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Sample records for active nucleation site

  1. Identification of ice nucleation active sites on feldspar dust particles.

    PubMed

    Zolles, Tobias; Burkart, Julia; Häusler, Thomas; Pummer, Bernhard; Hitzenberger, Regina; Grothe, Hinrich

    2015-03-19

    Mineral dusts originating from Earth's crust are known to be important atmospheric ice nuclei. In agreement with earlier studies, feldspar was found as the most active of the tested natural mineral dusts. Here we investigated in closer detail the reasons for its activity and the difference in the activity of the different feldspars. Conclusions are drawn from scanning electron microscopy, X-ray powder diffraction, infrared spectroscopy, and oil-immersion freezing experiments. K-feldspar showed by far the highest ice nucleation activity. Finally, we give a potential explanation of this effect, finding alkali-metal ions having different hydration shells and thus an influence on the ice nucleation activity of feldspar surfaces. PMID:25584435

  2. Identification of Ice Nucleation Active Sites on Feldspar Dust Particles

    PubMed Central

    2015-01-01

    Mineral dusts originating from Earth’s crust are known to be important atmospheric ice nuclei. In agreement with earlier studies, feldspar was found as the most active of the tested natural mineral dusts. Here we investigated in closer detail the reasons for its activity and the difference in the activity of the different feldspars. Conclusions are drawn from scanning electron microscopy, X-ray powder diffraction, infrared spectroscopy, and oil-immersion freezing experiments. K-feldspar showed by far the highest ice nucleation activity. Finally, we give a potential explanation of this effect, finding alkali-metal ions having different hydration shells and thus an influence on the ice nucleation activity of feldspar surfaces. PMID:25584435

  3. Insights Into the Effects of Internal Variability, External Variability, and Active Sites on Heterogeneous Ice Nucleation

    NASA Astrophysics Data System (ADS)

    Beydoun, H.; Sullivan, R. C.; Polen, M.

    2015-12-01

    Heterogeneous ice nucleation (HIN) remains one of the outstanding problems in cloud physics and atmospheric science. Experimental challenges in properly simulating HIN processes with relevant atmospheric conditions have largely contributed to the absence of a consistent and comprehensive parameterization. Here we formulate a new ice active surface site-based stochastic model of HIN with the unique feature of invoking a continuum assumption on the ice nucleation activity (contact angle) of an aerosol particle's surface. The result is a particle specific property g that defines a distribution of local surface ice nucleation rates. Upon integration this yields a full freezing probability function for an ice nucleating particle. Current cold plate droplet freezing measurements provide a great resource for studying the freezing ability of many atmospheric aerosol systems. A method based on statistical significance and critical area analysis is presented that can resolve the two-dimensional nature of the ice nucleation ability of aerosol particles: variability in active sites and freezing rates along an individual particle's surface, as well as variability between two particles of the same type in an aerosol population. When applied to published experimental data, the method demonstrates its ability to comprehensively interpret droplet freezing spectra of variable particle mass and surface area concentrations. By fitting the high concentration freezing curves to a statistically significant active site density function, the lower concentration freezing curves are successfully fitted via a process of random sampling from the statistically significant distribution. Using the new scheme, comprehensive parameterizations that can track the frozen fraction of cloud droplets in larger atmospheric models are derived.

  4. Ice nucleation properties of mineral dust particles: Determination of onset RHi, IN active fraction, nucleation time-lag, and the effect of active sites on contact angles

    SciTech Connect

    Kulkarni, Gourihar R.; Dobbie, Steven

    2010-01-08

    A newly developed ice nucleation experimental set up was used to investigate the heterogeneous ice nucleation properties of three Saharan and one Spanish dust particle samples. It is observed that the spread in the onset relative humidities with respect to ice (RHi) for Saharan dust particles varies from 104% to 110%, whereas for the Spanish dust from 106% to 110%. The elemental composition analysis shows a prominent Ca feature in the Spanish dust sample which could potentially explain the differences in nucleation threshold. Although spread in the onset RHi for Saharan dust samples were in agreement, their active fractions and nucleation time-lags calculated at various temperature and RHi conditions, for two Saharan dust samples, were not found to be in complete agreement. This could be because of the subtle variation in the elemental composition of the dust samples, and the surface irregularities like steps, cracks, cavities etc. A combination of classical nucleation theory and active site theory is used to understand the importance of these surface irregularities, expressed in terms of active sites, on the nucleability parameter (contact angle) that is widely used in the ice cloud modeling studies. These calculations show that the surface irregularities reduce the contact angle by approximately 10 degrees.

  5. Molecular Study of the Effects of Chemical Processing on Heterogeneous Ice Nucleation: Role of Active Sites and Product Formation

    NASA Astrophysics Data System (ADS)

    Sihvonen, S.; Schill, G. P.; Murphy, K. A.; Mueller, K.; Tolbert, M. A.; Freedman, M. A.

    2014-12-01

    Mineral dust aerosol is the largest global source of ice nuclei, but the identity of the active sites for nucleation is unknown. During atmospheric transport, mineral dust aerosol can encounter and react with sulfuric acid, which affects the ice nucleation activity either due to changes to reactive surface sites or product formation. In this study, we reacted two types of clays found in mineral dust, kaolinite and montmorillonite, with sulfuric acid. Variation in the mineral due to acid treatment was separated from product formation through rinsing techniques. The samples were subsequently reacted with a probe molecule, (3,3,3-trifluoropropyl)dimethylchlorosilane, that selectively binds to edge hydroxyl groups that are bonded to a silicon atom with three bridging oxygens. Hydroxyl groups are considered potential active sites, because they can hydrogen bond with water and facilitate ice nucleation. Attachment to these sites was quantified by 19F magic angle spinning nuclear magnetic resonance (MAS NMR) of the 19F atoms on the probe molecule, which provided a direct correlation of the number of hydroxyl groups. Our results indicate that the number of edge-site hydroxyl groups increases with exposure to acid. Ice nucleation measurements indicate that the sulfuric acid-treated mineral is less ice active than the untreated mineral. Surprisingly, no difference between the nucleation activity of the untreated mineral and acid-treated, rinsed mineral is observed. As a result, we hypothesize that once a critical density of active sites is reached for ice nucleation, there is no further change in nucleation activity despite a continued increase in active sites. We additionally propose that the reduced activity of the acid-treated mineral is due to product formation that blocks active sites on the mineral, rather than changes to active sites.

  6. Immersion freezing of supermicron mineral dust particles: freezing results, testing different schemes for describing ice nucleation, and ice nucleation active site densities.

    PubMed

    Wheeler, M J; Mason, R H; Steunenberg, K; Wagstaff, M; Chou, C; Bertram, A K

    2015-05-14

    Ice nucleation on mineral dust particles is known to be an important process in the atmosphere. To accurately implement ice nucleation on mineral dust particles in atmospheric simulations, a suitable theory or scheme is desirable to describe laboratory freezing data in atmospheric models. In the following, we investigated ice nucleation by supermicron mineral dust particles [kaolinite and Arizona Test Dust (ATD)] in the immersion mode. The median freezing temperature for ATD was measured to be approximately -30 °C compared with approximately -36 °C for kaolinite. The freezing results were then used to test four different schemes previously used to describe ice nucleation in atmospheric models. In terms of ability to fit the data (quantified by calculating the reduced chi-squared values), the following order was found for ATD (from best to worst): active site, pdf-α, deterministic, single-α. For kaolinite, the following order was found (from best to worst): active site, deterministic, pdf-α, single-α. The variation in the predicted median freezing temperature per decade change in the cooling rate for each of the schemes was also compared with experimental results from other studies. The deterministic model predicts the median freezing temperature to be independent of cooling rate, while experimental results show a weak dependence on cooling rate. The single-α, pdf-α, and active site schemes all agree with the experimental results within roughly a factor of 2. On the basis of our results and previous results where different schemes were tested, the active site scheme is recommended for describing the freezing of ATD and kaolinite particles. We also used our ice nucleation results to determine the ice nucleation active site (INAS) density for the supermicron dust particles tested. Using the data, we show that the INAS densities of supermicron kaolinite and ATD particles studied here are smaller than the INAS densities of submicron kaolinite and ATD particles

  7. Immersion freezing of supermicron mineral dust particles: freezing results, testing different schemes for describing ice nucleation, and ice nucleation active site densities.

    PubMed

    Wheeler, M J; Mason, R H; Steunenberg, K; Wagstaff, M; Chou, C; Bertram, A K

    2015-05-14

    Ice nucleation on mineral dust particles is known to be an important process in the atmosphere. To accurately implement ice nucleation on mineral dust particles in atmospheric simulations, a suitable theory or scheme is desirable to describe laboratory freezing data in atmospheric models. In the following, we investigated ice nucleation by supermicron mineral dust particles [kaolinite and Arizona Test Dust (ATD)] in the immersion mode. The median freezing temperature for ATD was measured to be approximately -30 °C compared with approximately -36 °C for kaolinite. The freezing results were then used to test four different schemes previously used to describe ice nucleation in atmospheric models. In terms of ability to fit the data (quantified by calculating the reduced chi-squared values), the following order was found for ATD (from best to worst): active site, pdf-α, deterministic, single-α. For kaolinite, the following order was found (from best to worst): active site, deterministic, pdf-α, single-α. The variation in the predicted median freezing temperature per decade change in the cooling rate for each of the schemes was also compared with experimental results from other studies. The deterministic model predicts the median freezing temperature to be independent of cooling rate, while experimental results show a weak dependence on cooling rate. The single-α, pdf-α, and active site schemes all agree with the experimental results within roughly a factor of 2. On the basis of our results and previous results where different schemes were tested, the active site scheme is recommended for describing the freezing of ATD and kaolinite particles. We also used our ice nucleation results to determine the ice nucleation active site (INAS) density for the supermicron dust particles tested. Using the data, we show that the INAS densities of supermicron kaolinite and ATD particles studied here are smaller than the INAS densities of submicron kaolinite and ATD particles

  8. Truncated Dual-Cap Nucleation Site Development

    NASA Technical Reports Server (NTRS)

    Matson, Douglas M.; Sander, Paul J.

    2012-01-01

    During heterogeneous nucleation within a metastable mushy-zone, several geometries for nucleation site development must be considered. Traditional spherical dual cap and crevice models are compared to a truncated dual cap to determine the activation energy and critical cluster growth kinetics in ternary Fe-Cr-Ni steel alloys. Results of activation energy results indicate that nucleation is more probable at grain boundaries within the solid than at the solid-liquid interface.

  9. Porous capsules with a large number of active sites: nucleation/growth under confined conditions.

    PubMed

    Garai, Somenath; Rubčić, Mirta; Bögge, Hartmut; Gouzerh, Pierre; Müller, Achim

    2015-03-01

    This work deals with the generation of large numbers of active sites and with ensuing nucleation/ growth processes on the inside wall of the cavity of porous nanocapsules of the type (pentagon)12(linker)30≡{(Mo(VI))Mo(VI)5}12{Mo(V)2(ligand)}30. A first example refers to sulfur dioxide capture through displacement of acetate ligands, while the grafted sulfite ligands are able to trap {MoO3H}(+) units thereby forming unusual {(O2SO)3MoO3H}(5-) assemblies. A second example relates to the generation of open coordination sites through release of carbon dioxide upon mild acidification of a carbonate-type capsule. When the reaction is performed in the presence of heptamolybdate ions, MoO4(2-) ions enter the cavity where they bind to the inside wall while forming new types of polyoxomolybdate architectures, thereby extending the molybdenum oxide skeleton of the capsule. Parallels can be drawn with Mo-storage proteins and supported MoO3 catalysts, making the results relevant to molybdenum biochemistry and to catalysis. PMID:25653204

  10. Can we define an asymptotic value for the ice active surface site density for heterogeneous ice nucleation?

    NASA Astrophysics Data System (ADS)

    Niedermeier, Dennis; Augustin-Bauditz, Stefanie; Hartmann, Susan; Wex, Heike; Ignatius, Karoliina; Stratmann, Frank

    2015-04-01

    The formation of ice in atmospheric clouds has a substantial influence on the radiative properties of clouds as well as on the formation of precipitation. Therefore much effort has been made to understand and quantify the major ice formation processes in clouds. Immersion freezing has been suggested to be a dominant primary ice formation process in low and mid-level clouds (mixed-phase cloud conditions). It also has been shown that mineral dust particles are the most abundant ice nucleating particles in the atmosphere and thus may play an important role for atmospheric ice nucleation (Murray et al., 2012). Additionally, biological particles like bacteria and pollen are suggested to be potentially involved in atmospheric ice formation, at least on a regional scale (Murray et al., 2012). In recent studies for biological particles (SNOMAX and birch pollen), it has been demonstrated that freezing is induced by ice nucleating macromolecules and that an asymptotic value for the mass density of these ice nucleating macromolecules can be determined (Hartmann et al., 2013; Augustin et al., 2013, Wex et al., 2014). The question arises whether such an asymptotic value can also be determined for the ice active surface site density ns, a parameter which is commonly used to describe the ice nucleation activity of e.g., mineral dust. Such an asymptotic value for ns could be an important input parameter for atmospheric modeling applications. In the presented study, we therefore investigated the immersion freezing behavior of droplets containing size-segregated, monodisperse feldspar particles utilizing the Leipzig Aerosol Cloud Interaction Simulator (LACIS). For all particle sizes considered in the experiments, we observed a leveling off of the frozen droplet fraction reaching a plateau within the heterogeneous freezing temperature regime (T > -38°C) which was proportional to the particle surface area. Based on these findings, we could determine an asymptotic value for the ice

  11. Thermal interaction effect on nucleation site distribution in subcooled boiling

    SciTech Connect

    Ling Zou; Barclay Joned

    2012-05-01

    An experimental work on subcooled boiling of refrigerant, R134a, to examine nucleation site distributions on both copper and stainless steel heating surfaces was performed. In order to obtain high fidelity active nucleation site density and distribution data, a high-speed digital camera was utilized to record bubble emission images from a view normal to heating surfaces. Statistical analyses on nucleation site data were done and their statistical distributions were obtained. Those experimentally observed nucleation site distributions were compared to the random spatial Poisson distribution. The comparisons showed that, rather than purely random, active nucleation site distributions on boiling surfaces are relatively more uniform. Experimental results also showed that on the copper heating surface, nucleation site distributions are slightly more uniform than on the stainless steel surface. This was concluded as the results of thermal interactions between nucleation sites with different solid thermal conductivities. A two dimensional thermal interaction model was then developed to quantitatively examine the thermal interactions between nucleation sites. The results give a reasonable explanation to the experimental observation on nucleation site distributions.

  12. Ice Nucleation Activity in Lichens

    PubMed Central

    Kieft, Thomas L.

    1988-01-01

    A newly discovered form of biological ice nucleus associated with lichens is described. Ice nucleation spectra of a variety of lichens from the southwestern United States were measured by the drop-freezing method. Several epilithic lichen samples of the genera Rhizoplaca, Xanthoparmelia, and Xanthoria had nuclei active at temperatures as warm as −2.3°C and had densities of 2.3 × 106 to more than 1 × 108 nuclei g−1 at −5°C (2 to 4 orders of magnitude higher than any plants infected with ice nucleation-active bacteria). Most lichens tested had nucleation activity above −8°C. Lichen substrates (rocks, plants, and soil) showed negligible activity above −8°C. Ice nucleation-active bacteria were not isolated from the lichens, and activity was not destroyed by heat (70°C) or sonication, indicating that lichen-associated ice nuclei are nonbacterial in origin and differ chemically from previously described biological ice nuclei. An axenic culture of the lichen fungus Rhizoplaca chrysoleuca showed detectable ice nucleation activity at −1.9°C and an ice nucleation density of 4.5 × 106 nuclei g−1 at −5°C. It is hypothesized that these lichens, which are both frost tolerant and dependent on atmospheric moisture, derive benefit in the form of increased moisture deposition as a result of ice nucleation. PMID:16347678

  13. Ice nucleation activity in lichens.

    PubMed

    Kieft, T L

    1988-07-01

    A newly discovered form of biological ice nucleus associated with lichens is described. Ice nucleation spectra of a variety of lichens from the southwestern United States were measured by the drop-freezing method. Several epilithic lichen samples of the genera Rhizoplaca, Xanthoparmelia, and Xanthoria had nuclei active at temperatures as warm as -2.3 degrees C and had densities of 2.3 x 10 to more than 1 x 10 nuclei g at -5 degrees C (2 to 4 orders of magnitude higher than any plants infected with ice nucleation-active bacteria). Most lichens tested had nucleation activity above -8 degrees C. Lichen substrates (rocks, plants, and soil) showed negligible activity above -8 degrees C. Ice nucleation-active bacteria were not isolated from the lichens, and activity was not destroyed by heat (70 degrees C) or sonication, indicating that lichen-associated ice nuclei are nonbacterial in origin and differ chemically from previously described biological ice nuclei. An axenic culture of the lichen fungus Rhizoplaca chrysoleuca showed detectable ice nucleation activity at -1.9 degrees C and an ice nucleation density of 4.5 x 10 nuclei g at -5 degrees C. It is hypothesized that these lichens, which are both frost tolerant and dependent on atmospheric moisture, derive benefit in the form of increased moisture deposition as a result of ice nucleation.

  14. Ice nucleation activity of polysaccharides

    NASA Astrophysics Data System (ADS)

    Bichler, Magdalena; Felgitsch, Laura; Haeusler, Thomas; Seidl-Seiboth, Verena; Grothe, Hinrich

    2015-04-01

    Heterogeneous ice nucleation is an important process in the atmosphere. It shows direct impact on our climate by triggering ice cloud formation and therefore it has much influence on the radiation balance of our planet (Lohmann et al. 2002; Mishchenko et al. 1996). The process itself is not completely understood so far and many questions remain open. Different substances have been found to exhibit ice nucleation activity (INA). Due to their vast differences in chemistry and morphology it is difficult to predict what substance will make good ice nuclei and which will not. Hence simple model substances must be found and be tested regarding INA. Our work aims at gaining to a deeper understanding of heterogeneous ice nucleation. We intend to find some reference standards with defined chemistry, which may explain the mechanisms of heterogeneous ice nucleation. A particular focus lies on biological carbohydrates in regards to their INA. Biological carbohydrates are widely distributed in all kingdoms of life. Mostly they are specific for certain organisms and have well defined purposes, e.g. structural polysaccharides like chitin (in fungi and insects) and pectin (in plants), which has also water-binding properties. Since they are widely distributed throughout our biosphere and mostly safe to use for nutrition purposes, they are well studied and easily accessible, rendering them ideal candidates as proxies. In our experiments we examined various carbohydrates, like the already mentioned chitin and pectin, as well as their chemical modifications. Lohmann U.; A Glaciation Indirect Aerosol Effect Caused by Soot Aerosols; J. Geoph. Res.; Vol. 24 No.4; pp 11-1 - 11-4; 2002 Mishchenko M.I., Rossow W.B., Macke A., Lacis A. A.; Sensitivity of Cirrus Cloud Albedo, Bidirectional Reflectance and Optical Thickness Retrieval Accuracy to Ice Particle Shape, J. Geoph. Res.; Vol. 101, No D12; pp. 16,973 - 16,985; 1996

  15. Can we define an asymptotic value for the ice active surface site density for heterogeneous ice nucleation?

    NASA Astrophysics Data System (ADS)

    Niedermeier, Dennis; Augustin-Bauditz, Stefanie; Hartmann, Susan; Wex, Heike; Ignatius, Karoliina; Stratmann, Frank

    2015-05-01

    The immersion freezing behavior of droplets containing size-segregated, monodisperse feldspar particles was investigated. For all particle sizes investigated, a leveling off of the frozen droplet fraction was observed reaching a plateau within the heterogeneous freezing temperature regime (T >- 38°C). The frozen fraction in the plateau region was proportional to the particle surface area. Based on these findings, an asymptotic value for ice active surface site density ns, which we named ns⋆, could be determined for the investigated feldspar sample. The comparison of these results with those of other studies not only elucidates the general feasibility of determining such an asymptotic value but also shows that the value of ns⋆ strongly depends on the method of the particle surface area determination. However, such an asymptotic value might be an important input parameter for atmospheric modeling applications. At least it shows that care should be taken when ns is extrapolated to lower or higher temperature.

  16. Potential Sites for Ice Nucleation on Aluminosilicate Clay Minerals and Related Materials.

    PubMed

    Freedman, Miriam Arak

    2015-10-01

    Few aerosol particles in clouds nucleate the formation of ice. The surface sites available for nucleus formation, which can include surface defects and functional groups, determine in part the activity of an aerosol particle toward ice formation. Although ice nucleation on particles has been widely studied, exploration of the specific sites at which the initial germ forms has been limited, but is important for predicting the microphysical properties of clouds, which impact climate. This Perspective focuses on what is currently known about surface sites for ice nucleation on aluminosilicate clay minerals, which are commonly found in ice residuals, as well as related materials. PMID:26722881

  17. Potential Sites for Ice Nucleation on Aluminosilicate Clay Minerals and Related Materials.

    PubMed

    Freedman, Miriam Arak

    2015-10-01

    Few aerosol particles in clouds nucleate the formation of ice. The surface sites available for nucleus formation, which can include surface defects and functional groups, determine in part the activity of an aerosol particle toward ice formation. Although ice nucleation on particles has been widely studied, exploration of the specific sites at which the initial germ forms has been limited, but is important for predicting the microphysical properties of clouds, which impact climate. This Perspective focuses on what is currently known about surface sites for ice nucleation on aluminosilicate clay minerals, which are commonly found in ice residuals, as well as related materials.

  18. The ice nucleation activity of extremophilic algae.

    PubMed

    Kviderova, Jana; Hajek, Josef; Worland, Roger M

    2013-01-01

    Differences in the level of cold acclimation and cryoprotection estimated as ice nucleation activity in snow algae (Chlamydomonas cf. nivalis and Chloromonas nivalis), lichen symbiotic algae (Trebouxia asymmetrica, Trebouxia erici and Trebouxia glomerata), and a mesophilic strain (Chlamydomonas reinhardti) were evaluated. Ice nucleation activity was measured using the freezing droplet method. Measurements were performed using suspensions of cells of A750 (absorbance at 750 nm) ~ 1, 0.1, 0.01 and 0.001 dilutions for each strain. The algae had lower ice nucleation activity, with the exception of Chloromonas nivalis contaminated by bacteria. The supercooling points of the snow algae were higher than those of lichen photobionts. The supercooling points of both, mesophilic and snow Chlamydomonas strains were similar. The lower freezing temperatures of the lichen algae may reflect either the more extreme and more variable environmental conditions of the original localities or the different cellular structure of the strains examined.

  19. Molecular Ice Nucleation Activity of Birch Pollen

    NASA Astrophysics Data System (ADS)

    Felgitsch, Laura; Bichler, Magdalena; Häusler, Thomas; Weiss, Victor U.; Marchetti-Deschmann, Martina; Allmaier, Günter; Grothe, Hinrich

    2015-04-01

    Heterogeneous ice nucleation plays a major part in ecosystem and climate. Due to the triggering of ice cloud formation it influences the radiation balance of the earth, but also on the ground it can be found to be important in many processes of nature. So far the process of heterogeneous ice nucleation is not fully understood and many questions remain to be answered. Biological ice nucleation is hereby from great interest, because it shows the highest freezing temperatures. Several bacteria and fungi act as ice nuclei. A famous example is Pseudomonas syringae, a bacterium in commercial use (Snomax®), which increases the freezing from homogeneous freezing temperatures of approx. -40° C (for small volumes as in cloud droplets) to temperatures up to -2° C. In 2001 it was found that birch pollen can trigger ice nucleation (Diehl et al. 2001; Diehl et al. 2002). For a long time it was believed that this is due to macroscopic features of the pollen surface. Recent findings of Bernhard Pummer (2012) show a different picture. The ice nuclei are not attached on the pollen surface directly, but on surface material which can be easily washed off. This shows that not only the surface morphology, but also specific molecules or molecular structures are responsible for the ice nucleation activity of birch pollen. With various analytic methods we work on elucidating the structure of these molecules as well as the mechanism with which they trigger ice nucleation. To solve this we use various instrumental analytic techniques like Nuclear Magnetic Resonance spectroscopy (NMR), Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI-MS), and Gas-phase Electrophoretic Mobility Molecular Analysis (GEMMA). Also standard techniques like various chromatographic separation techniques and solvent extraction are in use. We state here that this feature might be due to the aggregation of small molecules, with agglomerates showing a specific surface structure. Our results

  20. Immersion freezing of ice nucleation active protein complexes

    NASA Astrophysics Data System (ADS)

    Hartmann, S.; Augustin, S.; Clauss, T.; Wex, H.; Šantl-Temkiv, T.; Voigtländer, J.; Niedermeier, D.; Stratmann, F.

    2013-06-01

    to the outer membrane of intact bacteria or membrane fragments, (c) the temperature range in which heterogeneous droplet freezing occurs, and the fraction of droplets being able to freeze, both depend on the actual number of INA protein complexes present in the droplet ensemble, and (d) possible artifacts suspected to occur in connection with the drop freezing method, i.e., the method frequently used by biologist for quantifying ice nucleation behaviour, are of minor importance, at least for substances such as P. syringae, which induce freezing at comparably high temperatures. The last statement implies that for single ice nucleation entities such as INA protein complexes, it is the number of entities present in the droplet population, and the entities' nucleation rate, which control the freezing behaviour of the droplet population. Quantities such as ice active surface site density are not suitable in this context. The results obtained in this study allow a different perspective on the quantification of the immersion freezing behaviour of bacterial ice nucleation.

  1. The ice nucleation activity of biological aerosols

    NASA Astrophysics Data System (ADS)

    Grothe, H.; Pummer, B.; Bauer, H.; Bernardi, J.

    2012-04-01

    Primary Biological Aerosol Particles (PBAPs), including bacteria, spores and pollen may be important for several atmospheric processes. Particularly, the ice nucleation caused by PBAPs is a topic of growing interest, since their impact on ice cloud formation and thus on radiative forcing, an important parameter in global climate is not yet fully understood. In laboratory model studies we investigated the ice nucleation activity of selected PBAPs. We studied the immersion mode freezing using water-oil emulsion, which we observed by optical microscopy. We particularly focused on pollen. We show that pollen of different species strongly differ in their ice nucleation behavior. The average freezing temperatures in laboratory experiments range from 240 K to 255 K. As the most efficient nuclei (silver birch, Scots pine and common juniper pollen) have a distribution area up to the Northern timberline, their ice nucleation activity might be a cryoprotective mechanism. For comparison the ice nucleation activity of Snomax, fungal spores, and mushrooms will be discussed as well. In the past, pollen have been rejected as important atmospheric IN, as they are not as abundant in the atmosphere as bacteria or mineral dust and are too heavy to reach higher altitudes. However, in our experiments (Pummer et al. 2011) it turned out that water, which had been in contact with pollen and then been separated from the bodies, nucleates as good as the pollen grains themselves. So the ice nuclei have to be easily-suspendable macromolecules (100-300 kDa) located on the pollen. Once extracted, they can be distributed further through the atmosphere than the heavy pollen grains and so augment the impact of pollen on ice cloud formation even in the upper troposphere. It is widely known, that material from the pollen, like allergens and sugars, can indeed leave the pollen body and be distributed independently. The most probable mechanism is the pollen grain bursting by rain, which releases

  2. Controllable Magnetization Processes Induced by Nucleation Sites in Permalloy Rings

    NASA Astrophysics Data System (ADS)

    Ying-Jiun Chen,; Chia-Jung Hsu,; Chun-Neng Liao,; Hao-Ting Huang,; Chiun-Peng Lee,; Yi-Hsun Chiu,; Tzu-Yun Tung,; Mei-Feng Lai,

    2010-02-01

    Different arrangements of notches as nucleation sites are demonstrated experimentally and numerically to effectively control the magnetization processes of permalloy rings. In the ring with notches at the same side with respect to field direction, two same-helicity vortex domain walls in the onion state lead to two-step switching going through flux-closure state; in the ring with diagonal notches two opposite-helicity vortex domain walls lead to one-step switching skipping flux-closure state. The switching processes are repeatable in contrast to rings without notches where helicites of two vortex domain walls are random so the switching processes can not be controlled.

  3. Thermodynamic Derivation of the Activation Energy for Ice Nucleation

    NASA Technical Reports Server (NTRS)

    Barahona, D.

    2015-01-01

    Cirrus clouds play a key role in the radiative and hydrological balance of the upper troposphere. Their correct representation in atmospheric models requires an understanding of the microscopic processes leading to ice nucleation. A key parameter in the theoretical description of ice nucleation is the activation energy, which controls the flux of water molecules from the bulk of the liquid to the solid during the early stages of ice formation. In most studies it is estimated by direct association with the bulk properties of water, typically viscosity and self-diffusivity. As the environment in the ice-liquid interface may differ from that of the bulk, this approach may introduce bias in calculated nucleation rates. In this work a theoretical model is proposed to describe the transfer of water molecules across the ice-liquid interface. Within this framework the activation energy naturally emerges from the combination of the energy required to break hydrogen bonds in the liquid, i.e., the bulk diffusion process, and the work dissipated from the molecular rearrangement of water molecules within the ice-liquid interface. The new expression is introduced into a generalized form of classical nucleation theory. Even though no nucleation rate measurements are used to fit any of the parameters of the theory the predicted nucleation rate is in good agreement with experimental results, even at temperature as low as 190 K, where it tends to be underestimated by most models. It is shown that the activation energy has a strong dependency on temperature and a weak dependency on water activity. Such dependencies are masked by thermodynamic effects at temperatures typical of homogeneous freezing of cloud droplets; however, they may affect the formation of ice in haze aerosol particles. The new model provides an independent estimation of the activation energy and the homogeneous ice nucleation rate, and it may help to improve the interpretation of experimental results and the

  4. Thermodynamic derivation of the activation energy for ice nucleation

    NASA Astrophysics Data System (ADS)

    Barahona, D.

    2015-12-01

    Cirrus clouds play a key role in the radiative and hydrological balance of the upper troposphere. Their correct representation in atmospheric models requires an understanding of the microscopic processes leading to ice nucleation. A key parameter in the theoretical description of ice nucleation is the activation energy, which controls the flux of water molecules from the bulk of the liquid to the solid during the early stages of ice formation. In most studies it is estimated by direct association with the bulk properties of water, typically viscosity and self-diffusivity. As the environment in the ice-liquid interface may differ from that of the bulk, this approach may introduce bias in calculated nucleation rates. In this work a theoretical model is proposed to describe the transfer of water molecules across the ice-liquid interface. Within this framework the activation energy naturally emerges from the combination of the energy required to break hydrogen bonds in the liquid, i.e., the bulk diffusion process, and the work dissipated from the molecular rearrangement of water molecules within the ice-liquid interface. The new expression is introduced into a generalized form of classical nucleation theory. Even though no nucleation rate measurements are used to fit any of the parameters of the theory the predicted nucleation rate is in good agreement with experimental results, even at temperature as low as 190 K, where it tends to be underestimated by most models. It is shown that the activation energy has a strong dependency on temperature and a weak dependency on water activity. Such dependencies are masked by thermodynamic effects at temperatures typical of homogeneous freezing of cloud droplets; however, they may affect the formation of ice in haze aerosol particles. The new model provides an independent estimation of the activation energy and the homogeneous ice nucleation rate, and it may help to improve the interpretation of experimental results and the

  5. Infrared Visualisation of Nucleate Boiling from an Isolated Site in a Hele-Shaw Cell

    NASA Astrophysics Data System (ADS)

    Barber, Jacqueline; Brutin, David; Tadrist, Lounes

    2010-11-01

    Nucleation, growth and detachment of HFE-7000 confined vapour bubbles are investigated locally using simultaneously an infrared camera with 10 μm spatial resolution and a visible camera. Bubbles are created from a 50 μm artificial nucleation site on a 100 μm Inconel film in a Hele-Shaw cell. A single bubble nucleation is investigated. Experiments are performed by varying both the convective inlet liquid mass flow rate, and the heat flux supplied at the wire. Bubble detachment diameters at the single artificial nucleation site and the associated effects on the heat transfer by the confinement influence are investigated at low Reynolds number. The experimental set-up enables observation in the 2D Hele-Shaw cell of the flow and of the bubble growth; this is achievable since the cell has one face transparent to infrared radiation. The infrared video resolution enables us to observe the presence of a bubble and its magnitude of thermal disturbance on the flow. The temperature profile of the bubble as it nucleates, grows and detaches from the wall can be measured from the infrared videos. The temperature change at the nucleation site highlights the frequency of the bubble detachment based on the temperature signal. From analysis of the visible and infrared videos, the nucleation site surface temperature, bubble detachment diameter and bubble nucleation frequency can be calculated.

  6. Evolution of Vapor Bubbles Nucleation Sites in Low Gravity

    NASA Technical Reports Server (NTRS)

    Buyevich, Yu A.; Webbon, Bruce W.

    1995-01-01

    When liquid is expelled by a vapor bubble growing at a nucleation site on a superheated surface, a thin microlayer underneath the bubble is left behind. It is evaporated from the free microlayer surface that provides for bubble growth. The average thickness of the microlayer determining the evaporation rate increases with time if the latter does not exceed a threshold value associated with the burn-out crisis. The bubble is described as a spherical segment with its flattened part adjoining the microlayer. This introduces two independent variables - the radius of the spherical part of the bubble surface and the polar angle that defines the relative area of the flattened part. They are to be found out from a set of two strongly nonlinear equations resulting from mass and momentum conservation laws. The first one depends on both microlayer thickness and nonmonotonously changing bubble base area. The second involves two major factors favoring bubble detachment - the buoyancy and a force due to the initial momentum of vapor input into the bubble. The former force depends on gravity whereas the latter one does not. It is why the limiting regimes of bubble evolution that correspond to normal or moderately reduced gravity and to microgravity feature drastically different properties. In the first case, the buoyancy dominates and the bubble evolves in such a manner as to become a full sphere at a moment that can be viewed as that of detachment. The detachment volume grows as gravity decreases. In the second case, the buoyancy is negligible and the bubble stays near the surface, while its volume continues to increase for a sufficiently long time. The findings are discussed in connection with experimental data obtained under different gravity conditions, some unpublished experiments being included. They help to understand why the pool boiling heat transfer coefficient frequently increases as gravity falls down and eventually vanishes.

  7. Ice nucleation temperature of individual leaves in relation to population sizes of ice nucleation active bacteria and frost injury.

    PubMed

    Hirano, S S; Baker, L S; Upper, C D

    1985-02-01

    Ice nucleation temperatures of individual leaves were determined by a tube nucleation test. With this assay, a direct quantitative relationship was obtained between the temperatures at which ice nucleation occurred on individual oat (Avena sativa L.) leaves and the population sizes of ice nucleation active (INA) bacteria present on those leaves. In the absence of INA bacteria, nucleation of supercooled growth-chamber grown oat leaves did not occur until temperatures were below approximately -5 degrees C. Both nucleation temperature and population size of INA bacteria were determined on the same individual, field-grown oat leaves. Leaves with higher ice nucleation temperatures harbored larger populations of INA bacteria than did leaves with lower nucleation temperatures. Log(10) mean populations of INA bacteria per leaf were 5.14 and 3.51 for leaves with nucleation temperatures of -2.5 degrees C and -3.0 degrees C, respectively. Nucleation frequencies (the ratio of ice nuclei to viable cells) of INA bacteria on leaves were lognormally distributed. Strains from two very different collections of Pseudomonas syringae and one of Erwinia herbicola were cultured on nutrient glycerol agar and tested for nucleation frequency at -5 degrees C. Nucleation frequencies of these bacterial strains were also lognormally distributed within each of the three sets. The tube nucleation test was used to determine the frequency with which individual leaves in an oat canopy harbored large populations of INA bacteria throughout the growing season. This test also predicted relative frost hazard to tomato (Lycopersicon esculentum Mill) plants. PMID:16664039

  8. Ice Nucleation Temperature of Individual Leaves in Relation to Population Sizes of Ice Nucleation Active Bacteria and Frost Injury

    PubMed Central

    Hirano, Susan S.; Baker, L. Stuart; Upper, Christen D.

    1985-01-01

    Ice nucleation temperatures of individual leaves were determined by a tube nucleation test. With this assay, a direct quantitative relationship was obtained between the temperatures at which ice nucleation occurred on individual oat (Avena sativa L.) leaves and the population sizes of ice nucleation active (INA) bacteria present on those leaves. In the absence of INA bacteria, nucleation of supercooled growth-chamber grown oat leaves did not occur until temperatures were below approximately −5°C. Both nucleation temperature and population size of INA bacteria were determined on the same individual, field-grown oat leaves. Leaves with higher ice nucleation temperatures harbored larger populations of INA bacteria than did leaves with lower nucleation temperatures. Log10 mean populations of INA bacteria per leaf were 5.14 and 3.51 for leaves with nucleation temperatures of −2.5°C and −3.0°C, respectively. Nucleation frequencies (the ratio of ice nuclei to viable cells) of INA bacteria on leaves were lognormally distributed. Strains from two very different collections of Pseudomonas syringae and one of Erwinia herbicola were cultured on nutrient glycerol agar and tested for nucleation frequency at −5°C. Nucleation frequencies of these bacterial strains were also lognormally distributed within each of the three sets. The tube nucleation test was used to determine the frequency with which individual leaves in an oat canopy harbored large populations of INA bacteria throughout the growing season. This test also predicted relative frost hazard to tomato (Lycopersicon esculentum Mill) plants. PMID:16664039

  9. Homogeneous ice nucleation from aqueous inorganic/organic particles representative of biomass burning: water activity, freezing temperatures, nucleation rates.

    PubMed

    Knopf, Daniel A; Rigg, Yannick J

    2011-02-10

    Homogeneous ice nucleation plays an important role in the formation of cirrus clouds with subsequent effects on the global radiative budget. Here we report on homogeneous ice nucleation temperatures and corresponding nucleation rate coefficients of aqueous droplets serving as surrogates of biomass burning aerosol. Micrometer-sized (NH(4))(2)SO(4)/levoglucosan droplets with mass ratios of 10:1, 1:1, 1:5, and 1:10 and aqueous multicomponent organic droplets with and without (NH(4))(2)SO(4) under typical tropospheric temperatures and relative humidities are investigated experimentally using a droplet conditioning and ice nucleation apparatus coupled to an optical microscope with image analysis. Homogeneous freezing was determined as a function of temperature and water activity, a(w), which was set at droplet preparation conditions. The ice nucleation data indicate that minor addition of (NH(4))(2)SO(4) to the aqueous organic droplets renders the temperature dependency of water activity negligible in contrast to the case of aqueous organic solution droplets. The mean homogeneous ice nucleation rate coefficient derived from 8 different aqueous droplet compositions with average diameters of ∼60 μm for temperatures as low as 195 K and a(w) of 0.82-1 is 2.18 × 10(6) cm(-3) s(-1). The experimentally derived freezing temperatures and homogeneous ice nucleation rate coefficients are in agreement with predictions of the water activity-based homogeneous ice nucleation theory when taking predictive uncertainties into account. However, the presented ice nucleation data indicate that the water activity-based homogeneous ice nucleation theory overpredicts the freezing temperatures by up to 3 K and corresponding ice nucleation rate coefficients by up to ∼2 orders of magnitude. A shift of 0.01 in a(w), which is well within the uncertainty of typical field and laboratory relative humidity measurements, brings experimental and predicted freezing temperatures and homogeneous ice

  10. Immersion freezing of ice nucleating active protein complexes

    NASA Astrophysics Data System (ADS)

    Hartmann, S.; Augustin, S.; Clauss, T.; Voigtländer, J.; Niedermeier, D.; Wex, H.; Stratmann, F.

    2012-08-01

    Biological particles, e.g. bacteria and their Ice Nucleating Active (INA) protein complexes, might play an important role for the ice formation in atmospheric mixed-phase clouds. Therefore, the immersion freezing behavior of INA protein complexes generated from a SnomaxTM solution/suspension was investigated as function of temperature in a range of -5 °C to -38 °C at the Leipzig Aerosol Cloud Interaction Simulator (LACIS). The immersion freezing of droplets containing small numbers of INA protein complexes occurs in a temperature range of -7 °C and -10 °C. The experiments performed in the lower temperature range, where all droplets freeze which contain at least one INA protein complex, are used to determine the average number of INA protein complexes present, assuming that the INA protein complexes are Poisson distributed over the droplet ensemble. Knowing the average number of INA protein complexes, the heterogeneous ice nucleation rate and rate coefficient of a single INA protein complex is determined by using the newly-developed CHESS model (stoCHastic model of idEntical poiSSon distributed ice nuclei). Therefore, we assume the ice nucleation process to be of stochastic nature, and a parameterization of the INA protein complex's nucleation rate. Analyzing the results of immersion freezing experiments from literature (SnomaxTM and Pseudomonas syringae bacteria), to results gained in this study, demonstrates that first, a similar temperature dependence of the heterogeneous ice nucleation rate for a single INA protein complex was found in all experiments, second, the shift of the ice fraction curves to higher temperatures can be explained consistently by a higher average number of INA protein complexes being present in the droplet ensemble, and finally the heterogeneous ice nucleation rate of one single INA protein complex might be also applicable for intact Pseudomonas syringae bacteria cells. The results obtained in this study allow a new perspective on the

  11. Urediospores of rust fungi are ice nucleation active at > -10 °C and harbor ice nucleation active bacteria

    NASA Astrophysics Data System (ADS)

    Morris, C. E.; Sands, D. C.; Glaux, C.; Samsatly, J.; Asaad, S.; Moukahel, A. R.; Gonçalves, F. L. T.; Bigg, E. K.

    2013-04-01

    Various features of the biology of the rust fungi and of the epidemiology of the plant diseases they cause illustrate the important role of rainfall in their life history. Based on this insight we have characterized the ice nucleation activity (INA) of the aerially disseminated spores (urediospores) of this group of fungi. Urediospores of this obligate plant parasite were collected from natural infections of 7 species of weeds in France, from coffee in Brazil and from field and greenhouse-grown wheat in France, the USA, Turkey and Syria. Immersion freezing was used to determine freezing onset temperatures and the abundance of ice nuclei in suspensions of washed spores. Microbiological analyses of spores from France, the USA and Brazil, and subsequent tests of the ice nucleation activity of the bacteria associated with spores were deployed to quantify the contribution of bacteria to the ice nucleation activity of the spores. All samples of spores were ice nucleation active, having freezing onset temperatures as high as -4 °C. Spores in most of the samples carried cells of ice nucleation-active strains of the bacterium Pseudomonas syringae (at rates of less than 1 bacterial cell per 100 urediospores), but bacterial INA accounted for only a small fraction of the INA observed in spore suspensions. Changes in the INA of spore suspensions after treatment with lysozyme suggest that the INA of urediospores involves a polysaccharide. Based on data from the literature, we have estimated the concentrations of urediospores in air at cloud height and in rainfall. These quantities are very similar to those reported for other biological ice nucleators in these same substrates. However, at cloud level convective activity leads to widely varying concentrations of particles of surface origin, so that mean concentrations can underestimate their possible effects on clouds. We propose that spatial and temporal concentrations of biological ice nucleators active at temperatures > -10

  12. Toxicity of smoke to epiphytic ice nucleation-active bacteria.

    PubMed

    Zagory, D; Lindow, S E; Parmeter, J R

    1983-07-01

    Wheat straw smoke aerosols and liquid smoke condensates reduced significantly both the viability and the ice-nucleating activity of Pseudomonas syringae pv. syringae and Erwinia herbicola in vitro and on leaf surfaces in vivo. Highly significant reductions in numbers of bacterial ice nuclei on the surface of both corn and almond were observed after exposure to smoke aerosols. At -5 degrees C, frost injury to corn seedlings colonized by ice nucleation-active bacteria was reduced after exposure to smoke aerosols. Effects on -9 degrees C ice nuclei, although significant, were less than on ice nuclei active at -5 degrees C. These results suggest that smoke from wildfires or smudge pots may reduce plant frost susceptibility and sources of ice nuclei important in other natural processes under some conditions. PMID:16346333

  13. Ice nucleation activity of bacteria isolated from cloud water

    NASA Astrophysics Data System (ADS)

    Joly, Muriel; Attard, Eléonore; Sancelme, Martine; Deguillaume, Laurent; Guilbaud, Caroline; Morris, Cindy E.; Amato, Pierre; Delort, Anne-Marie

    2013-05-01

    Some Gamma-Proteobacteria can catalyze ice formation thereby potentially contributing to the induction of precipitation in supercooled clouds and subsequently to bacterial deposition. Forty-four bacterial strains from cloud water were screened for their capacity to induce freezing. Seven strains (16%) were active at -8 °C or warmer and were identified as Pseudomonas syringae, Xanthomonas spp. and Pseudoxanthomonas sp. Phylogenetic analysis revealed that the P. syringae strains in clouds at the Puy de Dôme belonged to clades that are among the most infrequently detected in the environment, while widespread clades were absent suggesting some extent of selection or unusual biogeography of the bacteria at the sampling site. Three strains induced freezing at -3 °C while the others nucleated ice at -4 °C to -6 °C. The freezing profiles revealed that the peaks of activity were centered around -3.5 °C, -5 °C and/or -8.5 °C depending on the strain. The frequency of ice-nuclei (IN) per cell at -6 °C was generally below 0.5% and reached up to 4.2% in one strain. We estimated that clouds influenced by vegetated areas would carry between less than 1 and ˜500 bacterial IN mL-1 of water active between -3 °C and -10 °C depending on the season. These data will contribute to modeling the impact of bacterial IN on precipitation at regional scales.

  14. Ice Nucleation Activity of Various Agricultural Soil Dust Aerosol Particles

    NASA Astrophysics Data System (ADS)

    Schiebel, Thea; Höhler, Kristina; Funk, Roger; Hill, Thomas C. J.; Levin, Ezra J. T.; Nadolny, Jens; Steinke, Isabelle; Suski, Kaitlyn J.; Ullrich, Romy; Wagner, Robert; Weber, Ines; DeMott, Paul J.; Möhler, Ottmar

    2016-04-01

    Recent investigations at the cloud simulation chamber AIDA (Aerosol Interactions and Dynamics in the Atmosphere) suggest that agricultural soil dust has an ice nucleation ability that is enhanced up to a factor of 10 compared to desert dust, especially at temperatures above -26 °C (Steinke et al., in preparation for submission). This enhancement might be caused by the contribution of very ice-active biological particles. In addition, soil dust aerosol particles often contain a considerably higher amount of organic matter compared to desert dust particles. To test agricultural soil dust as a source of ice nucleating particles, especially for ice formation in warm clouds, we conducted a series of laboratory measurements with different soil dust samples to extend the existing AIDA dataset. The AIDA has a volume of 84 m3 and operates under atmospherically relevant conditions over wide ranges of temperature, pressure and humidity. By controlled adiabatic expansions, the ascent of an air parcel in the troposphere can be simulated. As a supplement to the AIDA facility, we use the INKA (Ice Nucleation Instrument of the KArlsruhe Institute of Technology) continuous flow diffusion chamber based on the design by Rogers (1988) to expose the sampled aerosol particles to a continuously increasing saturation ratio by keeping the aerosol temperature constant. For our experiments, soil dust was dry dispersed into the AIDA vessel. First, fast saturation ratio scans at different temperatures were performed with INKA, sampling soil dust aerosol particles directly from the AIDA vessel. Then, we conducted the AIDA expansion experiment starting at a preset temperature. The combination of these two different methods provides a robust data set on the temperature-dependent ice activity of various agriculture soil dust aerosol particles with a special focus on relatively high temperatures. In addition, to extend the data set, we investigated the role of biological and organic matter in more

  15. Improving ice nucleation activity of zein film through layer-by-layer deposition of extracellular ice nucleators.

    PubMed

    Shi, Ke; Yu, Hailong; Lee, Tung-Ching; Huang, Qingrong

    2013-11-13

    Zein protein has been of scientific interest in the development of biodegradable functional food packaging. This study aimed at developing a novel zein-based biopolymer film with ice nucleation activity through layer-by-layer deposition of biogenic ice nucleators, that is, extracellular ice nucleators (ECINs) isolated from Erwinia herbicola , onto zein film surface. The adsorption behaviors and mechanisms were investigated using quartz crystal microbalance with dissipation monitoring (QCM-D). On unmodified zein surface, the highest ECINs adsorption occurred at pH 5.0; on UV/ozone treated zein surface followed by deposition of poly(diallyldimethylammonium chloride) (PDADMAC) layer, the optimum condition for ECINs adsorption occurred at pH 7.0 and I 0.05 M, where the amount of ECINs adsorbed was also higher than that on unmodified zein surface. QCM-D analyses further revealed a two-step adsorption process on unmodified zein surfaces, compared to a one-step adsorption process on PDADMAC-modified zein surface. Also, significantly, in order to quantify the ice nucleation activity of ECINs-coated zein films, an empirical method was developed to correlate the number of ice nucleators with the ice nucleation temperature measured by differential scanning calorimetry. Calculated using this empirical method, the highest ice nucleation activity of ECINs on ECINs-modified zein film reached 64.1 units/mm(2), which was able to elevate the ice nucleation temperature of distilled water from -15.5 °C to -7.3 °C.

  16. Experimental analysis of bubble growth, departure and interactions during pool boiling on artificial nucleation sites

    SciTech Connect

    Siedel, S.; Cioulachtjian, S.; Bonjour, J.

    2008-09-15

    The present work describes experimental results of pentane pool boiling, simplified to the cases of boiling on a single or on two adjacent nucleation sites. Bubbles growths have been recorded by a high speed camera under various wall superheat conditions. Bubble volume has been plotted as a function of time, and an experimental growth law has been proposed. Oscillations were observed during growth, showing the interaction of one bubble with the preceding bubble released from the same nucleation site. Lateral coalescence has been visualized and the images have brought to the fore the capillary effects on the distortion of the interface. (author)

  17. Urediospores of Puccinia spp. and other rusts are warm-temperature ice nucleators and harbor ice nucleation active bacteria

    NASA Astrophysics Data System (ADS)

    Morris, C. E.; Sands, D. C.; Glaux, C.; Samsatly, J.; Asaad, S.; Moukahel, A. R.; Gonçalves, F. L. T.; Bigg, E. K.

    2012-10-01

    In light of various features of the biology of the rust fungi and of the epidemiology of the plant diseases they cause that illustrate the important role of rainfall in their life history, we have characterized the ice nucleation activity (INA) of the aerially disseminated spores (urediospores) of this group of fungi. Urediospores of this obligate plant parasite were collected from natural infections from 7 species of weeds in France, from coffee in Brazil and from field and greenhouse-grown wheat in France, the USA, Turkey and Syria. Immersion freezing was used to determine freezing onset temperatures and the abundance of ice nuclei in suspensions of washed spores. Microbiological analyses of spores and subsequent tests of the ice nucleation activity of the bacteria associated with spores were deployed to quantify the contribution of bacteria to the ice nucleation activity of the spores. All samples of spores were ice nucleation active having freezing onset temperatures as warm as -4 °C. Spores in most of the samples carried cells of ice nucleation-active strains of the bacterium Pseudomonas syringae (at rates of less than 1 bacterial cell per 100 urediospores), but bacterial INA accounted for only a small fraction of the INA observed in spore suspensions. Changes in the INA of spore suspensions after treatment with lysozyme suggest that the INA of urediospores involves a polysaccharide. Based on data from the literature, we have estimated the concentrations of urediospores in air at cloud height and in rainfall. These quantities are very similar to those reported for other biological ice nucleators in these same substrates. We suggest that air sampling techniques have ignored the spatial and temporal variability of atmospheric concentrations that occur under conditions propitious for precipitation that could increase their local abundance intermittently. Nevertheless, we propose that the relative low abundance of warm-temperature biological ice nucleators in the

  18. Activation energy paths for graphene nucleation and growth on Cu.

    PubMed

    Kim, HoKwon; Mattevi, Cecilia; Calvo, M Reyes; Oberg, Jenny C; Artiglia, Luca; Agnoli, Stefano; Hirjibehedin, Cyrus F; Chhowalla, Manish; Saiz, Eduardo

    2012-04-24

    The synthesis of wafer-scale single crystal graphene remains a challenge toward the utilization of its intrinsic properties in electronics. Until now, the large-area chemical vapor deposition of graphene has yielded a polycrystalline material, where grain boundaries are detrimental to its electrical properties. Here, we study the physicochemical mechanisms underlying the nucleation and growth kinetics of graphene on copper, providing new insights necessary for the engineering synthesis of wafer-scale single crystals. Graphene arises from the crystallization of a supersaturated fraction of carbon-adatom species, and its nucleation density is the result of competition between the mobility of the carbon-adatom species and their desorption rate. As the energetics of these phenomena varies with temperature, the nucleation activation energies can span over a wide range (1-3 eV) leading to a rational prediction of the individual nuclei size and density distribution. The growth-limiting step was found to be the attachment of carbon-adatom species to the graphene edges, which was independent of the Cu crystalline orientation.

  19. Ice Nucleation Activity in the Widespread Soil Fungus Mortierella alpina

    NASA Astrophysics Data System (ADS)

    Fröhlich-Nowoisky, J.; Hill, T. C. J.; Pummer, B. G.; Franc, G. D.; Pöschl, U.

    2014-08-01

    Biological residues in soil dust are a potentially strong source of atmospheric ice nuclei (IN). So far, however, the abundance, diversity, sources, seasonality, and role of biological - in particular, fungal - IN in soil dust have not been characterized. By analysis of the culturable fungi in topsoils, from a range of different land use and ecosystem types in south-east Wyoming, we found ice nucleation active (INA) fungi to be both widespread and abundant, particularly in soils with recent inputs of decomposable organic matter. Across all investigated soils, 8% of fungal isolates were INA. All INA isolates initiated freezing at -5 to -6 °C, and belonged to a single zygomycotic species, Mortierella alpina (Mortierellales, Mortierellomycotina). By contrast, the handful of fungal species so far reported as INA all belong within the Ascomycota or Basidiomycota phyla. M. alpina is known to be saprobic, widespread in soil and present in air and rain. Sequencing of the ITS region and the gene for γ-linolenic-elongase revealed four distinct clades, affiliated to different soil types. The IN produced by M. alpina seem to be proteinaceous, <300 kDa in size, and can be easily washed off the mycelium. Ice nucleating fungal mycelium will ramify topsoils and probably also release cell-free IN into it. If these IN survive decomposition or are adsorbed onto mineral surfaces, their contribution might accumulate over time, perhaps to be transported with soil dust and influencing its ice nucleating properties.

  20. Cellulose and Their Characteristic Ice Nucleation Activity- Freezing on a Chip

    NASA Astrophysics Data System (ADS)

    Häusler, Thomas; Felgitsch, Laura; Grothe, Hinrich

    2016-04-01

    The influence of clouds on the Earth's climate system is well known (IPCC, 2013). Cloud microphysics determines for example cloud lifetime and precipitation properties. Clouds are cooling the climate system by reflecting incoming solar radiation and warm its surface by trapping outgoing infrared radiation (Baker and Peter, 2008). In all these processes, aerosol particles play a crucial role by acting as cloud condensation nuclei (CCN) for liquid droplets and as an ice nucleation particle (INP) for the formation of ice particles. Freezing processes at higher temperatures than -38°C occur heterogeneously (Pruppacher and Klett 1997). Therefore aerosol particles act like a catalyst, which reduces the energy barrier for nucleation. The nucleation mechanisms, especially the theory of functional sites are not entirely understood. It remains unclear which class of compound nucleates ice. Here we present a unique technique to perform drop- freezing experiments in a more efficient way. A self-made freezing- chip will be presented. Measurements done to proof the efficiency of our setup as well as advantages compared with other setups will be discussed. Furthermore we present a proxy for biological INPs, microcrystalline cellulose. Cellulose is the main component of herbal cell walls (about 50 wt%). It is a polysaccharide consisting of a linear chain of several hundred to many thousands of β(1→4) linked D-glucose units. Cellulose can contribute to the diverse spectrum of ice nucleation particles. We present results of the nucleation activity measurements of MCCs as well as the influence of concentration, preparation or chemical modification.

  1. Freezing activities of flavonoids in solutions containing different ice nucleators.

    PubMed

    Kuwabara, Chikako; Wang, Donghui; Kasuga, Jun; Fukushi, Yukiharu; Arakawa, Keita; Koyama, Toshie; Inada, Takaaki; Fujikawa, Seizo

    2012-06-01

    In this study, we examined the effects on freezing of 26 kinds of flavonoid compounds, which were randomly selected as compounds with structures similar to those of flavonoid compounds existing in deep supercooling xylem parenchyma cells (XPCs) in trees, in solutions containing different kinds of ice nucleators, including the ice nucleation bacterium (INB) Erwinia ananas, INB Xanthomonas campestris, silver iodide, phloroglucinol and unidentified airborne impurities in buffered Milli-Q water (BMQW). Cumulative freezing spectra were obtained in each solution by cooling 2 μL droplets at 0.2 °C/min by a droplet freezing assay. Freezing temperature of 50% droplets (FT(50)) was obtained from each spectra in a separate analysis with more than 20 droplets and mean FT(50) were obtained from more than five separate analyses using more than 100 droplets in total in each flavonoid. Supercooling-promoting activities (SCA) or ice nucleation-enhancing activities (INA) of these flavonoids were determined by the difference in FT(50) between control solutions without flavonoids and experimental solutions with flavonoids. In mean values, most of the compounds examined exhibited SCA in solutions containing the INB E. ananas, INB X. campestris, silver iodide, and phloroglucinol although the magnitudes of their activities were different depending on the ice nucleator. In solutions containing the INB E. ananas, 10 compounds exhibited SCAs with significant differences (p<0.05) in the range of 1.4-4.2 °C. In solutions containing silver iodide, 23 compounds exhibited SCAs with significant differences in the range of 2.0-7.1 °C. In solutions containing phloroglucinol, six compounds exhibited SCAs with significant differences in the range of 2.4-3.5 °C. In solutions containing the INB X. campestris, only three compounds exhibited SCAs with significant differences in the range of 0.9-2.3 °C. In solutions containing unidentified airborne impurities (BMQW alone), on the other hand, many

  2. Freezing activities of flavonoids in solutions containing different ice nucleators.

    PubMed

    Kuwabara, Chikako; Wang, Donghui; Kasuga, Jun; Fukushi, Yukiharu; Arakawa, Keita; Koyama, Toshie; Inada, Takaaki; Fujikawa, Seizo

    2012-06-01

    In this study, we examined the effects on freezing of 26 kinds of flavonoid compounds, which were randomly selected as compounds with structures similar to those of flavonoid compounds existing in deep supercooling xylem parenchyma cells (XPCs) in trees, in solutions containing different kinds of ice nucleators, including the ice nucleation bacterium (INB) Erwinia ananas, INB Xanthomonas campestris, silver iodide, phloroglucinol and unidentified airborne impurities in buffered Milli-Q water (BMQW). Cumulative freezing spectra were obtained in each solution by cooling 2 μL droplets at 0.2 °C/min by a droplet freezing assay. Freezing temperature of 50% droplets (FT(50)) was obtained from each spectra in a separate analysis with more than 20 droplets and mean FT(50) were obtained from more than five separate analyses using more than 100 droplets in total in each flavonoid. Supercooling-promoting activities (SCA) or ice nucleation-enhancing activities (INA) of these flavonoids were determined by the difference in FT(50) between control solutions without flavonoids and experimental solutions with flavonoids. In mean values, most of the compounds examined exhibited SCA in solutions containing the INB E. ananas, INB X. campestris, silver iodide, and phloroglucinol although the magnitudes of their activities were different depending on the ice nucleator. In solutions containing the INB E. ananas, 10 compounds exhibited SCAs with significant differences (p<0.05) in the range of 1.4-4.2 °C. In solutions containing silver iodide, 23 compounds exhibited SCAs with significant differences in the range of 2.0-7.1 °C. In solutions containing phloroglucinol, six compounds exhibited SCAs with significant differences in the range of 2.4-3.5 °C. In solutions containing the INB X. campestris, only three compounds exhibited SCAs with significant differences in the range of 0.9-2.3 °C. In solutions containing unidentified airborne impurities (BMQW alone), on the other hand, many

  3. Ice nucleation active particles are efficiently removed by precipitating clouds

    PubMed Central

    Stopelli, Emiliano; Conen, Franz; Morris, Cindy E.; Herrmann, Erik; Bukowiecki, Nicolas; Alewell, Christine

    2015-01-01

    Ice nucleation in cold clouds is a decisive step in the formation of rain and snow. Observations and modelling suggest that variations in the concentrations of ice nucleating particles (INPs) affect timing, location and amount of precipitation. A quantitative description of the abundance and variability of INPs is crucial to assess and predict their influence on precipitation. Here we used the hydrological indicator δ18O to derive the fraction of water vapour lost from precipitating clouds and correlated it with the abundance of INPs in freshly fallen snow. Results show that the number of INPs active at temperatures ≥ −10 °C (INPs−10) halves for every 10% of vapour lost through precipitation. Particles of similar size (>0.5 μm) halve in number for only every 20% of vapour lost, suggesting effective microphysical processing of INPs during precipitation. We show that INPs active at moderate supercooling are rapidly depleted by precipitating clouds, limiting their impact on subsequent rainfall development in time and space. PMID:26553559

  4. Ice nucleation active particles are efficiently removed by precipitating clouds.

    PubMed

    Stopelli, Emiliano; Conen, Franz; Morris, Cindy E; Herrmann, Erik; Bukowiecki, Nicolas; Alewell, Christine

    2015-01-01

    Ice nucleation in cold clouds is a decisive step in the formation of rain and snow. Observations and modelling suggest that variations in the concentrations of ice nucleating particles (INPs) affect timing, location and amount of precipitation. A quantitative description of the abundance and variability of INPs is crucial to assess and predict their influence on precipitation. Here we used the hydrological indicator δ(18)O to derive the fraction of water vapour lost from precipitating clouds and correlated it with the abundance of INPs in freshly fallen snow. Results show that the number of INPs active at temperatures ≥ -10 °C (INPs-10) halves for every 10% of vapour lost through precipitation. Particles of similar size (>0.5 μm) halve in number for only every 20% of vapour lost, suggesting effective microphysical processing of INPs during precipitation. We show that INPs active at moderate supercooling are rapidly depleted by precipitating clouds, limiting their impact on subsequent rainfall development in time and space.

  5. Classical Nucleation Theory Description of Active Colloid Assembly

    NASA Astrophysics Data System (ADS)

    Redner, Gabriel S.; Wagner, Caleb G.; Baskaran, Aparna; Hagan, Michael F.

    2016-09-01

    Nonaligning self-propelled particles with purely repulsive excluded volume interactions undergo athermal motility-induced phase separation into a dilute gas and a dense cluster phase. Here, we use enhanced sampling computational methods and analytic theory to examine the kinetics of formation of the dense phase. Despite the intrinsically nonequilibrium nature of the phase transition, we show that the kinetics can be described using an approach analogous to equilibrium classical nucleation theory, governed by an effective free energy of cluster formation with identifiable bulk and surface terms. The theory captures the location of the binodal, nucleation rates as a function of supersaturation, and the cluster size distributions below the binodal, while discrepancies in the metastable region reveal additional physics about the early stages of active crystal formation. The success of the theory shows that a framework similar to equilibrium thermodynamics can be obtained directly from the microdynamics of an active system, and can be used to describe the kinetics of evolution toward nonequilibrium steady states.

  6. Ice nucleation active particles are efficiently removed by precipitating clouds

    NASA Astrophysics Data System (ADS)

    Stopelli, Emiliano; Conen, Franz; Morris, Cindy E.; Herrmann, Erik; Bukowiecki, Nicolas; Alewell, Christine

    2015-11-01

    Ice nucleation in cold clouds is a decisive step in the formation of rain and snow. Observations and modelling suggest that variations in the concentrations of ice nucleating particles (INPs) affect timing, location and amount of precipitation. A quantitative description of the abundance and variability of INPs is crucial to assess and predict their influence on precipitation. Here we used the hydrological indicator δ18O to derive the fraction of water vapour lost from precipitating clouds and correlated it with the abundance of INPs in freshly fallen snow. Results show that the number of INPs active at temperatures ≥ -10 °C (INPs-10) halves for every 10% of vapour lost through precipitation. Particles of similar size (>0.5 μm) halve in number for only every 20% of vapour lost, suggesting effective microphysical processing of INPs during precipitation. We show that INPs active at moderate supercooling are rapidly depleted by precipitating clouds, limiting their impact on subsequent rainfall development in time and space.

  7. Ice nucleation active particles are efficiently removed by precipitating clouds.

    PubMed

    Stopelli, Emiliano; Conen, Franz; Morris, Cindy E; Herrmann, Erik; Bukowiecki, Nicolas; Alewell, Christine

    2015-01-01

    Ice nucleation in cold clouds is a decisive step in the formation of rain and snow. Observations and modelling suggest that variations in the concentrations of ice nucleating particles (INPs) affect timing, location and amount of precipitation. A quantitative description of the abundance and variability of INPs is crucial to assess and predict their influence on precipitation. Here we used the hydrological indicator δ(18)O to derive the fraction of water vapour lost from precipitating clouds and correlated it with the abundance of INPs in freshly fallen snow. Results show that the number of INPs active at temperatures ≥ -10 °C (INPs-10) halves for every 10% of vapour lost through precipitation. Particles of similar size (>0.5 μm) halve in number for only every 20% of vapour lost, suggesting effective microphysical processing of INPs during precipitation. We show that INPs active at moderate supercooling are rapidly depleted by precipitating clouds, limiting their impact on subsequent rainfall development in time and space. PMID:26553559

  8. Ice nucleation activity in the widespread soil fungus Mortierella alpina

    NASA Astrophysics Data System (ADS)

    Fröhlich-Nowoisky, Janine; Hill, Thomas C. J.; Pummer, Bernhard G.; Yordanova, Petya; Franc, Gary D.; Pöschl, Ulrich

    2015-04-01

    Biological residues in soil dust are a potentially strong source of atmospheric ice nucleators (IN). However, the sources and characteristics of biological - in particular, fungal - IN in soil dust have not been characterized. By analysis of the culturable fungi in topsoils, from a range of different land use and ecosystem types in south-east Wyoming, we found ice nucleation active (INA, i.e., inducing ice formation in the probed range of temperature and concentration) fungi to be both widespread and abundant, particularly in soils with recent inputs of decomposable organic matter. For example, in harvested and ploughed sugar beet and potato fields, and in the organic horizon beneath Lodgepole pine forest, their relative abundances and concentrations among the cultivable fungi were 25% (8 x 103 CFU g-1), 17% (4.8 x 103 CFU g-1) and 17% (4 x 103 CFU g-1), respectively. Across all investigated soils, 8% (2.9 x 103 CFU g-1) of fungal isolates were INA. All INA isolates initiated freezing at -5° C to -6° C and all belonged to a single zygomycotic species, Mortierella alpina (Mortierellales, Mortierellomycotina). By contrast, the handful of fungal species so far reported as INA all belong within the Ascomycota or Basidiomycota phyla. Mortierella alpina is known to be saprobic (utilizing non-living organic matter), widespread in soil and present in air and rain. Sequencing of the ITS region and the gene for γ-linolenic elongase revealed four distinct clades, affiliated to different soil types. The IN produced by M. alpina seem to be extracellular proteins of 100-300 kDa in size which are not anchored in the fungal cell wall. Ice nucleating fungal mycelium will ramify topsoils and probably also release cell-free IN into it. If these IN survive decomposition or are adsorbed onto mineral surfaces, these small cell-free IN might contribute to the as yet uncharacterized pool of atmospheric IN released by soils as dusts.

  9. Effects of atmospheric conditions on ice nucleation activity of Pseudomonas

    NASA Astrophysics Data System (ADS)

    Attard, E.; Yang, H.; Delort, A.-M.; Amato, P.; Pöschl, U.; Glaux, C.; Koop, T.; Morris, C. E.

    2012-11-01

    Although ice nuclei from bacterial origin are known to be efficient at the highest temperatures known for ice catalysts, quantitative data are still needed to assess their role in cloud processes. Here we studied the effects of three typical cloud conditions (i) acidic pH (ii) NO2 and O3 exposure and (iii) UV-A exposure on the ice nucleation activity (INA) of four Pseudomonas strains. Three of the Pseudomonas syringae strains were isolated from cloud water and the phyllosphere and Pseudomonas fluorescens strain CGina-01 was isolated from Antarctic glacier ice melt. Among the three conditions tested, acidic pH caused the most significant effects on INA likely due to denaturation of the ice nucleation protein complex. Exposure to NO2 and O3 gases had no significant or only weak effects on the INA of two P. syringae strains whereas the INA of P. fluorescens CGina-01 was significantly affected. The INA of the third P. syringae strain showed variable responses to NO2 and O3 exposure. These differences in the INA of different Pseudomonas suggest that the response to atmospheric conditions could be strain-specific. After UV-A exposure, a substantial loss of viability of all four strains was observed whereas their INA decreased only slightly. This corroborates the notion that under certain conditions dead bacterial cells can maintain their INA. Overall, the negative effects of the three environmental factors on INA were more significant at the warmer temperatures. Our results suggest that in clouds where temperatures are near 0 °C, the importance of bacterial ice nucleation in precipitation processes could be reduced by some environmental factors.

  10. Effects of atmospheric conditions on ice nucleation activity of Pseudomonas

    NASA Astrophysics Data System (ADS)

    Attard, E.; Yang, H.; Delort, A.-M.; Amato, P.; Pöschl, U.; Glaux, C.; Koop, T.; Morris, C. E.

    2012-04-01

    Although ice nuclei from bacterial origin are known to be efficient at the highest temperatures known for ice catalysts, quantitative data are still needed to assess their role in cloud processes. Here we studied the effects of three typical cloud conditions (i) acidic pH (ii) NO2 and O3 exposure and (iii) UV-A exposure on the ice nucleation activity (INA) of four Pseudomonas strains. Three of the Pseudomonas syringae strains were isolated from cloud water and the phyllosphere and Pseudomonas fluorescens strain CGina-01 was isolated from Antarctic glacier ice melt. Among the three conditions tested, acidic pH caused the most significant effects on INA likely due to denaturation of the ice nucleation protein complex. Exposure to NO2 and O3 gases had no significant or only weak effects on the INA of two P. syringae strains whereas the INA of P. fluorescens CGina-01 was significantly affected. The INA of the third P. syringae strain showed variable responses to NO2 and O3 exposure. These differences in the INA of different Pseudomonas suggest that the response to atmospheric conditions could be strain-specific. After UV-A exposure, a substantial loss of viability of all four strains was observed whereas their INA decreased only slightly. This corroborates the notion that under certain conditions dead bacterial cells can maintain their INA. Overall, the negative effects of the three environmental factors on INA were more significant at the warmer temperatures. Our results suggest that in clouds where temperatures are near 0 °C, the importance of bacterial ice nucleation in precipitation processes could be reduced by some environmental factors.

  11. Rocket effluent - Its ice nucleation activity and related properties

    NASA Technical Reports Server (NTRS)

    Parungo, F. P.; Allee, P. A.

    1978-01-01

    To investigate the possibility of inadvertent weather modification from rocket effluent, aerosol samples were collected from an instrumented aircraft subsequent to the Voyager I and II launches. The aerosol's morphology, concentration and size distribution were examined with an electron microscope. The elemental compositions of individual particles were analyzed with an X-ray energy spectrometer. Ice nucleus concentration was measured with a subfreezing thermal diffusion chamber. The particles' physical and chemical properties were related to their ice nucleation activity. A laboratory experiment on rocket propellant exhaust was conducted under controlled conditions. Both laboratory and field experimental results indicated that rocket propellant exhaust can produce active ice nuclei. Their consequences for potential inadvertant weather modification demand additional study.

  12. Rocket effluent: Its ice nucleation activity and related properties

    NASA Technical Reports Server (NTRS)

    Parungo, F. P.; Allee, P. A.

    1978-01-01

    To investigate the possibility of inadvertent weather modification from rocket effluent, aerosol samples were collected from an instrumented aircraft subsequent to the Voyager 1 and 2 launches. The aerosol's morphology, concentration, and size distribution were examined with an electron microscope. The elemental compositions of individual particles were analyzed with an X-ray energy spectrometer. Ice nucleus concentration was measured with a thermal diffusion chamber. The particles' physical and chemical properties were related to their ice nucleation activity. A laboratory experiment on rocket propellant exhaust was conducted under controlled conditions. Both laboratory and field experimental results indicated that rocket propellant exhaust can produce active ice nuclei and modify local weather in suitable meteorological conditions.

  13. Locating the nucleation sites for protein encapsulated gold nanoclusters: a molecular dynamics and fluorescence study.

    PubMed

    Russell, B A; Kubiak-Ossowska, K; Mulheran, P A; Birch, D J S; Chen, Y

    2015-09-14

    Fluorescent gold nanoclusters encapsulated by proteins have attracted considerable attention in recent years for their unique properties as new fluorescence probes for biological sensing and imaging. However, fundamental questions, such as the nucleation sites of gold nanoclusters within proteins and the fluorescence mechanism remain unsolved. Here we present a study of the location of gold nanoclusters within bovine serum albumin (BSA) combining both fully atomistic molecular dynamic (MD) simulations and fluorescence spectroscopic studies. The MD simulations show gold clusters growing close to a number of cysteine sites across all three domains of BSA, although just two major sites in domains IIB and IA were found to accommodate large clusters comprising more than 12 atoms. The dependence of the fluorescence on pH is found to be compatible with possible nucleation sites in domains IIB and IA. Furthermore, the energy transfer between tryptophan and gold nanoclusters reveals a separation of 29.7 Å, further indicating that gold nanoclusters were most likely located in the major nucleation site in domain IIB. The disclosure of the precise location of the gold nanoclusters and their surrounding amino acid residues should help better understanding of their fluorescence mechanism and aid their optimization as fluorescent nanoprobes.

  14. Inducing crystallization of poly(3-hexylthiophene) nanowires by well-defined nucleation sites

    NASA Astrophysics Data System (ADS)

    Acevedo-Cartagena, Daniel; Zhang, Yue; Trabanino, Elvira; Briseno, Alejandro; Hayward, Ryan; Alejandro Briseno Collaboration; Ryan Hayward Team

    2014-03-01

    Solution crystallization of conjugated polymers promises a facile way to fabricate nano-scale structures with desirable properties for improving organic-based electronic devices. The addition of well-defined nucleation sites to a supersaturated solution can induce crystallization and allow for control over structural features. We identified conditions when homogenous nucleation of a model semicrystalline polymer, poly(3-hexylthiophene), P3HT, is suppressed, allowing for controlled crystallization into nanowires upon addition of well-defined nucleation sites. The hysteresis window between crystallization and melting temperatures of P3HT nanowires is tuned using concentration, molecular weight of the polymer, and solvent quality. We show that in this manner short P3HT nanowires (``seeds'') can be extended, though obtaining well controlled extension into linear structure remains an open challenge. In a similar fashion, graphene or graphite coated substrates were found to be excellent nucleating agents for growth of nanowire films. Northeast Alliance for Graduate Education and the Professoriate (NEAGEP), National Science Foundation Graduate Research Fellowship.

  15. Sensitivity of partially purified ice nucleation activity of Fusarium acuminatum SRSF 616.

    PubMed

    Humphreys, T L; Castrillo, L A; Lee, M R

    2001-05-01

    Factors that affect bacterial ice nucleation, including growth medium, growth phase, nutrient deprivation, and cold-temperature exposure, were investigated in the ice nucleation active (INA) fungus Fusarium acuminatum SRSF 616. Ice nucleation activity remained relatively constant throughout the growth cycle, and the cell-free culture supernatant consistently displayed higher ice nucleation activity than the hyphal pellet. Although nutrient starvation and low-temperature exposure enhance bacterial ice nucleation activity, reducing the concentration of C, N, or P in synthetischer nährstoffarmer broth (SNB) did not increase fungal ice nucleation activity, nor did exposure to 4 degrees C or 15 degrees C. From the SNB supernatant, selected INA chromatography fractions were obtained that demonstrated increased sensitivity to proteinase K and heat compared with culture supernatant. We propose that partial purification of the fungal ice nuclei resulted in removal of low-molecular-weight stabilizing factors. PMID:11400053

  16. Size-resolved measurements of ice nucleating particles at North American and European sites

    NASA Astrophysics Data System (ADS)

    Mason, R.; Si, M.; Chou, C.; Irish, V.; Dickie, R.; Elizondo, P.; Wong, R.; Brintnell, M.; Elsasser, M.; Lassar, W.; Pierce, K.; Leaitch, W. R.; Macdonald, A. M.; Platt, A.; Desiree, T. S.; Sarda Esteve, R.; Schiller, C. L.; Suski, K. J.; Hill, T. C. J.; Abbatt, J.; Huffman, J. A.; DeMott, P. J.; Bertram, A. K.

    2015-12-01

    Ice nucleating particles (INPs) are a small fraction of the total aerosol population capable of catalyzing ice formation under atmospheric conditions, and may therefore influence the albedo and lifetime of mixed-phase and ice clouds. Compared to ambient measurements of the total number concentration of INPs, relatively little data exists on the size distribution of INPs in the atmosphere. Information on the size of INPs may be useful in source identification, modeling their transport in the atmosphere, and determining the degree to which common INP instrumentation captures the full atmospheric INP population. Measured using the micro-orifice uniform deposit impactor-droplet freezing technique (MOUDI-DFT), we report immersion-mode INP number concentrations as a function of particle size at ground-level sites in North America and Europe, including Arctic, alpine, coastal, marine, agricultural, and suburban environments. On average, more than 91 % of INPs active at -15 °C were found to be supermicron in size and 62 % were in the coarse mode (> 2.5 μm). While these percentages decreased with decreasing freezing temperature, many INPs remained in the supermicron with nearly half of those active at -25 °C belonging to the coarse mode.

  17. Application of Ice Nucleation - Active Bacteria to Food

    NASA Astrophysics Data System (ADS)

    Arai, Soichi; Watanabe, Michiko

    Ice nucleation-active bacteria act as nuclei and are able to freeze water without supercooling to a great degree. They are known as a major cause of the frost damage to crops. We have been trying with success to positively apply these bacteria to freeze texturing of food materials, freeze concentration of fresh liquid foods, formation of new physical properties of foods by freezing, and so forth. The most useful species for these applications is Xanthomonas campestris which has recently been designated as a food additive by the Japan Ministry of Health and Welfare and produced on an industrial scale. This paper reviews these topics, with some practical examples quoted primarily from our studies.

  18. Biological Ice Nucleation Activity in Cloud Water (Invited)

    NASA Astrophysics Data System (ADS)

    Delort, A.

    2013-12-01

    Ice nucleation active (INA) biological particles, in particular microorganisms, were studied in cloud water. Twelve cloud samples were collected over a period of 16 months from the puy de Dôme summit (1465 m, France) using sterile cloud droplet impactors. The samples were characterized through biological (cultures, cell counts) and physico-chemical measurements (pH, ion concentrations, carbon content...), and biological ice nuclei were investigated by droplet-freezing assays from -3°C to -13°C. The concentration of total INA particles within this temperature range typically varied from ~1 to ~100 per mL of cloud water; the concentrations of biological IN were several orders of magnitude higher than the values previously reported for precipitations. At -12°C, at least 76% of the IN were biological in origin, i.e. they were inactivated by heating at 95°C, and at temperatures above -8°C only biological material could induce ice. By culture, 44 Pseudomonas-like strains of bacteria were isolated from cloud water samples; 16% of them were found INA at the temperature of -8°C and they were identified as Pseudomonas syringae, Xanthomonas sp. and Pseudoxanthomonas sp.. Two strains induced freezing at as warm as -2°C, positioning them among the most active ice nucleators described so far. We estimated that, in average, 0.18% and more than 1%.of the bacterial cells present in clouds (~104 mL-1) are INA at the temperatures of -8°C and -12°C, respectively.

  19. Direct measurement of activation time and nucleation rate in capillary-condensed water nanomeniscus

    SciTech Connect

    Sung, Baekman; Kim, Jongwoo; Stambaugh, Corey; Chang, Sung-Jin; Jhe, Wonho

    2013-11-18

    We demonstrate real-time observation of nucleation of the single water nanomeniscus formed via capillary condensation. We directly measure (i) activation time by time-resolved atomic force microscopy and (ii) nucleation rate by statistical analysis of its exponential distribution, which is the experimental evidence that the activation process is stochastic and follows the Poisson statistics. It implies that formation of the water nanomeniscus is triggered by nucleation, which requires activation for producing a nucleus. We also find the dependence of the nucleation rate on the tip-sample distance and temperature.

  20. Characterizing Ice Nucleating Particles Emitted from Agricultural Activities and Natural Landscapes

    NASA Astrophysics Data System (ADS)

    Suski, K. J.; Levin, E. J.; DeMott, P. J.; Kreidenweis, S. M.; Hill, T. C. J.

    2015-12-01

    Soil dust and plant fragment emissions from agricultural harvesting and natural ecosystems are two potentially large, yet unquantified and largely uncharacterized, sources of ice nucleating particles (INPs). Both organic and mineral components have been shown to contribute to the ice-nucleating ability of soil dust, but apart from the likely presence of ice nucleation-active bacteria, little is known about the ice nucleating potential of plant tissues. This work aims to identify and differentiate the organic and inorganic contributions of soil and plant INP sources emitted from harvesting activities and natural landscapes. For this purpose, the CSU Continuous Flow Diffusion Chamber (CFDC) and the Ice Spectrometer (IS) were utilized in a combination of ambient measurements and laboratory studies. Small variability and low INP numbers (< 10 L-1 at -30 °C) characterized measurements made in air over the grazed Pawnee National Grassland in Colorado, while more variable INP over croplands around the DOE-ARM SGP site in Oklahoma appear linked to regional wind, humidity, and rainfall conditions. Harvesting of milo (grain sorghum), soybean, and wheat at an experimental research farm in Kansas resulted in spikes of INPs, with wheat harvesting producing the largest INP concentrations (up to 100 L-1 at -30 °C). In-situ use of heating tubes upstream of the CFDC to deactivate organic INP showed that milo and wheat harvest emissions showed a stronger reduction of INPs at warm temperatures than soybean emissions, suggesting a larger contribution of organics to their INP activity. Further characterization of the sources and organic and inorganic contributions to terrestrially emitted INPs by comparison to laboratory studies on collected soil dust and plant samples will also be presented.

  1. Identification and quantification of ice nucleation active microorganisms by digital droplet PCR (ddPCR)

    NASA Astrophysics Data System (ADS)

    Linden, Martin; Pöschl, Ulrich; Fröhlich-Nowoisky, Janine

    2015-04-01

    Several bioaerosol types, including bacteria, fungi, pollen and lichen, have been identified as sources of biological ice nucleators (IN) which induce ice formation already at temperatures as high as -10 °C or above. Accordingly, they potentially contribute widely to environmental ice nucleation in the atmosphere and are of great interest in the study of natural heterogenous ice nucleation processes. Ice nucleation active microorganisms have been found and studied among bacteria (Proteobacteria) and fungi (phyla Basidiomycota and Ascomycota). The mechanisms enabling the microorganisms to ice nucleation are subject to ongoing research. While it has been demonstrated that whole cells can act as ice nucleators in the case of bacteria due to the presence of specific membrane proteins, cell-free ice nucleation active particles seem to be responsible for this phenomenon in fungi and lichen. The identification and quantification of these ice nucleation active microorganisms and their IN in atmospheric samples is crucial to understand their contribution to the pool of atmospheric IN. This is not a trivial task since the respective microorganisms are often prevalent in lowest concentrations and a variety of states, be it viable cells, spores or cell debris from dead cells. Molecular biology provides tools to identify and quantify ice nucleation active microorganisms independent of their state by detecting genetic markers specific for the organism of interest. Those methods are not without their drawbacks in terms of sample material concentration required or reliable standardization. Digital Droplet Polymerase Chain Reaction (ddPCR) was chosen for our demands as a more elegant, quick and specific method in the investigation of ice nucleation active microorganisms in atmospheric samples. The advantages of ddPCR lie in the simultaneous detection and quantification of genetic markers and their original copy numbers in a sample. This is facilitated by the fractionation of the

  2. Spores of most common airborne fungi reveal no ice nucleation activity

    NASA Astrophysics Data System (ADS)

    Pummer, B. G.; Atanasova, L.; Bauer, H.; Bernardi, J.; Druzhinina, I. S.; Grothe, H.

    2013-06-01

    Fungal spores are ubiquitous biological aerosols, which are considered to show ice nucleation (IN) activity. In this study the respective IN activity was tested in oil emulsion in the immersion freezing mode. The focus was laid on species of economical, ecological or sanitary significance. For the first time, not only common moulds, but also edible mushrooms (Basidiomycota, Agaricomycetes) were investigated, as they contribute massively to the total amount of fungal spores in the atmosphere. Only Fusarium avenaceum showed freezing events at low subzero-temperatures, while the other investigated fungal spores showed no significant IN activity. Furthermore, we selected a set of fungal strains from different sites and exposed them to occasional freezing stress during cultivation. Although the total protein expression was altered by this treatment, it had no significant impact on the IN activity.

  3. Enhancing effect of 4-hydroxy-3-nitrophenylacetic acid on transcription of the ice nucleation-active gene of Xanthomonas campestris.

    PubMed

    Watanabe, M; Watanabe, J; Michigami, Y

    1994-12-01

    Cultivation of an ice nucleation-active strain of Xanthomonas campestris in the presence (1 ppm) of 4-hydroxy-3-nitrophenylacetic acid resulted in enhancement of its ice-nucleation activity. Both the ice-nucleation-active protein, InaX, and its mRNA were effectively expressed in the bacterial cells cultured in the presence of this compound. This indicates that this compound stimulated the biosynthesis of the ice-nucleation-active protein. PMID:7765721

  4. Anti-ice nucleating activity of polyphenol compounds against silver iodide.

    PubMed

    Koyama, Toshie; Inada, Takaaki; Kuwabara, Chikako; Arakawa, Keita; Fujikawa, Seizo

    2014-10-01

    Freeze-avoiding organisms survive sub-zero temperatures without freezing in several ways, such as removal of ice nucleating agents (INAs), production of polyols, and dehydration. Another way is production of anti-ice nucleating agents (anti-INAs), such as has been reported for several antifreeze proteins (AFPs) and polyphenols, that inhibit ice nucleation by inactivating INAs. In this study, the anti-ice nucleating activity of five polyphenol compounds, including flavonoid and tannin compounds of both biological and synthetic origin, against silver iodide (AgI) was examined by measuring the ice nucleation temperature in emulsified polyphenol solutions containing AgI particles. The emulsified solutions eliminated the influence of contamination by unidentified INAs, thus enabling examination of the anti-ice nucleating activity of the polyphenols against AgI alone. Results showed that all five polyphenol compounds used here have anti-ice nucleating activities that are unique compared with other known anti-INAs, such as fish AFPs (type I and III) and synthetic polymers (poly(vinyl alcohol), poly(vinylpyrrolidone) and poly(ethylene glycol)). All five polyphenols completely inactivated the ice nucleating activity of AgI even at relatively low temperatures, and the first ice nucleation event was observed at temperatures between -14.1 and -19.4°C, compared with between -8.6 and -11.8°C for the fish AFPs and three synthetic polymers. These anti-ice nucleating activities of the polyphenols at such low temperatures are promising properties for practical applications where freezing should be prevented.

  5. Anti-ice nucleating activity of polyphenol compounds against silver iodide.

    PubMed

    Koyama, Toshie; Inada, Takaaki; Kuwabara, Chikako; Arakawa, Keita; Fujikawa, Seizo

    2014-10-01

    Freeze-avoiding organisms survive sub-zero temperatures without freezing in several ways, such as removal of ice nucleating agents (INAs), production of polyols, and dehydration. Another way is production of anti-ice nucleating agents (anti-INAs), such as has been reported for several antifreeze proteins (AFPs) and polyphenols, that inhibit ice nucleation by inactivating INAs. In this study, the anti-ice nucleating activity of five polyphenol compounds, including flavonoid and tannin compounds of both biological and synthetic origin, against silver iodide (AgI) was examined by measuring the ice nucleation temperature in emulsified polyphenol solutions containing AgI particles. The emulsified solutions eliminated the influence of contamination by unidentified INAs, thus enabling examination of the anti-ice nucleating activity of the polyphenols against AgI alone. Results showed that all five polyphenol compounds used here have anti-ice nucleating activities that are unique compared with other known anti-INAs, such as fish AFPs (type I and III) and synthetic polymers (poly(vinyl alcohol), poly(vinylpyrrolidone) and poly(ethylene glycol)). All five polyphenols completely inactivated the ice nucleating activity of AgI even at relatively low temperatures, and the first ice nucleation event was observed at temperatures between -14.1 and -19.4°C, compared with between -8.6 and -11.8°C for the fish AFPs and three synthetic polymers. These anti-ice nucleating activities of the polyphenols at such low temperatures are promising properties for practical applications where freezing should be prevented. PMID:25086201

  6. Spores of many common airborne fungi reveal no ice nucleation activity in oil immersion freezing experiments

    NASA Astrophysics Data System (ADS)

    Pummer, B. G.; Atanasova, L.; Bauer, H.; Bernardi, J.; Druzhinina, I. S.; Fröhlich-Nowoisky, J.; Grothe, H.

    2013-12-01

    Fungal spores are ubiquitous biological aerosols, which are considered to act as ice nuclei. In this study the ice nucleation (IN) activity of spores harvested from 29 fungal strains belonging to 21 different species was tested in the immersion freezing mode by microscopic observation of water-in-oil emulsions. Spores of 8 of these strains were also investigated in a microdroplet freezing array instrument. The focus was laid on species of economical, ecological or sanitary significance. Besides common molds (Ascomycota), some representatives of the widespread group of mushrooms (Basidiomycota) were also investigated. Fusarium avenaceum was the only sample showing IN activity at relatively high temperatures (about 264 K), while the other investigated fungal spores showed no freezing above 248 K. Many of the samples indeed froze at homogeneous ice nucleation temperatures (about 237 K). In combination with other studies, this suggests that only a limited number of species may act as atmospheric ice nuclei. This would be analogous to what is already known for the bacterial ice nuclei. Apart from that, we selected a set of fungal strains from different sites and exposed them to occasional freezing stress during their cultivation. This was in order to test if the exposure to a cold environment encourages the expression of ice nuclei during growth as a way of adaptation. Although the total protein expression was altered by this treatment, it had no significant impact on the IN activity.

  7. Preferential sites for InAsP/InP quantum wire nucleation using molecular dynamics

    NASA Astrophysics Data System (ADS)

    Nuñez-Moraleda, Bernardo; Pizarro, Joaquin; Guerrero, Elisa; Guerrero-Lebrero, Maria P.; Yáñez, Andres; Molina, Sergio Ignacio; Galindo, Pedro Luis

    2014-11-01

    In this paper, stress fields at the surface of the capping layer of self-assembled InAsP quantum wires grown on an InP (001) substrate have been determined from atomistic models using molecular dynamics and Stillinger-Weber potentials. To carry out these calculations, the quantum wire compositional distribution was extracted from previous works, where the As and P distributions were determined by electron energy loss spectroscopy and high-resolution aberration-corrected Z-contrast imaging. Preferential sites for the nucleation of wires on the surface of the capping layer were studied and compared with (i) previous simulations using finite element analysis to solve anisotropic elastic theory equations and (ii) experimentally measured locations of stacked wires. Preferential nucleation sites of stacked wires were determined by the maximum stress location at the MD model surface in good agreement with experimental results and those derived from finite element analysis. This indicates that MD simulations based on empirical potentials provide a suitable and flexible tool to study strain dependent atom processes.

  8. Ice nucleating particles at a coastal marine boundary layer site: correlations with aerosol type and meteorological conditions

    NASA Astrophysics Data System (ADS)

    Mason, R. H.; Si, M.; Li, J.; Chou, C.; Dickie, R.; Toom-Sauntry, D.; Pöhlker, C.; Yakobi-Hancock, J. D.; Ladino, L. A.; Jones, K.; Leaitch, W. R.; Schiller, C. L.; Abbatt, J. P. D.; Huffman, J. A.; Bertram, A. K.

    2015-11-01

    Information on what aerosol particle types are the major sources of ice nucleating particles (INPs) in the atmosphere is needed for climate predictions. To determine which aerosol particles are the major sources of immersion-mode INPs at a coastal site in Western Canada, we investigated correlations between INP number concentrations and both concentrations of different atmospheric particles and meteorological conditions. We show that INP number concentrations are strongly correlated with the number concentrations of fluorescent bioparticles between -15 and -25 °C, and that the size distribution of INPs is most consistent with the size distribution of fluorescent bioparticles. We conclude that biological particles were likely the major source of ice nuclei at freezing temperatures between -15 and -25 °C at this site for the time period studied. At -30 °C, INP number concentrations are also well correlated with number concentrations of the total aerosol particles ≥ 0.5 μm, suggesting that non-biological particles may have an important contribution to the population of INPs active at this temperature. As we found that black carbon particles were unlikely to be a major source of ice nuclei during this study, these non-biological INPs may include mineral dust. Furthermore, correlations involving chemical tracers of marine aerosols and marine biological activity, sodium and methanesulfonic acid, indicate that the majority of INPs measured at the coastal site likely originated from terrestrial rather than marine sources. Finally, six existing empirical parameterizations of ice nucleation were tested to determine if they accurately predict the measured INP number concentrations. We found that none of the parameterizations selected are capable of predicting INP number concentrations with high accuracy over the entire temperature range investigated. This finding illustrates that additional measurements are needed to improve parameterizations of INPs and their

  9. Integrating laboratory and field data to quantify the immersion freezing ice nucleation activity of mineral dust particles

    DOE PAGES

    DeMott, P. J.; Prenni, A. J.; McMeeking, G. R.; Sullivan, R. C.; Petters, M. D.; Tobo, Y.; Niemand, M.; Möhler, O.; Snider, J. R.; Wang, Z.; et al

    2014-06-27

    freezing surface active site density parameterization for mineral dust particles, developed separately from AIDA experimental data alone, shows excellent agreement for data collected in a descent through a Saharan aerosol layer. These studies support the utility of laboratory measurements to obtain atmospherically-relevant data on the ice nucleation properties of dust and other particle types, and suggest the suitability of considering all mineral dust as a single type of ice nucleating particle as a useful first order approximation in numerical modeling investigations.« less

  10. Integrating laboratory and field data to quantify the immersion freezing ice nucleation activity of mineral dust particles

    DOE PAGES

    DeMott, P. J.; Prenni, A. J.; McMeeking, G. R.; Sullivan, R. C.; Petters, M. D.; Tobo, Y.; Niemand, M.; Möhler, O.; Snider, J. R.; Wang, Z.; et al

    2015-01-13

    correction, to predictions of the immersion freezing surface active site density parameterization for mineral dust particles, developed separately from AIDA experimental data alone, shows excellent agreement for data collected in a descent through a Saharan aerosol layer. These studies support the utility of laboratory measurements to obtain atmospherically relevant data on the ice nucleation properties of dust and other particle types, and suggest the suitability of considering all mineral dust as a single type of ice nucleating particle as a useful first-order approximation in numerical modeling investigations.« less

  11. Ice nucleation activity in various tissues of Rhododendron flower buds: their relevance to extraorgan freezing.

    PubMed

    Ishikawa, Masaya; Ishikawa, Mikiko; Toyomasu, Takayuki; Aoki, Takayuki; Price, William S

    2015-01-01

    Wintering flower buds of cold hardy Rhododendron japonicum cooled slowly to subfreezing temperatures are known to undergo extraorgan freezing, whose mechanisms remain obscure. We revisited this material to demonstrate why bud scales freeze first in spite of their lower water content, why florets remain deeply supercooled and how seasonal adaptive responses occur in regard to extraorgan freezing in flower buds. We determined ice nucleation activity (INA) of various flower bud tissues using a test tube-based assay. Irrespective of collection sites, outer and inner bud scales that function as ice sinks in extraorgan freezing had high INA levels whilst florets that remain supercooled and act as a water source lacked INA. The INA level of bud scales was not high in late August when flower bud formation was ending, but increased to reach the highest level in late October just before the first autumnal freeze. The results support the following hypothesis: the high INA in bud scales functions as the subfreezing sensor, ensuring the primary freezing in bud scales at warmer subzero temperatures, which likely allows the migration of floret water to the bud scales and accumulation of icicles within the bud scales. The low INA in the florets helps them remain unfrozen by deep supercooling. The INA in the bud scales was resistant to grinding and autoclaving at 121(∘)C for 15 min, implying the intrinsic nature of the INA rather than of microbial origin, whilst the INA in stem bark was autoclaving-labile. Anti-nucleation activity (ANA) was implicated in the leachate of autoclaved bud scales, which suppresses the INA at millimolar levels of concentration and likely differs from the colligative effects of the solutes. The tissue INA levels likely contribute to the establishment of freezing behaviors by ensuring the order of freezing in the tissues: from the primary freeze to the last tissue remaining unfrozen.

  12. Ice nucleation activity in various tissues of Rhododendron flower buds: their relevance to extraorgan freezing.

    PubMed

    Ishikawa, Masaya; Ishikawa, Mikiko; Toyomasu, Takayuki; Aoki, Takayuki; Price, William S

    2015-01-01

    Wintering flower buds of cold hardy Rhododendron japonicum cooled slowly to subfreezing temperatures are known to undergo extraorgan freezing, whose mechanisms remain obscure. We revisited this material to demonstrate why bud scales freeze first in spite of their lower water content, why florets remain deeply supercooled and how seasonal adaptive responses occur in regard to extraorgan freezing in flower buds. We determined ice nucleation activity (INA) of various flower bud tissues using a test tube-based assay. Irrespective of collection sites, outer and inner bud scales that function as ice sinks in extraorgan freezing had high INA levels whilst florets that remain supercooled and act as a water source lacked INA. The INA level of bud scales was not high in late August when flower bud formation was ending, but increased to reach the highest level in late October just before the first autumnal freeze. The results support the following hypothesis: the high INA in bud scales functions as the subfreezing sensor, ensuring the primary freezing in bud scales at warmer subzero temperatures, which likely allows the migration of floret water to the bud scales and accumulation of icicles within the bud scales. The low INA in the florets helps them remain unfrozen by deep supercooling. The INA in the bud scales was resistant to grinding and autoclaving at 121(∘)C for 15 min, implying the intrinsic nature of the INA rather than of microbial origin, whilst the INA in stem bark was autoclaving-labile. Anti-nucleation activity (ANA) was implicated in the leachate of autoclaved bud scales, which suppresses the INA at millimolar levels of concentration and likely differs from the colligative effects of the solutes. The tissue INA levels likely contribute to the establishment of freezing behaviors by ensuring the order of freezing in the tissues: from the primary freeze to the last tissue remaining unfrozen. PMID:25859249

  13. Ice nucleation activity in various tissues of Rhododendron flower buds: their relevance to extraorgan freezing

    PubMed Central

    Ishikawa, Masaya; Ishikawa, Mikiko; Toyomasu, Takayuki; Aoki, Takayuki; Price, William S.

    2015-01-01

    Wintering flower buds of cold hardy Rhododendron japonicum cooled slowly to subfreezing temperatures are known to undergo extraorgan freezing, whose mechanisms remain obscure. We revisited this material to demonstrate why bud scales freeze first in spite of their lower water content, why florets remain deeply supercooled and how seasonal adaptive responses occur in regard to extraorgan freezing in flower buds. We determined ice nucleation activity (INA) of various flower bud tissues using a test tube-based assay. Irrespective of collection sites, outer and inner bud scales that function as ice sinks in extraorgan freezing had high INA levels whilst florets that remain supercooled and act as a water source lacked INA. The INA level of bud scales was not high in late August when flower bud formation was ending, but increased to reach the highest level in late October just before the first autumnal freeze. The results support the following hypothesis: the high INA in bud scales functions as the subfreezing sensor, ensuring the primary freezing in bud scales at warmer subzero temperatures, which likely allows the migration of floret water to the bud scales and accumulation of icicles within the bud scales. The low INA in the florets helps them remain unfrozen by deep supercooling. The INA in the bud scales was resistant to grinding and autoclaving at 121∘C for 15 min, implying the intrinsic nature of the INA rather than of microbial origin, whilst the INA in stem bark was autoclaving-labile. Anti-nucleation activity (ANA) was implicated in the leachate of autoclaved bud scales, which suppresses the INA at millimolar levels of concentration and likely differs from the colligative effects of the solutes. The tissue INA levels likely contribute to the establishment of freezing behaviors by ensuring the order of freezing in the tissues: from the primary freeze to the last tissue remaining unfrozen. PMID:25859249

  14. Analysis of the Effect of Water Activity on Ice Formation Using a New Theory of Nucleation

    NASA Technical Reports Server (NTRS)

    Barahona, Donifan

    2013-01-01

    In this work a new theory of nucleation is developed and used to investigate the effect of water activity on the formation of ice within super-cooled droplets. The new theory is based on a novel concept where the interface is assumed to be made of liquid molecules trapped by the solid matrix. Using this concept new expressions are developed for the critical ice germ size and the nucleation work, with explicit dependencies on temperature and water activity. However unlike previous approaches, the new theory does not depend on the interfacial tension between liquid and ice. Comparison against experimental results shows that the new theory is able to reproduce the observed effect of water activity on nucleation rate and freezing temperature. It allows for the first time a theoretical derivation of the constant shift in water activity between melting and nucleation. The new theory offers a consistent thermodynamic view of ice nucleation, simple enough to be applied in atmospheric models of cloud formation.

  15. Heterogeneous ice nucleation in aqueous solutions: the role of water activity.

    PubMed

    Zobrist, B; Marcolli, C; Peter, T; Koop, T

    2008-05-01

    Heterogeneous ice nucleation experiments have been performed with four different ice nuclei (IN), namely nonadecanol, silica, silver iodide and Arizona test dust. All IN are either immersed in the droplets or located at the droplets surface. The IN were exposed to various aqueous solutions, which consist of (NH4)2SO4, H2SO4, MgCl2, NaCl, LiCl, Ca(NO3)2, K2CO3, CH3COONa, ethylene glycol, glycerol, malonic acid, PEG300 or a NaCl/malonic acid mixture. Freezing was studied using a differential scanning calorimeter and a cold finger cell. The results show that the heterogeneous ice freezing temperatures decrease with increasing solute concentration; however, the magnitude of this effect is solute dependent. In contrast, when the results are analyzed in terms of the solution water activity a very consistent behavior emerges: heterogeneous ice nucleation temperatures for all four IN converge each onto a single line, irrespective of the nature of the solute. We find that a constant offset with respect to the ice melting point curve, Deltaaw,het, can describe the observed freezing temperatures for each IN. Such a behavior is well-known for homogeneous ice nucleation from supercooled liquid droplets and has led to the development of water-activity-based ice nucleation theory. The large variety of investigated solutes together with different general types of ice nuclei studied (monolayers, ionic crystals, covalently bound network-forming compounds, and a mixture of chemically different crystallites) underlines the general applicability of water-activity-based ice nucleation theory also for heterogeneous ice nucleation in the immersion mode. Finally, the ice nucleation efficiencies of the various IN, as well as the atmospheric implication of the developed parametrization are discussed. PMID:18363389

  16. Soot Aerosol Particles as Cloud Condensation Nuclei: from Ice Nucleation Activity to Ice Crystal Morphology

    NASA Astrophysics Data System (ADS)

    Pirim, Claire; Ikhenazene, Raouf; Ortega, Isamel Kenneth; Carpentier, Yvain; Focsa, Cristian; Chazallon, Bertrand; Ouf, François-Xavier

    2016-04-01

    Emissions of solid-state particles (soot) from engine exhausts due to incomplete fuel combustion is considered to influence ice and liquid water cloud droplet activation [1]. The activity of these aerosols would originate from their ability to be important centers of ice-particle nucleation, as they would promote ice formation above water homogeneous freezing point. Soot particles are reported to be generally worse ice nuclei than mineral dust because they activate nucleation at higher ice-supersaturations for deposition nucleation and at lower temperatures for immersion freezing than ratios usually expected for homogeneous nucleation [2]. In fact, there are still numerous opened questions as to whether and how soot's physico-chemical properties (structure, morphology and chemical composition) can influence their nucleation ability. Therefore, systematic investigations of soot aerosol nucleation activity via one specific nucleation mode, here deposition nucleation, combined with thorough structural and compositional analyzes are needed in order to establish any association between the particles' activity and their physico-chemical properties. In addition, since the morphology of the ice crystals can influence their radiative properties [3], we investigated their morphology as they grow over both soot and pristine substrates at different temperatures and humidity ratios. In the present work, Combustion Aerosol STandart soot samples were produced from propane using various experimental conditions. Their nucleation activity was studied in deposition mode (from water vapor), and monitored using a temperature-controlled reactor in which the sample's relative humidity is precisely measured with a cryo-hygrometer. Formation of water/ice onto the particles is followed both optically and spectroscopically, using a microscope coupled to a Raman spectrometer. Vibrational signatures of hydroxyls (O-H) emerge when the particle becomes hydrated and are used to characterize ice

  17. Ferritin protein nanocages use ion channels, catalytic sites, and nucleation channels to manage iron/oxygen chemistry.

    PubMed

    Theil, Elizabeth C

    2011-04-01

    The ferritin superfamily is composed of ancient, nanocage proteins with an internal cavity, 60% of total volume, that reversibly synthesize solid minerals of hydrated ferric oxide; the minerals are iron concentrates for cell nutrition as well as antioxidants due to ferrous and oxygen consumption during mineralization. The cages have multiple iron entry/exit channels, oxidoreductase enzyme sites, and, in eukaryotes, Fe(III)O nucleation channels with clustered exits that extend protein activity to include facilitated mineral growth. Ferritin protein cage differences include size, amino acid sequence, and location of the active sites, oxidant substrate and crystallinity of the iron mineral. Genetic regulation depends on iron and oxygen signals, which in animals includes direct ferrous signaling to RNA to release and to ubiquitin-ligases to degrade the protein repressors. Ferritin biosynthesis forms, with DNA, mRNA and the protein product, a feedback loop where the genetic signals are also protein substrates. The ferritin protein nanocages, which are required for normal iron homeostasis and are finding current use in the delivery of nanodrugs, novel nanomaterials, and nanocatalysts, are likely contributors to survival and success during the transition from anaerobic to aerobic life.

  18. Active control of the nucleation temperature enhances freezing survival of multipotent mesenchymal stromal cells.

    PubMed

    Lauterboeck, L; Hofmann, N; Mueller, T; Glasmacher, B

    2015-12-01

    Cryopreservation is a technique that has been extensively used for storage of multipotent mesenchymal stromal cells (MSCs) in regenerative medicine. Therefore, improving current cryopreservation procedures in terms of increasing cell viability and functionality is important. In this study, we optimized the cryopreservation protocol of MSCs derived from the common marmoset Callithrix jacchus (cj), which can be used as a non-human primate model in various pathological and transplantation studies and have a great potential for regenerative medicine. We have investigated the effect of the active control of the nucleation temperature using induced nucleation at a broad range of temperatures and two different dimethylsulfoxide concentrations (Me2SO, 5% (v/v) and 10%, (v/v)) to evaluate the overall effect on the viability, metabolic activity and recovery of cells after thawing. Survival rate and metabolic activity displayed an optimum when ice formation was induced at -10 °C. Cryomicroscopy studies indicated differences in ice crystal morphologies as well as differences in intracellular ice formation with different nucleation temperatures. High subzero nucleation temperatures resulted in larger extracellular ice crystals and cellular dehydration, whereas low subzero nucleation temperatures resulted in smaller ice crystals and intracellular ice formation. PMID:26499840

  19. Topical Application of Ice-Nucleating-Active Bacteria Decreases Insect Cold Tolerance †

    PubMed Central

    Strong-Gunderson, Janet M.; Lee, Richard E.; Lee, Marcia R.

    1992-01-01

    The majority of overwintering insects avoid lethal freezing by lowering the temperature at which ice spontaneously nucleates within their body fluids. We examined the effect of ice-nucleating-active bacteria on the cold-hardiness of the lady beetle, Hippodamia convergens, a freeze-intolerant species that overwinters by supercooling to ca. −16°C. Topical application of the ice-nucleating-active bacteria Pseudomonas syringae increased the supercooling point to temperatures as high as −3°C. This decrease in cold tolerance was maintained for at least 3 days after treatment. Various treatment doses (108, 106, and 104 bacteria per ml) and modes of action (bacterial ingestion and topical application) were also compared. At the highest concentration of topically applied P. syringae, 50% of the beetles froze between −2 and −4°C. After topical application at the lowest concentration, 50% of the individuals froze by −11°C. In contrast, beetles fed bacteria at this concentration did not begin to freeze until −10°C, and 50% were frozen only at temperatures of −13°C or less. In addition to reducing the supercooling capacity in H. convergens, ice-nucleating-active bacteria also significantly reduced the cold-hardiness of four additional insects. These data demonstrate that ice-nucleating-active bacteria can be used to elevate the supercooling point and thereby decrease insect cold tolerance. The results of this study support the proposition that ice-nucleating-active bacteria may be used as a biological insecticide for the control of insect pests during the winter. Images PMID:16348764

  20. Isolation of ice-nucleating active bacteria from the freeze-tolerant frog, Rana sylvatica.

    PubMed

    Lee, M R; Lee, R E; Strong-Gunderson, J M; Minges, S R

    1995-08-01

    Ice-nucleating active (INA) bacteria were isolated from the gut of field-collected freeze-tolerant wood frogs (Rana sylvatica) collected in winter. Thirteen strains of Pseudomonas fluorescens, four strains of Pseudomonas putida, and two strains of Enterobacter agglomerans had ice-nucleating activity. Each of the INA pseudomonad strains was psychrophilic. P. putida strains were differentiated from P. fluorescens strains by gelatinase, lecithinase, and lipase production. The maximum nucleation temperatures (Tmax) of aqueous suspensions (10(9) bacteria/ml) of the four INA P. putida strains ranged from -1.6 to -3.0 degrees C, which places this INA species among the most potent known biological nucleators. Ingestion of INA P. putida isolated from R. sylvatica by another freeze-tolerant frog. Pseudacris crucifer, decreased the capacity of this frog to supercool and remain unfrozen at -2 degrees C. This is the first report of INA bacteria isolated from a vertebrate, and suggests that, as part of the gut flora in some posthibernation freeze-tolerant wood frogs, these bacteria may play a role in enhancing winter survival by promoting ice nucleation at high subzero temperatures (ca. -2 degrees C). PMID:7656570

  1. Analysis of supercooling-facilitating (anti-ice nucleation) activity of flavonol glycosides.

    PubMed

    Kasuga, Jun; Fukushi, Yukiharu; Kuwabara, Chikako; Wang, Donghui; Nishioka, Atsushi; Fujikawa, Emiko; Arakawa, Keita; Fujikawa, Seizo

    2010-04-01

    Deep supercooling xylem parenchyma cells (XPCs) of katsura tree (Cercidiphyllum japonicum) contain four kinds of flavonol glycosides with high supercooling-facilitating (anti-ice nucleation) activities. These flavonol glycosides have very similar structures, but their supercooling-facilitating activities are very different. In this study, we analyzed the supercooling-facilitating activities of 12 kinds of flavonol glycosides in order to determine the chemical structures that might affect supercooling-facilitating activity. All of the flavonol glycosides tested showed supercooling-facilitating activity, although the magnitudes of activity differed among the compounds. It was clear that the combination of the position of attachment of the glycosyl moiety, the kind of attached glycosyl moiety and the structure of aglycone determined the magnitude of anti-ice nucleation activity. However, there is still some ambiguity preventing the exact identification of features that affect the magnitude of supercooling-facilitating activity.

  2. Pre-activation of ice-nucleating particles by the pore condensation and freezing mechanism

    NASA Astrophysics Data System (ADS)

    Wagner, Robert; Kiselev, Alexei; Möhler, Ottmar; Saathoff, Harald; Steinke, Isabelle

    2016-02-01

    In spite of the resurgence in ice nucleation research a comparatively small number of studies deal with the phenomenon of pre-activation in heterogeneous ice nucleation. Fifty years ago, it was shown that various mineral dust and volcanic ash particles can be pre-activated to become nuclei for ice crystal formation even at temperatures as high as 270-271 K. Pre-activation was achieved under ice-subsaturated conditions without any preceding macroscopic ice growth by just temporarily cooling the particles to temperatures below 228 K. A two-step mechanism involving capillary condensation of supercooled water and subsequent homogeneous freezing was proposed to account for the particles' enhanced ice nucleation ability at high temperatures. This work reinvestigates the efficiency of the proposed pre-activation mechanism in temperature-cycling experiments performed in a large cloud chamber with suspended particles. We find the efficiency to be highest for the clay mineral illite as well as for highly porous materials like zeolite and diatomaceous earth, whereas most aerosols generated from desert dust surface samples did not reveal a measurable pre-activation ability. The pre-activation efficiency is linked to particle pores in a certain size range. As estimated by model calculations, only pores with diameters between about 5 and 8 nm contribute to pre-activation under ice-subsaturated conditions. This range is set by a combination of requirements from the negative Kelvin effect for condensation and a critical size of ice embryos for ice nucleation and melting. In contrast to the early study, pre-activation is only observed for temperatures below 260 K. Above that threshold, the particles' improved ice nucleation ability disappears due to the melting of ice in the pores.

  3. Role of ice nucleation and antifreeze activities in pathogenesis and growth of snow molds.

    PubMed

    Snider, C S; Hsiang, T; Zhao, G; Griffith, M

    2000-04-01

    ABSTRACT We examined the ability of snow molds to grow at temperatures from -5 to 30 degrees C and to influence the growth of ice through assays for ice nucleation and antifreeze activities. Isolates of Coprinus psychromorbidus (low temperature basidiomycete variant), Microdochium nivale, Typhula phacorrhiza, T. ishikariensis, T. incarnata, and T. canadensis all grew at -5 degrees C, whereas Sclerotinia borealis and S. homoeocarpa did not grow at temperatures below 4 degrees C. The highest threshold ice nucleation temperature was -7 degrees C. Because snow molds are most damaging to their hosts at temperatures above this, our results imply that the pathogenesis of these fungi is not dependent on ice nucleation activity to cause freeze-wounding of host plants. All snow molds that grew at subzero temperatures also exhibited antifreeze activity in the growth medium and in the soluble and insoluble hyphal fractions, with the exception of M. nivale and one isolate of T. canadensis. The lack of high ice nucleation activity combined with the presence of antifreeze activity in all fungal fractions indicates that snow molds can moderate their environment to inhibit or modify intra- and extracellular ice formation, which helps explain their ability to grow at subzero temperatures under snow cover.

  4. Strain analysis for the prediction of the preferential nucleation sites of stacked quantum dots by combination of FEM and APT

    PubMed Central

    2013-01-01

    The finite elements method (FEM) is a useful tool for the analysis of the strain state of semiconductor heterostructures. It has been used for the prediction of the nucleation sites of stacked quantum dots (QDs), but often using either simulated data of the atom positions or two-dimensional experimental data, in such a way that it is difficult to assess the validity of the predictions. In this work, we assess the validity of the FEM method for the prediction of stacked QD nucleation sites using three-dimensional experimental data obtained by atom probe tomography (APT). This also allows us to compare the simulation results with the one obtained experimentally. Our analysis demonstrates that FEM and APT constitute a good combination to resolve strain–stress problems of epitaxial semiconductor structures. PMID:24308663

  5. Cavitation nucleation

    NASA Astrophysics Data System (ADS)

    Crum, Lawrence A.

    2001-05-01

    For his dissertation research at Harvard, Bob Apfel chose the subject of homogeneous nucleation, and conceived of some ingenious experiments to test existing theories. By selecting a small microdroplet of liquid, he could make the reasonable assumption that no inhomogeneities were present to serve as preferential sites for liquid rupture. However, Bob also studied dirty liquids, as well as very clean ones, and wrote some seminal papers on inhomogeneous nucleation, in which he developed the Golden rule: Know thy liquid! Currently, considerable attention has been devoted to the study of cavitation generation in vivo, particularly in blood, and, for this case, the nucleation conditions are much different than those for normal liquids. In this presentation, I will review some of Bob's pioneering studies and present some of our latest studies of cavitation inception, both in vitro and in vivo.

  6. Water activity as the determinant for homogeneous ice nucleation in aqueous solutions

    PubMed

    Koop; Luo; Tsias; Peter

    2000-08-10

    The unique properties of water in the supercooled (metastable) state are not fully understood. In particular, the effects of solutes and mechanical pressure on the kinetics of the liquid-to-solid phase transition of supercooled water and aqueous solutions to ice have remained unresolved. Here we show from experimental data that the homogeneous nucleation of ice from supercooled aqueous solutions is independent of the nature of the solute, but depends only on the water activity of the solution--that is, the ratio between the water vapour pressures of the solution and of pure water under the same conditions. In addition, we show that the presence of solutes and the application of pressure have a very similar effect on ice nucleation. We present a thermodynamic theory for homogeneous ice nucleation, which expresses the nucleation rate coefficient as a function of water activity and pressure. Recent observations from clouds containing ice are in good agreement with our theory and our results should help to overcome one of the main weaknesses of numerical models of the atmosphere, the formulation of cloud processes.

  7. Bubble nucleation in stout beers

    NASA Astrophysics Data System (ADS)

    Lee, W. T.; McKechnie, J. S.; Devereux, M. G.

    2011-05-01

    Bubble nucleation in weakly supersaturated solutions of carbon dioxide—such as champagne, sparkling wines, and carbonated beers—is well understood. Bubbles grow and detach from nucleation sites: gas pockets trapped within hollow cellulose fibers. This mechanism appears not to be active in stout beers that are supersaturated solutions of nitrogen and carbon dioxide. In their canned forms these beers require additional technology (widgets) to release the bubbles which will form the head of the beer. We extend the mathematical model of bubble nucleation in carbonated liquids to the case of two gases and show that this nucleation mechanism is active in stout beers, though substantially slower than in carbonated beers and confirm this by observation. A rough calculation suggests that despite the slowness of the process, applying a coating of hollow porous fibers to the inside of a can or bottle could be a potential replacement for widgets.

  8. Isolation and purification of human biliary vesicles with potent cholesterol-nucleation-promoting activity.

    PubMed

    Miquel, J F; Rigotti, A; Rojas, E; Brandan, E; Nervi, F

    1992-02-01

    1. Cholesterol nucleation is a critical step in the formation of cholesterol gallstones. This nucleation takes place after aggregation and fusion of cholesterol-rich biliary vesicles, a process probably modulated by biliary proteins. The present study was conducted to identify specific proteins associated with native cholesterol-rich biliary vesicles and to explore their effect on the cholesterol-nucleation time of supersaturated artificial bile. 2. Hepatic bile was obtained from six patients with cholesterol gallstone disease. Biliary vesicles were isolated by ultracentrifugation and were purified by gel filtration chromatography. A small amount of protein (less than 1% by weight) remained associated with the purified cholesterol-rich biliary vesicles. The electrophoretic profile of these proteins was remarkably similar in all six patients, showing the presence of at least six polypeptides (of molecular mass from 52 to 200 kDa), five of them having carbohydrate residues (except the 52 kDa one). The effect of reconstituted biliary vesicle solutions, containing their specific vesicular proteins, on cholesterol-nucleation time was studied by mixing the vesicle solution with artificial supersaturated bile. A potent cholesterol-pronucleating activity, reflected in a 20-70% reduction in nucleation time, was present in the biliary vesicle solutions compared with control solutions having a similar lipid composition. The pronucleating activity disappeared on heating and was not detected in the micellar fraction containing the major proportion of biliary proteins. 3. These results indicate that cholesterol-rich biliary vesicles containing a unique and defined glycoprotein profile can be isolated and purified from human hepatic bile. The potent cholesterol-pronucleating activity of the biliary vesicles from patients with gallstones was unrelated to their lipid composition or cholesterol content.(ABSTRACT TRUNCATED AT 250 WORDS)

  9. Conversion of Atmospheric Aerosol by Bacteria and Their Influence on Ice-Nucleation Activity

    NASA Astrophysics Data System (ADS)

    Kos, G.; Shawi, M.; Ariya, P. A.

    2004-05-01

    The presence of microorganisms such as bacteria and fungi in the boundary layer of the atmosphere has been established for some time. These species can also convert organic aerosol species (e.g. dicarboxylic acids), a transformation that was so far assumed to occur only via physico-chemical pathways. As a result, the ice nucleation activity of certain aerosol species can be altered by biochemical transformations including metabolite production and bacterial growth and these new species as well as the microorganisms themselves can act as ice nuclei. In this study we have used dicarboxylic acids (DCA) as model nutrients, which are commonly observed in the aerosol population of the boundary layer. Pseudomonas syringae and Erwinia herbicolae are two types of bacteria that have been found to possess ice nucleation ability, caused by lipoglycoprotein, which consists of a sequence of amino acids that favor the formation of ice. The main objective was to look into the conversion of DCA by bacterial species, their ice nucleating ability and the identification of metabolites from bacterial activity. Furthermore, the influence of different parameters on the ice nucleation of bacteria was investigated. A Freezing Nuclei apparatus was used in order to assess the freezing temperature of a population of small drops to study both homogenous and heterogeneous nucleation of different concentrations of malonic acid containing bacterial species. An acid concentration in the lower Fg/l-range was chosen, matching earlier observations in an urban environment. Other varied parameters include the pH and bacterial membrane shearing. All labware was sterilized prior to use and airtight containers minimized external contamination. Malonic acid concentration was determined by gas chromatography with mass spectrometric detection (GC-MS) after esterification with a mixture of borontrifluoride and 1-propanol, modified from Kawamura, 1991. Malonic acid and its metabolites were identified by

  10. Perturbation of bacterial ice nucleation activity by a grass antifreeze protein.

    PubMed

    Tomalty, Heather E; Walker, Virginia K

    2014-09-26

    Certain plant-associating bacteria produce ice nucleation proteins (INPs) which allow the crystallization of water at high subzero temperatures. Many of these microbes are considered plant pathogens since the formed ice can damage tissues, allowing access to nutrients. Intriguingly, certain plants that host these bacteria synthesize antifreeze proteins (AFPs). Once freezing has occurred, plant AFPs likely function to inhibit the growth of large damaging ice crystals. However, we postulated that such AFPs might also serve as defensive mechanisms against bacterial-mediated ice nucleation. Recombinant AFP derived from the perennial ryegrass Lolium perenne (LpAFP) was combined with INP preparations originating from the grass epiphyte, Pseudomonas syringae. The presence of INPs had no effect on AFP activity, including thermal hysteresis and ice recrystallization inhibition. Strikingly, the ice nucleation point of the INP was depressed up to 1.9°C in the presence of LpAFP, but a recombinant fish AFP did not lower the INP-imposed freezing point. Assays with mutant LpAFPs and the visualization of bacterially-displayed fluorescent plant AFP suggest that INP and LpAFP can interact. Thus, we postulate that in addition to controlling ice growth, plant AFPs may also function as a defensive strategy against the damaging effects of ice-nucleating bacteria.

  11. Perturbation of bacterial ice nucleation activity by a grass antifreeze protein.

    PubMed

    Tomalty, Heather E; Walker, Virginia K

    2014-09-26

    Certain plant-associating bacteria produce ice nucleation proteins (INPs) which allow the crystallization of water at high subzero temperatures. Many of these microbes are considered plant pathogens since the formed ice can damage tissues, allowing access to nutrients. Intriguingly, certain plants that host these bacteria synthesize antifreeze proteins (AFPs). Once freezing has occurred, plant AFPs likely function to inhibit the growth of large damaging ice crystals. However, we postulated that such AFPs might also serve as defensive mechanisms against bacterial-mediated ice nucleation. Recombinant AFP derived from the perennial ryegrass Lolium perenne (LpAFP) was combined with INP preparations originating from the grass epiphyte, Pseudomonas syringae. The presence of INPs had no effect on AFP activity, including thermal hysteresis and ice recrystallization inhibition. Strikingly, the ice nucleation point of the INP was depressed up to 1.9°C in the presence of LpAFP, but a recombinant fish AFP did not lower the INP-imposed freezing point. Assays with mutant LpAFPs and the visualization of bacterially-displayed fluorescent plant AFP suggest that INP and LpAFP can interact. Thus, we postulate that in addition to controlling ice growth, plant AFPs may also function as a defensive strategy against the damaging effects of ice-nucleating bacteria. PMID:25193694

  12. A new approach for freezing of aqueous solutions under active control of the nucleation temperature.

    PubMed

    Petersen, Ansgar; Schneider, Hendrik; Rau, Guenter; Glasmacher, Birgit

    2006-10-01

    An experimental setup for controlled freezing of aqueous solutions is introduced. The special feature is a mechanism to actively control the nucleation temperature via electrofreezing: an ice nucleus generated at a platinum electrode by the application of an electric high voltage pulse initiates the crystallization of the sample. Using electrofreezing, the nucleation temperature in pure water can be precisely adjusted to a desired value over the whole temperature range between a maximum temperature Tn(max) close to the melting point and the temperature of spontaneous nucleation. However, the presence of additives can inhibit the nucleus formation. The influence of hydroxyethylstarch (HES), glucose, glycerol, additives commonly used in cryobiology, and NaCl on Tn(max) were investigated. While the decrease showed to be moderate for the non-ionic additives, the hindrance of nucleation by ionic NaCl makes the direct application of electrofreezing in solutions with physiological salt concentrations impossible. Therefore, in the multi-sample freezing device presented in this paper, the ice nucleus is produced in a separate volume of pure water inside an electrode cap. This way, the nucleus formation becomes independent of the sample composition. Using electrofreezing rather than conventional seeding methods allows automated freezing of many samples under equal conditions. Experiments performed with model solutions show the reliability and repeatability of this method to start crystallization in the test samples at different specified temperatures. The setup was designed to freeze samples of small volume for basic investigations in the field of cryopreservation and freeze-drying, but the mode of operation might be interesting for many other applications where a controlled nucleation of aqueous solutions is of importance. PMID:16887112

  13. Frost injury and heterogeneous ice nucleation in leaves of tuber-bearing solanum species : ice nucleation activity of external source of nucleants.

    PubMed

    Rajashekar, C B; Li, P H; Carter, J V

    1983-04-01

    The heterogeneous ice nucleation characteristics and frost injury in supercooled leaves upon ice formation were studied in nonhardened and cold-hardened species and crosses of tuber-bearing Solanum. The ice nucleation activity of the leaves was low at temperatures just below 0 degrees C and further decreased as a result of cold acclimation. In the absence of supercooling, the nonhardened and cold-hardened leaves tolerated extracellular freezing between -3.5 degrees and -8.5 degrees C. However, if ice initiation in the supercooled leaves occurred at any temperature below -2.6 degrees C, the leaves were lethally injured.To prevent supercooling in these leaves, various nucleants were tested for their ice nucleating ability. One% aqueous suspensions of fluorophlogopite and acetoacetanilide were found to be effective in ice nucleation of the Solanum leaves above -1 degrees C. They had threshold temperatures of -0.7 degrees and -0.8 degrees C, respectively, for freezing in distilled H(2)O. Although freezing could be initiated in the Solanum leaves above -1 degrees C with both the nucleants, 1% aqueous fluorophlogopite suspension showed overall higher ice nucleation activity than acetoacetanilide and was nontoxic to the leaves. The cold-hardened leaves survived between -2.5 degrees and -6.5 degrees using 1% aqueous fluorophlogopite suspension as a nucleant. The killing temperatures in the cold-hardened leaves were similar to those determined using ice as a nucleant. However, in the nonhardened leaves, use of fluorophlogopite as a nucleant resulted in lethal injury at higher temperatures than those estimated using ice as a nucleant. PMID:16662901

  14. Heterogeneous ice nucleation activity of bacteria: new laboratory experiments at simulated cloud conditions

    NASA Astrophysics Data System (ADS)

    Möhler, O.; Georgakopoulos, D. G.; Morris, C. E.; Benz, S.; Ebert, V.; Hunsmann, S.; Saathoff, H.; Schnaiter, M.; Wagner, R.

    2008-10-01

    The ice nucleation activities of five different Pseudomonas syringae, Pseudomonas viridiflava and Erwinia herbicola bacterial species and of Snomax™ were investigated in the temperature range between -5 and -15°C. Water suspensions of these bacteria were directly sprayed into the cloud chamber of the AIDA facility of Forschungszentrum Karlsruhe at a temperature of -5.7°C. At this temperature, about 1% of the Snomax™ cells induced immersion freezing of the spray droplets before the droplets evaporated in the cloud chamber. The living cells didn't induce any detectable immersion freezing in the spray droplets at -5.7°C. After evaporation of the spray droplets the bacterial cells remained as aerosol particles in the cloud chamber and were exposed to typical cloud formation conditions in experiments with expansion cooling to about -11°C. During these experiments, the bacterial cells first acted as cloud condensation nuclei to form cloud droplets. Then, only a minor fraction of the cells acted as heterogeneous ice nuclei either in the condensation or the immersion mode. The results indicate that the bacteria investigated in the present study are mainly ice active in the temperature range between -7 and -11°C with an ice nucleation (IN) active fraction of the order of 10-4. In agreement to previous literature results, the ice nucleation efficiency of Snomax™ cells was much larger with an IN active fraction of 0.2 at temperatures around -8°C.

  15. Plants as sources of airborne bacteria, including ice nucleation-active bacteria.

    PubMed

    Lindemann, J; Constantinidou, H A; Barchet, W R; Upper, C D

    1982-11-01

    Vertical wind shear and concentration gradients of viable, airborne bacteria were used to calculate the upward flux of viable cells above bare soil and canopies of several crops. Concentrations at soil or canopy height varied from 46 colony-forming units per m over young corn and wet soil to 663 colony-forming units per m over dry soil and 6,500 colony-forming units per m over a closed wheat canopy. In simultaneous samples, concentrations of viable bacteria in the air 10 m inside an alfalfa field were fourfold higher than those over a field with dry, bare soil immediately upwind. The upward flux of viable bacteria over alfalfa was three- to fourfold greater than over dry soil. Concentrations of ice nucleation-active bacteria were higher over plants than over soil. Thus, plant canopies may constitute a major source of bacteria, including ice nucleation-active bacteria, in the air.

  16. Hypervalent iodine compounds as potent antibacterial agents against ice nucleation active (INA) Pseudomonas syringae.

    PubMed

    Menkissoglu-Spiroudi, U; Karamanoli, K; Spyroudis, S; Constantinidou, H I

    2001-08-01

    Twenty-three hypervalent iodine compounds belonging to aryliodonium salts, 1, aryliodonium ylides, 2, and (diacyloxyiodo)arenes, 3, were tested for their antibacterial activities against ice nucleation active (INA) Pseudomonas syringae, and the MIC and EC(50) values were determined. All of the compounds examined caused a dose-dependent decrease in bacterial growth rates. Aryliodonium salts, especially those with electron-withdrawing groups, exhibit higher antibacterial activities with MIC = 8-16 ppm, whereas the nature of the anion does not seem to affect the activities of the diaryliodonium salts. PMID:11513659

  17. The Fifth International Ice Nucleation Workshop Activities FIN-1 and FIN-2: Overview and Selected Results

    NASA Astrophysics Data System (ADS)

    Moehler, O.; Cziczo, D. J.; DeMott, P. J.; Hiranuma, N.; Petters, M. D.

    2015-12-01

    The role of aerosol particles for ice formation in clouds is one of the largest uncertainties in understanding the Earth's weather and climate systems, which is related to the poor knowledge of ice nucleation microphysics or of the nature and atmospheric abundance of ice nucleating particles (INPs). During the recent years, new mobile instruments were developed for measuring the concentration, size and chemical composition of INPs, which were tested during the three-part Fifth International Ice Nucleation (FIN) workshop. The FIN activities addressed not only instrument issues, but also important science topics like the nature of atmospheric INP and cloud ice residuals, the ice nucleation activity of relevant atmospheric aerosols, or the parameterization of ice formation in atmospheric weather and climate models. The first activity FIN-1 was conducted during November 2014 at the AIDA cloud chamber. It involved co-locating nine single particle mass spectrometers to evaluate how well they resolve the INP and ice residual composition and how spectra from different instruments compare for relevant atmospheric aerosols. We conducted about 90 experiments with mineral, carbonaceous and biological aerosol types, some also coated with organic and inorganic compounds. The second activity FIN-2 was conducted during March 2015 at the AIDA facility. A total of nine mobile INP instruments directly sampled from the AIDA aerosol chambers. Wet suspension and filter samples were also taken for offline INP processing. A refereed blind intercomparison was conducted during two days of the FIN-2 activity. The third activity FIN-3 will take place at the Desert Research Institute's Storm Peak Laboratory (SPL) in order to test the instruments' performance in the field. This contribution will introduce the FIN activities, summarize first results from the formal part of FIN-2, and discuss selected results, mainly from FIN-1 for the effect of coating on the ice nucleation (IN) by mineral

  18. Ice nucleation active particles in continental air samples over Mainz, Germany

    NASA Astrophysics Data System (ADS)

    Pummer, Bernhard G.; Pöschl, Ulrich; Fröhlich-Nowoisky, Janine

    2016-04-01

    Aerosol particles are of central importance for atmospheric chemistry and physics, climate and public health. Some of these particles possess ice nucleation activity (INA), which is highly relevant for cloud formation and precipitation. In 2010, air filter samples were collected with a high-volume filter sampler separating fine and coarse particles (aerodynamic cut-off diameter 3 μm) in Mainz, Germany. In this study, the INA of the atmospheric particles deposited on these filters was determined. Therefore,they were extracted with ultrapure water, which was then measured in a droplet freezing assay, as described in Fröhlich-Nowoisky et al. (2015). The determined concentration of ice nucleators (INs) was between 0.3 and 2per m³ at 266 K, and between5 and 75 per m³ at 260 K. The INs were further characterized by different treatments, like heating (308 K, 371 K), filtration (0.1 μm, 300 kDa), and digestion with papain (10 mg/ml). We further investigated, which atmospheric conditions (e.g. weather) and distinguished events (e.g. dust storms, volcanic eruptions, and pollen peaks) influenced the number and nature of these INs. Fröhlich-Nowoisky, J., Hill, T. C. J., Pummer, B. G., Yordanova, P., Franc, G. D., and Pöschl, U.: Ice nucleation activity in the widespread soil fungus Mortierella alpina, Biogeosci., 12, 1057-1071, doi:10.5194/bg-12-1057-2015, 2015.

  19. Ligand-induced activation of a formin–NPF pair leads to collaborative actin nucleation

    PubMed Central

    Graziano, Brian R.; Jonasson, Erin M.; Pullen, Jessica G.; Gould, Christopher J.

    2013-01-01

    Formins associate with other nucleators and nucleation-promoting factors (NPFs) to stimulate collaborative actin assembly, but the mechanisms regulating these interactions have been unclear. Yeast Bud6 has an established role as an NPF for the formin Bni1, but whether it also directly regulates the formin Bnr1 has remained enigmatic. In this paper, we analyzed NPF-impaired alleles of bud6 in a bni1Δ background and found that Bud6 stimulated Bnr1 activity in vivo. Furthermore, Bud6 bound directly to Bnr1, but its NPF effects were masked by a short regulatory sequence, suggesting that additional factors may be required for activation. We isolated a novel in vivo binding partner of Bud6, Yor304c-a/Bil1, which colocalized with Bud6 and functioned in the Bnr1 pathway for actin assembly. Purified Bil1 bound to the regulatory sequence in Bud6 and triggered NPF effects on Bnr1. These observations define a new mode of formin regulation, which has important implications for understanding NPF-nucleator pairs in diverse systems. PMID:23671312

  20. Effect of Plant Species and Environmental Conditions on Ice Nucleation Activity of Pseudomonas syringae on Leaves.

    PubMed

    O'brien, R D; Lindow, S E

    1988-09-01

    Selected plant species and environmental conditions were investigated for their influences on expression of ice nucleation activity by 15 Pseudomonas syringae strains grown on plants in constant-temperature growth chamber studies. Ice nucleation frequencies (INFs), the fraction of cells that expressed ice nucleation at -5 or -9 degrees C, of individual strains varied greatly, both on plants and in culture. This suggests that the probability of frost injury, which is proportional to the number of ice nuclei on leaf surfaces, is strongly determined by the particular bacterial strains that are present on a leaf surface. The INFs of strains were generally higher when they were grown on plants than when they were grown in culture. In addition, INFs in culture did not correlate closely with INFs on plants, suggesting that frost injury prediction should be based on INF measurements of cells grown on plants rather than in culture. The relative INFs of individual strains varied with plant host and environment. However, none of seven plant species tested optimized the INFs of all 15 strains. Similarly, incubation for 48 h at near 100% relative humidity with short photoperiods did not always decrease the INF when compared with a 72 h, 40% relative humidity, long-photoperiod incubation. Pathogenic strains on susceptible hosts were not associated with higher or lower INFs relative to their INFs on nonsusceptible plant species. The ice nucleation activity of individual bacterial strains on plants therefore appears to be controlled by complex and interacting factors such as strain genotype, environment, and host plant species. PMID:16347741

  1. Hygroscopic growth and activation of uncoated and coated soot particles and their relation to ice nucleation

    NASA Astrophysics Data System (ADS)

    Ziese, M.; Henning, S.; Mildenberger, K.; Stratmann, F.; Möhler, O.; Benz, S.; Buchholz, A.; Mentel, Th.; Aida/Lacis-Mobile-Team

    2009-04-01

    Measurements of the hygroscopic growth (HTDMA, LACIS-mobile), activation behavior (DMT-CCNC) - scope of this paper - and ice nucleation (AIDA chamber) were performed to estimate the cloud-forming potential of pure and coated soot particles. Globally, soot particles contribute up to 2.5 % to the atmospheric aerosol. In the framework of the investigations described here, soot particles were generated either applying a graphite-spark-generator (GFG1000) or a flame-soot-generator (Mini-CAST). With respect to the hygroscopic growth and activation behavior, the influences of the carrier-gas (GFG-soot), the OC-content (CAST-soot) and of different coating materials were investigated. Differences in the hygroscopic growth and activation behavior of GFG generated soot particles were found for the two carrier-gases considered. If nitrogen was used, neither hygroscopic growth nor activation were observed. In contrast, when argon was used, particles featured a slight hygroscopic growth and were easier to activate. Hygroscopic growth increases with decreasing OC-content of the CAST-soot, up to growth factor 1.04 at 98.4 % relative humidity. Lower OC-contents also result in the particles being activated more easily. Coating with sulfuric acid enhances the hygroscopic growth and activation behavior of CAST-soot for different OC-contents. If the soot (GFG & CAST) was coated with dicarboxylic acids (oxalic and succinic acid), no enhancement of hygroscopic growth and activation was observed. This is most likely due to evaporation of the coating material. In comparison to the hygroscopic growth and activation behavior, the same trends were observed in the ice-nucleation behavior. That is, the more active a particle is as cloud condensation nuclei, the better it functions as ice nuclei. GFG-soot with argon as carrier-gas acts as a better ice nuclei than GFG-soot with nitrogen. For the CAST-soot the ice-nucleation activity decreases with increasing OC-content. Coating with sulfuric acid

  2. Anti-ice nucleation activity in xylem extracts from trees that contain deep supercooling xylem parenchyma cells.

    PubMed

    Kasuga, Jun; Mizuno, Kaoru; Arakawa, Keita; Fujikawa, Seizo

    2007-12-01

    Boreal hardwood species, including Japanese white birch (Betula platyphylla Sukat. var. japonica Hara), Japanese chestnut (Castanea crenata Sieb. et Zucc.), katsura tree (Cercidiphyllum japonicum Sieb. et Zucc.), Siebold's beech (Fagus crenata Blume), mulberry (Morus bombycis Koidz.), and Japanese rowan (Sorbus commixta Hedl.), had xylem parenchyma cells (XPCs) that adapt to subfreezing temperatures by deep supercooling. Crude extracts from xylem in all these trees were found to have anti-ice nucleation activity that promoted supercooling capability of water as measured by a droplet freezing assay. The magnitude of increase in supercooling capability of water droplets in the presence of ice-nucleation bacteria, Erwinia ananas, was higher in the ranges from 0.1 to 1.7 degrees C on addition of crude xylem extracts than freezing temperature of water droplets on addition of glucose in the same concentration (100 mosmol/kg). Crude xylem extracts from C. japonicum provided the highest supercooling capability of water droplets. Our additional examination showed that crude xylem extracts from C. japonicum exhibited anti-ice nucleation activity toward water droplets containing a variety of heterogeneous ice nucleators, including ice-nucleation bacteria, not only E. ananas but also Pseudomonas syringae (NBRC3310) or Xanthomonas campestris, silver iodide or airborne impurities. However, crude xylem extracts from C. japonicum did not affect homogeneous ice nucleation temperature as analyzed by emulsified micro-water droplets. The possible role of such anti-ice nucleation activity in crude xylem extracts in deep supercooling of XPCs is discussed.

  3. Anti-ice nucleation activity in xylem extracts from trees that contain deep supercooling xylem parenchyma cells.

    PubMed

    Kasuga, Jun; Mizuno, Kaoru; Arakawa, Keita; Fujikawa, Seizo

    2007-12-01

    Boreal hardwood species, including Japanese white birch (Betula platyphylla Sukat. var. japonica Hara), Japanese chestnut (Castanea crenata Sieb. et Zucc.), katsura tree (Cercidiphyllum japonicum Sieb. et Zucc.), Siebold's beech (Fagus crenata Blume), mulberry (Morus bombycis Koidz.), and Japanese rowan (Sorbus commixta Hedl.), had xylem parenchyma cells (XPCs) that adapt to subfreezing temperatures by deep supercooling. Crude extracts from xylem in all these trees were found to have anti-ice nucleation activity that promoted supercooling capability of water as measured by a droplet freezing assay. The magnitude of increase in supercooling capability of water droplets in the presence of ice-nucleation bacteria, Erwinia ananas, was higher in the ranges from 0.1 to 1.7 degrees C on addition of crude xylem extracts than freezing temperature of water droplets on addition of glucose in the same concentration (100 mosmol/kg). Crude xylem extracts from C. japonicum provided the highest supercooling capability of water droplets. Our additional examination showed that crude xylem extracts from C. japonicum exhibited anti-ice nucleation activity toward water droplets containing a variety of heterogeneous ice nucleators, including ice-nucleation bacteria, not only E. ananas but also Pseudomonas syringae (NBRC3310) or Xanthomonas campestris, silver iodide or airborne impurities. However, crude xylem extracts from C. japonicum did not affect homogeneous ice nucleation temperature as analyzed by emulsified micro-water droplets. The possible role of such anti-ice nucleation activity in crude xylem extracts in deep supercooling of XPCs is discussed. PMID:17936742

  4. Measurement of ice nucleation-active bacteria on plants and in precipitation by quantitative PCR.

    PubMed

    Hill, Thomas C J; Moffett, Bruce F; Demott, Paul J; Georgakopoulos, Dimitrios G; Stump, William L; Franc, Gary D

    2014-02-01

    Ice nucleation-active (INA) bacteria may function as high-temperature ice-nucleating particles (INP) in clouds, but their effective contribution to atmospheric processes, i.e., their potential to trigger glaciation and precipitation, remains uncertain. We know little about their abundance on natural vegetation, factors that trigger their release, or persistence of their ice nucleation activity once airborne. To facilitate these investigations, we developed two quantitative PCR (qPCR) tests of the ina gene to directly count INA bacteria in environmental samples. Each of two primer pairs amplified most alleles of the ina gene and, taken together, they should amplify all known alleles. To aid primer design, we collected many new INA isolates. Alignment of their partial ina sequences revealed new and deeply branching clades, including sequences from Pseudomonas syringae pv. atropurpurea, Ps. viridiflava, Pantoea agglomerans, Xanthomonas campestris, and possibly Ps. putida, Ps. auricularis, and Ps. poae. qPCR of leaf washings recorded ∼10(8) ina genes g(-1) fresh weight of foliage on cereals and 10(5) to 10(7) g(-1) on broadleaf crops. Much lower populations were found on most naturally occurring vegetation. In fresh snow, ina genes from various INA bacteria were detected in about half the samples but at abundances that could have accounted for only a minor proportion of INP at -10°C (assuming one ina gene per INA bacterium). Despite this, an apparent biological source contributed an average of ∼85% of INP active at -10°C in snow samples. In contrast, a thunderstorm hail sample contained 0.3 INA bacteria per INP active at -10°C, suggesting a significant contribution to this sample. PMID:24317082

  5. Measurement of ice nucleation-active bacteria on plants and in precipitation by quantitative PCR.

    PubMed

    Hill, Thomas C J; Moffett, Bruce F; Demott, Paul J; Georgakopoulos, Dimitrios G; Stump, William L; Franc, Gary D

    2014-02-01

    Ice nucleation-active (INA) bacteria may function as high-temperature ice-nucleating particles (INP) in clouds, but their effective contribution to atmospheric processes, i.e., their potential to trigger glaciation and precipitation, remains uncertain. We know little about their abundance on natural vegetation, factors that trigger their release, or persistence of their ice nucleation activity once airborne. To facilitate these investigations, we developed two quantitative PCR (qPCR) tests of the ina gene to directly count INA bacteria in environmental samples. Each of two primer pairs amplified most alleles of the ina gene and, taken together, they should amplify all known alleles. To aid primer design, we collected many new INA isolates. Alignment of their partial ina sequences revealed new and deeply branching clades, including sequences from Pseudomonas syringae pv. atropurpurea, Ps. viridiflava, Pantoea agglomerans, Xanthomonas campestris, and possibly Ps. putida, Ps. auricularis, and Ps. poae. qPCR of leaf washings recorded ∼10(8) ina genes g(-1) fresh weight of foliage on cereals and 10(5) to 10(7) g(-1) on broadleaf crops. Much lower populations were found on most naturally occurring vegetation. In fresh snow, ina genes from various INA bacteria were detected in about half the samples but at abundances that could have accounted for only a minor proportion of INP at -10°C (assuming one ina gene per INA bacterium). Despite this, an apparent biological source contributed an average of ∼85% of INP active at -10°C in snow samples. In contrast, a thunderstorm hail sample contained 0.3 INA bacteria per INP active at -10°C, suggesting a significant contribution to this sample.

  6. Measurement of Ice Nucleation-Active Bacteria on Plants and in Precipitation by Quantitative PCR

    PubMed Central

    Moffett, Bruce F.; DeMott, Paul J.; Georgakopoulos, Dimitrios G.; Stump, William L.; Franc, Gary D.

    2014-01-01

    Ice nucleation-active (INA) bacteria may function as high-temperature ice-nucleating particles (INP) in clouds, but their effective contribution to atmospheric processes, i.e., their potential to trigger glaciation and precipitation, remains uncertain. We know little about their abundance on natural vegetation, factors that trigger their release, or persistence of their ice nucleation activity once airborne. To facilitate these investigations, we developed two quantitative PCR (qPCR) tests of the ina gene to directly count INA bacteria in environmental samples. Each of two primer pairs amplified most alleles of the ina gene and, taken together, they should amplify all known alleles. To aid primer design, we collected many new INA isolates. Alignment of their partial ina sequences revealed new and deeply branching clades, including sequences from Pseudomonas syringae pv. atropurpurea, Ps. viridiflava, Pantoea agglomerans, Xanthomonas campestris, and possibly Ps. putida, Ps. auricularis, and Ps. poae. qPCR of leaf washings recorded ∼108 ina genes g−1 fresh weight of foliage on cereals and 105 to 107 g−1 on broadleaf crops. Much lower populations were found on most naturally occurring vegetation. In fresh snow, ina genes from various INA bacteria were detected in about half the samples but at abundances that could have accounted for only a minor proportion of INP at −10°C (assuming one ina gene per INA bacterium). Despite this, an apparent biological source contributed an average of ∼85% of INP active at −10°C in snow samples. In contrast, a thunderstorm hail sample contained 0.3 INA bacteria per INP active at −10°C, suggesting a significant contribution to this sample. PMID:24317082

  7. The formin mDia2 stabilizes microtubules independently of its actin nucleation activity

    PubMed Central

    Bartolini, Francesca; Moseley, James B.; Schmoranzer, Jan; Cassimeris, Lynne; Goode, Bruce L.; Gundersen, Gregg G.

    2008-01-01

    A critical microtubule (MT) polarization event in cell migration is the Rho/mDia-dependent stabilization of a subset of MTs oriented toward the direction of migration. Although mDia nucleates actin filaments, it is unclear whether this or a separate activity of mDia underlies MT stabilization. We generated two actin mutants (K853A and I704A) in a constitutively active version of mDia2 containing formin homology domains 1 and 2 (FH1FH2) and found that they still induced stable MTs and bound to the MT TIP proteins EB1 and APC, which have also been implicated in MT stabilization. A dimerization-impaired mutant of mDia2 (W630A) also generated stable MTs in cells. We examined whether FH1FH2mDia2 had direct activity on MTs in vitro and found that it bound directly to MTs, stabilized MTs against cold- and dilution-induced disassembly, and reduced the rates of growth and shortening during MT assembly and disassembly, respectively. These results indicate that mDia2 has a novel MT stabilization activity that is separate from its actin nucleation activity. PMID:18458159

  8. Characterizing protein crystal nucleation

    NASA Astrophysics Data System (ADS)

    Akella, Sathish V.

    We developed an experimental microfluidic based technique to measure the nucleation rates and successfully applied the technique to measure nucleation rates of lysozyme crystals. The technique involves counting the number of samples which do not have crystals as a function of time. Under the assumption that nucleation is a Poisson process, the fraction of samples with no crystals decays exponentially with the decay constant proportional to nucleation rate and volume of the sample. Since nucleation is a random and rare event, one needs to perform measurements on large number of samples to obtain good statistics. Microfluidics offers the solution of producing large number of samples at minimal material consumption. Hence, we developed a microfluidic method and measured nucleation rates of lysozyme crystals in supersaturated protein drops, each with volume of ˜ 1 nL. Classical Nucleation Theory (CNT) describes the kinetics of nucleation and predicts the functional form of nucleation rate in terms of the thermodynamic quantities involved, such as supersaturation, temperature, etc. We analyzed the measured nucleation rates in the context of CNT and obtained the activation energy and the kinetic pre-factor characterizing the nucleation process. One conclusion is that heterogeneous nucleation dominates crystallization. We report preliminary studies on selective enhancement of nucleation in one of the crystal polymorprhs of lysozyme (spherulite) using amorphous mesoporous bioactive gel-glass te{naomi06, naomi08}, CaO.P 2O5.SiO2 (known as bio-glass) with 2-10 nm pore-size diameter distribution. The pores act as heterogeneous nucleation centers and claimed to enhance the nucleation rates by molecular confinement. The measured kinetic profiles of crystal fraction of spherulites indicate that the crystallization of spherulites may be proceeding via secondary nucleation pathways.

  9. Observation of nucleation mode particle burst and new particle formation events at an urban site in Hong Kong

    NASA Astrophysics Data System (ADS)

    Wang, Dawei; Guo, Hai; Cheung, Kalam; Gan, Fuxing

    2014-12-01

    Particle number (PN) concentrations and particle size distributions (PSD) in the size range of 5.5-350 nm were continuously measured from 22 December 2010 to 20 January 2011 at an urban site in Hong Kong when northeastern monsoon prevailed. Apart from the PN peaks appeared in traffic rush hours (i.e. 08:00-09:00 and 17:00-18:00), a distinct peak of PN concentrations in the afternoon (11:00-16:00) was observed during the sampling period. Concurrent measurement data of PSD, ozone (O3) and proxy sulfuric acid (H2SO4) concentrations revealed that the afternoon peaks observed were likely due to new particle formation (NPF) via photochemical reactions. These NPF events were frequently observed under a clean and dry weather in Hong Kong. The occurrence of NPF was closely associated with high solar radiation (SR), low relative humidity (RH) and low condensation sink (CS) in the atmosphere. Besides the NPF events, we also found four nucleation mode particle burst events, typically with increased number concentrations of nucleation mode particles (Nnuc) without growth to larger size particles. These burst events were generally accompanied by high-level primary air pollutants, i.e. sulfur dioxide (SO2), nitrogen oxide (NOx) and carbon monoxide (CO), low SR and high CS conditions. The very different characteristics of the burst events from those of the NPF events indicated that these nucleation mode particle burst events were not caused by the photochemical reactions, but by the primary emission from the local combustion source(s).

  10. Probing the Biomimetic Ice Nucleation Inhibition Activity of Poly(vinyl alcohol) and Comparison to Synthetic and Biological Polymers

    PubMed Central

    2015-01-01

    Nature has evolved many elegant solutions to enable life to flourish at low temperatures by either allowing (tolerance) or preventing (avoidance) ice formation. These processes are typically controlled by ice nucleating proteins or antifreeze proteins, which act to either promote nucleation, prevent nucleation or inhibit ice growth depending on the specific need, respectively. These proteins can be expensive and their mechanisms of action are not understood, limiting their translation, especially into biomedical cryopreservation applications. Here well-defined poly(vinyl alcohol), synthesized by RAFT/MADIX polymerization, is investigated for its ice nucleation inhibition (INI) activity, in contrast to its established ice growth inhibitory properties and compared to other synthetic polymers. It is shown that ice nucleation inhibition activity of PVA has a strong molecular weight dependence; polymers with a degree of polymerization below 200 being an effective inhibitor at just 1 mg.mL–1. Other synthetic and natural polymers, both with and without hydroxyl-functional side chains, showed negligible activity, highlighting the unique ice/water interacting properties of PVA. These findings both aid our understanding of ice nucleation but demonstrate the potential of engineering synthetic polymers as new biomimetics to control ice formation/growth processes PMID:26258729

  11. Probing the Biomimetic Ice Nucleation Inhibition Activity of Poly(vinyl alcohol) and Comparison to Synthetic and Biological Polymers.

    PubMed

    Congdon, Thomas; Dean, Bethany T; Kasperczak-Wright, James; Biggs, Caroline I; Notman, Rebecca; Gibson, Matthew I

    2015-09-14

    Nature has evolved many elegant solutions to enable life to flourish at low temperatures by either allowing (tolerance) or preventing (avoidance) ice formation. These processes are typically controlled by ice nucleating proteins or antifreeze proteins, which act to either promote nucleation, prevent nucleation or inhibit ice growth depending on the specific need, respectively. These proteins can be expensive and their mechanisms of action are not understood, limiting their translation, especially into biomedical cryopreservation applications. Here well-defined poly(vinyl alcohol), synthesized by RAFT/MADIX polymerization, is investigated for its ice nucleation inhibition (INI) activity, in contrast to its established ice growth inhibitory properties and compared to other synthetic polymers. It is shown that ice nucleation inhibition activity of PVA has a strong molecular weight dependence; polymers with a degree of polymerization below 200 being an effective inhibitor at just 1 mg.mL(-1). Other synthetic and natural polymers, both with and without hydroxyl-functional side chains, showed negligible activity, highlighting the unique ice/water interacting properties of PVA. These findings both aid our understanding of ice nucleation but demonstrate the potential of engineering synthetic polymers as new biomimetics to control ice formation/growth processes.

  12. Probing the Biomimetic Ice Nucleation Inhibition Activity of Poly(vinyl alcohol) and Comparison to Synthetic and Biological Polymers.

    PubMed

    Congdon, Thomas; Dean, Bethany T; Kasperczak-Wright, James; Biggs, Caroline I; Notman, Rebecca; Gibson, Matthew I

    2015-09-14

    Nature has evolved many elegant solutions to enable life to flourish at low temperatures by either allowing (tolerance) or preventing (avoidance) ice formation. These processes are typically controlled by ice nucleating proteins or antifreeze proteins, which act to either promote nucleation, prevent nucleation or inhibit ice growth depending on the specific need, respectively. These proteins can be expensive and their mechanisms of action are not understood, limiting their translation, especially into biomedical cryopreservation applications. Here well-defined poly(vinyl alcohol), synthesized by RAFT/MADIX polymerization, is investigated for its ice nucleation inhibition (INI) activity, in contrast to its established ice growth inhibitory properties and compared to other synthetic polymers. It is shown that ice nucleation inhibition activity of PVA has a strong molecular weight dependence; polymers with a degree of polymerization below 200 being an effective inhibitor at just 1 mg.mL(-1). Other synthetic and natural polymers, both with and without hydroxyl-functional side chains, showed negligible activity, highlighting the unique ice/water interacting properties of PVA. These findings both aid our understanding of ice nucleation but demonstrate the potential of engineering synthetic polymers as new biomimetics to control ice formation/growth processes. PMID:26258729

  13. Heterogeneous ice nucleation activity of bacteria: new laboratory experiments at simulated cloud conditions

    NASA Astrophysics Data System (ADS)

    Möhler, O.; Georgakopoulos, D. G.; Morris, C. E.; Benz, S.; Ebert, V.; Hunsmann, S.; Saathoff, H.; Schnaiter, M.; Wagner, R.

    2008-04-01

    The ice nucleation activities of five different Pseudomonas syringae, Pseudomonas viridiflava and Erwinia herbicola bacterial species and of SnomaxTM were investigated in the temperature range between -5 and -15°C. Water suspensions of these bacteria were directly spray into the cloud chamber of the AIDA facility of Forschungszentrum Karlsruhe at a temperature of -5.7°. At this temperature, about 1% of the SnomaxTM cells induced freezing of the spray droplets before they evaporated in the cloud chamber. The other suspensions of living cells didn't induce any measurable ice concentration during spray formation at -5.7°. The remaining aerosol was exposed to typical cloud activation conditions in subsequent experiments with expansion cooling to about -11°C. During these experiments, the bacterial cells first acted as cloud condensation nuclei to form cloud droplets and then eventually acted as ice nuclei to freeze the droplets. The results indicate that the bacteria investigated in the present study are mainly ice active in the temperature range between -7 and -11°C with an INA fraction of the order of 10-4. The ice nucleation efficiency of SnomaxTM cells was much larger with an INA fraction of 0.2 at temperatures around -8°C.

  14. Cloud condensation nuclei and ice nucleation activity of hydrophobic and hydrophilic soot particles.

    PubMed

    Koehler, Kirsten A; DeMott, Paul J; Kreidenweis, Sonia M; Popovicheva, Olga B; Petters, Markus D; Carrico, Christian M; Kireeva, Elena D; Khokhlova, Tatiana D; Shonija, Natalia K

    2009-09-28

    Cloud condensation nuclei (CCN) activity and ice nucleation behavior (for temperaturesactivity at or below water supersaturations required for wettable, insoluble particles (the Kelvin limit). TC1 soot particles, despite classification as hydrophilic, did not show CCN activity at or below the Kelvin limit. We attribute this result to the microporosity of this soot. In contrast, oxidized, non-porous, and hydrophilic TOS particles exhibited CCN activation at very near the Kelvin limit, with a small percentage of these particles CCN-active even at lower supersaturations. Due to containing a range of surface coverage of organic and inorganic hydrophilic and hygroscopic compounds, up to approximately 35% of hygroscopic AEC particles were active as CCN, with a small percentage of these particles CCN-active at lower supersaturations. In ice nucleation experiments below -40 degrees C, AEC particles nucleated ice near the expected condition for homogeneous freezing of water from aqueous solutions. In

  15. Relationships between cold hardiness, and ice nucleating activity, glycerol and protein contents in the hemolymph of caterpillars, Aporia crataegi L.

    PubMed

    Li, N G

    2012-01-01

    Insects in Siberia must tolerate some of the coldest conditions on earth. The relationship between hemolymph ice nucleating activity, glycerol and total protein concentrations, and cold hardiness was explored in Aporia crataegi L. (Lepidoptera: Pieridae). Cold-hardened overwintering caterpillars were collected at a time of year when temperatures are regularly below -50 degree C, and warm-acclimated at +22 degree C, to see how changes in the physical and chemical properties of the hemolymph influence their cold hardiness potential. Warm acclimation led to a decrease in glycerol and proteins content in the hemolymph, which was associated with the decrease in ice nucleating activity and dramatic loss of cold hardiness potential of the caterpillars. It is suggested that one of the effects of cryoprotection in the freeze tolerant insects, caused by glycerol, might be associated with its ability to form larger aggregates of ice nucleating polypeptides that initiate the ice nucleation at high subzero temperatures. Such ice nucleating structures seem to ensure a high probability of ice nucleation at relatively high temperatures, which may contribute to the extraordinary cold hardiness of A. crataegi caterpillars, which may tolerate temperatures below -85 degree С.

  16. Effect of an Ice-Nucleating Activity Agent on Subzero Survival of Nematode Juveniles

    PubMed Central

    Wergin, William P.; Yaklich, Robert W.; Carta, Lynn K.; Erbe, Eric F.; Murphy, Charles A.

    2000-01-01

    Juveniles of five species of nematodes, Caenorhabditis elegans, Panagrellus redivivus, Pratylenchus agilis, Pristionchus pacificus, and Distolabrellus veechi, were added to solutions with (treatment) and without (control) a commercial ice-nucleating activity (INA) agent. Ten-microliter droplets of the solutions containing the juveniles were placed on glass microscope slides and transferred to a temperaturecontrolled freeze plate where the temperature was reduced to -6 to -8 °C. At this temperature, the droplets containing the INA agent froze while those without the agent remained liquid. After 2 minutes, the temperature of the plate was raised to 24 °C, and the slides were examined with a light microscope to determine the viability of the juveniles. The results showed that usually most juveniles (43% to 88%, depending on species) in solutions that did not contain the INA agent (controls) were active, indicating that the juveniles were capable of supercooling and were thereby protected from the subzero temperatures. Alternatively, less than 10% of the juveniles that had frozen for 2 minutes in solutions containing the INA agent remained viable, indicating that inoculative freezing of the solution was lethal to the supercooled juveniles. Our results suggest that, in geographical areas where winter temperatures may not be sufficiently low or sustained to freeze soil, the addition of an INA agent may help induce ice nucleation and thereby reduce the populations of nematode species that are unable to survive when the soil solution is frozen. PMID:19270966

  17. Neutron-induced nucleation inside bubble chambers using Freon 115 as the active medium

    NASA Astrophysics Data System (ADS)

    Ghilea, M. C.; Meyerhofer, D. D.; Sangster, T. C.

    2011-08-01

    Neutron imaging is used in inertial confinement fusion (ICF) experiments to measure the core symmetry of imploded targets. Liquid bubble chambers have the potential to obtain higher resolution images of the targets for a shorter source-target distance than typical scintillator arrays. Due to the fact that nucleation models used in gel detectors research cannot always give correct estimates for the neutron-induced bubble density inside a liquid bubble chamber, an improved theoretical model to describe the mechanism of bubble formation for Freon 115 as the active medium has been developed. It shows that the size of the critical radius for the nucleation process determines the mechanism of bubble formation and the sensitivity of the active medium to the 14.1-MeV incident neutrons resulting from ICF implosions. The bubble-growth mechanism is driven by the excitation of the medium electronic levels and not by electrons ejected from the medium's atoms as happens for the bubble chambers used to detect charged particles. The model accurately predicts the neutron-induced bubble density measured on OMEGA with both liquid bubble chambers and gel detectors.

  18. Effect of an ice-nucleating activity agent on subzero survival of nematode juveniles.

    PubMed

    Wergin, W P; Yaklich, R W; Carta, L K; Erbe, E F; Murphy, C A

    2000-06-01

    Juveniles of five species of nematodes, Caenorhabditis elegans, Panagrellus redivivus, Pratylenchus agilis, Pristionchus pacificus, and Distolabrellus veechi, were added to solutions with (treatment) and without (control) a commercial ice-nucleating activity (INA) agent. Ten-microliter droplets of the solutions containing the juveniles were placed on glass microscope slides and transferred to a temperaturecontrolled freeze plate where the temperature was reduced to -6 to -8 degrees C. At this temperature, the droplets containing the INA agent froze while those without the agent remained liquid. After 2 minutes, the temperature of the plate was raised to 24 degrees C, and the slides were examined with a light microscope to determine the viability of the juveniles. The results showed that usually most juveniles (43% to 88%, depending on species) in solutions that did not contain the INA agent (controls) were active, indicating that the juveniles were capable of supercooling and were thereby protected from the subzero temperatures. Alternatively, less than 10% of the juveniles that had frozen for 2 minutes in solutions containing the INA agent remained viable, indicating that inoculative freezing of the solution was lethal to the supercooled juveniles. Our results suggest that, in geographical areas where winter temperatures may not be sufficiently low or sustained to freeze soil, the addition of an INA agent may help induce ice nucleation and thereby reduce the populations of nematode species that are unable to survive when the soil solution is frozen. PMID:19270966

  19. Effect of Fe coating of nucleation sites on epitaxial growth of Fe oxide nanocrystals on Si substrates

    NASA Astrophysics Data System (ADS)

    Ishibe, Takafumi; Watanabe, Kentaro; Nakamura, Yoshiaki

    2016-08-01

    We studied the effect of Fe coating on the epitaxial growth of Fe3O4 nanocrystals (NCs) over Fe-coated Ge epitaxial nuclei on Si(111). To completely cover Ge nuclei with Fe, some amount of Fe (>8 monolayers) must be deposited. Such covering is a key to epitaxial growth because an Fe coating layer prevents the oxidation of Ge surfaces during Fe3O4 formation, resulting in the epitaxial growth of Fe3O4 on them. This study demonstrates that an appropriate Fe coating of nucleation sites leads to the epitaxial growth of Fe3O4 NCs on Si substrates, indicating the realization of environmentally friendly and low-cost Fe3O4 NCs as the resistance random access memory material.

  20. Stress-determined nucleation sites above GaAs-capped arrays of InAs quantum dots

    NASA Astrophysics Data System (ADS)

    Latini, V.; Placidi, E.; Arciprete, F.; Tisbi, E.; Patella, F.; Magri, R.

    2016-09-01

    We studied the stress field at the surface of GaAs capping layers of variable thicknesses burying InAs quantum dot arrays using the Finite Element method to solve numerically the equations of the elastic field. The aim is to determine the stress-determined favorable sites for dot nucleation. We show that: (i) depending on the cap thickness, dot distances, and array orientation, sudden transitions in the stress-strain fields occur, leading from a vertical alignment of the dots to an anti-aligned correlation. We find that just few determined positions are favorable for dot nucleation and exclude some other sites previously indicated as favorable in the literature; (ii) the critical thicknesses at which the switch between the vertical alignment and the anti-aligned positions occurs depend on the distance between the dots in a square array and on the ratio between the two different distances if the arrays are rectangular; (iii) the transitions occur within a few nanometer range of the capping layer thickness, and the elastic field undergoes large changes in its properties before and after the transition. This behavior has been revealed by a very accurate fit of the tangential stress field using appropriate fit functions. The fit and parameter functions allow to easily reproduce the stress field in different contexts and are useful in growth simulation models. The results suggest that by properly engineering the capping layer thicknesses in the layers of a stack, it is possible to obtain different three-dimensional quantum dot lattices starting from an initial fixed dot array. Our results are in agreement with the available experimental data.

  1. The microtubule nucleation activity of centrobin in both the centrosome and cytoplasm

    PubMed Central

    Shin, Wonjung; Yu, Nam-Kyung; Kaang, Bong-Kiun; Rhee, Kunsoo

    2015-01-01

    Centrobin resides in daughter centriole and play a critical role in centriole duplication. Nucleation and stabilization of microtubules are known biological activities of centrobin. Here, we report a specific localization of centrobin outside the centrosome. Centrobin was associated with the stable microtubules. In hippocampal cells, centrobin formed cytoplasmic dots in addition to the localization at both centrosomes with the mother and daughter centrioles. Such specific localization pattern suggests that cytoplasmic centrobin is not just a reserved pool for centrosomal localization but also has a specific role in the cytoplasm. In fact, centrobin enhanced microtubule formation outside as well as inside the centrosome. These results propose specific roles of the cytoplasmic centrobin for noncentrosomal microtubule formation in specific cell types and during the cell cycle. PMID:26083938

  2. Cloning and sequencing of an ice nucleation active gene of Erwinia uredovora.

    PubMed

    Michigami, Y; Watabe, S; Abe, K; Obata, H; Arai, S

    1994-04-01

    An ice nucleation activity gene, named inaU, of the bacterium Erwinia uredovora KUIN-3 has been sequenced. This gene encodes a protein of 1034 amino acid residues, and its expression product, inaU protein, has an 832-amino acid residue segment consisting of 52 repeats of closely related 16-amino acid motifs (R-domain), flanked by N- and C-terminal sequences (N- and C-domains, respectively). The primary structure of the inaU protein is similar to those of the inaA, inaW, and inaZ gene products of Erwinia ananas, Pseudomonas fluorescens, and Pseudomonas syringae, respectively, but is smaller than any of these products in terms of the size of the R-domain. PMID:7764866

  3. Observation and Analysis of Particle Nucleation at a Forest Site in Southeastern US

    EPA Science Inventory

    This study examines the characteristics of new particle formation at a forest site in the Southeast U.S. Particle size distributions above a Loblolly pine plantation were measured between November, 2005 and September, 2007 and analyzed by event type and frequency as well as relat...

  4. Characterization of the ice nucleation activity of an airborne Penicillium species

    NASA Astrophysics Data System (ADS)

    Yordanova, Petya; Hill, Thomas C. J.; Pummer, Bernhard G.; Franc, Gary D.; Pöschl, Ulrich; Fröhlich-Nowoisky, Janine

    2016-04-01

    Microorganisms are ubiquitous both on and above the Earth. Several bacterial and fungal spe-cies are the focus of atmospheric studies due to their ability to trigger ice formation at high subzero temperatures. Thus, they have potential to modify cloud albedo, lifetime and precipita-tion, and ultimately the hydrological cycle. Several fungal strains have already been identified as possessing ice nucleation (IN) activity, and recent studies have shown that IN active fungi are present in the cultivable community of air and soil samples [1, 2]. However, the abundance, diversity, and sources of fungal ice nuclei in the atmosphere are still poorly characterized. In this study, fungal colonies obtained from air samples were screened for IN activity in the droplet-freezing assay described in Fröhlich-Nowoisky et al., 2015 [2]. Out of 128 tested iso-lates, two were found to catalyze ice formation at temperatures up to -4°C. By DNA analysis, both isolates were classified as Penicillium spp. The freezing activity of both was further char-acterized after different filtration, heat, and enzymatic treatments in the temperature range from ‑4°C to ‑15°C. Preliminary results show that a proteinaceous compound is responsible for the IN activity. Furthermore, ongoing experiments indicate that the activity is associated only with the hyphae. [1] Huffman, et al. (2013): Atmos. Chem. Phys., 13, 6151-6164. [2] Fröhlich-Nowoisky et al. (2015): Biogeosciences, 12: 1057-1071.

  5. Characterization of the ice nucleation activity of an airborne Penicillium species

    NASA Astrophysics Data System (ADS)

    Yordanova, Petya; Hill, Thomas C. J.; Pummer, Bernhard G.; Franc, Gary D.; Pöschl, Ulrich; Fröhlich-Nowoisky, Janine

    2016-04-01

    Microorganisms are ubiquitous both on and above the Earth. Several bacterial and fungal spe-cies are the focus of atmospheric studies due to their ability to trigger ice formation at high subzero temperatures. Thus, they have potential to modify cloud albedo, lifetime and precipita-tion, and ultimately the hydrological cycle. Several fungal strains have already been identified as possessing ice nucleation (IN) activity, and recent studies have shown that IN active fungi are present in the cultivable community of air and soil samples [1, 2]. However, the abundance, diversity, and sources of fungal ice nuclei in the atmosphere are still poorly characterized. In this study, fungal colonies obtained from air samples were screened for IN activity in the droplet-freezing assay described in Fröhlich-Nowoisky et al., 2015 [2]. Out of 128 tested iso-lates, two were found to catalyze ice formation at temperatures up to -4°C. By DNA analysis, both isolates were classified as Penicillium spp. The freezing activity of both was further char-acterized after different filtration, heat, and enzymatic treatments in the temperature range from -4°C to -15°C. Preliminary results show that a proteinaceous compound is responsible for the IN activity. Furthermore, ongoing experiments indicate that the activity is associated only with the hyphae. [1] Huffman, et al. (2013): Atmos. Chem. Phys., 13, 6151-6164. [2] Fröhlich-Nowoisky et al. (2015): Biogeosciences, 12: 1057-1071.

  6. Site-selective nucleation and controlled growth of gold nanostructures in tobacco mosaic virus nanotubulars.

    PubMed

    Zhou, Kun; Zhang, Jianting; Wang, Qiangbin

    2015-06-01

    Site-selective biomineralization of Au nanostructures in the interior channel of Tobacco Mosaic Virus (TMV) is achieved by mutating threonine 103 in TMV to cysteine (T103C-TMV) to introduce the strong coordination interaction between the arrayed sulfhydryl ligands and gold species. By finely tuning the reaction conditions, Au nanoparticle chains and Au nanorods are successfully and exclusively synthesized inside the T103C-TMV nanotubes. PMID:25612918

  7. Nucleation process of an M2 earthquake in a deep gold mine in South Africa inferred from on-fault foreshock activity

    NASA Astrophysics Data System (ADS)

    Yabe, Y.; Nakatani, M.; Naoi, M.; Philipp, J.; Janssen, C.; Kawakata, H.; Dresen, G. H.; Ogasawara, H.

    2014-12-01

    We observed foreshock activity of an Mw2.2 earthquake (the mainshock) that occurred in a gabbroic dyke at a depth of about 3.3 km from the surface in a deep gold mine in South Africa. Foreshock activity, selectively occurring on a plane on which the mainshock would occur, lasted for at least six months until the mainshock. Rock samples in the mainshock source region were recovered by drilling afterward. Indication of ancient hydrothermal alteration on the rupture plane of the mainshock suggests that the foreshock activity occurred on a pre-existing weakness, probably a healed joint, to nucleate the mainshock. The foreshocks during the three months leading up to the mainshock concentrated to three clusters (F1-F3), which, we interpreted, represent the nucleation at multiple sites. The temporal variation in the foreshock activity in the three months can be well explained by the temporal variation of the stressing state in the source region of the mainshock due to nearby mining. One of these clusters (cluster F2) showed an accelerated activity from about 10 days before the mainshock, while activity over the entire foreshock area was rather constant. The foreshock sources in the final 41 hours, during which the stress state was constant, migrated from F2 to F1 that neighbored to the mainshock hypocenter, suggesting coalescence of the two nuclei. The occurrence of mainshock was 0.4-2.3 days earlier than the time expected from an extrapolation of the accelerated foreshock activity in F2. The nucleation of mainshock may have been advanced to the criticality for dynamic instability in a stepwise manner upon the coalescence of nuclei.While the heterogeneity of geological structures obscures the straightforward manifestation of self-driven quasi-static nucleation, the present careful analysis suggests that some essence of such nucleation as known from the fracture theory and laboratory experiments was caught in the pre-M2 AE data on a natural joint at a depth of 3.3 km.

  8. Effect of starting microstructure upon the nucleation sites and distribution of graphite particles during a graphitising anneal of an experimental medium-carbon machining steel

    SciTech Connect

    Inam, A. Brydson, R. Edmonds, D.V.

    2015-08-15

    The potential for using graphite particles as an internal lubricant during machining is considered. Graphite particles were found to form during graphitisation of experimental medium-carbon steel alloyed with Si and Al. The graphite nucleation sites were strongly influenced by the starting microstructure, whether ferrite–pearlite, bainite or martensite, as revealed by light and electron microscopy. Favourable nucleation sites in the ferrite–pearlite starting microstructure were, not unexpectedly, found to be located within pearlite colonies, no doubt due to the presence of abundant cementite as a source of carbon. In consequence, the final distribution of graphite nodules in ferrite–pearlite microstructures was less uniform than for the bainite microstructure studied. In the case of martensite, this study found a predominance of nucleation at grain boundaries, again leading to less uniform graphite dispersions. - Highlights: • Metallography of formation of graphite particles in experimental carbon steel. • Potential for using graphite in steel as an internal lubricant during machining. • Microstructure features expected to influence improved machinability studied. • Influence of pre-anneal starting microstructure on graphite nucleation sites. • Influence of pre-anneal starting microstructure on graphite distribution. • Potential benefit is new free-cutting steel compositions without e.g. Pb alloying.

  9. Study on the ice nucleation activity of fungal spores (Ascomycota and Basidiomycota)

    NASA Astrophysics Data System (ADS)

    Pummer, B. G.; Atanasova, L.; Bauer, H.; Bernardi, J.; Druzhinina, I. S.; Grothe, H.

    2012-04-01

    Biogenic ice nucleation (IN) in the atmosphere is a topic of growing interest, as, according to IPCC, the impact of IN on global climate is crucial to perform reliable climate model calculations. About 20 years ago IN activity of a few lichen and Fusarium species [1,2] was reported, while all other investigated fungi were IN-negative. However, as the fungal kingdom is vast, many abundant species, especially the Basidiomycota (most mushrooms), were not tested before. Furthermore, the focus of the past studies was on the IN activity of the mycelium as a cryoprotective mechanism, and not on the airborne spores. We carried out oil immersion measurements [3] with spores from 17 different fungal species of ecological, economical or sanitary importance. Most of these species have not been investigated before, like exponents of Aspergillus, Trichoderma and Agaricales (most mushrooms). Apart from F. avenaceum, spores of all measured species showed moderate or no IN activity, supporting the hypothesis that significant IN activity is a rather exclusive property of only a few species within the fungal kingdom. [1] Kieft TL and Ruscetti T: J. Bacteriol. 172, 3519-3523, 1990. [2] Pouleur S et al.: Appl. Environ. Microbiol., 58, 2960-2964, 1992. [3] Marcolli C et al.: Atmos. Chem. Phys. 7, 5081-5091, 2007.

  10. Bacterial ice nucleation: significance and molecular basis.

    PubMed

    Gurian-Sherman, D; Lindow, S E

    1993-11-01

    Several bacterial species are able to catalyze ice formation at temperatures as warm as -2 degrees C. These microorganisms efficiently catalyze ice formation at temperatures much higher than most organic or inorganic substances. Because of their ubiquity on the surfaces of frost-sensitive plants, they are responsible for initiating ice formation, which results in frost injury. The high temperature of ice catalysis conferred by bacterial ice nuclei makes them useful in ice nucleation-limited processes such as artificial snow production, the freezing of some food products, and possibly in future whether modification schemes. The rarity of other ice nuclei active at high subfreezing temperature, and the ease and sensitivity with which ice nuclei can be quantified, have made the use of a promoterless bacterial ice nucleation gene valuable as a reporter of transcription. Target genes to which this promoter is fused can be used in cells in natural habitats. Warm-temperature ice nucleation sites have also been extensively studied at a molecular level. Nucleation sites active at high temperatures (above -5 degrees C) are probably composed of bacterial ice nucleation protein molecules that form functionally aligned aggregates. Models of ice nucleation proteins predict that they form a planar array of hydrogen binding groups that closely complement that of an ice crystal face. Moreover, interdigitation of these molecules may produce a large contiguous template for ice formation.

  11. Bacterial ice nucleation: significance and molecular basis.

    PubMed

    Gurian-Sherman, D; Lindow, S E

    1993-11-01

    Several bacterial species are able to catalyze ice formation at temperatures as warm as -2 degrees C. These microorganisms efficiently catalyze ice formation at temperatures much higher than most organic or inorganic substances. Because of their ubiquity on the surfaces of frost-sensitive plants, they are responsible for initiating ice formation, which results in frost injury. The high temperature of ice catalysis conferred by bacterial ice nuclei makes them useful in ice nucleation-limited processes such as artificial snow production, the freezing of some food products, and possibly in future whether modification schemes. The rarity of other ice nuclei active at high subfreezing temperature, and the ease and sensitivity with which ice nuclei can be quantified, have made the use of a promoterless bacterial ice nucleation gene valuable as a reporter of transcription. Target genes to which this promoter is fused can be used in cells in natural habitats. Warm-temperature ice nucleation sites have also been extensively studied at a molecular level. Nucleation sites active at high temperatures (above -5 degrees C) are probably composed of bacterial ice nucleation protein molecules that form functionally aligned aggregates. Models of ice nucleation proteins predict that they form a planar array of hydrogen binding groups that closely complement that of an ice crystal face. Moreover, interdigitation of these molecules may produce a large contiguous template for ice formation. PMID:8224607

  12. Activation energy distributions predicted by dispersive kinetic models for nucleation and denucleation: anomalous diffusion resulting from quantization.

    PubMed

    Skrdla, Peter J

    2011-06-23

    The activation energy distributions underpinning the two complementary dispersive kinetic models described by the author in a recent work (Skrdla, P. J. J. Phys. Chem. A 2009, 113, 9329) are derived and investigated. In the case of nucleation rate-limited conversions, which exhibit "acceleratory" sigmoidal transients (a kind of S-shaped stretched exponential conversion profile), an activation energy distribution visually similar to the Maxwell-Boltzmann (M-B) distribution is recovered, consistent with the original derivation of that model. In the case of predominantly "deceleratory" conversions, the activation energy distribution is skewed from normal in the opposite direction. While the "M-B-like" activation energy distribution supports the empirical observation of a rate enhancement as a function of the conversion time in nucleation rate-limited processes, the complementary distribution, with its pronounced low-energy tail, reflects a slow-down in the specific rate as the conversion progresses, consistent with experimentally observed denucleation rate-limited conversions. Activation energy distributions were also plotted for real-world data (Qu, H.; Louhi-Kultanen, M.; Kallas, J. Cryst. Growth Des. 2007, 7, 724), depicting the impact of various additives on the nucleation rate-limited kinetics of the solvent-mediated phase transformation of the crystalline drug carbamazepine. Last, by coupling the author's dispersive kinetic description of the time-dependent activation energy for nucleation to the classical description of the critical nucleus energy provided by the Kelvin equation, an accelerated hopping mechanism for the diffusion of monomers to the growing embryo surface was observed. That hopping mechanism was rationalized by modifying the Einstein-Smoluchowski (E-S) equation to allow it to describe the "supra-brownian" molecular motion thought to lie at the heart of nucleation kinetics.

  13. Significance of the C-terminal domain of Erwinia uredovora ice nucleation-active protein (Ina U).

    PubMed

    Michigami, Y; Abe, K; Obata, H; Arai, S

    1995-12-01

    Ice nucleation-active (Ina) proteins of bacterial origin comprise three distinct domains, i.e., N-terminal (N-), central repeat (R-), and C-terminal (C-) domains, among which the R-domain is essential, and its length may be correlated with the ice nucleation activity. In addition, the short C-terminal domain of about 50 amino acid residues is indispensable for the activity. Using the Ina U protein of Erwinia uredovora, we carried out precise mutational analyses of its C-terminus. The ice nucleation activity (T50) assay showed that the C-terminal 12 amino acids were not necessary, and a deletion mutant (delta C29) with a new C-terminal, Met29 (numbered from the first amino acid residue of the C-domain and corresponding to Met1022), exhibited almost the same activity as the wild-type Ina U protein did. However, deletion of the C-terminal 13 residues including Met29 resulted in almost complete loss of the activity. In the deletion mutant (delta C29), amino acid replacement of the C-terminus, Met29, showed that the activity was retained when Met29 was replaced with a neutral, aromatic, or basic amino acid (Gly, Phe, or Lys), but was lost on the replacement with an acidic amino acid (Asp or Glu). In addition, two other residues in the C-terminal region commonly present in all Ina proteins were examined as to their importance, and it was shown that one of these residues, Tyr27, is important for the activity, although it is not exclusively required; the activity was lost to a great extent when this residue was replaced with Gly or Ala, but to a lesser extent when it was replaced with Leu. These results suggest that significance of the secondary and/or tertiary structure of the C-terminal region of the Ina U protein for the ice nucleation activity. PMID:8720147

  14. Ion Mediated Nucleation: how is it Influenced by Changes in the Solar Activity?

    NASA Astrophysics Data System (ADS)

    D'Auria, R.; Turco, R. P.

    2003-12-01

    Recently it has been pointed out that tropospheric cloudiness can be correlated with the galactic cosmic rays (GCRs) intensity [Svensmark and Friis-Christensen, 1997]. A possible explanation for such a correlation relies on the fact that GCRs are the main ionization source in the upper troposphere, hence, throughout ionic mediated nucleation, they could possibly influence the global cloud condensation nuclei (CCN) formation [e.g., Yu, 2001; Dickinson, 1975]. Because the GCRs are modulated by the interaction between the solar wind and the Earth's magnetosphere and their intensity generally decreases with increasing solar activity, subtle changes in the solar activity could indirectly affect the Earth's climate. We have been studying the very first steps of ionic nucleation considering the molecular species of atmospheric interest (e.g.,water, nitric acid, sulfuric acid, ammonia etc.). In our approach the formation and evolution of ionic clusters is followed by resolving the time dependent kinetic aggregation process and considering the ions sources (ultimately the atmospheric ionization of neutral species) and sinks. We show how in typical atmospheric conditions stable populations of molecular ions forms. The novelty of our work consists in the determination of the kinetic parameters that govern the molecular ions growth (i.e., the forward and reverse clustering reaction constants for each cluster type and size) at a microscopic level. In fact a thermochemistry data base is built for the species of interest by integrating laboratory measurements, quantum mechanical calculations and, when appropriate, results from the macroscopic liquid droplet model [Thomson, 1928]. Such database is than used to retrieve the reverse clustering reaction coefficients for the molecular ion type and size and for the environmental conditions (pressure and temperature) of interest. The forward reaction is instead determined by calculating the ionic-neutral collisional rate or is assumed

  15. Salt site performance assessment activities

    SciTech Connect

    Kircher, J.F.; Gupta, S.K.

    1983-01-01

    During this year the first selection of the tools (codes) for performance assessments of potential salt sites have been tentatively selected and documented; the emphasis has shifted from code development to applications. During this period prior to detailed characterization of a salt site, the focus is on bounding calculations, sensitivity and with the data available. The development and application of improved methods for sensitivity and uncertainty analysis is a focus for the coming years activities and the subject of a following paper in these proceedings. Although the assessments to date are preliminary and based on admittedly scant data, the results indicate that suitable salt sites can be identified and repository subsystems designed which will meet the established criteria for protecting the health and safety of the public. 36 references, 5 figures, 2 tables.

  16. Parameterization of the Cloud Nucleating Activity of Fresh, Aged, and Internally-Mixed Organic Aerosols

    NASA Astrophysics Data System (ADS)

    Kreidenweis, S.; Petters, M.; Demott, P.; Prenni, A.; Ziemann, P.

    2006-12-01

    Carbonaceous particle types affect global climate, visibility, and human health, but their primary and secondary sources, sinks, and tropospheric lifetimes are highly uncertain. The size and hygroscopicity of particles, and in particular their activity as cloud condensation nuclei (CCN), plays a large role in determining their atmospheric impacts and lifetimes. However, hygroscopicity is difficult to parameterize for many organic species for which no thermodynamic data exist, and for complex, multicomponent aerosols of undefined composition. We propose a simple method to describe the relationship between dry particle diameter and CCN activity using a single hygroscopicity parameter, κ. We derive values of κ from fitting of experimental CCN-activity data from the literature and from recent experiments, including oxidation-aged organic particles and secondary organic aerosols. Values of κ are between 0.5 and 2 for highly-CCN- active salts such as sodium chloride, between 0.01 and 0.5 for slightly to very hygroscopic organic aerosols such as those produced in biomass burning and as secondary organic aerosols, and 0 for nonhygroscopic components. The hygroscopicity of internal mixtures can be calculated as a volume fraction weighted average of the hygroscopicity parameters of the individual species comprising the mixture. Aging of aerosol, understood as changes in hygroscopicity due to condensation of hydrophilic species, coagulation of aerosol populations, or heterogeneous chemical reactions, are described conveniently by changes in κ. Our studies show that oxidative aging that proceeds by addition of functional groups to the CHx carbon backbone leads to only small changes in κ, and thus the process alone is inefficient at rendering small, initially- hydrophobic primary organic particles capable of being scavenged by cloud-drop nucleation. Other processes, such as coagulation and condensation, control the rate of hydrophobic-to-hydrophilic conversion of primary

  17. Characterization of airborne ice-nucleation-active bacteria and bacterial fragments

    NASA Astrophysics Data System (ADS)

    Šantl-Temkiv, Tina; Sahyoun, Maher; Finster, Kai; Hartmann, Susan; Augustin-Bauditz, Stefanie; Stratmann, Frank; Wex, Heike; Clauss, Tina; Nielsen, Niels Woetmann; Sørensen, Jens Havskov; Korsholm, Ulrik Smith; Wick, Lukas Y.; Karlson, Ulrich Gosewinkel

    2015-05-01

    Some bacteria have the unique capacity of synthesising ice-nucleation-active (INA) proteins and exposing them at their outer membrane surface. As INA bacteria enter the atmosphere, they may impact the formation of clouds and precipitation. We studied members of airborne bacterial communities for their capacity to catalyse ice formation and we report on the excretion of INA proteins by airborne Pseudomonas sp. We also observed for the first time that INA biological fragments <220 nm were present in precipitation samples (199 and 482 INA fragments per L of precipitation), which confirms the presence of submicron INA biological fragments in the atmosphere. During 14 precipitation events, strains affiliated with the genus Pseudomonas, which are known to carry ina genes, were dominant. A screening for INA properties revealed that ∼12% of the cultivable bacteria caused ice formation at ≤-7 °C. They had likely been emitted to the atmosphere from terrestrial surfaces, e.g. by convective transport. We tested the ability of isolated INA strains to produce outer membrane vesicles and found that two isolates could do so. However, only very few INA vesicles were released per INA cell. Thus, the source of the submicron INA proteinaceous particles that we detected in the atmosphere remains to be elucidated.

  18. E-cadherin junction formation involves an active kinetic nucleation process

    SciTech Connect

    Biswas, Kabir H.; Hartman, Kevin L.; Yu, Cheng -han; Harrison, Oliver J.; Song, Hang; Smith, Adam W.; Huang, William Y. C.; Lin, Wan -Chen; Guo, Zhenhuan; Padmanabhan, Anup; Troyanovsky, Sergey M.; Dustin, Michael L.; Shapiro, Lawrence; Honig, Barry; Zaidel-Bar, Ronen; Groves, Jay T.

    2015-08-19

    Epithelial (E)-cadherin-mediated cell–cell junctions play important roles in the development and maintenance of tissue structure in multicellular organisms. E-cadherin adhesion is thus a key element of the cellular microenvironment that provides both mechanical and biochemical signaling inputs. Here, we report in vitro reconstitution of junction-like structures between native E-cadherin in living cells and the extracellular domain of E-cadherin in a supported membrane. Junction formation in this hybrid live cell-supported membrane configuration requires both active processes within the living cell and a supported membrane with low E-cad-ECD mobility. The hybrid junctions recruit α-catenin and exhibit remodeled cortical actin. Observations suggest that the initial stages of junction formation in this hybrid system depend on the trans but not the cis interactions between E-cadherin molecules, and proceed via a nucleation process in which protrusion and retraction of filopodia play a key role.

  19. E-cadherin junction formation involves an active kinetic nucleation process

    PubMed Central

    Biswas, Kabir H.; Hartman, Kevin L.; Yu, Cheng-han; Harrison, Oliver J.; Song, Hang; Smith, Adam W.; Huang, William Y. C.; Lin, Wan-Chen; Guo, Zhenhuan; Padmanabhan, Anup; Troyanovsky, Sergey M.; Dustin, Michael L.; Shapiro, Lawrence; Honig, Barry; Zaidel-Bar, Ronen; Groves, Jay T.

    2015-01-01

    Epithelial (E)-cadherin-mediated cell−cell junctions play important roles in the development and maintenance of tissue structure in multicellular organisms. E-cadherin adhesion is thus a key element of the cellular microenvironment that provides both mechanical and biochemical signaling inputs. Here, we report in vitro reconstitution of junction-like structures between native E-cadherin in living cells and the extracellular domain of E-cadherin (E-cad-ECD) in a supported membrane. Junction formation in this hybrid live cell-supported membrane configuration requires both active processes within the living cell and a supported membrane with low E-cad-ECD mobility. The hybrid junctions recruit α-catenin and exhibit remodeled cortical actin. Observations suggest that the initial stages of junction formation in this hybrid system depend on the trans but not the cis interactions between E-cadherin molecules, and proceed via a nucleation process in which protrusion and retraction of filopodia play a key role. PMID:26290581

  20. E-cadherin junction formation involves an active kinetic nucleation process

    DOE PAGES

    Biswas, Kabir H.; Hartman, Kevin L.; Yu, Cheng -han; Harrison, Oliver J.; Song, Hang; Smith, Adam W.; Huang, William Y. C.; Lin, Wan -Chen; Guo, Zhenhuan; Padmanabhan, Anup; et al

    2015-08-19

    Epithelial (E)-cadherin-mediated cell–cell junctions play important roles in the development and maintenance of tissue structure in multicellular organisms. E-cadherin adhesion is thus a key element of the cellular microenvironment that provides both mechanical and biochemical signaling inputs. Here, we report in vitro reconstitution of junction-like structures between native E-cadherin in living cells and the extracellular domain of E-cadherin in a supported membrane. Junction formation in this hybrid live cell-supported membrane configuration requires both active processes within the living cell and a supported membrane with low E-cad-ECD mobility. The hybrid junctions recruit α-catenin and exhibit remodeled cortical actin. Observations suggest thatmore » the initial stages of junction formation in this hybrid system depend on the trans but not the cis interactions between E-cadherin molecules, and proceed via a nucleation process in which protrusion and retraction of filopodia play a key role.« less

  1. Evaluating the Role of Aerosol Mixing State in Cloud Droplet Nucleation using a New Activation Parameterization

    NASA Astrophysics Data System (ADS)

    Rothenberg, D. A.; Wang, C.

    2013-12-01

    An important source contributing to uncertainty in simulations with global climate models arises from the influence of aerosols on cloud properties. These so-called aerosol indirect effects arise from a single coupling in the model, representing how aerosols activate and serve as cloud condensation nuclei and ultimately cloud droplets. While it is possible to build explicit numerical models which describe this process in detail, these class of tools are untenable for use in global climate models due to their complexity. Instead, physically- or empirically-based parameterizations of activation are used in their place to efficiently approximate cloud droplet nucleation as a function of a few meteorological and aerosol physical/chemical properties. As global climate models are outfitted with more complex, size- and mixing state-resolving aerosol models, activation parameterizations are increasingly called upon to handle aerosol populations against which their performance has not been explicitly benchmarked. Here, a simple scheme is proposed to evaluate the performance of activation parameterizations against a spectrum of mixing states, and two schemes commonly used in global models are studied using this framework. It is shown that each scheme exhibits systematic biases when a complex mixing state is present. To help resolve these issues, a new scheme is derived using Polynomial Chaos Expansion to build meta-models representing a full complexity parcel model. The meta-models are shown to accurately handle activation in both single-mode and mixture cases. In addition, a global sensitivity analysis is applied to benchmark the performance of the meta-models and the activation parameterizations against a detailed parcel model, and it is shown that the meta-models tend to more accurately attribute variability in activation dynamics to each input parameter and their interactions with others when compared to the physically-based parameterizations. A variety of experiments

  2. Enhanced High-Temperature Ice Nucleation Ability of Crystallized Aerosol Particles after Pre-Activation at Low Temperature

    NASA Astrophysics Data System (ADS)

    Wagner, R.; Moehler, O.; Saathoff, H.; Schnaiter, M.

    2014-12-01

    The term pre-activation in heterogeneous ice nucleation describes the observation that the ice nucleation ability of solid ice nuclei may improve after they have already been involved in ice crystal formation or have been exposed to a temperature lower than 235 K. This can be explained by the retention of small ice embryos in cavities or crevices at the particle surface or by the capillary condensation and freezing of supercooled water, respectively. In recent cloud chamber experiments with crystallized aqueous ammonium sulfate, oxalic acid, and succinic acid solution droplets, we have unraveled a further pre-activation mechanism under ice subsaturated conditions which does not require the preceding growth of ice on the seed aerosol particles (Wagner, R. et al., J. Geophys. Res. Atmos., 119, doi: 10.1002/2014JD021741). First cloud expansion experiments were performed at a high temperature (267 - 244 K) where the crystallized particles did not promote any heterogeneous ice nucleation. Ice nucleation at this temperature, however, could be triggered by temporarily cooling the crystallized particles to a lower temperature. This is because upon crystallization, residuals of the aqueous solution are trapped within the crystals. These captured liquids can freeze when cooled below their respective homogeneous or heterogeneous freezing temperature, leading to the formation of ice pockets in the crystalline particles. When warmed again to the higher temperature, ice formation by the pre-activated particles occurred via depositional and deliquescence-induced ice growth, with ice active fractions ranging from 1 to 4% and 4 to 20%, respectively. Pre-activation disappeared above the eutectic temperature, which for the organic acids are close to the melting point of ice. This mechanism could therefore contribute to the very small fraction of atmospheric aerosol particles that are still ice active well above 263 K.

  3. Deep supercooling xylem parenchyma cells of katsura tree (Cercidiphyllum japonicum) contain flavonol glycosides exhibiting high anti-ice nucleation activity.

    PubMed

    Kasuga, Jun; Hashidoko, Yasuyuki; Nishioka, Atsushi; Yoshiba, Megumi; Arakawa, Keita; Fujikawa, Seizo

    2008-09-01

    Xylem parenchyma cells (XPCs) of boreal hardwood species adapt to sub-freezing temperatures by deep supercooling to maintain a liquid state of intracellular water near -40 degrees C. Our previous study found that crude xylem extracts from such tree species exhibited anti-ice nucleation activity to promote supercooling of water. In the present study, thus, we attempted to identify the causative substances of supercooling. Crude xylem extracts from katsura tree (Cercidiphyllum japonicum), of which XPCs exhibited deep supercooling to -40 degrees C, were prepared by methanol extraction. The crude extracts were purified by liquid-liquid extraction and then by silica gel column chromatography. Although all the fractions obtained after each purification step exhibited some levels of anti-ice nucleation activity, only the most active fraction was retained to proceed to the subsequent level of purification. High-performance liquid chromatography (HPLC) analysis of a fraction with the highest level of activity revealed four peaks with high levels of anti-ice nucleation activity in the range of 2.8-9.0 degrees C. Ultraviolet (UV), mass and nuclear magnetic resonance (NMR) spectra revealed that these four peaks corresponded to quercetin-3-O-beta-glucoside (Q3G), kaempferol-7-O-beta-glucoside (K7G), 8-methoxykaempferol-3-O-beta-glucoside (8MK3G) and kaempferol-3-O-beta-glucoside (K3G). Microscopic observations confirmed the presence of flavonoids in cytoplasms of XPCs. These results suggest that diverse kinds of anti-ice nucleation substances, including flavonol glycosides, may have important roles in deep supercooling of XPCs. PMID:18518920

  4. Deep supercooling xylem parenchyma cells of katsura tree (Cercidiphyllum japonicum) contain flavonol glycosides exhibiting high anti-ice nucleation activity.

    PubMed

    Kasuga, Jun; Hashidoko, Yasuyuki; Nishioka, Atsushi; Yoshiba, Megumi; Arakawa, Keita; Fujikawa, Seizo

    2008-09-01

    Xylem parenchyma cells (XPCs) of boreal hardwood species adapt to sub-freezing temperatures by deep supercooling to maintain a liquid state of intracellular water near -40 degrees C. Our previous study found that crude xylem extracts from such tree species exhibited anti-ice nucleation activity to promote supercooling of water. In the present study, thus, we attempted to identify the causative substances of supercooling. Crude xylem extracts from katsura tree (Cercidiphyllum japonicum), of which XPCs exhibited deep supercooling to -40 degrees C, were prepared by methanol extraction. The crude extracts were purified by liquid-liquid extraction and then by silica gel column chromatography. Although all the fractions obtained after each purification step exhibited some levels of anti-ice nucleation activity, only the most active fraction was retained to proceed to the subsequent level of purification. High-performance liquid chromatography (HPLC) analysis of a fraction with the highest level of activity revealed four peaks with high levels of anti-ice nucleation activity in the range of 2.8-9.0 degrees C. Ultraviolet (UV), mass and nuclear magnetic resonance (NMR) spectra revealed that these four peaks corresponded to quercetin-3-O-beta-glucoside (Q3G), kaempferol-7-O-beta-glucoside (K7G), 8-methoxykaempferol-3-O-beta-glucoside (8MK3G) and kaempferol-3-O-beta-glucoside (K3G). Microscopic observations confirmed the presence of flavonoids in cytoplasms of XPCs. These results suggest that diverse kinds of anti-ice nucleation substances, including flavonol glycosides, may have important roles in deep supercooling of XPCs.

  5. A novel cryoprotective protein (CRP) with high activity from the ice-nucleating bacterium, Pantoea agglomerans IFO12686.

    PubMed

    Koda, N; Asaeda, T; Yamade, K; Kawahara, H; Obata, H

    2001-04-01

    The ice-nucleating bacterium, Pantoea agglomerans IFO12686, induces the cryoprotective protein (CRP) by cold acclimation at 12 degrees C. The CRP was purified to apparent homogeneity by various chromatographies. We found that the purified CRP was a monomer of approximately 29,000 according to gel filtration chromatography and SDS-PAGE, and was a heat-stable protein. The CRP could protect freeze-labile enzymes, lactate dehydrogenase (LDH), alcohol dehydrogenase (ADH) and isocitrate dehydrogenase (iCDH), against freezing-thawing denaturation. The activity of the CRP was about 3.5 x 10(4) times more effective than bovine serum albumin (BSA) and 2 x 10(6) times than COR26 from the ice-nucleating bacterium Pseudomonas fluorescens KUIN-1. We confirmed that the CRP was a novel protein, as judged by the a different molecule mass from the already-known cryoprotectants, and has an extremely high cryoprotective activity. PMID:11388469

  6. Measurements of BC-Containing Aerosol and Ice Nucleation Active Residuals in Colorado.

    NASA Astrophysics Data System (ADS)

    Katich, J. M.

    2015-12-01

    A recent ice nucleation (IN) chamber inter-comparison study (FIN-3) provided an opportunity to deploy two single particle soot photometers (SP2s) to the Stormpeak Laboratory in the mountains of Colorado in September of 2015. Aerosol was sampled from ambient air, as well as from behind both a coarse-mode aerosol concentrator and an ice nucleation chamber providing ice residuals. The SP2s characterized the size and mixing state of refractory black carbon-containing particles. Initial analyses of laboratory and ambient data collected over 3 weeks will be presented, with an emphasis on both coarse mode BC observations and BC contributions to ice residuals. The results will help constrain the role of BC from local and regional sources on heterogeneous ice nucleation.

  7. Heterogeneous nucleation or homogeneous nucleation?

    NASA Astrophysics Data System (ADS)

    Liu, X. Y.

    2000-06-01

    The generic heterogeneous effect of foreign particles on three dimensional nucleation was examined both theoretically and experimentally. It shows that the nucleation observed under normal conditions includes a sequence of progressive heterogeneous processes, characterized by different interfacial correlation function f(m,x)s. At low supersaturations, nucleation will be controlled by the process with a small interfacial correlation function f(m,x), which results from a strong interaction and good structural match between the foreign bodies and the crystallizing phase. At high supersaturations, nucleation on foreign particles having a weak interaction and poor structural match with the crystallizing phase (f(m,x)→1) will govern the kinetics. This frequently leads to the false identification of homogeneous nucleation. Genuine homogeneous nucleation, which is the up-limit of heterogeneous nucleation, may not be easily achievable under gravity. In order to check these results, the prediction is confronted with nucleation experiments of some organic and inorganic crystals. The results are in excellent agreement with the theory.

  8. Geographic, seasonal, and precipitation chemistry influence on the abundance and activity of biological ice nucleators in rain and snow

    PubMed Central

    Christner, Brent C.; Cai, Rongman; Morris, Cindy E.; McCarter, Kevin S.; Foreman, Christine M.; Skidmore, Mark L.; Montross, Scott N.; Sands, David C.

    2008-01-01

    Biological ice nucleators (IN) function as catalysts for freezing at relatively warm temperatures (warmer than −10 °C). We examined the concentration (per volume of liquid) and nature of IN in precipitation collected from Montana and Louisiana, the Alps and Pyrenees (France), Ross Island (Antarctica), and Yukon (Canada). The temperature of detectable ice-nucleating activity for more than half of the samples was ≥ −5 °C based on immersion freezing testing. Digestion of the samples with lysozyme (i.e., to hydrolyze bacterial cell walls) led to reductions in the frequency of freezing (0–100%); heat treatment greatly reduced (95% average) or completely eliminated ice nucleation at the measured conditions in every sample. These behaviors were consistent with the activity being bacterial and/or proteinaceous in origin. Statistical analysis revealed seasonal similarities between warm-temperature ice-nucleating activities in snow samples collected over 7 months in Montana. Multiple regression was used to construct models with biogeochemical data [major ions, total organic carbon (TOC), particle, and cell concentration] that were accurate in predicting the concentration of microbial cells and biological IN in precipitation based on the concentration of TOC, Ca2+, and NH4+, or TOC, cells, Ca2+, NH4+, K+, PO43−, SO42−, Cl−, and HCO3−. Our results indicate that biological IN are ubiquitous in precipitation and that for some geographic locations the activity and concentration of these particles is related to the season and precipitation chemistry. Thus, our research suggests that biological IN are widespread in the atmosphere and may affect meteorological processes that lead to precipitation. PMID:19028877

  9. Transgenic ice nucleation-active Enterobacter cloacae reduces cold hardiness of corn borer and cotton bollworm larvae.

    PubMed

    Tang, Chaorong; Sun, Fuzai; Zhang, Xinjian; Zhao, Tingchang; Qi, Jiyan

    2004-12-27

    The ice nucleation (IN) gene iceA of Erwinia ananas 110 was integrated into the chromosomes of two Enterobacter cloacae strains (Enc1.2022 and Enc1.181). These two newly derived transgenic strains, designated Enc2022-I and Enc181-I, respectively, possessed ice nucleation activity at -2.5 degrees C, significantly higher than their parent strains (active at approx -10 degrees C or lower). After ingesting these transgenic bacteria, the mean supercooling points (SCPs) of corn borer and cotton bollworm larvae were -3 to -4 degrees C, significantly higher than those of untreated controls. The SCPs remained significantly elevated over the 9-day period after ingestion, which matched well with the efficient gut colonization of the bacteria during this period. All treated larvae froze and eventually died after exposure for 6 h to a temperature of -7 degrees C, and more than 95% died after 12 h at -5 degrees C. In contrast, few or none of the untreated control larvae froze and died under the same conditions. Furthermore, the growth ability of these transgenic ice nucleation-active (INA) En. cloacae strains on corn leaves was reduced, compared to that of wild-type epiphytic E. ananas, as revealed by pot tests conducted in both greenhouse and outdoor conditions. The stable colonization in insect guts and their lower affinity to plants would make these transgenic INA bacteria useful as a novel tool for biological control of insect pests in agricultural fields. PMID:16329857

  10. Formin 1 Regulates Ectoplasmic Specialization in the Rat Testis Through Its Actin Nucleation and Bundling Activity.

    PubMed

    Li, Nan; Mruk, Dolores D; Wong, Chris K C; Han, Daishu; Lee, Will M; Cheng, C Yan

    2015-08-01

    During spermatogenesis, developing spermatids and preleptotene spermatocytes are transported across the adluminal compartment and the blood-testis barrier (BTB), respectively, so that spermatids line up near the luminal edge to prepare for spermiation, whereas preleptotene spermatocytes enter the adluminal compartment to differentiate into late spermatocytes to prepare for meiosis I/II. These cellular events involve actin microfilament reorganization at the testis-specific, actin-rich Sertoli-spermatid and Sertoli-Sertoli cell junction called apical and basal ectoplasmic specialization (ES). Formin 1, an actin nucleation protein known to promote actin microfilament elongation and bundling, was expressed at the apical ES but limited to stage VII of the epithelial cycle, whereas its expression at the basal ES/BTB stretched from stage III to stage VI, diminished in stage VII, and was undetectable in stage VIII tubules. Using an in vitro model of studying Sertoli cell BTB function by RNA interference and biochemical assays to monitor actin bundling and polymerization activity, a knockdown of formin 1 in Sertoli cells by approximately 70% impeded the tight junction-permeability function. This disruptive effect on the tight junction barrier was mediated by a loss of actin microfilament bundling and actin polymerization capability mediated by changes in the localization of branched actin-inducing protein Arp3 (actin-related protein 3), and actin bundling proteins Eps8 (epidermal growth factor receptor pathway substrate 8) and palladin, thereby disrupting cell adhesion. Formin 1 knockdown in vivo was found to impede spermatid adhesion, transport, and polarity, causing defects in spermiation in which elongated spermatids remained embedded into the epithelium in stage IX tubules, mediated by changes in the spatiotemporal expression of Arp3, Eps8, and palladin. In summary, formin 1 is a regulator of ES dynamics.

  11. A detailed study of ice nucleation by feldspar minerals

    NASA Astrophysics Data System (ADS)

    Whale, T. F.; Murray, B. J.; Wilson, T. W.; Carpenter, M. A.; Harrison, A.; Holden, M. A.; Vergara Temprado, J.; Morris, J.; O'Sullivan, D.

    2015-12-01

    Immersion mode heterogeneous ice nucleation plays a crucial role in controlling the composition of mixed phase clouds, which contain both supercooled liquid water and ice particles. The amount of ice in mixed phase clouds can affect cloud particle size, lifetime and extent and so affects radiative properties and precipitation. Feldspar minerals are probably the most important minerals for ice nucleation in mixed phase clouds because they nucleate ice more efficiently than other components of atmospheric mineral dust (Atkinson et al. 2013). The feldspar class of minerals is complex, containing numerous chemical compositions, several crystal polymorphs and wide variations in microscopic structure. Here we present the results of a study into ice nucleation by a wide range of different feldspars. We found that, in general, alkali feldspars nucleate ice more efficiently than plagioclase feldspars. However, we also found that particular alkali feldspars nucleate ice relatively inefficiently, suggesting that chemical composition is not the only important factor that dictates the ice nucleation efficiency of feldspar minerals. Ice nucleation by feldspar is described well by the singular model and is probably site specific in nature. The alkali feldspars that do not nucleate ice efficiently possess relatively homogenous structure on the micrometre scale suggesting that the important sites for nucleation are related to surface topography. Ice nucleation active site densities for the majority of tested alkali feldspars are similar to those found by Atkinson et al (2013), meaning that the validity of global aerosol modelling conducted in that study is not affected. Additionally, we have found that ice nucleation by feldspars is strongly influenced, both positively and negatively, by the solute content of droplets. Most other nucleants we have tested are unaffected by solutes. This provides insight into the mechanism of ice nucleation by feldspars and could be of importance

  12. The presence of complete but masked freezing nuclei in various artificially constructed ice nucleation-active proteobacteria.

    PubMed

    Yankofsky, S A; Nadler, T; Kaplan, H

    1997-05-01

    Disparate gamma-subdivision proteobacteria artificially endowed with the same ice gene of enteric origin acquired water-freezing potential at -12 degrees C, but expressed it to varying extents under identical conditions of culture as well as after being subjected to certain post-culture treatments. Varying rates of cell-bound ice nucleus synthesis were probably not the root cause of these observed interspecies differences in nucleation-active cell frequency because potentially functional but masked ice-forming templates were found in the outer cell envelope of even initially inactive individuals taken from physiologically uniform populations of virtually all tested species. We therefore propose that the extent of bacterial ice nucleation generally reflects species-specified extent of ice nucleus sequestration. PMID:9099634

  13. A kinetic model describing cell growth and production of highly active, recombinant ice nucleation protein in Escherichia coli.

    PubMed

    Palaiomylitou, M A; Matis, K A; Zouboulis, A I; Kyriakidis, D A

    2002-05-01

    A structured kinetic model, which describes the production of the recombinant ice nucleation protein in different conditions, was applied. The model parameters were estimated based on the variation of the specific growth rate and the intracellular product concentration during cultivation. The equations employed relate the cellular plasmid content or plasmid copy number with the cloned-gene expression; these correlations were successfully tested on the experimental data. The optimal nutrient conditions for the growth of Escherichia coli expressing the inaZ gene of Pseudomonas syringae were determined for the production of active ice nucleation protein. The kinetics of the cultures expressing the inaZ gene were studied in a bioreactor at different growth temperatures and nutrient conditions. PMID:11920448

  14. Spatial Variability in Ultrafine Particles at Five Sites in Southern Ontario, Canada During BAQS-Met 2007 Campaign: Implication of Regional Nucleation Events

    NASA Astrophysics Data System (ADS)

    Jeong, C.; McGuire, M.; Evans, G.; Rachel, R. Y.; Slowik, J. G.; Abbatt, J. P.; Popescu, R.; Murphy, J.; Zeromskiene, K. G.; Mozurkewich, M.; Leaitch, R.

    2008-12-01

    Ultrafine particle (UFP) measurements were simultaneously conducted in five urban and rural areas; Toronto, Egbert, Ridgetown, Bear Creek, and Harrow in Ontario, Canada as part of the Border Air Quality and Meteorology Study (BAQS-Met 2007). The number and size distributions of UFP in the size range of 14 to 93 nm were measured by a Fast Mobility Particle Sizer (FMPS, TSI 3091) and four Scanning Mobility Particle Sizers (SMPS) from June 19 to July 8, 2007. Continuous measurements of PM2.5 mass and gaseous pollutants (NH3, CO, SO2, NOx, O3) were also performed at the sites. The highest particle concentrations were observed at the rural site in Harrow, whereas lower concentrations were found in Toronto, a metropolitan area. The variability of hourly averaged UFP concentrations were significantly higher at the Harrow and Bear Creek sites indicating low background levels and frequent occurrence of strong particle nucleation events. Regional particle nucleation events were classified by assessing particle formation and growth rates at the five monitoring sites. The influences of pre-existing particles, gaseous pollutants and meteorological parameters on the classified particle nucleation events were evaluated. Spatial variability of UFP was examined by using the coefficient of divergence (COD) of each size bin of UFP. The COD provides relative measure of homogeneity in UPF concentrations in the southern Ontario. On average, the COD value was lower between Harrow and Bear Creek than between Harrow and Ridgetown. The COD values for smaller particles in the size range (14nm-22nm) tended to be higher than the levels for larger particles (25nm-93nm) suggesting size dependent homogeneity. In order to regional distribution and dispersion of UFP with distance, cumulative semivariogram (CSV) technique was used for UFP number concentrations at five sites. Detailed results over the measurement periods will be presented and discussed.

  15. [Advances in the application research of bacterial ice nucleation active (ina) genes].

    PubMed

    Tang, Chao-Rong; Sun, Fu-Zai; Zhao, Ting-Chang

    2002-07-01

    For recent years, the research has been focused on the ina gene application in the field of biological ice nucleation. This paper reviewed the application of ina genes in bacterial cell surface display, construction of reporter gene systems, killing insect pests through induced freezing, sensitive detection of pathogenic bacteria contaminating foods, breeding of cold resistant varieties. A brief introduction of the ina gene application in killing insect pests in China was also made in this review. PMID:12385233

  16. Nucleation in Synoptically Forced Cirrostratus

    NASA Technical Reports Server (NTRS)

    Lin, R.-F.; Starr, D. OC.; Reichardt, J.; DeMott, P. J.

    2004-01-01

    Formation and evolution of cirrostratus in response to weak, uniform and constant synoptic forcing is simulated using a one-dimensional numerical model with explicit microphysics, in which the particle size distribution in each grid box is fully resolved. A series of tests of the model response to nucleation modes (homogeneous-freezing-only/heterogeneous nucleation) and heterogeneous nucleation parameters are performed. In the case studied here, nucleation is first activated in the prescribed moist layer. A continuous cloud-top nucleation zone with a depth depending on the vertical humidity gradient and one of the nucleation parameters is developed afterward. For the heterogeneous nucleation cases, intermittent nucleation zones in the mid-upper portion of the cloud form where the relative humidity is on the rise, because existent ice crystals do not uptake excess water vapor efficiently, and ice nuclei (IN) are available. Vertical resolution as fine as 1 m is required for realistic simulation of the homogeneous-freezing-only scenario, while the model resolution requirement is more relaxed in the cases where heterogeneous nucleation dominates. Bulk microphysical and optical properties are evaluated and compared. Ice particle number flux divergence, which is due to the vertical gradient of the gravity-induced particle sedimentation, is constantly and rapidly changing the local ice number concentration, even in the nucleation zone. When the depth of the nucleation zone is shallow, particle number concentration decreases rapidly as ice particles grow and sediment away from the nucleation zone. When the depth of the nucleation zone is large, a region of high ice number concentration can be sustained. The depth of nucleation zone is an important parameter to be considered in parametric treatments of ice cloud generation.

  17. The adsorption theory of heterogeneous nucleation and its application to ice nucleation

    NASA Astrophysics Data System (ADS)

    Laaksonen, A.; Malila, J.

    2015-12-01

    In the classical picture of heterogeneous nucleation, spherical liquid caps, characterized by a contact angle, appear on a surface at supersaturated conditions, and if these caps are larger than so called critical size, they grow spontaneously, whereas smaller caps will evaporate. In reality, vapor adsorption takes place already at subsaturated conditions, and depending on the substrate-vapor interactions, the adsorbed layer may consist of clusters centered on so called active sites. The extent of adsorption can be calculated using adsorption isotherms which give the average adsorption layer thickness as a function of vapor saturation ratio, provided that adsorption constants (characterizing the substrate-vapor interactions) are known. We recently proposed a new theory (Laaksonen, J. Phys. Chem. A., 2015) that combines adsorption and heterogeneous nucleation so that it can be used to calculate both the adsorption layer thickness at subsaturated conditions, as well as the onset supersaturation for nucleation. We showed that the new theory performs much better than the classical theory both with flat surfaces, and in the case of water vapor nucleating on SiO2, TiO2, and Ag2O nanoparticles (Laaksonen and Malila, ACPD, in press). Here, we review the new theory, and compare its predictive capability to that of the classical heterogeneous nucleation theory. We furthermore discuss the potential use of the new theory for calculation of condensation and deposition mode ice nucleation in the atmosphere.

  18. Ldb1-nucleated transcription complexes function as primary mediators of global erythroid gene activation

    PubMed Central

    Li, LiQi; Freudenberg, Johannes; Cui, Kairong; Dale, Ryan; Song, Sang-Hyun; Dean, Ann; Zhao, Keji

    2013-01-01

    Erythropoiesis is dependent on the lineage-specific transcription factors Gata1, Tal1, and Klf1. Several erythroid genes have been shown to require all 3 factors for their expression, suggesting that they function synergistically; however, there is little direct evidence for widespread cooperation. Gata1 and Tal1 can assemble within higher-order protein complexes (Ldb1 complexes) that include the adapter molecules Lmo2 and Ldb1. Ldb1 proteins are capable of coassociation, and long-range Ldb1-mediated oligomerization of enhancer- and promoter-bound Ldb1 complexes has been shown to be required for β-globin gene expression. In this study, we generated a genomewide map of Ldb1 complex binding sites that revealed widespread binding at erythroid genes and at known erythroid enhancer elements. Ldb1 complex binding sites frequently colocalized with Klf1 binding sites and with consensus binding motifs for other erythroid transcription factors. Transcriptomic analysis demonstrated a strong correlation between Ldb1 complex binding and Ldb1 dependency for gene expression and identified a large cohort of genes coregulated by Ldb1 complexes and Klf1. Together, these results provide a foundation for defining the mechanism and scope of Ldb1 complex activity during erythropoiesis. PMID:23610375

  19. Direct Quantification of Ice Nucleation Active Bacteria in Aerosols and Precipitation: Their Potential Contribution as Ice Nuclei

    NASA Astrophysics Data System (ADS)

    Hill, T. C.; DeMott, P. J.; Garcia, E.; Moffett, B. F.; Prenni, A. J.; Kreidenweis, S. M.; Franc, G. D.

    2013-12-01

    Ice nucleation active (INA) bacteria are a potentially prodigious source of highly active (≥-12°C) atmospheric ice nuclei, especially from agricultural land. However, we know little about the conditions that promote their release (eg, daily or seasonal cycles, precipitation, harvesting or post-harvest decay of litter) or their typical contribution to the pool of boundary layer ice nucleating particles (INP). To initiate these investigations we developed a quantitative Polymerase Chain Reaction (qPCR) test of the ina gene, the gene that codes for the ice nucleating protein, to directly count INA bacteria in environmental samples. The qPCR test amplifies most forms of the gene and is highly sensitive, able to detect perhaps a single gene copy (ie, a single bacterium) in DNA extracted from precipitation. Direct measurement of the INA bacteria is essential because environmental populations will be a mixture of living, viable-but-not culturable, moribund and dead cells, all of which may retain ice nucleating proteins. Using the qPCR test on leaf washings of plants from three farms in Wyoming, Colorado and Nebraska we found INA bacteria to be abundant on crops, especially on cereals. Mid-summer populations on wheat and barley were ~108/g fresh weigh of foliage. Broadleaf crops, such as corn, alfalfa, sugar beet and potato supported 105-107/g. Unexpectedly, however, in the absence of a significant physical disturbance, such as harvesting, we were unable to detect the ina gene in aerosols sampled above the crops. Likewise, in fresh snow samples taken over two winters, ina genes from a range of INA bacteria were detected in about half the samples but at abundances that equated to INA bacterial numbers that accounted for only a minor proportion of INP active at -10°C. By contrast, in a hail sample from a summer thunderstorm we found 0.3 INA bacteria per INP at -10°C and ~0.5 per hail stone. Although the role of the INA bacteria as warm-temperature INP in these samples

  20. Microtubule nucleation and organization in dendrites.

    PubMed

    Delandre, Caroline; Amikura, Reiko; Moore, Adrian W

    2016-07-01

    Dendrite branching is an essential process for building complex nervous systems. It determines the number, distribution and integration of inputs into a neuron, and is regulated to create the diverse dendrite arbor branching patterns characteristic of different neuron types. The microtubule cytoskeleton is critical to provide structure and exert force during dendrite branching. It also supports the functional requirements of dendrites, reflected by differential microtubule architectural organization between neuron types, illustrated here for sensory neurons. Both anterograde and retrograde microtubule polymerization occur within growing dendrites, and recent studies indicate that branching is enhanced by anterograde microtubule polymerization events in nascent branches. The polarities of microtubule polymerization events are regulated by the position and orientation of microtubule nucleation events in the dendrite arbor. Golgi outposts are a primary microtubule nucleation center in dendrites and share common nucleation machinery with the centrosome. In addition, pre-existing dendrite microtubules may act as nucleation sites. We discuss how balancing the activities of distinct nucleation machineries within the growing dendrite can alter microtubule polymerization polarity and dendrite branching, and how regulating this balance can generate neuron type-specific morphologies. PMID:27097122

  1. Effects of surface-active organic matter on carbon dioxide nucleation in atmospheric wet aerosols: a molecular dynamics study.

    PubMed

    Daskalakis, Vangelis; Charalambous, Fevronia; Panagiotou, Fostira; Nearchou, Irene

    2014-11-21

    Organic matter (OM) uptake in cloud droplets produces water-soluble secondary organic aerosols (SOA) via aqueous chemistry. These play a significant role in aerosol properties. We report the effects of OM uptake in wet aerosols, in terms of the dissolved-to-gas carbon dioxide nucleation using molecular dynamics (MD) simulations. Carbon dioxide has been implicated in the natural rainwater as well as seawater acidity. Variability of the cloud and raindrop pH is assumed in space and time, as regional emissions, local human activities and geophysical characteristics differ. Rain scavenging of inorganic SOx, NOx and NH3 plays a major role in rain acidity in terms of acid-base activity, however carbon dioxide solubility also remains a key parameter. Based on the MD simulations we propose that the presence of surface-active OM promotes the dissolved-to-gas carbon dioxide nucleation in wet aerosols, even at low temperatures, strongly decreasing carbon dioxide solubility. A discussion is made on the role of OM in controlling the pH of a cloud or raindrop, as a consequence, without involving OM ionization equilibrium. The results are compared with experimental and computational studies in the literature. PMID:25272147

  2. Effects of surface-active organic matter on carbon dioxide nucleation in atmospheric wet aerosols: a molecular dynamics study.

    PubMed

    Daskalakis, Vangelis; Charalambous, Fevronia; Panagiotou, Fostira; Nearchou, Irene

    2014-11-21

    Organic matter (OM) uptake in cloud droplets produces water-soluble secondary organic aerosols (SOA) via aqueous chemistry. These play a significant role in aerosol properties. We report the effects of OM uptake in wet aerosols, in terms of the dissolved-to-gas carbon dioxide nucleation using molecular dynamics (MD) simulations. Carbon dioxide has been implicated in the natural rainwater as well as seawater acidity. Variability of the cloud and raindrop pH is assumed in space and time, as regional emissions, local human activities and geophysical characteristics differ. Rain scavenging of inorganic SOx, NOx and NH3 plays a major role in rain acidity in terms of acid-base activity, however carbon dioxide solubility also remains a key parameter. Based on the MD simulations we propose that the presence of surface-active OM promotes the dissolved-to-gas carbon dioxide nucleation in wet aerosols, even at low temperatures, strongly decreasing carbon dioxide solubility. A discussion is made on the role of OM in controlling the pH of a cloud or raindrop, as a consequence, without involving OM ionization equilibrium. The results are compared with experimental and computational studies in the literature.

  3. Heterogeneous nucleation of aspartame from aqueous solutions

    NASA Astrophysics Data System (ADS)

    Kubota, Noriaki; Kinno, Hiroaki; Shimizu, Kenji

    1990-03-01

    Waiting times, the time from the instant of quenching needed for a first nucleus to appear, were measured at constant supercoolings for primary nucleation of aspartame (α-L-aspartyl-L-phenylalanine methylester) from aqueous solutions, which were sealed into glass ampoules (solution volume = 3.16 cm 3). Since the waiting time became shorter by filtering the solution prior to quenching, the nucleation was concluded to be heterogeneously induced. The measured waiting time consisted of two parts: time needed for the nucleus to grow to a detactable size (growth time) and stochastic time needed for nucleation (true waiting time). The distribution of the true waiting time, is well explained by a stochastic model, in which nucleation is regarded to occur heterogeneously and in a stochastic manner by two kinds of active sites. The active sites are estimated to be located on foreign particles in which such elements as Si, Al and Mg were contained. The amount of each element is very small in the order of magnitude of ppb (mass basis) of the whole solution. The growth time was correlated with the degree of supercooling.

  4. The nature of the water nucleation sites on TiO2(110) surfacesrelvealed by ambient pressure x-ray photoelectron spectroscopy

    SciTech Connect

    Ketteler, Guido; Yamamoto, Susumu; Bluhm, Hendrik; Andersson,Klas; Starr, David E.; Ogletree, D. Frank; Ogasawara, Hirohito; Nilsson,Anders; Salmeron, Miquel

    2007-05-01

    X-ray photoelectron spectroscopy at ambient conditions of pressure (up to 1.5 Torr) and temperature (265Knucleation sites for subsequent water adsorption. The adsorption enthalpy of water binding to these sites is {approx}70 kJ/mol, much stronger than that in the bulk liquid (45 kJ/mol). A model is proposed that relates the structure of the oxide surface to its hydrophilic character.

  5. Biological contribution to ice nucleation active particles in clouds at the puy de Dôme atmospheric station, France

    NASA Astrophysics Data System (ADS)

    Amato, Pierre; Joly, Muriel; Deguillaume, Laurent; Delort, Anne-Marie

    2015-04-01

    The distribution, abundance and nature of ice nucleation active particles in the atmosphere are major sources of uncertainty in the prediction of cloud coverage, precipitation patterns and climate. Some biological ice nuclei (IN) induce freezing at temperatures at which most other atmospheric particles exhibit no detectable activity (> -10°C), but their actual contribution to the pool of IN in clouds remains poorly known. In order to help elucidating this, cloud water was collected aseptically from the summit of Puy de Dome (1465m a.s.l., France) within contrasted meteorological and physico-chemical situations. Total and biological (i.e. heat-sensitive) IN were quantified by droplet-freezing assay between -5°C and -14°C. We observed that freezing was systematically induced by biological material, between -6°C and -8°C in 92{%} of the samples. Its removal by heat treatment consistently led to a decrease of the onset freezing temperature, by 3°C or more in most samples. At -10°C, 0 to 220 biological IN mL-1 of cloud water were measured (i.e. 0 to 22 m-3 of cloud air), and these represented 65{%} to 100{%} of the total IN. Based on back-trajectories and on physico-chemical analyses, the high variability observed resulted probably from a source effect, with IN originating mostly from continental sources. Bacteria concentration in the air at altitude relevant for clouds typically ranges from ˜102 to ˜105 cells m-3. Assuming that biological IN measured in cloud water samples at -8°C were all bacteria, ice nucleation active bacteria represented at maximum 0.6{%} of the total bacteria cells present (3.1{%} at -12°C). These results should help elucidating the role of biological and bacterial IN on cloud microphysics and their impact on precipitation at local scale. References: Joly, M., Amato, P., Deguillaume, L., Monier, M., Hoose, C., and Delort A-M (2014). Quantification of ice nuclei active at near 0°C temperatures in low altitude clouds at the puy de Dome

  6. Characterization and Quantification of Intrinsic Ice Nucleators in Winter Rye (Secale cereale) Leaves.

    PubMed

    Brush, R. A.; Griffith, M.; Mlynarz, A.

    1994-02-01

    Extracellular ice formation in frost-tolerant organisms is often initiated at specific sites by ice nucleators. In this study, we examined ice nucleation activity (INA) in the frost-tolerant plant winter rye (Secale cereale). Plants were grown at 20[deg]C, at 5[deg]C with a long day, and at 5[deg]C with a short day (5[deg]C-SD). The threshold temperature for INA was -5 to -12[deg]C in winter rye leaves from all three growth treatments. Epiphytic ice nucleation-active bacteria could not account for INA observed in the leaves. Therefore, the INA must have been produced endogenously. Intrinsic rye ice nucleators were quantified and characterized using single mesophyll cell suspensions obtained by pectolytic degradation of the leaves. The most active ice nucleators in mesophyll cell suspensions exhibited a threshold ice nucleation temperature of -7[deg]C and occurred infrequently at the rate of one nucleator per 105 cells. Rye cells were treated with chemicals and enzymes to characterize the ice nucleators, which proved to be complexes of proteins, carbohydrates, and phospholipids, in which both disulfide bonds and free sulfhydryl groups were important for activity. Carbohydrates and phospholipids were important components of ice nucleators derived from 20[deg]C leaves, whereas the protein component was more important in 5[deg]C-SD leaves. This difference in composition or structure of the ice nucleators, combined with a tendency for more frequent INA, suggests that more ice nucleators are produced in 5[deg]C-SD leaves. These additional ice nucleators may be a component of the mechanism for freezing tolerance observed in winter rye. PMID:12232122

  7. A water activity based model of heterogeneous ice nucleation kinetics for freezing of water and aqueous solution droplets.

    PubMed

    Knopf, Daniel A; Alpert, Peter A

    2013-01-01

    Immersion freezing of water and aqueous solutions by particles acting as ice nuclei (IN) is a common process of heterogeneous ice nucleation which occurs in many environments, especially in the atmosphere where it results in the glaciation of clouds. Here we experimentally show, using a variety of IN types suspended in various aqueous solutions, that immersion freezing temperatures and kinetics can be described solely by temperature, T, and solution water activity, a(w), which is the ratio of the vapour pressure of the solution and the saturation water vapour pressure under the same conditions and, in equilibrium, equivalent to relative humidity (RH). This allows the freezing point and corresponding heterogeneous ice nucleation rate coefficient, J(het), to be uniquely expressed by T and a(w), a result we term the a(w) based immersion freezing model (ABIFM). This method is independent of the nature of the solute and accounts for several varying parameters, including cooling rate and IN surface area, while providing a holistic description of immersion freezing and allowing prediction of freezing temperatures, J(het), frozen fractions, ice particle production rates and numbers. Our findings are based on experimental freezing data collected for various IN surface areas, A, and cooling rates, r, of droplets variously containing marine biogenic material, two soil humic acids, four mineral dusts, and one organic monolayer acting as IN. For all investigated IN types we demonstrate that droplet freezing temperatures increase as A increases. Similarly, droplet freezing temperatures increase as the cooling rate decreases. The log10(J(het)) values for the various IN types derived exclusively by Tand a(w), provide a complete description of the heterogeneous ice nucleation kinetics. Thus, the ABIFM can be applied over the entire range of T, RH, total particulate surface area, and cloud activation timescales typical of atmospheric conditions. Lastly, we demonstrate that ABIFM can

  8. CCN activation and efficiency of nucleation and impaction removal process of biomass burning aerosols in Brazil: preliminary results.

    NASA Astrophysics Data System (ADS)

    Sánchez Gácita, Madeleine; Longo, Karla M.; Freitas, Saulo R.; Martin, Scot T.

    2015-04-01

    The biomass burning activity constitutes an important source of aerosols and trace gases to the atmosphere globally. In South America, during the dry season, aerosols prevenient from biomass burning are typically transported to long distances from its sources before being removed though contributing significantly to the aerosol budget on a continental scale. The uncertainties in the magnitude of the impacts on the hydrological cycle, the radiation budget and the biogeochemical cycles on a continental scale are still noteworthy. The still unknowns on the efficiency of biomass burning aerosol to act as cloud condensation nuclei (CCN) and the effectiveness of the nucleation and impaction scavenging mechanisms in removing them from the atmosphere contribute to such uncertainties. In the present work, the explicit modelling of the early stages of cloud development using a parcel model for the typical conditions of the dry season and dry-to-wet transition periods in Amazonia allowed an estimation of the efficiency of nucleation scavenging process and the ability of South American biomass burning aerosol to act as CCN. Additionally, the impaction scavenging was simulated for the same aerosol population following a method based on the widely used concept of the efficiency of collision between a raindrop and an aerosol particle. DMPS and H-TDMA data available in the literature for biomass burning aerosol population in the region indicated the presence of a nearly hydrophobic fraction (on average, with specific hygroscopic parameter κ=0.04, and relative abundance of 73 %) and nearly hygroscopic fraction (κ=0.13, 27 %), externally mixed. The hygroscopic parameters and relative abundances of each hygroscopic group, as well as the weighted average specific hygroscopic parameter for the entire population κ=0.06, were used in calculations of aerosol activation and population mass and number concentration scavenged by nucleation. Results from both groups of simulations are

  9. Ice nucleation activity of diesel soot particles at cirrus relevant temperature conditions: Effects of hydration, secondary organics coating, soot morphology, and coagulation

    NASA Astrophysics Data System (ADS)

    Kulkarni, Gourihar; China, Swarup; Liu, Shang; Nandasiri, Manjula; Sharma, Noopur; Wilson, Jacqueline; Aiken, Allison C.; Chand, Duli; Laskin, Alexander; Mazzoleni, Claudio; Pekour, Mikhail; Shilling, John; Shutthanandan, Vaithiyalingam; Zelenyuk, Alla; Zaveri, Rahul A.

    2016-04-01

    Ice formation by diesel soot particles was investigated at temperatures ranging from -40 to -50°C. Size-selected soot particles were physically and chemically aged in an environmental chamber, and their ice nucleating properties were determined using a continuous flow diffusion type ice nucleation chamber. Bare (freshly formed), hydrated, and compacted soot particles, as well as α-pinene secondary organic aerosol (SOA)-coated soot particles at high relative humidity conditions, showed ice formation activity at subsaturation conditions with respect to water but below the homogeneous freezing threshold conditions. However, SOA-coated soot particles at dry conditions were observed to freeze at homogeneous freezing threshold conditions. Overall, our results suggest that heterogeneous ice nucleation activity of freshly emitted diesel soot particles are sensitive to some of the aging processes that soot can undergo in the atmosphere.

  10. Preferential Nucleation during Polymorphic Transformations

    PubMed Central

    Sharma, H.; Sietsma, J.; Offerman, S. E.

    2016-01-01

    Polymorphism is the ability of a solid material to exist in more than one phase or crystal structure. Polymorphism may occur in metals, alloys, ceramics, minerals, polymers, and pharmaceutical substances. Unresolved are the conditions for preferential nucleation during polymorphic transformations in which structural relationships or special crystallographic orientation relationships (OR’s) form between the nucleus and surrounding matrix grains. We measured in-situ and simultaneously the nucleation rates of grains that have zero, one, two, three and four special OR’s with the surrounding parent grains. These experiments show a trend in which the activation energy for nucleation becomes smaller – and therefore nucleation more probable - with increasing number of special OR’s. These insights contribute to steering the processing of polymorphic materials with tailored properties, since preferential nucleation affects which crystal structure forms, the average grain size and texture of the material, and thereby - to a large extent - the final properties of the material. PMID:27484579

  11. Preferential Nucleation during Polymorphic Transformations

    NASA Astrophysics Data System (ADS)

    Sharma, H.; Sietsma, J.; Offerman, S. E.

    2016-08-01

    Polymorphism is the ability of a solid material to exist in more than one phase or crystal structure. Polymorphism may occur in metals, alloys, ceramics, minerals, polymers, and pharmaceutical substances. Unresolved are the conditions for preferential nucleation during polymorphic transformations in which structural relationships or special crystallographic orientation relationships (OR’s) form between the nucleus and surrounding matrix grains. We measured in-situ and simultaneously the nucleation rates of grains that have zero, one, two, three and four special OR’s with the surrounding parent grains. These experiments show a trend in which the activation energy for nucleation becomes smaller – and therefore nucleation more probable - with increasing number of special OR’s. These insights contribute to steering the processing of polymorphic materials with tailored properties, since preferential nucleation affects which crystal structure forms, the average grain size and texture of the material, and thereby - to a large extent - the final properties of the material.

  12. Preferential Nucleation during Polymorphic Transformations.

    PubMed

    Sharma, H; Sietsma, J; Offerman, S E

    2016-08-03

    Polymorphism is the ability of a solid material to exist in more than one phase or crystal structure. Polymorphism may occur in metals, alloys, ceramics, minerals, polymers, and pharmaceutical substances. Unresolved are the conditions for preferential nucleation during polymorphic transformations in which structural relationships or special crystallographic orientation relationships (OR's) form between the nucleus and surrounding matrix grains. We measured in-situ and simultaneously the nucleation rates of grains that have zero, one, two, three and four special OR's with the surrounding parent grains. These experiments show a trend in which the activation energy for nucleation becomes smaller - and therefore nucleation more probable - with increasing number of special OR's. These insights contribute to steering the processing of polymorphic materials with tailored properties, since preferential nucleation affects which crystal structure forms, the average grain size and texture of the material, and thereby - to a large extent - the final properties of the material.

  13. Preferential Nucleation during Polymorphic Transformations.

    PubMed

    Sharma, H; Sietsma, J; Offerman, S E

    2016-01-01

    Polymorphism is the ability of a solid material to exist in more than one phase or crystal structure. Polymorphism may occur in metals, alloys, ceramics, minerals, polymers, and pharmaceutical substances. Unresolved are the conditions for preferential nucleation during polymorphic transformations in which structural relationships or special crystallographic orientation relationships (OR's) form between the nucleus and surrounding matrix grains. We measured in-situ and simultaneously the nucleation rates of grains that have zero, one, two, three and four special OR's with the surrounding parent grains. These experiments show a trend in which the activation energy for nucleation becomes smaller - and therefore nucleation more probable - with increasing number of special OR's. These insights contribute to steering the processing of polymorphic materials with tailored properties, since preferential nucleation affects which crystal structure forms, the average grain size and texture of the material, and thereby - to a large extent - the final properties of the material. PMID:27484579

  14. Catalysis: Elusive active site in focus

    NASA Astrophysics Data System (ADS)

    Labinger, Jay A.

    2016-08-01

    The identification of the active site of an iron-containing catalyst raises hopes of designing practically useful catalysts for the room-temperature conversion of methane to methanol, a potential fuel for vehicles. See Letter p.317

  15. Metadynamics studies of crystal nucleation

    PubMed Central

    Giberti, Federico; Salvalaglio, Matteo; Parrinello, Michele

    2015-01-01

    Crystallization processes are characterized by activated events and long timescales. These characteristics prevent standard molecular dynamics techniques from being efficiently used for the direct investigation of processes such as nucleation. This short review provides an overview on the use of metadynamics, a state-of-the-art enhanced sampling technique, for the simulation of phase transitions involving the production of a crystalline solid. In particular the principles of metadynamics are outlined, several order parameters are described that have been or could be used in conjunction with metadynamics to sample nucleation events and then an overview is given of recent metadynamics results in the field of crystal nucleation. PMID:25866662

  16. Cryo-EM structure of the activated NAIP2-NLRC4 inflammasome reveals nucleated polymerization

    PubMed Central

    Zhang, Liman; Chen, Shuobing; Ruan, Jianbin; Wu, Jiayi; Tong, Alexander B.; Yin, Qian; Li, Yang; David, Liron; Lu, Alvin; Wang, Wei Li; Marks, Carolyn; Ouyang, Qi; Zhang, Xinzheng; Mao, Youdong; Wu, Hao

    2015-01-01

    The NLR family apoptosis inhibitory proteins (NAIPs) bind conserved bacterial ligands, such as the bacterial rod protein PrgJ, and recruit NLR family CARD-containing protein 4 (NLRC4) as the inflammasome adapter to activate innate immunity. We found that the PrgJ-NAIP2-NLRC4 inflammasome is assembled into multisubunit disk-like structures through a unidirectional adenosine triphosphatase polymerization, primed with a single PrgJ-activated NAIP2 per disk. Cryo–electron microscopy (cryo-EM) reconstruction at subnanometer resolution revealed a ~90° hinge rotation accompanying NLRC4 activation. Unlike in the related heptameric Apaf-1 apoptosome, in which each subunit needs to be conformationally activated by its ligand before assembly, a single PrgJ-activated NAIP2 initiates NLRC4 polymerization in a domino-like reaction to promote the disk assembly. These insights reveal the mechanism of signal amplification in NAIP-NLRC4 inflammasomes. PMID:26449474

  17. Cryo-EM structure of the activated NAIP2-NLRC4 inflammasome reveals nucleated polymerization.

    PubMed

    Zhang, Liman; Chen, Shuobing; Ruan, Jianbin; Wu, Jiayi; Tong, Alexander B; Yin, Qian; Li, Yang; David, Liron; Lu, Alvin; Wang, Wei Li; Marks, Carolyn; Ouyang, Qi; Zhang, Xinzheng; Mao, Youdong; Wu, Hao

    2015-10-23

    The NLR family apoptosis inhibitory proteins (NAIPs) bind conserved bacterial ligands, such as the bacterial rod protein PrgJ, and recruit NLR family CARD-containing protein 4 (NLRC4) as the inflammasome adapter to activate innate immunity. We found that the PrgJ-NAIP2-NLRC4 inflammasome is assembled into multisubunit disk-like structures through a unidirectional adenosine triphosphatase polymerization, primed with a single PrgJ-activated NAIP2 per disk. Cryo-electron microscopy (cryo-EM) reconstruction at subnanometer resolution revealed a ~90° hinge rotation accompanying NLRC4 activation. Unlike in the related heptameric Apaf-1 apoptosome, in which each subunit needs to be conformationally activated by its ligand before assembly, a single PrgJ-activated NAIP2 initiates NLRC4 polymerization in a domino-like reaction to promote the disk assembly. These insights reveal the mechanism of signal amplification in NAIP-NLRC4 inflammasomes. PMID:26449474

  18. A Distributed Activation Energy Model of Thermodynamically Inhibited Nucleation and Growth Reactions and its Application to the beta-delta Phase Transition of HMX

    SciTech Connect

    Burnham, A K; Weese, R K; Weeks, B L

    2004-06-18

    Detailed and global models are presented for thermodynamically inhibited nucleation-growth reactions and applied to the {beta}-{delta} Phase Transition of HMX (nitramine octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine). The detailed model contains separate kinetic parameters for the nucleation process, including an activation energy distribution resulting from a distribution of defect energies, and for movement of the resulting reaction interface within a single particle. A thermodynamic inhibition term is added to both processes so that the rates go to zero at the transition temperature. The global model adds the thermodynamic inhibition term to the extended Prout-Tompkins nucleation-growth formalism for single particles or powders. Model parameters are calibrated from differential scanning calorimetry data. The activation energy for nucleation (333 kJ/mol) is substantially higher than that for growth (29.3 kJ/mol). Use of a small activation energy distribution ({approx}400 J/mol) for the defects improves the fit to a powered sample for both the early and late stages of the transition. The effective overall activation energy for the global model (208.8 kJ/mol) is in between that of nucleation and growth. Comparison of the two models with experiment indicates the thermodynamic inhibition term is more important than the energy distribution feature for this transition. Based on the applicability of the Prout-Tompkins kinetics approach to a wide range of organic and inorganic materials, both models should have equally broad applicability for thermodynamically constrained reactions.

  19. A Distributed Activation Energy Model of Thermodynamically Inhibited Nucleation and Growth Reactions and its Application to the Phase Transition of HMX

    SciTech Connect

    Burnham, A K; Weese, R K; Weeks, B L

    2004-07-20

    Detailed and global models are presented for thermodynamically inhibited nucleation-growth reactions and applied to the {beta}-{delta} Phase Transition of HMX (nitramine octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine). The detailed model contains separate kinetic parameters for the nucleation process, including an activation energy distribution resulting from a distribution of defect energies, and for movement of the resulting reaction interface within a single particle. A thermodynamic inhibition term is added to both processes so that the rates go to zero at the transition temperature. The global model adds the thermodynamic inhibition term to the extended Prout-Tompkins nucleation-growth formalism for single particles or powders. Model parameters are calibrated from differential scanning calorimetry data. The activation energy for nucleation (333 kJ/mol) is substantially higher than that for growth (29.3 kJ/mol). Use of a small activation energy distribution ({approx}400 J/mol) for the defects improves the fit to a powered sample for both the early and late stages of the transition. The effective overall activation energy for the global model (208.8 kJ/mol) is in between that of nucleation and growth. Comparison of the two models with experiment indicates the thermodynamic inhibition term is more important than the energy distribution feature for this transition. Based on the applicability of the Prout-Tompkins kinetics approach to a wide range of organic and inorganic materials, both models should have equally broad applicability for thermodynamically constrained reactions.

  20. Low dielectric response in enzyme active site

    PubMed Central

    Mertz, Edward L.; Krishtalik, Lev I.

    2000-01-01

    The kinetics of charge transfer depend crucially on the dielectric reorganization of the medium. In enzymatic reactions that involve charge transfer, atomic dielectric response of the active site and of its surroundings determines the efficiency of the protein as a catalyst. We report direct spectroscopic measurements of the reorganization energy associated with the dielectric response in the active site of α-chymotrypsin. A chromophoric inhibitor of the enzyme is used as a spectroscopic probe. We find that water strongly affects the dielectric reorganization in the active site of the enzyme in solution. The reorganization energy of the protein matrix in the vicinity of the active site is similar to that of low-polarity solvents. Surprisingly, water exhibits an anomalously high dielectric response that cannot be described in terms of the dielectric continuum theory. As a result, sequestering the active site from the aqueous environment inside low-dielectric enzyme body dramatically reduces the dielectric reorganization. This reduction is particularly important for controlling the rate of enzymatic reactions. PMID:10681440

  1. Sensitivities of immersion freezing: Reconciling classical nucleation theory and deterministic expressions

    NASA Astrophysics Data System (ADS)

    Ervens, Barbara; Feingold, Graham

    2013-06-01

    Ice particle number concentrations are often described deterministically, i.e., ice nucleation is singular and occurs on active sites unambiguously at a given temperature. Other approaches are based on classical nucleation theory (CNT) that describes ice nucleation stochastically as a function of time and nucleation rate. Sensitivity studies of CNT for immersion freezing performed here show that ice nucleation has by far the lowest sensitivity to time as compared to temperature, ice nucleus (IN) diameter, and contact angle. Sensitivities generally decrease with decreasing temperature. Our study helps to reconcile the apparent differences in stochastic and singular freezing behavior, and suggests that over a wide range of temperatures and IN parameters, time-independent CNT-based expressions for immersion freezing may be derived for use in large-scale models.

  2. The Science of Chocolate: Interactive Activities on Phase Transitions, Emulsification, and Nucleation

    ERIC Educational Resources Information Center

    Rowat, Amy C.; Hollar, Kathryn A.; Stone, Howard A.; Rosenberg, Daniel

    2011-01-01

    Nearly everyone loves chocolate, which makes this an excellent topic for communicating scientific concepts to the general public and to students in the classroom. Here we present the outline and activities for an interactive presentation on the science of chocolate for nonspecialists and their children ages 6 and up. We design the presentation…

  3. Observations of Ice Nucleation and Propagation in Plants Using Infrared Video Thermography.

    PubMed

    Wisniewski, M.; Lindow, S. E.; Ashworth, E. N.

    1997-02-01

    We evaluated the use of infrared (IR) video thermography to observe directly ice nucleation and propagation in plants. An imaging radiometer with an HgCdTe long-wave (8-12 [mu]m) detector was utilized to image the thermal response of plants during freezing. IR images were analyzed in real time and recorded on videotape. Information on the videotape was subsequently accessed and analyzed utilizing IR image analysis software. Freezing of water droplets as small as 0.5 [mu]L was clearly detectable with the radiometer. Additionally, a comparison of temperature tracking data collected by the radiometer with data collected with thermocouples showed close correspondence. Monitoring of an array of plant species under different freezing conditions revealed that ice nucleation and propagation are readily observable by thermal imaging. In many instances, the ice nucleation-active bacterium Pseudomonas syringae placed on test plants could be seen to initiate freezing of the whole plant. Apparent ice nucleation by intrinsic nucleators, despite the presence of ice nucleation-active bacteria, was also evident in some species. Floral bud tissues of peach (Prunus persica) could be seen to supercool below the temperature of stem tissues, and ice nucleation at the site of insertion of the thermocouple was frequently observed. Rates of propagation of ice in different tissues were also easily measured by thermal imaging. This study demonstrates that IR thermography is an excellent method for studying ice nucleation and propagation in plants.

  4. Observations of Ice Nucleation and Propagation in Plants Using Infrared Video Thermography.

    PubMed

    Wisniewski, M.; Lindow, S. E.; Ashworth, E. N.

    1997-02-01

    We evaluated the use of infrared (IR) video thermography to observe directly ice nucleation and propagation in plants. An imaging radiometer with an HgCdTe long-wave (8-12 [mu]m) detector was utilized to image the thermal response of plants during freezing. IR images were analyzed in real time and recorded on videotape. Information on the videotape was subsequently accessed and analyzed utilizing IR image analysis software. Freezing of water droplets as small as 0.5 [mu]L was clearly detectable with the radiometer. Additionally, a comparison of temperature tracking data collected by the radiometer with data collected with thermocouples showed close correspondence. Monitoring of an array of plant species under different freezing conditions revealed that ice nucleation and propagation are readily observable by thermal imaging. In many instances, the ice nucleation-active bacterium Pseudomonas syringae placed on test plants could be seen to initiate freezing of the whole plant. Apparent ice nucleation by intrinsic nucleators, despite the presence of ice nucleation-active bacteria, was also evident in some species. Floral bud tissues of peach (Prunus persica) could be seen to supercool below the temperature of stem tissues, and ice nucleation at the site of insertion of the thermocouple was frequently observed. Rates of propagation of ice in different tissues were also easily measured by thermal imaging. This study demonstrates that IR thermography is an excellent method for studying ice nucleation and propagation in plants. PMID:12223611

  5. Surface fractal dimension, water adsorption efficiency, and cloud nucleation activity of insoluble aerosol

    PubMed Central

    Laaksonen, Ari; Malila, Jussi; Nenes, Athanasios; Hung, Hui-Ming; Chen, Jen-Ping

    2016-01-01

    Surface porosity affects the ability of a substance to adsorb gases. The surface fractal dimension D is a measure that indicates the amount that a surface fills a space, and can thereby be used to characterize the surface porosity. Here we propose a new method for determining D, based on measuring both the water vapour adsorption isotherm of a given substance, and its ability to act as a cloud condensation nucleus when introduced to humidified air in aerosol form. We show that our method agrees well with previous methods based on measurement of nitrogen adsorption. Besides proving the usefulness of the new method for general surface characterization of materials, our results show that the surface fractal dimension is an important determinant in cloud drop formation on water insoluble particles. We suggest that a closure can be obtained between experimental critical supersaturation for cloud drop activation and that calculated based on water adsorption data, if the latter is corrected using the surface fractal dimension of the insoluble cloud nucleus. PMID:27138171

  6. Surface fractal dimension, water adsorption efficiency, and cloud nucleation activity of insoluble aerosol

    NASA Astrophysics Data System (ADS)

    Laaksonen, Ari; Malila, Jussi; Nenes, Athanasios; Hung, Hui-Ming; Chen, Jen-Ping

    2016-05-01

    Surface porosity affects the ability of a substance to adsorb gases. The surface fractal dimension D is a measure that indicates the amount that a surface fills a space, and can thereby be used to characterize the surface porosity. Here we propose a new method for determining D, based on measuring both the water vapour adsorption isotherm of a given substance, and its ability to act as a cloud condensation nucleus when introduced to humidified air in aerosol form. We show that our method agrees well with previous methods based on measurement of nitrogen adsorption. Besides proving the usefulness of the new method for general surface characterization of materials, our results show that the surface fractal dimension is an important determinant in cloud drop formation on water insoluble particles. We suggest that a closure can be obtained between experimental critical supersaturation for cloud drop activation and that calculated based on water adsorption data, if the latter is corrected using the surface fractal dimension of the insoluble cloud nucleus.

  7. Surface fractal dimension, water adsorption efficiency, and cloud nucleation activity of insoluble aerosol.

    PubMed

    Laaksonen, Ari; Malila, Jussi; Nenes, Athanasios; Hung, Hui-Ming; Chen, Jen-Ping

    2016-01-01

    Surface porosity affects the ability of a substance to adsorb gases. The surface fractal dimension D is a measure that indicates the amount that a surface fills a space, and can thereby be used to characterize the surface porosity. Here we propose a new method for determining D, based on measuring both the water vapour adsorption isotherm of a given substance, and its ability to act as a cloud condensation nucleus when introduced to humidified air in aerosol form. We show that our method agrees well with previous methods based on measurement of nitrogen adsorption. Besides proving the usefulness of the new method for general surface characterization of materials, our results show that the surface fractal dimension is an important determinant in cloud drop formation on water insoluble particles. We suggest that a closure can be obtained between experimental critical supersaturation for cloud drop activation and that calculated based on water adsorption data, if the latter is corrected using the surface fractal dimension of the insoluble cloud nucleus. PMID:27138171

  8. Surface fractal dimension, water adsorption efficiency, and cloud nucleation activity of insoluble aerosol.

    PubMed

    Laaksonen, Ari; Malila, Jussi; Nenes, Athanasios; Hung, Hui-Ming; Chen, Jen-Ping

    2016-05-03

    Surface porosity affects the ability of a substance to adsorb gases. The surface fractal dimension D is a measure that indicates the amount that a surface fills a space, and can thereby be used to characterize the surface porosity. Here we propose a new method for determining D, based on measuring both the water vapour adsorption isotherm of a given substance, and its ability to act as a cloud condensation nucleus when introduced to humidified air in aerosol form. We show that our method agrees well with previous methods based on measurement of nitrogen adsorption. Besides proving the usefulness of the new method for general surface characterization of materials, our results show that the surface fractal dimension is an important determinant in cloud drop formation on water insoluble particles. We suggest that a closure can be obtained between experimental critical supersaturation for cloud drop activation and that calculated based on water adsorption data, if the latter is corrected using the surface fractal dimension of the insoluble cloud nucleus.

  9. Gut colonization by an ice nucleation active bacterium, Erwinia (Pantoea) ananas reduces the cold hardiness of mulberry pyralid larvae.

    PubMed

    Watanabe, K; Sato, M

    1999-06-01

    To evaluate the suitability of using ice nucleation active (INA) bacteria for the biological control of insect pests, the supercooling point (SCP) of larvae of mulberry pyralid, Glyphodes duplicalis, and silkworm, Bombyx mori, ingesting INA strains of Erwinia (Pantoea) ananas and Pseudomonas syringae was determined. Mean SCP of the guts of silkworm larvae ingesting INA strains of E. ananas ranged from -2.5 to -2.8 degrees C, being 5 degrees C higher than that in control treatments. Similarly, mean SCP of mulberry pyralid larvae ingesting INA strain of E. ananas, which can grow well in the gut, was -4.7 degrees C at 3 days after treatment, being 6.5 degrees C higher than that in control treatments. On the other hand, mean SCP of the larvae-ingesting INA strain of P. syringae, which cannot grow in the gut, was -9.0 degrees C at 3 days after treatment, rising by only 2.5 degrees C higher than that in the control treatments. In addition, more than 80% of the larvae of mulberry pyralid ingesting the INA strain of E. ananas froze and eventually died when exposed to -6 degrees C for 18 h, while only 36% of the larvae ingesting the INA strain of P. syringae, or approximately 20% of the control larvae, froze and died. Thus, the gut colonization by INA strains of E. ananas reduced remarkably the cold hardiness of the insects. These findings suggest that INA strains of E. ananas could be effective as a potential biological control agent of insect pests. PMID:10413571

  10. Polo-like kinase 1 regulates Nlp, a centrosome protein involved in microtubule nucleation.

    PubMed

    Casenghi, Martina; Meraldi, Patrick; Weinhart, Ulrike; Duncan, Peter I; Körner, Roman; Nigg, Erich A

    2003-07-01

    In animal cells, most microtubules are nucleated at centrosomes. At the onset of mitosis, centrosomes undergo a structural reorganization, termed maturation, which leads to increased microtubule nucleation activity. Centrosome maturation is regulated by several kinases, including Polo-like kinase 1 (Plk1). Here, we identify a centrosomal Plk1 substrate, termed Nlp (ninein-like protein), whose properties suggest an important role in microtubule organization. Nlp interacts with two components of the gamma-tubulin ring complex and stimulates microtubule nucleation. Plk1 phosphorylates Nlp and disrupts both its centrosome association and its gamma-tubulin interaction. Overexpression of an Nlp mutant lacking Plk1 phosphorylation sites severely disturbs mitotic spindle formation. We propose that Nlp plays an important role in microtubule organization during interphase, and that the activation of Plk1 at the onset of mitosis triggers the displacement of Nlp from the centrosome, allowing the establishment of a mitotic scaffold with enhanced microtubule nucleation activity.

  11. Active Sites Environmental Monitoring Program: Action levels

    SciTech Connect

    Ashwood, J.S.; Ashwood, T.L.

    1991-10-01

    The Active Sites Environmental Monitoring Program (ASEMP) was established at Oak Ridge National Laboratory to provide for early leak detection and to monitor performance of the active low-level waste disposal facilities in Solid Waste Storage Area (SWSA) 6 and the transuranic waste storage areas in SWSA 5 North. Early leak detection is accomplished by sampling runoff, groundwater, and perched water in burial trenches. Sample results are compared to action levels that represent background contamination by naturally occurring and fallout-derived radionuclides. 15 refs., 3 figs., 12 tabs.

  12. Mto2 multisite phosphorylation inactivates non-spindle microtubule nucleation complexes during mitosis.

    PubMed

    Borek, Weronika E; Groocock, Lynda M; Samejima, Itaru; Zou, Juan; de Lima Alves, Flavia; Rappsilber, Juri; Sawin, Kenneth E

    2015-08-05

    Microtubule nucleation is highly regulated during the eukaryotic cell cycle, but the underlying molecular mechanisms are largely unknown. During mitosis in fission yeast Schizosaccharomyces pombe, cytoplasmic microtubule nucleation ceases simultaneously with intranuclear mitotic spindle assembly. Cytoplasmic nucleation depends on the Mto1/2 complex, which binds and activates the γ-tubulin complex and also recruits the γ-tubulin complex to both centrosomal (spindle pole body) and non-centrosomal sites. Here we show that the Mto1/2 complex disassembles during mitosis, coincident with hyperphosphorylation of Mto2 protein. By mapping and mutating multiple Mto2 phosphorylation sites, we generate mto2-phosphomutant strains with enhanced Mto1/2 complex stability, interaction with the γ-tubulin complex and microtubule nucleation activity. A mutant with 24 phosphorylation sites mutated to alanine, mto2[24A], retains interphase-like behaviour even in mitotic cells. This provides a molecular-level understanding of how phosphorylation 'switches off' microtubule nucleation complexes during the cell cycle and, more broadly, illuminates mechanisms regulating non-centrosomal microtubule nucleation.

  13. Mto2 multisite phosphorylation inactivates non-spindle microtubule nucleation complexes during mitosis

    PubMed Central

    Borek, Weronika E.; Groocock, Lynda M.; Samejima, Itaru; Zou, Juan; de Lima Alves, Flavia; Rappsilber, Juri; Sawin, Kenneth E.

    2015-01-01

    Microtubule nucleation is highly regulated during the eukaryotic cell cycle, but the underlying molecular mechanisms are largely unknown. During mitosis in fission yeast Schizosaccharomyces pombe, cytoplasmic microtubule nucleation ceases simultaneously with intranuclear mitotic spindle assembly. Cytoplasmic nucleation depends on the Mto1/2 complex, which binds and activates the γ-tubulin complex and also recruits the γ-tubulin complex to both centrosomal (spindle pole body) and non-centrosomal sites. Here we show that the Mto1/2 complex disassembles during mitosis, coincident with hyperphosphorylation of Mto2 protein. By mapping and mutating multiple Mto2 phosphorylation sites, we generate mto2-phosphomutant strains with enhanced Mto1/2 complex stability, interaction with the γ-tubulin complex and microtubule nucleation activity. A mutant with 24 phosphorylation sites mutated to alanine, mto2[24A], retains interphase-like behaviour even in mitotic cells. This provides a molecular-level understanding of how phosphorylation ‘switches off' microtubule nucleation complexes during the cell cycle and, more broadly, illuminates mechanisms regulating non-centrosomal microtubule nucleation. PMID:26243668

  14. High ice nucleation activity located in blueberry stem bark is linked to primary freeze initiation and adaptive freezing behaviour of the bark.

    PubMed

    Kishimoto, Tadashi; Yamazaki, Hideyuki; Saruwatari, Atsushi; Murakawa, Hiroki; Sekozawa, Yoshihiko; Kuchitsu, Kazuyuki; Price, William S; Ishikawa, Masaya

    2014-01-01

    Controlled ice nucleation is an important mechanism in cold-hardy plant tissues for avoiding excessive supercooling of the protoplasm, for inducing extracellular freezing and/or for accommodating ice crystals in specific tissues. To understand its nature, it is necessary to characterize the ice nucleation activity (INA), defined as the ability of a tissue to induce heterogeneous ice nucleation. Few studies have addressed the precise localization of INA in wintering plant tissues in respect of its function. For this purpose, we recently revised a test tube INA assay and examined INA in various tissues of over 600 species. Extremely high levels of INA (-1 to -4 °C) in two wintering blueberry cultivars of contrasting freezing tolerance were found. Their INA was much greater than in other cold-hardy species and was found to be evenly distributed along the stems of the current year's growth. Concentrations of active ice nuclei in the stem were estimated from quantitative analyses. Stem INA was localized mainly in the bark while the xylem and pith had much lower INA. Bark INA was located mostly in the cell wall fraction (cell walls and intercellular structural components). Intracellular fractions had much less INA. Some cultivar differences were identified. The results corresponded closely with the intrinsic freezing behaviour (extracellular freezing) of the bark, icicle accumulation in the bark and initial ice nucleation in the stem under dry surface conditions. Stem INA was resistant to various antimicrobial treatments. These properties and specific localization imply that high INA in blueberry stems is of intrinsic origin and contributes to the spontaneous initiation of freezing in extracellular spaces of the bark by acting as a subfreezing temperature sensor. PMID:25082142

  15. High ice nucleation activity located in blueberry stem bark is linked to primary freeze initiation and adaptive freezing behaviour of the bark.

    PubMed

    Kishimoto, Tadashi; Yamazaki, Hideyuki; Saruwatari, Atsushi; Murakawa, Hiroki; Sekozawa, Yoshihiko; Kuchitsu, Kazuyuki; Price, William S; Ishikawa, Masaya

    2014-07-31

    Controlled ice nucleation is an important mechanism in cold-hardy plant tissues for avoiding excessive supercooling of the protoplasm, for inducing extracellular freezing and/or for accommodating ice crystals in specific tissues. To understand its nature, it is necessary to characterize the ice nucleation activity (INA), defined as the ability of a tissue to induce heterogeneous ice nucleation. Few studies have addressed the precise localization of INA in wintering plant tissues in respect of its function. For this purpose, we recently revised a test tube INA assay and examined INA in various tissues of over 600 species. Extremely high levels of INA (-1 to -4 °C) in two wintering blueberry cultivars of contrasting freezing tolerance were found. Their INA was much greater than in other cold-hardy species and was found to be evenly distributed along the stems of the current year's growth. Concentrations of active ice nuclei in the stem were estimated from quantitative analyses. Stem INA was localized mainly in the bark while the xylem and pith had much lower INA. Bark INA was located mostly in the cell wall fraction (cell walls and intercellular structural components). Intracellular fractions had much less INA. Some cultivar differences were identified. The results corresponded closely with the intrinsic freezing behaviour (extracellular freezing) of the bark, icicle accumulation in the bark and initial ice nucleation in the stem under dry surface conditions. Stem INA was resistant to various antimicrobial treatments. These properties and specific localization imply that high INA in blueberry stems is of intrinsic origin and contributes to the spontaneous initiation of freezing in extracellular spaces of the bark by acting as a subfreezing temperature sensor.

  16. High ice nucleation activity located in blueberry stem bark is linked to primary freeze initiation and adaptive freezing behaviour of the bark

    PubMed Central

    Kishimoto, Tadashi; Yamazaki, Hideyuki; Saruwatari, Atsushi; Murakawa, Hiroki; Sekozawa, Yoshihiko; Kuchitsu, Kazuyuki; Price, William S.; Ishikawa, Masaya

    2014-01-01

    Controlled ice nucleation is an important mechanism in cold-hardy plant tissues for avoiding excessive supercooling of the protoplasm, for inducing extracellular freezing and/or for accommodating ice crystals in specific tissues. To understand its nature, it is necessary to characterize the ice nucleation activity (INA), defined as the ability of a tissue to induce heterogeneous ice nucleation. Few studies have addressed the precise localization of INA in wintering plant tissues in respect of its function. For this purpose, we recently revised a test tube INA assay and examined INA in various tissues of over 600 species. Extremely high levels of INA (−1 to −4 °C) in two wintering blueberry cultivars of contrasting freezing tolerance were found. Their INA was much greater than in other cold-hardy species and was found to be evenly distributed along the stems of the current year's growth. Concentrations of active ice nuclei in the stem were estimated from quantitative analyses. Stem INA was localized mainly in the bark while the xylem and pith had much lower INA. Bark INA was located mostly in the cell wall fraction (cell walls and intercellular structural components). Intracellular fractions had much less INA. Some cultivar differences were identified. The results corresponded closely with the intrinsic freezing behaviour (extracellular freezing) of the bark, icicle accumulation in the bark and initial ice nucleation in the stem under dry surface conditions. Stem INA was resistant to various antimicrobial treatments. These properties and specific localization imply that high INA in blueberry stems is of intrinsic origin and contributes to the spontaneous initiation of freezing in extracellular spaces of the bark by acting as a subfreezing temperature sensor. PMID:25082142

  17. Characterization of active sites in zeolite catalysts

    SciTech Connect

    Eckert, J.; Bug, A.; Nicol, J.M.

    1997-11-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). Atomic-level details of the interaction of adsorbed molecules with active sites in catalysts are urgently needed to facilitate development of more effective and/or environmentally benign catalysts. To this end the authors have carried out neutron scattering studies combined with theoretical calculations of the dynamics of small molecules inside the cavities of zeolite catalysts. The authors have developed the use of H{sub 2} as a probe of adsorption sites by observing the hindered rotations of the adsorbed H{sub 2} molecule, and they were able to show that an area near the four-rings is the most likely adsorption site for H{sub 2} in zeolite A while adsorption of H{sub 2} near cations located on six-ring sites decreases in strength as Ni {approximately} Co > Ca > Zn {approximately} Na. Vibrational and rotational motions of ethylene and cyclopropane adsorption complexes were used as a measure for zeolite-adsorbate interactions. Preliminary studies of the binding of water, ammonia, and methylamines were carried out in a number of related guest-host materials.

  18. Factors Affecting Ice Nucleation in Plant Tissues

    PubMed Central

    Ashworth, Edward N.; Davis, Glen A.; Anderson, Jeffrey A.

    1985-01-01

    Factors affecting the ice nucleation temperature of plants and plant tissues were examined. The mass of a sample had a marked effect on ice nucleation temperature. Small tissue samples supercooled to −10°C and were not accurate predictors of the nucleation temperature of intact plants in either laboratory or field experiments. This effect was not unique to plant tissues and was observed in autoclaved and control soil samples. Ice nucleation temperatures of bean, corn, cotton, and soybean seedlings were influenced by the length of subzero exposure, presence of ice nucleation active bacteria, and leaf surface wetness. The number of factors influencing ice nucleation temperature suggested that predicting the freezing behavior of plants in the field will be complex. PMID:16664524

  19. Transient nucleation in glasses

    NASA Technical Reports Server (NTRS)

    Kelton, K. F.

    1991-01-01

    Nucleation rates in condensed systems are frequently not at their steady state values. Such time dependent (or transient) nucleation is most clearly observed in devitrification studies of metallic and silicate glasses. The origin of transient nucleation and its role in the formation and stability of desired phases and microstructures are discussed. Numerical models of nucleation in isothermal and nonisothermal situations, based on the coupled differential equations describing cluster evolution within the classical theory, are presented. The importance of transient nucleation in glass formation and crystallization is discussed.

  20. Active site of ribulosebisphosphate carboxylase/oxygenase

    SciTech Connect

    Hartman, F.C.; Stringer, C.D.; Milanez, S.; Lee, E.H.

    1985-01-01

    Previous affinity labeling studies and comparative sequence analyses have identified two different lysines at the active site of ribulosebisphosphate carboxylase/oxygenase and have suggested their essentiality to function. The essential lysines occupy positions 166 and 329 in the Rhodospirillum rubrum enzyme and positions 175 and 334 in the spinach enzyme. Based on the pH-dependencies of inactivations of the two enzymes by trinitrobenzene sulfonate, Lys-166 (R. rubrum enzyme) exhibits a pK/sub a/ of 7.9 and Lys-334 (spinach enzyme) exhibits a pK/sub a/ of 9.0. These low pK/sub a/ values as well as the enhanced nucleophilicities of the lysyl residues argue that both are important to catalysis rather than to substrate binding. Lys-166 may correspond to the essential base that initiates catalysis and that displays a pK/sub a/ of 7.5 in the pH-curve for V/sub max//K/sub m/. Cross-linking experiments with 4,4'-diisothiocyano-2,2'-disulfonate stilbene demonstrate that the two active-site lysines are within 12 A. 50 refs., 7 figs., 1 tab.

  1. Alteration of Heterogeneous Ice Nucleation Properties Induced by Particle Aging

    NASA Astrophysics Data System (ADS)

    Sullivan, R. C.; Polen, M.; Beydoun, H.; Lawlis, E.; Ahern, A.; Jahn, L.; Hill, T. C. J.

    2015-12-01

    Aerosol particles that can serve as ice nuclei frequently experience rapid and extensive chemical aging during atmospheric transport. This is known to significantly alter some ice nucleation modes of the few types of ice nucleation particle systems where aging effects have been simulated, such as for mineral dust. Yet much of our understanding of atmospheric particle freezing properties is derived from measurements of fresh or unaged particles. We know almost nothing regarding how atmospheric aging might alter the freezing properties of biomass burning aerosol or biological particle nucleants. We have investigated the effects of simulated aging using a chamber reactor on the heterogeneous ice nucleation properties of biomass burning aerosol (BBA) and ice-active bacteria particles. Some types of aging were found to enhance the freezing ability of BBA, exhibited as a shift in a portion of the droplet freezing curve to warmer temperatures by a few °C. Ice-active bacteria were found to consistently loose their most ice-active nucleants after repeated aging cycles. The bacterial systems always retained significantly efficient ice active sites that still allowed them to induce freezing at mild/warm temperatures, despite this decrease in freezing ability. A comprehensive series of online single-particle mass spectrometry and offline spectromicroscopic analysis of individual particles was used to determine how the aging altered the aerosol's composition, and gain mechanistic insights into how this in turn altered the freezing properties. Our new ice nucleation framework that uses a continuous distribution of ice active site ability (contact angle) was used to interpret the droplet freezing spectra and understand how aging alters the internal and external variability, and rigidity, of the ice active sites.

  2. Active Sites Environmental Monitoring Program: Program plan

    SciTech Connect

    Ashwood, T.L.; Wickliff, D.S.; Morrissey, C.M.

    1992-02-01

    The Active Sites Environmental Monitoring Program (ASEMP), initiated in 1989, provides early detection and performance monitoring of transuranic (TRU) waste and active low-level waste (LLW) facilities at Oak Ridge National Laboratory (ORNL) in accordance with US Department of Energy (DOE) Order 5820.2A. Active LLW facilities in Solid Waste Storage Area (SWSA) 6 include Tumulus I and Tumulus II, the Interim Waste Management Facility (IWMF), LLW silos, high-range wells, asbestos silos, and fissile wells. The tumulus pads and IWMF are aboveground, high-strength concrete pads on which concrete vaults containing metal boxes of LLW are placed; the void space between the boxes and vaults is filled with grout. Eventually, these pads and vaults will be covered by an engineered multilayered cap. All other LLW facilities in SWSA 6 are below ground. In addition, this plan includes monitoring of the Hillcut Disposal Test Facility (HDTF) in SWSA 6, even though this facility was completed prior to the data of the DOE order. In SWSA 5 North, the TRU facilities include below-grade engineered caves, high-range wells, and unlined trenches. All samples from SWSA 6 are screened for alpha and beta activity, counted for gamma-emitting isotopes, and analyzed for tritium. In addition to these analytes, samples from SWSA 5 North are analyzed for specific transuranic elements.

  3. Supercooling ability in two populations of the land snail Helix pomatia (Gastropoda: Helicidae) and ice-nucleating activity of gut bacteria.

    PubMed

    Nicolai, Annegret; Vernon, Philippe; Lee, Marcia; Ansart, Armelle; Charrier, Maryvonne

    2005-02-01

    The land snail Helix pomatia (Gastropoda: Helicidae) is widely distributed in Northern and Central Europe where it may experience subzero temperatures during winter months. Its supercooling ability was studied in two populations of H. pomatia. One population originated from Southern Sweden (Gotaland) and the other from Central France (Auvergne). In the experimental design, they were acclimated, over 2 weeks, to artificial winter conditions (hibernation, T=5 degrees C). The Swedish snails showed a rather limited supercooling ability (temperature of crystallization, T(c)=-6.4+/-0.8 degrees C), significantly greater, however, than the supercooling capacity of the population from France (T(c)=-4.6+/-1.4 degrees C). In artificial spring conditions (3 months of hibernation followed by a progressive acclimation, over 2 weeks, to activity at T=20 degrees C), both populations exhibited a similar high T(c) (-2.0+/-1.0 degrees C). The lower T(c) of hibernating Swedish snails could be due to a greater loss of body water, accompanied by a higher concentration of solutes in the hemolymph. In both populations, the variation in hemolymph osmolality measured between hibernating (250-270 mOsm kg(-1)) and active (165-215 mOsm kg(-1)) snails may be explained by the variation in body water mass and did not suggest the production of colligative cryoprotectants. Moreover, the three bacterial strains, Buttiauxella sp., Kluyvera sp., and Tatumella sp. (Enterobacteriaceae) which were isolated from fed snails, but absent in starved snails, did not show any ice-nucleating activity at temperatures higher than -9 degrees C. Only the strain Kluyvera sp. initiated nucleation at -9 degrees C. This strain, therefore, is a weak, also termed a Type III or Class C ice-nucleating active bacterium, but with no influence on the supercooling ability of individual snails. In summary, fluctuations in body water mass of hibernating snail populations, triggering changes in osmolyte concentration, rather than

  4. Supercooling ability in two populations of the land snail Helix pomatia (Gastropoda: Helicidae) and ice-nucleating activity of gut bacteria.

    PubMed

    Nicolai, Annegret; Vernon, Philippe; Lee, Marcia; Ansart, Armelle; Charrier, Maryvonne

    2005-02-01

    The land snail Helix pomatia (Gastropoda: Helicidae) is widely distributed in Northern and Central Europe where it may experience subzero temperatures during winter months. Its supercooling ability was studied in two populations of H. pomatia. One population originated from Southern Sweden (Gotaland) and the other from Central France (Auvergne). In the experimental design, they were acclimated, over 2 weeks, to artificial winter conditions (hibernation, T=5 degrees C). The Swedish snails showed a rather limited supercooling ability (temperature of crystallization, T(c)=-6.4+/-0.8 degrees C), significantly greater, however, than the supercooling capacity of the population from France (T(c)=-4.6+/-1.4 degrees C). In artificial spring conditions (3 months of hibernation followed by a progressive acclimation, over 2 weeks, to activity at T=20 degrees C), both populations exhibited a similar high T(c) (-2.0+/-1.0 degrees C). The lower T(c) of hibernating Swedish snails could be due to a greater loss of body water, accompanied by a higher concentration of solutes in the hemolymph. In both populations, the variation in hemolymph osmolality measured between hibernating (250-270 mOsm kg(-1)) and active (165-215 mOsm kg(-1)) snails may be explained by the variation in body water mass and did not suggest the production of colligative cryoprotectants. Moreover, the three bacterial strains, Buttiauxella sp., Kluyvera sp., and Tatumella sp. (Enterobacteriaceae) which were isolated from fed snails, but absent in starved snails, did not show any ice-nucleating activity at temperatures higher than -9 degrees C. Only the strain Kluyvera sp. initiated nucleation at -9 degrees C. This strain, therefore, is a weak, also termed a Type III or Class C ice-nucleating active bacterium, but with no influence on the supercooling ability of individual snails. In summary, fluctuations in body water mass of hibernating snail populations, triggering changes in osmolyte concentration, rather than

  5. Controlled calcite nucleation on polarized calcite single crystal substrates in the presence of polyacrylic acid

    NASA Astrophysics Data System (ADS)

    Wada, Norio; Horiuchi, Naohiro; Nakamura, Miho; Nozaki, Kosuke; Hiyama, Tetsuo; Nagai, Akiko; Yamashita, Kimihiro

    2015-04-01

    We studied theoretically and experimentally the effects of the surface electric field generated by polarization and polyacrylic acid (PAA) additives on the heterogeneous nucleation of calcite on the calcite single crystal substrates with (10.4), (10.0) and (00.1) orientations. A set of "in-situ" experiments with optical microscopy was performed to determine the waiting time of CaCO3 nucleation, defined as the time interval between the onset of the diffusion of CO2 and the appearance of the first visible precipitation. Calcite was nucleated on the oriented calcite substrates through diffusion of NH3 and CO2 gas from a solid ammonium carbonate into calcium chloride solutions. A theoretical analysis showed that the surface electric field of the polarized calcite substrate decrease the activation energy for nucleation and consequently promotes nucleation. Experimentally, the surface electric field and PAA addition were found to decrease both contact angles and waiting times, and as a result, promote the heterogeneous nucleation. Combined effect of PAA and surface electric field further reduced contact angles and waiting times regardless of orientation differences of the calcite substrates. The cooperation acts remarkably on N-surface of the respective calcite substrates. The results were explained by the Cassie's equation, a classical heterogeneous nucleation theory under a surface electric field, and matching of the charged sites on the PAA chain with the ion arrangement on the calcite substrate.

  6. Nucleation of nuclear bodies.

    PubMed

    Dundr, Miroslav

    2013-01-01

    The nucleus is a complex organelle containing numerous highly dynamic, structurally stable domains and bodies, harboring functions that have only begun to be defined. However, the molecular mechanisms for their formation are still poorly understood. Recently it has been shown that a nuclear body can form de novo by self-organization. But little is known regarding what triggers the formation of a nuclear body and how subsequent assembly steps are orchestrated. Nuclear bodies are frequently associated with specific active gene loci that directly contribute to their formation. Both coding and noncoding RNAs can initiate the assembly of nuclear bodies with which they are physiologically associated. Thus, the formation of nuclear bodies occurs via recruitment and consequent accumulation of resident proteins in the nuclear bodies by nucleating RNA acting as a seeder. In this chapter I describe how to set up an experimental cell system to probe de novo biogenesis of a nuclear body by nucleating RNA and nuclear body components tethered on chromatin. PMID:23980018

  7. Ice-nucleating bacteria from the guts of two sub-antarctic beetles, hydromedion sparsutum and perimylops antarcticus (Perimylopidae)

    PubMed

    Worland; Block

    1999-02-01

    The site of ice nucleation in the freeze-tolerant, sub-Antarctic beetle Hydromedion sparsutum has been investigated. Ice+ bacteria, active at above -2.0 degrees C, were isolated from the guts of beetles and identified as a fluorescent Pseudomonas species. Other possible sites of nucleation, including the hemolymph, were examined but had a lower activity. Ice+ bacteria were isolated from mixed populations, isolated from the guts of adult beetles, and grown on nutrient agar plates and in nutrient broth. Nucleation activity of the broth culture peaked after only 2 days although the number of live cells continued to increase until day 6. These cultures were used to determine the maximum nucleation activity of a bacterial suspension in sterile distilled water (-3.4 degrees C) and the dilution factor required to cause a 50% reduction in activity (10(4)). The original bacterial suspension had an absorbance of 0.5 measured at 660 nm and contained 6 x 10(11) bacteria per milliliter. From this it is estimated that only 1 in 10(6) bacteria possessed the highest levels of ice-nucleating activity. Other insect species, including Perimylops antarcticus, which are found in habitats similar to that of H. sparsutum, were examined for the presence of ice+ bacteria. All contained ice-nucleating bacteria in their guts but with a lower level of activity than in H. sparsutum. Copyright 1999 Academic Press. PMID:10079130

  8. Heterogeneous Nucleation and Growth of Nanoparticles at Environmental Interfaces.

    PubMed

    Jun, Young-Shin; Kim, Doyoon; Neil, Chelsea W

    2016-09-20

    Mineral nucleation is a phase transformation of aqueous components to solids with an accompanying creation of new surfaces. In this evolutional, yet elusive, process, nuclei often form at environmental interfaces, which provide remarkably reactive sites for heterogeneous nucleation and growth. Naturally occurring nucleation processes significantly contribute to the biogeochemical cycles of important components in the Earth's crust, such as iron and manganese oxide minerals and calcium carbonate. However, in recent decades, these cycles have been significantly altered by anthropogenic activities, which affect the aqueous chemistry and equilibrium of both surface and subsurface systems. These alterations can trigger the dissolution of existing minerals and formation of new nanoparticles (i.e., nucleation and growth) and consequently change the porosity and permeability of geomedia in subsurface environments. Newly formed nanoparticles can also actively interact with components in natural and engineered aquatic systems, including those posing a significant hazard such as arsenic. These interactions can bilaterally influence the fate and transport of both newly formed nanoparticles and aqueous components. Due to their importance in natural and engineered processes, heterogeneous nucleation at environmental interfaces has started to receive more attention. However, a lack of time-resolved in situ analyses makes the evaluation of heterogeneous nucleation challenging because the physicochemical properties of both the nuclei and surfaces significantly and dynamically change with time and aqueous chemistry. This Account reviews our in situ kinetic studies of the heterogeneous nucleation and growth behaviors of iron(III) (hydr)oxide, calcium carbonate, and manganese (hydr)oxide minerals in aqueous systems. In particular, we utilized simultaneous small-angle and grazing incidence small-angle X-ray scattering (SAXS/GISAXS) to investigate in situ and in real-time the effects of

  9. Nucleation in an Ultra Low Ionization Environment

    NASA Astrophysics Data System (ADS)

    Pedersen, J. O.; Enghoff, M. B.; Paling, S.; Svensmark, H.

    2010-12-01

    Atmospheric ions can enhance the nucleation of aerosols, as has been established by experiments, observation, and theory. In the clean marine atmosphere ionization is mainly caused by cosmic rays which in turn are controlled by the activity of the Sun, thus providing a potential link between solar activity and climate. In order to understand the effect ions may have on the production of cloud condensation nuclei the overall contribution of ion induced nucleation to the global production of secondary aerosols must be determined. One issue with determining this contribution is that several mechanisms for nucleation exist and it can be difficult to determine the relative importance of the various mechanisms in a given nucleation event when both ion induced and electrically neutral nucleation mechanisms are at work at the same time. We have carried out nucleation experiments in the Boulby Underground Laboratory, located 1100 meters below ground, thus reducing the flux of ionizing cosmic radiation by six orders of magnitude. Similarly we have reduced the gamma background by shielding the experiment in lead and copper. Finally we have used air stored for several weeks and passed through an active charcoal filter in order to reduce the Radon concentration. In this way we have been able to make nucleation experiments with very low ionizing background, meaning that we can rule out ion induced nucleation as a contributing mechanism. Our experimental setup is a 50 L electropolished stainless steel reactor at near atmospheric conditions. The chamber contains clean air with the addition of water vapor, ozone, and SO2. Using UV lights at 254 nm ozone is photolyzed, leading to the production of sulfuric acid and thus aerosols. An 18 MBq Caesium-137 gamma ray source with various amounts of lead in front allows us to alter the ionization in our chamber. By making series of nucleation bursts with varying amounts of ionizing radiation we then gauge the relative importance of ion

  10. Control of active sites in flocculation: Concept of equivalent active sites''

    SciTech Connect

    Behl, S.; Moudgil, B.M. . Dept. of Materials Science and Engineering)

    1993-12-01

    Flocculation and dispersion of solids are strong functions of the amount and conformation of the adsorbed polymer. Regions of dispersion and flocculation of solids with particular polymer molecules may be deduced from saturation adsorption data. The concept of equivalent active sites'' is proposed to explain flocculation and dispersion behavior irrespective of the amount or conformation of the adsorbed polymer. The concept has been further extended to study the selective flocculation process.

  11. Diamond nucleation using polyethene

    DOEpatents

    Morell, Gerardo; Makarov, Vladimir; Varshney, Deepak; Weiner, Brad

    2013-07-23

    The invention presents a simple, non-destructive and non-abrasive method of diamond nucleation using polyethene. It particularly describes the nucleation of diamond on an electrically viable substrate surface using polyethene via chemical vapor deposition (CVD) technique in a gaseous environment.

  12. Diamond Nucleation Using Polyethene

    NASA Technical Reports Server (NTRS)

    Morell, Gerardo (Inventor); Makarov, Vladimir (Inventor); Varshney, Deepak (Inventor); Weiner, Brad (Inventor)

    2013-01-01

    The invention presents a simple, non-destructive and non-abrasive method of diamond nucleation using polyethene. It particularly describes the nucleation of diamond on an electrically viable substrate surface using polyethene via chemical vapor deposition (CVD) technique in a gaseous environment.

  13. Ice Nucleation in Deep Convection

    NASA Technical Reports Server (NTRS)

    Jensen, Eric; Ackerman, Andrew; Stevens, David; Gore, Warren J. (Technical Monitor)

    2001-01-01

    The processes controlling production of ice crystals in deep, rapidly ascending convective columns are poorly understood due to the difficulties involved with either modeling or in situ sampling of these violent clouds. A large number of ice crystals are no doubt generated when droplets freeze at about -40 C. However, at higher levels, these crystals are likely depleted due to precipitation and detrainment. As the ice surface area decreases, the relative humidity can increase well above ice saturation, resulting in bursts of ice nucleation. We will present simulations of these processes using a large-eddy simulation model with detailed microphysics. Size bins are included for aerosols, liquid droplets, ice crystals, and mixed-phase (ice/liquid) hydrometers. Microphysical processes simulated include droplet activation, freezing, melting, homogeneous freezing of sulfate aerosols, and heterogeneous ice nucleation. We are focusing on the importance of ice nucleation events in the upper part of the cloud at temperatures below -40 C. We will show that the ultimate evolution of the cloud in this region (and the anvil produced by the convection) is sensitive to these ice nucleation events, and hence to the composition of upper tropospheric aerosols that get entrained into the convective column.

  14. Experimental Studies in Ice Nucleation

    NASA Astrophysics Data System (ADS)

    Wright, Timothy Peter

    data show that the time dependence for all investigated materials was weak. The drop freezing assay was then employed to test the hypothesis that certain macromolecules derived from burst pollen could be efficient ice nuclei. In a new method, air samples were collected during the height of the 2013 pollen season using a particle-in-liquid impinger and the solutions were transferred to the drop freezing assay to be analyzed for ice nuclei activity. The IN concentration in collected rainwater was analyzed and compared to IN concentrations near the ground to determine if potential IN enhancement due to pollen bursting at the surface was also found within clouds. No general trend was observed between ambient pollen counts and observed IN concentrations, suggesting that ice nuclei multiplication via pollen sac rupturing and the subsequent release of macromolecules was not prevalent for the pollen types and meteorological conditions typically encountered in the Southeastern US. Additional field tests were performed in conjunction with the Wideband Integrated Bioaerosol Sensor which used UV fluorescence to determine the possible fraction of biological aerosol present at the measurement site. This instrument was operated in parallel with the particle-in-liquid impinger allowing for a comparison of ambient immersion mode ice nuclei and fluorescent particle concentrations. Two case studies provided evidence that the active release of biological ice nuclei was causally coordinated with the arrival of a cold-frontal boundary, which can loft the nuclei to seed the frontal cloud rain band.

  15. Potential function of added minerals as nucleation sites and effect of humic substances on mineral formation by the nitrate-reducing Fe(II)-oxidizer Acidovorax sp. BoFeN1.

    PubMed

    Dippon, Urs; Pantke, Claudia; Porsch, Katharina; Larese-Casanova, Phil; Kappler, Andreas

    2012-06-19

    The mobility of toxic metals and the transformation of organic pollutants in the environment are influenced and in many cases even controlled by iron minerals. Therefore knowing the factors influencing iron mineral formation and transformation by Fe(II)-oxidizing and Fe(III)-reducing bacteria is crucial for understanding the fate of contaminants and for the development of remediation technologies. In this study we followed mineral formation by the nitrate-reducing Fe(II)-oxidizing strain Acidovorax sp. BoFeN1 in the presence of the crystalline Fe(III) (oxyhydr)oxides goethite, magnetite and hematite added as potential nucleation sites. Mössbauer spectroscopy analysis of minerals precipitated by BoFeN1 in (57)Fe(II)-spiked microbial growth medium showed that goethite was formed in the absence of mineral additions as well as in the presence of goethite or hematite. The presence of magnetite minerals during Fe(II) oxidation induced the formation of magnetite in addition to goethite, while the addition of humic substances along with magnetite also led to goethite but no magnetite. This study showed that mineral formation not only depends on the aqueous geochemical conditions but can also be affected by the presence of mineral nucleation sites that initiate precipitation of the same underlying mineral phases.

  16. Nonequilibrium thermodynamics of nucleation

    SciTech Connect

    Schweizer, M.; Sagis, L. M. C.

    2014-12-14

    We present a novel approach to nucleation processes based on the GENERIC framework (general equation for the nonequilibrium reversible-irreversible coupling). Solely based on the GENERIC structure of time-evolution equations and thermodynamic consistency arguments of exchange processes between a metastable phase and a nucleating phase, we derive the fundamental dynamics for this phenomenon, based on continuous Fokker-Planck equations. We are readily able to treat non-isothermal nucleation even when the nucleating cores cannot be attributed intensive thermodynamic properties. In addition, we capture the dynamics of the time-dependent metastable phase being continuously expelled from the nucleating phase, and keep rigorous track of the volume corrections to the dynamics. Within our framework the definition of a thermodynamic nuclei temperature is manifest. For the special case of nucleation of a gas phase towards its vapor-liquid coexistence, we illustrate that our approach is capable of reproducing recent literature results obtained by more microscopic considerations for the suppression of the nucleation rate due to nonisothermal effects.

  17. Cytoplasmic nucleation and atypical branching nucleation generate endoplasmic microtubules in Physcomitrella patens.

    PubMed

    Nakaoka, Yuki; Kimura, Akatsuki; Tani, Tomomi; Goshima, Gohta

    2015-01-01

    The mechanism underlying microtubule (MT) generation in plants has been primarily studied using the cortical MT array, in which fixed-angled branching nucleation and katanin-dependent MT severing predominate. However, little is known about MT generation in the endoplasm. Here, we explored the mechanism of endoplasmic MT generation in protonemal cells of Physcomitrella patens. We developed an assay that utilizes flow cell and oblique illumination fluorescence microscopy, which allowed visualization and quantification of individual MT dynamics. MT severing was infrequently observed, and disruption of katanin did not severely affect MT generation. Branching nucleation was observed, but it showed markedly variable branch angles and was occasionally accompanied by the transport of nucleated MTs. Cytoplasmic nucleation at seemingly random locations was most frequently observed and predominated when depolymerized MTs were regrown. The MT nucleator γ-tubulin was detected at the majority of the nucleation sites, at which a single MT was generated in random directions. When γ-tubulin was knocked down, MT generation was significantly delayed in the regrowth assay. However, nucleation occurred at a normal frequency in steady state, suggesting the presence of a γ-tubulin-independent backup mechanism. Thus, endoplasmic MTs in this cell type are generated in a less ordered manner, showing a broader spectrum of nucleation mechanisms in plants.

  18. Simulations of Ice Nucleation by Model AgI Disks and Plates.

    PubMed

    Zielke, Stephen A; Bertram, Allan K; Patey, G N

    2016-03-10

    Silver iodide is one of the most effective ice nuclei known. We use molecular dynamics simulations to investigate ice nucleation by AgI disks and plates with radii ranging from 1.15 to 2.99 nm. It is shown that disks and plates in this size range are effective ice nuclei, nucleating bulk ice at temperatures as warm as 14 K below the equilibrium freezing temperature, on simulation time scales (up to a few hundred nanoseconds). Ice nucleated on the Ag exposed surface of AgI disks and plates. Shortly after supercooling an ice cluster forms on the AgI surface. The AgI-stabilized ice cluster fluctuates in size as time progresses, but, once formed, it is constantly present. Eventually, depending on the disk or plate size and the degree of supercooling, a cluster fluctuation achieves critical size, and ice nucleates and rapidly grows to fill the simulation cell. Larger AgI disks and plates support larger ice clusters and hence can nucleate ice at warmer temperatures. This work may be useful for understanding the mechanism of ice nucleation on nanoparticles and active sites of larger atmospheric particles. PMID:26878341

  19. Dissecting the active site of a photoreceptor protein

    NASA Astrophysics Data System (ADS)

    Hoff, Wouter; Hara, Miwa; Ren, Jie; Moghadam, Farzaneh; Xie, Aihua; Kumauchi, Masato

    While enzymes are quite large molecules, functionally important chemical events are often limited to a small region of the protein: the active site. The physical and chemical properties of residues at such active sites are often strongly altered compared to the same groups dissolved in water. Understanding such effects is important for unraveling the mechanisms underlying protein function and for protein engineering, but has proven challenging. Here we report on our ongoing efforts on using photoactive yellow protein (PYP), a bacterial photoreceptor, as a model system for such effects. We will report on the following questions: How many residues affect active site properties? Are these residues in direct physical contact with the active site? Can functionally important residues be recognized in the crystal structure of a protein? What structural resolution is needed to understand active sites? What spectroscopic techniques are most informative? Which weak interactions dominate active site properties?

  20. Mars Surveyor Project Landing Site Activities

    NASA Technical Reports Server (NTRS)

    Gulick, Virginia C.; Briggs, Geoffrey; Saunders, R. Stephen; Gilmore, Martha; Soderblom, Larry

    1999-01-01

    The Mars Surveyor Program --now a cooperative program led by NASA and CNES along with other international partners -- is underway. It has the primary science objective of furthering our understanding of the biological potential and possible biological history of Mars and has the complementary objective of improving our understanding of martian climate evolution and planetary history The missions will develop technology and acquire data necessary for eventual human Exploration. Launches of orbiters, landers and rovers will take place in 2001 and in 2003; in 2005 a complete system will be launched capable of returning samples to Earth by 2008. A key aspect of the program is the selection of landing sites. This abstract 1) reports on the status of the landing site selection process that begins with the 2001 lander mission and 2) outlines be opportunities for the Mars community to provide input into the landing site selection process.

  1. Mars Surveyor Project Landing Site Activities

    NASA Technical Reports Server (NTRS)

    Gulick, V. C.; Briggs, Geoffrey; Saunders, R. Stephen; Gilmore, Martha; Soderblom, Larry

    1999-01-01

    The Mars Surveyor Program -- now a cooperative program led by NASA and CNES along with other international partners -- is underway. It has the primary science objective of furthering our understanding of the biological potential and possible biological history of Mars and has the complementary objective of improving our understanding of martian climate evolution and planetary history. The missions will develop technology and acquire data necessary for eventual human exploration. Launches of orbiters, landers and rovers will take place in 2001 and in 2003; in 2005 a complete system will be launched capable of returning samples to Earth by 2008. A key aspect of the program is the selection of landing sites. This abstract 1) reports on the status of the landing site selection process that begins with the 2001 lander mission and 2) outlines the opportunities for the Mars community to provide input into the landing site selection process.

  2. Non-extensive treatment of surface nucleation on glass particles

    NASA Astrophysics Data System (ADS)

    Nascimento, Marcio Luis Ferreira

    2012-12-01

    Experimental data of phase transformation kinetics was used to fit a new model based on a non-extensive formalism derived from Tsallis thermostatistics and another based on the Johnson-Mehl-Avrami-Yerofeyev-Kolmogorov (JMAYK) theory. For this we considered the same experimental parameters such as crystal geometric factor g, the density of nucleation sites, NS and crystal growth rates U on glass powders. The kinetics of nucleation and growth of diopside crystals (MgOṡCaOṡ2SiO2) on the glass surface at 825 °C (Tg˜727 °C) were studied. Treatments for sinter-crystallization were performed in compacts of diopside glass particles by varying the treatment time. The crystallized fraction of the samples subjected to such treatments, which develop from the particles’ surface toward their volume, was characterized by means of optical microscopy and X-ray diffraction. The two models were then fitted to the measured crystallized fraction data and compared to each other. It was found that surface nucleation occurs very rapidly from a random number of active sites. The JMAYK theory describes the case of fast heterogeneous nucleation from a constant number of sites on the glass surface. The Tsallis approach is better than the JMAYK model considering that the q factor equals 1.268±0.062 and does not require taking into account the change in crystallization mode from three dimensional to one dimensional as JMAYK predicts, and this is advantageous. Furthermore, Tsallis thermostatistics contains the Austin-Rickett model as a special and limiting case study for this system. A generalized Avrami plot is also presented.

  3. Activation of Inhibitors by Sortase Triggers Irreversible Modification of the Active Site*S

    PubMed Central

    Maresso, Anthony W.; Wu, Ruiying; Kern, Justin W.; Zhang, Rongguang; Janik, Dorota; Missiakas, Dominique M.; Duban, Mark-Eugene; Joachimiak, Andrzej; Schneewind, Olaf

    2011-01-01

    Sortases anchor surface proteins to the cell wall of Gram-positive pathogens through recognition of specific motif sequences. Loss of sortase leads to large reductions in virulence, which identifies sortase as a target for the development of antibacterials. By screening 135,625 small molecules for inhibition, we report here that aryl (β-amino)ethyl ketones inhibit sortase enzymes from staphylococci and bacilli. Inhibition of sortases occurs through an irreversible, covalent modification of their active site cysteine. Sortases specifically activate this class of molecules via β-elimination, generating a reactive olefin intermediate that covalently modifies the cysteine thiol. Analysis of the three-dimensional structure of Bacillus anthracis sortase B with and without inhibitor provides insights into the mechanism of inhibition and reveals binding pockets that can be exploited for drug discovery. PMID:17545669

  4. The bifunctional active site of s-adenosylmethionine synthetase. Roles of the active site aspartates.

    PubMed

    Taylor, J C; Markham, G D

    1999-11-12

    S-Adenosylmethionine (AdoMet) synthetase catalyzes the biosynthesis of AdoMet in a unique enzymatic reaction. Initially the sulfur of methionine displaces the intact tripolyphosphate chain (PPP(i)) from ATP, and subsequently PPP(i) is hydrolyzed to PP(i) and P(i) before product release. The crystal structure of Escherichia coli AdoMet synthetase shows that the active site contains four aspartate residues. Aspartate residues Asp-16* and Asp-271 individually provide the sole protein ligand to one of the two required Mg(2+) ions (* denotes a residue from a second subunit); aspartates Asp-118 and Asp-238* are proposed to interact with methionine. Each aspartate has been changed to an uncharged asparagine, and the metal binding residues were also changed to alanine, to assess the roles of charge and ligation ability on catalytic efficiency. The resultant enzyme variants all structurally resemble the wild type enzyme as indicated by circular dichroism spectra and are tetramers. However, all have k(cat) reductions of approximately 10(3)-fold in AdoMet synthesis, whereas the MgATP and methionine K(m) values change by less than 3- and 8-fold, respectively. In the partial reaction of PPP(i) hydrolysis, mutants of the Mg(2+) binding residues have >700-fold reduced catalytic efficiency (k(cat)/K(m)), whereas the D118N and D238*N mutants are impaired less than 35-fold. The catalytic efficiency for PPP(i) hydrolysis by Mg(2+) site mutants is improved by AdoMet, like the wild type enzyme. In contrast AdoMet reduces the catalytic efficiency for PPP(i) hydrolysis by the D118N and D238*N mutants, indicating that the events involved in AdoMet activation are hindered in these methionyl binding site mutants. Ca(2+) uniquely activates the D271A mutant enzyme to 15% of the level of Mg(2+), in contrast to the approximately 1% Ca(2+) activation of the wild type enzyme. This indicates that the Asp-271 side chain size is a discriminator between the activating ability of Ca(2+) and the

  5. Easy alignment and effective nucleation activity of ramie fibers in injection-molded poly(lactic acid) biocomposites.

    PubMed

    Xu, Huan; Liu, Chun-Yan; Chen, Chen; Hsiao, Benjamin S; Zhong, Gan-Ji; Li, Zhong-Ming

    2012-10-01

    The poly(lactic acid) (PLA)/ramie fiber biocomposites were fabricated, which exhibited considerable reinforcement effect comparable to the glass fiber at the same loading. The attempts were made to understand the flow-induced morphology of ramie fibers and PLA crystals in the injection-molded PLA/ramie fiber biocomposites, thus revealing its relationship to biocomposite mechanical properties. The polarized optical microscopy (POM) and two-dimensional wide-angle X-ray diffraction (2D-WAXD) were for the first time used to determine the distribution of nature fibers, which interestingly showed the ramie fibers aligned well along the flow direction over the whole thickness of injection-molded parts, instead of skin-core structure. This easy alignment of ramie fibers during the common processing was ascribed to the intrinsically high flexibility of ramie fibers and strong interfacial interaction between PLA chains and cellulose molecules of ramie fibers. Both 2D-WAXD and differential scanning calorimeter (DSC) measurements suggested that the PLA matrix in its ramie biocomposites had rather high orientation degree and crystallinity, which was attributed to effective heterogeneous nucleation induced by ramie fibers and local shearing field in the vicinity of fiber surface. Remarkable improvement of mechanical and thermo-mechanical properties was achieved for PLA/ramie fiber biocomposites, without sacrifice of toughness and ductility. Addition of 30wt% ramie fibers increased the tensile strength and modulus of PLA/ramie fiber biocomposites from 65.6 and 1468 MPa for pure PLA to 91.3 and 2977 MPa, respectively. These superior mechanical properties were ascribed to easy alignment of ramie fibers, high crystallinity of PLA, and favorable interfacial adhesion as revealed by scanning electron microscopy (SEM) observation and theoretical analysis based on dynamic mechanical analysis (DMA) data.

  6. A simple ice nucleation spectrometer.

    PubMed

    Wharton, David A; Mutch, Jodi S; Wilson, Peter W; Marshall, Craig J; Lim, Miang

    2004-01-01

    The construction of a simple ice nucleation spectrometer is described. It uses 10 microliter droplets loaded into glass capillary tubes which are then inserted into an aluminium holder. Each holder takes six capillary tubes surrounding a central thermocouple. Four holders are placed into a cooling block, cooled by fluid from a programmable refrigerated circulator, and the thermocouples interfaced to a computer to record temperatures. Freezing of each sample is detected by an exotherm on the temperature recording, with 24 samples recorded per run. The spectrometer was tested using deionized water, an extract from a New Zealand alpine cockroach and an extract of lawn grass. The cockroach extract is estimated to contain about 10(3) more nucleators, active at -5 degrees C, than the grass extract. PMID:15618985

  7. Atmospheric nucleation: highlights of the EUCAARI project and future directions

    NASA Astrophysics Data System (ADS)

    Kerminen, V.-M.; Petäjä, T.; Manninen, H. E.; Paasonen, P.; Nieminen, T.; Sipilä, M.; Junninen, H.; Ehn, M.; Gagné, S.; Laakso, L.; Riipinen, I.; Vehkamäki, H.; Kurten, T.; Ortega, I. K.; Dal Maso, M.; Brus, D.; Hyvärinen, A.; Lihavainen, H.; Leppä, J.; Lehtinen, K. E. J.; Mirme, A.; Mirme, S.; Hõrrak, U.; Berndt, T.; Stratmann, F.; Birmili, W.; Wiedensohler, A.; Metzger, A.; Dommen, J.; Baltensperger, U.; Kiendler-Scharr, A.; Mentel, T. F.; Wildt, J.; Winkler, P. M.; Wagner, P. E.; Petzold, A.; Minikin, A.; Plass-Dülmer, C.; Pöschl, U.; Laaksonen, A.; Kulmala, M.

    2010-07-01

    Within the project EUCAARI (European Integrated project on Aerosol Cloud Climate and Air Quality interactions), atmospheric nucleation was studied by (i) developing and testing new air ion and cluster spectrometers, (ii) conducting homogeneous nucleation experiments for sulphate and organic systems in the laboratory, (iii) investigating atmospheric nucleation mechanism under field conditions, and (iv) applying new theoretical and modelling tools for data interpretation and development of parameterisations. The current paper provides a synthesis of the obtained results and identifies the remaining major knowledge gaps related to atmospheric nucleation. The most important technical achievement of the project was the development of new instruments for measuring sub-3 nm particle populations, along with the extensive application of these instruments in both the laboratory and the field. All the results obtained during EUCAARI indicate that sulphuric acid plays a central role in atmospheric nucleation, in addition to which other vapours, especially organic ones, are needed to explain the nucleation and the subsequent growth processes. Both our field and laboratory data demonstrate that the nucleation rate scales to the first or second power of the nucleating vapour concentration(s). This agrees with the few earlier field observations, but is in stark contrast with classical thermodynamic nucleation theories. The average formation rates of 2-nm particles were found to vary by almost two orders of magnitude between the different EUCAARI sites, whereas the formation rates of charged 2-nm particles varied very little between the sites. Overall, our observations are indicative of frequent, yet moderate, ion-induced nucleation usually outweighed by much stronger neutral nucleation events in the lower troposphere. The most concrete outcome of the EUCAARI nucleation studies are the new semi-empirical nucleation rate parameterizations based on field observations, along with

  8. Atmospheric nucleation: highlights of the EUCAARI project and future directions

    NASA Astrophysics Data System (ADS)

    Kerminen, V.-M.; Petäjä, T.; Manninen, H. E.; Paasonen, P.; Nieminen, T.; Sipilä, M.; Junninen, H.; Ehn, M.; Gagné, S.; Laakso, L.; Riipinen, I.; Vehkamäki, H.; Kurten, T.; Ortega, I. K.; Dal Maso, M.; Brus, D.; Hyvärinen, A.; Lihavainen, H.; Leppä, J.; Lehtinen, K. E. J.; Mirme, A.; Mirme, S.; Hõrrak, U.; Berndt, T.; Stratmann, F.; Birmili, W.; Wiedensohler, A.; Metzger, A.; Dommen, J.; Baltensperger, U.; Kiendler-Scharr, A.; Mentel, T. F.; Wildt, J.; Winkler, P. M.; Wagner, P. E.; Petzold, A.; Minikin, A.; Plass-Dülmer, C.; Pöschl, U.; Laaksonen, A.; Kulmala, M.

    2010-11-01

    Within the project EUCAARI (European Integrated project on Aerosol Cloud Climate and Air Quality interactions), atmospheric nucleation was studied by (i) developing and testing new air ion and cluster spectrometers, (ii) conducting homogeneous nucleation experiments for sulphate and organic systems in the laboratory, (iii) investigating atmospheric nucleation mechanism under field conditions, and (iv) applying new theoretical and modelling tools for data interpretation and development of parameterisations. The current paper provides a synthesis of the obtained results and identifies the remaining major knowledge gaps related to atmospheric nucleation. The most important technical achievement of the project was the development of new instruments for measuring sub-3 nm particle populations, along with the extensive application of these instruments in both the laboratory and the field. All the results obtained during EUCAARI indicate that sulphuric acid plays a central role in atmospheric nucleation. However, also vapours other than sulphuric acid are needed to explain the nucleation and the subsequent growth processes, at least in continental boundary layers. Candidate vapours in this respect are some organic compounds, ammonia, and especially amines. Both our field and laboratory data demonstrate that the nucleation rate scales to the first or second power of the nucleating vapour concentration(s). This agrees with the few earlier field observations, but is in stark contrast with classical thermodynamic nucleation theories. The average formation rates of 2-nm particles were found to vary by almost two orders of magnitude between the different EUCAARI sites, whereas the formation rates of charged 2-nm particles varied very little between the sites. Overall, our observations are indicative of frequent, yet moderate, ion-induced nucleation usually outweighed by much stronger neutral nucleation events in the continental lower troposphere. The most concrete outcome of

  9. The active site of ribulose-bisphosphate carboxylase/oxygenase

    SciTech Connect

    Hartman, F.C.

    1991-01-01

    The active site of ribulose-bisphosphate carboxylase/oxygenase requires interacting domains of adjacent, identical subunits. Most active-site residues are located within the loop regions of an eight-stranded {beta}/{alpha}-barrel which constitutes the larger C-terminal domain; additional key residues are located within a segment of the smaller N-terminal domain which partially covers the mouth of the barrel. Site-directed mutagenesis of the gene encoding the enzyme from Rhodospirillum rubrum has been used to delineate functions of active-site residues. 6 refs., 2 figs.

  10. Ice-nucleating bacteria control the order and dynamics of interfacial water.

    PubMed

    Pandey, Ravindra; Usui, Kota; Livingstone, Ruth A; Fischer, Sean A; Pfaendtner, Jim; Backus, Ellen H G; Nagata, Yuki; Fröhlich-Nowoisky, Janine; Schmüser, Lars; Mauri, Sergio; Scheel, Jan F; Knopf, Daniel A; Pöschl, Ulrich; Bonn, Mischa; Weidner, Tobias

    2016-04-01

    Ice-nucleating organisms play important roles in the environment. With their ability to induce ice formation at temperatures just below the ice melting point, bacteria such as Pseudomonas syringae attack plants through frost damage using specialized ice-nucleating proteins. Besides the impact on agriculture and microbial ecology, airborne P. syringae can affect atmospheric glaciation processes, with consequences for cloud evolution, precipitation, and climate. Biogenic ice nucleation is also relevant for artificial snow production and for biomimetic materials for controlled interfacial freezing. We use interface-specific sum frequency generation (SFG) spectroscopy to show that hydrogen bonding at the water-bacteria contact imposes structural ordering on the adjacent water network. Experimental SFG data and molecular dynamics simulations demonstrate that ice-active sites within P. syringae feature unique hydrophilic-hydrophobic patterns to enhance ice nucleation. The freezing transition is further facilitated by the highly effective removal of latent heat from the nucleation site, as apparent from time-resolved SFG spectroscopy. PMID:27152346

  11. Ice-nucleating bacteria control the order and dynamics of interfacial water.

    PubMed

    Pandey, Ravindra; Usui, Kota; Livingstone, Ruth A; Fischer, Sean A; Pfaendtner, Jim; Backus, Ellen H G; Nagata, Yuki; Fröhlich-Nowoisky, Janine; Schmüser, Lars; Mauri, Sergio; Scheel, Jan F; Knopf, Daniel A; Pöschl, Ulrich; Bonn, Mischa; Weidner, Tobias

    2016-04-01

    Ice-nucleating organisms play important roles in the environment. With their ability to induce ice formation at temperatures just below the ice melting point, bacteria such as Pseudomonas syringae attack plants through frost damage using specialized ice-nucleating proteins. Besides the impact on agriculture and microbial ecology, airborne P. syringae can affect atmospheric glaciation processes, with consequences for cloud evolution, precipitation, and climate. Biogenic ice nucleation is also relevant for artificial snow production and for biomimetic materials for controlled interfacial freezing. We use interface-specific sum frequency generation (SFG) spectroscopy to show that hydrogen bonding at the water-bacteria contact imposes structural ordering on the adjacent water network. Experimental SFG data and molecular dynamics simulations demonstrate that ice-active sites within P. syringae feature unique hydrophilic-hydrophobic patterns to enhance ice nucleation. The freezing transition is further facilitated by the highly effective removal of latent heat from the nucleation site, as apparent from time-resolved SFG spectroscopy.

  12. Ice-nucleating bacteria control the order and dynamics of interfacial water

    PubMed Central

    Pandey, Ravindra; Usui, Kota; Livingstone, Ruth A.; Fischer, Sean A.; Pfaendtner, Jim; Backus, Ellen H. G.; Nagata, Yuki; Fröhlich-Nowoisky, Janine; Schmüser, Lars; Mauri, Sergio; Scheel, Jan F.; Knopf, Daniel A.; Pöschl, Ulrich; Bonn, Mischa; Weidner, Tobias

    2016-01-01

    Ice-nucleating organisms play important roles in the environment. With their ability to induce ice formation at temperatures just below the ice melting point, bacteria such as Pseudomonas syringae attack plants through frost damage using specialized ice-nucleating proteins. Besides the impact on agriculture and microbial ecology, airborne P. syringae can affect atmospheric glaciation processes, with consequences for cloud evolution, precipitation, and climate. Biogenic ice nucleation is also relevant for artificial snow production and for biomimetic materials for controlled interfacial freezing. We use interface-specific sum frequency generation (SFG) spectroscopy to show that hydrogen bonding at the water-bacteria contact imposes structural ordering on the adjacent water network. Experimental SFG data and molecular dynamics simulations demonstrate that ice-active sites within P. syringae feature unique hydrophilic-hydrophobic patterns to enhance ice nucleation. The freezing transition is further facilitated by the highly effective removal of latent heat from the nucleation site, as apparent from time-resolved SFG spectroscopy. PMID:27152346

  13. Savannah River Site prioritization of transition activities

    SciTech Connect

    Finley, R.H.

    1993-11-01

    Effective management of SRS conversion from primarily a production facility to other missions (or Decontamination and Decommissioning (D&D)) requires a systematic and consistent method of prioritizing the transition activities. This report discusses the design of a prioritizing method developed to achieve systematic and consistent methods of prioritizing these activities.

  14. DOE site performance assessment activities. Radioactive Waste Technical Support Program

    SciTech Connect

    Not Available

    1990-07-01

    Information on performance assessment capabilities and activities was collected from eight DOE sites. All eight sites either currently dispose of low-level radioactive waste (LLW) or plan to dispose of LLW in the near future. A survey questionnaire was developed and sent to key individuals involved in DOE Order 5820.2A performance assessment activities at each site. The sites surveyed included: Hanford Site (Hanford), Idaho National Engineering Laboratory (INEL), Los Alamos National Laboratory (LANL), Nevada Test Site (NTS), Oak Ridge National Laboratory (ORNL), Paducah Gaseous Diffusion Plant (Paducah), Portsmouth Gaseous Diffusion Plant (Portsmouth), and Savannah River Site (SRS). The questionnaire addressed all aspects of the performance assessment process; from waste source term to dose conversion factors. This report presents the information developed from the site questionnaire and provides a comparison of site-specific performance assessment approaches, data needs, and ongoing and planned activities. All sites are engaged in completing the radioactive waste disposal facility performance assessment required by DOE Order 5820.2A. Each site has achieved various degrees of progress and have identified a set of critical needs. Within several areas, however, the sites identified common needs and questions.

  15. Safety Oversight of Decommissioning Activities at DOE Nuclear Sites

    SciTech Connect

    Zull, Lawrence M.; Yeniscavich, William

    2008-01-15

    The Defense Nuclear Facilities Safety Board (Board) is an independent federal agency established by Congress in 1988 to provide nuclear safety oversight of activities at U.S. Department of Energy (DOE) defense nuclear facilities. The activities under the Board's jurisdiction include the design, construction, startup, operation, and decommissioning of defense nuclear facilities at DOE sites. This paper reviews the Board's safety oversight of decommissioning activities at DOE sites, identifies the safety problems observed, and discusses Board initiatives to improve the safety of decommissioning activities at DOE sites. The decommissioning of former defense nuclear facilities has reduced the risk of radioactive material contamination and exposure to the public and site workers. In general, efforts to perform decommissioning work at DOE defense nuclear sites have been successful, and contractors performing decommissioning work have a good safety record. Decommissioning activities have recently been completed at sites identified for closure, including the Rocky Flats Environmental Technology Site, the Fernald Closure Project, and the Miamisburg Closure Project (the Mound site). The Rocky Flats and Fernald sites, which produced plutonium parts and uranium materials for defense needs (respectively), have been turned into wildlife refuges. The Mound site, which performed R and D activities on nuclear materials, has been converted into an industrial and technology park called the Mound Advanced Technology Center. The DOE Office of Legacy Management is responsible for the long term stewardship of these former EM sites. The Board has reviewed many decommissioning activities, and noted that there are valuable lessons learned that can benefit both DOE and the contractor. As part of its ongoing safety oversight responsibilities, the Board and its staff will continue to review the safety of DOE and contractor decommissioning activities at DOE defense nuclear sites.

  16. Mutations of fumarase that distinguish between the active site and a nearby dicarboxylic acid binding site.

    PubMed Central

    Weaver, T.; Lees, M.; Banaszak, L.

    1997-01-01

    Two mutant forms of fumarase C from E. coli have been made using PCR and recombinant DNA. The recombinant form of the protein included a histidine arm on the C-terminal facilitating purification. Based on earlier studies, two different carboxylic acid binding sites, labeled A- and B-, were observed in crystal structures of the wild type and inhibited forms of the enzyme. A histidine at each of the sites was mutated to an asparagine. H188N at the A-site resulted in a large decrease in specific activity, while the H129N mutation at the B-site had essentially no effect. From the results, we conclude that the A-site is indeed the active site, and a dual role for H188 as a potential catalytic base is proposed. Crystal structures of the two mutant proteins produced some unexpected results. Both mutations reduced the affinity for the carboxylic acids at their respective sites. The H129N mutant should be particularly useful in future kinetic studies because it sterically blocks the B-site with the carboxyamide of asparagine assuming the position of the ligand's carboxylate. In the H188N mutation at the active site, the new asparagine side chain still interacts with an active site water that appears to have moved slightly as a result of the mutation. PMID:9098893

  17. Ionizable Side Chains at Catalytic Active Sites of Enzymes

    PubMed Central

    Jimenez-Morales, David; Liang, Jie

    2012-01-01

    Catalytic active sites of enzymes of known structure can be well defined by a modern program of computational geometry. The CASTp program was used to define and measure the volume of the catalytic active sites of 573 enzymes in the Catalytic Site Atlas database. The active sites are identified as catalytic because the amino acids they contain are known to participate in the chemical reaction catalyzed by the enzyme. Acid and base side chains are reliable markers of catalytic active sites. The catalytic active sites have 4 acid and 5 base side chains, in an average volume of 1072 Å3. The number density of acid side chains is 8.3 M (in chemical units); the number density of basic side chains is 10.6 M. The catalytic active site of these enzymes is an unusual electrostatic and steric environment in which side chains and reactants are crowded together in a mixture more like an ionic liquid than an ideal infinitely dilute solution. The electrostatics and crowding of reactants and side chains seems likely to be important for catalytic function. In three types of analogous ion channels, simulation of crowded charges accounts for the main properties of selectivity measured in a wide range of solutions and concentrations. It seems wise to use mathematics designed to study interacting complex fluids when making models of the catalytic active sites of enzymes. PMID:22484856

  18. Homogeneous nucleation of nitrogen

    NASA Astrophysics Data System (ADS)

    Iland, Kristina; Wedekind, Jan; Wölk, Judith; Strey, Reinhard

    2009-03-01

    We investigated the homogeneous nucleation of nitrogen in a cryogenic expansion chamber [A. Fladerer and R. Strey, J. Chem. Phys. 124, 164710 (2006)]. Gas mixtures of nitrogen and helium as carrier gas were adiabatically expanded and cooled down from an initial temperature of 83 K until nucleation occurred. This onset was detected by constant angle light scattering at nitrogen vapor pressures of 1.3-14.2 kPa and temperatures of 42-54 K. An analytical fit function well describes the experimental onset pressures with an error of ±15%. We estimate the size of the critical nucleus with the Gibbs-Thomson equation yielding critical sizes of about 50 molecules at the lowest and 70 molecules at the highest temperature. In addition, we estimate the nucleation rate and compare it with nucleation theories. The predictions of classical nucleation theory (CNT) are 9 to 19 orders of magnitude below the experimental results and show a stronger temperature dependence. The Reguera-Reiss theory [Phys. Rev. Lett. 93, 165701 (2004)] predicts the correct temperature dependence at low temperatures and decreases the absolute deviation to 7-13 orders of magnitude. We present an empirical correction function to CNT describing our experimental results. These correction parameters are remarkably close to the ones of argon [Iland et al., J. Chem. Phys. 127, 154506 (2007)] and even those of water [J. Wölk and R. Strey, J. Phys. Chem. B 105, 11683 (2001)].

  19. Effect of solute on the nucleation and propagation of ice.

    PubMed

    Charoenrein, S; Goddard, M; Reid, D S

    1991-01-01

    Using the emulsion technique, we have studied nucleation of ice in aqueous solutions containing silver iodide or Pseudomonas syringae. Using a Differential Scanning Calorimeter (DSC), we determined characteristic temperatures of nucleation, and also rates of nucleation at selected temperatures. The freezing point depression induced by added solute is linearly related to the lowering of both homogeneous and heterogeneous nucleation temperature. Nucleation kinetics depend on a fifth power function of the temperature. Solute is found to affect the parameters of this relationship in different ways, dependent upon the nature of the catalytic site for ice nucleation. We have also studied the effect of composition on the linear propagation velocity (LPV) of ice in undercooled solutions contained in a U-tube. We have determined velocities in a range of concentrations of sugar solution at the same undercooling, and also as a function of undercooling. The role of added polymer has also been investigated. It is affected by the sugar concentration. PMID:1746327

  20. Ice nucleation by water-soluble macromolecules

    NASA Astrophysics Data System (ADS)

    Pummer, B. G.; Budke, C.; Augustin-Bauditz, S.; Niedermeier, D.; Felgitsch, L.; Kampf, C. J.; Huber, R. G.; Liedl, K. R.; Loerting, T.; Moschen, T.; Schauperl, M.; Tollinger, M.; Morris, C. E.; Wex, H.; Grothe, H.; Pöschl, U.; Koop, T.; Fröhlich-Nowoisky, J.

    2015-04-01

    Cloud glaciation is critically important for the global radiation budget (albedo) and for initiation of precipitation. But the freezing of pure water droplets requires cooling to temperatures as low as 235 K. Freezing at higher temperatures requires the presence of an ice nucleator, which serves as a template for arranging water molecules in an ice-like manner. It is often assumed that these ice nucleators have to be insoluble particles. We point out that also free macromolecules which are dissolved in water can efficiently induce ice nucleation: the size of such ice nucleating macromolecules (INMs) is in the range of nanometers, corresponding to the size of the critical ice embryo. As the latter is temperature-dependent, we see a correlation between the size of INMs and the ice nucleation temperature as predicted by classical nucleation theory. Different types of INMs have been found in a wide range of biological species and comprise a variety of chemical structures including proteins, saccharides, and lipids. Our investigation of the fungal species Acremonium implicatum, Isaria farinosa, and Mortierella alpina shows that their ice nucleation activity is caused by proteinaceous water-soluble INMs. We combine these new results and literature data on INMs from fungi, bacteria, and pollen with theoretical calculations to develop a chemical interpretation of ice nucleation and water-soluble INMs. This has atmospheric implications since many of these INMs can be released by fragmentation of the carrier cell and subsequently may be distributed independently. Up to now, this process has not been accounted for in atmospheric models.

  1. Colloids and Nucleation

    NASA Technical Reports Server (NTRS)

    Ackerson, Bruce

    1997-01-01

    The objectives of the work funded under this grant were to develop a microphotographic technique and use it to monitor the nucleation and growth of crystals of hard colloidal spheres. Special attention is given to the possible need for microgravity studies in future experiments. A number of persons have been involved in this work. A masters student, Keith Davis, began the project and developed a sheet illumination apparatus and an image processing system for detection and analysis. His work on a segmentation program for image processing was sufficient for his master's research and has been published. A post doctoral student Bernie Olivier and a graduate student Yueming He, who originally suggested the sheet illumination, were funded by another source but along with Keith made photographic series of several samples (that had been made by Keith Davis). Data extraction has been done by Keith, Bernie, Yueming and two undergraduates employed on the grant. Results are published in Langmuir. These results describe the sheet lighting technique as one which illuminates not only the Bragg scattering crystal, but all the crystals. Thus, accurate crystal counts can be made for nucleation rate measurements. The strange crystal length scale reduction, observed in small angle light scattering (SALS) studies, following the initial nucleation and growth period, has been observed directly. The Bragg scattering (and dark) crystal size decreases in the crossover region. This could be an effect due to gravitational forces or due to over- compression of the crystal during growth. Direct observations indicate a complex morphology for the resulting hard sphere crystals. The crystal edges are fairly sharp but the crystals have a large degree of internal structure. This structure is a result of (unstable) growth and not aggregation. As yet unpublished work compares growth exponents data with data obtained by SALS. The nucleation rate density is determined over a broad volume fraction range

  2. Characteristics of Microcracks in the Nucleation Stage of Natural Earthquake

    NASA Astrophysics Data System (ADS)

    Fujinawa, Y.; Noda, Y.; Takahashi, K.; Kobayashi, M.; Takamatsu, K.; Natsumeda, J.

    2013-12-01

    At the last AGU Fall meeting we reported that that an electric field measurement using special antenna could detect micro-cracks appearing in the nucleation stage. Here we report several results of analysis on the phenomena. 1) Detection Distance: Some events of B-type variation have clear first and second phases (Fig.1). The S-P time is 25ms corresponding to 181m of the epicentral distance. Almost events have no apparent P phases due to the small strength. The detection distance of P phase is about 200m. But a B-1 type suggests detection distance of some 11km, much larger than the AE emission observation. Moreover, the converted seismic wave to electric mode at the conductivity contrast can be detected at several tens km (Fujinawa et al., 2011). The characteristic electric field variation induced by crack through electro-kinetic mechanism can be discussed on the systematic formulations ( Pride, 1994). There are four kinds of wave, slow P and fast P (ordinary p wave), S-wave (ordinary S wave) and electromagnetic wave. Events containing P phase have occasionally small forerunners at about the origin time (EM in Figure 1). The arrival time difference agrees with the electric wave propagation velocity suggesting that that it is the EM pahse.. 2) Correspondence to main shock: The seismological approaches (e.g., Kato et al., 2012) showed that there were two slow seismic slip events as well as microearthquake activities around the forshocks and mainshock. Those activities were whole limited in the epicentral zone, about 300 km northeast from our observation site. Our observational evidence including temporal evolution of the microcrack activity suggest that the micro-cracks of B-type at the edge of the rupture area are related to the nucleation process of the main shock , the asperity. We propose that the nucleation process is not limited at around the asperity. 3). Intermittent Criticality There appeared undulation of microcrack activity after the most active period

  3. Nucleation in an ultra low ionization environment

    NASA Astrophysics Data System (ADS)

    Olaf Pepke Pedersen, Jens; Bødker Enghoff, Martin; Paling, Sean; Svensmark, Henrik

    2010-05-01

    Atmospheric ions can enhance the nucleation of aerosols, as has been established by experiments, observation, and theory. In the clean marine atmosphere ionization is mainly caused by cosmic rays which in turn are controlled by the activity of the Sun, thus providing a potential link between solar activity and climate. In order to understand the effect ions may have on the formation of cloud condensation nuclei and thus the Earth's radiation budget the overall contribution of ion induced nucleation to the global production of secondary aerosols must be determined. One issue with determining this contribution is that several mechanisms for nucleation exist and it can be difficult to determine the relative importance of the various mechanisms in a given nucleation event when both ion induced and electrically neutral nucleation mechanisms are at work at the same time. We have carried out nucleation experiments in the Boulby Underground Laboratory, located 1100 meters below ground, thus reducing the flux of ionizing cosmic radiation by six orders of magnitude. Similarly we have reduced the gamma background by shielding the experiment in lead and copper. Finally we have used air stored for several weeks and passed through an active charcoal filter in order to reduce the Radon concentration. In this way we have been able to make nucleation experiments with very low ionizing background, meaning that we can rule out ion induced nucleation as a contributing mechanism. Our experimental setup is a 50 L electropolished stainless steel reactor at near atmospheric conditions. The chamber contains clean air with the addition of water vapour, ozone, and sulphur dioxide. Using UV lights at 254 nm ozone is photolyzed, leading to the production of sulphuric acid and thus aerosols. An 18 MBq Caesium-137 gamma ray source with various amounts of lead in front allows us to alter the ionization in our chamber. By making series of nucleation bursts with varying amounts of ionizing

  4. Structural and Biochemical Characterization of Two Binding Sites for Nucleation-promoting Factor WASp-VCA on Arp2/3 Complex

    SciTech Connect

    S Ti; C Jurgenson; B Nolen; T Pollard

    2011-12-31

    Actin-related protein (Arp) 2/3 complex mediates the formation of actin filament branches during endocytosis and at the leading edge of motile cells. The pathway of branch formation is ambiguous owing to uncertainty regarding the stoichiometry and location of VCA binding sites on Arp2/3 complex. Isothermal titration calorimetry showed that the CA motif from the C terminus of fission yeast WASP (Wsp1p) bound to fission yeast and bovine Arp2/3 complex with a stoichiometry of 2 to 1 and very different affinities for the two sites (K{sub d}s of 0.13 and 1.6 {micro}M for fission yeast Arp2/3 complex). Equilibrium binding, kinetic, and cross-linking experiments showed that (i) CA at high-affinity site 1 inhibited Arp2/3 complex binding to actin filaments, (ii) low-affinity site 2 had a higher affinity for CA when Arp2/3 complex was bound to actin filaments, and (iii) Arp2/3 complex had a much higher affinity for free CA than VCA cross-linked to an actin monomer. Crystal structures showed the C terminus of CA bound to the low-affinity site 2 on Arp3 of bovine Arp2/3 complex. The C helix is likely to bind to the barbed end groove of Arp3 in a position for VCA to deliver the first actin subunit to the daughter filament.

  5. Active site - a site of binding of affinity inhibitors in baker's yeast inorganic pyrophosphatase

    SciTech Connect

    Svyato, I.E.; Sklyankina, V.A.; Avaeva, S.M.

    1986-03-20

    The interaction of the enzyme-substrate complex with methyl phosphate, O-phosphoethanolamine, O-phosphopropanolamine, N-acetylphosphoserine, and phosphoglyolic acid, as well as pyrophosphatase, modified by monoesters of phosphoric acid, with pyrophosphate and tripolyphosphate, was investigated. It was shown that the enzyme containing the substrate in the active site does not react with monophosphates, but modified pyrophosphatase entirely retains the ability to bind polyanions to the regulatory site. It is concluded that the inactivation of baker's yeast inorganic pyrophosphatase by monoesters of phosphoric acid, which are affinity inhibitors of it, is the result of modification of the active site of the enzyme.

  6. Particle Characterization and Ice Nucleation Efficiency of Field-Collected Aerosol Particles

    NASA Astrophysics Data System (ADS)

    Wang, B.; Gilles, M. K.; Laskin, A.; Moffet, R.; Nizkorodov, S.; Roedel, T.; Sterckx, L.; Tivanski, A.; Knopf, D. A.

    2011-12-01

    Atmospheric ice formation by heterogeneous nucleation is one of the least understood processes resulting in cirrus and mixed-phase clouds which affect the global radiation budget, the hydrological cycle, and water vapor distribution. In particular, how organic aerosol affect ice nucleation is not well understood. Here we report on heterogeneous ice nucleation from particles collected during the CalNex campaign at the Caltech campus site, Pasadena, on May 19, 2010 at 6am-12pm (A2) and 12pm-6pm (A3) and May 23 at 6am-12pm (B2) and 6pm-12am (B4). The ice nucleation onsets and water uptake were determined as a function of temperature (200-273 K) and relative humidity with respect to ice (RHice). The ice nucleation efficiency was related to the particle chemical composition. Single particle characterization was provided by using computer controlled scanning electron microscopy with energy dispersive analysis of X-rays (CCSEM/EDX) and scanning transmission X-ray microscopy with near edge X-ray absorption fine structure spectroscopy (STXM/NEXAFS). The STXM/NEXAFS analysis indicates that the morning sample (A2) constitutes organic particles and organic particles with soot and inorganic inclusions. The afternoon sample (A3) is dominated by organic particles with a potentially higher degree of oxidation associated with soot. The B2 sample shows a higher number fraction of magnesium-containing particle indicative of a marine source and ~93% of the particles contained sulfur besides oxygen and carbon as derived from CCSEM/EDX analysis. The B4 sample lacks the strong marine influence and shows higher organic content. Above 230 K, we observed water uptake followed by condensation freezing at mean RH of 93-100% and 89-95% for A2 and A3, respectively. This indicates that the aged A3 particles are efficient ice nuclei (IN) for condensation freezing. Below 230 K A2 and A3 induced deposition ice nucleation between 125-155% RHice (at mean values of 134-150% RHice). The B2 and B4

  7. A review of phosphate mineral nucleation in biology and geobiology.

    PubMed

    Omelon, Sidney; Ariganello, Marianne; Bonucci, Ermanno; Grynpas, Marc; Nanci, Antonio

    2013-10-01

    Relationships between geological phosphorite deposition and biological apatite nucleation have often been overlooked. However, similarities in biological apatite and phosphorite mineralogy suggest that their chemical formation mechanisms may be similar. This review serves to draw parallels between two newly described phosphorite mineralization processes, and proposes a similar novel mechanism for biologically controlled apatite mineral nucleation. This mechanism integrates polyphosphate biochemistry with crystal nucleation theory. Recently, the roles of polyphosphates in the nucleation of marine phosphorites were discovered. Marine bacteria and diatoms have been shown to store and concentrate inorganic phosphate (Pi) as amorphous, polyphosphate granules. Subsequent release of these P reserves into the local marine environment as Pi results in biologically induced phosphorite nucleation. Pi storage and release through an intracellular polyphosphate intermediate may also occur in mineralizing oral bacteria. Polyphosphates may be associated with biologically controlled apatite nucleation within vertebrates and invertebrates. Historically, biological apatite nucleation has been attributed to either a biochemical increase in local Pi concentration or matrix-mediated apatite nucleation control. This review proposes a mechanism that integrates both theories. Intracellular and extracellular amorphous granules, rich in both calcium and phosphorus, have been observed in apatite-biomineralizing vertebrates, protists, and atremate brachiopods. These granules may represent stores of calcium-polyphosphate. Not unlike phosphorite nucleation by bacteria and diatoms, polyphosphate depolymerization to Pi would be controlled by phosphatase activity. Enzymatic polyphosphate depolymerization would increase apatite saturation to the level required for mineral nucleation, while matrix proteins would simultaneously control the progression of new biological apatite formation.

  8. Understanding cirrus ice crystal number variability for different heterogeneous ice nucleation spectra

    NASA Astrophysics Data System (ADS)

    Sullivan, Sylvia C.; Morales Betancourt, Ricardo; Barahona, Donifan; Nenes, Athanasios

    2016-03-01

    Along with minimizing parameter uncertainty, understanding the cause of temporal and spatial variability of the nucleated ice crystal number, Ni, is key to improving the representation of cirrus clouds in climate models. To this end, sensitivities of Ni to input variables like aerosol number and diameter provide valuable information about nucleation regime and efficiency for a given model formulation. Here we use the adjoint model of the adjoint of a cirrus formation parameterization (Barahona and Nenes, 2009b) to understand Ni variability for various ice-nucleating particle (INP) spectra. Inputs are generated with the Community Atmosphere Model version 5, and simulations are done with a theoretically derived spectrum, an empirical lab-based spectrum and two field-based empirical spectra that differ in the nucleation threshold for black carbon particles and in the active site density for dust. The magnitude and sign of Ni sensitivity to insoluble aerosol number can be directly linked to nucleation regime and efficiency of various INP. The lab-based spectrum calculates much higher INP efficiencies than field-based ones, which reveals a disparity in aerosol surface properties. Ni sensitivity to temperature tends to be low, due to the compensating effects of temperature on INP spectrum parameters; this low temperature sensitivity regime has been experimentally reported before but never deconstructed as done here.

  9. Understanding cirrus ice crystal number variability for different heterogeneous ice nucleation spectra

    DOE PAGES

    Sullivan, Sylvia C.; Morales Betancourt, Ricardo; Barahona, Donifan; Nenes, Athanasios

    2016-03-03

    Along with minimizing parameter uncertainty, understanding the cause of temporal and spatial variability of the nucleated ice crystal number, Ni, is key to improving the representation of cirrus clouds in climate models. To this end, sensitivities of Ni to input variables like aerosol number and diameter provide valuable information about nucleation regime and efficiency for a given model formulation. Here we use the adjoint model of the adjoint of a cirrus formation parameterization (Barahona and Nenes, 2009b) to understand Ni variability for various ice-nucleating particle (INP) spectra. Inputs are generated with the Community Atmosphere Model version 5, and simulations are donemore » with a theoretically derived spectrum, an empirical lab-based spectrum and two field-based empirical spectra that differ in the nucleation threshold for black carbon particles and in the active site density for dust. The magnitude and sign of Ni sensitivity to insoluble aerosol number can be directly linked to nucleation regime and efficiency of various INP. The lab-based spectrum calculates much higher INP efficiencies than field-based ones, which reveals a disparity in aerosol surface properties. Ni sensitivity to temperature tends to be low, due to the compensating effects of temperature on INP spectrum parameters; this low temperature sensitivity regime has been experimentally reported before but never deconstructed as done here.« less

  10. A novel approach to predict active sites of enzyme molecules.

    PubMed

    Chou, Kuo-Chen; Cai, Yu-dong

    2004-04-01

    Enzymes are critical in many cellular signaling cascades. With many enzyme structures being solved, there is an increasing need to develop an automated method for identifying their active sites. However, given the atomic coordinates of an enzyme molecule, how can we predict its active site? This is a vitally important problem because the core of an enzyme molecule is its active site from the viewpoints of both pure scientific research and industrial application. In this article, a topological entity was introduced to characterize the enzymatic active site. Based on such a concept, the covariant discriminant algorithm was formulated for identifying the active site. As a paradigm, the serine hydrolase family was demonstrated. The overall success rate by jackknife test for a data set of 88 enzyme molecules was 99.92%, and that for a data set of 50 independent enzyme molecules was 99.91%. Meanwhile, it was shown through an example that the prediction algorithm can also be used to find any typographic error of a PDB file in annotating the constituent amino acids of catalytic triad and to suggest a possible correction. The very high success rates are due to the introduction of a covariance matrix in the prediction algorithm that makes allowance for taking into account the coupling effects among the key constituent atoms of active site. It is anticipated that the novel approach is quite promising and may become a useful high throughput tool in enzymology, proteomics, and structural bioinformatics. PMID:14997541

  11. Elucidating Key Motifs Required for Arp2/3-Dependent and Independent Actin Nucleation by Las17/WASP

    PubMed Central

    Urbanek, Agnieszka N.; Smaczynska-de Rooij, Iwona I.

    2016-01-01

    Actin nucleation is the key rate limiting step in the process of actin polymerization, and tight regulation of this process is critical to ensure actin filaments form only at specific times and at defined regions of the cell. Arp2/3 is a well-characterised protein complex that can promote nucleation of new filaments, though its activity requires additional nucleation promotion factors (NPFs). The best recognized of these factors are the WASP family of proteins that contain binding motifs for both monomeric actin and for Arp2/3. Previously we demonstrated that the yeast WASP homologue, Las17, in addition to activating Arp2/3 can also nucleate actin filaments de novo, independently of Arp2/3. This activity is dependent on its polyproline rich region. Through biochemical and in vivo analysis we have now identified key motifs within the polyproline region that are required for nucleation and elongation of actin filaments, and have addressed the role of the WH2 domain in the context of actin nucleation without Arp2/3. We have also demonstrated that full length Las17 is able to bind liposomes giving rise to the possibility of direct linkage of nascent actin filaments to specific membrane sites to which Las17 has been recruited. Overall, we propose that Las17 functions as the key initiator of de novo actin filament formation at endocytic sites by nucleating, elongating and tethering nascent filaments which then serve as a platform for Arp2/3 recruitment and function. PMID:27637067

  12. Elucidating Key Motifs Required for Arp2/3-Dependent and Independent Actin Nucleation by Las17/WASP.

    PubMed

    Allwood, Ellen G; Tyler, Joe J; Urbanek, Agnieszka N; Smaczynska-de Rooij, Iwona I; Ayscough, Kathryn R

    2016-01-01

    Actin nucleation is the key rate limiting step in the process of actin polymerization, and tight regulation of this process is critical to ensure actin filaments form only at specific times and at defined regions of the cell. Arp2/3 is a well-characterised protein complex that can promote nucleation of new filaments, though its activity requires additional nucleation promotion factors (NPFs). The best recognized of these factors are the WASP family of proteins that contain binding motifs for both monomeric actin and for Arp2/3. Previously we demonstrated that the yeast WASP homologue, Las17, in addition to activating Arp2/3 can also nucleate actin filaments de novo, independently of Arp2/3. This activity is dependent on its polyproline rich region. Through biochemical and in vivo analysis we have now identified key motifs within the polyproline region that are required for nucleation and elongation of actin filaments, and have addressed the role of the WH2 domain in the context of actin nucleation without Arp2/3. We have also demonstrated that full length Las17 is able to bind liposomes giving rise to the possibility of direct linkage of nascent actin filaments to specific membrane sites to which Las17 has been recruited. Overall, we propose that Las17 functions as the key initiator of de novo actin filament formation at endocytic sites by nucleating, elongating and tethering nascent filaments which then serve as a platform for Arp2/3 recruitment and function. PMID:27637067

  13. Nucleation of Ice

    NASA Astrophysics Data System (ADS)

    Molinero, Valeria

    2009-03-01

    The freezing of water into ice is a ubiquitous transformation in nature, yet the microscopic mechanism of homogeneous nucleation of ice has not yet been elucidated. One of the reasons is that nucleation happens in time scales that are too fast for an experimental characterization and two slow for a systematic study with atomistic simulations. In this work we use coarse-grained molecular dynamics simulations with the monatomic model of water mW[1] to shed light into the mechanism of homogeneous nucleation of ice and its relationship to the thermodynamics of supercooled water. Cooling of bulk water produces either crystalline ice or low- density amorphous ice (LDA) depending on the quenching rate. We find that ice crystallization occurs faster at temperatures close to the liquid-liquid transition, defined as the point of maximum inflection of the density with respect to the temperature. At the liquid-liquid transition, the time scale of nucleation becomes comparable to the time scale of relaxation within the liquid phase, determining --effectively- the end of the metastable liquid state. Our results imply that no ultraviscous liquid water can exist at temperatures just above the much disputed glass transition of water. We discuss how the scenario is changed when water is in confinement, and the relationship of the mechanism of ice nucleation to that of other liquids that present the same phase behavior, silicon [2] and germanium [3]. [4pt] [1] Molinero, V. & Moore, E. B. Water modeled as an intermediate element between carbon and silicon. Journal of Physical Chemistry B (2008). Online at http://pubs.acs.org/cgi- bin/abstract.cgi/jpcbfk/asap/abs/jp805227c.html [0pt] [2] Molinero, V., Sastry, S. & Angell, C. A. Tuning of tetrahedrality in a silicon potential yields a series of monatomic (metal-like) glass formers of very high fragility. Physical Review Letters 97, 075701 (2006).

  14. Growth exponents in surface models with non-active sites

    NASA Astrophysics Data System (ADS)

    Santos, M.; Figueiredo, W.; Aarão Reis, F. D. A.

    2006-11-01

    In this work, we studied the role played by the inactive sites present on the substrate of a growing surface. In our model, one particle sticks at the surface if the site where it falls is an active site. However, we allow the deposited particle to diffuse along the surface in accordance with some mechanism previously defined. Using Monte Carlo simulations, and some analytical results, we have investigated the model in (1+1) and (2+1) dimensions considering different relaxation mechanisms. We show that the consideration of non-active sites is a crucial point in the model. In fact, we have seen that the saturation regime is not observed for any value of the density of inactive sites. Besides, the growth exponent β turns to be one, at long times, whatever the mechanism of diffusion we consider in one and two dimensions.

  15. A small ribozyme with dual-site kinase activity

    PubMed Central

    Biondi, Elisa; Maxwell, Adam W.R.; Burke, Donald H.

    2012-01-01

    Phosphoryl transfer onto backbone hydroxyls is a recognized catalytic activity of nucleic acids. We find that kinase ribozyme K28 possesses an unusually complex active site that promotes (thio)phosphorylation of two residues widely separated in primary sequence. After allowing the ribozyme to radiolabel itself by phosphoryl transfer from [γ-32P]GTP, DNAzyme-mediated cleavage yielded two radiolabeled cleavage fragments, indicating phosphorylation sites within each of the two cleavage fragments. These sites were mapped by alkaline digestion and primer extension pausing. Enzymatic digestion and mutational analysis identified nucleotides important for activity and established the active structure as being a constrained pseudoknot with unusual connectivity that may juxtapose the two reactive sites. Nuclease sensitivities for nucleotides near the pseudoknot core were altered in the presence of GTPγS, indicating donor-induced folding. The 5′ target site was more strongly favored in full-length ribozyme K28 (128 nt) than in truncated RNAs (58 nt). Electrophoretic mobilities of self-thiophosphorylated products on organomercurial gels are distinct from the 5′ mono-thiophosphorylated product produced by reaction with polynucleotide kinase, potentially indicating simultaneous labeling of both sites within individual RNA strands. Our evidence supports a single, compact structure with local dynamics, rather than global rearrangement, as being responsible for dual-site phosphorylation. PMID:22618879

  16. GRB2 Nucleates T Cell Receptor-Mediated LAT Clusters That Control PLC-γ1 Activation and Cytokine Production.

    PubMed

    Bilal, Mahmood Yousif; Houtman, Jon C D

    2015-01-01

    GRB2 is a ubiquitously expressed adaptor protein required for signaling downstream of multiple receptors. To address the role of GRB2 in receptor-mediated signaling, the expression of GRB2 was suppressed in human CD4+ T cells and its role downstream of the T cell receptor (TCR) was examined. Interestingly, GRB2 deficient T cells had enhanced signaling from complexes containing the TCR. However, GRB2 deficient T cells had substantially reduced production of IL-2 and IFN-γ. This defect was attributed to diminished formation of linker for activation of T cells (LAT) signaling clusters, which resulted in reduced MAP kinase activation, calcium flux, and PLC-γ1 recruitment to LAT signaling clusters. Add back of wild-type GRB2, but not a novel N-terminal SH3 domain mutant, rescued LAT microcluster formation, calcium mobilization, and cytokine release, providing the first direct evidence that GRB2, and its ability to bind to SH3 domain ligands, is required for establishing LAT microclusters. Our data demonstrate that the ability of GRB2 to facilitate protein clusters is equally important in regulating TCR-mediated functions as its capacity to recruit effector proteins. This highlights that GRB2 regulates signaling downstream of adaptors and receptors by both recruiting effector proteins and regulating the formation of signaling complexes.

  17. Kinetics of Ice Nucleation Confined in Nanoporous Alumina.

    PubMed

    Suzuki, Yasuhito; Steinhart, Martin; Butt, Hans-Jürgen; Floudas, George

    2015-09-01

    The nucleation mechanism of water (heterogeneous/homogeneous) can be regulated by confinement within nanoporous alumina. The kinetics of ice nucleation is studied in confinement by employing dielectric permittivity as a probe. Both heterogeneous and homogeneous nucleation, obtained at low and high undercooling, respectively, are stochastic in nature. The temperature interval of metastability extends over ∼4 and 0.4 °C for heterogeneous and homogeneous nucleation, respectively. Nucleation within a pore is spread to all pores in the template. We have examined a possible coupling of all pores through a heat wave and a sound wave, with the latter being a more realistic scenario. In addition, dielectric spectroscopy indicates that prior to crystallization undercooled water molecules relax with an activation energy of ∼50 kJ/mol, and this process acts as precursor to ice nucleation. PMID:26241561

  18. Ice nucleation in nature: supercooling point (SCP) measurements and the role of heterogeneous nucleation.

    PubMed

    Wilson, P W; Heneghan, A F; Haymet, A D J

    2003-02-01

    In biological systems, nucleation of ice from a supercooled aqueous solution is a stochastic process and always heterogeneous. The average time any solution may remain supercooled is determined only by the degree of supercooling and heterogeneous nucleation sites it encounters. Here we summarize the many and varied definitions of the so-called "supercooling point," also called the "temperature of crystallization" and the "nucleation temperature," and exhibit the natural, inherent width associated with this quantity. We describe a new method for accurate determination of the supercooling point, which takes into account the inherent statistical fluctuations of the value. We show further that many measurements on a single unchanging sample are required to make a statistically valid measure of the supercooling point. This raises an interesting difference in circumstances where such repeat measurements are inconvenient, or impossible, for example for live organism experiments. We also discuss the effect of solutes on this temperature of nucleation. Existing data appear to show that various solute species decrease the nucleation temperature somewhat more than the equivalent melting point depression. For non-ionic solutes the species appears not to be a significant factor whereas for ions the species does affect the level of decrease of the nucleation temperature.

  19. Scavenging of ice-nucleating microorganisms from the atmosphere by artificial rain events

    NASA Astrophysics Data System (ADS)

    Hanlon, Regina; Powers, Craig; Failor, Kevin; Vinatzer, Boris; Schmale, David

    2015-04-01

    Little is known about how microorganisms are scavenged from the atmosphere during rainfall. Microorganisms are abundant and diverse in rain (precipitation) collected near the surface of the earth. Some of these rain-associated microorganisms produce proteins that catalyze the nucleation of ice crystals at significantly warmer temperatures than would normally be required for ice formation, suggesting that they may play important roles in weather, including the onset of precipitation. We conducted a series of field experiments to test the hypothesis that ice-nucleating microorganisms are scavenged from the atmosphere by rainfall. Thirteen artificial rain events were conducted off the side of the Smart Road Bridge in Blacksburg, VA, USA. In each event, sterile water was dispensed over the side of the bridge (simulated rainfall), and recovered in sterile containers following gravitational settling from the side of the bridge to an open fallow agricultural field below (a distance of ~55m from the release site to the collection site). Microbes scavenged from the artificial rain events were cultured on six different types of agar media (R2A, TSA, CA; +/- cycloheximide) and the ice nucleation activity was examined for colonies cultured from the different media types. Mean CFUs scavenged by artificial rain ranged from 83 to 196 CFUs/mL across all six media types. Ice-nucleating microorganisms were recovered from 85% (11/13) of the simulated rain events, and represented about 1% of the total number of colonies assayed from each event. Strikingly, this percentage is nearly identical to the percentage of culturable ice-nucleating microorganisms occurring in about half of the natural rain events studied to date in Blacksburg, Virginia. This work expands our knowledge of the scavenging properties of rain, and suggests that at least some ice nucleators in natural precipitation events may have been stripped from the atmosphere during rainfall, thus negating their potential role in

  20. A parameterization of cloud droplet nucleation

    SciTech Connect

    Ghan, S.J.; Chuang, C.C.; Penner, J.E.

    1994-01-01

    Droplet nucleation is a fundamental cloud process. The number of aerosols activated to form cloud droplets influences not only the number of aerosols scavenged by clouds but also the size of the cloud droplets. Cloud droplet size influences the cloud albedo and the conversion of cloud water to precipitation. Global aerosol models are presently being developed with the intention of coupling with global atmospheric circulation models to evaluate the influence of aerosols and aerosol-cloud interactions on climate. If these and other coupled models are to address issues of aerosol-interactions, the droplet nucleation process must be adequately represented. Ghan et al. have introduced a droplet nucleation parameterization for a single aerosol type that offers certain advantages over the popular Twomey parameterization. Here we describe the generalization of that parameterization to the case of multiple aerosol types, with estimation of aerosol mass as well as number activated.

  1. Architecture and active site of particulate methane monooxygenase

    PubMed Central

    Culpepper, Megen A.; Rosenzweig, Amy C.

    2012-01-01

    Particulate methane monooxygenase (pMMO) is an integral membrane metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria, organisms that live on methane gas as their sole carbon source. Understanding pMMO function has important implications for bioremediation applications and for the development of new, environmentally friendly catalysts for the direct conversion of methane to methanol. Crystal structures of pMMOs from three different methanotrophs reveal a trimeric architecture, consisting of three copies each of the pmoB, pmoA, and pmoC subunits. There are three distinct metal centers in each protomer of the trimer, mononuclear and dinuclear copper sites in the periplasmic regions of pmoB and a mononuclear site within the membrane that can be occupied by copper or zinc. Various models for the pMMO active site have been proposed within these structural constraints, including dicopper, tricopper, and diiron centers. Biochemical and spectroscopic data on pMMO and recombinant soluble fragments, denoted spmoB proteins, indicate that the active site involves copper and is located at the site of the dicopper center in the pmoB subunit. Initial spectroscopic evidence for O2 binding at this site has been obtained. Despite these findings, questions remain about the active site identity and nuclearity and will be the focus of future studies. PMID:22725967

  2. Methanopyrus kandleri topoisomerase V contains three distinct AP lyase active sites in addition to the topoisomerase active site.

    PubMed

    Rajan, Rakhi; Osterman, Amy; Mondragón, Alfonso

    2016-04-20

    Topoisomerase V (Topo-V) is the only topoisomerase with both topoisomerase and DNA repair activities. The topoisomerase activity is conferred by a small alpha-helical domain, whereas the AP lyase activity is found in a region formed by 12 tandem helix-hairpin-helix ((HhH)2) domains. Although it was known that Topo-V has multiple repair sites, only one had been mapped. Here, we show that Topo-V has three AP lyase sites. The atomic structure and Small Angle X-ray Scattering studies of a 97 kDa fragment spanning the topoisomerase and 10 (HhH)2 domains reveal that the (HhH)2 domains extend away from the topoisomerase domain. A combination of biochemical and structural observations allow the mapping of the second repair site to the junction of the 9th and 10th (HhH)2 domains. The second site is structurally similar to the first one and to the sites found in other AP lyases. The 3rd AP lyase site is located in the 12th (HhH)2 domain. The results show that Topo-V is an unusual protein: it is the only known protein with more than one (HhH)2 domain, the only known topoisomerase with dual activities and is also unique by having three AP lyase repair sites in the same polypeptide. PMID:26908655

  3. Methanopyrus kandleri topoisomerase V contains three distinct AP lyase active sites in addition to the topoisomerase active site

    PubMed Central

    Rajan, Rakhi; Osterman, Amy; Mondragón, Alfonso

    2016-01-01

    Topoisomerase V (Topo-V) is the only topoisomerase with both topoisomerase and DNA repair activities. The topoisomerase activity is conferred by a small alpha-helical domain, whereas the AP lyase activity is found in a region formed by 12 tandem helix-hairpin-helix ((HhH)2) domains. Although it was known that Topo-V has multiple repair sites, only one had been mapped. Here, we show that Topo-V has three AP lyase sites. The atomic structure and Small Angle X-ray Scattering studies of a 97 kDa fragment spanning the topoisomerase and 10 (HhH)2 domains reveal that the (HhH)2 domains extend away from the topoisomerase domain. A combination of biochemical and structural observations allow the mapping of the second repair site to the junction of the 9th and 10th (HhH)2 domains. The second site is structurally similar to the first one and to the sites found in other AP lyases. The 3rd AP lyase site is located in the 12th (HhH)2 domain. The results show that Topo-V is an unusual protein: it is the only known protein with more than one (HhH)2 domain, the only known topoisomerase with dual activities and is also unique by having three AP lyase repair sites in the same polypeptide. PMID:26908655

  4. Role of the conducting layer substrate on TiO2 nucleation when using microwave activated chemical bath deposition

    NASA Astrophysics Data System (ADS)

    Zumeta, I.; Espinosa, R.; Ayllón, J. A.; Vigil, E.

    2002-12-01

    Nanostructured TiO2 is used in novel dye sensitized solar cells. Because of their interaction with light, thin TiO2 films are also used as coatings for self-cleaning glasses and tiles. Microwave activated chemical bath deposition represents a simple and cost-effective way to obtain nanostructured TiO2 films. It is important to study, in this technique, the role of the conducting layer used as the substrate. The influence of microwave-substrate interactions on TiO2 deposition is analysed using different substrate positions, employing substrates with different conductivities, and also using different microwave radiation powers for film deposition. We prove that a common domestic microwave oven with a large cavity and inhomogeneous radiation field can be used with equally satisfactory results. The transmittance spectra of the obtained films were studied and used to analyse film thickness and to obtain gap energy values. The results, regarding different indium-tin oxide resistivities and different substrate positions in the oven cavity, show that the interaction of the microwave field with the conducting layer is determinant in layer deposition. It has also been found that film thickness increases with the power of the applied radiation while the gap energies of the TiO2 films decrease approaching the 3.2 eV value reported for bulk anatase. This indicates that these films are not crystalline and it agrees with x-ray spectra that do not reveal any peak.

  5. Ice nucleation by soil dust compared to desert dust aerosols

    NASA Astrophysics Data System (ADS)

    Moehler, O.; Steinke, I.; Ullrich, R.; Höhler, K.; Schiebel, T.; Hoose, C.; Funk, R.

    2015-12-01

    A minor fraction of atmospheric aerosol particles, so-called ice-nucleating particles (INPs), initiates the formation of the ice phase in tropospheric clouds and thereby markedly influences the Earth's weather and climate systems. Whether an aerosol particle acts as an INP depends on its size, morphology and chemical compositions. The INP fraction of certain aerosol types also strongly depends on the temperature and the relative humidity. Because both desert dust and soil dust aerosols typically comprise a variety of different particles, it is difficult to assess and predict their contribution to the atmospheric INP abundance. This requires both accurate modelling of the sources and atmospheric distribution of atmospheric dust components and detailed investigations of their ice nucleation activities. The latter can be achieved in laboratory experiments and parameterized for use in weather and climate models as a function of temperature and particle surface area, a parameter called ice-nucleation active site (INAS) density. Concerning ice nucleation activity studies, the soil dust is of particular interest because it contains a significant fraction of organics and biological components, both with the potential for contributing to the atmospheric INP abundance at relatively high temperatures compared to mineral components. First laboratory ice nucleation experiments with a few soil dust samples indicated their INP fraction to be comparable or slightly enhanced to that of desert dust. We have used the AIDA (Aerosol Interaction and Dynamics in the Atmosphere) cloud simulation chamber to study the immersion freezing ability of four different arable soil dusts, sampled in Germany, China and Argentina. For temperatures higher than about -20°C, we found the INP fraction of aerosols generated from these samples by a dry dispersion technique to be significantly higher compared to various desert dust aerosols also investigated in AIDA experiments. In this contribution, we

  6. Cross-Linking Studies of Lysozyme Nucleation

    NASA Technical Reports Server (NTRS)

    Forsythe, Elizabeth; Pusey, Marc

    2000-01-01

    Tetragonal chicken egg white crystals consist of 4(sub 3) helices running in alternating directions, the helix rows having a two fold symmetry with each other. The unit cell consists of one complete tetrameric turn from each of two adjacent helices (an octamer). PBC analysis indicates that the helix intermolecular bonds are the strongest in the crystal, therefore likely formed first. AFM analysis of the (110) surface shows only complete helices, no half steps or bisected helices being found, while AFM line scans to measure the growth step increments show that they are multiples of the 4(sub 3) helix tetramer dimensions. This supports our thesis that the growth units are in fact multiples of the four molecule 4(sub 3) helix unit, the "average" growth unit size for the (110) face being an octamer (two turns about the helix) and the (101) growth unit averaging about the size of a hexamer. In an effort to better understand the species involved in the crystal nucleation and growth process, we have initiated an experimental program to study the species formed in solution compared to what is found in the crystal through covalent cross-linking studies. These experiments use the heterobifunctional cross-linking agent aminoethyl-4-azidonitroanaline (AEANA). An aliphatic amine at one end is covalently attached to the protein by a carbodiimide-mediated reaction, and a photo reactive group at the other can be used to initiate crosslinking. Modifications to the parent structure can be used to alter the distance between the two reactive groups and thus the cross-linking agents "reach". In practice, the cross-linking agent is first coupled to the asp101 side chain through the amine group. Asp101 lies within the active site cleft, and previous work with fluorescent probes had shown that derivatives at this site still crystallize in the tetragonal space group. This was also found to be the case with the AEANA derivative, which gave red tetragonal crystals. The protein now has a

  7. A Comparative Study of Nucleation Parameterizations: 2. Three-Dimensional Model Application and Evaluation

    EPA Science Inventory

    Following the examination and evaluation of 12 nucleation parameterizations presented in part 1, 11 of them representing binary, ternary, kinetic, and cluster‐activated nucleation theories are evaluated in the U.S. Environmental Protection Agency Community Multiscale Air Quality ...

  8. Bleb Nucleation through Membrane Peeling

    NASA Astrophysics Data System (ADS)

    Alert, Ricard; Casademunt, Jaume

    2016-02-01

    We study the nucleation of blebs, i.e., protrusions arising from a local detachment of the membrane from the cortex of a cell. Based on a simple model of elastic linkers with force-dependent kinetics, we show that bleb nucleation is governed by membrane peeling. By this mechanism, the growth or shrinkage of a detached membrane patch is completely determined by the linker kinetics, regardless of the energetic cost of the detachment. We predict the critical nucleation radius for membrane peeling and the corresponding effective energy barrier. These may be typically smaller than those predicted by classical nucleation theory, implying a much faster nucleation. We also perform simulations of a continuum stochastic model of membrane-cortex adhesion to obtain the statistics of bleb nucleation times as a function of the stress on the membrane. The determinant role of membrane peeling changes our understanding of bleb nucleation and opens new directions in the study of blebs.

  9. Mutations in C4orf26, encoding a peptide with in vitro hydroxyapatite crystal nucleation and growth activity, cause amelogenesis imperfecta.

    PubMed

    Parry, David A; Brookes, Steven J; Logan, Clare V; Poulter, James A; El-Sayed, Walid; Al-Bahlani, Suhaila; Al Harasi, Sharifa; Sayed, Jihad; Raïf, El Mostafa; Shore, Roger C; Dashash, Mayssoon; Barron, Martin; Morgan, Joanne E; Carr, Ian M; Taylor, Graham R; Johnson, Colin A; Aldred, Michael J; Dixon, Michael J; Wright, J Tim; Kirkham, Jennifer; Inglehearn, Chris F; Mighell, Alan J

    2012-09-01

    Autozygosity mapping and clonal sequencing of an Omani family identified mutations in the uncharacterized gene, C4orf26, as a cause of recessive hypomineralized amelogenesis imperfecta (AI), a disease in which the formation of tooth enamel fails. Screening of a panel of 57 autosomal-recessive AI-affected families identified eight further families with loss-of-function mutations in C4orf26. C4orf26 encodes a putative extracellular matrix acidic phosphoprotein expressed in the enamel organ. A mineral nucleation assay showed that the protein's phosphorylated C terminus has the capacity to promote nucleation of hydroxyapatite, suggesting a possible function in enamel mineralization during amelogenesis.

  10. Active Sites Environmental Monitoring Program: Mid-FY 1991 report

    SciTech Connect

    Ashwood, T.L.; Wickliff, D.S.; Morrissey, C.M.

    1991-10-01

    This report summarizes the activities of the Active Sites Environmental Monitoring Program (ASEMP) from October 1990 through March 1991. The ASEMP was established in 1989 by Solid Waste Operations and the Environmental Sciences Division to provide early detection and performance monitoring at active low-level radioactive waste (LLW) disposal sites in Solid Waste Storage Area (SWSA) 6 and transuranic (TRU) waste storage sites in SWSA 5 as required by chapters II and III of US Department of Energy Order 5820.2A. Monitoring results continue to demonstrate the no LLW is being leached from the storage vaults on the tumulus pads. Loading of vaults on Tumulus II began during this reporting period and 115 vaults had been loaded by the end of March 1991.

  11. Deposition nucleation viewed as homogeneous or immersion freezing in pores and cavities

    NASA Astrophysics Data System (ADS)

    Marcolli, C.

    2013-06-01

    filled with water. Water in pores can freeze in immersion mode at T > 235 K if the pore walls contain an active site. Pore analysis of clay minerals shows that kaolinites exhibit pore structures with pore diameters of 20-50 nm. The mesoporosity of illites and montmorillonites is characterized by pores with T = 2-5 nm. The number and size of pores is distinctly increased in acid treated montmorillonites like K10. Many clay minerals and mineral dusts show a strong increase in ice nucleation efficiency when temperature is decreased below 235 K. Such an increase is difficult to explain when ice nucleation is supposed to occur by a deposition mechanism, but evident when assuming freezing in pores, because for homogeneous ice nucleation only small pore volumes are needed, while heterogeneous ice nucleation requires larger pore structures to contain at least one active site for immersion nucleation. Together, these pieces of evidence strongly suggest that ice nucleation within pores should be the prevailing freezing mechanism of clay minerals for RHw below water saturation. Extending the analysis to other types of ice nuclei shows that freezing in pores and cracks is probably the prevailing ice nucleation mechanism for glassy and volcanic ash aerosols at RHw below water saturation. Freezing of water in carbon nanotubes might be of significance for ice nucleation by soot aerosols. No case could be identified that gives clear evidence of ice nucleation by water vapor deposition on a solid surface. Inspection of ice nuclei with a close lattice match to ice, such as silver iodide or SnomaxTM, show that for high ice nucleation efficiency below water saturation the presence of impurities or cracks on the surface may be essential. Soluble impurities promote the formation of a liquid phase below water saturation in patches on the surface or as a complete surface layer that offers an environment for immersion freezing. If porous aerosol particles come in contact with semivolatile vapors

  12. Active chemisorption sites in functionalized ionic liquids for carbon capture.

    PubMed

    Cui, Guokai; Wang, Jianji; Zhang, Suojiang

    2016-07-25

    Development of novel technologies for the efficient and reversible capture of CO2 is highly desired. In the last decade, CO2 capture using ionic liquids has attracted intensive attention from both academia and industry, and has been recognized as a very promising technology. Recently, a new approach has been developed for highly efficient capture of CO2 by site-containing ionic liquids through chemical interaction. This perspective review focuses on the recent advances in the chemical absorption of CO2 using site-containing ionic liquids, such as amino-based ionic liquids, azolate ionic liquids, phenolate ionic liquids, dual-functionalized ionic liquids, pyridine-containing ionic liquids and so on. Other site-containing liquid absorbents such as amine-based solutions, switchable solvents, and functionalized ionic liquid-amine blends are also investigated. Strategies have been discussed for how to activate the existent reactive sites and develop novel reactive sites by physical and chemical methods to enhance CO2 absorption capacity and reduce absorption enthalpy. The carbon capture mechanisms of these site-containing liquid absorbents are also presented. Particular attention has been paid to the latest progress in CO2 capture in multiple-site interactions by amino-free anion-functionalized ionic liquids. In the last section, future directions and prospects for carbon capture by site-containing ionic liquids are outlined.

  13. Active chemisorption sites in functionalized ionic liquids for carbon capture.

    PubMed

    Cui, Guokai; Wang, Jianji; Zhang, Suojiang

    2016-07-25

    Development of novel technologies for the efficient and reversible capture of CO2 is highly desired. In the last decade, CO2 capture using ionic liquids has attracted intensive attention from both academia and industry, and has been recognized as a very promising technology. Recently, a new approach has been developed for highly efficient capture of CO2 by site-containing ionic liquids through chemical interaction. This perspective review focuses on the recent advances in the chemical absorption of CO2 using site-containing ionic liquids, such as amino-based ionic liquids, azolate ionic liquids, phenolate ionic liquids, dual-functionalized ionic liquids, pyridine-containing ionic liquids and so on. Other site-containing liquid absorbents such as amine-based solutions, switchable solvents, and functionalized ionic liquid-amine blends are also investigated. Strategies have been discussed for how to activate the existent reactive sites and develop novel reactive sites by physical and chemical methods to enhance CO2 absorption capacity and reduce absorption enthalpy. The carbon capture mechanisms of these site-containing liquid absorbents are also presented. Particular attention has been paid to the latest progress in CO2 capture in multiple-site interactions by amino-free anion-functionalized ionic liquids. In the last section, future directions and prospects for carbon capture by site-containing ionic liquids are outlined. PMID:27243042

  14. Paper-based assay of antioxidant activity using analyte-mediated on-paper nucleation of gold nanoparticles as colorimetric probes.

    PubMed

    Choleva, Tatiana G; Kappi, Foteini A; Giokas, Dimosthenis L; Vlessidis, Athanasios G

    2015-02-20

    With the increasing interest in the health benefits arising from the consumption of dietary products rich in antioxidants, there exists a clear demand for easy-to-use and cost-effective tests that can be used for the identification of the antioxidant power of food products. Paper-based analytical devices constitute a remarkable platform for such expedient and low-cost assays with minimal external resources but efforts in this direction are still scarce. In this work we introduce a new paper-based device in the form of a sensor patch that enables the determination of antioxidant activity through analyte-driven on-paper formation of gold nanoparticles. The principle of detection capitalizes, for the first time, on the on-paper nucleation of gold ions to its respective nanoparticles, upon reduction by antioxidant compounds present in an aqueous sample. The ensuing chromatic transitions, induced on the paper surface, are used as an optical "signature" of the antioxidant strength of the solution. The response of the paper-based sensor was evaluated against a large variety of antioxidant species and the respective dose response curves were constructed. On the basis of these data, the contribution of each species according to its chemical structure was elucidated. For the analysis of real samples, a concentration-dependent colorimetric response was established against Gallic acid equivalents over a linear range of 10 μM-1.0 mM, with detection limits at the low and ultra-low μM levels (i.e. <1.0 μM) and satisfactory precision (RSD=3.6-12.6%). The sensor has been tested for the assessment of antioxidant activity in real samples (teas and wines) and the results correlated well with commonly used antioxidant detection methods. Importantly, the sensor performed favorably for long periods of time when stored at moisture-free and low temperature conditions without losing its activity thus posing as an attractive alternative to the assessment of antioxidant activity without

  15. Studies on the active site of pig plasma amine oxidase.

    PubMed Central

    Collison, D; Knowles, P F; Mabbs, F E; Rius, F X; Singh, I; Dooley, D M; Cote, C E; McGuirl, M

    1989-01-01

    Amine oxidase from pig plasma (PPAO) has two bound Cu2+ ions and at least one pyrroloquinoline quinone (PQQ) moiety as cofactors. It is shown that recovery of activity by copper-depleted PPAO is linear with respect to added Cu2+ ions. Recovery of e.s.r. and optical spectral characteristics of active-site copper parallel the recovery of catalytic activity. These results are consistent with both Cu2+ ions contributing to catalysis. Further e.s.r. studies indicate that the two copper sites in PPAO, unlike those in amine oxidases from other sources, are chemically distinct. These comparative studies establish that non-identity of the Cu2+ ions in PPAO is not a requirement for amine oxidase activity. It is shown through the use of a new assay procedure that there are two molecules of PQQ bound per molecule of protein in PPAO; only the more reactive of these PQQ moieties is required for activity. PMID:2559715

  16. Realizing controllable graphene nucleation by regulating the competition of hydrogen and oxygen during chemical vapor deposition heating.

    PubMed

    Zhang, Haoran; Zhang, Yaqian; Zhang, Yanhui; Chen, Zhiying; Sui, Yanping; Ge, Xiaoming; Deng, Rongxuan; Yu, Guanghui; Jin, Zhi; Liu, Xinyu

    2016-08-24

    Oxygen can passivate Cu surface active sites when graphene nucleates. Thus, the nucleation density is decreased. The CuO/Cu substrate was chosen for graphene domain synthesis in our study. The results indicate that the CuO/Cu substrate is beneficial for large-scale, single-crystal graphene domain synthesis. Graphene grown on the CuO/Cu substrate exhibits fewer nucleation sites than on Cu foils, suggesting that graphene follows an oxygen-dominating growth. Hydrogen treatment via a heating process could weaken the surface oxygen's role in limiting graphene nucleation under the competition of hydrogen and oxygen and could transfer the synthesis of graphene into a hydrogen-dominating growth. However, the competition only exists during the chemical vapor deposition heating process. For non-hydrogen heated samples, oxygen-dominating growth is experienced even though the samples are annealed in hydrogen for a long time after the heating process. With the temperature increases, the role of hydrogen gradually decreases. The balance of hydrogen and oxygen is adjusted by introducing hydrogen gas at a different heating temperatures. The oxygen concentration on the substrate surface is believed to determine the reactions mechanisms based on the secondary ion mass spectrometry test results. This study provides a new method for the controllable synthesis of graphene nucleation during a heating process. PMID:27506467

  17. Computer simulation of the active site of human serum cholinesterase

    SciTech Connect

    Kefang Jiao; Song Li; Zhengzheng Lu

    1996-12-31

    The first 3D-structure of acetylchelinesterase from Torpedo California electric organ (T.AChE) was published by JL. Sussman in 1991. We have simulated 3D-structure of human serum cholinesterase (H.BuChE) and the active site of H.BuChE. It is discovered by experiment that the residue of H.BuChE is still active site after a part of H.BuChE is cut. For example, the part of 21KD + 20KD is active site of H.BuChE. The 20KD as it is. Studies on these peptides by Hemelogy indicate that two active peptides have same negative electrostatic potential maps diagram. These negative electrostatic areas attached by acetyl choline with positive electrostatic potency. We predict that 147...236 peptide of AChE could be active site because it was as 20KD as with negative electrostatic potential maps. We look forward to proving from other ones.

  18. Molecular Characterization of an Ice Nucleation Protein Variant (InaQ) from Pseudomonas syringae and the Analysis of Its Transmembrane Transport Activity in Escherichia coli

    PubMed Central

    Li, Qianqian; Yan, Qi; Chen, Jinsi; He, Yan; Wang, Jing; Zhang, Hongxing; Yu, Ziniu; Li, Lin

    2012-01-01

    The ice nucleation protein (INP) of Pseudomonas syringae has gained scientific interest not only because of its pathogenicity of foliar necroses but also for its wide range of potential applications, such as in snow making, frozen food preparation, and surface-display system development. However, studies on the transport activity of INP remain lacking. In the present study, a newly identified INP-gene variant, inaQ, from a P. syringae MB03 strain was cloned. Its structural domains, signal sequences, and the hydrophilicity or hydrophobicity of each domain, were then characterized. The deduced amino acid sequence of InaQ shares similar protein domains with three P. syringae INPs, namely, InaK, InaZ, and InaV, which were identified as an N-terminal domain, a central repeating domain, and a C-terminal domain. The expression of the full-length InaQ and of various truncated variants was induced in Escherichia coli to analyze their transmembrane transport and surface-binding activities, while using the green fluorescence protein (GFP) as the fusion partner. With two transmembrane segments and a weak secretion signal, the N-terminal domain (InaQ-N) alone was found to be responsible for the transport process as well as for the binding to the outer membrane, whereas the C-terminal region was nonfunctional in protein transport. Increased membrane transport and surface-binding capacities were induced by a low isopropyl-β-D-thiogalactoside concentration (0.1 mmol/l) but not by culture temperatures (15 ºC to 37 ºC). Furthermore, by constructing the GFP-fused proteins with a single InaQ-N, as well as two and three tandemly aligned InaQ-N molecules, the transport and membrane-binding activities of these proteins were compared using Western blot analysis, immmunofluorescence microscopy, and assays of the GFP specific fluorescence intensity of subcellular fractions and flow cytometry, which showed that the increase of InaQ-N repeats resulted in a coordinated increase of the

  19. On the Ice Nucleation Spectrum

    NASA Technical Reports Server (NTRS)

    Barahona, D.

    2012-01-01

    This work presents a novel formulation of the ice nucleation spectrum, i.e. the function relating the ice crystal concentration to cloud formation conditions and aerosol properties. The new formulation is physically-based and explicitly accounts for the dependency of the ice crystal concentration on temperature, supersaturation, cooling rate, and particle size, surface area and composition. This is achieved by introducing the concepts of ice nucleation coefficient (the number of ice germs present in a particle) and nucleation probability dispersion function (the distribution of ice nucleation coefficients within the aerosol population). The new formulation is used to generate ice nucleation parameterizations for the homogeneous freezing of cloud droplets and the heterogeneous deposition ice nucleation on dust and soot ice nuclei. For homogeneous freezing, it was found that by increasing the dispersion in the droplet volume distribution the fraction of supercooled droplets in the population increases. For heterogeneous ice nucleation the new formulation consistently describes singular and stochastic behavior within a single framework. Using a fundamentally stochastic approach, both cooling rate independence and constancy of the ice nucleation fraction over time, features typically associated with singular behavior, were reproduced. Analysis of the temporal dependency of the ice nucleation spectrum suggested that experimental methods that measure the ice nucleation fraction over few seconds would tend to underestimate the ice nuclei concentration. It is shown that inferring the aerosol heterogeneous ice nucleation properties from measurements of the onset supersaturation and temperature may carry significant error as the variability in ice nucleation properties within the aerosol population is not accounted for. This work provides a simple and rigorous ice nucleation framework where theoretical predictions, laboratory measurements and field campaign data can be

  20. Resonant active sites in catalytic ammonia synthesis: A structural model

    NASA Astrophysics Data System (ADS)

    Cholach, Alexander R.; Bryliakova, Anna A.; Matveev, Andrey V.; Bulgakov, Nikolai N.

    2016-03-01

    Adsorption sites Mn consisted of n adjacent atoms M, each bound to the adsorbed species, are considered within a realistic model. The sum of bonds Σ lost by atoms in a site in comparison with the bulk atoms was used for evaluation of the local surface imperfection, while the reaction enthalpy at that site was used as a measure of activity. The comparative study of Mn sites (n = 1-5) at basal planes of Pt, Rh, Ir, Fe, Re and Ru with respect to heat of N2 dissociative adsorption QN and heat of Nad + Had → NHad reaction QNH was performed using semi-empirical calculations. Linear QN(Σ) increase and QNH(Σ) decrease allowed to specify the resonant Σ for each surface in catalytic ammonia synthesis at equilibrium Nad coverage. Optimal Σ are realizable for Ru2, Re2 and Ir4 only, whereas other centers meet steric inhibition or unreal crystal structure. Relative activity of the most active sites in proportion 5.0 × 10- 5: 4.5 × 10- 3: 1: 2.5: 3.0: 1080: 2270 for a sequence of Pt4, Rh4, Fe4(fcc), Ir4, Fe2-5(bcc), Ru2, Re2, respectively, is in agreement with relevant experimental data. Similar approach can be applied to other adsorption or catalytic processes exhibiting structure sensitivity.

  1. Inhibition of bacterial ice nucleation by polyglycerol polymers.

    PubMed

    Wowk, Brian; Fahy, Gregory M

    2002-02-01

    The simple linear polymer polyglycerol (PGL) was found to apparently bind and inhibit the ice nucleating activity of proteins from the ice nucleating bacterium Pseudomonas syringae. PGL of molecular mass 750 Da was added to a solution consisting of 1 ppm freeze-dried P. syringae 31A in water. Differential ice nucleator spectra were determined by measuring the distribution of freezing temperatures in a population of 98 drops of 1 microL volume. The mean freezing temperature was lowered from -6.8 degrees C (control) to -8.0,-9.4,-12.5, and -13.4 degrees C for 0.001, 0.01, 0.1, and 1% w/w PGL concentrations, respectively (SE < 0.2 degrees C). PGL was found to be an ineffective inhibitor of seven defined organic ice nucleating agents, whereas the general ice nucleation inhibitor polyvinyl alcohol (PVA) was found to be effective against five of the seven. The activity of PGL therefore seems to be specific against bacterial ice nucleating protein. PGL alone was an ineffective inhibitor of ice nucleation in small volumes of environmental or laboratory water samples, suggesting that the numerical majority of ice nucleating contaminants in nature may be of nonbacterial origin. However, PGL was more effective than PVA at suppressing initial ice nucleation events in large volumes, suggesting a ubiquitous sparse background of bacterial ice nucleating proteins with high nucleation efficiency. The combination of PGL and PVA was particularly effective for reducing ice formation in solutions used for cryopreservation by vitrification.

  2. Multi-site Phosphorylation Regulates Bim Stability and Apoptotic Activity

    PubMed Central

    Hübner, Anette; Barrett, Tamera; Flavell, Richard A.; Davis, Roger J.

    2008-01-01

    The pro-apoptotic BH3-only protein Bim is established to be an important mediator of signaling pathways that induce cell death. Multi-site phosphorylation of Bim by several members of the MAP kinase group is implicated as a regulatory mechanism that controls the apoptotic activity of Bim. To test the role of Bim phosphorylation in vivo, we constructed mice with a series of mutant alleles that express phosphorylation-defective Bim proteins. We show that mutation of the phosphorylation site Thr-112 causes decreased binding of Bim to the anti-apoptotic protein Bcl2 and can increase cell survival. In contrast, mutation of the phosphorylation sites Ser-55, Ser-65, and Ser-73 can cause increased apoptosis because of reduced proteasomal degradation of Bim. Together, these data indicate that phosphorylation can regulate Bim by multiple mechanisms and that the phosphorylation of Bim on different sites can contribute to the sensitivity of cellular apoptotic responses. PMID:18498746

  3. A Hydrophobic Pocket in the Active Site of Glycolytic Aldolase Mediates Interactions with Wiskott-Aldrich Syndrome Protein

    SciTech Connect

    St-Jean,M.; Izard, T.; Sygusch, J.

    2007-01-01

    Aldolase plays essential catalytic roles in glycolysis and gluconeogenesis. However, aldolase is a highly abundant protein that is remarkably promiscuous in its interactions with other cellular proteins. In particular, aldolase binds to highly acidic amino acid sequences, including the C-terminus of the Wiskott-Aldrich syndrome protein, an actin nucleation promoting factor. Here we report the crystal structure of tetrameric rabbit muscle aldolase in complex with a C-terminal peptide of Wiskott-Aldrich syndrome protein. Aldolase recognizes a short, 4-residue DEWD motif (residues 498-501), which adopts a loose hairpin turn that folds about the central aromatic residue, enabling its tryptophan side chain to fit into a hydrophobic pocket in the active site of aldolase. The flanking acidic residues in this binding motif provide further interactions with conserved aldolase active site residues, Arg-42 and Arg-303, aligning their side chains and forming the sides of the hydrophobic pocket. The binding of Wiskott-Aldrich syndrome protein to aldolase precludes intramolecular interactions of its C-terminus with its active site, and is competitive with substrate as well as with binding by actin and cortactin. Finally, based on this structure a novel naphthol phosphate-based inhibitor of aldolase was identified and its structure in complex with aldolase demonstrated mimicry of the Wiskott-Aldrich syndrome protein-aldolase interaction. The data support a model whereby aldolase exists in distinct forms that regulate glycolysis or actin dynamics.

  4. Water in the Active Site of Ketosteroid Isomerase

    PubMed Central

    Hanoian, Philip; Hammes-Schiffer, Sharon

    2011-01-01

    Classical molecular dynamics simulations were utilized to investigate the structural and dynamical properties of water in the active site of ketosteroid isomerase (KSI) to provide insight into the role of these water molecules in the enzyme-catalyzed reaction. This reaction is thought to proceed via a dienolate intermediate that is stabilized by hydrogen bonding with residues Tyr16 and Asp103. A comparative study was performed for the wild-type (WT) KSI and the Y16F, Y16S, and Y16F/Y32F/Y57F (FFF) mutants. These systems were studied with three different bound ligands: equilenin, which is an intermediate analog, and the intermediate states of two steroid substrates. Several distinct water occupation sites were identified in the active site of KSI for the WT and mutant systems. Three additional sites were identified in the Y16S mutant that were not occupied in WT KSI or the other mutants studied. The number of water molecules directly hydrogen bonded to the ligand oxygen was approximately two waters in the Y16S mutant, one water in the Y16F and FFF mutants, and intermittent hydrogen bonding of one water molecule in WT KSI. The molecular dynamics trajectories of the Y16F and FFF mutants reproduced the small conformational changes of residue 16 observed in the crystal structures of these two mutants. Quantum mechanical/molecular mechanical calculations of 1H NMR chemical shifts of the protons in the active site hydrogen-bonding network suggest that the presence of water in the active site does not prevent the formation of short hydrogen bonds with far-downfield chemical shifts. The molecular dynamics simulations indicate that the active site water molecules exchange much more frequently for WT KSI and the FFF mutant than for the Y16F and Y16S mutants. This difference is most likely due to the hydrogen-bonding interaction between Tyr57 and an active site water molecule that is persistent in the Y16F and Y16S mutants but absent in the FFF mutant and significantly less

  5. Activation of phenylalanine hydroxylase by phenylalanine does not require binding in the active site.

    PubMed

    Roberts, Kenneth M; Khan, Crystal A; Hinck, Cynthia S; Fitzpatrick, Paul F

    2014-12-16

    Phenylalanine hydroxylase (PheH), a liver enzyme that catalyzes the hydroxylation of excess phenylalanine in the diet to tyrosine, is activated by phenylalanine. The lack of activity at low levels of phenylalanine has been attributed to the N-terminus of the protein's regulatory domain acting as an inhibitory peptide by blocking substrate access to the active site. The location of the site at which phenylalanine binds to activate the enzyme is unknown, and both the active site in the catalytic domain and a separate site in the N-terminal regulatory domain have been proposed. Binding of catecholamines to the active-site iron was used to probe the accessibility of the active site. Removal of the regulatory domain increases the rate constants for association of several catecholamines with the wild-type enzyme by ∼2-fold. Binding of phenylalanine in the active site is effectively abolished by mutating the active-site residue Arg270 to lysine. The k(cat)/K(phe) value is down 10⁴ for the mutant enzyme, and the K(m) value for phenylalanine for the mutant enzyme is >0.5 M. Incubation of the R270K enzyme with phenylalanine also results in a 2-fold increase in the rate constants for catecholamine binding. The change in the tryptophan fluorescence emission spectrum seen in the wild-type enzyme upon activation by phenylalanine is also seen with the R270K mutant enzyme in the presence of phenylalanine. Both results establish that activation of PheH by phenylalanine does not require binding of the amino acid in the active site. This is consistent with a separate allosteric site, likely in the regulatory domain.

  6. Chemical Modification of Papain and Subtilisin: An Active Site Comparison

    ERIC Educational Resources Information Center

    St-Vincent, Mireille; Dickman, Michael

    2004-01-01

    An experiment using methyle methanethiosulfonate (MMTS) and phenylmethylsulfonyl flouride (PMSF) to specifically modify the cysteine and serine residues in the active sites of papain and subtilism respectively is demonstrated. The covalent modification of these enzymes and subsequent rescue of papain shows the beginning biochemist that proteins…

  7. Energy transfer at the active sites of heme proteins

    SciTech Connect

    Dlott, D.D.; Hill, J.R.

    1995-12-31

    Experiments using a picosecond pump-probe apparatus at the Picosecond Free-electron Laser Center at Stanford University, were performed to investigate the relaxation of carbon monoxide bound to the active sites of heme proteins. The significance of these experiments is two-fold: (1) they provide detailed information about molecular dynamics occurring at the active sites of proteins; and (2) they provide insight into the nature of vibrational relaxation processes in condensed matter. Molecular engineering is used to construct various molecular systems which are studied with the FEL. We have studied native proteins, mainly myoglobin obtained from different species, mutant proteins produced by genetic engineering using recombinant DNA techniques, and a variety of model systems which mimic the structures of the active sites of native proteins, which are produced using molecular synthesis. Use of these different systems permits us to investigate how specific molecular structural changes affect dynamical processes occurring at the active sites. This research provides insight into the problems of how different species needs are fulfilled by heme proteins which have greatly different functionality, which is induced by rather small structural changes.

  8. Changes in active site histidine hydrogen bonding trigger cryptochrome activation.

    PubMed

    Ganguly, Abir; Manahan, Craig C; Top, Deniz; Yee, Estella F; Lin, Changfan; Young, Michael W; Thiel, Walter; Crane, Brian R

    2016-09-01

    Cryptochrome (CRY) is the principal light sensor of the insect circadian clock. Photoreduction of the Drosophila CRY (dCRY) flavin cofactor to the anionic semiquinone (ASQ) restructures a C-terminal tail helix (CTT) that otherwise inhibits interactions with targets that include the clock protein Timeless (TIM). All-atom molecular dynamics (MD) simulations indicate that flavin reduction destabilizes the CTT, which undergoes large-scale conformational changes (the CTT release) on short (25 ns) timescales. The CTT release correlates with the conformation and protonation state of conserved His378, which resides between the CTT and the flavin cofactor. Poisson-Boltzmann calculations indicate that flavin reduction substantially increases the His378 pKa Consistent with coupling between ASQ formation and His378 protonation, dCRY displays reduced photoreduction rates with increasing pH; however, His378Asn/Arg variants show no such pH dependence. Replica-exchange MD simulations also support CTT release mediated by changes in His378 hydrogen bonding and verify other responsive regions of the protein previously identified by proteolytic sensitivity assays. His378 dCRY variants show varying abilities to light-activate TIM and undergo self-degradation in cellular assays. Surprisingly, His378Arg/Lys variants do not degrade in light despite maintaining reactivity toward TIM, thereby implicating different conformational responses in these two functions. Thus, the dCRY photosensory mechanism involves flavin photoreduction coupled to protonation of His378, whose perturbed hydrogen-bonding pattern alters the CTT and surrounding regions. PMID:27551082

  9. Transient nucleation in condensed systems

    NASA Technical Reports Server (NTRS)

    Kelton, K. F.; Greer, A. L.; Thompson, C. V.

    1983-01-01

    Using classical nucleation theory we consider transient nucleation occurring in a one-component, condensed system under isothermal conditions. We obtain an exact closed-form expression for the time dependent cluster populations. In addition, a more versatile approach is developed: a numerical simulation technique which models directly the reactions by which clusters are produced. This simulation demonstrates the evolution of cluster populations and nucleation rate in the transient regime. Results from the simulation are verified by comparison with exact analytical solutions for the steady state. Experimental methods for measuring transient nucleation are assessed, and it is demonstrated that the observed behavior depends on the method used. The effect of preexisting cluster distributions is studied. Previous analytical and numerical treatments of transient nucleation are compared to the solutions obtained from the simulation. The simple expressions of Kashchiev are shown to give good descriptions of the nucleation behavior.

  10. Conformational Transitions in Human AP Endonuclease 1 and Its Active Site Mutant during Abasic Site Repair†

    PubMed Central

    Kanazhevskaya, Lyubov Yu.; Koval, Vladimir V.; Zharkov, Dmitry O.; Strauss, Phyllis R.; Fedorova, Olga S.

    2010-01-01

    AP endonuclease 1 (APE 1) is a crucial enzyme of the base excision repair pathway (BER) in human cells. APE1 recognizes apurinic/apyrimidinic (AP) sites and makes a nick in the phosphodiester backbone 5′ to them. The conformational dynamics and presteady-state kinetics of wild-type APE1 and its active site mutant, Y171F-P173L-N174K, have been studied. To observe conformational transitions occurring in the APE1 molecule during the catalytic cycle, we detected intrinsic tryptophan fluorescence of the enzyme under single turnover conditions. DNA duplexes containing a natural AP site, its tetrahydrofuran analogue, or a 2′-deoxyguanosine residue in the same position were used as specific substrates or ligands. The stopped-flow experiments have revealed high flexibility of the APE1 molecule and the complexity of the catalytic process. The fluorescent traces indicate that wild-type APE1 undergoes at least four conformational transitions during the processing of abasic sites in DNA. In contrast, nonspecific interactions of APE1 with undamaged DNA can be described by a two-step kinetic scheme. Rate and equilibrium constants were extracted from the stopped-flow and fluorescence titration data for all substrates, ligands, and products. A replacement of three residues at the enzymatic active site including the replacement of tyrosine 171 with phenylalanine in the enzyme active site resulted in a 2 × 104-fold decrease in the reaction rate and reduced binding affinity. Our data indicate the important role of conformational changes in APE1 for substrate recognition and catalysis. PMID:20575528

  11. Nanoindentation. Simulation of defect nucleation in a crystal.

    PubMed

    Gouldstone, A; Van Vliet, K J; Suresh, S

    2001-06-01

    Nanoindentation is the penetration of a surface to nanometre depths using an indenting device. It can be simulated using the Bragg bubble-raft model, in which a close-packed array of soap bubbles corresponds to the equilibrium positions of atoms in a crystalline solid. Here we show that homogeneous defect nucleation occurs within a crystal when its surface roughness is comparable to the radius of the indenter tip, and that the depth of the nucleation site below the surface is proportional to the half-width of the contact. Our results may explain the unusually high local stress required for defect nucleation in nano-indented face-centred cubic crystals.

  12. N-methyl-D-aspartate recognition site ligands modulate activity at the coupled glycine recognition site.

    PubMed

    Hood, W F; Compton, R P; Monahan, J B

    1990-03-01

    In synaptic plasma membranes from rat forebrain, the potencies of glycine recognition site agonists and antagonists for modulating [3H]1-[1-(2-thienyl)cyclohexyl]piperidine ([3H]TCP) binding and for displacing strychnine-insensitive [3H]glycine binding are altered in the presence of N-methyl-D-aspartate (NMDA) recognition site ligands. The NMDA competitive antagonist, cis-4-phosphonomethyl-2-piperidine carboxylate (CGS 19755), reduces [3H]glycine binding, and the reduction can be fully reversed by the NMDA recognition site agonist, L-glutamate. Scatchard analysis of [3H]glycine binding shows that in the presence of CGS 19755 there is no change in Bmax (8.81 vs. 8.79 pmol/mg of protein), but rather a decrease in the affinity of glycine (KD of 0.202 microM vs. 0.129 microM). Similar decreases in affinity are observed for the glycine site agonists, D-serine and 1-aminocyclopropane-1-carboxylate, in the presence of CGS 19755. In contrast, the affinity of glycine antagonists, 1-hydroxy-3-amino-2-pyrrolidone and 1-aminocyclobutane-1-carboxylate, at this [3H]glycine recognition site increases in the presence of CGS 19755. The functional consequence of this change in affinity was addressed using the modulation of [3H]TCP binding. In the presence of L-glutamate, the potency of glycine agonists for the stimulation of [3H]TCP binding increases, whereas the potency of glycine antagonists decreases. These data are consistent with NMDA recognition site ligands, through their interactions at the NMDA recognition site, modulating activity at the associated glycine recognition site.

  13. Control of active sites in selective flocculation: I -- Mathematical model

    SciTech Connect

    Behl, S.; Moudgil, B.M.; Prakash, T.S. . Dept. of Materials Science and Engineering)

    1993-12-01

    Heteroflocculation has been determined to be another major reason for loss in selectivity for flocculation process. In a mathematical model developed earlier, conditions for controlling heteroflocculation were discussed. Blocking active sites to control selective adsorption of a flocculant oil a desirable solid surface is discussed. It has been demonstrated that the lower molecular weight fraction of a flocculant which is incapable of flocculating the particles is an efficient site blocking agent. The major application of selective flocculation has been in mineral processing but many potential uses exist in biological and other colloidal systems. These include purification of ceramic powders, separating hazardous solids from chemical waste, and removal of deleterious components from paper pulp.

  14. Ice nucleation of bioaerosols - a resumee

    NASA Astrophysics Data System (ADS)

    Pummer, Bernhard G.; Atanasova, Lea; Bauer, Heidi; Bernardi, Johannes; Chazallon, Bertrand; Druzhinina, Irina S.; Grothe, Hinrich

    2013-04-01

    The role of biological particles for ice nucleation (IN) is still debated. Here, we present a summary of investigation and comparison of different ice nuclei. Apart from the bacterial ice nucleation proteins in Snomax, we further investigated a broad spectrum of pollen and fungal spores in the search for ice nucleation activity. Apart from Snomax, only few samples showed vital IN activity, like Fusarium avenaceum spores and Betula pendula pollen. Chemical characterization accentuated the differences between bacterial and pollen ice nuclei. Exposure to natural stresses, like UV and NOx, led to a significant decrease in IN activity. Furthermore, the releasable fraction of the pollen material, which includes the ice nuclei, was extracted with water and dried up. These residues were investigated with Raman spectroscopy and compared with the spectra of whole pollen grains. Measurements clearly demonstrated that the aqueous fraction contained mainly saccharides, lipids and proteins, but no sporopollenin, which is the bulk material of the outer pollen wall. Fungal spores of ecologically, economically or otherwise relevant species were also investigated. Most species showed no significant IN activity at all. A few species showed a slight increase in freezing temperature, but still significantly below the activity of the most active pollen or mineral dusts. Only Fusarium avenaceum showed strong IN activity. Cultivation of Fusarium and Trichoderma (close relatives of Fusarium) at different temperatures showed changes in total protein expression, but no impact on the IN activity.

  15. The site of activation of factor X by cancer procoagulant.

    PubMed

    Gordon, S G; Mourad, A M

    1991-12-01

    Cancer procoagulant (CP) is a cysteine proteinase found in a variety of malignant cells and tissues and in human amnion-chorion tissue. It initiates coagulation by activating factor X. However, the amino acid sequence of the substrate protein that determines the cleavage site of cysteine proteinases is different from that of the serine proteinases that normally activate factor X, such as factor IXa, VIIa and Russell's Viper Venom (RVV). Therefore, it was of interest to determine the site of cleavage of human factor X by CP. Purified CP was incubated with purified factor X and the reaction mixture was electrophoresed on a 10% Tris-tricine SDS-PAGE gel. The proteins were electroeluted on to a polyvinylidene difluoride (PVDF) membrane, and stained with Coomassie blue. The heavy chain of activated factor X was cut out of the PVDF membrane and sequenced with an Applied Biosystems 477A with on-line HPLC. The primary cleavage sequence was Asp-Ala-Ala-Asp-Leu-Asp-Pro-; two other secondary sequences Ser-Ile-Thr-Trp-Lys-Pro- and Glu-Asn-Pro-Phe-Asp-Leu were found. The penultimate amino acid on the carbonyl side of the hydrolysed amide bond plays a critical role for the recognition of the cleavage site of cysteine proteinases. These data indicate that the penultimate amino acid for the primary cleavage site of factor X by CP is proline-20 and for the secondary sites, proline-13 and proline-28. This is in contrast to arginine-52 that determines the specificity of the cleavage by normal serine proteinase activation.(ABSTRACT TRUNCATED AT 250 WORDS)

  16. Experimental and Theoretical Studies of Nucleation in Supercooled Liquid Silicon. Final Program Report

    SciTech Connect

    Im, J.

    2004-04-29

    The original objectives of the present program consisted of two specific nucleation-related research activities; (1) to provide a set of experimental data that will enable the quantitative examination of classical nucleation theory, and (2) to describe the phenomenon of nucleation by developing general expressions of nucleation that include both the thermal and athermal components and that correctly consider and incorporate the transient effects that arise from the nonstationary cluster distribution profile.

  17. Active-Site-Accessible, Porphyrinic Metal;#8722;Organic Framework Materials

    SciTech Connect

    Farha, Omar K.; Shultz, Abraham M.; Sarjeant, Amy A.; Nguyen, SonBinh T.; Hupp, Joseph T.

    2012-02-06

    On account of their structural similarity to cofactors found in many metallo-enzymes, metalloporphyrins are obvious potential building blocks for catalytically active, metal-organic framework (MOF) materials. While numerous porphyrin-based MOFs have already been described, versions featuring highly accessible active sites and permanent microporosity are remarkably scarce. Indeed, of the more than 70 previously reported porphyrinic MOFs, only one has been shown to be both permanently microporous and contain internally accessible active sites for chemical catalysis. Attempts to generalize the design approach used in this single successful case have failed. Reported here, however, is the synthesis of an extended family of MOFs that directly incorporate a variety of metalloporphyrins (specifically Al{sup 3+}, Zn{sup 2+}, Pd{sup 2+}, Mn{sup 3+}, and Fe{sup 3+} complexes). These robust porphyrinic materials (RPMs) feature large channels and readily accessible active sites. As an illustrative example, one of the manganese-containing RPMs is shown to be catalytically competent for the oxidation of alkenes and alkanes.

  18. Functional constituents of the active site of human neutrophil collagenase.

    PubMed

    Mookhtiar, K A; Wang, F; Van Wart, H E

    1986-05-01

    A series of chemical modification reactions has been carried out to identify functional constituents of the active site of human neutrophil collagenase. The enzyme is reversibly inhibited by the transition metal chelating agent 1,10-phenanthroline, and inhibition is fully reversed by zinc. Removal of weakly bound metal ions by gel filtration inactivates collagenase, and activity is fully restored on immediate readdition of calcium. The enzyme is unaffected by reagents that modify serine, cysteine, and arginine residues. However, reaction with the carboxyl reagents cyclohexylmorpholinocarbodiimide and Woodward's Reagent K lowers the activity of the enzyme substantially. Acetylimidazole inactivates the enzyme, but activity is completely restored on addition of hydroxylamine. The enzyme is also inactivated by tetranitromethane, indicating that it contains an essential tyrosine residue. Acylation of collagenase with diethyl pyrocarbonate, diketene, acetic anhydride, or trinitrobenzenesulfonate inactivates the enzyme, and activity is not restored on addition of hydroxylamine, indicating the presence of an essential lysine residue.

  19. Promotion and nucleation of carbonate precipitation during microbial iron reduction.

    PubMed

    Zeng, Z; Tice, M M

    2014-07-01

    Iron-bearing early diagenetic carbonate cements are common in sedimentary rocks, where they are thought to be associated with microbial iron reduction. However, little is yet known about how local environments around actively iron-reducing cells affect carbonate mineral precipitation rates and compositions. Precipitation experiments with the iron-reducing bacterium Shewanella oneidensis MR-1 were conducted to examine the potential role of cells in promoting precipitation and to explore the possible range of precipitate compositions generated in varying fluid compositions. Actively iron-reducing cells induced increased carbonate mineral saturation and nucleated precipitation on their poles. However, precipitation only occurred when calcium was present in solution, suggesting that cell surfaces lowered local ferrous iron concentrations by adsorption or intracellular iron oxide precipitation even as they locally raised pH. Resultant precipitates were a range of thermodynamically unstable calcium-rich siderites that would likely act as precursors to siderite, calcite, or even dolomite in nature. By modifying local pH, providing nucleation sites, and altering metal ion concentrations around cell surfaces, iron-reducing micro-organisms could produce a wide range of carbonate cements in natural sediments. PMID:24862734

  20. Promotion and nucleation of carbonate precipitation during microbial iron reduction.

    PubMed

    Zeng, Z; Tice, M M

    2014-07-01

    Iron-bearing early diagenetic carbonate cements are common in sedimentary rocks, where they are thought to be associated with microbial iron reduction. However, little is yet known about how local environments around actively iron-reducing cells affect carbonate mineral precipitation rates and compositions. Precipitation experiments with the iron-reducing bacterium Shewanella oneidensis MR-1 were conducted to examine the potential role of cells in promoting precipitation and to explore the possible range of precipitate compositions generated in varying fluid compositions. Actively iron-reducing cells induced increased carbonate mineral saturation and nucleated precipitation on their poles. However, precipitation only occurred when calcium was present in solution, suggesting that cell surfaces lowered local ferrous iron concentrations by adsorption or intracellular iron oxide precipitation even as they locally raised pH. Resultant precipitates were a range of thermodynamically unstable calcium-rich siderites that would likely act as precursors to siderite, calcite, or even dolomite in nature. By modifying local pH, providing nucleation sites, and altering metal ion concentrations around cell surfaces, iron-reducing micro-organisms could produce a wide range of carbonate cements in natural sediments.

  1. Nest predation increases with parental activity: Separating nest site and parental activity effects

    USGS Publications Warehouse

    Martin, T.E.; Scott, J.; Menge, C.

    2000-01-01

    Alexander Skutch hypothesized that increased parental activity can increase the risk of nest predation. We tested this hypothesis using ten open-nesting bird species in Arizona, USA. Parental activity was greater during the nestling than incubation stage because parents visited the nest frequently to feed their young during the nestling stage. However, nest predation did not generally increase with parental activity between nesting stages across the ten study species. Previous investigators have found similar results. We tested whether nest site effects might yield higher predation during incubation because the most obvious sites are depredated most rapidly. We conducted experiments using nest sites from the previous year to remove parental activity. Our results showed that nest sites have highly repeatable effects on nest predation risk; poor nest sites incurred rapid predation and caused predation rates to be greater during the incubation than nestling stage. This pattern also was exhibited in a bird species with similar (i.e. controlled) parental activity between nesting stages. Once nest site effects are taken into account, nest predation shows a strong proximate increase with parental activity during the nestling stage within and across species. Parental activity and nest sites exert antagonistic influences on current estimates of nest predation between nesting stages and both must be considered in order to understand current patterns of nest predation, which is an important source of natural selection.

  2. Studies in SiO(2)-based glass systems devitrifying by nucleation and growth

    NASA Astrophysics Data System (ADS)

    Krishnamurthy, Lakshmi Narayan

    Experimental and computational studies have been made on SiOsb2-based glasses crystallizing by homogenous nucleation (nucleation occurring randomly in space and time), heterogenous nucleation (nucleation occurring at specific sites through the glass), or non-polymorphic nucleation (nucleation occurring in systems where the composition of the crystallizing phase is different from that of the glass phase). A comprehensive computer model based on the classical theory of nucleation has been developed to simulate the process of crystallization occurring in differential thermal analysis experiments. The model, which takes into account the mode of the crystallization as well as the finite-size of the glass particles used in the measurements, is used to study homogenous and heterogenous crystallization of Lisb2O.2SiOsb2 glasses. The first measurements in any system of the composition dependence of the time-dependent nucleation rate are presented. An analysis of the steady-state nucleation rates in Nasb2O.2CaO.3SiOsb2 glasses made with different SiOsb2 concentrations show that the data are consistent with predictions from the classical theory of nucleation, assuming a composition-dependent interfacial energy. Further measurements of the transient nucleation rates resulting from multi-step annealing treatments support this claim, though small systematic differences suggest possible deviations from the kinetic model for nucleation.

  3. Actin nucleation and elongation factors: mechanisms and interplay.

    PubMed

    Chesarone, Melissa A; Goode, Bruce L

    2009-02-01

    Cells require actin nucleators to catalyze the de novo assembly of filaments and actin elongation factors to control the rate and extent of polymerization. Nucleation and elongation factors identified to date include Arp2/3 complex, formins, Ena/VASP, and newcomers Spire, Cobl, and Lmod. Here, we discuss recent advances in understanding their activities and mechanisms and new evidence for their cooperation and interaction in vivo. Earlier models had suggested that different nucleators function independently to assemble distinct actin arrays. However, more recent observations indicate that the construction of most cellular actin networks depends on the activities of multiple actin assembly-promoting factors working in concert.

  4. The role of collagen in bone apatite formation in the presence of hydroxyapatite nucleation inhibitors

    PubMed Central

    Nudelman, Fabio; Pieterse, Koen; George, Anne; Bomans, Paul H. H.; Friedrich, Heiner; Brylka, Laura J.; Hilbers, Peter A. J.; de With, Gijsbertus; Sommerdijk, Nico A. J. M.

    2011-01-01

    Bone is a composite material, in which collagen fibrils form a scaffold for a highly organized arrangement of uniaxially oriented apatite crystals1,2. In the periodic 67 nm cross-striated pattern of the collagen fibril3–5, the less dense 40-nm-long gap zone has been implicated as the place where apatite crystals nucleate from an amorphous phase, and subsequently grow6–9. This process is believed to be directed by highly acidic non-collagenous proteins6,7,9–11; however, the role of the collagen matrix12–14 during bone apatite mineralization remains unknown. Here, combining nanometre-scale resolution cryogenic transmission electron microscopy and cryogenic electron tomography15 with molecular modelling, we show that collagen functions in synergy with inhibitors of hydroxyapatite nucleation to actively control mineralization. The positive net charge close to the C-terminal end of the collagen molecules promotes the infiltration of the fibrils with amorphous calcium phosphate (ACP). Furthermore, the clusters of charged amino acids, both in gap and overlap regions, form nucleation sites controlling the conversion of ACP into a parallel array of oriented apatite crystals. We developed a model describing the mechanisms through which the structure, supramolecular assembly and charge distribution of collagen can control mineralization in the presence of inhibitors of hydroxyapatite nucleation. PMID:20972429

  5. A unifying model for adsorption and nucleation of vapors on solid surfaces.

    PubMed

    Laaksonen, Ari

    2015-04-23

    Vapor interaction with solid surfaces is traditionally described with adsorption isotherms in the undersaturated regime and with heterogeneous nucleation theory in the supersaturated regime. A class of adsorption isotherms is based on the idea of vapor molecule clustering around so-called active sites. However, as the isotherms do not account for the surface curvature effects of the clusters, they predict an infinitely thick adsorption layer at saturation and do not recognize the existence of the supersaturated regime. The classical heterogeneous nucleation theory also builds on the idea of cluster formation, but describes the interactions between the surface and the cluster with a single parameter, the contact angle, which provides limited information compared with adsorption isotherms. Here, a new model of vapor adsorption on nonporous solid surfaces is derived. The basic assumption is that adsorption proceeds via formation of molecular clusters, modeled as liquid caps. The equilibrium of the individual clusters with the vapor phase is described with the Frenkel-Halsey-Hill (FHH) adsorption theory modified with the Kelvin equation that corrects for the curvature effect on vapor pressure. The new model extends the FHH adsorption isotherm to be applicable both at submonolayer surface coverages and at supersaturated conditions. It shows good agreement with experimental adsorption data from 12 different adsorbent-adsorbate systems. The model predictions are also compared against heterogeneous nucleation data, and they show much better agreement than predictions of the classical heterogeneous nucleation theory. PMID:25831213

  6. Heterogeneous Formation of Polar Stratospheric Clouds- Part 1: Nucleation of Nitric Acid Trihydrate (NAT)

    NASA Technical Reports Server (NTRS)

    Hoyle, C. R.; Engel, I.; Luo, B. P.; Pitts, M. C.; Poole, L. R.; Grooss, J.-U.; Peter, T.

    2013-01-01

    Satellite-based observations during the Arctic winter of 2009/2010 provide firm evidence that, in contrast to the current understanding, the nucleation of nitric acid trihydrate (NAT) in the polar stratosphere does not only occur on preexisting ice particles. In order to explain the NAT clouds observed over the Arctic in mid-December 2009, a heterogeneous nucleation mechanism is required, occurring via immersion freezing on the surface of solid particles, likely of meteoritic origin. For the first time, a detailed microphysical modelling of this NAT formation pathway has been carried out. Heterogeneous NAT formation was calculated along more than sixty thousand trajectories, ending at Cloud Aerosol Lidar with Orthogonal Polarization (CALIOP) observation points. Comparing the optical properties of the modelled NAT with these observations enabled a thorough validation of a newly developed NAT nucleation parameterisation, which has been built into the Zurich Optical and Microphysical box Model (ZOMM). The parameterisation is based on active site theory, is simple to implement in models and provides substantial advantages over previous approaches which involved a constant rate of NAT nucleation in a given volume of air. It is shown that the new method is capable of reproducing observed polar stratospheric clouds (PSCs) very well, despite the varied conditions experienced by air parcels travelling along the different trajectories. In a companion paper, ZOMM is applied to a later period of the winter, when ice PSCs are also present, and it is shown that the observed PSCs are also represented extremely well under these conditions.

  7. The role of collagen in bone apatite formation in the presence of hydroxyapatite nucleation inhibitors.

    PubMed

    Nudelman, Fabio; Pieterse, Koen; George, Anne; Bomans, Paul H H; Friedrich, Heiner; Brylka, Laura J; Hilbers, Peter A J; de With, Gijsbertus; Sommerdijk, Nico A J M

    2010-12-01

    Bone is a composite material in which collagen fibrils form a scaffold for a highly organized arrangement of uniaxially oriented apatite crystals. In the periodic 67 nm cross-striated pattern of the collagen fibril, the less dense 40-nm-long gap zone has been implicated as the place where apatite crystals nucleate from an amorphous phase, and subsequently grow. This process is believed to be directed by highly acidic non-collagenous proteins; however, the role of the collagen matrix during bone apatite mineralization remains unknown. Here, combining nanometre-scale resolution cryogenic transmission electron microscopy and cryogenic electron tomography with molecular modelling, we show that collagen functions in synergy with inhibitors of hydroxyapatite nucleation to actively control mineralization. The positive net charge close to the C-terminal end of the collagen molecules promotes the infiltration of the fibrils with amorphous calcium phosphate (ACP). Furthermore, the clusters of charged amino acids, both in gap and overlap regions, form nucleation sites controlling the conversion of ACP into a parallel array of oriented apatite crystals. We developed a model describing the mechanisms through which the structure, supramolecular assembly and charge distribution of collagen can control mineralization in the presence of inhibitors of hydroxyapatite nucleation.

  8. Final Report: "Collaborative Project. Understanding the Chemical Processes That Affect Growth Rates of Freshly Nucleated Particles"

    SciTech Connect

    Smith, James N.; McMurry, Peter H.

    2015-11-12

    This final technical report describes our research activities that have, as the ultimate goal, the development of a model that explains growth rates of freshly nucleated particles. The research activities, which combine field observations with laboratory experiments, explore the relationship between concentrations of gas-phase species that contribute to growth and the rates at which those species are taken up. We also describe measurements of the chemical composition of freshly nucleated particles in a variety of locales, as well as properties (especially hygroscopicity) that influence their effects on climate. Our measurements include a self-organized, DOE-ARM funded project at the Southern Great Plains site, the New Particle Formation Study (NPFS), which took place during spring 2013. NPFS data are available to the research community on the ARM data archive, providing a unique suite observations of trace gas and aerosols that are associated with the formation and growth of atmospheric aerosol particles.

  9. Active sites in char gasification: Final technical report

    SciTech Connect

    Wojtowicz, M.; Lilly, W.D.; Perkins, M.T.; Hradil, G.; Calo, J.M.; Suuberg, E.M.

    1987-09-01

    Among the key variables in the design of gasifiers and combustors is the reactivity of the chars which must be gasified or combusted. Significant loss of unburned char is unacceptable in virtually any process; the provision of sufficient residence time for complete conversion is essential. A very wide range of reactivities are observed, depending upon the nature of the char in a process. The current work focuses on furthering the understanding of gasification reactivities of chars. It has been well established that the reactivity of char to gasification generally depends upon three principal factors: (1) the concentration of ''active sites'' in the char; (2) mass transfer within the char; and (3) the type and concentration of catalytic impurities in the char. The present study primarily addresses the first factor. The subject of this research is the origin, nature, and fate of active sites in chars derived from parent hydrocarbons with coal-like structure. The nature and number of the active sites and their reactivity towards oxygen are examined in ''model'' chars derived from phenol-formaldehyde type resins. How the active sites are lost by the process of thermal annealing during heat treatment of chars are studied, and actual rate for the annealing process is derived. Since intrinsic char reactivities are of primary interest in the present study, a fair amount of attention was given to the model char synthesis and handling so that the effect of catalytic impurities and oxygen-containing functional groups in the chemical structure of the material were minimized, if not completely eliminated. The project would not be considered complete without comparing characteristic features of synthetic chars with kinetic behavior exhibited by natural chars, including coal chars.

  10. On Capillary Rise and Nucleation

    ERIC Educational Resources Information Center

    Prasad, R.

    2008-01-01

    A comparison of capillary rise and nucleation is presented. It is shown that both phenomena result from a balance between two competing energy factors: a volume energy and a surface energy. Such a comparison may help to introduce nucleation with a topic familiar to the students, capillary rise. (Contains 1 table and 3 figures.)

  11. Nucleation of Crystals in Solution

    NASA Astrophysics Data System (ADS)

    Vekilov, Peter G.

    2010-07-01

    Solution crystallization is an essential part of processes in the chemical and pharmaceutical industries and a major step in physiological and pathological phenomena. Crystallization starts with nucleation and control of nucleation is crucial for the control of the number, size, perfection, polymorphism and other characteristics of the crystalline materials. Recently, there have been significant advances in the understanding of the mechanism of nucleation of crystals in solution. The most significant of these is the two-step mechanism of nucleation, according to which the crystalline nucleus appears inside pre-existing metastable clusters of size several hundred nanometers, which consist of dense liquid and are suspended in the solution. While initially proposed for protein crystals, the applicability of this mechanism has been demonstrated for small molecule organic materials, colloids, and biominerals. This mechanism helps to explain several long-standing puzzles of crystal nucleation in solution: nucleation rates which are many orders of magnitude lower than theoretical predictions, nucleation kinetic dependencies with steady or receding parts at increasing supersaturation, the role of heterogeneous substrates for polymorph selection, the significance of the dense protein liquid, and others. More importantly, this mechanism provides powerful tools for control of the nucleation process by varying the solution thermodynamic parameters so that the volume occupied by the dense liquid shrinks or expands.

  12. Surface nanobubbles nucleate microdroplets.

    PubMed

    Zhang, Xuehua; Lhuissier, Henri; Sun, Chao; Lohse, Detlef

    2014-04-11

    When a hydrophobic solid is in contact with water, surface nanobubbles often form at the interface. They have a lifetime many orders of magnitude longer than expected. Here, we show that they even withstand a temperature increase to temperatures close to the boiling point of bulk water; i.e., they do not nucleate larger bubbles ("superstability"). On the contrary, when the vapor-liquid contact line passes a nanobubble, a liquid film remains around it, which, after pinch-off, results in a microdroplet in which the nanobubbles continue to exist. Finally, the microdroplet evaporates and the nanobubble consequently bursts. Our results support that pinning plays a crucial role for nanobubble stability. PMID:24765973

  13. Brownian aggregation rate of colloid particles with several active sites

    SciTech Connect

    Nekrasov, Vyacheslav M.; Yurkin, Maxim A.; Chernyshev, Andrei V.; Polshchitsin, Alexey A.; Yakovleva, Galina E.; Maltsev, Valeri P.

    2014-08-14

    We theoretically analyze the aggregation kinetics of colloid particles with several active sites. Such particles (so-called “patchy particles”) are well known as chemically anisotropic reactants, but the corresponding rate constant of their aggregation has not yet been established in a convenient analytical form. Using kinematic approximation for the diffusion problem, we derived an analytical formula for the diffusion-controlled reaction rate constant between two colloid particles (or clusters) with several small active sites under the following assumptions: the relative translational motion is Brownian diffusion, and the isotropic stochastic reorientation of each particle is Markovian and arbitrarily correlated. This formula was shown to produce accurate results in comparison with more sophisticated approaches. Also, to account for the case of a low number of active sites per particle we used Monte Carlo stochastic algorithm based on Gillespie method. Simulations showed that such discrete model is required when this number is less than 10. Finally, we applied the developed approach to the simulation of immunoagglutination, assuming that the formed clusters have fractal structure.

  14. Active Sites Environmental Monitoring Program: FY 1991 report

    SciTech Connect

    Ashwood, T.L.; Hicks, D.S.; Morrissey, C.M.

    1992-11-01

    This report summarizes the activities of the Active Sites Environmental Monitoring Program (ASEMP) from April 1991 through September 1991. The ASEMP was established in 1989 by Solid Waste Operations (SWO) and the Environmental Sciences Division, both of Oak Ridge National Laboratory, to provide early detection and performance monitoring at active low-level (radioactive) waste (LLW) disposal sites in Solid Waste Storage Area (SWSA) 6 and transuranic (TRU) waste storage sites in SWSA 5 as required by chapters II and III of US Department of Energy Order 5820.2A. A new set of action levels was developed on the basis of a statistical analysis of background contamination. These new action levels have been used to evaluate results in this report. Results of ASEMP monitoring continue to demonstrate that no LLW (except [sup 3]H) is being leached from the storage vaults on the tumulus pads. Loading of vaults on Tumulus II, which began in early FY 1991, was >90% complete at the end of September 1991. Results of sampling of groundwater and surface waters is presented.

  15. Inhibition and active-site modelling of prolidase.

    PubMed

    King, G F; Crossley, M J; Kuchel, P W

    1989-03-15

    Consideration of the active-site model of prolidase led us to examine azetidine, pyrrolidine and piperidine substrate analogs as potential in vivo inhibitors of the enzyme. One of these, N-benzyloxycarbonyl-L-proline, was shown to be a potent competitive inhibitor of porcine kidney prolidase (Ki = 90 microM); its rapid protein-mediated permeation of human and sheep erythrocytes suggests that it may be effective in vivo. The higher homolog, N-benzyloxycarbonyl-L-pipecolic acid, was also a potent inhibitor of the enzyme while the antihypertensive drugs, captopril and enalaprilat, were shown to have mild and no inhibitory effects, respectively. Analysis of inhibitor action and consideration of X-ray crystallographic data of relevant Mn2+ complexes allowed the active-site model of prolidase to be further refined; a new model is presented in which the substrate acts as a bidentate ligand towards the active-site manganous ion. Various aspects of the new model help to explain why Mn2+ has been 'chosen' by the enzyme in preference to other biologically available metal ions. PMID:2924773

  16. Nucleation rate in monotectic alloys

    NASA Astrophysics Data System (ADS)

    Falk, F.

    Cooling a melt of a monotectic system into the miscibility gap results in nucleation of fluid droplets in a fluid matrix prior to solidification. For homogeneous nucleation the temperature dependence of the nucleation rate is calculated. As material parameters the chemical potential of the species involved, the diffusion constant of the fluid, and the surface tension between adjacent phases are important. Since their temperature dependence is not well known from experiments, different theoretical models are used and their influence is discussed. The surface tension turns out to be the most crucial parameter in determining the nucleation rate. For AlIn numerical results are presented. In this system the undercooling with respect to homogeneous nucleation increases from zero at the critical point to 100 K at a composition near the monotectic point.

  17. Characterization of Ice Nucleating Particles at the Western US Coast

    NASA Astrophysics Data System (ADS)

    Rocci, K.; McCluskey, C. S.; Hill, T. C. J.; DeMott, P. J.; Kreidenweis, S. M.

    2015-12-01

    In temperate climates, ice nucleating particles (INPs) are vital for precipitation initiation. Because INPs may affect precipitation efficiency, and thereby the supply of water resources, it is paramount to have a clear understanding of both natural and anthropogenic sources of INPs. This is especially important to understand in California where drought continues to be a major problem. The CalWater 2015 field campaign, which took place in California from January 15 - March 9, 2015, included comprehensive characterizations of aerosols and their ice nucleating ability via ground-, air-, and ship-based measurements. As part of this campaign, we characterized and analyzed the intra-air mass differences of INPs at a coastal site (Bodega Bay) using immersion freezing measurements of particles collected on filters. Aerosol filters collected throughout the campaign were characterized by their loading and dominant type using meteorology, aerosol size distributions, aerosol composition, and trace gas concentration data. Samples contained a variety of aerosol influences, including biomass burning, nitrogen pollution, sulfur pollution, and sea spray. This study had a particular focus on the INP activity spectra of sea spray aerosol (SSA). We used the online aerosol data to infer variations in SSA types and heat-treated specific samples to look for the presence of heat-labile biological INPs. Furthermore, we ran the NOAA HYSPLIT model to obtain back trajectories for samples dominated by SSA. We found that air masses dominated by distinct terrestrial source types are not well distinguished by their INP number concentrations. However, we did see significantly higher (up to 5000-fold) INP number concentrations in SSA samples taken at the coast compared with number concentrations in samples obtained over open ocean. This difference could be attributable to differences in overall aerosol abundance, which will be evaluated in future studies. Overall, our findings suggest that an

  18. Three separate classes of bacterial ice nucleation structures.

    PubMed Central

    Turner, M A; Arellano, F; Kozloff, L M

    1990-01-01

    Studies of the properties of the ice nucleation structure exposed on the surfaces of various bacteria such as Pseudomonas syringae, Erwinia herbicola, or various strains of Ice+ recombinant Escherichia coli have shown that there are clearly three major related but chemically distinct types of structures on these cells. First, the ability of Ice+ cells to nucleate super-cooled D2O has been examined, and it has been found that this ability (relative to the ability of the same cells to nucleate super-cooled H2O) exhibited three characteristic nucleating patterns. The rarest structure, called class A, is found on only a small fraction of cells in a culture, nucleates H2O at temperatures above -4.4 degrees C, and is an effective nucleator of super-cooled D2O. A second class of structure, called class B, is found on a larger portion of the cells, nucleates H2O between -4.8 and -5.7 degrees C, and is a relatively poor nucleator of super-cooled D2O. The class C structure is found on almost all cells and nucleates at -7.6 degrees C or colder. These three classes of structures were also differentiated by their sensitivities to low concentrations of water-miscible organic solvents such as dioxane or dimethyl sulfoxide. Depending on the specific bacterial strain, the addition of these solvents to bacterial suspensions lowered the nucleation activity of the class A structure by 1,000-fold or more. The nucleation activities of class B structures in the same culture were highly resistant to these compounds and were lowered only by 20 to 40%. The class C structures were more sensitive than Class B structures were, and the nucleation activities decreased 70 to 90%. Finally, the pH sensitivity of these three classes of structures was examined. The class A structure was destroyed in buffers at pH 4.5 lower but was stable in buffers at higher pHs. The class B structure was less sensitive to acidic buffers but was destroyed at pH 5.5 or lower and was stable at higher pHs. However, the

  19. Hotspots organize clathrin-mediated endocytosis by efficient recruitment and retention of nucleating resources

    PubMed Central

    Nunez, Daniel; Antonescu, Costin; Mettlen, Marcel; Liu, Allen; Schmid, Sandra L.; Loerke, Dinah; Danuser, Gaudenz

    2011-01-01

    The formation of clathrin-coated pits (CCPs) at the plasma membrane has been reported to sometimes occur repeatedly at predefined sites. However, defining such CCP `hotspots' structurally and mechanistically has been difficult due to the dynamic and heterogeneous nature of CCPs. Here we explore the molecular requirements for hotspots using a global assay of CCP dynamics. Our data confirmed that a subset of CCPs is nucleated at spatially distinct sites. The degree of clustering of nucleation events at these sites is dependent on the integrity of cortical actin, and the availability of certain resources, including the adaptor protein AP-2 and the phospholipid PI(4,5)P2. We observe that modulation in the expression of FCHo1 and 2, which have been reported to initiate CCPs, affect only the number of nucleations. Modulation in the expression levels of other accessory proteins, such as SNX9, affects the spatial clustering of CCPs but not the number of nucleations. Based on these findings we distinguish two classes of accessory proteins in clathrin-mediated endocytosis (CME): nucleation factors and nucleation organizers. Finally, we observe that clustering of transferrin receptors spatially randomizes pit nucleation and thus reduces the role of hotspots. Based on these data, we propose that hotspots are specialized cortical actin patches that organize CCP nucleations from within the cell by more efficient recruitment and/or retention of resources required for CCP nucleation partially due to the action of nucleation organizers. PMID:21883765

  20. The adsorption of fungal ice-nucleating proteins on mineral dusts: a terrestrial reservoir of atmospheric ice-nucleating particles

    NASA Astrophysics Data System (ADS)

    O'Sullivan, Daniel; Murray, Benjamin J.; Ross, James; Webb, Michael E.

    2016-04-01

    The occurrence of ice-nucleating particles (INPs) in our atmosphere has a profound impact on the properties and lifetime of supercooled clouds. However, the identities, sources and abundances of airborne particles capable of efficiently nucleating ice at relatively low supercoolings (T > -15 °C) remain enigmatic. Recently, several studies have suggested that unidentified biogenic residues in soil dusts are likely to be an important source of these efficient atmospheric INPs. While it has been shown that cell-free proteins produced by common soil-borne fungi are exceptional INPs, whether these fungi are a source of ice-nucleating biogenic residues in soils has yet to be shown. In particular, it is unclear whether upon adsorption to soil mineral particles, the activity of fungal ice-nucleating proteins is retained or is reduced, as observed for other soil enzymes. Here we show that proteins from a common soil fungus (Fusarium avenaceum) do in fact preferentially bind to and impart their ice-nucleating properties to the common clay mineral kaolinite. The ice-nucleating activity of the proteinaceous INPs is found to be unaffected by adsorption to the clay, and once bound the proteins do not readily desorb, retaining much of their activity even after multiple washings with pure water. The atmospheric implications of the finding that nanoscale fungal INPs can effectively determine the nucleating abilities of lofted soil dusts are discussed.

  1. Druggability analysis and classification of protein tyrosine phosphatase active sites

    PubMed Central

    Ghattas, Mohammad A; Raslan, Noor; Sadeq, Asil; Al Sorkhy, Mohammad; Atatreh, Noor

    2016-01-01

    Protein tyrosine phosphatases (PTP) play important roles in the pathogenesis of many diseases. The fact that no PTP inhibitors have reached the market so far has raised many questions about their druggability. In this study, the active sites of 17 PTPs were characterized and assessed for its ability to bind drug-like molecules. Consequently, PTPs were classified according to their druggability scores into four main categories. Only four members showed intermediate to very druggable pocket; interestingly, the rest of them exhibited poor druggability. Particularly focusing on PTP1B, we also demonstrated the influence of several factors on the druggability of PTP active site. For instance, the open conformation showed better druggability than the closed conformation, while the tight-bound water molecules appeared to have minimal effect on the PTP1B druggability. Finally, the allosteric site of PTP1B was found to exhibit superior druggability compared to the catalytic pocket. This analysis can prove useful in the discovery of new PTP inhibitors by assisting researchers in predicting hit rates from high throughput or virtual screening and saving unnecessary cost, time, and efforts via prioritizing PTP targets according to their predicted druggability. PMID:27757011

  2. Current activities handbook: formerly utilized sites remedial action program

    SciTech Connect

    1981-02-27

    This volume is one of a series produced under contract with the DOE, by Politech Corporation to develop a legislative and regulatory data base to assist the FUSRAP management in addressing the institutional and socioeconomic issues involved in carrying out the Formerly Utilized Sites Remedial Action Program. This Information Handbook series contains information about all relevant government agencies at the Federal and state levels, the pertinent programs they administer, each affected state legislature, and current Federal and state legislative and regulatory initiatives. This volume is a compilation of information about the activities each of the thirteen state legislatures potentially affected by the Formerly Utilized Sites Remedial Action Program. It contains a description of the state legislative procedural rules and a schedule of each legislative session; a summary of pending relevant legislation; the name and telephone number of legislative and state agency contacts; and the full text of all bills identified.

  3. Climate Impacts of Ice Nucleation

    NASA Technical Reports Server (NTRS)

    Gettelman, Andrew; Liu, Xiaohong; Barahona, Donifan; Lohmann, Ulrike; Chen, Celia

    2012-01-01

    Several different ice nucleation parameterizations in two different General Circulation Models (GCMs) are used to understand the effects of ice nucleation on the mean climate state, and the Aerosol Indirect Effects (AIE) of cirrus clouds on climate. Simulations have a range of ice microphysical states that are consistent with the spread of observations, but many simulations have higher present-day ice crystal number concentrations than in-situ observations. These different states result from different parameterizations of ice cloud nucleation processes, and feature different balances of homogeneous and heterogeneous nucleation. Black carbon aerosols have a small (0.06 Wm(exp-2) and not statistically significant AIE when included as ice nuclei, for nucleation efficiencies within the range of laboratory measurements. Indirect effects of anthropogenic aerosols on cirrus clouds occur as a consequence of increasing anthropogenic sulfur emissions with different mechanisms important in different models. In one model this is due to increases in homogeneous nucleation fraction, and in the other due to increases in heterogeneous nucleation with coated dust. The magnitude of the effect is the same however. The resulting ice AIE does not seem strongly dependent on the balance between homogeneous and heterogeneous ice nucleation. Regional effects can reach several Wm2. Indirect effects are slightly larger for those states with less homogeneous nucleation and lower ice number concentration in the base state. The total ice AIE is estimated at 0.27 +/- 0.10 Wm(exp-2) (1 sigma uncertainty). This represents a 20% offset of the simulated total shortwave AIE for ice and liquid clouds of 1.6 Wm(sup-2).

  4. Climate Impacts of Ice Nucleation

    SciTech Connect

    Gettelman, A.; Liu, Xiaohong; Barahona, Donifan; Lohmann, U.; Chen, Chih-Chieh

    2012-10-19

    [1] Several different ice nucleation parameterizations in two different General Circulation Models (GCMs) are used to understand the effects of ice nucleation on the mean climate state, and the Aerosol Indirect Effects (AIE) of cirrus clouds on climate. Simulations have a range of ice microphysical states that are consistent with the spread of observations, but many simulations have higher present-day ice crystal number concentrations than in-situ observations. These different states result from different parameterizations of ice cloud nucleation processes, and feature different balances of homogeneous and heterogeneous nucleation. Black carbon aerosols have a small (-0.06 Wm-2) and not statistically significant AIE when included as ice nuclei, for nucleation efficiencies within the range of laboratory measurements. Indirect effects of anthropogenic aerosols on cirrus clouds occur as a consequence of increasing anthropogenic sulfur emissions with different mechanisms important in different models. In one model this is due to increases in homogeneous nucleation fraction, and in the other due to increases in heterogeneous nucleation with coated dust. The magnitude of the effect is the same however. The resulting ice AIE does not seem strongly dependent on the balance between homogeneous and heterogeneous ice nucleation. Regional effects can reach several Wm-2. Indirect effects are slightly larger for those states with less homogeneous nucleation and lower ice number concentration in the base state. The total ice AIE is estimated at 0.27 ± 0.10 Wm-2 (1σ uncertainty). Finally, this represents a 20% offset of the simulated total shortwave AIE for ice and liquid clouds of -1.6 Wm-2.

  5. Entropic effect on the rate of dislocation nucleation.

    PubMed

    Ryu, Seunghwa; Kang, Keonwook; Cai, Wei

    2011-03-29

    Dislocation nucleation is essential to our understanding of plastic deformation, ductility, and mechanical strength of crystalline materials. Molecular dynamics simulation has played an important role in uncovering the fundamental mechanisms of dislocation nucleation, but its limited timescale remains a significant challenge for studying nucleation at experimentally relevant conditions. Here we show that dislocation nucleation rates can be accurately predicted over a wide range of conditions by determining the activation free energy from umbrella sampling. Our data reveal very large activation entropies, which contribute a multiplicative factor of many orders of magnitude to the nucleation rate. The activation entropy at constant strain is caused by thermal expansion, with negligible contribution from the vibrational entropy. The activation entropy at constant stress is significantly larger than that at constant strain, as a result of thermal softening. The large activation entropies are caused by anharmonic effects, showing the limitations of the harmonic approximation widely used for rate estimation in solids. Similar behaviors are expected to occur in other nucleation processes in solids. PMID:21402933

  6. Ice nucleation efficiency of natural dust samples in the immersion mode

    NASA Astrophysics Data System (ADS)

    Kaufmann, Lukas; Marcolli, Claudia; Hofer, Julian; Pinti, Valeria; Hoyle, Christopher R.; Peter, Thomas

    2016-09-01

    A total of 12 natural surface dust samples, which were surface-collected on four continents, most of them in dust source regions, were investigated with respect to their ice nucleation activity. Dust collection sites were distributed across Africa, South America, the Middle East, and Antarctica. Mineralogical composition has been determined by means of X-ray diffraction. All samples proved to be mixtures of minerals, with major contributions from quartz, calcite, clay minerals, K-feldspars, and (Na, Ca)-feldspars. Reference samples of these minerals were investigated with the same methods as the natural dust samples. Furthermore, Arizona test dust (ATD) was re-evaluated as a benchmark. Immersion freezing of emulsion and bulk samples was investigated by differential scanning calorimetry. For emulsion measurements, water droplets with a size distribution peaking at about 2 µm, containing different amounts of dust between 0.5 and 50 wt % were cooled until all droplets were frozen. These measurements characterize the average freezing behaviour of particles, as they are sensitive to the average active sites present in a dust sample. In addition, bulk measurements were conducted with one single 2 mg droplet consisting of a 5 wt % aqueous suspension of the dusts/minerals. These measurements allow the investigation of the best ice-nucleating particles/sites available in a dust sample. All natural dusts, except for the Antarctica and ATD samples, froze in a remarkably narrow temperature range with the heterogeneously frozen fraction reaching 10 % between 244 and 250 K, 25 % between 242 and 246 K, and 50 % between 239 and 244 K. Bulk freezing occurred between 255 and 265 K. In contrast to the natural dusts, the reference minerals revealed ice nucleation temperatures with 2-3 times larger scatter. Calcite, dolomite, dolostone, and muscovite can be considered ice nucleation inactive. For microcline samples, a 50 % heterogeneously frozen fraction occurred above 245 K for all

  7. Electrostatic fields in the active sites of lysozymes.

    PubMed

    Sun, D P; Liao, D I; Remington, S J

    1989-07-01

    Considerable experimental evidence is in support of several aspects of the mechanism that has been proposed for the catalytic activity of lysozyme. However, the enzymatically catalyzed hydrolysis of polysaccharides proceeds over 5 orders of magnitude faster than that of model compounds that mimic the configuration of the substrate in the active site of the enzyme. Although several possible explanations for this rate enhancement have been discussed elsewhere, a definitive mechanism has not emerged. Here we report striking results obtained by classical electrodynamics, which suggest that bond breakage and the consequent separation of charge in lysozyme is promoted by a large electrostatic field across the active site cleft, produced in part by a very asymmetric distribution of charged residues on the enzyme surface. Lysozymes unrelated in amino acid sequence have similar distributions of charged residues and electric fields. The results reported here suggest that the electrostatic component of the rate enhancement is greater than 9 kcal.mol-1. Thus, electrostatic interactions may play a more important role in the enzymatic mechanism than has generally been appreciated.

  8. Histidine at the active site of Neurospora tyrosinase.

    PubMed

    Pfiffner, E; Lerch, K

    1981-10-13

    The involvement of histidyl residues as potential ligands to the binuclear active-site copper of Neurospora tyrosinase was explored by dye-sensitized photooxidation. The enzymatic activity of the holoenzyme was shown to be unaffected by exposure to light in the presence of methylene blue; however, irradiation of the apoenzyme under the same conditions led to a progressive loss of its ability to be reactivated with Cu2+. This photoinactivation was paralleled by a decrease in the histidine content whereas the number of histidyl residues in the holoenzyme remained constant. Copper measurements of photooxidized, reconstituted apoenzyme demonstrated the loss of binding of one copper atom per mole of enzyme as a consequence of photosensitized oxidation of three out of nine histidine residues. Their sequence positions were determined by a comparison of the relative yields of the histidine containing peptides of photooxidized holo- and apotyrosinases. The data obtained show the preferential modification of histidyl residues 188, 193, and 289 and suggest that they constitute metal ligands to one of the two active-site copper atoms. Substitution of copper by cobalt was found to afford complete protection of the histidyl residues from being modified by dye-sensitized photooxidation. PMID:6458322

  9. Twin nucleation and migration in FeCr single crystals

    SciTech Connect

    Patriarca, L.; Abuzaid, Wael; Sehitoglu, Huseyin; Maier, Hans J.; Chumlyakov, Y.

    2013-01-15

    Tension and compression experiments were conducted on body-centered cubic Fe -47.8 at pct. Cr single crystals. The critical resolved shear stress (CRSS) magnitudes for slip nucleation, twin nucleation and twin migration were established. We show that the nucleation of slip occurs at a CRSS of about 88 MPa, while twinning nucleates at a CRSS of about 191 MPa with an associated load drop. Following twin nucleation, twin migration proceeds at a CRSS that is lower than the initiation stress ( Almost-Equal-To 114-153 MPa). The experimental results of the nucleation stresses indicate that the Schmid law holds to a first approximation for the slip and twin nucleation cases, but to a lesser extent for twin migration particularly when considerable slip strains preceded twinning. The CRSSs were determined experimentally using digital image correlation (DIC) in conjunction with electron back scattering diffraction (EBSD). The DIC measurements enabled pinpointing the precise stress on the stress-strain curves where twins or slip were activated. The crystal orientations were obtained using EBSD and used to determine the activated twin and slip systems through trace analysis. - Highlights: Black-Right-Pointing-Pointer Digital image correlation allows to capture slip/twin initiation for bcc FeCr. Black-Right-Pointing-Pointer Crystal orientations from EBSD allow slip/twin system indexing. Black-Right-Pointing-Pointer Nucleation of slip always precedes twinning. Black-Right-Pointing-Pointer Twin growth is sustained with a lower stress than required for nucleation. Black-Right-Pointing-Pointer Twin-slip interactions provide high hardening at the onset of plasticity.

  10. A fractal study for nucleate pool boiling heat transfer of nanofluids

    NASA Astrophysics Data System (ADS)

    Xiao, Boqi; Jiang, Guoping; Chen, Lingxia

    2010-01-01

    In this paper, a fractal model for nucleate pool boiling heat transfer of nanofluids is developed based on the fractal distribution of nanoparticles and nucleation sites on boiling surfaces. The model shows the dependences of the heat flux on nanoparticle size and the nanoparticle volume fraction of the suspension, the fractal dimension of the nanoparticle and nucleation site, temperature of nanofluids and properties of fluids. The fractal model predictions show that the natural convection stage continues relatively longer in the case of nanofluids. The addition of nanoparticles causes a decrease of the pool nucleate boiling heat transfer. The nucleate pool boiling heat transfer coefficient is decreased by increasing particle concentration. An excellent agreement between the proposed model predictions and experimental data is found. The validity of the fractal model for nucleate pool boiling heat transfer is thus verified.

  11. Dew nucleation and growth

    NASA Astrophysics Data System (ADS)

    Beysens, Daniel

    2006-11-01

    Dew is the condensation of water vapor into liquid droplets on a substrate. It is characterized by an initial heterogeneous nucleation on a substrate and a further growth of droplets. The presence of a substrate that geometrically constrains the growth is the origin of the peculiarities and richness of the phenomenon. A key point is the drop interaction through drop fusion or coalescence, which leads to scaling in the growth and gives universality to the process. As a matter of fact, growth dynamics are only dependent on substrate and drop dimensionality. Coalescence events lead to temporal and spatio-temporal fluctuations in the substrate coverage, drop configuration, etc., which give rise to a very peculiar dynamics. When the substrate is a liquid or a liquid crystal, the drop pattern can exhibit special spatial order, such as crystalline, hexatic phases and fractal contours. Condensation on a solid substrate near its melting point can make the drop jump. The applications of monitoring dew formation are manifold. Examples can be found in medicine (sterilization process), agriculture (green houses) and hydrology (production of drinkable water). To cite this article: D. Beysens, C. R. Physique 7 (2006).

  12. Nucleation and structural growth of cluster crystals

    NASA Astrophysics Data System (ADS)

    Leitold, Christian; Dellago, Christoph

    2016-08-01

    We study the nucleation of crystalline cluster phases in the generalized exponential model with exponent n = 4. Due to the finite value of this pair potential for zero separation, at high densities the system forms cluster crystals with multiply occupied lattice sites. Here, we investigate the microscopic mechanisms that lead to the formation of cluster crystals from a supercooled liquid in the low-temperature region of the phase diagram. Using molecular dynamics and umbrella sampling, we calculate the free energy as a function of the size of the largest crystalline nucleus in the system, and compare our results with predictions from classical nucleation theory. Employing bond-order parameters based on a Voronoi tessellation to distinguish different crystal structures, we analyze the average composition of crystalline nuclei. We find that even for conditions where a multiply occupied fcc crystal is the thermodynamically stable phase, the nucleation into bcc cluster crystals is strongly preferred. Furthermore, we study the particle mobility in the supercooled liquid and in the cluster crystal. In the cluster crystal, the motion of individual particles is captured by a simple reaction-diffusion model introduced previously to model the kinetics of hydrogen bonds.

  13. Nucleation and structural growth of cluster crystals.

    PubMed

    Leitold, Christian; Dellago, Christoph

    2016-08-21

    We study the nucleation of crystalline cluster phases in the generalized exponential model with exponent n = 4. Due to the finite value of this pair potential for zero separation, at high densities the system forms cluster crystals with multiply occupied lattice sites. Here, we investigate the microscopic mechanisms that lead to the formation of cluster crystals from a supercooled liquid in the low-temperature region of the phase diagram. Using molecular dynamics and umbrella sampling, we calculate the free energy as a function of the size of the largest crystalline nucleus in the system, and compare our results with predictions from classical nucleation theory. Employing bond-order parameters based on a Voronoi tessellation to distinguish different crystal structures, we analyze the average composition of crystalline nuclei. We find that even for conditions where a multiply occupied fcc crystal is the thermodynamically stable phase, the nucleation into bcc cluster crystals is strongly preferred. Furthermore, we study the particle mobility in the supercooled liquid and in the cluster crystal. In the cluster crystal, the motion of individual particles is captured by a simple reaction-diffusion model introduced previously to model the kinetics of hydrogen bonds. PMID:27544116

  14. Trichodiene synthase. Identification of active site residues by site-directed mutagenesis.

    PubMed

    Cane, D E; Shim, J H; Xue, Q; Fitzsimons, B C; Hohn, T M

    1995-02-28

    Derivatization of 5,5'-dithiobis(2-nitrobenzoic acid)-treated trichodiene synthase with [methyl-14C]methyl methanethiosulfonate and analysis of the derived tryptic peptides suggested the presence of two cysteine residues at the active site. The corresponding C146A and C190A mutants were constructed by site-directed mutagenesis. The C190A mutant displayed partial but significantly reduced activity, with a reduction in kcat/Km of 3000 compared to the wild-type trichodiene synthase, while the C146A mutant was essentially inactive. A hybrid trichodiene synthase, constructed from amino acids 1-309 of the Fusarium sporotrichioides enzyme and amino acids 310-383 of the Gibberella pulicaris cyclase, had steady state kinetic parameters nearly identical to those of the wild-type F. sporotrichioides enzyme. From this parent hybrid, a series of mutants was constructed by site-directed mutagenesis in which the amino acids in the base-rich region, 302-306 (DRRYR), were systematically modified. Three of these mutants were overexpressed and purified to homogeneity. The importance of Arg304 for catalysis was established by the observation that the R304K mutant showed a more than 25-fold increase in Km, as well as a 200-fold reduction in kcat. In addition, analysis of the incubation products of the R304K mutant by gas chromatography-mass spectrometry (GC-MS) indicated that farnesyl diphosphate was converted not only to trichodiene but to at least two additional C15H24 hydrocarbons, mle 204. Replacement of the Tyr305 residue of trichodiene synthase with Phe had little effect on kcat, while increasing the Km by a factor of ca. 7-8.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7873527

  15. Measuring surface dislocation nucleation in defect-scarce nanostructures.

    PubMed

    Chen, Lisa Y; He, Mo-rigen; Shin, Jungho; Richter, Gunther; Gianola, Daniel S

    2015-07-01

    Linear defects in crystalline materials, known as dislocations, are central to the understanding of plastic deformation and mechanical strength, as well as control of performance in a variety of electronic and photonic materials. Despite nearly a century of research on dislocation structure and interactions, measurements of the energetics and kinetics of dislocation nucleation have not been possible, as synthesizing and testing pristine crystals absent of defects has been prohibitively challenging. Here, we report experiments that directly measure the surface dislocation nucleation strengths in high-quality 〈110〉 Pd nanowhiskers subjected to uniaxial tension. We find that, whereas nucleation strengths are weakly size- and strain-rate-dependent, a strong temperature dependence is uncovered, corroborating predictions that nucleation is assisted by thermal fluctuations. We measure atomic-scale activation volumes, which explain both the ultrahigh athermal strength as well as the temperature-dependent scatter, evident in our experiments and well captured by a thermal activation model. PMID:25985457

  16. Laboratory Studies of Ice Nucleation on Volcanic Ash

    NASA Astrophysics Data System (ADS)

    Tolbert, M. A.; Schill, G. P.; Genareau, K. D.

    2014-12-01

    Ice nucleation on volcanic ash controls both ash aggregation and cloud glaciation, which affect human respiratory health, atmospheric transport, and global climate. We have performed laboratory studies of the depositional and immersion freezing efficiency of three distinct samples of volcanic ash using Raman Microscopy coupled to an environmental cell. Ash from the Fuego (Basaltic Ash, Guatemala), Soufriere Hills (Andesetic Ash, Montserrat), and Taupo (Rhyolitic Ash, New Zealand) volcanoes were chosen to represent different geographical locations and silica content. All ash samples were quantitatively analyzed for both percent crystallinity and mineralogy using X-ray diffraction. We find that all three samples of volcanic ash are excellent depositional ice nuclei, nucleating ice at ice saturation ratios of 1.05 ± 0.1. For immersion freezing, however, only the Taupo ash exhibited efficient heterogeneous ice nucleation activity. Similar to recent studies on mineral dust, we suggest that the mineralogy of volcanic ash may dictate its ice nucleation activity in the immersion mode.

  17. SUCCESS Evidence for Cirrus Cloud Ice Nucleation Mechanisms

    NASA Technical Reports Server (NTRS)

    Jensen, Eric; Gore, Warren J. Y. (Technical Monitor)

    1997-01-01

    During the SUCCESS mission, several measurements were made which should improve our understanding of ice nucleation processes in cirrus clouds. Temperature and water vapor concentration were made with a variety of instruments on the NASA DC-8. These observations should provide accurate upper tropospheric humidities. In particular, we will evaluate what humidities are required for ice nucleation. Preliminary results suggest that substantial supersaturations frequently exist in the upper troposphere. The leading-edge region of wave-clouds (where ice nucleation occurs) was sampled extensively at temperatures near -40 and -60C. These observations should give precise information about conditions required for ice nucleation. In addition, we will relate the observed aerosol composition and size distributions to the ice formation observed to evaluate the role of soot or mineral particles on ice nucleation. As an alternative technique for determining what particles act as ice nuclei, numerous samples of aerosols inside ice crystals were taken. In some cases, large numbers of aerosols were detected in each crystal, indicating that efficient scavenging occurred. Analysis of aerosols in ice crystals when only one particle per crystal was detected should help with the ice nucleation issue. Direct measurements of the ice nucleating activity of ambient aerosols drawn into airborne cloud chambers were also made. Finally, measurements of aerosols and ice crystals in contrails should indicate whether aircraft exhaust soot particles are effective ice nuclei.

  18. The nucleation kinetics of ammonium metavanadate precipitated by ammonium chloride

    NASA Astrophysics Data System (ADS)

    Du, Guangchao; Sun, Zhaohui; Xian, Yong; Jing, Han; Chen, Haijun; Yin, Danfeng

    2016-05-01

    The nucleation kinetics of ammonium metavanadate (NH4VO3) was investigated under conditions of the simulated process for precipitation of NH4VO3 from the vanadium-containing solution. Induction periods for the nucleation of NH4VO3 were experimentally determined as a function of supersaturation at temperatures from 30 to 45 °C. Using the classical nucleation theory, the interfacial tension between NH4VO3 and supersaturated solution, the nucleation rate and critical radius of nucleus for the homogeneous nucleation of NH4VO3 were estimated. With temperature increasing, the calculated interfacial tension gradually decreased from 29.78 mJ/m2 at 30 °C to 23.66 mJ/m2 at 45 °C. The nucleation rate was found to proportionally increase but the critical radius of nucleus exponentially decreased, with increase in supersaturation ratio at a constant temperature. The activation energy for NH4VO3 nucleation was obtained from the relationship between temperature and induction period, ranging from 79.17 kJ/mol at S=25 to 115.50 kJ/mol at S=15. FT-IR and Raman spectrum indicated that the crystals obtained in the precipitation process were NH4VO3.

  19. The copper active site of CBM33 polysaccharide oxygenases.

    PubMed

    Hemsworth, Glyn R; Taylor, Edward J; Kim, Robbert Q; Gregory, Rebecca C; Lewis, Sally J; Turkenburg, Johan P; Parkin, Alison; Davies, Gideon J; Walton, Paul H

    2013-04-24

    The capacity of metal-dependent fungal and bacterial polysaccharide oxygenases, termed GH61 and CBM33, respectively, to potentiate the enzymatic degradation of cellulose opens new possibilities for the conversion of recalcitrant biomass to biofuels. GH61s have already been shown to be unique metalloenzymes containing an active site with a mononuclear copper ion coordinated by two histidines, one of which is an unusual τ-N-methylated N-terminal histidine. We now report the structural and spectroscopic characterization of the corresponding copper CBM33 enzymes. CBM33 binds copper with high affinity at a mononuclear site, significantly stabilizing the enzyme. X-band EPR spectroscopy of Cu(II)-CBM33 shows a mononuclear type 2 copper site with the copper ion in a distorted axial coordination sphere, into which azide will coordinate as evidenced by the concomitant formation of a new absorption band in the UV/vis spectrum at 390 nm. The enzyme's three-dimensional structure contains copper, which has been photoreduced to Cu(I) by the incident X-rays, confirmed by X-ray absorption/fluorescence studies of both aqueous solution and intact crystals of Cu-CBM33. The single copper(I) ion is ligated in a T-shaped configuration by three nitrogen atoms from two histidine side chains and the amino terminus, similar to the endogenous copper coordination geometry found in fungal GH61. PMID:23540833

  20. Activation of muscarinic acetylcholine receptors via their allosteric binding sites.

    PubMed Central

    Jakubík, J; Bacáková, L; Lisá, V; el-Fakahany, E E; Tucek, S

    1996-01-01

    Ligands that bind to the allosteric-binding sites on muscarinic acetylcholine receptors alter the conformation of the classical-binding sites of these receptors and either diminish or increase their affinity for muscarinic agonists and classical antagonists. It is not known whether the resulting conformational change also affects the interaction between the receptors and the G proteins. We have now found that the muscarinic receptor allosteric modulators alcuronium, gallamine, and strychnine (acting in the absence of an agonist) alter the synthesis of cAMP in Chinese hamster ovary (CHO) cells expressing the M2 or the M4 subtype of muscarinic receptors in the same direction as the agonist carbachol. In addition, most of their effects on the production of inositol phosphates in CHO cells expressing the M1 or the M3 muscarinic receptor subtypes are also similar to (although much weaker than) those of carbachol. The agonist-like effects of the allosteric modulators are not observed in CHO cells that have not been transfected with the gene for any of the subtypes of muscarinic receptors. The effects of alcuronium on the formation of cAMP and inositol phosphates are not prevented by the classical muscarinic antagonist quinuclidinyl benzilate. These observations demonstrate for the first time that the G protein-mediated functional responses of muscarinic receptors can be evoked not only from their classical, but also from their allosteric, binding sites. This represents a new mechanism of receptor activation. PMID:8710935

  1. Radiation inactivation study of aminopeptidase: probing the active site

    NASA Astrophysics Data System (ADS)

    Jamadar, V. K.; Jamdar, S. N.; Mohan, Hari; Dandekar, S. P.; Harikumar, P.

    2004-04-01

    Ionizing radiation inactivated purified chicken intestinal aminopeptidase in media saturated with gases in the order N 2O>N 2>air. The D 37 values in the above conditions were 281, 210 and 198 Gy, respectively. OH radical scavengers such as t-butanol and isopropanol effectively nullified the radiation-induced damage in N 2O. The radicals (SCN) 2•-, Br 2•- and I 2•- inactivated the enzyme, pointing to the involvement of aromatic amino acids and cysteine in its catalytic activity. The enzyme exhibited fluorescence emission at 340 nm which is characteristic of tryptophan. The radiation-induced loss of activity was accompanied by a decrease in the fluorescence of the enzyme suggesting a predominant influence on tryptophan residues. The enzyme inhibition was associated with a marked increase in the Km and a decrease in the Vmax and kcat values, suggesting an irreversible alteration in the catalytic site. The above observations were confirmed by pulse radiolysis studies.

  2. Mimicking enzymatic active sites on surfaces for energy conversion chemistry.

    PubMed

    Gutzler, Rico; Stepanow, Sebastian; Grumelli, Doris; Lingenfelder, Magalí; Kern, Klaus

    2015-07-21

    Metal-organic supramolecular chemistry on surfaces has matured to a point where its underlying growth mechanisms are well understood and structures of defined coordination environments of metal atoms can be synthesized in a controlled and reproducible procedure. With surface-confined molecular self-assembly, scientists have a tool box at hand which can be used to prepare structures with desired properties, as for example a defined oxidation number and spin state of the transition metal atoms within the organic matrix. From a structural point of view, these coordination sites in the supramolecular structure resemble the catalytically active sites of metallo-enzymes, both characterized by metal centers coordinated to organic ligands. Several chemical reactions take place at these embedded metal ions in enzymes and the question arises whether these reactions also take place using metal-organic networks as catalysts. Mimicking the active site of metal atoms and organic ligands of enzymes in artificial systems is the key to understanding the selectivity and efficiency of enzymatic reactions. Their catalytic activity depends on various parameters including the charge and spin configuration in the metal ion, but also on the organic environment, which can stabilize intermediate reaction products, inhibits catalytic deactivation, and serves mostly as a transport channel for the reactants and products and therefore ensures the selectivity of the enzyme. Charge and spin on the transition metal in enzymes depend on the one hand on the specific metal element, and on the other hand on its organic coordination environment. These two parameters can carefully be adjusted in surface confined metal-organic networks, which can be synthesized by virtue of combinatorial mixing of building synthons. Different organic ligands with varying functional groups can be combined with several transition metals and spontaneously assemble into ordered networks. The catalytically active metal

  3. Polarizability of the active site of cytochrome c reduces the activation barrier for electron transfer

    NASA Astrophysics Data System (ADS)

    Dinpajooh, Mohammadhasan; Martin, Daniel R.; Matyushov, Dmitry V.

    2016-06-01

    Enzymes in biology’s energy chains operate with low energy input distributed through multiple electron transfer steps between protein active sites. The general challenge of biological design is how to lower the activation barrier without sacrificing a large negative reaction free energy. We show that this goal is achieved through a large polarizability of the active site. It is polarized by allowing a large number of excited states, which are populated quantum mechanically by electrostatic fluctuations of the protein and hydration water shells. This perspective is achieved by extensive mixed quantum mechanical/molecular dynamics simulations of the half reaction of reduction of cytochrome c. The barrier for electron transfer is consistently lowered by increasing the number of excited states included in the Hamiltonian of the active site diagonalized along the classical trajectory. We suggest that molecular polarizability, in addition to much studied electrostatics of permanent charges, is a key parameter to consider in order to understand how enzymes work.

  4. Polarizability of the active site of cytochrome c reduces the activation barrier for electron transfer

    PubMed Central

    Dinpajooh, Mohammadhasan; Martin, Daniel R.; Matyushov, Dmitry V.

    2016-01-01

    Enzymes in biology’s energy chains operate with low energy input distributed through multiple electron transfer steps between protein active sites. The general challenge of biological design is how to lower the activation barrier without sacrificing a large negative reaction free energy. We show that this goal is achieved through a large polarizability of the active site. It is polarized by allowing a large number of excited states, which are populated quantum mechanically by electrostatic fluctuations of the protein and hydration water shells. This perspective is achieved by extensive mixed quantum mechanical/molecular dynamics simulations of the half reaction of reduction of cytochrome c. The barrier for electron transfer is consistently lowered by increasing the number of excited states included in the Hamiltonian of the active site diagonalized along the classical trajectory. We suggest that molecular polarizability, in addition to much studied electrostatics of permanent charges, is a key parameter to consider in order to understand how enzymes work. PMID:27306204

  5. Spectroscopic Definition of the Ferroxidase Site in M Ferritin: Comparison of Binuclear Substrate vs. Cofactor Active Sites

    PubMed Central

    Schwartz, Jennifer K.; Liu, Xiaofeng S.; Tosha, Takehiko; Theil, Elizabeth C.; Solomon, Edward I.

    2008-01-01

    Maxi ferritins, 24 subunit protein nanocages, are essential in humans, plants, bacteria, and other animals for the concentration and storage of iron as hydrated ferric oxide, while minimizing free radical generation or use by pathogens. Formation of the precursors to these ferric oxides is catalyzed at a non-heme biferrous substrate site, which has some parallels with the cofactor sites in other biferrous enzymes. A combination of circular dichroism (CD), magnetic circular dichroism (MCD), and variable-temperature, variable-field MCD (VTVH MCD) has been used to probe Fe(II) binding to the substrate active site in frog M ferritin. These data determined that the active site within each subunit consists of two inequivalent five-coordinate (5C) ferrous centers that are weakly anti-ferromagnetically coupled, consistent with a μ-1,3 carboxylate bridge. The active site ligand set is unusual and likely includes a terminal water bound to each Fe(II) center. The Fe(II) ions bind to the active sites in a concerted manner, and cooperativity among the sites in each subunit is observed, potentially providing a mechanism for the control of ferritin iron loading. Differences in geometric and electronic structure – including a weak ligand field, availability of two water ligands at the biferrous substrate site, and the single carboxylate bridge in ferritin – coincide with the divergent reaction pathways observed between this substrate site and the previously studied cofactor active sites. PMID:18576633

  6. Nucleation process of an M2 earthquake in a deep gold mine in South Africa inferred from on-fault foreshock activity

    NASA Astrophysics Data System (ADS)

    Yabe, Yasuo; Nakatani, Masao; Naoi, Makoto; Philipp, Joachim; Janssen, Christoph; Watanabe, Takayoshi; Katsura, Taishi; Kawakata, Hironori; Georg, Dresen; Ogasawara, Hiroshi

    2015-08-01

    Using a network of sensitive high-frequency acoustic emission sensors, we observed foreshock activity of an Mw 2.2 earthquake (main shock) in a deep gold mine in South Africa. Foreshock activity, which selectively occurred on a part of the rupture plane of the forthcoming main shock, lasted for at least 6 months until the main shock. Rock samples recovered from the main shock source region showed evidence of ancient hydrothermal alteration on the main shock rupture plane, suggesting that the foreshock activity occurred on a preexisting weakness. The foreshocks during 3 months before the main shock were concentrated in three clusters (F1-F3), which we interpret as representing localized preslip at multiple sites. While the location of mining area, the source of stress perturbations, changed with time, the locations of foreshock clusters did not change, suggesting that the preslip patches were controlled by strength heterogeneity rather than stress distribution. Activity over the entire foreshock area was generally constant, but the largest cluster (F2) showed accelerated activity starting at least 7 days before the main shock, while mining stress did not increase in this period. The main shock initiated at a point close to F1, away from F2. All the six foreshocks during the final 41 h occurred in F1 and F2 and in-between. These suggest that in the last stage of the preparation process of the main shock, preslip patches interacted with each other through the stress concentration ahead of the expanding preslip patch (F2), which should be the only driving force of the preparation process under the constant external load.

  7. An active-site lysine in avian liver phosphoenolpyruvate carboxykinase

    SciTech Connect

    Guidinger, P.F.; Nowak, T. )

    1991-09-10

    The participation of lysine in the catalysis by avian liver phosphoenolpyruvate carboxykinase was studied by chemical modification and by a characterization of the modified enzyme. The rate of inactivation by 2,4-pentanedione is pseudo-first-order and linearly dependent on reagent concentration with a second-order rate constant of 0.36 {plus minus} 0.025 M{sup {minus}1} min{sup {minus}1}. Inactivation by pyridoxal 5{prime}-phosphate of the reversible reaction catalyzed by phosphoenolpyruvate carboxykinase follows bimolecular kinetics with a second-order rate constant of 7,700 {plus minus} 860 m{sup {minus}1} min{sup {minus}1}. Treatment of the enzyme or one lysine residue modified concomitant with 100% loss in activity. A stoichiometry of 1:1 is observed when either the reversible or the irreversible reactions catalyzed by the enzyme are monitored. A study of k{sub obs} vs pH suggests this active-site lysine has a pK{sub a} of 8.1 and a pH-independent rate constant of inactivation of 47,700 m{sup {minus}1} min{sup {minus}1}. Proton relaxation rate measurements suggest that pyridoxal 5{prime}-phosphate modification alters binding of the phosphate-containing substrates. {sup 31}P NMR relaxation rate measurements show altered binding of the substrates in the ternary enzyme {center dot}Mn{sup 2+}{center dot}substrate complex. Circular dichroism studies show little change in secondary structure of pyridoxal 5{prime}-phosphate modified phosphoenolpyruvate carboxykinase. These results indicate that avian liver phosphoenolpyruvate carboxykinase has one reactive lysine at the active site and it is involved in the binding and activation of the phosphate-containing substrates.

  8. Perchlorate Reductase Is Distinguished by Active Site Aromatic Gate Residues.

    PubMed

    Youngblut, Matthew D; Tsai, Chi-Lin; Clark, Iain C; Carlson, Hans K; Maglaqui, Adrian P; Gau-Pan, Phonchien S; Redford, Steven A; Wong, Alan; Tainer, John A; Coates, John D

    2016-04-22

    Perchlorate is an important ion on both Earth and Mars. Perchlorate reductase (PcrAB), a specialized member of the dimethylsulfoxide reductase superfamily, catalyzes the first step of microbial perchlorate respiration, but little is known about the biochemistry, specificity, structure, and mechanism of PcrAB. Here we characterize the biophysics and phylogeny of this enzyme and report the 1.86-Å resolution PcrAB complex crystal structure. Biochemical analysis revealed a relatively high perchlorate affinity (Km = 6 μm) and a characteristic substrate inhibition compared with the highly similar respiratory nitrate reductase NarGHI, which has a relatively much lower affinity for perchlorate (Km = 1.1 mm) and no substrate inhibition. Structural analysis of oxidized and reduced PcrAB with and without the substrate analog SeO3 (2-) bound to the active site identified key residues in the positively charged and funnel-shaped substrate access tunnel that gated substrate entrance and product release while trapping transiently produced chlorate. The structures suggest gating was associated with shifts of a Phe residue between open and closed conformations plus an Asp residue carboxylate shift between monodentate and bidentate coordination to the active site molybdenum atom. Taken together, structural and mutational analyses of gate residues suggest key roles of these gate residues for substrate entrance and product release. Our combined results provide the first detailed structural insight into the mechanism of biological perchlorate reduction, a critical component of the chlorine redox cycle on Earth.

  9. Eel calcitonin binding site distribution and antinociceptive activity in rats

    SciTech Connect

    Guidobono, F.; Netti, C.; Sibilia, V.; Villa, I.; Zamboni, A.; Pecile, A.

    1986-03-01

    The distribution of binding site for (/sup 125/I)-eel-calcitonin (ECT) to rat central nervous system, studied by an autoradiographic technique, showed concentrations of binding in the diencephalon, the brain stem and the spinal cord. Large accumulations of grains were seen in the hypothalamus, the amygdala, in the fasciculus medialis prosencephali, in the fasciculus longitudinalis medialis, in the ventrolateral part of the periventricular gray matter, in the lemniscus medialis and in the raphe nuclei. The density of grains in the reticular formation and in the nucleus tractus spinalis nervi trigemini was more moderate. In the spinal cord, grains were scattered throughout the dorsal horns. Binding of the ligand was displaced equally by cold ECT and by salmon CT(sCT), indicating that both peptides bind to the same receptors. Human CT was much weaker than sCT in displacing (/sup 125/I)-ECT binding. The administration of ECT into the brain ventricles of rats dose-dependently induced a significant and long-lasting enhancement of hot-plate latencies comparable with that obtained with sCT. The antinociceptive activity induced by ECT is compatible with the topographical distribution of binding sites for the peptide and is a further indication that fish CTs are active in the mammalian brain.

  10. Perchlorate Reductase Is Distinguished by Active Site Aromatic Gate Residues.

    PubMed

    Youngblut, Matthew D; Tsai, Chi-Lin; Clark, Iain C; Carlson, Hans K; Maglaqui, Adrian P; Gau-Pan, Phonchien S; Redford, Steven A; Wong, Alan; Tainer, John A; Coates, John D

    2016-04-22

    Perchlorate is an important ion on both Earth and Mars. Perchlorate reductase (PcrAB), a specialized member of the dimethylsulfoxide reductase superfamily, catalyzes the first step of microbial perchlorate respiration, but little is known about the biochemistry, specificity, structure, and mechanism of PcrAB. Here we characterize the biophysics and phylogeny of this enzyme and report the 1.86-Å resolution PcrAB complex crystal structure. Biochemical analysis revealed a relatively high perchlorate affinity (Km = 6 μm) and a characteristic substrate inhibition compared with the highly similar respiratory nitrate reductase NarGHI, which has a relatively much lower affinity for perchlorate (Km = 1.1 mm) and no substrate inhibition. Structural analysis of oxidized and reduced PcrAB with and without the substrate analog SeO3 (2-) bound to the active site identified key residues in the positively charged and funnel-shaped substrate access tunnel that gated substrate entrance and product release while trapping transiently produced chlorate. The structures suggest gating was associated with shifts of a Phe residue between open and closed conformations plus an Asp residue carboxylate shift between monodentate and bidentate coordination to the active site molybdenum atom. Taken together, structural and mutational analyses of gate residues suggest key roles of these gate residues for substrate entrance and product release. Our combined results provide the first detailed structural insight into the mechanism of biological perchlorate reduction, a critical component of the chlorine redox cycle on Earth. PMID:26940877

  11. Investigating the discrepancy between wet-suspension- and dry-dispersion-derived ice nucleation efficiency of mineral particles

    NASA Astrophysics Data System (ADS)

    Emersic, C.; Connolly, P. J.; Boult, S.; Campana, M.; Li, Z.

    2015-10-01

    Cloud chamber investigations into ice nucleation by mineral particles were compared with results from cold-stage droplet freezing experiments. Kaolinite, NX-illite, and K-feldspar were examined, and K-feldspar was revealed to be the most ice-active mineral particle sample, in agreement with recent cold-stage studies. The ice nucleation efficiencies, as quantified using the ice-active surface site density method, were found to be in agreement with previous studies for the lower temperatures; however, at higher temperatures the efficiency was between a factor of 10 and 1000 higher than those inferred from cold-stage experiments. Numerical process modelling of cloud formation during the experiments, using the cold-stage-derived parameterisations to initiate the ice phase, revealed the cold-stage-derived parameterisations to consistently underpredict the number of ice crystals relative to that observed. We suggest the reason for the underestimation of ice in the model is that the slope of the cold-stage-derived ice-active surface site density vs. temperature curves are too steep, which results in an underestimation of the number of ice crystals at higher temperatures during the expansion. These ice crystals suppress further freezing due to the Bergeron-Findeison process. A coagulation model was used to investigate the idea that the mineral particles coagulate in suspension. This model suggests that coagulation during the experiments may be sufficient to significantly remove the particles for the suspension by sedimentation or reduce the total particle surface area available for ice nucleation to take place. Aggregation was confirmed to take place in mineral suspensions using dynamic light-scattering measurements. However, it is not proven that aggregation of the mineral particles is able to reduce the surface area available for ice nucleation. The implication is that the mineral particles may be more important at nucleating ice at high temperatures than previously

  12. An Active Site Water Network in the Plasminogen Activator Pla from Yersinia pestis

    SciTech Connect

    Eren, Elif; Murphy, Megan; Goguen, Jon; van den Berg, Bert

    2010-08-13

    The plasminogen activator Pla from Yersinia pestis is an outer membrane protease (omptin) that is important for the virulence of plague. Here, we present the high-resolution crystal structure of wild-type, enzymatically active Pla at 1.9 {angstrom}. The structure shows a water molecule located between active site residues D84 and H208, which likely corresponds to the nucleophilic water. A number of other water molecules are present in the active site, linking residues important for enzymatic activity. The R211 sidechain in loop L4 is close to the nucleophilic water and possibly involved in the stabilization of the oxyanion intermediate. Subtle conformational changes of H208 result from the binding of lipopolysaccharide to the outside of the barrel, explaining the unusual dependence of omptins on lipopolysaccharide for activity. The Pla structure suggests a model for the interaction with plasminogen substrate and provides a more detailed understanding of the catalytic mechanism of omptin proteases.

  13. Metal active site elasticity linked to activation of homocysteine in methionine synthases

    SciTech Connect

    Koutmos, Markos; Pejchal, Robert; Bomer, Theresa M.; Matthews, Rowena G.; Smith, Janet L.; Ludwig, Martha L.

    2008-04-02

    Enzymes possessing catalytic zinc centers perform a variety of fundamental processes in nature, including methyl transfer to thiols. Cobalamin-independent (MetE) and cobalamin-dependent (MetH) methionine synthases are two such enzyme families. Although they perform the same net reaction, transfer of a methyl group from methyltetrahydrofolate to homocysteine (Hcy) to form methionine, they display markedly different catalytic strategies, modular organization, and active site zinc centers. Here we report crystal structures of zinc-replete MetE and MetH, both in the presence and absence of Hcy. Structural investigation of the catalytic zinc sites of these two methyltransferases reveals an unexpected inversion of zinc geometry upon binding of Hcy and displacement of an endogenous ligand in both enzymes. In both cases a significant movement of the zinc relative to the protein scaffold accompanies inversion. These structures provide new information on the activation of thiols by zinc-containing enzymes and have led us to propose a paradigm for the mechanism of action of the catalytic zinc sites in these and related methyltransferases. Specifically, zinc is mobile in the active sites of MetE and MetH, and its dynamic nature helps facilitate the active site conformational changes necessary for thiol activation and methyl transfer.

  14. Active Sites Environmental Monitoring Program: Program plan. Revision 1

    SciTech Connect

    Ashwood, T.L.; Wickliff, D.S.; Morrissey, C.M.

    1992-02-01

    The Active Sites Environmental Monitoring Program (ASEMP), initiated in 1989, provides early detection and performance monitoring of transuranic (TRU) waste and active low-level waste (LLW) facilities at Oak Ridge National Laboratory (ORNL) in accordance with US Department of Energy (DOE) Order 5820.2A. Active LLW facilities in Solid Waste Storage Area (SWSA) 6 include Tumulus I and Tumulus II, the Interim Waste Management Facility (IWMF), LLW silos, high-range wells, asbestos silos, and fissile wells. The tumulus pads and IWMF are aboveground, high-strength concrete pads on which concrete vaults containing metal boxes of LLW are placed; the void space between the boxes and vaults is filled with grout. Eventually, these pads and vaults will be covered by an engineered multilayered cap. All other LLW facilities in SWSA 6 are below ground. In addition, this plan includes monitoring of the Hillcut Disposal Test Facility (HDTF) in SWSA 6, even though this facility was completed prior to the data of the DOE order. In SWSA 5 North, the TRU facilities include below-grade engineered caves, high-range wells, and unlined trenches. All samples from SWSA 6 are screened for alpha and beta activity, counted for gamma-emitting isotopes, and analyzed for tritium. In addition to these analytes, samples from SWSA 5 North are analyzed for specific transuranic elements.

  15. Analysis of isothermal and cooling-rate-dependent immersion freezing by a unifying stochastic ice nucleation model

    DOE PAGES

    Alpert, Peter A.; Knopf, Daniel A.

    2016-02-24

    Immersion freezing is an important ice nucleation pathway involved in the formation of cirrus and mixed-phase clouds. Laboratory immersion freezing experiments are necessary to determine the range in temperature, T, and relative humidity, RH, at which ice nucleation occurs and to quantify the associated nucleation kinetics. Typically, isothermal (applying a constant temperature) and cooling-rate-dependent immersion freezing experiments are conducted. In these experiments it is usually assumed that the droplets containing ice nucleating particles (INPs) all have the same INP surface area (ISA); however, the validity of this assumption or the impact it may have on analysis and interpretation of the experimentalmore » data is rarely questioned. Descriptions of ice active sites and variability of contact angles have been successfully formulated to describe ice nucleation experimental data in previous research; however, we consider the ability of a stochastic freezing model founded on classical nucleation theory to reproduce previous results and to explain experimental uncertainties and data scatter. A stochastic immersion freezing model based on first principles of statistics is presented, which accounts for variable ISA per droplet and uses parameters including the total number of droplets, Ntot, and the heterogeneous ice nucleation rate coefficient, Jhet(T). This model is applied to address if (i) a time and ISA-dependent stochastic immersion freezing process can explain laboratory immersion freezing data for different experimental methods and (ii) the assumption that all droplets contain identical ISA is a valid conjecture with subsequent consequences for analysis and interpretation of immersion freezing. The simple stochastic model can reproduce the observed time and surface area dependence in immersion freezing experiments for a variety of methods such as: droplets on a cold-stage exposed to air or surrounded by an oil matrix, wind and acoustically

  16. Analysis of isothermal and cooling-rate-dependent immersion freezing by a unifying stochastic ice nucleation model

    NASA Astrophysics Data System (ADS)

    Alpert, Peter A.; Knopf, Daniel A.

    2016-02-01

    Immersion freezing is an important ice nucleation pathway involved in the formation of cirrus and mixed-phase clouds. Laboratory immersion freezing experiments are necessary to determine the range in temperature, T, and relative humidity, RH, at which ice nucleation occurs and to quantify the associated nucleation kinetics. Typically, isothermal (applying a constant temperature) and cooling-rate-dependent immersion freezing experiments are conducted. In these experiments it is usually assumed that the droplets containing ice nucleating particles (INPs) all have the same INP surface area (ISA); however, the validity of this assumption or the impact it may have on analysis and interpretation of the experimental data is rarely questioned. Descriptions of ice active sites and variability of contact angles have been successfully formulated to describe ice nucleation experimental data in previous research; however, we consider the ability of a stochastic freezing model founded on classical nucleation theory to reproduce previous results and to explain experimental uncertainties and data scatter. A stochastic immersion freezing model based on first principles of statistics is presented, which accounts for variable ISA per droplet and uses parameters including the total number of droplets, Ntot, and the heterogeneous ice nucleation rate coefficient, Jhet(T). This model is applied to address if (i) a time and ISA-dependent stochastic immersion freezing process can explain laboratory immersion freezing data for different experimental methods and (ii) the assumption that all droplets contain identical ISA is a valid conjecture with subsequent consequences for analysis and interpretation of immersion freezing. The simple stochastic model can reproduce the observed time and surface area dependence in immersion freezing experiments for a variety of methods such as: droplets on a cold-stage exposed to air or surrounded by an oil matrix, wind and acoustically levitated droplets

  17. Nucleation and growth of zinc from chloride concentrated solutions

    SciTech Connect

    Trejo, G.; Ortega B, R.; Meas V, Y.; Ozil, P.; Chainet, E.; Nguyen, B.

    1998-12-01

    The electrodeposition of metals is a complex phenomenon influenced by a number of factors that modify the rates of nucleation and growth and determine the properties of the deposits. In this work the authors study the influence of the zinc chloride (ZnCl{sub 2}) concentration on the zinc nucleation process on glassy carbon, in a KCl electrolyte under conditions close to those employed in commercial acid deposition baths for zinc. The electrochemical study was performed using cyclic voltammetry and potentiostatic current-time transients. The charge-transfer coefficient and the formal potential for ZnCl{sub 2} reduction were evaluated from cyclic voltammetry experiments. The nucleation process was analyzed by comparing the transients obtained with the known dimensionless (i/i{sub m}){sup 2} vs. t/t{sub m} response for instantaneous or progressive nucleation. The results show that the nucleation process and the number density of sites are dependent on ZnCl{sub 2} concentration. Scanning electron microscopy analysis of the deposits shows that the deposits are homogeneous and compact although a change in the morphology is observed as a function of ZnCl{sub 2} concentration. Evaluation of the corrosion resistance reveals the influence of the nucleation process on the subsequent corrosion resistance of the zinc deposits.

  18. Active Site and Laminarin Binding in Glycoside Hydrolase Family 55*

    PubMed Central

    Bianchetti, Christopher M.; Takasuka, Taichi E.; Deutsch, Sam; Udell, Hannah S.; Yik, Eric J.; Bergeman, Lai F.; Fox, Brian G.

    2015-01-01

    The Carbohydrate Active Enzyme (CAZy) database indicates that glycoside hydrolase family 55 (GH55) contains both endo- and exo-β-1,3-glucanases. The founding structure in the GH55 is PcLam55A from the white rot fungus Phanerochaete chrysosporium (Ishida, T., Fushinobu, S., Kawai, R., Kitaoka, M., Igarashi, K., and Samejima, M. (2009) Crystal structure of glycoside hydrolase family 55 β-1,3-glucanase from the basidiomycete Phanerochaete chrysosporium. J. Biol. Chem. 284, 10100–10109). Here, we present high resolution crystal structures of bacterial SacteLam55A from the highly cellulolytic Streptomyces sp. SirexAA-E with bound substrates and product. These structures, along with mutagenesis and kinetic studies, implicate Glu-502 as the catalytic acid (as proposed earlier for Glu-663 in PcLam55A) and a proton relay network of four residues in activating water as the nucleophile. Further, a set of conserved aromatic residues that define the active site apparently enforce an exo-glucanase reactivity as demonstrated by exhaustive hydrolysis reactions with purified laminarioligosaccharides. Two additional aromatic residues that line the substrate-binding channel show substrate-dependent conformational flexibility that may promote processive reactivity of the bound oligosaccharide in the bacterial enzymes. Gene synthesis carried out on ∼30% of the GH55 family gave 34 active enzymes (19% functional coverage of the nonredundant members of GH55). These active enzymes reacted with only laminarin from a panel of 10 different soluble and insoluble polysaccharides and displayed a broad range of specific activities and optima for pH and temperature. Application of this experimental method provides a new, systematic way to annotate glycoside hydrolase phylogenetic space for functional properties. PMID:25752603

  19. Fluorescence Studies of Protein Crystal Nucleation

    NASA Technical Reports Server (NTRS)

    Pusey, Marc L.

    1999-01-01

    Fluorescence can be used to study protein crystal nucleation through methods such as anisotropy, quenching, and resonance energy transfer (FRET), to follow pH and ionic strength changes, and follow events occurring at the growth interface. We have postulated, based upon a range of experimental evidence that the growth unit of tetragonal hen egg white lysozyme is an octamer. Several fluorescent derivatives of chicken egg white lysozyme have been prepared. The fluorescent probes lucifer yellow (LY), cascade blue, and 5-((2-aminoethyl)aminonapthalene-1-sulfonic acid (EDANS), have been covalently attached to ASP 101. All crystallize in the characteristic tetragonal form, indicating that the bound probes are likely laying within the active site cleft. Crystals of the LY and EDANS derivatives have been found to diffract to at least 1.7 A. A second group of derivatives is to the N-terminal amine group, and these do not crystallize as this site is part of the contact region between the adjacent 43 helix chains. However derivatives at these sites would not interfere with formation of the 43 helices in solution. Preliminary FRET studies have been carried out using N-terminal bound pyrene acetic acid (Ex 340 nm, Em 376 nm) lysozyme as a donor and LY (Ex -425 nm, Em 525 nm) labeled lysozyme as an acceptor. FRET data have been obtained at pH 4.6, 0.1 M NaAc buffer, at 5 and 7% NaCl, 4 C. The corresponding Csat values are 0.471 and 0.362 mg/ml (approximately 3.3 and approximately 2.5 x 10(exp -5) M respectively). The data at both salt concentrations show a consistent trend of decreasing fluorescence intensity of the donor species (PAA) with increasing total protein concentration. This decrease is more pronounced at 7% NaCl, consistent with the expected increased intermolecular interactions at higher salt concentrations reflected in the lower solubility. The calculated average distance between any two protein molecules at 5 x 10(exp -6) M is approximately 70nm, well beyond the

  20. Active site loop conformation regulates promiscuous activity in a lactonase from Geobacillus kaustophilus HTA426.

    PubMed

    Zhang, Yu; An, Jiao; Yang, Guang-Yu; Bai, Aixi; Zheng, Baisong; Lou, Zhiyong; Wu, Geng; Ye, Wei; Chen, Hai-Feng; Feng, Yan; Manco, Giuseppe

    2015-01-01

    Enzyme promiscuity is a prerequisite for fast divergent evolution of biocatalysts. A phosphotriesterase-like lactonase (PLL) from Geobacillus kaustophilus HTA426 (GkaP) exhibits main lactonase and promiscuous phosphotriesterase activities. To understand its catalytic and evolutionary mechanisms, we investigated a "hot spot" in the active site by saturation mutagenesis as well as X-ray crystallographic analyses. We found that position 99 in the active site was involved in substrate discrimination. One mutant, Y99L, exhibited 11-fold improvement over wild-type in reactivity (kcat/Km) toward the phosphotriesterase substrate ethyl-paraoxon, but showed 15-fold decrease toward the lactonase substrate δ-decanolactone, resulting in a 157-fold inversion of the substrate specificity. Structural analysis of Y99L revealed that the mutation causes a ∼6.6 Å outward shift of adjacent loop 7, which may cause increased flexibility of the active site and facilitate accommodation and/or catalysis of organophosphate substrate. This study provides for the PLL family an example of how the evolutionary route from promiscuity to specificity can derive from very few mutations, which promotes alteration in the conformational adjustment of the active site loops, in turn draws the capacity of substrate binding and activity.

  1. Active Site Loop Conformation Regulates Promiscuous Activity in a Lactonase from Geobacillus kaustophilus HTA426

    PubMed Central

    Zhang, Yu; An, Jiao; Yang, Guang-Yu; Bai, Aixi; Zheng, Baisong; Lou, Zhiyong; Wu, Geng; Ye, Wei; Chen, Hai-Feng; Feng, Yan; Manco, Giuseppe

    2015-01-01

    Enzyme promiscuity is a prerequisite for fast divergent evolution of biocatalysts. A phosphotriesterase-like lactonase (PLL) from Geobacillus kaustophilus HTA426 (GkaP) exhibits main lactonase and promiscuous phosphotriesterase activities. To understand its catalytic and evolutionary mechanisms, we investigated a “hot spot” in the active site by saturation mutagenesis as well as X-ray crystallographic analyses. We found that position 99 in the active site was involved in substrate discrimination. One mutant, Y99L, exhibited 11-fold improvement over wild-type in reactivity (kcat/Km) toward the phosphotriesterase substrate ethyl-paraoxon, but showed 15-fold decrease toward the lactonase substrate δ-decanolactone, resulting in a 157-fold inversion of the substrate specificity. Structural analysis of Y99L revealed that the mutation causes a ∼6.6 Å outward shift of adjacent loop 7, which may cause increased flexibility of the active site and facilitate accommodation and/or catalysis of organophosphate substrate. This study provides for the PLL family an example of how the evolutionary route from promiscuity to specificity can derive from very few mutations, which promotes alteration in the conformational adjustment of the active site loops, in turn draws the capacity of substrate binding and activity. PMID:25706379

  2. Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site.

    PubMed

    Sunden, Fanny; Peck, Ariana; Salzman, Julia; Ressl, Susanne; Herschlag, Daniel

    2015-01-01

    Enzymes enable life by accelerating reaction rates to biological timescales. Conventional studies have focused on identifying the residues that have a direct involvement in an enzymatic reaction, but these so-called 'catalytic residues' are embedded in extensive interaction networks. Although fundamental to our understanding of enzyme function, evolution, and engineering, the properties of these networks have yet to be quantitatively and systematically explored. We dissected an interaction network of five residues in the active site of Escherichia coli alkaline phosphatase. Analysis of the complex catalytic interdependence of specific residues identified three energetically independent but structurally interconnected functional units with distinct modes of cooperativity. From an evolutionary perspective, this network is orders of magnitude more probable to arise than a fully cooperative network. From a functional perspective, new catalytic insights emerge. Further, such comprehensive energetic characterization will be necessary to benchmark the algorithms required to rationally engineer highly efficient enzymes. PMID:25902402

  3. Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site.

    PubMed

    Sunden, Fanny; Peck, Ariana; Salzman, Julia; Ressl, Susanne; Herschlag, Daniel

    2015-01-01

    Enzymes enable life by accelerating reaction rates to biological timescales. Conventional studies have focused on identifying the residues that have a direct involvement in an enzymatic reaction, but these so-called 'catalytic residues' are embedded in extensive interaction networks. Although fundamental to our understanding of enzyme function, evolution, and engineering, the properties of these networks have yet to be quantitatively and systematically explored. We dissected an interaction network of five residues in the active site of Escherichia coli alkaline phosphatase. Analysis of the complex catalytic interdependence of specific residues identified three energetically independent but structurally interconnected functional units with distinct modes of cooperativity. From an evolutionary perspective, this network is orders of magnitude more probable to arise than a fully cooperative network. From a functional perspective, new catalytic insights emerge. Further, such comprehensive energetic characterization will be necessary to benchmark the algorithms required to rationally engineer highly efficient enzymes.

  4. Fluorescence Studies of Lysozyme Nucleation

    NASA Technical Reports Server (NTRS)

    Pusey, Marc L.; Smith, Lori

    1998-01-01

    Fluorescence is one of the most powerful tools available for the study of macromolecules. For example, fluorescence can be used to study self association through methods such as anisotropy (the rotational rate of the molecule in solution), quenching (the accessibility of a bound probe to the bulk solution), and resonance energy transfer (measurement of the distance between two species). Fluorescence can also be used to study the local environment of the probe molecules, and the changes in that environment which accompany crystal nucleation and growth. However fluorescent techniques have been very much underutilized in macromolecular growth studies. One major advantage is that the fluorescent species generally must be at low concentration, typically ca 10-5 to 10-6 M. Thus one can study a very wide range of solution conditions, ranging from very high to very low protein concentration, he latter of which are not readily accessible to scattering techniques. We have prepared a number of fluorescent derivatives of chicken egg white lysozyme (CEWL). Fluorescent probes have been attached to two different sites, ASP 101 and the N-terrninal amine, with a sought for use in different lines of study. Preliminary resonance energy transfer studies have been -carried out using pyrene acetic acid (Ex 340 mn, Em 376 nm) lysozyme as a donor and cascade blue (Ex 377 run, Em 423 nm) labeled lysozyme as an acceptor. The emission of both the pyrene and cascade blue probes was followed as a function of the salt protein concentrations. The data show an increase in cascade blue and a concomitant decrease in the pyrene fluorescence as either the salt or protein concentrations are increased, suggesting that the two species are approaching each other close enough for resonance energy transfer to occur. This data can be analyzed to measure the distance between the probe molecules and, knowing their locations on the protein molecule their distances from and orientations with respect to each

  5. Metals in the active site of native protein phosphatase-1.

    PubMed

    Heroes, Ewald; Rip, Jens; Beullens, Monique; Van Meervelt, Luc; De Gendt, Stefan; Bollen, Mathieu

    2015-08-01

    Protein phosphatase-1 (PP1) is a major protein Ser/Thr phosphatase in eukaryotic cells. Its activity depends on two metal ions in the catalytic site, which were identified as manganese in the bacterially expressed phosphatase. However, the identity of the metal ions in native PP1 is unknown. In this study, total reflection X-ray fluorescence (TXRF) was used to detect iron and zinc in PP1 that was purified from rabbit skeletal muscle. Metal exchange experiments confirmed that the distinct substrate specificity of recombinant and native PP1 is determined by the nature of their associated metals. We also found that the iron level associated with native PP1 is decreased by incubation with inhibitor-2, consistent with a function of inhibitor-2 as a PP1 chaperone. PMID:25890482

  6. A marine biogenic source of atmospheric ice-nucleating particles

    SciTech Connect

    Wilson, T. W.; Ladino, L. A.; Alpert, Peter A.; Breckels, M. N.; Brooks, I. M.; Browse, J.; Burrows, Susannah M.; Carslaw, K. S.; Huffman, J. A.; Judd, C.; Kilthau, W. P.; Mason, R. H.; McFiggans, Gordon; Miller, L. A.; Najera, J.; Polishchuk, E. A.; Rae, S.; Schiller, C. L.; Si, M.; Vergara Temprado, J.; Whale, Thomas; Wong, J P S; Wurl, O.; Yakobi-Hancock, J. D.; Abbatt, JPD; Aller, Josephine Y.; Bertram, Allan K.; Knopf, Daniel A.; Murray, Benjamin J.

    2015-09-09

    The formation of ice in clouds is facilitated by the presence of airborne ice nucleating particles1,2. Sea spray is one of the major global sources of atmospheric particles, but it is unclear to what extent these particles are capable of nucleating ice3–11. Here we show that material in the sea surface microlayer, which is enriched in surface active organic material representative of that found in sub-micron sea- spray aerosol12–21, nucleates ice under conditions that occur in mixed-phase clouds and high-altitude ice clouds. The ice active material is likely biogenic and is less than ~0.2 ?m in size. We also show that organic material (exudate) released by a common marine diatom nucleates ice when separated from cells and propose that organic material associated with phytoplankton cell exudates are a candidate for the observed ice nucleating ability of the microlayer samples. By combining our measurements with global model simulations of marine organic aerosol, we show that ice nucleating particles of marine origin are dominant in remote marine environments, such as the Southern Ocean, the North Pacific and the North Atlantic.

  7. Relationship between Ice Nucleation Frequency of Bacteria and Frost Injury.

    PubMed

    Lindow, S E; Hirano, S S; Barchet, W R; Arny, D C; Upper, C D

    1982-10-01

    Not every cell of a given bacterial isolate that has ice-nucleating properties can serve as an ice nucleus at any given time and temperature. The ratio between the number of ice nuclei and number of bacterial cells in a culture (i.e. nucleation frequency) was found to vary with incubation temperature, growth medium composition, culture age, and genotype. Optimal conditions for ice nucleus production in vitro included incubation of the bacterial cells at 20 to 24 degrees C on nutrient agar containing glycerol. The relationship between nucleation frequency and frost injury was examined by subjecting corn seedlings to -4 degrees C immediately after they were sprayed with bacterial suspensions with different nucleation frequencies and by following both ice nucleus concentration and bacterial population size on leaves of corn seedlings as a function of time after bacterial application. The amount of frost injury to growth chamber-grown corn seedlings at -4 degrees C was a function of the number of ice nuclei active at that temperature on the leaves. The number of ice nuclei, in turn, is the product of the nucleation frequency and population size of ice-nucleation-active bacteria present on the leaves. PMID:16662619

  8. Metavanadate at the active site of the phosphatase VHZ.

    PubMed

    Kuznetsov, Vyacheslav I; Alexandrova, Anastassia N; Hengge, Alvan C

    2012-09-01

    Vanadate is a potent modulator of a number of biological processes and has been shown by crystal structures and NMR spectroscopy to interact with numerous enzymes. Although these effects often occur under conditions where oligomeric forms dominate, the crystal structures and NMR data suggest that the inhibitory form is usually monomeric orthovanadate, a particularly good inhibitor of phosphatases because of its ability to form stable trigonal-bipyramidal complexes. We performed a computational analysis of a 1.14 Å structure of the phosphatase VHZ in complex with an unusual metavanadate species and compared it with two classical trigonal-bipyramidal vanadate-phosphatase complexes. The results support extensive delocalized bonding to the apical ligands in the classical structures. In contrast, in the VHZ metavanadate complex, the central, planar VO(3)(-) moiety has only one apical ligand, the nucleophilic Cys95, and a gap in electron density between V and S. A computational analysis showed that the V-S interaction is primarily ionic. A mechanism is proposed to explain the formation of metavanadate in the active site from a dimeric vanadate species that previous crystallographic evidence has shown to be able to bind to the active sites of phosphatases related to VHZ. Together, the results show that the interaction of vanadate with biological systems is not solely reliant upon the prior formation of a particular inhibitory form in solution. The catalytic properties of an enzyme may act upon the oligomeric forms primarily present in solution to generate species such as the metavanadate ion observed in the VHZ structure. PMID:22876963

  9. Particle Nucleation and Growth During the NIFTy Experiment

    NASA Astrophysics Data System (ADS)

    Barthelmie, R. J.; Pryor, S. C.; Spaulding, A. M.; Rossner, A.; Crimmins, B.; Hopke, P. K.; Mauldin, L.; Jobson, T.; Petaja, T.

    2008-12-01

    The measurements presented herein are being collected in order to assess the frequency and characteristics of nucleation events and high ultra-fine particle concentrations in this rural (but regionally polluted) setting, including the chemical composition of the ultra-fine particles, the principal mechanisms of nucleation, limitations on nucleation and growth and the ultimate fate of the resulting ultra-fine particles. We present a year of data from continuous measurements of particle size distributions (6 to 400 nm) at three- levels above and within a deciduous forest in southern Indiana (in the Ohio River Valley). These data are collected using two SMPS and one FMPS, and are supplemented with data concerning the spatial extent and the composition of ultra-fine particles using samples collected during May 2008 as part of the Nucleation In ForesTs (NIFTY) campaign. The long-term measurements indicate evidence of class A nucleation events on approximately 1 day in 5, and lesser magnitude or less well defined events on another 15% of days. These data indicate nucleation is most frequently observed in spring, but occurs in all seasons and subsequent growth is more rapid during leaf-on. During the NIFTY field experiment we enhanced the ongoing data collection at the forest site to include sulfuric acid, ammonia and VOC concentrations, and particle composition using two MOUDI-nano-MOUDI combinations. Preliminary analyses of these data indicate that the sub-32 nm diameter particles are almost completely ammonium-sulfate or ammonium-bisulfate and associated water but there is evidence that continued growth is aided by the addition of condensable organics. We further instrumented two additional sites - one directly south of the forest in a relatively rural setting, and one to the north in the city of Indianapolis. Results from these sites indicate strong evidence that the events are regional but the sites differ in terms of the magnitude of the events and the relative

  10. Zymogen Activation and Subcellular Activity of Subtilisin Kexin Isozyme 1/Site 1 Protease*

    PubMed Central

    da Palma, Joel Ramos; Burri, Dominique Julien; Oppliger, Joël; Salamina, Marco; Cendron, Laura; de Laureto, Patrizia Polverino; Seidah, Nabil Georges; Kunz, Stefan; Pasquato, Antonella

    2014-01-01

    The proprotein convertase subtilisin kexin isozyme 1 (SKI-1)/site 1 protease (S1P) plays crucial roles in cellular homeostatic functions and is hijacked by pathogenic viruses for the processing of their envelope glycoproteins. Zymogen activation of SKI-1/S1P involves sequential autocatalytic processing of its N-terminal prodomain at sites B′/B followed by the herein newly identified C′/C sites. We found that SKI-1/S1P autoprocessing results in intermediates whose catalytic domain remains associated with prodomain fragments of different lengths. In contrast to other zymogen proprotein convertases, all incompletely matured intermediates of SKI-1/S1P showed full catalytic activity toward cellular substrates, whereas optimal cleavage of viral glycoproteins depended on B′/B processing. Incompletely matured forms of SKI-1/S1P further process cellular and viral substrates in distinct subcellular compartments. Using a cell-based sensor for SKI-1/S1P activity, we found that 9 amino acid residues at the cleavage site (P1–P8) and P1′ are necessary and sufficient to define the subcellular location of processing and to determine to what extent processing of a substrate depends on SKI-1/S1P maturation. In sum, our study reveals novel and unexpected features of SKI-1/S1P zymogen activation and subcellular specificity of activity toward cellular and pathogen-derived substrates. PMID:25378398

  11. Identification of a novel ice-nucleating bacterium of Antarctic origin and its ice nucleation properties.

    PubMed

    Obata, H; Muryoi, N; Kawahara, H; Yamade, K; Nishikawa, J

    1999-03-01

    A novel ice-nucleating bacterium (INB) was isolated from Ross Island, Antarctica. INBs could be isolated more frequently than was generally thought. INB strain IN-74 was found in the white colony group. Strain IN-74 was identified from its taxonomic characteristics as a novel INB, Pseudomonas antarctica IN-74. When strain IN-74 was cultured aerobically in a medium consisting of the ice-nucleating broth (pH 7.0) for 6 days at 4 degrees C, the ice-nucleating activity of strain IN-74 cells was obtained. Strain IN-74 cells produced ice nuclei only at extremely low growth temperatures. The nuclei appeared to be less thermolabile than those of INB Pseudomonas fluorescens KUIN-1. The freezing difference spectra in D2O and H2O at ice-nucleating temperature for strain IN-74 cells and conventional INBs (Pseudomonas fluorescens KUIN-1, Pseudomonas viridiflava KUIN-2, and Pseudomonas syringae C-9) exhibited different curves. PMID:10191036

  12. Bacterial ice nucleation: a factor in frost injury to plants.

    PubMed

    Lindow, S E; Arny, D C; Upper, C D

    1982-10-01

    Heterogeneous ice nuclei are necessary, and the common epiphytic ice nucleation active (INA) bacteria Pseudomonas syringae van Hall and Erwinia herbicola (Löhnis) Dye are sufficient to incite frost injury to sensitive plants at -5 degrees C. The ice nucleation activity of the bacteria occurs at the same temperatures at which frost injury to sensitive plants occurs in nature. Bacterial ice nucleation on leaves can be detected at about -2 degrees C, whereas the leaves themselves, i.e. without INA bacteria, contain nuclei active only at much lower temperatures. The temperature at which injury to plants occurs is predictable on the basis of the ice nucleation activity of leaf discs, which in turn depends on the number and ice nucleation activity of their resident bacteria. Bacterial isolates which are able to incite injury to corn at -5 degrees C are always active as ice nuclei at -5 degrees C. INA bacteria incited frost injury to all of the species of sensitive plants tested. PMID:16662618

  13. Development of a gene reporter system in moderately halophilic bacteria by employing the ice nucleation gene of Pseudomonas syringae.

    PubMed Central

    Arvanitis, N; Vargas, C; Tegos, G; Perysinakis, A; Nieto, J J; Ventosa, A; Drainas, C

    1995-01-01

    The expression of the ice nucleation gene inaZ of Pseudomonas syringae in several moderate halophiles was investigated to establish its utility as a reporter for promoter activity and gene expression studies in these biotechnologically and environmentally important bacteria. A promoterless version of inaZ was introduced in two different restriction sites and at both orientations in a recombinant plasmid able to replicate in moderate halophiles and, in particular, within the sequence of its pHE1 part, a native plasmid of Halomonas elongata. One orientation of both recombinant constructs expressed high levels of ice nucleation activity in H. elongata and Volcaniella eurihalina cells, indicating that inaZ was probably introduced in the correct orientation downstream of putative native promoters. A recombinant construct carrying a tandem duplication of inaZ at the same orientation gave significantly higher ice nucleation activity, showing that inaZ is appropriate for gene dosage studies. The ice nucleation gene was also expressed in H. elongata and V. eurihalina under the control of Pbla (the promoter of the beta-lactamase gene of Escherichia coli) and Ppdc (the promoter of the pyruvate decarboxylase gene of Zymomonas mobilis). One of the inaZ reporter plasmids expressing high levels of ice nucleation activity under the control of a native putative promoter was also transferred in Halomonas subglaciescola, Halomonas meridiana, Halomonas halodurans, and Deleya halophila. In all cases, Ice+ transconjugants were successfully isolated, demonstrating that inaZ is expressed in a wide spectrum of moderately halophilic species. PMID:8526492

  14. The adsorption of fungal ice-nucleating proteins on mineral dusts: a terrestrial reservoir of atmospheric ice-nucleating particles

    NASA Astrophysics Data System (ADS)

    O'Sullivan, Daniel; Murray, Benjamin J.; Ross, James F.; Webb, Michael E.

    2016-06-01

    The occurrence of ice-nucleating particles (INPs) in our atmosphere has a profound impact on the properties and lifetime of supercooled clouds. To date, the identities, sources and abundances of particles capable of nucleating ice at relatively low supercoolings (T > -15 °C) remain enigmatic. While biomolecules such as proteins and carbohydrates have been implicated as important high-temperature INPs, the lack of knowledge on the environmental fates of these species makes it difficult to assess their potential atmospheric impacts. Here we show that such nanoscale ice-nucleating proteins from a common soil-borne fungus (Fusarium avenaceum) preferentially bind to and confer their ice-nucleating properties to kaolinite. The ice-nucleating activity of the proteinaceous INPs is unaffected by adsorption to the clay, and once bound the proteins do not readily desorb, retaining much of the activity even after multiple washings with pure water. The atmospheric implications of the finding that biological residues can confer their ice-nucleating ability to dust particles are discussed.

  15. Site-specific PEGylation of lidamycin and its antitumor activity.

    PubMed

    Li, Liang; Shang, Boyang; Hu, Lei; Shao, Rongguang; Zhen, Yongsu

    2015-05-01

    In this study, N-terminal site-specific mono-PEGylation of the recombinant lidamycin apoprotein (rLDP) of lidamycin (LDM) was prepared using a polyethyleneglycol (PEG) derivative (M w 20 kDa) through a reactive terminal aldehyde group under weak acidic conditions (pH 5.5). The biochemical properties of mPEG-rLDP-AE, an enediyne-integrated conjugate, were analyzed by SDS-PAGE, RP-HPLC, SEC-HPLC and MALDI-TOF. Meanwhile, in vitro and in vivo antitumor activity of mPEG-rLDP-AE was evaluated by MTT assays and in xenograft model. The results indicated that mPEG-rLDP-AE showed significant antitumor activity both in vitro and in vivo. After PEGylation, mPEG-rLDP still retained the binding capability to the enediyne AE and presented the physicochemical characteristics similar to that of native LDP. It is of interest that the PEGylation did not diminish the antitumor efficacy of LDM, implying the possibility that this derivative may function as a payload to deliver novel tumor-targeted drugs. PMID:26579455

  16. Hybrid [FeFe]-hydrogenases with modified active sites show remarkable residual enzymatic activity.

    PubMed

    Siebel, Judith F; Adamska-Venkatesh, Agnieszka; Weber, Katharina; Rumpel, Sigrun; Reijerse, Edward; Lubitz, Wolfgang

    2015-02-24

    [FeFe]-hydrogenases are to date the only enzymes for which it has been demonstrated that the native inorganic binuclear cofactor of the active site Fe2(adt)(CO)3(CN)2 (adt = azadithiolate = [S-CH2-NH-CH2-S](2-)) can be synthesized on the laboratory bench and subsequently inserted into the unmaturated enzyme to yield fully functional holo-enzyme (Berggren, G. et al. (2013) Nature 499, 66-70; Esselborn, J. et al. (2013) Nat. Chem. Biol. 9, 607-610). In the current study, we exploit this procedure to introduce non-native cofactors into the enzyme. Mimics of the binuclear subcluster with a modified bridging dithiolate ligand (thiodithiolate, N-methylazadithiolate, dimethyl-azadithiolate) and three variants containing only one CN(-) ligand were inserted into the active site of the enzyme. We investigated the activity of these variants for hydrogen oxidation as well as proton reduction and their structural accommodation within the active site was analyzed using Fourier transform infrared spectroscopy. Interestingly, the monocyanide variant with the azadithiolate bridge showed ∼50% of the native enzyme activity. This would suggest that the CN(-) ligands are not essential for catalytic activity, but rather serve to anchor the binuclear subsite inside the protein pocket through hydrogen bonding. The inserted artificial cofactors with a propanedithiolate and an N-methylazadithiolate bridge as well as their monocyanide variants also showed residual activity. However, these activities were less than 1% of the native enzyme. Our findings indicate that even small changes in the dithiolate bridge of the binuclear subsite lead to a rather strong decrease of the catalytic activity. We conclude that both the Brønsted base function and the conformational flexibility of the native azadithiolate amine moiety are essential for the high catalytic activity of the native enzyme. PMID:25633077

  17. Analysis of feedbacks between nucleation rate, survival probability and cloud condensation nuclei formation

    NASA Astrophysics Data System (ADS)

    Westervelt, D. M.; Pierce, J. R.; Adams, P. J.

    2014-06-01

    Aerosol nucleation is an important source of particle number in the atmosphere. However, in order to become cloud condensation nuclei (CCN), freshly nucleated particles must undergo significant condensational growth while avoiding coagulational scavenging. In an effort to quantify the contribution of nucleation to CCN, this work uses the GEOS-Chem-TOMAS global aerosol model to calculate changes in CCN concentrations against a broad range of nucleation rates and mechanisms. We then quantify the factors that control CCN formation from nucleation, including daily nucleation rates, growth rates, coagulation sinks, condensation sinks, survival probabilities, and CCN formation rates, in order to examine feedbacks that may limit growth of nucleated particles to CCN. Nucleation rate parameterizations tested in GEOS-Chem-TOMAS include ternary nucleation (with multiple tuning factors), activation nucleation (with two pre-factors), binary nucleation, and ion-mediated nucleation. We find that nucleation makes a significant contribution to boundary layer CCN(0.2%), but this contribution is only modestly sensitive to the choice of nucleation scheme, ranging from 49 to 78% increase in concentrations over a control simulation with no nucleation. Moreover, a two order-of-magnitude increase in the globally averaged nucleation rate (via changes to tuning factors) results in small changes (less than 10%) to global CCN(0.2%) concentrations. To explain this, we present a simple theory showing that survival probability has an exponentially decreasing dependence on the square of the condensation sink. This functional form stems from a negative correlation between condensation sink and growth rate and a positive correlation between condensation sink and coagulational scavenging. Conceptually, with a fixed condensable vapor budget (sulfuric acid and organics), any increase in CCN concentrations due to higher nucleation rates necessarily entails an increased aerosol surface area in the

  18. Influence of surface morphology on the immersion mode ice nucleation efficiency of hematite particles

    SciTech Connect

    Hiranuma, N.; Hoffmann, N.; Kiselev, A.; Dreyer, A.; Zhang, K.; Kulkarni, G.; Koop, T.; Möhler, O.

    2014-01-01

    In this paper, the effect of the morphological modification of aerosol particles with respect to heterogeneous ice nucleation is comprehensively investigated for laboratory-generated hematite particles as a model substrate for atmospheric dust particles. The surface-area-scaled ice nucleation efficiencies of monodisperse cubic hematite particles and milled hematite particles were measured with a series of expansion cooling experiments using the Aerosol Interaction and Dynamics in the Atmosphere (AIDA) cloud simulation chamber. Complementary offline characterization of physico-chemical properties of both hematite subsets were also carried out with scanning electron microscopy (SEM), energy dispersive X-ray (EDX) spectroscopy, dynamic light scattering (DLS), and an electro-kinetic particle charge detector to further constrain droplet-freezing measurements of hematite particles. Additionally, an empirical parameterization derived from our laboratory measurements was implemented in the single-column version of the Community Atmospheric Model version 5 (CAM5) to investigate the model sensitivity in simulated ice crystal number concentration on different ice nucleation efficiencies. From an experimental perspective, our results show that the immersion mode ice nucleation efficiency of milled hematite particles is almost an order of magnitude higher at -35.2 °C < T < -33.5 °C than that of the cubic hematite particles, indicating a substantial effect of morphological irregularities on immersion mode freezing. Our modeling results similarly show that the increased droplet-freezing rates of milled hematite particles lead to about one order magnitude higher ice crystal number in the upper troposphere than cubic hematite particles. Finally and overall, our results suggest that the surface irregularities and associated active sites lead to greater ice activation through droplet freezing.

  19. Classical nucleation theory from a dynamical approach to nucleation.

    PubMed

    Lutsko, James F; Durán-Olivencia, Miguel A

    2013-06-28

    It is shown that diffusion-limited classical nucleation theory (CNT) can be recovered as a simple limit of the recently proposed dynamical theory of nucleation based on fluctuating hydrodynamics [J. F. Lutsko, J. Chem. Phys. 136, 034509 (2012)]. The same framework is also used to construct a more realistic theory in which clusters have finite interfacial width. When applied to the dilute solution/dense solution transition in globular proteins, it is found that the extension gives corrections to the nucleation rate even for the case of small supersaturations due to changes in the monomer distribution function and to the excess free energy. It is also found that the monomer attachment/detachment picture breaks down at high supersaturations corresponding to clusters smaller than about 100 molecules. The results also confirm the usual assumption that most important corrections to CNT can be achieved by means of improved estimates of the free energy barrier. The theory also illustrates two topics that have received considerable attention in the recent literature on nucleation: the importance sub-dominant corrections to the capillary model for the free energy and of the correct choice of the reaction coordinate.

  20. Molecular organisation of the ice nucleation protein InaV from Pseudomonas syringae.

    PubMed

    Schmid, D; Pridmore, D; Capitani, G; Battistutta, R; Neeser, J R; Jann, A

    1997-09-15

    A new ice nucleation gene from Pseudomonas syringae was isolated and overexpressed as a fully active protein in Escherichia coli in order to gain experimental data about the structure of ice nucleation proteins. No evidence of a signal sequence or secondary glycosylation was found. Differences in the extent of aggregation were shown to modulate the ice nucleation activity. The circular dichroism spectrum of the purified protein indicated the presence of beta-sheet structure. This finding supports a recently proposed hypothetical model for the structure of ice nucleation proteins, which provides a plausible explanation for their aggregation tendency. PMID:9323042

  1. In Situ Conductance Analysis of Zinc Oxide Nucleation and Coalescence during Atomic Layer Deposition on Metal Oxides and Polymers.

    PubMed

    Sweet, William J; Parsons, Gregory N

    2015-07-01

    Real time in situ conductance is collected continuously during atomic layer deposition (ALD) of zinc oxide films, and trends are used to study ALD nucleation on polypropylene, nylon-6, SiO2, TiO2, and Al2O3 substrates. The detailed conductance change during the ALD cycle is ascribed to changes in surface band bending upon precursor/reactant exposure. Conductive pathways form earlier on the inorganic surfaces than on the polymers, with Al2O3 substrates showing more rapid nucleation than SiO2 or TiO2, consistent with the expected density of nucleation sites (e.g., hydroxyl groups) on these different materials. The measured conductance is ohmic, and both two- and four-electrode configurations show the same data trends. Detailed analysis of conductivity at deposition temperatures between 100 and 175 °C shows faster conductivity decay at higher temperature during the water purge step, ascribed to thermally activated water desorption kinetics. Analysis of real-time conductivity during ALD of other material systems could provide further insight into key aspects of film nucleation and nuclei coalescence.

  2. Characterization of the active site of chloroperoxidase using physical techniques

    SciTech Connect

    Hall, K.S.

    1986-01-01

    Chloroperoxidase (CPO) and Cytochrome P-450, two very different hemeproteins, have been shown to have similar active sites by several techniques. Recent work has demonstrated thiolate ligation from a cysteine residue to the iron in P-450. A major portion of this research has been devoted to obtaining direct evidence that CPO also has a thiolate 5th ligand from a cysteine residue. This information will provide the framework for a detailed analysis of the structure-function relationships between peroxidases, catalase and cytochrome P-450 hemeproteins. To determine whether the 5th ligand is a cysteine, methionine or a unique amino acid, specific isotope enrichment experiments were used. Preliminary /sup 1/H-NMR studies show that the carbon monoxide-CPO complex has a peak in the upfield region corresponding to alpha-protons of a thiolate amino acid. C. fumago was grown on 95% D/sub 2/O media with a small amount of /sup 1/H-cysteine added. Under these conditions C. fumago slows down the biosynthesis of cysteine by at least 50% and utilizes the exogenous cysteine in the media. GC-MS was able to show that the methylene protons next to the sulfur atom in cysteine are 80-90% protonated while these positions in methionine are approximately 73% deuterated. Comparison of the /sup 1/H-NMR spectra of CO-CPO and CO-CPO indicate the presence of a cysteine ligand in chloroperoxidase.

  3. N6-Methyldeoxyadenosine Marks Active Transcription Start Sites in Chlamydomonas

    PubMed Central

    Chen, Kai; Deng, Xin; Yu, Miao; Han, Dali; Hao, Ziyang; Liu, Jianzhao; Lu, Xingyu; Dore, Louis C; Weng, Xiaocheng; Ji, Quanjiang; Mets, Laurens; He, Chuan

    2015-01-01

    SUMMARY N6-methyldeoxyadenosine (6mA or m6A) is a DNA modification preserved in prokaryotes to eukaryotes. It is widespread in bacteria, and functions in DNA mismatch repair, chromosome segregation, and virulence regulation. In contrast, the distribution and function of 6mA in eukaryotes have been unclear. Here we present a comprehensive analysis of the 6mA landscape in the genome of Chlamydomonas using new sequencing approaches. We identified the 6mA modification in 84% of genes in Chlamydomonas. We found that 6mA mainly locates at ApT dinucleotides around transcription start sites (TSS) with a bimodal distribution, and appears to mark active genes. A periodic pattern of 6mA deposition was also observed at base resolution, which is associated with nucleosome distribution near the TSS, suggesting a possible role in nucleosome positioning. The new genome-wide mapping of 6mA and its unique distribution in the Chlamydomonas genome suggest potential regulatory roles of 6mA in gene expression in eukaryotic organisms. PMID:25936837

  4. Detection limit for activation measurements in ultralow background sites

    NASA Astrophysics Data System (ADS)

    Trache, Livius; Chesneanu, D.; Margineanu, R.; Pantelica, A.; Ghita, D. G.; Burducea, I.; Straticiuc, M.; Tang, X. D.

    2014-09-01

    We used 12C +13C fusion at the beam energies E = 6, 7 and 8 MeV to determine the sensitivity and the limits of activation method measurements in ultralow background sites. A 13C beam of 0.5 μA from the 3 MV Tandem accelerator of the Horia Hulubei National Institute of Physics and Nuclear Engineering - IFIN HH impinged on thick graphite targets. After about 24 hrs of irradiation targets were measured in two different laboratories: one with a heavy shielded Ge detector in the institute (at the surface) and one located underground in the microBequerel laboratory, in the salt mine of Slanic-Prahova, Romania. The 1369- and 2754 keV peaks from 24Na deactivation were clearly observed in the γ-ray spectra obtained for acquisitions lasting a few hours, or a few days. Determination of the detection limit in evaluating the cross sections for the target irradiated at Ec . m = 3 MeV indicates the fact that it is possible to measure gamma spectrum in underground laboratory down to Ec . m = 2 . 6 MeV. Cleaning the spectra with beta-gamma coincidences and increasing beam intensity 20 times will take as further down. The measurements are motivated by the study of the 12 C +12 C reaction at astrophysical energies.

  5. Disturbance opens recruitment sites for bacterial colonization in activated sludge.

    PubMed

    Vuono, David C; Munakata-Marr, Junko; Spear, John R; Drewes, Jörg E

    2016-01-01

    Little is known about the role of immigration in shaping bacterial communities or the factors that may dictate success or failure of colonization by bacteria from regional species pools. To address these knowledge gaps, the influence of bacterial colonization into an ecosystem (activated sludge bioreactor) was measured through a disturbance gradient (successive decreases in the parameter solids retention time) relative to stable operational conditions. Through a DNA sequencing approach, we show that the most abundant bacteria within the immigrant community have a greater probability of colonizing the receiving ecosystem, but mostly as low abundance community members. Only during the disturbance do some of these bacterial populations significantly increase in abundance beyond background levels and in few cases become dominant community members post-disturbance. Two mechanisms facilitate the enhanced enrichment of immigrant populations during disturbance: (i) the availability of resources left unconsumed by established species and (ii) the increased availability of niche space for colonizers to establish and displace resident populations. Thus, as a disturbance decreases local diversity, recruitment sites become available to promote colonization. This work advances our understanding of microbial resource management and diversity maintenance in complex ecosystems. PMID:25727891

  6. Active Site Characterization of Proteases Sequences from Different Species of Aspergillus.

    PubMed

    Morya, V K; Yadav, Virendra K; Yadav, Sangeeta; Yadav, Dinesh

    2016-09-01

    A total of 129 proteases sequences comprising 43 serine proteases, 36 aspartic proteases, 24 cysteine protease, 21 metalloproteases, and 05 neutral proteases from different Aspergillus species were analyzed for the catalytically active site residues using MEROPS database and various bioinformatics tools. Different proteases have predominance of variable active site residues. In case of 24 cysteine proteases of Aspergilli, the predominant active site residues observed were Gln193, Cys199, His364, Asn384 while for 43 serine proteases, the active site residues namely Asp164, His193, Asn284, Ser349 and Asp325, His357, Asn454, Ser519 were frequently observed. The analysis of 21 metalloproteases of Aspergilli revealed Glu298 and Glu388, Tyr476 as predominant active site residues. In general, Aspergilli species-specific active site residues were observed for different types of protease sequences analyzed. The phylogenetic analysis of these 129 proteases sequences revealed 14 different clans representing different types of proteases with diverse active site residues.

  7. A proposed definition of the 'activity' of surface sites on lactose carriers for dry powder inhalation.

    PubMed

    Grasmeijer, Floris; Frijlink, Henderik W; de Boer, Anne H

    2014-06-01

    A new definition of the activity of surface sites on lactose carriers for dry powder inhalation is proposed which relates to drug detachment during dispersion. The new definition is expected to improve the understanding of 'carrier surface site activity', which stimulates the unambiguous communication about this subject and may aid in the rational design and interpretation of future formulation studies. In contrast to the currently prevailing view on carrier surface site activity, it follows from the newly proposed definition that carrier surface site activity depends on more variables than just the physicochemical properties of the carrier surface. Because the term 'active sites' is ambiguous, it is recommended to use the term 'highly active sites' instead to denote carrier surface sites with a relatively high activity. PMID:24613490

  8. Ice-active proteins from New Zealand snow tussocks, Chionochloa macra AND C. rigida.

    PubMed

    Wharton, D A; Selvanesan, L; Marshall, C J

    2010-01-01

    The ice active protein profile of New Zealand snow tussocks Chionochloa macra and C. rigida consisted of ice nucleation activity but no antifreeze or recrystallization inhibition activity. The ice nucleation activity was similar in the two species, despite them being collected at different altitudes and at different times. The activity is intrinsic to the plant and is associated with the surface of the leaves. Snow tussocks collect water from fog. Nucleation sites on the surface of their leaves may aid the efficiency of this process. PMID:20919453

  9. Nanoindentation. Simulation of defect nucleation in a crystal.

    PubMed

    Gouldstone, A; Van Vliet, K J; Suresh, S

    2001-06-01

    Nanoindentation is the penetration of a surface to nanometre depths using an indenting device. It can be simulated using the Bragg bubble-raft model, in which a close-packed array of soap bubbles corresponds to the equilibrium positions of atoms in a crystalline solid. Here we show that homogeneous defect nucleation occurs within a crystal when its surface roughness is comparable to the radius of the indenter tip, and that the depth of the nucleation site below the surface is proportional to the half-width of the contact. Our results may explain the unusually high local stress required for defect nucleation in nano-indented face-centred cubic crystals. PMID:11395759

  10. Foam nucleation system for fluoropolymers

    SciTech Connect

    Buckmaster, M.D.; Randa, S.K.

    1988-08-16

    A foamable composition is described comprising a melt-processible fluoropolymer containing a nucleating amount of boron nitride and a synergistic amount of at least one inorganic salt that is thermally stable at the fluoropolymer extrusion temperature, and consists of a metal cation and a polyatomic anion.

  11. Comparison of parameterizations for homogeneous and heterogeneous ice nucleation

    NASA Astrophysics Data System (ADS)

    Koop, T.; Zobrist, B.

    2009-04-01

    The formation of ice particles from liquid aqueous aerosols is of central importance for the physics and chemistry of high altitude clouds. In this paper, we present new laboratory data on ice nucleation and compare them with two different parameterizations for homogeneous as well as heterogeneous ice nucleation. In particular, we discuss and evaluate the effect of solutes and ice nuclei. One parameterization is the λ-approach which correlates the depression of the freezing temperature of aqueous droplets in comparison to pure water droplets, Tf, with the corresponding depression, Tm, of the equilibrium ice melting point: Tf = λ × Tm. Here, λ is independent of concentration and a constant that is specific for a particular solute or solute/ice nucleus combination. The other approach is water-activity-based ice nucleation theory which describes the effects of solutes on the freezing temperature Tf via their effect on water activity: aw(Tf) = awi(Tf) + aw. Here, awi is the water activity of ice and aw is a constant that depends on the ice nucleus but is independent of the type of solute. We present new data on both homogeneous and heterogeneous ice nucleation with varying types of solutes and ice nuclei. We evaluate and discuss the advantages and limitations of the two approaches for the prediction of ice nucleation in laboratory experiments and atmospheric cloud models.

  12. Measurements to Fill Knowledge Gaps on Ice Nucleating Particle Sources over Oceans

    NASA Astrophysics Data System (ADS)

    DeMott, P. J.; Hill, T. C.; Ruppel, M. J.; Prather, K. A.; Collins, D. B.; Axson, J. L.; Lee, T.; Hwang, C. Y.; Sullivan, R. C.; McMeeking, G. R.; Mason, R.; Bertram, A. K.; Mayol-Bracero, O. L.; Lewis, E. R.

    2013-12-01

    Measurements of the temperature spectrum of ice nucleating particle concentrations by two methods in recent specialized laboratory sea spray studies and field campaigns in the Northern Hemisphere will be discussed and compared with historical data from over Southern Oceans. In general, new measurements of the condensation/immersion freezing activation spectra of realistically-generated laboratory sea spray particles (by wave generation or plunging water bubble production) are consistent with previous measurements made over oceans. The number concentrations of ice nuclei tend to be lower than are measured over land regions, at least for modestly supercooled cloud conditions. Certain but complex connections of ice nucleating particle production to ocean microbiological processes affecting the chemical composition of the sea surface microlayer are seen, but the nature of the ice nucleating units of particles remains to be identified. Associations of ice nucleating particle concentrations with heterotrophic bacterial concentrations were noted in some experiments, while correlation with chlorophyll-a concentration in seawater was clearly identified in laboratory simulations of phytoplankton blooms. These data may ultimately serve as the basis for parameterization development for ice initiation in numerical model simulations of mixed-phase clouds. Atmospheric measurements have been made at island sites, via aircraft, and from ship-based filter collections in the Northern Hemisphere. The immersion freezing spectra of these particles are similar to those found in recent laboratory studies and historical measurements, but show the expected natural variability by location. The majority of particles detected thus far as ice nuclei from sea spray and in marine air show minimal or episodic/variable direct participation of biological ice nucleating organisms on the basis of sensitivity to high temperatures (95°C). However, assembled measurements are still sparse, the nuclei

  13. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  14. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  15. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  16. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  17. 10 CFR 63.16 - Review of site characterization activities. 2

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of... conduct of site characterization activities at the Yucca Mountain site, DOE shall report the nature and... activities at the Yucca Mountain site, NRC staff shall be permitted to visit and inspect the locations...

  18. Ice Nucleation Properties of Oxidized Carbon Nanomaterials.

    PubMed

    Whale, Thomas F; Rosillo-Lopez, Martin; Murray, Benjamin J; Salzmann, Christoph G

    2015-08-01

    Heterogeneous ice nucleation is an important process in many fields, particularly atmospheric science, but is still poorly understood. All known inorganic ice nucleating particles are relatively large in size and tend to be hydrophilic. Hence it is not obvious that carbon nanomaterials should nucleate ice. However, in this paper we show that four different readily water-dispersible carbon nanomaterials are capable of nucleating ice. The tested materials were carboxylated graphene nanoflakes, graphene oxide, oxidized single walled carbon nanotubes and oxidized multiwalled carbon nanotubes. The carboxylated graphene nanoflakes have a diameter of ∼30 nm and are among the smallest entities observed so far to nucleate ice. Overall, carbon nanotubes were found to nucleate ice more efficiently than flat graphene species, and less oxidized materials nucleated ice more efficiently than more oxidized species. These well-defined carbon nanomaterials may pave the way to bridging the gap between experimental and computational studies of ice nucleation. PMID:26267196

  19. The effect of nucleation and crystal growth on isotope fractionation

    NASA Astrophysics Data System (ADS)

    Wang, Z.; Gaetani, G. A.; Liu, C.; Hu, P.; Cohen, A. L.

    2011-12-01

    A set of "free-drift" experiments is conducted to precipitate aragonites from seawater at controlled temperature (25-55oC) and CO2 degassing rate in the lab. These experiments help to calibrate a coupled degassing-nucleation-crystal growth model, which not only can reproduce measured pH and alkalinity over the course of the experiments, but also predict crystal size within a factor of two of the measured values, the activation energy of the precipitation reaction constant to be 24.3±1.3 kJ/mol, the surface energy of aragonite crystals that is consistent with estimation by atomistic simulation and crystal morphology. Forward simulation of our precipitation experiments using calibrated parameters reveal the supersaturation of seawater arrives at a critical value (~13-50 in our experiment) before nucleation initiates and when the concentration of the total dissolved inorganic carbon (DIC) reduces to that of Ca. This result cannot be explained by classical nucleation theory (CNT), but is consistent with recently proposed "two-step" nucleation model, implying solution chemistry determines when the nucleation starts but the surface properties of crystal (surface energy and crystal morphology) determine the size of the crystal. It also requires not only carbonate ions but all other DIC species within a sphere of a-few-micron radius actively participate into the nucleation process. This model is then used as a framework to understand oxygen and Mg isotope fractionation between carbonates and fluid. Our results suggest nucleation and crystal growth will affect isotope fractionation at different levels depending on experimental conditions. A quantitative analysis using our model can help reconcile the isotope fractionation factors determined by various experimental approaches.

  20. Identification & Characterization of Fungal Ice Nucleation Proteins

    NASA Astrophysics Data System (ADS)

    Scheel, Jan Frederik; Kunert, Anna Theresa; Kampf, Christopher Johannes; Mauri, Sergio; Weidner, Tobias; Pöschl, Ulrich; Fröhlich-Nowoisky, Janine

    2016-04-01

    Freezing of water at relatively warm subfreezing temperatures is dependent on ice nucleation catalysis facilitated by ice nuclei (IN). These IN can be of various origins and although extensive research was done and progress was achieved, the nature and mechanisms leading to an effective IN are to date still poorly understood. Some of the most important processes of our geosphere like the water cycle are highly dependent on effective ice nucleation at temperatures between -2°C - -8°C, a temperature range which is almost exclusively covered by biological IN (BioIN). BioIN are usually macromolecular structures of biological polymers. Sugars as well as proteins have been reported to serve as IN and the best characterized BioIN are ice nucleation proteins (IN-P) from gram negative bacteria. Fungal strains from Fusarium spp. were described to be effective IN at subfreezing temperatures up to -2°C already 25 years ago and more and more fungal species are described to serve as efficient IN. Fungal IN are also thought to be proteins or at least contain a proteinaceous compound, but to date the fungal IN-P primary structure as well as their coding genetic elements of all IN active fungi are unknown. The aim of this study is a.) to identify the proteins and their coding genetic elements from IN active fungi (F. acuminatum, F. avenaceum, M. alpina) and b.) to characterize the mechanisms by which fungal IN serve as effective IN. We designed an interdisciplinary approach using biological, analytical and physical methods to identify fungal IN-P and describe their biological, chemical, and physical properties.

  1. Controls of functional group chemistry on calcium carbonate nucleation: Insights into systematics of biomolecular innovations for skeletal mineralization?

    NASA Astrophysics Data System (ADS)

    Dove, P. M.; Hamm, L. M.; Giuffre, A. J.

    2012-12-01

    Living organisms produce skeletal structures within a complex matrix of organic macromolecules that guide the nucleation and growth of crystalline structures into the organic-inorganic composites we know as biominerals. This type of biomolecule-directed mineralization is an ancient process as evidenced by structures in the fossil record that date to the Ediacaran (ca. 549 Ma). Our understanding of template-directed biomineralization, however, is largely based upon assumptions from studies that: 1) qualitatively demonstrate some chemical functionalities influence the nucleating mineral phase and morphology; 2) propose proteins are the primary driver to template-directed mineralization and 3) propose the ubiquitous polysaccharides are inert components. Thus, a mechanistic basis for how the underlying chemistry of macromolecules controls nucleation kinetics and thermodynamics in template-directed nucleation is not well established. Moreover, there is not yet a good appreciation for how patterns of skeletal mineralization evolved with biochemical innovations in response to environmental changes over geologic timescales. In small steps toward understanding biochemical controls on biomineralization, we test the hypothesis that the kinetics and thermodynamics of calcium carbonate (CaCO3) formation is regulated by a systematic relationship to the functional group chemistry of macromolecules. A long-term goal is to establish the energetic basis for biochemical motifs that are seen (and not seen) at sites of calcification across the phylogenetic tree. Two types of studies were conducted. The first measured nucleation rates on model biomolecular substrates with termini that are found in proteins associated with sites of calcification (-COOH, -PO4, and -SH) and two alkanethiol chain lengths (16-C and 11-C) at a variety of chemical driving forces. The measurements show functional group chemistry and molecule conformation regulate rates by a predictable relation to interfacial

  2. GAS HYDRATES AT TWO SITES OF AN ACTIVE CONTINENTAL MARGIN.

    USGS Publications Warehouse

    Kvenvolden, K.A.

    1985-01-01

    Sediment containing gas hydrates from two distant Deep Sea Drilling Project sites (565 and 568), located about 670 km apart on the landward flank of the Middle America Trench, was studied to determine the geochemical conditions that characterize the occurrence of gas hydrates. Site 565 was located in the Pacific Ocean offshore the Nicoya Peninsula of Costa Rica in 3,111 m of water. The depth of the hole at this site was 328 m, and gas hydrates were recovered from 285 and 319 m. Site 568 was located about 670 km to the northwest offshore Guatemala in 2,031 m of water. At this site the hole penetrated to 418 m, and gas hydrates were encountered at 404 m.

  3. Control of active sites in selective flocculation: III -- Mechanism of site blocking

    SciTech Connect

    Behl, S.; Moudgil, B.M. . Dept. of Materials Science and Engineering)

    1993-12-01

    It has been shown in Parts I and II of this paper that heteroflocculation can be controlled by poisoning the sites for flocculant adsorption using a site blocking agent (SBA). An efficient SBA was determined to be the lower molecular weight fraction of the flocculant. In this paper, the underlying mechanism of SBA action is described. Also, the mathematical model detailed in Part I is used to determine the effect of different SBAs on apatite-dolomite separation efficiency. It has been demonstrated that the depression in flocculation is directly related to the site blocking parameter ([bar [Phi

  4. Dynamically achieved active site precision in enzyme catalysis.

    PubMed

    Klinman, Judith P

    2015-02-17

    CONSPECTUS: The grand challenge in enzymology is to define and understand all of the parameters that contribute to enzymes' enormous rate accelerations. The property of hydrogen tunneling in enzyme reactions has moved the focus of research away from an exclusive focus on transition state stabilization toward the importance of the motions of the heavy atoms of the protein, a role for reduced barrier width in catalysis, and the sampling of a protein conformational landscape to achieve a family of protein substates that optimize enzyme-substrate interactions and beyond. This Account focuses on a thermophilic alcohol dehydrogenase for which the chemical step of hydride transfer is rate determining across a wide range of experimental conditions. The properties of the chemical coordinate have been probed using kinetic isotope effects, indicating a transition in behavior below 30 °C that distinguishes nonoptimal from optimal C-H activation. Further, the introduction of single site mutants has the impact of either enhancing or eliminating the temperature dependent transition in catalysis. Biophysical probes, which include time dependent hydrogen/deuterium exchange and fluorescent lifetimes and Stokes shifts, have also been pursued. These studies allow the correlation of spatially resolved transitions in protein motions with catalysis. It is now possible to define a long-range network of protein motions in ht-ADH that extends from a dimer interface to the substrate binding domain across to the cofactor binding domain, over a distance of ca. 30 Å. The ongoing challenge to obtaining spatial and temporal resolution of catalysis-linked protein motions is discussed.

  5. Earthquake nucleation in weak subducted carbonates

    NASA Astrophysics Data System (ADS)

    Kurzawski, Robert M.; Stipp, Michael; Niemeijer, André R.; Spiers, Christopher J.; Behrmann, Jan H.

    2016-09-01

    Ocean-floor carbonate- and clay-rich sediments form major inputs to subduction zones, especially at low-latitude convergent plate margins. Therefore, knowledge of their frictional behaviour is fundamental for understanding plate-boundary earthquakes. Here we report results of mechanical tests performed on simulated fault gouges prepared from ocean-floor carbonates and clays, cored during IODP drilling offshore Costa Rica. Clay-rich gouges show internal friction coefficients (that is, the slope of linearized shear stress versus normal stress data) of μint = 0.44 - 0.56, irrespective of temperature and pore-fluid pressure (Pf). By contrast, μint for the carbonate gouge strongly depends on temperature and pore-fluid pressure, with μint decreasing dramatically from 0.84 at room temperature and Pf = 20 MPa to 0.27 at T = 140 °C and Pf = 120 MPa. This effect provides a fundamental mechanism of shear localization and earthquake generation in subduction zones, and makes carbonates likely nucleation sites for plate-boundary earthquakes. Our results imply that rupture nucleation is prompted by a combination of temperature-controlled frictional instability and temperature- and pore-pressure-dependent weakening of calcareous fault gouges.

  6. Thermodynamics of ice nucleation in liquid water.

    PubMed

    Wang, Xin; Wang, Shui; Xu, Qinzhi; Mi, Jianguo

    2015-01-29

    We present a density functional theory approach to investigate the thermodynamics of ice nucleation in supercooled water. Within the theoretical framework, the free-energy functional is constructed by the direct correlation function of oxygen-oxygen of the equilibrium water, and the function is derived from the reference interaction site model in consideration of the interactions of hydrogen-hydrogen, hydrogen-oxygen, and oxygen-oxygen. The equilibrium properties, including vapor-liquid and liquid-solid phase equilibria, local structure of hexagonal ice crystal, and interfacial structure and tension of water-ice are calculated in advance to examine the basis for the theory. The predicted phase equilibria and the water-ice surface tension are in good agreement with the experimental data. In particular, the critical nucleus radius and free-energy barrier during ice nucleation are predicted. The critical radius is similar to the simulation value, suggesting that the current theoretical approach is suitable in describing the thermodynamic properties of ice crystallization.

  7. Lethal Factor Active-Site Mutations Affect Catalytic Activity In Vitro

    PubMed Central

    Hammond, S. E.; Hanna, P. C.

    1998-01-01

    The lethal factor (LF) protein of Bacillus anthracis lethal toxin contains the thermolysin-like active-site and zinc-binding consensus motif HEXXH (K. R. Klimpel, N. Arora, and S. H. Leppla, Mol. Microbiol. 13:1093–1100, 1994). LF is hypothesized to act as a Zn2+ metalloprotease in the cytoplasm of macrophages, but no proteolytic activities have been previously shown on any target substrate. Here, synthetic peptides are hydrolyzed by LF in vitro. Mass spectroscopy and peptide sequencing of isolated cleavage products separated by reverse-phase high-pressure liquid chromatography indicate that LF seems to prefer proline-containing substrates. Substitution mutations within the consensus active-site residues completely abolish all in vitro catalytic functions, as does addition of 1,10-phenanthroline, EDTA, and certain amino acid hydroxamates, including the novel zinc metalloprotease inhibitor ZINCOV. In contrast, the protease inhibitors bestatin and lysine CMK, previously shown to block LF activity on macrophages, did not block LF activity in vitro. These data provide the first direct evidence that LF may act as an endopeptidase. PMID:9573135

  8. Monoclonal antibody against the active site of caeruloplasmin and the ELISA system detecting active caeruloplasmin.

    PubMed

    Hiyamuta, S; Ito, K

    1994-04-01

    Serum caeruloplasmin deficiency is a characteristic biochemical abnormality found in patients with Wilson's disease, but the mechanism of this disease is unknown. Although the phenylenediamine oxidase activity of serum caeruloplasmin is markedly low in patients with Wilson's disease, mRNA of caeruloplasmin exists to some extent. To investigate the deficiency of caeruloplasmin oxidase activity in Wilson's disease, we generated 14 monoclonal antibodies (MAbs) and selected ID1, which had the strongest reactivity, and ID2, which had neutralizing ability. We also established a system to measure active caeruloplasmin specifically using these MAbs. These MAbs and the system will be useful tools in analyzing the active site of caeruloplasmin in patients with Wilson's disease.

  9. The role of elastic anisotropy, length scale and crystallographic slip in fatigue crack nucleation

    NASA Astrophysics Data System (ADS)

    Sweeney, C. A.; Vorster, W.; Leen, S. B.; Sakurada, E.; McHugh, P. E.; Dunne, F. P. E.

    2013-05-01

    Fatigue crack nucleation in polycrystal ferritic steel is investigated through experimental observation of multiple large-grained, notched, four-point bend tests combined with explicit microstructural representation of the same samples using crystal plasticity finite element techniques in order to assess fatigue indicator parameters, together with the roles of elastic anisotropy and length scale effects in slip development, and hence in crack nucleation. Elastic anisotropy has been demonstrated to play a pivotal role in the distribution and magnitude of polycrystal slip relative to observed crack nucleation sites in the context of constrained cyclic microplasticity. Length scale effects were found not to alter substantively the distributions or magnitudes of slip relative to the observed crack nucleation site, but in detailed analyses of an experimental sample, the location of highest magnitude of geometrically necessary dislocations was found to coincide precisely with the position of predicted peak plasticity and the experimentally observed crack nucleation site. The distributions of microplasticity within polycrystal samples were found to change quite significantly between the first yield and after multiple cycles. As a result, the effective plastic strain per cycle was found to be a better indicator of fatigue crack nucleation than peak effective plastic strain. In nine independently tested and analysed polycrystal samples, the cyclic effective plastic strain and crystallographic system peak accumulated slip were found to be good indicators of a fatigue crack nucleation site.

  10. Robotics and Automation Activities at the Savannah River Site: A Site Report for SUBWOG 39F

    SciTech Connect

    Teese, G.D.

    1995-09-28

    The Savannah River Site has successfully used robots, teleoperators, and remote video to reduce exposure to ionizing radiation, improve worker safety, and improve the quality of operations. Previous reports have described the use of mobile teleoperators in coping with a high level liquid waste spill, the removal of highly contaminated equipment, and the inspection of nuclear reactor vessels. This report will cover recent applications at the Savannah River, as well as systems which SRS has delivered to other DOE site customers.

  11. Control of active sites in selective flocculation: II -- Role of site blocking agents

    SciTech Connect

    Behl, S.; Moudgil, B.M. . Dept. of Materials Science and Engineering)

    1993-12-01

    Control of heteroflocculation using a lower molecular weight fraction of the flocculant as a site blocking agent is demonstrated in the apatite-dolomite-polyethylene oxide system. The most effective SBA (site blocking agent) was determined to be the highest molecular weight fraction of the flocculant itself which was not capable of flocculating any of the components of the mixture. In the presence of the SBA, flocculant adsorption decreased significantly on apatite particles, thereby inhibiting coflocculation.

  12. Surface structure, crystallographic and ice-nucleating properties of cellulose

    NASA Astrophysics Data System (ADS)

    Hiranuma, Naruki; Möhler, Ottmar; Kiselev, Alexei; Saathoff, Harald; Weidler, Peter; Shutthanandan, Shuttha; Kulkarni, Gourihar; Jantsch, Evelyn; Koop, Thomas

    2015-04-01

    Increasing evidence of the high diversity and efficient freezing ability of biological ice-nucleating particles is driving a reevaluation of their impact upon climate. Despite their potential importance, little is known about their atmospheric abundance and ice nucleation efficiency, especially non-proteinaceous ones, in comparison to non-biological materials (e.g., mineral dust). Recently, microcrystalline cellulose (MCC; non-proteinaceous plant structural polymer) has been identified as a potential biological ice-nucleating particle. However, it is still uncertain if the ice-nucleating activity is specific to the MCC structure or generally relevant to all cellulose materials, such that the results of MCC can be representatively scaled up to the total cellulose content in the atmosphere to address its role in clouds and the climate system. Here we use the helium ion microscopy (HIM) imaging and the X-ray diffraction (XRD) technique to characterize the nanoscale surface structure and crystalline properties of the two different types of cellulose (MCC and fibrous cellulose extracted from natural wood pulp) as model proxies for atmospheric cellulose particles and to assess their potential accessibility for water molecules. To complement these structural characterizations, we also present the results of immersion freezing experiments using the cold stage-based droplet freezing BINARY (Bielefeld Ice Nucleation ARaY) technique. The HIM results suggest that both cellulose types have a complex porous morphology with capillary spaces between the nanoscale fibrils over the microfiber surface. These surface structures may make cellulose accessible to water. The XRD results suggest that the structural properties of both cellulose materials are in agreement (i.e., P21 space group; a=7.96 Å, b=8.35 Å, c=10.28 Å) and comparable to the crystallographic properties of general monoclinic cellulose (i.e., Cellulose Iβ). The results obtained from the BINARY measurements suggest

  13. Mutation at a Strictly Conserved, Active Site Tyrosine in the Copper Amine Oxidase Leads to Uncontrolled Oxygenase Activity

    SciTech Connect

    Chen, Zhi-wei; Datta, Saumen; DuBois, Jennifer L.; Klinman, Judith P.; Mathews, F. Scott

    2010-09-07

    The copper amine oxidases carry out two copper-dependent processes: production of their own redox-active cofactor (2,4,5-trihydroxyphenylalanine quinone, TPQ) and the subsequent oxidative deamination of substrate amines. Because the same active site pocket must facilitate both reactions, individual active site residues may serve multiple roles. We have examined the roles of a strictly conserved active site tyrosine Y305 in the copper amine oxidase from Hansenula polymorpha kinetically, spetroscopically (Dubois and Klinman (2006) Biochemistry 45, 3178), and, in the present work, structurally. While the Y305A enzyme is almost identical to the wild type, a novel, highly oxygenated species replaces TPQ in the Y305F active sites. This new structure not only provides the first direct detection of peroxy intermediates in cofactor biogenesis but also indicates the critical control of oxidation chemistry that can be conferred by a single active site residue.

  14. Role of nucleation in nanodiamond film growth

    SciTech Connect

    Lifshitz, Y.; Lee, C.H.; Wu, Y.; Zhang, W.J.; Bello, I.; Lee, S.T.

    2006-06-12

    Nanodiamond films were deposited using different microwave plasma chemical vapor deposition schemes following several nucleation pretreatment methods. The nucleation efficiency and the films structure were investigated using scanning and transmission electron microscopy and Raman spectroscopy. C{sub 2} dimer growth (CH{sub 4} and H{sub 2} in 90% Ar) cannot nucleate diamond and works only on existing diamond surfaces. The methyl radical process (up to 20% CH{sub 4} in H{sub 2}) allows some nucleation probability on appropriate substrates. Prolonged bias enhanced nucleation initiates both diamond nucleation and growth. C{sub 2} dimer growth results in pure nanodiamond free of amorphous carbon, while prolonged bias enhanced nucleation forms an amorphous carbon/nanodiamond composite.

  15. Nucleation and interfacial adsorption in ternary systems.

    PubMed

    Philippe, T

    2015-03-01

    Nucleation is studied in incompressible ternary fluids by examining the topology of the overall landscape of the energy surface. Minimum free energy paths for nucleation (MFEPs) of a single nucleus in an infinite matrix are computed with the string method in the framework of the continuum theory of nucleation for the regular solution. Properties of the critical nucleus are compared with the predictions of the classical nucleation theory. MFEPs are found to exhibit complex nucleation pathways with non-monotonic variations of compositions in the interfacial region, specifically adsorption of a component. In the symmetric regular solution, the minority component is found to segregate at the interface during nucleation with a concomitant depletion of the nucleus core, resulting in unpredicted partition of the non-selective component. Despite increasing the gradient energy, such inhomogeneity in composition is shown to lower the nucleation barrier. PMID:25747088

  16. Measuring induction times and crystal nucleation rates.

    PubMed

    Brandel, Clément; ter Horst, Joop H

    2015-01-01

    A large variation is observed in induction times measured under equal conditions in 1 ml solutions. Ruling out experimental errors, this variation originates from the nucleation process. The induction time distribution is explained by the stochastic nature of nucleation if the number of nuclei formed is approaching 1 per vial. Accurate heterogeneous crystal nucleation rates were determined from the induction time distributions on a 1 ml scale for racemic diprophylline in two solvents. The difference in nucleation behaviour in the two solvents originates from the energy barrier for nucleation, which is much higher in the solvent in which induction times are much longer. In addition the pre-exponential factor for the crystal nucleation rate in both solvents is rather low compared to predictions using Classical Nucleation Theory. Unfortunately, concentration and surface characteristics of the effective heterogeneous particles are not known which clouds a further molecular interpretation.

  17. Sigmoid kinetics of protein crystal nucleation

    NASA Astrophysics Data System (ADS)

    Nanev, Christo N.; Tonchev, Vesselin D.

    2015-10-01

    A non-linear differential equation expressing the new phase nucleation rate in the different steps of the process (non-stationary and stationary nucleation and in the plateau region) is derived from basic principles of the nucleation theory. It is shown that one and the same sigmoid (logistic) function describes both nucleation scenarios: the one according to the classical theory, and the other according to the modern two-stage mechanism of protein crystal formation. Comparison to experimental data on both insulin crystal nucleation kinetics and on bovine β-lactoglobulin crystallization indicates a good agreement with the sigmoidal prediction. Experimental data for electrochemical nucleation and glass crystallization obey the same sigmoid time dependence, and suggest universality of this nucleation kinetics law.

  18. Diamond nucleation under bias conditions

    SciTech Connect

    Stoeckel, R.; Stammler, M.; Janischowsky, K.; Ley, L.; Albrecht, M.; Strunk, H.P.

    1998-01-01

    The so-called bias pretreatment allows the growth of heteroepitaxial diamond films by plasma chemical vapor deposition on silicon (100) surfaces. We present plan-view and cross-sectional transmission electron micrographs of the substrate surface at different phases of the bias pretreatment. These observations are augmented by measurements of the etch rates of Si, SiC, and different carbon modifications under plasma conditions and the size distribution of oriented diamond crystals grown after bias pretreatment. Based on these results a new model for diamond nucleation under bias conditions is proposed. First, a closed layer of nearly epitaxially oriented cubic SiC with a thickness of about 10 nm is formed. Subplantation of carbon into this SiC layer causes a supersaturation with carbon and results in the subcutaneous formation of epitaxially oriented nucleation centers in the SiC layer. Etching of the SiC during the bias pretreatment as well as during diamond growth brings these nucleation centers to the sample surface and causes the growth of diamonds epitaxially oriented on the Si/SiC substrate. {copyright} {ital 1998 American Institute of Physics.}

  19. Identification of promiscuous ene-reductase activity by mining structural databases using active site constellations

    PubMed Central

    Steinkellner, Georg; Gruber, Christian C.; Pavkov-Keller, Tea; Binter, Alexandra; Steiner, Kerstin; Winkler, Christoph; Łyskowski, Andrzej; Schwamberger, Orsolya; Oberer, Monika; Schwab, Helmut; Faber, Kurt; Macheroux, Peter; Gruber, Karl

    2014-01-01

    The exploitation of catalytic promiscuity and the application of de novo design have recently opened the access to novel, non-natural enzymatic activities. Here we describe a structural bioinformatic method for predicting catalytic activities of enzymes based on three-dimensional constellations of functional groups in active sites (‘catalophores’). As a proof-of-concept we identify two enzymes with predicted promiscuous ene-reductase activity (reduction of activated C–C double bonds) and compare them with known ene-reductases, that is, members of the Old Yellow Enzyme family. Despite completely different amino acid sequences, overall structures and protein folds, high-resolution crystal structures reveal equivalent binding modes of typical Old Yellow Enzyme substrates and ligands. Biochemical and biocatalytic data show that the two enzymes indeed possess ene-reductase activity and reveal an inverted stereopreference compared with Old Yellow Enzymes for some substrates. This method could thus be a tool for the identification of viable starting points for the development and engineering of novel biocatalysts. PMID:24954722

  20. The Global Distribution of Atmospheric Ice Nucleating Particles

    NASA Astrophysics Data System (ADS)

    Vergara Temprado, J.; Wilson, T. W.; Burrows, S. M.; Murray, B. J.; Carslaw, K. S.

    2015-12-01

    Ice nucleating particles (INP) affect the amount of ice in clouds, changing many of their properties. However, the relevance of different aerosol species towards causing atmospheric ice nucleation in different contexts is not well-understood. In this presentation, I will show the simulated spatial and seasonal distributions of ice nucleating particles from K-feldspar (the ice-active component of desert dust), marine organics (from sea spray) and black carbon (from combustion). The global distribution of these materials is simulated using two global aerosol model (GLOMAP-mode and EMAC). The contribution of each aerosol species to the INP distribution is calculated using parameterizations of their ice nucleating ability developed from laboratory studies of the materials involved, founding good agreement with INP observations. We found that K-feldspar dominates the atmospheric distribution of ice nucleating particles; however, marine organic INPs and black carbon are important regionally in some seasons. This study advances our understanding of which aerosol species have to be included in order to adequately describe the global and regional distribution of INPs in models.

  1. Crystallographic Analysis of Nucleation at Hardness Indentations in High-Purity Aluminum

    NASA Astrophysics Data System (ADS)

    Xu, Chaoling; Zhang, Yubin; Lin, Fengxiang; Wu, Guilin; Liu, Qing; Juul Jensen, Dorte

    2016-08-01

    Nucleation at Vickers hardness indentations has been studied in high-purity aluminum cold-rolled 12 pct. Electron channeling contrast was used to measure the size of the indentations and to detect nuclei, while electron backscattering diffraction was used to determine crystallographic orientations. It is found that indentations are preferential nucleation sites. The crystallographic orientations of the deformed grains affect the hardness and the nucleation potentials at the indentations. Higher hardness gives increased nucleation probabilities. Orientation relationships between nuclei developed at different indentations within one original grain are analyzed and it is found that the orientation distribution of the nuclei is far from random. It is suggested that it relates to the orientations present near the indentation tips which in turn depend on the orientation of the selected grain in which they form. Finally, possible nucleation mechanisms are briefly discussed.

  2. An ionizable active-site tryptophan imparts catalase activity to a peroxidase core.

    PubMed

    Loewen, Peter C; Carpena, Xavi; Vidossich, Pietro; Fita, Ignacio; Rovira, Carme

    2014-05-21

    Catalase peroxidases (KatG's) are bifunctional heme proteins that can disproportionate hydrogen peroxide (catalatic reaction) despite their structural dissimilarity with monofunctional catalases. Using X-ray crystallography and QM/MM calculations, we demonstrate that the catalatic reaction of KatG's involves deprotonation of the active-site Trp, which plays a role similar to that of the distal His in monofunctional catalases. The interaction of a nearby mobile arginine with the distal Met-Tyr-Trp essential adduct (in/out) acts as an electronic switch, triggering deprotonation of the adduct Trp.

  3. Actin nucleation at the centrosome controls lymphocyte polarity

    PubMed Central

    Obino, Dorian; Farina, Francesca; Malbec, Odile; Sáez, Pablo J.; Maurin, Mathieu; Gaillard, Jérémie; Dingli, Florent; Loew, Damarys; Gautreau, Alexis; Yuseff, Maria-Isabel; Blanchoin, Laurent; Théry, Manuel; Lennon-Duménil, Ana-Maria

    2016-01-01

    Cell polarity is required for the functional specialization of many cell types including lymphocytes. A hallmark of cell polarity is the reorientation of the centrosome that allows repositioning of organelles and vesicles in an asymmetric fashion. The mechanisms underlying centrosome polarization are not fully understood. Here we found that in resting lymphocytes, centrosome-associated Arp2/3 locally nucleates F-actin, which is needed for centrosome tethering to the nucleus via the LINC complex. Upon lymphocyte activation, Arp2/3 is partially depleted from the centrosome as a result of its recruitment to the immune synapse. This leads to a reduction in F-actin nucleation at the centrosome and thereby allows its detachment from the nucleus and polarization to the synapse. Therefore, F-actin nucleation at the centrosome—regulated by the availability of the Arp2/3 complex—determines its capacity to polarize in response to external stimuli. PMID:26987298

  4. Nuclear Site Security in the Event of Terrorist Activity

    SciTech Connect

    Thomson, M.L.; Sims, J.

    2008-07-01

    This paper, presented as a poster, identifies why ballistic protection should now be considered at nuclear sites to counter terrorist threats. A proven and flexible form of multi purpose protection is described in detail with identification of trial results that show its suitability for this role. (authors)

  5. Cell-cycle dependent phosphorylation of yeast pericentrin regulates γ-TuSC-mediated microtubule nucleation.

    PubMed

    Lin, Tien-Chen; Neuner, Annett; Schlosser, Yvonne T; Scharf, Annette N D; Weber, Lisa; Schiebel, Elmar

    2014-01-01

    Budding yeast Spc110, a member of γ-tubulin complex receptor family (γ-TuCR), recruits γ-tubulin complexes to microtubule (MT) organizing centers (MTOCs). Biochemical studies suggest that Spc110 facilitates higher-order γ-tubulin complex assembly (Kollman et al., 2010). Nevertheless the molecular basis for this activity and the regulation are unclear. Here we show that Spc110 phosphorylated by Mps1 and Cdk1 activates γ-TuSC oligomerization and MT nucleation in a cell cycle dependent manner. Interaction between the N-terminus of the γ-TuSC subunit Spc98 and Spc110 is important for this activity. Besides the conserved CM1 motif in γ-TuCRs (Sawin et al., 2004), a second motif that we named Spc110/Pcp1 motif (SPM) is also important for MT nucleation. The activating Mps1 and Cdk1 sites lie between SPM and CM1 motifs. Most organisms have both SPM-CM1 (Spc110/Pcp1/PCNT) and CM1-only (Spc72/Mto1/Cnn/CDK5RAP2/myomegalin) types of γ-TuCRs. The two types of γ-TuCRs contain distinct but conserved C-terminal MTOC targeting domains.DOI: http://dx.doi.org/10.7554/eLife.02208.001. PMID:24842996

  6. Preliminary siting activities for new waste handling facilities at the Idaho National Engineering Laboratory

    SciTech Connect

    Taylor, D.D.; Hoskinson, R.L.; Kingsford, C.O.; Ball, L.W.

    1994-09-01

    The Idaho Waste Processing Facility, the Mixed and Low-Level Waste Treatment Facility, and the Mixed and Low-Level Waste Disposal Facility are new waste treatment, storage, and disposal facilities that have been proposed at the Idaho National Engineering Laboratory (INEL). A prime consideration in planning for such facilities is the selection of a site. Since spring of 1992, waste management personnel at the INEL have been involved in activities directed to this end. These activities have resulted in the (a) identification of generic siting criteria, considered applicable to either treatment or disposal facilities for the purpose of preliminary site evaluations and comparisons, (b) selection of six candidate locations for siting,and (c) site-specific characterization of candidate sites relative to selected siting criteria. This report describes the information gathered in the above three categories for the six candidate sites. However, a single, preferred site has not yet been identified. Such a determination requires an overall, composite ranking of the candidate sites, which accounts for the fact that the sites under consideration have different advantages and disadvantages, that no single site is superior to all the others in all the siting criteria, and that the criteria should be assigned different weighing factors depending on whether a site is to host a treatment or a disposal facility. Stakeholder input should now be solicited to help guide the final selection. This input will include (a) siting issues not already identified in the siting, work to date, and (b) relative importances of the individual siting criteria. Final site selection will not be completed until stakeholder input (from the State of Idaho, regulatory agencies, the public, etc.) in the above areas has been obtained and a strategy has been developed to make a composite ranking of all candidate sites that accounts for all the siting criteria.

  7. Active Layer and Moisture Measurements for Intensive Site 0 and 1, Barrow, Alaska

    DOE Data Explorer

    John Peterson

    2015-04-17

    These are measurements of Active Layer Thickness collected along several lines beginning in September, 2011 to the present. The data were collected at several time periods along the Site0 L2 Line, the Site1 AB Line, and an ERT Monitoring Line near Area A in Site1.

  8. Communication. Kinetics of scavenging of small, nucleating clusters. First nucleation theorem and sum rules

    DOE PAGES

    Malila, Jussi; McGraw, Robert; Laaksonen, Ari; Lehtinen, Kari E. J.

    2015-01-07

    Despite recent advances in monitoring nucleation from a vapor at close-to-molecular resolution, the identity of the critical cluster, forming the bottleneck for the nucleation process, remains elusive. During past twenty years, the first nucleation theorem has been often used to extract the size of the critical cluster from nucleation rate measurements. However, derivations of the first nucleation theorem invoke certain questionable assumptions that may fail, e.g., in the case of atmospheric new particle formation, including absence of subcritical cluster losses and heterogeneous nucleation on pre-existing nanoparticles. Here we extend the kinetic derivation of the first nucleation theorem to give amore » general framework to include such processes, yielding sum rules connecting the size dependent particle formation and loss rates to the corresponding loss-free nucleation rate and the apparent critical size from a naïve application of the first nucleation theorem that neglects them.« less

  9. Communication. Kinetics of scavenging of small, nucleating clusters. First nucleation theorem and sum rules

    SciTech Connect

    Malila, Jussi; McGraw, Robert; Laaksonen, Ari; Lehtinen, Kari E. J.

    2015-01-07

    Despite recent advances in monitoring nucleation from a vapor at close-to-molecular resolution, the identity of the critical cluster, forming the bottleneck for the nucleation process, remains elusive. During past twenty years, the first nucleation theorem has been often used to extract the size of the critical cluster from nucleation rate measurements. However, derivations of the first nucleation theorem invoke certain questionable assumptions that may fail, e.g., in the case of atmospheric new particle formation, including absence of subcritical cluster losses and heterogeneous nucleation on pre-existing nanoparticles. Here we extend the kinetic derivation of the first nucleation theorem to give a general framework to include such processes, yielding sum rules connecting the size dependent particle formation and loss rates to the corresponding loss-free nucleation rate and the apparent critical size from a naïve application of the first nucleation theorem that neglects them.

  10. Structural mechanism of RuBisCO activation by carbamylation of the active site lysine

    PubMed Central

    Stec, Boguslaw

    2012-01-01

    Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is a crucial enzyme in carbon fixation and the most abundant protein on earth. It has been studied extensively by biochemical and structural methods; however, the most essential activation step has not yet been described. Here, we describe the mechanistic details of Lys carbamylation that leads to RuBisCO activation by atmospheric CO2. We report two crystal structures of nitrosylated RuBisCO from the red algae Galdieria sulphuraria with O2 and CO2 bound at the active site. G. sulphuraria RuBisCO is inhibited by cysteine nitrosylation that results in trapping of these gaseous ligands. The structure with CO2 defines an elusive, preactivation complex that contains a metal cation Mg2+ surrounded by three H2O/OH molecules. Both structures suggest the mechanism for discriminating gaseous ligands by their quadrupole electric moments. We describe conformational changes that allow for intermittent binding of the metal ion required for activation. On the basis of these structures we propose the individual steps of the activation mechanism. Knowledge of all these elements is indispensable for engineering RuBisCO into a more efficient enzyme for crop enhancement or as a remedy to global warming. PMID:23112176

  11. Using catalytic atom maps to predict the catalytic functions present in enzyme active sites.

    PubMed

    Nosrati, Geoffrey R; Houk, K N

    2012-09-18

    Catalytic atom maps (CAMs) are minimal models of enzyme active sites. The structures in the Protein Data Bank (PDB) were examined to determine if proteins with CAM-like geometries in their active sites all share the same catalytic function. We combined the CAM-based search protocol with a filter based on the weighted contact number (WCN) of the catalytic residues, a measure of the "crowdedness" of the microenvironment around a protein residue. Using this technique, a CAM based on the Ser-His-Asp catalytic triad of trypsin was able to correctly identify catalytic triads in other enzymes within 0.5 Å rmsd of the CAM with 96% accuracy. A CAM based on the Cys-Arg-(Asp/Glu) active site residues from the tyrosine phosphatase active site achieved 89% accuracy in identifying this type of catalytic functionality. Both of these CAMs were able to identify active sites across different fold types. Finally, the PDB was searched to locate proteins with catalytic functionality similar to that present in the active site of orotidine 5'-monophosphate decarboxylase (ODCase), whose mechanism is not known with certainty. A CAM, based on the conserved Lys-Asp-Lys-Asp tetrad in the ODCase active site, was used to search the PDB for enzymes with similar active sites. The ODCase active site has a geometry similar to that of Schiff base-forming Class I aldolases, with lowest aldolase rmsd to the ODCase CAM at 0.48 Å. The similarity between this CAM and the aldolase active site suggests that ODCase has the correct catalytic functionality present in its active site for the generation of a nucleophilic lysine. PMID:22909276

  12. Using Catalytic Atom Maps to Predict the Catalytic Functions Present in Enzyme Active Sites

    PubMed Central

    Nosrati, Geoffrey R.; Houk, K. N.

    2012-01-01

    Catalytic Atom Maps (CAMs) are minimal models of enzyme active sites. The structures in the Protein Data Bank (PDB) were examined to determine if proteins with CAM-like geometries in their active sites all share the same catalytic function. We combined the CAM-based search protocol with a filter based on the weighted contact number (WCN) of the catalytic residues, a measure of the “crowdedness” of the microenvironment around a protein residue. Using this technique, a CAM based on the Ser-His-Asp catalytic triad of trypsin was able to correctly identify catalytic triads in other enzymes within 0.5 Å RMSD of the Catalytic Atom Map with 96% accuracy. A CAM based on the Cys-Arg-(Asp/Glu) active site residues from the tyrosine phosphatase active site achieved 89% accuracy in identifying this type of catalytic functionality. Both of these Catalytic Atom Maps were able to identify active sites across different fold types. Finally, the PDB was searched to locate proteins with catalytic functionality similar to that present in the active site of orotidine 5′-monophosphate decarboxylase (ODCase), whose mechanism is not known with certainty. A CAM, based on the conserved Lys-Asp-Lys-Asp tetrad in the ODCase active site, was used to search the PDB for enzymes with similar active sites. The ODCase active site has a geometry similar to that of Schiff base-forming Class I aldolases, with lowest aldolase RMSD to the ODCase CAM at 0.48 Å. The similarity between this CAM and the aldolase active site suggests that ODCase has the correct catalytic functionality present in its active site for the generation of a nucleophilic lysine. PMID:22909276

  13. The composition of nucleation and Aitken modes particles during coastal nucleation events: evidence for marine secondary organic contribution

    NASA Astrophysics Data System (ADS)

    Vaattovaara, P.; Huttunen, P. E.; Yoon, Y. J.; Joutsensaari, J.; Lehtinen, K. E. J.; O'Dowd, C. D.; Laaksonen, A.

    2006-04-01

    Newly-formed nanometer-sized particles have been observed at coastal and marine environments worldwide. Interestingly, organic species have so far not been detected in those newly-formed nucleation mode particles. In this study, we applied the UFO-TDMA (ultrafine organic tandem differential mobility analyzer) method to study the possible existence of an organic fraction in recently formed coastal nucleation mode particles (d<20 nm) at the Mace Head research station. Furthermore, effects of those nucleation events to potential CCN (cloud condensation nuclei) were studied. The coastal events were typical for the Mace Head region and they occurred at low tide conditions during efficient solar radiation and high biological activity (HBA, i.e. a high mass concentration of chlorophyll a of the ocean) in spring 2002. Additionally, a PHA-UCPC (pulse height analyzer ultrafine condensation particle counter) technique was used to study the composition of newly-formed particles formed in low tide conditions during a lower biological activity (LBA, i.e. a lower mass concentration of chlorophyll a of the ocean) in October 2002. The overall results of the UFO-TDMA and the PHA-UCPC measurements indicate that those coastally/marinely formed nucleation mode particles include a remarkable fraction of secondary organic products, beside iodine oxides, which are likely to be responsible for the nucleation. During clean marine air mass conditions, the origin of those secondary organic oxidation compounds can be related to marine/coastal biota and thus a major fraction of the organics may originate from biosynthetic production of alkenes such as isoprene and their oxidation by iodine, hydroxyl radical, and ozone. During modified marine conditions, also anthropogenic secondary organic compounds may contribute to the nucleation mode organic mass, in addition to biogenic secondary organic compounds. Thus, the UFO-TDMA results suggest that the secondary organic compounds may, in addition to

  14. Active-Site Hydration and Water Diffusion in Cytochrome P450cam: A Highly Dynamic Process

    SciTech Connect

    Miao, Yinglong; Baudry, Jerome Y

    2011-01-01

    Long-timescale molecular dynamics simulations (300 ns) are performed on both the apo- (i.e., camphor-free) and camphor-bound cytochrome P450cam (CYP101). Water diffusion into and out of the protein active site is observed without biased sampling methods. During the course of the molecular dynamics simulation, an average of 6.4 water molecules is observed in the camphor-binding site of the apo form, compared to zero water molecules in the binding site of the substrate-bound form, in agreement with the number of water molecules observed in crystal structures of the same species. However, as many as 12 water molecules can be present at a given time in the camphor-binding region of the active site in the case of apo-P450cam, revealing a highly dynamic process for hydration of the protein active site, with water molecules exchanging rapidly with the bulk solvent. Water molecules are also found to exchange locations frequently inside the active site, preferentially clustering in regions surrounding the water molecules observed in the crystal structure. Potential-of-mean-force calculations identify thermodynamically favored trans-protein pathways for the diffusion of water molecules between the protein active site and the bulk solvent. Binding of camphor in the active site modifies the free-energy landscape of P450cam channels toward favoring the diffusion of water molecules out of the protein active site.

  15. Parameterization of an Active Thermal Erosion Site, Caribou Creek, Alaska

    NASA Astrophysics Data System (ADS)

    Busey, R.; Bolton, W. R.; Cherry, J. E.; Hinzman, L. D.

    2012-12-01

    Thermokarst features are thought to be an important mechanism for landscape change in permafrost-dominated cold regions, but few such features have been incorporated into full featured landscape models. The root of this shortcoming is that historic observations are not detailed enough to parameterize a model, and the models typically do not include the relevant processes for thermal erosion. A new, dynamic thermokarst feature has been identified at the Caribou-Poker Creek Research Watershed (CPCRW) in the boreal forest of Interior Alaska. Located adjacent to a traditional use trail, this feature terminates directly in Caribou Creek. Erosion within the feature is driven predominantly by fluvial interflow. CPCRW is a Long-Term Ecological Research site underlain by varying degrees of relatively warm, discontinuous permafrost. This poster will describe the suite of measurements that have been undertaken to parameterize the ERODE model for this site, including thorough surveys, time lapse- and aerial photography, and 3-D structure from motion algorithms.

  16. Blogs and Social Network Sites as Activity Systems: Exploring Adult Informal Learning Process through Activity Theory Framework

    ERIC Educational Resources Information Center

    Heo, Gyeong Mi; Lee, Romee

    2013-01-01

    This paper uses an Activity Theory framework to explore adult user activities and informal learning processes as reflected in their blogs and social network sites (SNS). Using the assumption that a web-based space is an activity system in which learning occurs, typical features of the components were investigated and each activity system then…

  17. Early Site Permit Demonstration Program: Recommendations for communication activities and public participation in the Early Site Permit Demonstration Program

    SciTech Connect

    Not Available

    1993-01-27

    On October 24, 1992, President Bush signed into law the National Energy Policy Act of 1992. The bill is a sweeping, comprehensive overhaul of the Nation`s energy laws, the first in more than a decade. Among other provisions, the National Energy Policy Act reforms the licensing process for new nuclear power plants by adopting a new approach developed by the US Nuclear Regulatory Commission (NRC) in 1989, and upheld in court in 1992. The NRC 10 CFR Part 52 rule is a three-step process that guarantees public participation at each step. The steps are: early site permit approval; standard design certifications; and, combined construction/operating licenses for nuclear power reactors. Licensing reform increases an organization`s ability to respond to future baseload electricity generation needs with less financial risk for ratepayers and the organization. Costly delays can be avoided because design, safety and siting issues will be resolved before a company starts to build a plant. Specifically, early site permit approval allows for site suitability and acceptability issues to be addressed prior to an organization`s commitment to build a plant. Responsibility for site-specific activities, including communications and public participation, rests with those organizations selected to try out early site approval. This plan has been prepared to assist those companies (referred to as sponsoring organizations) in planning their communications and public involvement programs. It provides research findings, information and recommendations to be used by organizations as a resource and starting point in developing their own plans.

  18. Active Site Structure and Peroxidase Activity of Oxidatively Modified Cytochrome c Species in Complexes with Cardiolipin.

    PubMed

    Capdevila, Daiana A; Oviedo Rouco, Santiago; Tomasina, Florencia; Tortora, Verónica; Demicheli, Verónica; Radi, Rafael; Murgida, Daniel H

    2015-12-29

    We report a resonance Raman and UV-vis characterization of the active site structure of oxidatively modified forms of cytochrome c (Cyt-c) free in solution and in complexes with cardiolipin (CL). The studied post-translational modifications of Cyt-c include methionine sulfoxidation and tyrosine nitration, which lead to altered heme axial ligation and increased peroxidase activity with respect to those of the wild-type protein. In spite of the structural and activity differences between the protein variants free in solution, binding to CL liposomes induces in all cases the formation of a spectroscopically identical bis-His axial coordination conformer that more efficiently promotes lipid peroxidation. The spectroscopic results indicate that the bis-His form is in equilibrium with small amounts of high-spin species, thus suggesting a labile distal His ligand as the basis for the CL-induced increase in enzymatic activity observed for all protein variants. For Cyt-c nitrated at Tyr74 and sulfoxidized at Met80, the measured apparent binding affinities for CL are ∼4 times larger than for wild-type Cyt-c. On the basis of these results, we propose that these post-translational modifications may amplify the pro-apoptotic signal of Cyt-c under oxidative stress conditions at CL concentrations lower than for the unmodified protein.

  19. Binary nucleation rates for ethanol/water mixtures in supersonic Laval nozzles: Analyses by the first and second nucleation theorems

    NASA Astrophysics Data System (ADS)

    Tanimura, Shinobu; Pathak, Harshad; Wyslouzil, Barbara E.

    2013-11-01

    We performed pressure trace measurements and small angle x-ray scattering measurements to determine the vapor-liquid nucleation rates of EtOH/H2O mixtures including pure EtOH and pure H2O in two supersonic Laval nozzles with different expansion rates. The nucleation rates varied from 0.9 × 1017 to 16 × 1017 cm-3 s-1 over the temperature range of 210 K to 230 K, EtOH activity range of 0 to 11.6, and H2O activity range of 0 to 124. The first and second nucleation theorems were applied to the nucleation rates to estimate the sizes, compositions, and excess energies of the critical clusters. The critical clusters contained from 4 to 15 molecules for pure H2O and EtOH/H2O clusters, and from 16 to 23 molecules for pure EtOH clusters. Comparing the excess energies of the pure H2O critical clusters with the results of a quantum-chemistry calculation suggested that the pre-factor of the theoretical nucleation rate is almost constant regardless of the monomer concentration. One possible explanation for this result is that cooling of the critical clusters limits the nucleation rate under the highly supersaturated conditions. The results of the analyses also yielded the relation between the surface energy and the composition of the critical clusters, where the latter are predicted to consist only of surface molecules. Applying this relationship to the EtOH/H2O bulk liquid mixtures, we estimated the EtOH mole fraction in the surface layer and found it is higher than that derived from the surface tension based on the Gibbs adsorption equation when the EtOH mole fraction in the liquid is higher than about 0.2 mol/mol. This discrepancy was attributed to the existence of the EtOH depletion layer just below the surface layer of the liquid.

  20. Stereospecific suppression of active site mutants by methylphosphonate substituted substrates reveals the stereochemical course of site-specific DNA recombination.

    PubMed

    Rowley, Paul A; Kachroo, Aashiq H; Ma, Chien-Hui; Maciaszek, Anna D; Guga, Piotr; Jayaram, Makkuni

    2015-07-13

    Tyrosine site-specific recombinases, which promote one class of biologically important phosphoryl transfer reactions in DNA, exemplify active site mechanisms for stabilizing the phosphate transition state. A highly conserved arginine duo (Arg-I; Arg-II) of the recombinase active site plays a crucial role in this function. Cre and Flp recombinase mutants lacking either arginine can be rescued by compensatory charge neutralization of the scissile phosphate via methylphosphonate (MeP) modification. The chemical chirality of MeP, in conjunction with mutant recombinases, reveals the stereochemical contributions of Arg-I and Arg-II. The SP preference of the native reaction is specified primarily by Arg-I. MeP reaction supported by Arg-II is nearly bias-free or RP-biased, depending on the Arg-I substituent. Positional conservation of the arginines does not translate into strict functional conservation. Charge reversal by glutamic acid substitution at Arg-I or Arg-II has opposite effects on Cre and Flp in MeP reactions. In Flp, the base immediately 5' to the scissile MeP strongly influences the choice between the catalytic tyrosine and water as the nucleophile for strand scission, thus between productive recombination and futile hydrolysis. The recombinase active site embodies the evolutionary optimization of interactions that not only favor the normal reaction but also proscribe antithetical side reactions. PMID:25999343

  1. Stereospecific suppression of active site mutants by methylphosphonate substituted substrates reveals the stereochemical course of site-specific DNA recombination.

    PubMed

    Rowley, Paul A; Kachroo, Aashiq H; Ma, Chien-Hui; Maciaszek, Anna D; Guga, Piotr; Jayaram, Makkuni

    2015-07-13

    Tyrosine site-specific recombinases, which promote one class of biologically important phosphoryl transfer reactions in DNA, exemplify active site mechanisms for stabilizing the phosphate transition state. A highly conserved arginine duo (Arg-I; Arg-II) of the recombinase active site plays a crucial role in this function. Cre and Flp recombinase mutants lacking either arginine can be rescued by compensatory charge neutralization of the scissile phosphate via methylphosphonate (MeP) modification. The chemical chirality of MeP, in conjunction with mutant recombinases, reveals the stereochemical contributions of Arg-I and Arg-II. The SP preference of the native reaction is specified primarily by Arg-I. MeP reaction supported by Arg-II is nearly bias-free or RP-biased, depending on the Arg-I substituent. Positional conservation of the arginines does not translate into strict functional conservation. Charge reversal by glutamic acid substitution at Arg-I or Arg-II has opposite effects on Cre and Flp in MeP reactions. In Flp, the base immediately 5' to the scissile MeP strongly influences the choice between the catalytic tyrosine and water as the nucleophile for strand scission, thus between productive recombination and futile hydrolysis. The recombinase active site embodies the evolutionary optimization of interactions that not only favor the normal reaction but also proscribe antithetical side reactions.

  2. Active site densities, oxygen activation and adsorbed reactive oxygen in alcohol activation on npAu catalysts.

    PubMed

    Wang, Lu-Cun; Friend, C M; Fushimi, Rebecca; Madix, Robert J

    2016-07-01

    The activation of molecular O2 as well as the reactivity of adsorbed oxygen species is of central importance in aerobic selective oxidation chemistry on Au-based catalysts. Herein, we address the issue of O2 activation on unsupported nanoporous gold (npAu) catalysts by applying a transient pressure technique, a temporal analysis of products (TAP) reactor, to measure the saturation coverage of atomic oxygen, its collisional dissociation probability, the activation barrier for O2 dissociation, and the facility with which adsorbed O species activate methanol, the initial step in the catalytic cycle of esterification. The results from these experiments indicate that molecular O2 dissociation is associated with surface silver, that the density of reactive sites is quite low, that adsorbed oxygen atoms do not spill over from the sites of activation onto the surrounding surface, and that methanol reacts quite facilely with the adsorbed oxygen atoms. In addition, the O species from O2 dissociation exhibits reactivity for the selective oxidation of methanol but not for CO. The TAP experiments also revealed that the surface of the npAu catalyst is saturated with adsorbed O under steady state reaction conditions, at least for the pulse reaction. PMID:27376884

  3. Ice nucleation efficiency of clay minerals in the immersion mode

    NASA Astrophysics Data System (ADS)

    Pinti, V.; Marcolli, C.; Zobrist, B.; Hoyle, C. R.; Peter, T.

    2012-07-01

    Emulsion and bulk freezing experiments were performed to investigate immersion ice nucleation on clay minerals in pure water, using various kaolinites, montmorillonites, illites as well as natural dust from the Hoggar Mountains in the Saharan region. Differential scanning calorimeter measurements were performed on three different kaolinites (KGa-1b, KGa-2 and K-SA), two illites (Illite NX and Illite SE) and four natural and acid-treated montmorillonites (SWy-2, STx-1b, KSF and K-10). The emulsion experiments provide information on the average freezing behaviour characterized by the average nucleation sites. These experiments revealed one to sometimes two distinct heterogeneous freezing peaks, which suggest the presence of a low number of qualitatively distinct average nucleation site classes. We refer to the peak at the lowest temperature as "standard peak" and to the one occurring in only some clay mineral types at higher temperatures as "special peak". Conversely, freezing in bulk samples is not initiated by the average nucleation sites, but by a very low number of "best sites". The kaolinites and montmorillonites showed quite narrow standard peaks with onset temperatures 238 Ksites with averaged median freezing temperature Tmedbest=257 K, but only some featuring a special peak (i.e. KSF, K-10, K-SA and SWy-2) with freezing onsets in the range 240-248 K. The illites showed broad standard peaks with freezing onsets at 244 K Tonstd<246 K and best sites with averaged median freezing temperature Tmedbest=262 K. The large difference between freezing temperatures of standard and best sites shows that characterizing ice nucleation efficiencies of dust particles on the basis of freezing onset temperatures from bulk experiments, as has been done in some atmospheric studies, is not appropriate. Our investigations demonstrate that immersion freezing temperatures of clay minerals strongly depend on the amount of clay mineral present per droplet and on

  4. Reducing the nucleation barrier in magnetocaloric Heusler alloys by nanoindentation

    NASA Astrophysics Data System (ADS)

    Niemann, R.; Hahn, S.; Diestel, A.; Backen, A.; Schultz, L.; Nielsch, K.; Wagner, M. F.-X.; Fähler, S.

    2016-06-01

    Magnetocaloric materials are promising as solid state refrigerants for more efficient and environmentally friendly cooling devices. The highest effects have been observed in materials that exhibit a first-order phase transition. These transformations proceed by nucleation and growth which lead to a hysteresis. Such irreversible processes are undesired since they heat up the material and reduce the efficiency of any cooling application. In this article, we demonstrate an approach to decrease the hysteresis by locally changing the nucleation barrier. We created artificial nucleation sites and analyzed the nucleation and growth processes in their proximity. We use Ni-Mn-Ga, a shape memory alloy that exhibits a martensitic transformation. Epitaxial films serve as a model system, but their high surface-to-volume ratio also allows for a fast heat transfer which is beneficial for a magnetocaloric regenerator geometry. Nanoindentation is used to create a well-defined defect. We quantify the austenite phase fraction in its proximity as a function of temperature which allows us to determine the influence of the defect on the transformation.

  5. Turn nucleation perturbs amyloid β self-assembly and cytotoxicity.

    PubMed

    Doran, Todd M; Anderson, Elizabeth A; Latchney, Sarah E; Opanashuk, Lisa A; Nilsson, Bradley L

    2012-08-10

    The accumulation of senile plaques composed of amyloid β (Aβ) fibrils is a hallmark of Alzheimer's disease, although prefibrillar oligomeric species are believed to be the primary neurotoxic congeners in the pathogenesis of Alzheimer's disease. Uncertainty regarding the mechanistic relationship between Aβ oligomer and fibril formation and the cytotoxicity of these aggregate species persists. β-Turn formation has been proposed to be a potential rate-limiting step during Aβ fibrillogenesis. The effect of turn nucleation on Aβ self-assembly was probed by systematically replacing amino acid pairs in the putative turn region of Aβ (residues 24-27) with d-ProGly ((D)PG), an effective turn-nucleating motif. The kinetic, thermodynamic, and cytotoxic effects of these mutations were characterized. It was found that turn formation dramatically accelerated Aβ fibril self-assembly dependent on the site of turn nucleation. The cytotoxicity of the three (D)PG-containing Aβ variants was significantly lower than that of wild-type Aβ40, presumably due to decreased oligomer populations as a function of a more rapid progression to mature fibrils; oligomer populations were not eliminated, however, suggesting that turn formation is also a feature of oligomer structures. These results indicate that turn nucleation is a critical step in Aβ40 fibril formation.

  6. Fracture Statistics: Universality vs. Nucleation

    NASA Astrophysics Data System (ADS)

    Shekhawat, Ashivni

    2012-02-01

    We reexamine several common assumptions about fracture strength, utilizing large-scale simulations of a fuse network model and applying both renormalization-group and nucleation theory methods. Statistical distributions of fracture strengths are believed to be universal and material independent. The universal Weibull and Gumbel distributions emerge as a consequence of the ``weakest-link hypothesis'' and have been studied in the classical theory of extreme value statistics. These distributions are also the fixed points of a renormalization group (RG) flow. However, the engineering community often ignores the Gumbel distribution and uses the Weibull form almost exclusively to fit experimental data. Further, such fits are often extrapolated beyond the available data to estimate the probability of rare events in a variety of applications ranging from structural reliability to insurance pricing. Our recent studies of the random fuse network model raises doubts about most of these practices. We find that the emergent distribution of fracture strengths is the Gumbel distribution. However, the extremely slow convergence to the universal Gumbel form renders it unusable at least in this case. On the other hand, we show that a non-universal distribution derived by using a Griffiths type nucleation theory (due to Duxbury et al.) converges rapidly even for moderate system sizes. We find that while extrapolating the RG based universal Gumbel distribution is perilous and gives wildly incorrect predictions, the nucleation based non-universal results can be extrapolated with confidence. It is entertaining that fracture provides wonderful examples of the statistical mechanics tools developed to study both continuous as well as abrupt phase transitions.

  7. Investigations of organic and microbiological atmospheric ice nucleating particles (Invited)

    NASA Astrophysics Data System (ADS)

    DeMott, P. J.; Hill, T. C.; Tobo, Y.; Prenni, A. J.; McMeeking, G. R.; Levin, E. J.; McCluskey, C.; Huffman, J. A.; Mason, R.; Bertram, A. K.; Kreidenweis, S. M.

    2013-12-01

    Measurements in a number of laboratory and field campaigns have offered the opportunity to compare and contrast ice nucleation by soil-and plant-based inorganic, organic, and microbiological particles versus ice nucleating particles (INP) actually sampled in the atmosphere. This presentation reviews these recent studies. Plants support sometimes prodigious populations of INA bacteria as well as fungi and other potential biological ice nucleating particles, such as fragments of plant tissues themselves. The means of release of plant-sourced INP to the atmosphere is not fully documented, but our recent studies have found clear cases of release of ice nuclei from disturbances such as rain, both in forests and over grasslands, and harvesting. Composition of such ice nuclei in air has been inferred at these times based on simultaneous measurements of ice nuclei and biological aerosols. At quiescent times, measurements of the labile fraction of ice nucleating particles in air over agricultural regions suggest that organic and possibly microbiological organisms dominate ice nuclei populations, but INA bacteria are only selective and modest contributors at the warmest activation temperatures. Our results therefore suggest the presence of a spectrum of biological and organic ice nucleating particles over land regions. The ice nucleating activity of mineral soils is well documented and the presence of these particles in air is certain on the basis of many measurement campaigns which identified mineral particles to represent up to half or more of ice nuclei sampled in parts of the free troposphere. Our recent measurements have also documented a clear organic ice nucleating particle source within arable, sagebrush, grassland and forest soils, a source that may dominate over the mineral ice nuclei in such soils. Investigations of their compositions will be described. These ice nuclei are strongly resistant to heat, and may represent a separate population and source compared to

  8. Advances in Understanding the Role of Aerosols on Ice Clouds from the Fifth International Ice Nucleation (FIN) Workshops

    NASA Astrophysics Data System (ADS)

    Cziczo, D. J.; Moehler, O.; DeMott, P. J.

    2015-12-01

    The relationship of ambient aerosol particles to the formation of ice-containing clouds is one of the largest uncertainties in understanding climate. This is due to several poorly understood processes including the microphysics of how particles nucleate ice, the number of effective heterogeneous ice nuclei and their atmospheric distribution, the role of anthropogenic activities in producing or changing the behavior of ice forming particles and the interplay between effective heterogeneous ice nuclei and homogeneous ice formation. Our team recently completed a three-part international workshop to improve our understanding of atmospheric ice formation. Termed the Fifth International Ice Nucleation (FIN) Workshops, our motivation was the limited number of measurements and a lack of understanding of how to compare data acquired by different groups. The first activity, termed FIN1, addressed the characterization of ice nucleating particle size, number and chemical composition. FIN2 addressed the determination of ice nucleating particle number density. Groups modeling ice nucleation joined FIN2 to provide insight on measurements critically needed to model atmospheric ice nucleation and to understand the performance of ice chambers. FIN1 and FIN2 took place at the Aerosol Interaction and Dynamics in the Atmosphere (AIDA) chamber at the Karlsruhe Institute of Technology. A particular emphasis of FIN1 and FIN2 was the use of 'blind' intercomparisons using a highly characterized, but unknown to the instrument operators, aerosol sample. The third activity, FIN3, took place at the Desert Research Institute's Storm Peak Laboratory (SPL). A high elevation site not subject to local emissions, SPL allowed for a comparison of ice chambers and subsequent analysis of the ice residuals under the challenging conditions of low particle loading, temperature and pressure found in the atmosphere. The presentation focuses on the improvement in understanding how mass spectra from different

  9. Stochastic analysis of nucleation rates.

    PubMed

    Johansson, Jonas

    2016-02-01

    We show that approximating the Becker-Döring equations with a Langevin equation results in multiplicative noise, which in turn leads to a family of possible Fokker-Planck equations according to the Ito-Stratonovich dilemma. Using a simple and general model for the attachment and detachment rates, we find that the Ito choice approximates the nucleation rate best and also coincides with the Fokker-Planck equation resulting from the common way to Taylor expand the original set of rate equations.

  10. Stochastic analysis of nucleation rates

    NASA Astrophysics Data System (ADS)

    Johansson, Jonas

    2016-02-01

    We show that approximating the Becker-Döring equations with a Langevin equation results in multiplicative noise, which in turn leads to a family of possible Fokker-Planck equations according to the Ito-Stratonovich dilemma. Using a simple and general model for the attachment and detachment rates, we find that the Ito choice approximates the nucleation rate best and also coincides with the Fokker-Planck equation resulting from the common way to Taylor expand the original set of rate equations.

  11. Properties of the seismic nucleation phase

    USGS Publications Warehouse

    Beroza, G.C.; Ellsworth, W.L.

    1996-01-01

    Near-source observations show that earthquakes begin abruptly at the P-wave arrival, but that this beginning is weak, with a low moment rate relative to the rest of the main shock. We term this initial phase of low moment rate the seismic nucleation phase. We have observed the seismic nucleation phase for a set of 48 earthquakes ranging in magnitude from 1.1-8.1. The size and duration of the seismic nucleation phase scale with the total seismic moment of the earthquake, suggesting that the process responsible for the seismic nucleation phase carries information about the eventual size of the earthquake. The seismic nucleation phase is characteristically followed by quadratic growth in the moment rate, consistent with self-similar rupture at constant stress drop. In this paper we quantify the properties of the seismic nucleation phase and offer several possible explanations for it.

  12. Nucleation and growth in alkaline zinc electrodeposition An Experimental and Theoretical study

    NASA Astrophysics Data System (ADS)

    Desai, Divyaraj

    The current work seeks to investigate the nucleation and growth of zinc electrodeposition in alkaline electrolyte, which is of commercial interest to alkaline zinc batteries for energy storage. The morphology of zinc growth places a severe limitation on the typical cycle life of such batteries. The formation of mossy zinc leads to a progressive deterioration of battery performance while zinc dendrites are responsible for sudden catastrophic battery failure. The problems are identified as the nucleation-controlled formation of mossy zinc and the transport-limited formation of dendritic zinc. Consequently, this thesis work seeks to investigate and accurately simulate the conditions under which such morphologies are formed. The nucleation and early-stage growth of Zn electrodeposits is studied on carbon-coated TEM grids. At low overpotentials, the morphology develops by aggregation at two distinct length scales: ~5 nm diameter monocrystalline nanoclusters form ~50nm diameter polycrystalline aggregates, and second, the aggregates form a branched network. Epitaxial (0002) growth above a critical overpotential leads to the formation of hexagonal single-crystals. A kinetic model is provided using the rate equations of vapor solidification to simulate the evolution of the different morphologies. On solving these equations, we show that aggregation is attributed to cluster impingement and cluster diffusion while single-crystal formation is attributed to direct attachment. The formation of dendritic zinc is investigated using in-operando transmission X-ray microscopy which is a unique technique for imaging metal electrodeposits. The nucleation density of zinc nuclei is lowered using polyaniline films to cover the active nucleation sites. The effect of overpotential is investigated and the morphology shows beautiful in-operando formation of symmetric zinc crystals. A linear perturbation model was developed to predict the growth and formation of these crystals to first

  13. Possible active site of the sweet-tasting protein thaumatin.

    PubMed

    Slootstra, J W; De Geus, P; Haas, H; Verrips, C T; Meloen, R H

    1995-10-01

    Epitopes on thaumatin and monellin were studied using the PEPSCAN-technology. The antibodies used were raised against thaumatin. Only antibodies that, in an ELISA, both recognized thaumatin and monellin were used in the PEPSCAN-analyses. On thaumatin two major overlapping epitopes were identified. On monellin no epitopes could be identified. The identified epitope region on thaumatin shares structural features with various peptide and protein sweeteners. It contains an aspartame-like site which is formed by Asp21 and Phe80, tips of the two extruding loops KGDAALDAGGR19-29 and CKRFGRPP77-84, which are spatially positioned next to each other. Furthermore, sub-sequences of the KGDAALDAGGR19-29 loop are similar to peptide-sweeteners such as L-Asp-D-Ala-L-Ala-methyl ester and L-Asp-D-Ala-Gly-methyl ester. Since the aspartame-like Asp21-Phe80 site and the peptide-sweetener-like sequences are also not present in non-sweet thaumatin-like proteins it is postulated that the KGDAALDAGGR19-29- and CKRFGRPP77-84 loop contain important sweet-taste determinants. This region has previously not been implicated as a sweet-taste determinant of thaumatin.

  14. Nck adaptors, besides promoting N-WASP mediated actin-nucleation activity at pedestals, influence the cellular levels of enteropathogenic Escherichia coli Tir effector.

    PubMed

    Nieto-Pelegrin, Elvira; Kenny, Brendan; Martinez-Quiles, Narcisa

    2014-01-01

    Enteropathogenic Escherichia coli (EPEC) binding to human intestinal cells triggers the formation of disease-associated actin rich structures called pedestals. The latter process requires the delivery, via a Type 3 secretion system, of the translocated Intimin receptor (Tir) protein into the host plasma membrane where binding of a host kinase-modified form to the bacterial surface protein Intimin triggers pedestal formation. Tir-Intimin interaction recruits the Nck adaptor to a Tir tyrosine phosphorylated residue where it activates neural Wiskott-Aldrich syndrome protein (N-WASP); initiating the major pathway to actin polymerization mediated by the actin-related protein (Arp) 2/3 complex. Previous studies with Nck-deficient mouse embryonic fibroblasts (MEFs) identified a key role for Nck in pedestal formation, presumed to reflect a lack of N-WASP activation. Here, we show the defect relates to reduced amounts of Tir within Nck-deficient cells. Indeed, Tir delivery and, thus, pedestal formation defects were much greater for MEFs than HeLa (human epithelial) cells. Crucially, the levels of two other effectors (EspB/EspF) within Nck-deficient MEFs were not reduced unlike that of Map (Mitochondrial associated protein) which, like Tir, requires CesT chaperone function for efficient delivery. Interestingly, drugs blocking various host protein degradation pathways failed to increase Tir cellular levels unlike an inhibitor of deacetylase activity (Trichostatin A; TSA). Treatments with TSA resulted in significant recovery of Tir levels, potentiation of actin polymerization and improvement in bacterial attachment to cells. Our findings have important implications for the current model of Tir-mediated actin polymerization and opens new lines of research in this area. PMID:25482634

  15. Time-dependent nucleation in partitioning systems

    SciTech Connect

    Kelton, K.F.; Narayan, K.L.

    1998-12-31

    Nucleation in multi-component systems is poorly understood, particularly when the rates of long-range diffusion are comparable with the rates of attachment at the cluster interface. For illustration, measurements of the time-dependent nucleation rates in silicate and metallic glasses are discussed. A new model for nucleation in partitioning systems, which explains many of devitrification microstructural features in bulk metallic glasses, is presented.

  16. Static-stress impact of the 1992 Landers earthquake sequence on nucleation and slip at the site of the 1999 M=7.1 Hector Mine earthquake, southern California

    USGS Publications Warehouse

    Parsons, Tom; Dreger, Douglas S.

    2000-01-01

    The proximity in time (∼7 years) and space (∼20 km) between the 1992 M=7.3 Landers earthquake and the 1999 M=7.1 Hector Mine event suggests a possible link between the quakes. We thus calculated the static stress changes following the 1992 Joshua Tree/Landers/Big Bear earthquake sequence on the 1999 M=7.1 Hector Mine rupture plane in southern California. Resolving the stress tensor into rake-parallel and fault-normal components and comparing with changes in the post-Landers seismicity rate allows us to estimate a coefficient of friction on the Hector Mine plane. Seismicity following the 1992 sequence increased at Hector Mine where the fault was unclamped. This increase occurred despite a calculated reduction in right-lateral shear stress. The dependence of seismicity change primarily on normal stress change implies a high coefficient of static friction (µ≥0.8). We calculated the Coulomb stress change using µ=0.8 and found that the Hector Mine hypocenter was mildly encouraged (0.5 bars) by the 1992 earthquake sequence. In addition, the region of peak slip during the Hector Mine quake occurred where Coulomb stress is calculated to have increased by 0.5–1.5 bars. In general, slip was more limited where Coulomb stress was reduced, though there was some slip where the strongest stress decrease was calculated. Interestingly, many smaller earthquakes nucleated at or near the 1999 Hector Mine hypocenter after 1992, but only in 1999 did an event spread to become a M=7.1 earthquake.

  17. Assessment of activation products in the Savannah River Site environment

    SciTech Connect

    Carlton, W.H.; Denham, M.

    1996-07-01

    This document assesses the impact of radioactive activation products released from SRS facilities since the first reactor became operational late in 1953. The isotopes reported here are those whose release resulted in the highest dose to people living near SRS: {sup 32}P, {sup 51}Cr, {sup 60}C, and {sup 65}Zn. Release pathways, emission control features, and annual releases to the aqueous and atmospheric environments are discussed. No single incident has resulted in a major acute release of activation products to the environment. The releases were the result of normal operations of the reactors and separations facilities. Releases declined over the years as better controls were established and production was reduced. The overall radiological impact of SRS activation product atmospheric releases from 1954 through 1994 on the offsite maximally exposed individual can be characterized by a total dose of 0.76 mrem. During the same period, such an individual received a total dose of 14,400 mrem from non-SRS sources of ionizing radiation present in the environment. SRS activation product aqueous releases between 1954 and 1994 resulted in a total dose of 54 mrem to the offsite maximally exposed individual. The impact of SRS activation product releases on offsite populations also has been evaluated.

  18. Binary Nucleation of Water and Sodium Chloride

    SciTech Connect

    Nemec, Thomas; Marsik, Frantisek; Palmer, Donald

    2005-01-01

    Nucleation processes in the binary water-sodium chloride system are investigated in the sense of the classical nucleation theory (CNT). The CNT is modified to be able to handle the electrolytic nature of the system and is employed to investigate the acceleration of the nucleation process due to the presence of sodium chloride in the steam. This phenomenon, frequently observed in the Wilson zone of steam turbines, is called early condensation. Therefore, the nucleation rates of the water-sodium chloride mixture are of key importance in the power cycle industry.

  19. Quantifying the density and utilization of active sites in non-precious metal oxygen electroreduction catalysts

    PubMed Central

    Sahraie, Nastaran Ranjbar; Kramm, Ulrike I.; Steinberg, Julian; Zhang, Yuanjian; Thomas, Arne; Reier, Tobias; Paraknowitsch, Jens-Peter; Strasser, Peter

    2015-01-01

    Carbon materials doped with transition metal and nitrogen are highly active, non-precious metal catalysts for the electrochemical conversion of molecular oxygen in fuel cells, metal air batteries, and electrolytic processes. However, accurate measurement of their intrinsic turn-over frequency and active-site density based on metal centres in bulk and surface has remained difficult to date, which has hampered a more rational catalyst design. Here we report a successful quantification of bulk and surface-based active-site density and associated turn-over frequency values of mono- and bimetallic Fe/N-doped carbons using a combination of chemisorption, desorption and 57Fe Mössbauer spectroscopy techniques. Our general approach yields an experimental descriptor for the intrinsic activity and the active-site utilization, aiding in the catalyst development process and enabling a previously unachieved level of understanding of reactivity trends owing to a deconvolution of site density and intrinsic activity. PMID:26486465

  20. Characterization of an Active Thermal Erosion Site, Caribou Creek, Alaska

    NASA Astrophysics Data System (ADS)

    Busey, R.; Bolton, W. R.; Cherry, J. E.; Hinzman, L. D.

    2013-12-01

    The goal of this project is to estimate volume loss of soil over time from this site, provide parameterizations on erodibility of ice rich permafrost and serve as a baseline for future landscape evolution simulations. Located in the zone of discontinuous permafrost, the interior region of Alaska (USA) is home to a large quantity of warm, unstable permafrost that is both high in ice content and has soil temperatures near the freezing point. Much of this permafrost maintains a frozen state despite the general warming air temperature trend in the region due to the presence of a thick insulating organic mat and a dense root network in the upper sub-surface of the soil column. At a rapidly evolving thermo-erosion site, located within the Caribou-Poker Creeks Research Watershed (part of the Bonanza Creek LTER) near Chatanika, Alaska (N65.140, W147.570), the protective organic layer and associated plants were disturbed by an adjacent traditional use trail and the shifting of a groundwater spring. These triggers have led to rapid geomorphological change on the landscape as the soil thaws and sediment is transported into the creek at the valley bottom. Since 2006 (approximately the time of initiation), the thermal erosion has grown to 170 meters length, 3 meters max depth, and 15 meters maximum width. This research combines several data sets: DGPS survey, imagery from an extremely low altitude pole-based remote sensing (3 to 5 meters above ground level), and imagery from an Unmanned Aerial System (UAS) at about 60m altitude.

  1. Molecular Basis for Enzymatic Sulfite Oxidation -- HOW THREE CONSERVED ACTIVE SITE RESIDUES SHAPE ENZYME ACTIVITY

    SciTech Connect

    Bailey, Susan; Rapson, Trevor; Johnson-Winters, Kayunta; Astashkin, Andrei; Enemark, John; Kappler, Ulrike

    2008-11-10

    Sulfite dehydrogenases (SDHs) catalyze the oxidation and detoxification of sulfite to sulfate, a reaction critical to all forms of life. Sulfite-oxidizing enzymes contain three conserved active site amino acids (Arg-55, His-57, and Tyr-236) that are crucial for catalytic competency. Here we have studied the kinetic and structural effects of two novel and one previously reported substitution (R55M, H57A, Y236F) in these residues on SDH catalysis. Both Arg-55 and His-57 were found to have key roles in substrate binding. An R55M substitution increased Km(sulfite)(app) by 2-3 orders of magnitude, whereas His-57 was required for maintaining a high substrate affinity at low pH when the imidazole ring is fully protonated. This effect may be mediated by interactions of His-57 with Arg-55 that stabilize the position of the Arg-55 side chain or, alternatively, may reflect changes in the protonation state of sulfite. Unlike what is seen for SDHWT and SDHY236F, the catalytic turnover rates of SDHR55M and SDHH57A are relatively insensitive to pH (~;;60 and 200 s-1, respectively). On the structural level, striking kinetic effects appeared to correlate with disorder (in SDHH57A and SDHY236F) or absence of Arg-55 (SDHR55M), suggesting that Arg-55 and the hydrogen bonding interactions it engages in are crucial for substrate binding and catalysis. The structure of SDHR55M has sulfate bound at the active site, a fact that coincides with a significant increase in the inhibitory effect of sulfate in SDHR55M. Thus, Arg-55 also appears to be involved in enabling discrimination between the substrate and product in SDH.

  2. Active Site Metal Occupancy and Cyclic Di-GMP Phosphodiesterase Activity of Thermotoga maritima HD-GYP.

    PubMed

    Miner, Kyle D; Kurtz, Donald M

    2016-02-16

    HD-GYPs make up a subclass of the metal-dependent HD phosphohydrolase superfamily and catalyze conversion of cyclic di(3',5')-guanosine monophosphate (c-di-GMP) to 5'-phosphoguanylyl-(3'→5')-guanosine (pGpG) and GMP. Until now, the only reported crystal structure of an HD-GYP that also exhibits c-di-GMP phosphodiesterase activity contains a His/carboxylate ligated triiron active site. However, other structural and phylogenetic correlations indicate that some HD-GYPs contain dimetal active sites. Here we provide evidence that an HD-GYP c-di-GMP phosphodiesterase, TM0186, from Thermotoga maritima can accommodate both di- and trimetal active sites. We show that an as-isolated iron-containing TM0186 has an oxo/carboxylato-bridged diferric site, and that the reduced (diferrous) form is necessary and sufficient to catalyze conversion of c-di-GMP to pGpG, but that conversion of pGpG to GMP requires more than two metals per active site. Similar c-di-GMP phosphodiesterase activities were obtained with divalent iron or manganese. On the basis of activity correlations with several putative metal ligand residue variants and molecular dynamics simulations, we propose that TM0186 can accommodate both di- and trimetal active sites. Our results also suggest that a Glu residue conserved in a subset of HD-GYPs is required for formation of the trimetal site and can also serve as a labile ligand to the dimetal site. Given the anaerobic growth requirement of T. maritima, we suggest that this HD-GYP can function in vivo with either divalent iron or manganese occupying di- and trimetal sites.

  3. Ultrasonic emissions during ice nucleation and propagation in plant xylem.

    PubMed

    Charrier, Guillaume; Pramsohler, Manuel; Charra-Vaskou, Katline; Saudreau, Marc; Améglio, Thierry; Neuner, Gilbert; Mayr, Stefan

    2015-08-01

    Ultrasonic acoustic emission analysis enables nondestructive monitoring of damage in dehydrating or freezing plant xylem. We studied acoustic emissions (AE) in freezing stems during ice nucleation and propagation, by combining acoustic and infrared thermography techniques and controlling the ice nucleation point. Ultrasonic activity in freezing samples of Picea abies showed two distinct phases: the first on ice nucleation and propagation (up to 50 AE s(-1) ; reversely proportional to the distance to ice nucleation point), and the second (up to 2.5 AE s(-1) ) after dissipation of the exothermal heat. Identical patterns were observed in other conifer and angiosperm species. The complex AE patterns are explained by the low water potential of ice at the ice-liquid interface, which induced numerous and strong signals. Ice propagation velocities were estimated via AE (during the first phase) and infrared thermography. Acoustic activity ceased before the second phase probably because the exothermal heating and the volume expansion of ice caused decreasing tensions. Results indicate cavitation events at the ice front leading to AE. Ultrasonic emission analysis enabled new insights into the complex process of xylem freezing and might be used to monitor ice propagation in natura.

  4. A rapid and direct method for the determination of active site accessibility in proteins based on ESI-MS and active site titrations.

    PubMed

    O'Farrell, Norah; Kreiner, Michaela; Moore, Barry D; Parker, Marie-Claire

    2006-11-01

    We have developed an electrospray ionisation mass spectrometry (ESI-MS) technique that can be applied to rapidly determine the number of intact active sites in proteins. The methodology relies on inhibiting the protein with an active-site irreversible inhibitor and then using ESI-MS to determine the extent of inhibition. We have applied this methodology to a test system: a serine protease, subtilisin Carlsberg, and monitored the extent of inhibition by phenylmethylsulfonyl fluoride (PMSF), an irreversible serine hydrolase inhibitor as a function of the changes in immobilisation and hydration conditions. Two types of enzyme preparation were investigated, lyophilised enzymes and protein-coated microcrystals (PCMC).

  5. Cyanide does more to inhibit heme enzymes, than merely serving as an active-site ligand.

    PubMed

    Parashar, Abhinav; Venkatachalam, Avanthika; Gideon, Daniel Andrew; Manoj, Kelath Murali

    2014-12-12

    The toxicity of cyanide is hitherto attributed to its ability to bind to heme proteins' active site and thereby inhibit their activity. It is shown herein that the long-held interpretation is inadequate to explain several observations in heme-enzyme reaction systems. Generation of cyanide-based diffusible radicals in heme-enzyme reaction milieu could shunt electron transfers (by non-active site processes), and thus be detrimental to the efficiency of oxidative outcomes.

  6. Marine Biology Field Trip Sites. Ocean Related Curriculum Activities.

    ERIC Educational Resources Information Center

    Pauls, John

    The ocean affects all of our lives. Therefore, awareness of and information about the interconnections between humans and oceans are prerequisites to making sound decisions for the future. Project ORCA (Ocean Related Curriculum Activities) has developed interdisciplinary curriculum materials designed to meet the needs of students and teachers…