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Sample records for aggregation dla model

  1. Modeling Solute Transport by DLA in Soils of Northeastern Egypt

    PubMed Central

    Hamed, Yasser Ahmed; Yasuda, Hiroshi; Persson, Magnus; Berndtsson, Ronny; Wang, Xin-ping

    2015-01-01

    Arid soils in Egypt display large variability in solute transport properties, causing problems in soil management. To characterize this variability, dye infiltration experiments were conducted on four plots representing three main soil types in northeastern Egypt. The plots represented both cultivated and uncultivated land use. The observed dye patterns displayed a large variability and especially the clay soils indicated a high degree of preferential flow. The loamy sand and sandy soils displayed a more uniform dye distribution indicating more homogeneous soil properties. The observed dye patterns were modeled using a diffusion limited aggregation (DLA) model. The DLA is a random walk model where model parameters can be optimized using genetic algorithms (GA). The DLA model reproduced the observed dye patterns for all soils in an excellent way. The best fit was obtained with a specific combination of directional random walk probabilities Pu, Pd, Pr, and Pl for each plot (correlation 0.97–0.99). To account for soil layers with different hydraulic properties a two layer DLA model was developed. For all plots the Pu (upward random walk probability) was higher for the upper more homogeneous soil layer. The overall results showed that spatial variability resulting from solute transport for the investigated soils can be modeled using a DLA approach. PMID:25790463

  2. Modeling solute transport by DLA in soils of northeastern Egypt.

    PubMed

    Hamed, Yasser Ahmed; Yasuda, Hiroshi; Persson, Magnus; Berndtsson, Ronny; Wang, Xin-ping

    2015-01-01

    Arid soils in Egypt display large variability in solute transport properties, causing problems in soil management. To characterize this variability, dye infiltration experiments were conducted on four plots representing three main soil types in northeastern Egypt. The plots represented both cultivated and uncultivated land use. The observed dye patterns displayed a large variability and especially the clay soils indicated a high degree of preferential flow. The loamy sand and sandy soils displayed a more uniform dye distribution indicating more homogeneous soil properties. The observed dye patterns were modeled using a diffusion limited aggregation (DLA) model. The DLA is a random walk model where model parameters can be optimized using genetic algorithms (GA). The DLA model reproduced the observed dye patterns for all soils in an excellent way. The best fit was obtained with a specific combination of directional random walk probabilities Pu, Pd, Pr, and Pl for each plot (correlation 0.97-0.99). To account for soil layers with different hydraulic properties a two layer DLA model was developed. For all plots the Pu (upward random walk probability) was higher for the upper more homogeneous soil layer. The overall results showed that spatial variability resulting from solute transport for the investigated soils can be modeled using a DLA approach.

  3. Electrochemical Growth of Ag Junctions and Diffusion Limited Aggregate (DLA) Fractal Simulation

    NASA Astrophysics Data System (ADS)

    Olson, Zak; Tuppan, Sam; Kim, Woo-Joong; Seattle University Team

    2015-03-01

    We attempt construction of a single atom connection between two copper wires. By applying a DC voltage across the wires when immersed in a silver nitrate solution, we deposit silver until a junction is formed. The deposited silver forms a fractal structure that can be simulated with a diffusion limited aggregation model.

  4. A new galactic chemical evolution model with dust: results for dwarf irregular galaxies and DLA systems

    NASA Astrophysics Data System (ADS)

    Gioannini, L.; Matteucci, F.; Vladilo, G.; Calura, F.

    2017-01-01

    We present a galactic chemical evolution model which adopts updated prescriptions for all the main processes governing the dust cycle. We follow in detail the evolution of the abundances of several chemical species (C, O, S, Si, Fe and Zn) in the gas and dust of a typical dwarf irregular galaxy. The dwarf irregular galaxy is assumed to evolve with a low but continuous level of star formation and experience galactic winds triggered by supernova (SN) explosions. We predict the evolution of the gas to dust ratio in such a galaxy and discuss critically the main processes involving dust, such as dust production by asymptotic giant branch stars and Type II SNe, destruction and accretion (gas condensation in clouds). We then apply our model to damped Lyman α (DLA) systems which are believed to be dwarf irregulars, as witnessed by their abundance patterns. Our main conclusions are the following. (i) We can reproduce the observed gas to dust ratio in dwarf galaxies. (ii) We find that the process of dust accretion plays a fundamental role in the evolution of dust and in certain cases it becomes the dominant process in the dust cycle. On the other hand, dust destruction seems to be a negligible process in irregulars. (iii) Concerning DLA systems, we show that the observed gas-phase abundances of silicon, normalized to volatile elements (zinc and sulfur), are in agreement with our model. (iv) The abundances of iron and silicon in DLA systems suggest that the two elements undergo a different history of dust formation and evolution. Our work casts light on the nature of iron-rich dust: the observed depletion pattern of iron is well reproduced only when an additional source of iron dust is considered. Here we explore the possibility of a contribution from Type Ia SNe as well as an efficient accretion of iron nanoparticles.

  5. Comparison of the Rates of Uni- and Bi-Molecular Diffusion Controlled Reactions on Circular, Filled Aggregate and DLA Fractal Aggregate in Two Dimensions.

    DTIC Science & Technology

    1987-05-07

    CLASSIFICATION Of THIS PAGIL(Whan Data Entered) It is found that the reaction rates of OLA agigregates are comnatible with * that of circular aggregates with...NOSC Wayne State University Code 521 Detroit, Michigan 49207 San Diego, California 91232 Or. W.E. Moerner I.B.M. Corporation Almaden Research Center 650

  6. Activity Based Costing within a DLA Depot’s Planning and Resource Management Department: A Model and Analysis

    DTIC Science & Technology

    1994-09-01

    protection in .local congressional districts and the continued pressures of a cold war environment all worked in concert to stifle any call to change...Logistics Center and. the Physical DistUýibution Department of the Naval Supply Center Oakland were all consolidated under the control of the DLA Defense...DLA command was titles Defense Distribution Region West (DDRW), and it was not long before funding pressures forced DLA to take over consolidated

  7. The galaxy counterpart of the high-metallicity and 16 kpc impact parameter DLA towards Q 0918+1636 - a challenge to galaxy formation models?

    NASA Astrophysics Data System (ADS)

    Sommer-Larsen, J.; Fynbo, J. P. U.

    2017-01-01

    The quasar Q0918+1636 (z = 3.07) has an intervening high-metallicity damped Lyman α absorber (DLA) along the line of sight, at a redshift of z = 2.58. The DLA is located at a large impact parameter of 16.2 kpc, and despite this large impact parameter, it has a very high metallicity (consistent with solar). In this paper, it is investigated whether a novel type of galaxy formation models, based on hydrodynamical/gravitational TreeSPH simulations invoking a new Supernova Type II feedback prescription, the Haardt & Madau most recent ultraviolet background radiation (UVB) field and explicit treatment of UVB self-shielding effects, can reproduce the observed characteristics of the DLA. Effects of UV radiation from young stellar populations in the galaxy, in particular in the photon energy range 10.36-13.61 eV (relating to Sulphur II abundance), are also considered in the analysis. It is found that (a) for L ˜ L⋆ galaxies (at z = 2.58), about 10 per cent of the sight-lines through the galaxies at impact parameter b = 16.2 kpc will display a Sulphur II column density of N({S II)} ≥ 10^{15.82} cm-2 (the observed value for the DLA), and (b) considering only cases where a near-solar metallicity will be detected at 16.2 kpc impact parameter, the (Bayesian) probability distribution of galaxy star formation rate peaks near the value observed for the DLA galaxy counterpart of 27^{+20}_{-9} { M_{⊙}} yr-1. It is argued that the bulk of the α-elements, like Sulphur, traced by the high metal column density, b = 16.2 kpc absorption lines, have been produced by evolving stars in the inner galaxy, and subsequently transported outwards by galactic winds.

  8. Model for amorphous aggregation processes

    NASA Astrophysics Data System (ADS)

    Stranks, Samuel D.; Ecroyd, Heath; van Sluyter, Steven; Waters, Elizabeth J.; Carver, John A.; von Smekal, Lorenz

    2009-11-01

    The amorphous aggregation of proteins is associated with many phenomena, ranging from the formation of protein wine haze to the development of cataract in the eye lens and the precipitation of recombinant proteins during their expression and purification. While much literature exists describing models for linear protein aggregation, such as amyloid fibril formation, there are few reports of models which address amorphous aggregation. Here, we propose a model to describe the amorphous aggregation of proteins which is also more widely applicable to other situations where a similar process occurs, such as in the formation of colloids and nanoclusters. As first applications of the model, we have tested it against experimental turbidimetry data of three proteins relevant to the wine industry and biochemistry, namely, thaumatin, a thaumatinlike protein, and α -lactalbumin. The model is very robust and describes amorphous experimental data to a high degree of accuracy. Details about the aggregation process, such as shape parameters of the aggregates and rate constants, can also be extracted.

  9. Thermodynamic modeling of asphaltene aggregation.

    PubMed

    Rogel, E

    2004-02-03

    A new molecular thermodynamic model for the description of the aggregation behavior of asphaltenes in different solvents is presented. This new model is relatively simple and strictly predictive and does not use any experimental information from asphaltene solutions. In this model, asphaltene aggregates are described as composed of an aromatic core formed by stacked aromatic sheets surrounded by aliphatic chains. The proposed model qualitatively predicts the asphaltene aggregation behavior in a series of different solvents. In particular, the experimental trends observed for the variation of aggregate size with (1) asphaltene molecular characteristics (condensation index, aromaticity, and chain length), (2) asphaltene concentration, (3) solvent characteristics, and (4) temperature have been successfully reproduced by the proposed model. The model also provides a plausible explanation for the existence or absence of a critical micelle concentration (cmc) for asphaltene solutions. Specifically, the model predicted that the asphaltenes with low aromaticities and low aromatic condensations do not exhibit cmc behavior. Finally, the obtained results clearly support the classical model for asphaltene aggregates.

  10. Aggregation models on hypergraphs

    NASA Astrophysics Data System (ADS)

    Alberici, Diego; Contucci, Pierluigi; Mingione, Emanuele; Molari, Marco

    2017-01-01

    Following a newly introduced approach by Rasetti and Merelli we investigate the possibility to extract topological information about the space where interacting systems are modelled. From the statistical datum of their observable quantities, like the correlation functions, we show how to reconstruct the activities of their constitutive parts which embed the topological information. The procedure is implemented on a class of polymer models on hypergraphs with hard-core interactions. We show that the model fulfils a set of iterative relations for the partition function that generalise those introduced by Heilmann and Lieb for the monomer-dimer case. After translating those relations into structural identities for the correlation functions we use them to test the precision and the robustness of the inverse problem. Finally the possible presence of a further interaction of peer-to-peer type is considered and a criterion to discover it is identified.

  11. Average shape of transport-limited aggregates.

    PubMed

    Davidovitch, Benny; Choi, Jaehyuk; Bazant, Martin Z

    2005-08-12

    We study the relation between stochastic and continuous transport-limited growth models. We derive a nonlinear integro-differential equation for the average shape of stochastic aggregates, whose mean-field approximation is the corresponding continuous equation. Focusing on the advection-diffusion-limited aggregation (ADLA) model, we show that the average shape of the stochastic growth is similar, but not identical, to the corresponding continuous dynamics. Similar results should apply to DLA, thus explaining the known discrepancies between average DLA shapes and viscous fingers in a channel geometry.

  12. Scaling behavior of generalized diffusion-limited aggregation: The correct form of the m-spoke model

    NASA Astrophysics Data System (ADS)

    Kassner, K.; Family, F.

    1989-05-01

    The potential of the original m-spoke model, conceived by Family and Hentschel (FH) [Faraday Discuss. Chem. Soc. 83, 139 (1987)], does not satisfy the correct boundary conditions for diffusion-limited aggregation (DLA) or dielectric breakdown. Moreover, while the suggested scaling forms hold, if the growth probability exponent η of the dielectric breakdown model is larger than 2, they are not generally valid for η<2. The correct potential of an m-spoke structure is given, and the scaling behavior of this new model is calculated. Since the scaling dependence on the cluster size N is determined by the local-field behavior, the exponent ν found by FH is recovered with the new potential. For a careful evaluation of the m dependence, however, a nonlocal quantity must be considered, leading to novel results. We conclude that only if the fractal dimension is m dependent can the asymptotic shape of DLA clusters be m-spoke-like.

  13. Canine DLA diversity: 3. Disease studies.

    PubMed

    Kennedy, L J; Barnes, A; Short, A; Brown, J J; Seddon, J; Fleeman, L; Brkljacic, M; Happ, G M; Catchpole, B; Ollier, W E R

    2007-04-01

    There are many millions of dogs worldwide, and these dogs have many different functions. The most obvious use is providing companionship, but there are also many working dogs, including guide dogs for the blind, hearing dogs, guard dogs and farm dogs, to mention a few. The health and welfare of these dogs is of great concern to dog owners, dog breeders and to those who use dogs in their work. Dogs spontaneously develop many diseases that are very similar to their human counterparts. Dogs may, therefore, provide exceptional animal models for such diseases. Identifying genetic markers in the dog may be easier than in humans, and may then provide useful information about genes that can be transferred to humans. This study looked for associations between DLA and two autoimmune diseases of the dog, diabetes and hypothyroidism. DLA associations were found for both of these diseases.

  14. Aggregate Models of Climate Change

    NASA Astrophysics Data System (ADS)

    Hooss, G.; Voss, R.; Hasselmann, K.; Maier-Reimer, E.; Joos, F.

    Integrated assessment of climate change generally requires the evaluation of many transient scenario simulations of century-timescale changes in atmospheric compo- sition and climate, desirably with the accuracy of state-of-the-art three-dimensional (3D) coupled atmosphere-ocean general circulation models (GCMs). Such multi- scenario GCM computations are possible through appropriate representation of the models in aggregate forms. For this purpose, we developed Nonlinear Impulse- response projections of 3D models of the global (oceanic and terrestrial) Carbon cycle and the atmosphere-ocean Climate System (NICCS). For higher CO2 forcing, appli- cability is extended beyond the linear response domain through explicit treatment of dominant nonlinear effects. The climate change module was furthermore augmented with spatial patterns of change in some of the most impact-relevant fields. Applied to three long-term CO2 emission scenarios, the model demonstrates (a) the minor rela- tive role of the terrestrial carbon sink through CO2 fertilization, and (b) the necessity to reduce fossil carbon emissions to a very small fraction of today's rates within the next few decades if a major climate change is to be avoided.

  15. DLA based compressed sensing for high resolution MR microscopy of neuronal tissue

    NASA Astrophysics Data System (ADS)

    Nguyen, Khieu-Van; Li, Jing-Rebecca; Radecki, Guillaume; Ciobanu, Luisa

    2015-10-01

    In this work we present the implementation of compressed sensing (CS) on a high field preclinical scanner (17.2 T) using an undersampling trajectory based on the diffusion limited aggregation (DLA) random growth model. When applied to a library of images this approach performs better than the traditional undersampling based on the polynomial probability density function. In addition, we show that the method is applicable to imaging live neuronal tissues, allowing significantly shorter acquisition times while maintaining the image quality necessary for identifying the majority of neurons via an automatic cell segmentation algorithm.

  16. Aggregation in ecosystem models and model stability

    NASA Astrophysics Data System (ADS)

    Giricheva, Evgeniya

    2015-05-01

    Using a multimodal approach to research ecosystems improves usage of available information on an object. This study presents several models of the Bering Sea ecosystem. The ecosystem is considered as a closed object, that is, the influence of the environment is not provided. We then add the links with the external medium in the models. The models differ in terms of the degree and method of grouping components. Our method is based on the differences in habitat and food source of groups, which allows us to determine the grouping of species with a greater effect on system dynamics. In particular, we determine whether benthic fish aggregation or pelagic fish aggregation can change the consumption structure of some groups of species, and consequently, the behavior of the entire model system.

  17. Teaching Aggregate Demand and Supply Models

    ERIC Educational Resources Information Center

    Wells, Graeme

    2010-01-01

    The author analyzes the inflation-targeting model that underlies recent textbook expositions of the aggregate demand-aggregate supply approach used in introductory courses in macroeconomics. He shows how numerical simulations of a model with inflation inertia can be used as a tool to help students understand adjustments in response to demand and…

  18. Diffusion-Limited Aggregation with Anisotropic Sticking Probability: A Tentative Model for River Networks

    NASA Astrophysics Data System (ADS)

    Kondoh, Hiroshi; Matsushita, Mitsugu

    1986-10-01

    Diffusion-limited aggregation (DLA) model with anisotropic sticking probability Ps is computer-simulated on two dimensional square lattice. The cluster grows from a seed particle at the origin in the positive y area with the absorption-type boundary along x-axis. The cluster is found to grow anisotropically as R//˜Nν// and R\\bot˜Nν\\bot, where R\\bot and R// are the radii of gyration of the cluster along x- and y-axes, respectively, and N is the particle number constituting the cluster. The two exponents are shown to become assymptotically ν//{=}2/3, ν\\bot{=}1/3 whenever the sticking anisotropy exists. It is also found that the present model is fairly consistent with Hack’s law of river networks, suggesting that it is a good candidate of a prototype model for the evolution of the river network.

  19. A competitive aggregation model for flash nanoprecipitation.

    PubMed

    Cheng, Janine Chungyin; Vigil, R D; Fox, R O

    2010-11-15

    Flash NanoPrecipitation (FNP) is a novel approach for producing functional nanoparticles stabilized by amphiphilic block copolymers. FNP involves the rapid mixing of a hydrophobic active (organic) and an amphiphilic di-block copolymer with a non-solvent (water) and subsequent co-precipitation of nanoparticles composed of both the organic and copolymer. During this process, the particle size distribution (PSD) is frozen and stabilized by the hydrophilic portion of the amphiphilic di-block copolymer residing on the particle surface. That is, the particle growth is kinetically arrested and thus a narrow PSD can be attained. To model the co-precipitation process, a bivariate population balance equation (PBE) has been formulated to account for the competitive aggregation of the organic and copolymer versus pure organic-organic or copolymer-copolymer aggregation. Aggregation rate kernels have been derived to account for the major aggregation events: free coupling, unimer insertion, and aggregate fusion. The resulting PBE is solved both by direct integration and by using the conditional quadrature method of moments (CQMOM). By solving the competitive aggregation model under well-mixed conditions, it is demonstrated that the PSD is controlled primarily by the copolymer-copolymer aggregation process and that the energy barrier to aggregate fusion plays a key role in determining the PSD. It is also shown that the characteristic aggregation times are smaller than the turbulent mixing time so that the FNP process is always mixing limited.

  20. Safety of treatment with DLA-identical or unrelated mesenchymal stromal cells in DLA-identical canine bone marrow transplantation

    PubMed Central

    Kornblit, Brian; Leisenring, Wendy M.; Santos, Erlinda B.; Storb, Rainer; Sandmaier, Brenda M.

    2013-01-01

    Background: Although in vitro and in vivo experiments have suggested that mesenchymal stromal cells (MSC) may have important immunomodulatory functions in allogeneic hematopoietic cell transplantation (HCT), results from clinical studies have been inconsistent. In the current study we investigate the safety of dog leukocyte antigen (DLA) identical or third party unrelated MSC in DLA-identical HCT. Results: There were no differences between treatment groups in depth of granulocyte or platelet nadirs, time to granulocyte or platelet engraftment, rate of acute GVHD or rejection. All dogs tolerated the MSC infusion well, although 2 dogs treated with unrelated MSC were euthanized on day 9 due to complications unrelated to the MSC infusion. While no formation of ectopic tissue was observed, GFP positive signals in bone marrow, spleen or liver were detected at time of necropsy in 75% and 50% of dogs treated with DLA-identical or unrelated MSC, respectively. Discussion: Treatment with DLA-identical or unrelated MSC in high dose DLA-identical HCT is safe, and provides a large animal HCT model in which to investigate immunological mechanisms and optimal treatment strategies for future human trials. Methods: Fourteen dogs were treated with 920 cGy total body irradiation (TBI) followed by transplantation of marrow from DLA-identical littermates and immunosuppression with cyclosporine. Prior to infusion of marrow, dogs received infusions of DLA-identical MSC from the marrow donor (n = 4), unrelated MSC (n = 4), or culture medium (n = 6), within 1 h of TBI. MSC obtained from relevant donors were ex-vivo expanded and transduced with GFP-retrovirus before infusion. PMID:23723082

  1. Population balance modeling of antibodies aggregation kinetics.

    PubMed

    Arosio, Paolo; Rima, Simonetta; Lattuada, Marco; Morbidelli, Massimo

    2012-06-21

    The aggregates morphology and the aggregation kinetics of a model monoclonal antibody under acidic conditions have been investigated. Growth occurs via irreversible cluster-cluster coagulation forming compact, fractal aggregates with fractal dimension of 2.6. We measured the time evolution of the average radius of gyration, , and the average hydrodynamic radius, , by in situ light scattering, and simulated the aggregation kinetics by a modified Smoluchowski's population balance equations. The analysis indicates that aggregation does not occur under diffusive control, and allows quantification of effective intermolecular interactions, expressed in terms of the Fuchs stability ratio (W). In particular, by introducing a dimensionless time weighed on W, the time evolutions of measured under various operating conditions (temperature, pH, type and concentration of salt) collapse on a single master curve. The analysis applies also to data reported in the literature when growth by cluster-cluster coagulation dominates, showing a certain level of generality in the antibodies aggregation behavior. The quantification of the stability ratio gives important physical insights into the process, including the Arrhenius dependence of the aggregation rate constant and the relationship between monomer-monomer and cluster-cluster interactions. Particularly, it is found that the reactivity of non-native monomers is larger than that of non-native aggregates, likely due to the reduction of the number of available hydrophobic patches during aggregation.

  2. Active matter model of Myxococcus xanthus aggregation

    NASA Astrophysics Data System (ADS)

    Patch, Adam; Bahar, Fatmagul; Liu, Guannan; Thutupalli, Shashi; Welch, Roy; Yllanes, David; Shaevitz, Joshua; Marchetti, M. Cristina

    Myxococcus xanthus is a soil-dwelling bacterium that exhibits several fascinating collective behaviors including streaming, swarming, and generation of fruiting bodies. A striking feature of M. xanthus is that it periodically reverses its motility direction. The first stage of fruiting body formation is characterized by the aggregation of cells on a surface into round mesoscopic structures. Experiments have shown that this aggregation relies heavily on regulation of the reversal rate and local mechanical interactions, suggesting motility-induced phase separation may play an important role. We have adapted self-propelled particle models to include cell reversal and motility suppression resulting from sporulation observed in aggregates. Using 2D molecular dynamics simulations, we map the phase behavior in the space of Péclet number and local density and examine the kinetics of aggregation for comparison to experiments.

  3. Structure and aggregation in model tetramethylurea solutions

    SciTech Connect

    Gupta, Rini; Patey, G. N.

    2014-08-14

    The structure of model aqueous tetramethylurea (TMU) solutions is investigated employing large-scale (32 000, 64 000 particles) molecular dynamics simulations. Results are reported for TMU mole fractions, X{sub t}, ranging from infinite dilution up to 0.07, and for two temperatures, 300 and 330 K. Two existing force fields for TMU-water solutions are considered. These are the GROMOS 53A6 united-atom TMU model combined with SPC/E water [TMU(GROMOS-UA)/W(SPC/E)], and the more frequently employed AMBER03 all-atom force field for TMU combined with the TIP3P water model [TMU(AMBER-AA)/W(TIP3P)]. It is shown that TMU has a tendency towards aggregation for both models considered, but the tendency is significantly stronger for the [TMU(AMBER-AA)/W(TIP3P)] force field. For this model signs of aggregation are detected at X{sub t} = 0.005, aggregation is a well established feature of the solution at X{sub t} = 0.02, and the aggregates increase further in size with increasing concentration. This is in agreement with at least some experimental studies, which report signals of aggregation in the low concentration regime. The TMU aggregates exhibit little structure and are simply loosely ordered, TMU-rich regions of solution. The [TMU(GROMOS-UA)/W(SPC/E)] model shows strong signs of aggregation only at higher concentrations (X{sub t} ≳ 0.04), and the aggregates appear more loosely ordered, and less well-defined than those occurring in the [TMU(AMBER-AA)/W(TIP3P)] system. For both models, TMU aggregation increases when the temperature is increased from 300 to 330 K, consistent with an underlying entropy driven, hydrophobic interaction mechanism. At X{sub t} = 0.07, the extra-molecular correlation length expected for microheterogeneous solutions has become comparable with the size of the simulation cell for both models considered, indicating that even the systems simulated here are sufficiently large only at low concentrations.

  4. Structure and aggregation in model tetramethylurea solutions.

    PubMed

    Gupta, Rini; Patey, G N

    2014-08-14

    The structure of model aqueous tetramethylurea (TMU) solutions is investigated employing large-scale (32,000, 64,000 particles) molecular dynamics simulations. Results are reported for TMU mole fractions, X(t), ranging from infinite dilution up to 0.07, and for two temperatures, 300 and 330 K. Two existing force fields for TMU-water solutions are considered. These are the GROMOS 53A6 united-atom TMU model combined with SPC/E water [TMU(GROMOS-UA)/W(SPC/E)], and the more frequently employed AMBER03 all-atom force field for TMU combined with the TIP3P water model [TMU(AMBER-AA)/W(TIP3P)]. It is shown that TMU has a tendency towards aggregation for both models considered, but the tendency is significantly stronger for the [TMU(AMBER-AA)/W(TIP3P)] force field. For this model signs of aggregation are detected at X(t) = 0.005, aggregation is a well established feature of the solution at X(t) = 0.02, and the aggregates increase further in size with increasing concentration. This is in agreement with at least some experimental studies, which report signals of aggregation in the low concentration regime. The TMU aggregates exhibit little structure and are simply loosely ordered, TMU-rich regions of solution. The [TMU(GROMOS-UA)/W(SPC/E)] model shows strong signs of aggregation only at higher concentrations (X(t) ≳ 0.04), and the aggregates appear more loosely ordered, and less well-defined than those occurring in the [TMU(AMBER-AA)/W(TIP3P)] system. For both models, TMU aggregation increases when the temperature is increased from 300 to 330 K, consistent with an underlying entropy driven, hydrophobic interaction mechanism. At X(t) = 0.07, the extra-molecular correlation length expected for microheterogeneous solutions has become comparable with the size of the simulation cell for both models considered, indicating that even the systems simulated here are sufficiently large only at low concentrations.

  5. DLA Pre-Award Contracting System

    DTIC Science & Technology

    1993-05-01

    Gulley DPSSO Bldg 33 Standards Cheryl Haines DISC-RMO Bldg 36 Lead Time Jeff Hammer DGSC-P Bldg 32 DPACS WorkloadjersonnedALT Judy Harroson DLA-Z...33 DPACS Functionality Lou JuIg DISC-RM Bldg 36 Resource Data Sandra King DLA-ZSM 3A675 Project Oversight Scotie Knott DGSC-P Bldg 33 Post Award Dave

  6. Aggregate vehicle travel forecasting model

    SciTech Connect

    Greene, D.L.; Chin, Shih-Miao; Gibson, R.

    1995-05-01

    This report describes a model for forecasting total US highway travel by all vehicle types, and its implementation in the form of a personal computer program. The model comprises a short-run, econometrically-based module for forecasting through the year 2000, as well as a structural, scenario-based longer term module for forecasting through 2030. The short-term module is driven primarily by economic variables. It includes a detailed vehicle stock model and permits the estimation of fuel use as well as vehicle travel. The longer-tenn module depends on demographic factors to a greater extent, but also on trends in key parameters such as vehicle load factors, and the dematerialization of GNP. Both passenger and freight vehicle movements are accounted for in both modules. The model has been implemented as a compiled program in the Fox-Pro database management system operating in the Windows environment.

  7. Methods and Models for the Aggregate.

    ERIC Educational Resources Information Center

    McKay, Rose; Segall, Mary

    1983-01-01

    Presents a community analysis plan used at the University of Colorado to develop a graduate-level community health nursing program. Examines a model that describes different possibilities for including the aggregate in community health nursing programs. States that community health nursing will be strengthened by developing associations between…

  8. Probabilistic prediction models for aggregate quarry siting

    USGS Publications Warehouse

    Robinson, G.R.; Larkins, P.M.

    2007-01-01

    Weights-of-evidence (WofE) and logistic regression techniques were used in a GIS framework to predict the spatial likelihood (prospectivity) of crushed-stone aggregate quarry development. The joint conditional probability models, based on geology, transportation network, and population density variables, were defined using quarry location and time of development data for the New England States, North Carolina, and South Carolina, USA. The Quarry Operation models describe the distribution of active aggregate quarries, independent of the date of opening. The New Quarry models describe the distribution of aggregate quarries when they open. Because of the small number of new quarries developed in the study areas during the last decade, independent New Quarry models have low parameter estimate reliability. The performance of parameter estimates derived for Quarry Operation models, defined by a larger number of active quarries in the study areas, were tested and evaluated to predict the spatial likelihood of new quarry development. Population density conditions at the time of new quarry development were used to modify the population density variable in the Quarry Operation models to apply to new quarry development sites. The Quarry Operation parameters derived for the New England study area, Carolina study area, and the combined New England and Carolina study areas were all similar in magnitude and relative strength. The Quarry Operation model parameters, using the modified population density variables, were found to be a good predictor of new quarry locations. Both the aggregate industry and the land management community can use the model approach to target areas for more detailed site evaluation for quarry location. The models can be revised easily to reflect actual or anticipated changes in transportation and population features. ?? International Association for Mathematical Geology 2007.

  9. Aggregate driver model to enable predictable behaviour

    NASA Astrophysics Data System (ADS)

    Chowdhury, A.; Chakravarty, T.; Banerjee, T.; Balamuralidhar, P.

    2015-09-01

    The categorization of driving styles, particularly in terms of aggressiveness and skill is an emerging area of interest under the broader theme of intelligent transportation. There are two possible discriminatory techniques that can be applied for such categorization; a microscale (event based) model and a macro-scale (aggregate) model. It is believed that an aggregate model will reveal many interesting aspects of human-machine interaction; for example, we may be able to understand the propensities of individuals to carry out a given task over longer periods of time. A useful driver model may include the adaptive capability of the human driver, aggregated as the individual propensity to control speed/acceleration. Towards that objective, we carried out experiments by deploying smartphone based application to be used for data collection by a group of drivers. Data is primarily being collected from GPS measurements including position & speed on a second-by-second basis, for a number of trips over a two months period. Analysing the data set, aggregate models for individual drivers were created and their natural aggressiveness were deduced. In this paper, we present the initial results for 12 drivers. It is shown that the higher order moments of the acceleration profile is an important parameter and identifier of journey quality. It is also observed that the Kurtosis of the acceleration profiles stores major information about the driving styles. Such an observation leads to two different ranking systems based on acceleration data. Such driving behaviour models can be integrated with vehicle and road model and used to generate behavioural model for real traffic scenario.

  10. Topological data analysis of biological aggregation models.

    PubMed

    Topaz, Chad M; Ziegelmeier, Lori; Halverson, Tom

    2015-01-01

    We apply tools from topological data analysis to two mathematical models inspired by biological aggregations such as bird flocks, fish schools, and insect swarms. Our data consists of numerical simulation output from the models of Vicsek and D'Orsogna. These models are dynamical systems describing the movement of agents who interact via alignment, attraction, and/or repulsion. Each simulation time frame is a point cloud in position-velocity space. We analyze the topological structure of these point clouds, interpreting the persistent homology by calculating the first few Betti numbers. These Betti numbers count connected components, topological circles, and trapped volumes present in the data. To interpret our results, we introduce a visualization that displays Betti numbers over simulation time and topological persistence scale. We compare our topological results to order parameters typically used to quantify the global behavior of aggregations, such as polarization and angular momentum. The topological calculations reveal events and structure not captured by the order parameters.

  11. Microwave extinction characteristics of nanoparticle aggregates

    NASA Astrophysics Data System (ADS)

    Wu, Y. P.; Cheng, J. X.; Liu, X. X.; Wang, H. X.; Zhao, F. T.; Wen, W. W.

    2016-07-01

    Structure of nanoparticle aggregates plays an important role in microwave extinction capacity. The diffusion-limited aggregation model (DLA) for fractal growth is utilized to explore the possible structures of nanoparticle aggregates by computer simulation. Based on the discrete dipole approximation (DDA) method, the microwave extinction performance by different nano-carborundum aggregates is numerically analyzed. The effects of the particle quantity, original diameter, fractal structure, as well as orientation on microwave extinction are investigated, and also the extinction characteristics of aggregates are compared with the spherical nanoparticle in the same volume. Numerical results give out that proper aggregation of nanoparticle is beneficial to microwave extinction capacity, and the microwave extinction cross section by aggregated granules is better than that of the spherical solid one in the same volume.

  12. Models for the optical simulations of fractal aggregated soot particles thinly coated with non-absorbing aerosols

    NASA Astrophysics Data System (ADS)

    Wu, Yu; Cheng, Tianhai; Zheng, Lijuan; Chen, Hao

    2016-10-01

    Light absorption enhancement of aged soot aerosols is highly sensitive to the morphologies and mixing states of soot aggregates and their non-absorbing coatings, such as organic materials. The quantification of these effects on the optical properties of thinly coated soot aerosols is simulated using an effective model with fixed volume fractions. Fractal aggregated soot was simulated using the diffusion limited aggregation (DLA) algorithm and discretized into soot dipoles. The dipoles of non-absorbing aerosols, whose number was fixed by the volume fraction, were further generated from the neighboring random edge dipoles. Their optical properties were calculated using the discrete dipole approximation (DDA) method and were compared with other commonly used models. The optical properties of thinly coated soot calculated using the fixed volume fraction model are close to (less than ~10% difference) the results of the fixed coating thickness model, except their asymmetry parameters (up to ~25% difference). In the optical simulations of thinly coated soot aerosols, this relative difference of asymmetry parameters and phase functions between these realistic models may be notable. The realizations of the fixed volume fraction model may introduce smaller variation of optical results than those of the fixed coating thickness model. Moreover, the core-shell monomers model and homogeneous aggregated spheres model with the Maxwell-Garnett (MG) theory may underestimate (up to ~20%) the cross sections of thinly coated soot aggregates. The single core-shell sphere model may largely overestimate (up to ~150%) the cross sections and single scattering albedo of thinly coated soot aggregates, and it underestimated (up to ~60%) their asymmetry parameters. It is suggested that the widely used single core-shell sphere approximation may not be suitable for the single scattering calculations of thinly coated soot aerosols.

  13. Understanding sexual harassment using aggregate construct models.

    PubMed

    Nye, Christopher D; Brummel, Bradley J; Drasgow, Fritz

    2014-11-01

    Sexual harassment has received a substantial amount of empirical attention over the past few decades, and this research has consistently shown that experiencing these behaviors has a detrimental effect on employees' well-being, job attitudes, and behaviors at work. However, these findings, and the conclusions that are drawn from them, make the implicit assumption that the empirical models used to examine sexual harassment are properly specified. This article presents evidence that properly specified aggregate construct models are more consistent with theoretical structures and definitions of sexual harassment and can result in different conclusions about the nomological network of harassment. Results from 3 large samples, 2 military and 1 from a civilian population, are used to illustrate the differences between aggregate construct and reflective indicator models of sexual harassment. These analyses suggested that the factor structure and the nomological network of sexual harassment differ when modeling harassment as an aggregate construct. The implications of these results for the continued study of sexual harassment are discussed. (PsycINFO Database Record (c) 2014 APA, all rights reserved).

  14. A nonlocal continuum model for biological aggregation.

    PubMed

    Topaz, Chad M; Bertozzi, Andrea L; Lewis, Mark A

    2006-10-01

    We construct a continuum model for biological aggregations in which individuals experience long-range social attraction and short-range dispersal. For the case of one spatial dimension, we study the steady states analytically and numerically. There exist strongly nonlinear states with compact support and steep edges that correspond to localized biological aggregations, or clumps. These steady-state clumps are reached through a dynamic coarsening process. In the limit of large population size, the clumps approach a constant density swarm with abrupt edges. We use energy arguments to understand the nonlinear selection of clump solutions, and to predict the internal density in the large population limit. The energy result holds in higher dimensions as well, and is demonstrated via numerical simulations in two dimensions.

  15. Topological Data Analysis of Biological Aggregation Models

    PubMed Central

    Topaz, Chad M.; Ziegelmeier, Lori; Halverson, Tom

    2015-01-01

    We apply tools from topological data analysis to two mathematical models inspired by biological aggregations such as bird flocks, fish schools, and insect swarms. Our data consists of numerical simulation output from the models of Vicsek and D'Orsogna. These models are dynamical systems describing the movement of agents who interact via alignment, attraction, and/or repulsion. Each simulation time frame is a point cloud in position-velocity space. We analyze the topological structure of these point clouds, interpreting the persistent homology by calculating the first few Betti numbers. These Betti numbers count connected components, topological circles, and trapped volumes present in the data. To interpret our results, we introduce a visualization that displays Betti numbers over simulation time and topological persistence scale. We compare our topological results to order parameters typically used to quantify the global behavior of aggregations, such as polarization and angular momentum. The topological calculations reveal events and structure not captured by the order parameters. PMID:25970184

  16. Modeling transport and aggregation of volcanic ash particles

    NASA Astrophysics Data System (ADS)

    Costa, Antonio; Folch, Arnau; Macedonio, Giovanni; Durant, Adam

    2010-05-01

    A complete description of ash aggregation processes in volcanic clouds is an very arduous task and the full coupling of ash transport and ash aggregation models is still computationally prohibitive. A large fraction of fine ash injected in the atmosphere during explosive eruptions aggregate because of complex interactions of surface liquid layers, electrostatic forces, and differences in settling velocities. The formation of aggregates of size and density different from those of the primary particles dramatically changes the sedimentation dynamics and results in lower atmospheric residence times of ash particles and in the formation of secondary maxima of tephra deposit. Volcanic ash transport models should include a full aggregation model accounting for all particle class interaction. However this approach would require prohibitive computational times. Here we present a simplified model for wet aggregation that accounts for both atmospheric and volcanic water transport. The aggregation model assumes a fractal relationship for the number of primary particles in aggregates, average efficiencies factors, and collision frequency functions accounting for Brownian motion, laminar and turbulent fluid shear, and differential settling velocity. We implemented the aggregation model in the WRF+FALL3D coupled modelling system and applied it to different eruptions where aggregation has been recognized to play an important role, such as the August and September 1992 Crater Peak eruptions and the 1980 Mt St Helens eruption. Moreover, understanding aggregation processes in volcanic clouds will contribute to mitigate the risks related with volcanic ash transport and sedimentation.

  17. Kinetic and hydrodynamic models of chemotactic aggregation

    NASA Astrophysics Data System (ADS)

    Chavanis, Pierre-Henri; Sire, Clément

    2007-10-01

    We derive general kinetic and hydrodynamic models of chemotactic aggregation that describe certain features of the morphogenesis of biological colonies (like bacteria, amoebae, endothelial cells or social insects). Starting from a stochastic model defined in terms of N coupled Langevin equations, we derive a nonlinear mean-field Fokker-Planck equation governing the evolution of the distribution function of the system in phase space. By taking the successive moments of this kinetic equation and using a local thermodynamic equilibrium condition, we derive a set of hydrodynamic equations involving a damping term. In the limit of small frictions, we obtain a hyperbolic model describing the formation of network patterns (filaments) and in the limit of strong frictions we obtain a parabolic model which is a generalization of the standard Keller-Segel model describing the formation of clusters (clumps). Our approach connects and generalizes several models introduced in the chemotactic literature. We discuss the analogy between bacterial colonies and self-gravitating systems and between the chemotactic collapse and the gravitational collapse (Jeans instability). We also show that the basic equations of chemotaxis are similar to nonlinear mean-field Fokker-Planck equations so that a notion of effective generalized thermodynamics can be developed.

  18. 76 FR 22681 - Defense Logistics Agency (DLA) Address Directory

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-22

    ... benefits the public in advising them where to send requests for review. DLA FOIA/Privacy Points of Contact are found at: http://www.dla.mil/foia-privacy/foia_poc.aspx . FOR FURTHER INFORMATION CONTACT:...

  19. RBC aggregation: laboratory data and models.

    PubMed

    Meiselman, H J; Neu, B; Rampling, M W; Baskurt, O K

    2007-01-01

    The reversible aggregation of red blood cells (RBC) into linear and three-dimensional structures continues to be of basic science and clinical interest: RBC aggregation affects low shear blood viscosity and microvascular flow dynamics, and can be markedly enhanced in several clinical states. Until fairly recently, most research efforts were focused on relations between suspending medium composition (i.e., protein levels, polymer type and concentration) and aggregate formation. However, there is now an increasing amount of experimental evidence indicating that RBC cellular properties can markedly affect aggregation, with the term "RBC aggregability" coined to describe the cell's intrinsic tendency to aggregate. Variations of aggregability can be large, with some changes of aggregation substantially greater than those resulting from pathologic states. The present review provides a brief overview of this topic, and includes such areas as donor-to-donor variations, polymer-plasma correlations, effects of RBC age, effects of enzymatic treatment, and current developments related to the mechanisms involved in RBC aggregation.

  20. Influence of dispersing additive on asphaltenes aggregation in model system

    NASA Astrophysics Data System (ADS)

    Gorshkov, A. M.; Shishmina, L. V.; Tukhvatullina, A. Z.; Ismailov, Yu R.; Ges, G. A.

    2016-09-01

    The work is devoted to investigation of the dispersing additive influence on asphaltenes aggregation in the asphaltenes-toluene-heptane model system by photon correlation spectroscopy method. The experimental relationship between the onset point of asphaltenes and their concentration in toluene has been obtained. The influence of model system composition on asphaltenes aggregation has been researched. The estimation of aggregative and sedimentation stability of asphaltenes in model system and system with addition of dispersing additive has been given.

  1. Aggregate Dynamics in AN Evolutionary Network Model

    NASA Astrophysics Data System (ADS)

    Seufert, Adrian M.; Schweitzer, Frank

    We analyze a model of interacting agents (e.g. prebiotic chemical species) which are represented by nodes of a network, whereas their interactions are mapped onto directed links between these nodes. On a fast time scale, each agent follows an eigendynamics based on catalytic support from other nodes, whereas on a much slower time scale the network evolves through selection and mutation of its nodes-agent. In the first part of the paper, we explain the dynamics of the model by means of characteristic snapshots of the network evolution and confirm earlier findings on crashes and recoveries in the network structure. In the second part, we focus on the aggregate behavior of the network dynamics. We show that the disruptions in the network structure are smoothed out, so that the average evolution can be described by a growth regime followed by a saturation regime, without an initial random regime. For the saturation regime, we obtain a logarithmic scaling between the average connectivity per node s and a parameter m, describing the average incoming connectivity, which is independent of the system size N.

  2. Scaling theory for the anisotropic behavior of generalized diffusion-limited aggregation clusters in two dimensions

    NASA Astrophysics Data System (ADS)

    Matsushita, Mitsugu; Family, Fereydoon; Honda, Katsuya

    1987-10-01

    A scaling description of the crossover from isotropic to anisotropic cluster growth for ordinary diffusion-limited aggregation (DLA) in two dimensions developed recently by Family and Hentschel is extended to the generalized DLA or η model. The dependence of various exponents necessary to characterize the anisotropic growth of the local-growth probability exponent η of the generalized DLA is obtained explicitly. The η dependence of the exponent β describing the variation of the crossover mass Nc on the degree of symmetry m,Nc~mβ, is derived. The results indicate that the anisotropic star-shaped clusters can be easily observed for η>1, while their appearance is much more difficult for η<1. All our results are consistent with those of computer simulations reported so far.

  3. On aggregation in spatial econometric modelling

    NASA Astrophysics Data System (ADS)

    Paelinck, Jean H. P.

    The spatial aggregation problem - also termed the modifiable areal unit problem - has attracted regular attention in spatial statistics and econometrics. In this study econometric aggregation analysis is used to investigate the formal composition of meso-areal parameters given micro-areal underlying relations with spatial dependence. Impact on stochastic terms (possible meso-areal spatial autocorrelation) is also studied. Finally consequences for meso-areal estimation are derived, the general finding having been that spatial aggregation leads to meso-region specific parameter values, with the estimation problems this implies.

  4. Modelling the structure of sludge aggregates

    PubMed Central

    Smoczyński, Lech; Ratnaweera, Harsha; Kosobucka, Marta; Smoczyński, Michał; Kalinowski, Sławomir; Kvaal, Knut

    2016-01-01

    ABSTRACT The structure of sludge is closely associated with the process of wastewater treatment. Synthetic dyestuff wastewater and sewage were coagulated using the PAX and PIX methods, and electro-coagulated on aluminium electrodes. The processes of wastewater treatment were supported with an organic polymer. The images of surface structures of the investigated sludge were obtained using scanning electron microscopy (SEM). The software image analysis permitted obtaining plots log A vs. log P, wherein A is the surface area and P is the perimeter of the object, for individual objects comprised in the structure of the sludge. The resulting database confirmed the ‘self-similarity’ of the structural objects in the studied groups of sludge, which enabled calculating their fractal dimension and proposing models for these objects. A quantitative description of the sludge aggregates permitted proposing a mechanism of the processes responsible for their formation. In the paper, also, the impact of the structure of the investigated sludge on the process of sedimentation, and dehydration of the thickened sludge after sedimentation, was discussed. PMID:26549812

  5. Modelling the structure of sludge aggregates.

    PubMed

    Smoczyński, Lech; Ratnaweera, Harsha; Kosobucka, Marta; Smoczyński, Michał; Kalinowski, Sławomir; Kvaal, Knut

    2016-01-01

    The structure of sludge is closely associated with the process of wastewater treatment. Synthetic dyestuff wastewater and sewage were coagulated using the PAX and PIX methods, and electro-coagulated on aluminium electrodes. The processes of wastewater treatment were supported with an organic polymer. The images of surface structures of the investigated sludge were obtained using scanning electron microscopy (SEM). The software image analysis permitted obtaining plots log A vs. log P, wherein A is the surface area and P is the perimeter of the object, for individual objects comprised in the structure of the sludge. The resulting database confirmed the 'self-similarity' of the structural objects in the studied groups of sludge, which enabled calculating their fractal dimension and proposing models for these objects. A quantitative description of the sludge aggregates permitted proposing a mechanism of the processes responsible for their formation. In the paper, also, the impact of the structure of the investigated sludge on the process of sedimentation, and dehydration of the thickened sludge after sedimentation, was discussed.

  6. Development of Transverse Modes Damped DLA Structure

    SciTech Connect

    Jing, C.; Kanareykin, A.; Schoessow, P.; Gai, W.; Konecny, R.; Power, J. G.; Conde, M.

    2009-01-22

    As the dimensions of accelerating structures become smaller and beam intensities higher, the transverse wakefields driven by the beam become quite large with even a slight misalignment of the beam from the geometric axis. These deflection modes can cause inter-bunch beam breakup and intra-bunch head-tail instabilities along the beam path, and thus BBU control becomes a critical issue. All new metal based accelerating structures, like the accelerating structures developed at SLAC or power extractors at CLIC, have designs in which the transverse modes are heavily damped. Similarly, minimizing the transverse wakefield modes (here the HEMmn hybrid modes in Dielectric-Loaded Accelerating (DLA) structures) is also very critical for developing dielectric based high energy accelerators. In this paper, we present the design of a 7.8 GHz transverse mode damped DLA structure currently under construction, along with plans for the experimental program.

  7. The Influence of DL-A Compatibility on the Survival of Hepatic Allografts in Unmodified Mongrel Dogs

    PubMed Central

    Ranson, John H. C.; Rapaport, Felix T.; Ferrebee, Joseph W.; Cannon, Frances D.; Adams, Peter X.; Localio, S. Arthur

    1974-01-01

    Heterotopic hepatic transplantation was performed in 26 pairs of littermate and non-littermate mongrel dogs selected by serological criteria of DL-A compatibility. No immunosuppression was given. In non-littermates, 11 recipients of DL-A incompatible allografts survived 10-22 days (mean 13.4 days). Mean serum bilirubin rose by the 6th day. Three recipients of DL-A compatible allografts survived 13, 41, and 60 days, (mean 38 days). Mean serum bilirubin rose by the 8th day. In littermates, 5 recipients of DL-A incompatible allografts survived 7-12 days (mean 10.2 days) and mean serum bilirubin rose by the 6th day. Four recipients of DL-A compatible allografts from phenotypically DL-A non-identical donors survived 58, 82, 90 and 128 days (mean 89.5 days). Mean serum bilirubin rose by the 29th day. In contrast, 3 recipients of DL-A phenotypically identical allografts survived 171, 536 and over 636 days respectively, with normal mean serum bilirubin levels. The results confirm the role of the DL-A system in hepatic transplantation in mongrel dogs, and suggest that this dog population may constitute a suitable experimental model parallelling the current situation with regard to HL-A compatibility testing in outbred human subjects. The relatively long survival of DL-A compatible heterotopic hepatic allografts, compared with similar transplants of skin, kidney and heart, also suggests a need for studies of possible alteration in parameters of humoral and cellular reactivity in these recipients. PMID:4599072

  8. MODELING AGGREGATE CHLORPYRIFOS EXPOSURE AND DOSE TO CHILDREN

    EPA Science Inventory

    To help address the aggregate exposure assessment needs of the Food Quality Protection Act, a physically-based probabilistic model (SHEDS-Pesticides, version 3) has been applied to estimate aggregate chlorpyrifos exposure and dose to children. Two age groups (0-4, 5-9 years) a...

  9. An aggregation model for ash particles in volcanic clouds

    NASA Astrophysics Data System (ADS)

    Costa, A.; Folch, A.; Macedonio, G.; Durant, A.

    2009-12-01

    A large fraction of fine ash particles injected into the atmosphere during explosive eruptions aggregate through complex interactions of surface liquid layers, electrostatic forces, and differences in particle settling velocities. The aggregates formed have a different size and density compared to primary particles formed during eruption which dramatically changes the dynamics of sedimentation from the volcanic cloud. Consequently, the lifetime of ash particles in the atmosphere is reduced and a distal mass deposition maximum is often generated in resulting tephra deposits. A complete and rigorous description of volcanic ash fallout requires the full coupling of models of volcanic cloud dynamics and dispersion, and ash particle transport, aggregation and sedimentation. Furthermore, volcanic ash transport models should include an aggregation model that accounts for the interaction of all particle size classes. The problem with this approach is that simulations would require excessively long computational times thereby prohibiting its application in an operational setting during an explosive volcanic eruption. Here we present a simplified model for ash particle transport and aggregation that includes the effects of water in the volcanic cloud and surrounding atmosphere. The aggregation model assumes a fractal relationship for the number of primary particles in aggregates, average sticking efficiency factors, and collision frequency functions that account for Brownian motion, laminar and turbulent fluid shear, and differential settling velocity. A parametric study on the key parameters of the model was performed. We implemented the aggregation model in the WRF+FALL3D coupled modelling system and applied it to different eruptions where aggregation has been recognized to play an important role, including the August and September 1992 Crater Peak eruptions and the 1980 Mt St Helens eruption. In these cases, mass deposited as a function of deposit area and the particle

  10. Aggregates, broccoli and cauliflower

    NASA Astrophysics Data System (ADS)

    Grey, Francois; Kjems, Jørgen K.

    1989-09-01

    Naturally grown structures with fractal characters like broccoli and cauliflower are discussed and compared with DLA-type aggregates. It is suggested that the branching density can be used to characterize the growth process and an experimental method to determine this parameter is proposed.

  11. Characterization and modeling of thermal diffusion and aggregation in nanofluids.

    SciTech Connect

    Gharagozloo, Patricia E.; Goodson, Kenneth E.

    2010-05-01

    Fluids with higher thermal conductivities are sought for fluidic cooling systems in applications including microprocessors and high-power lasers. By adding high thermal conductivity nanoscale metal and metal oxide particles to a fluid the thermal conductivity of the fluid is enhanced. While particle aggregates play a central role in recent models for the thermal conductivity of nanofluids, the effect of particle diffusion in a temperature field on the aggregation and transport has yet to be studied in depth. The present work separates the effects of particle aggregation and diffusion using parallel plate experiments, infrared microscopy, light scattering, Monte Carlo simulations, and rate equations for particle and heat transport in a well dispersed nanofluid. Experimental data show non-uniform temporal increases in thermal conductivity above effective medium theory and can be well described through simulation of the combination of particle aggregation and diffusion. The simulation shows large concentration distributions due to thermal diffusion causing variations in aggregation, thermal conductivity and viscosity. Static light scattering shows aggregates form more quickly at higher concentrations and temperatures, which explains the increased enhancement with temperature reported by other research groups. The permanent aggregates in the nanofluid are found to have a fractal dimension of 2.4 and the aggregate formations that grow over time are found to have a fractal dimension of 1.8, which is consistent with diffusion limited aggregation. Calculations show as aggregates grow the viscosity increases at a faster rate than thermal conductivity making the highly aggregated nanofluids unfavorable, especially at the low fractal dimension of 1.8. An optimum nanoparticle diameter for these particular fluid properties is calculated to be 130 nm to optimize the fluid stability by reducing settling, thermal diffusion and aggregation.

  12. Kinetic model for astaxanthin aggregation in water-methanol mixtures

    NASA Astrophysics Data System (ADS)

    Giovannetti, Rita; Alibabaei, Leila; Pucciarelli, Filippo

    2009-07-01

    The aggregation of astaxanthin in hydrated methanol was kinetically studied in the temperature range from 10 °C to 50 °C, at different astaxanthin concentrations and solvent composition. A kinetic model for the formation and transformation of astaxanthin aggregated has been proposed. Spectrophotometric studies showed that monomeric astaxanthin decayed to H-aggregates that after-wards formed J-aggregates when water content was 50% and the temperature lower than 20 °C; at higher temperatures, very stable J-aggregates were formed directly. Monomer formed very stable H-aggregates when the water content was greater than 60%; in these conditions H-aggregates decayed into J-aggregates only when the temperature was at least 50 °C. Through these findings it was possible to establish that the aggregation reactions took place through a two steps consecutive reaction with first order kinetic constants and that the values of these depended on the solvent composition and temperature.

  13. A particle dynamic model of red blood cell aggregation kinetics.

    PubMed

    Fenech, Marianne; Garcia, Damien; Meiselman, Herbert J; Cloutier, Guy

    2009-11-01

    To elucidate the relationship between microscopic red blood cell (RBC) interactions and macroscopic rheological behavior, we propose a two-dimensional particle model capable of mimicking the main characteristics of RBC aggregation kinetics. The mechanical model of RBCs sheared in Couette flow is based on Newton law. We assumed a hydrodynamic force to move particles, a force to describe aggregation and an elasticity force. The role of molecular mass and concentration of neutral polymers on aggregation [Neu, B., and H. J. Meiselman. Biophys. J. 83:2482-2490, 2002] could be mimicked. Specifically, it was shown that for any shear rate (SR), the mean aggregate size (MAS) grew with time until it reached a constant value, which is consistent with in vitro experiments. It was also demonstrated that we could mimic the modal relationship between MAS and SR and the occurrence of maximum aggregation at about 0.1 s(-1). As anticipated, simulations indicated that an increase in aggregation force augmented MAS. Further, augmentation of the depletion layer thickness influenced MAS only for SR close to zero, which is a new finding. To conclude, our contribution reveals that the aggregation force intensity and SR influence the steady state MAS, and that the depletion and layer thickness affect the aggregation speed.

  14. Modeling the impact of soil aggregate size on selenium immobilization

    NASA Astrophysics Data System (ADS)

    Kausch, M. F.; Pallud, C. E.

    2013-03-01

    Soil aggregates are mm- to cm-sized microporous structures separated by macropores. Whereas fast advective transport prevails in macropores, advection is inhibited by the low permeability of intra-aggregate micropores. This can lead to mass transfer limitations and the formation of aggregate scale concentration gradients affecting the distribution and transport of redox sensitive elements. Selenium (Se) mobilized through irrigation of seleniferous soils has emerged as a major aquatic contaminant. In the absence of oxygen, the bioavailable oxyanions selenate, Se(VI), and selenite, Se(IV), can be microbially reduced to solid, elemental Se, Se(0), and anoxic microzones within soil aggregates are thought to promote this process in otherwise well-aerated soils. To evaluate the impact of soil aggregate size on selenium retention, we developed a dynamic 2-D reactive transport model of selenium cycling in a single idealized aggregate surrounded by a macropore. The model was developed based on flow-through-reactor experiments involving artificial soil aggregates (diameter: 2.5 cm) made of sand and containing Enterobacter cloacae SLD1a-1 that reduces Se(VI) via Se(IV) to Se(0). Aggregates were surrounded by a constant flow providing Se(VI) and pyruvate under oxic or anoxic conditions. In the model, reactions were implemented with double-Monod rate equations coupled to the transport of pyruvate, O2, and Se species. The spatial and temporal dynamics of the model were validated with data from experiments, and predictive simulations were performed covering aggregate sizes 1-2.5 cm in diameter. Simulations predict that selenium retention scales with aggregate size. Depending on O2, Se(VI), and pyruvate concentrations, selenium retention was 4-23 times higher in 2.5 cm aggregates compared to 1 cm aggregates. Under oxic conditions, aggregate size and pyruvate concentrations were found to have a positive synergistic effect on selenium retention. Promoting soil aggregation on

  15. Measuring and modeling hemoglobin aggregation below the freezing temperature.

    PubMed

    Rosa, Mónica; Lopes, Carlos; Melo, Eduardo P; Singh, Satish K; Geraldes, Vitor; Rodrigues, Miguel A

    2013-08-01

    Freezing of protein solutions is required for many applications such as storage, transport, or lyophilization; however, freezing has inherent risks for protein integrity. It is difficult to study protein stability below the freezing temperature because phase separation constrains solute concentration in solution. In this work, we developed an isochoric method to study protein aggregation in solutions at -5, -10, -15, and -20 °C. Lowering the temperature below the freezing point in a fixed volume prevents the aqueous solution from freezing, as pressure rises until equilibrium (P,T) is reached. Aggregation rates of bovine hemoglobin (BHb) increased at lower temperature (-20 °C) and higher BHb concentration. However, the addition of sucrose substantially decreased the aggregation rate and prevented aggregation when the concentration reached 300 g/L. The unfolding thermodynamics of BHb was studied using fluorescence, and the fraction of unfolded protein as a function of temperature was determined. A mathematical model was applied to describe BHb aggregation below the freezing temperature. This model was able to predict the aggregation curves for various storage temperatures and initial concentrations of BHb. The aggregation mechanism was revealed to be mediated by an unfolded state, followed by a fast growth of aggregates that readily precipitate. The aggregation kinetics increased for lower temperature because of the higher fraction of unfolded BHb closer to the cold denaturation temperature. Overall, the results obtained herein suggest that the isochoric method could provide a relatively simple approach to obtain fundamental thermodynamic information about the protein and the aggregation mechanism, thus providing a new approach to developing accelerated formulation studies below the freezing temperature.

  16. Impact of diffusion limited aggregates of impurities on nematic ordering

    NASA Astrophysics Data System (ADS)

    Harkai, S.; Ambrožič, M.; Kralj, S.

    2017-02-01

    We study the impact of random bond-type disorder on two-dimensional (2D) orientational ordering of nematic liquid crystal (LC) configurations. The lattice Lebwohl-Lasher pseudospin model is used to model orientational ordering perturbed by frozen-in rod-like impurities of concentration p exhibiting the isotropic orientational probability distribution. The impurities are either (i) randomly spatially distributed or (ii) form diffusion limited aggregation (DLA)-type patterns characterized by the fractal dimensions df, where we consider cases df ∼ 1.7 and df ∼ 1.9. The degree of orientational ordering is quantified in terms of the orientational pair correlation function G(r) . Simulations reveal that the DLA pattern imposed disorder has a significantly weaker impact for a given concentration of impurities. Furthermore, if samples are quenched from the isotropic LC phase, then the fractal dimension is relatively strongly imprinted on quantitative characteristics of G(r) .

  17. Kinetic Model for 1D aggregation of yeast ``prions''

    NASA Astrophysics Data System (ADS)

    Kunes, Kay; Cox, Daniel; Singh, Rajiv

    2004-03-01

    Mammalian prion proteins (PrP) are of public health interest because of mad cow and chronic wasting diseases. Yeast have proteins which can undergo similar reconformation and aggregation processes to PrP; yeast forms are simpler to experimentally study and model. Recent in vitro studies of the SUP35 protein(1), showed long aggregates and pure exponential growth of the misfolded form. To explain this data, we have extended a previous model of aggregation kinetics(2). The model assumes reconformation only upon aggregation, and includes aggregate fissioning and an initial nucleation barrier. We find for sufficiently small nucleation rates or seeding by small dimer concentrations that we can achieve the requisite exponential growth and long aggregates. We will compare to a more realistic stochastic kinetics model and present prelimary attempts to describe recent experiments on SUP35 strains. *-Supported by U.S. Army Congressionally Mandated Research Fund. 1) P. Chien and J.S. Weissman, Nature 410, 223 (2001); http://online.kitp.ucsb.edu/online/bionet03/collins/. 2) J. Masel, V.A.> Jansen, M.A. Nowak, Biophys. Chem. 77, 139 (1999).

  18. Forecasting Pell Program Applications Using Structural Aggregate Models.

    ERIC Educational Resources Information Center

    Cavin, Edward S.

    1995-01-01

    Demand for Pell Grant financial aid has become difficult to predict when using the current microsimulation model. This paper proposes an alternative model that uses aggregate data (based on individuals' microlevel decisions and macrodata on family incomes, college costs, and opportunity wages) and avoids some limitations of simple linear models.…

  19. Generic model for tunable colloidal aggregation in multidirectional fields.

    PubMed

    Kogler, Florian; Velev, Orlin D; Hall, Carol K; Klapp, Sabine H L

    2015-10-07

    Based on Brownian Dynamics computer simulations in two dimensions we investigate aggregation scenarios of colloidal particles with directional interactions induced by multiple external fields. To this end we propose a model which allows continuous change in the particle interactions from point-dipole-like to patchy-like (with four patches). We show that, as a result of this change, the non-equilibrium aggregation occurring at low densities and temperatures transforms from conventional diffusion-limited cluster aggregation (DLCA) to slippery DLCA involving rotating bonds; this is accompanied by a pronounced change of the underlying lattice structure of the aggregates from square-like to hexagonal ordering. Increasing the temperature we find a transformation to a fluid phase, consistent with results of a simple mean-field density functional theory.

  20. Continuum modeling of deformation and aggregation of red blood cells.

    PubMed

    Yoon, Daegeun; You, Donghyun

    2016-07-26

    In order to gain better understanding for rheology of an isolated red blood cell (RBC) and a group of multiple RBCs, new continuum models for describing mechanical properties of cellular structures of an RBC and inter-cellular interactions among multiple RBCs are developed. The viscous property of an RBC membrane, which characterizes dynamic behaviors of an RBC under stress loading and unloading processes, is determined using a generalized Maxwell model. The present model is capable of predicting stress relaxation and stress-strain hysteresis, of which prediction is not possible using the commonly used Kelvin-Voigt model. Nonlinear elasticity of an RBC is determined using the Yeoh hyperelastic material model in a framework of continuum mechanics using finite-element approximation. A novel method to model inter-cellular interactions among multiple adjacent RBCs is also developed. Unlike the previous modeling approaches for aggregation of RBCs, where interaction energy for aggregation is curve-fitted using a Morse-type potential function, the interaction energy is analytically determined. The present aggregation model, therefore, allows us to predict various effects of physical parameters such as the osmotic pressure, the thickness of a glycocalyx layer, the penetration depth, and the permittivity, on the depletion and electrostatic energy among RBCs. Simulations for elongation and recovery deformation of an RBC and for aggregation of multiple RBCs are conducted to evaluate the efficacy of the present continuum modeling methods.

  1. Multiscale measurement error models for aggregated small area health data.

    PubMed

    Aregay, Mehreteab; Lawson, Andrew B; Faes, Christel; Kirby, Russell S; Carroll, Rachel; Watjou, Kevin

    2016-08-01

    Spatial data are often aggregated from a finer (smaller) to a coarser (larger) geographical level. The process of data aggregation induces a scaling effect which smoothes the variation in the data. To address the scaling problem, multiscale models that link the convolution models at different scale levels via the shared random effect have been proposed. One of the main goals in aggregated health data is to investigate the relationship between predictors and an outcome at different geographical levels. In this paper, we extend multiscale models to examine whether a predictor effect at a finer level hold true at a coarser level. To adjust for predictor uncertainty due to aggregation, we applied measurement error models in the framework of multiscale approach. To assess the benefit of using multiscale measurement error models, we compare the performance of multiscale models with and without measurement error in both real and simulated data. We found that ignoring the measurement error in multiscale models underestimates the regression coefficient, while it overestimates the variance of the spatially structured random effect. On the other hand, accounting for the measurement error in multiscale models provides a better model fit and unbiased parameter estimates.

  2. Modelling of strongly coupled particle growth and aggregation

    NASA Astrophysics Data System (ADS)

    Gruy, F.; Touboul, E.

    2013-02-01

    The mathematical modelling of the dynamics of particle suspension is based on the population balance equation (PBE). PBE is an integro-differential equation for the population density that is a function of time t, space coordinates and internal parameters. Usually, the particle is characterized by a unique parameter, e.g. the matter volume v. PBE consists of several terms: for instance, the growth rate and the aggregation rate. So, the growth rate is a function of v and t. In classical modelling, the growth and the aggregation are independently considered, i.e. they are not coupled. However, current applications occur where the growth and the aggregation are coupled, i.e. the change of the particle volume with time is depending on its initial value v0, that in turn is related to an aggregation event. As a consequence, the dynamics of the suspension does not obey the classical Von Smoluchowski equation. This paper revisits this problem by proposing a new modelling by using a bivariate PBE (with two internal variables: v and v0) and by solving the PBE by means of a numerical method and Monte Carlo simulations. This is applied to a physicochemical system with a simple growth law and a constant aggregation kernel.

  3. Fractality à la carte: a general particle aggregation model.

    PubMed

    Nicolás-Carlock, J R; Carrillo-Estrada, J L; Dossetti, V

    2016-01-19

    In nature, fractal structures emerge in a wide variety of systems as a local optimization of entropic and energetic distributions. The fractality of these systems determines many of their physical, chemical and/or biological properties. Thus, to comprehend the mechanisms that originate and control the fractality is highly relevant in many areas of science and technology. In studying clusters grown by aggregation phenomena, simple models have contributed to unveil some of the basic elements that give origin to fractality, however, the specific contribution from each of these elements to fractality has remained hidden in the complex dynamics. Here, we propose a simple and versatile model of particle aggregation that is, on the one hand, able to reveal the specific entropic and energetic contributions to the clusters' fractality and morphology, and, on the other, capable to generate an ample assortment of rich natural-looking aggregates with any prescribed fractal dimension.

  4. Cement-aggregate compatibility and structure property relationships including modelling

    SciTech Connect

    Jennings, H.M.; Xi, Y.

    1993-07-15

    The role of aggregate, and its interface with cement paste, is discussed with a view toward establishing models that relate structure to properties. Both short (nm) and long (mm) range structure must be considered. The short range structure of the interface depends not only on the physical distribution of the various phases, but also on moisture content and reactivity of aggregate. Changes that occur on drying, i.e. shrinkage, may alter the structure which, in turn, feeds back to alter further drying and shrinkage. The interaction is dynamic, even without further hydration of cement paste, and the dynamic characteristic must be considered in order to fully understand and model its contribution to properties. Microstructure and properties are two subjects which have been pursued somewhat separately. This review discusses both disciplines with a view toward finding common research goals in the future. Finally, comment is made on possible chemical reactions which may occur between aggregate and cement paste.

  5. Fractality à la carte: a general particle aggregation model

    PubMed Central

    Nicolás-Carlock, J. R.; Carrillo-Estrada, J. L.; Dossetti, V.

    2016-01-01

    In nature, fractal structures emerge in a wide variety of systems as a local optimization of entropic and energetic distributions. The fractality of these systems determines many of their physical, chemical and/or biological properties. Thus, to comprehend the mechanisms that originate and control the fractality is highly relevant in many areas of science and technology. In studying clusters grown by aggregation phenomena, simple models have contributed to unveil some of the basic elements that give origin to fractality, however, the specific contribution from each of these elements to fractality has remained hidden in the complex dynamics. Here, we propose a simple and versatile model of particle aggregation that is, on the one hand, able to reveal the specific entropic and energetic contributions to the clusters’ fractality and morphology, and, on the other, capable to generate an ample assortment of rich natural-looking aggregates with any prescribed fractal dimension. PMID:26781204

  6. Fractality à la carte: a general particle aggregation model

    NASA Astrophysics Data System (ADS)

    Nicolás-Carlock, J. R.; Carrillo-Estrada, J. L.; Dossetti, V.

    2016-01-01

    In nature, fractal structures emerge in a wide variety of systems as a local optimization of entropic and energetic distributions. The fractality of these systems determines many of their physical, chemical and/or biological properties. Thus, to comprehend the mechanisms that originate and control the fractality is highly relevant in many areas of science and technology. In studying clusters grown by aggregation phenomena, simple models have contributed to unveil some of the basic elements that give origin to fractality, however, the specific contribution from each of these elements to fractality has remained hidden in the complex dynamics. Here, we propose a simple and versatile model of particle aggregation that is, on the one hand, able to reveal the specific entropic and energetic contributions to the clusters’ fractality and morphology, and, on the other, capable to generate an ample assortment of rich natural-looking aggregates with any prescribed fractal dimension.

  7. Markov Modeling with Soft Aggregation for Safety and Decision Analysis

    SciTech Connect

    COOPER,J. ARLIN

    1999-09-01

    The methodology in this report improves on some of the limitations of many conventional safety assessment and decision analysis methods. A top-down mathematical approach is developed for decomposing systems and for expressing imprecise individual metrics as possibilistic or fuzzy numbers. A ''Markov-like'' model is developed that facilitates combining (aggregating) inputs into overall metrics and decision aids, also portraying the inherent uncertainty. A major goal of Markov modeling is to help convey the top-down system perspective. One of the constituent methodologies allows metrics to be weighted according to significance of the attribute and aggregated nonlinearly as to contribution. This aggregation is performed using exponential combination of the metrics, since the accumulating effect of such factors responds less and less to additional factors. This is termed ''soft'' mathematical aggregation. Dependence among the contributing factors is accounted for by incorporating subjective metrics on ''overlap'' of the factors as well as by correspondingly reducing the overall contribution of these combinations to the overall aggregation. Decisions corresponding to the meaningfulness of the results are facilitated in several ways. First, the results are compared to a soft threshold provided by a sigmoid function. Second, information is provided on input ''Importance'' and ''Sensitivity,'' in order to know where to place emphasis on considering new controls that may be necessary. Third, trends in inputs and outputs are tracked in order to obtain significant information% including cyclic information for the decision process. A practical example from the air transportation industry is used to demonstrate application of the methodology. Illustrations are given for developing a structure (along with recommended inputs and weights) for air transportation oversight at three different levels, for developing and using cycle information, for developing Importance and

  8. Multiscale modelling of nucleosome core particle aggregation

    NASA Astrophysics Data System (ADS)

    Lyubartsev, Alexander P.; Korolev, Nikolay; Fan, Yanping; Nordenskiöld, Lars

    2015-02-01

    The nucleosome core particle (NCP) is the basic building block of chromatin. Under the influence of multivalent cations, isolated mononucleosomes exhibit a rich phase behaviour forming various columnar phases with characteristic NCP-NCP stacking. NCP stacking is also a regular element of chromatin structure in vivo. Understanding the mechanism of nucleosome stacking and the conditions leading to self-assembly of NCPs is still incomplete. Due to the complexity of the system and the need to describe electrostatics properly by including the explicit mobile ions, novel modelling approaches based on coarse-grained (CG) methods at the multiscale level becomes a necessity. In this work we present a multiscale CG computer simulation approach to modelling interactions and self-assembly of solutions of NCPs induced by the presence of multivalent cations. Starting from continuum simulations including explicit three-valent cobalt(III)hexammine (CoHex3+) counterions and 20 NCPs, based on a previously developed advanced CG NCP model with one bead per amino acid and five beads per two DNA base pair unit (Fan et al 2013 PLoS One 8 e54228), we use the inverse Monte Carlo method to calculate effective interaction potentials for a ‘super-CG’ NCP model consisting of seven beads for each NCP. These interaction potentials are used in large-scale simulations of up to 5000 NCPs, modelling self-assembly induced by CoHex3+. The systems of ‘super-CG’ NCPs form a single large cluster of stacked NCPs without long-range order in agreement with experimental data for NCPs precipitated by the three-valent polyamine, spermidine3+.

  9. A draft model aggregated code of ethics for bioethicists.

    PubMed

    Baker, Robert

    2005-01-01

    Bioethicists function in an environment in which their peers--healthcare executives, lawyers, nurses, physicians--assert the integrity of their fields through codes of professional ethics. Is it time for bioethics to assert its integrity by developing a code of ethics? Answering in the affirmative, this paper lays out a case by reviewing the historical nature and function of professional codes of ethics. Arguing that professional codes are aggregative enterprises growing in response to a field's historical experiences, it asserts that bioethics now needs to assert its integrity and independence and has already developed a body of formal statements that could be aggregated to create a comprehensive code of ethics for bioethics. A Draft Model Aggregated Code of Ethics for Bioethicists is offered in the hope that analysis and criticism of this draft code will promote further discussion of the nature and content of a code of ethics for bioethicists.

  10. Study of interstellar extinction by aggregate dust model

    NASA Astrophysics Data System (ADS)

    Bhattacharjee, C.; Das, H. S.; Sen, A. K.

    Extinction generally occurs whenever electromagnetic radiation propagates through a medium containing small particles. The spectral dependence of extinction, or extinction curve, is a function of the composition, structure and size distribution of the particles. The study of interstellar extinction is important because they provide essential information for understanding the properties of the dust. In this work we have considered the aggregate dust model to interpret the extinction efficiency (Qext) of interstellar dust in the wavelength range 0.11-3.4 µm. Using Superposition T-matrix code with Ballistic Cluster-Cluster Aggregate (BCCA) aggregate having 64 number of monomers with graphite, astronomical silicates and amorphous carbon, the normalized extinction efficiency has been calculated for a well defined size distribution within a size range 0.001 to 0.077 micron of extinction near wavelength 2175 Å. The calculated normalized extinction efficiency curve is well matched with observed extinction efficiency.

  11. 32 CFR Appendix H to Part 323 - DLA Exemption Rules

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... PROGRAM DEFENSE LOGISTICS AGENCY PRIVACY PROGRAM Pt. 323, App. H Appendix H to Part 323—DLA Exemption Rules Exempted Records Systems. All systems of records maintained by the Defense Logistics Agency...

  12. Development of a Ferroelectric Based Tunable DLA Structure

    SciTech Connect

    Kanareykin, A.; Schoessow, P.; Jing, C.; Nenasheva, E.; Power, J. G.; Gai, W.

    2009-01-22

    An experimental demonstration of a tunable Dielectric Loaded Accelerating (DLA)[1] structure is planned using a nonlinear ferroelectric with temperature- or voltage-controllable permittivity. We designed and tested two prototype Ka-band double layer ferroelectric-ceramic structures (cylindrical and planar) consisting of linear ceramic layers (dielectric constant of 6.8) and BST(M) composite ferroelectric layers of 400-800 {mu}m thickness and dielectric constant of 450-550. The frequency shift by temperature variation of the cylindrical Ka-band tunable DLA of 14 MHz/ deg. K has been demonstrated leading to an overall DLA structure frequency tuning range of 140-280 MHz with 10-20 deg. K temperature variation. The Ka band prototype DLA structure demonstrated a 6 MHz frequency tuning range for a dc bias field design at 25 kV/cm field strength.

  13. A local PDE model of aggregation formation in bacterial colonies

    NASA Astrophysics Data System (ADS)

    Chavy-Waddy, Paul-Christopher; Kolokolnikov, Theodore

    2016-10-01

    We study pattern formation in a model of cyanobacteria motion recently proposed by Galante, Wisen, Bhaya and Levy. By taking a continuum limit of their model, we derive a novel fourth-order nonlinear parabolic PDE equation that governs the behaviour of the model. This PDE is {{u}t}=-{{u}xx}-{{u}xxxx}+α {{≤ft(\\frac{{{u}x}{{u}xx}}{u}\\right)}x} . We then derive the instability thresholds for the onset of pattern formation. We also compute analytically the spatial profiles of the steady state aggregation density. These profiles are shown to be of the form \\text{sec}{{\\text{h}}p} where the exponent p is related to the parameters of the model. Full numerical simulations give a favorable comparison between the continuum and the underlying discrete system, and show that the aggregation profiles are stable above the critical threshold.

  14. Balancing aggregation and smoothing errors in inverse models

    DOE PAGES

    Turner, A. J.; Jacob, D. J.

    2015-06-30

    Inverse models use observations of a system (observation vector) to quantify the variables driving that system (state vector) by statistical optimization. When the observation vector is large, such as with satellite data, selecting a suitable dimension for the state vector is a challenge. A state vector that is too large cannot be effectively constrained by the observations, leading to smoothing error. However, reducing the dimension of the state vector leads to aggregation error as prior relationships between state vector elements are imposed rather than optimized. Here we present a method for quantifying aggregation and smoothing errors as a function ofmore » state vector dimension, so that a suitable dimension can be selected by minimizing the combined error. Reducing the state vector within the aggregation error constraints can have the added advantage of enabling analytical solution to the inverse problem with full error characterization. We compare three methods for reducing the dimension of the state vector from its native resolution: (1) merging adjacent elements (grid coarsening), (2) clustering with principal component analysis (PCA), and (3) applying a Gaussian mixture model (GMM) with Gaussian pdfs as state vector elements on which the native-resolution state vector elements are projected using radial basis functions (RBFs). The GMM method leads to somewhat lower aggregation error than the other methods, but more importantly it retains resolution of major local features in the state vector while smoothing weak and broad features.« less

  15. Social Aggregation in Pea Aphids: Experiment and Random Walk Modeling

    PubMed Central

    Nilsen, Christa; Paige, John; Warner, Olivia; Mayhew, Benjamin; Sutley, Ryan; Lam, Matthew; Bernoff, Andrew J.; Topaz, Chad M.

    2013-01-01

    From bird flocks to fish schools and ungulate herds to insect swarms, social biological aggregations are found across the natural world. An ongoing challenge in the mathematical modeling of aggregations is to strengthen the connection between models and biological data by quantifying the rules that individuals follow. We model aggregation of the pea aphid, Acyrthosiphon pisum. Specifically, we conduct experiments to track the motion of aphids walking in a featureless circular arena in order to deduce individual-level rules. We observe that each aphid transitions stochastically between a moving and a stationary state. Moving aphids follow a correlated random walk. The probabilities of motion state transitions, as well as the random walk parameters, depend strongly on distance to an aphid's nearest neighbor. For large nearest neighbor distances, when an aphid is essentially isolated, its motion is ballistic with aphids moving faster, turning less, and being less likely to stop. In contrast, for short nearest neighbor distances, aphids move more slowly, turn more, and are more likely to become stationary; this behavior constitutes an aggregation mechanism. From the experimental data, we estimate the state transition probabilities and correlated random walk parameters as a function of nearest neighbor distance. With the individual-level model established, we assess whether it reproduces the macroscopic patterns of movement at the group level. To do so, we consider three distributions, namely distance to nearest neighbor, angle to nearest neighbor, and percentage of population moving at any given time. For each of these three distributions, we compare our experimental data to the output of numerical simulations of our nearest neighbor model, and of a control model in which aphids do not interact socially. Our stochastic, social nearest neighbor model reproduces salient features of the experimental data that are not captured by the control. PMID:24376691

  16. Social aggregation in pea aphids: experiment and random walk modeling.

    PubMed

    Nilsen, Christa; Paige, John; Warner, Olivia; Mayhew, Benjamin; Sutley, Ryan; Lam, Matthew; Bernoff, Andrew J; Topaz, Chad M

    2013-01-01

    From bird flocks to fish schools and ungulate herds to insect swarms, social biological aggregations are found across the natural world. An ongoing challenge in the mathematical modeling of aggregations is to strengthen the connection between models and biological data by quantifying the rules that individuals follow. We model aggregation of the pea aphid, Acyrthosiphon pisum. Specifically, we conduct experiments to track the motion of aphids walking in a featureless circular arena in order to deduce individual-level rules. We observe that each aphid transitions stochastically between a moving and a stationary state. Moving aphids follow a correlated random walk. The probabilities of motion state transitions, as well as the random walk parameters, depend strongly on distance to an aphid's nearest neighbor. For large nearest neighbor distances, when an aphid is essentially isolated, its motion is ballistic with aphids moving faster, turning less, and being less likely to stop. In contrast, for short nearest neighbor distances, aphids move more slowly, turn more, and are more likely to become stationary; this behavior constitutes an aggregation mechanism. From the experimental data, we estimate the state transition probabilities and correlated random walk parameters as a function of nearest neighbor distance. With the individual-level model established, we assess whether it reproduces the macroscopic patterns of movement at the group level. To do so, we consider three distributions, namely distance to nearest neighbor, angle to nearest neighbor, and percentage of population moving at any given time. For each of these three distributions, we compare our experimental data to the output of numerical simulations of our nearest neighbor model, and of a control model in which aphids do not interact socially. Our stochastic, social nearest neighbor model reproduces salient features of the experimental data that are not captured by the control.

  17. An evolutionary explanation of the aggregation model of species coexistence.

    PubMed Central

    Rohlfs, Marko; Hoffmeister, Thomas S

    2003-01-01

    In ecology, the 'aggregation model of coexistence' provides a powerful concept to explain the unexpectedly high species richness of insects on ephemeral resources like dung pats, fruits, etc. It suggests that females aggregate their eggs across resource patches, which leads to an increased intraspecific competition within occupied patches and a relatively large number of patches that remain unoccupied. This provides competitor-free patches for heterospecifics, facilitating species coexistence. At first glance, deliberately causing competition among the females' own offspring and leaving resources to heterospecific competitors seems altruistic and incompatible with individual fitness maximization, raising the question of how natural selection operates in favour of egg aggregation on ephemeral resource patches. Allee effects that lead to fitness maxima at intermediate egg densities have been suggested, but not yet detected. Using drosophilid flies on decaying fruits as a study system, we demonstrate a hump-shaped relationship between egg density and individual survival probability, with maximum survivorship at intermediate densities. This pattern clearly selects for egg aggregation and resolves the possible conflict between the ecological concept of species coexistence on ephemeral resources and evolutionary theory. PMID:12952629

  18. Modelling cellular aggregation induced by chemotaxis and phototaxis.

    PubMed

    Fatehi, Hasnaa; Meyer-Hermann, Michael; Figge, Marc Thilo

    2010-12-01

    We use a generic agent-based model to investigate cellular aggregation in response to cell-cell interactions. Cells secrete soluble chemokines that are detected by other cells which carry specific receptors for this chemokine. In a process termed 'chemotaxis' the direction of motility of cells is determined by the concentration gradient of chemokines. 'Phototaxis' relies on the detection of light by intracellular receptors. In particular, we consider the case where intercellular signalling is induced by light that is emitted by the cells themselves. While chemotaxis is a frequently analysed and modelled intercellular communication path, phototaxis is only rarely investigated. We characterize and compare the collective response of cells to these mechanisms and show that chemotaxis and phototaxis can be distinguished by the emerging aggregation profile. This result provides a guideline to differentiate between these cell-cell interactions under specific circumstances in experiment.

  19. Modeling of chemical inhibition from amyloid protein aggregation kinetics

    PubMed Central

    2014-01-01

    Backgrounds The process of amyloid proteins aggregation causes several human neuropathologies. In some cases, e.g. fibrillar deposits of insulin, the problems are generated in the processes of production and purification of protein and in the pump devices or injectable preparations for diabetics. Experimental kinetics and adequate modelling of chemical inhibition from amyloid aggregation are of practical importance in order to study the viable processing, formulation and storage as well as to predict and optimize the best conditions to reduce the effect of protein nucleation. Results In this manuscript, experimental data of insulin, Aβ42 amyloid protein and apomyoglobin fibrillation from recent bibliography were selected to evaluate the capability of a bivariate sigmoid equation to model them. The mathematical functions (logistic combined with Weibull equation) were used in reparameterized form and the effect of inhibitor concentrations on kinetic parameters from logistic equation were perfectly defined and explained. The surfaces of data were accurately described by proposed model and the presented analysis characterized the inhibitory influence on the protein aggregation by several chemicals. Discrimination between true and apparent inhibitors was also confirmed by the bivariate equation. EGCG for insulin (working at pH = 7.4/T = 37°C) and taiwaniaflavone for Aβ42 were the compounds studied that shown the greatest inhibition capacity. Conclusions An accurate, simple and effective model to investigate the inhibition of chemicals on amyloid protein aggregation has been developed. The equation could be useful for the clear quantification of inhibitor potential of chemicals and rigorous comparison among them. PMID:24572069

  20. Modeling Tritium and Chloride 36 Transport Through an Aggregated Oxisol

    NASA Astrophysics Data System (ADS)

    Nkedi-Kizza, P.; Biggar, J. W.; van Genuchten, M. Th.; Wierenga, P. J.; Selim, H. M.; Davidson, J. M.; Nielsen, D. R.

    1983-06-01

    Breakthrough curves (BTC's) of 3H2O and 36Cl simultaneously displaced through columns of various-sized aggregates of an Ione Oxisol soil were measured under water-saturated steady flow conditions. The data were simulated using two conceptual models. In model I, all soil water was assumed to be mobile with a physical equilibrium existing in the system. For model II, soil water was partitioned into mobile and immobile regions. Convective diffusive solute transport was limited to the mobile water region. Transfer of a tracer between the two soil water regions was assumed to occur at a rate proportional to the difference in tracer concentration between the two regions. Sorption Of 3H2O and 36Cl was considered to be an instantaneous linear and reversible process. The two unknown parameters in model I and the four unknown parameters in model II were estimated by fitting model predictions to the experimental data. Model I could only describe BTC's obtained from columns packed with small aggregates (0.5-1 mm) and for displacements run at small fluxes (0.2 cm/h), whereas model II described all the BTC's well. Peclet numbers P in model II, as measured on each separate column, were essentially constant, indicating a linear relationship between the apparent diffusion coefficient D and the mobile pore water velocity vm. The fraction of soil water that is mobile, Φ, and the mass transfer coefficient α were found to be a function of the physical and chemical properties of the porous medium (aggregate size, pore water velocity, and solution concentration).

  1. Aggregation of model asphaltenes: a molecular dynamics study

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

    Natural asphaltenes are defined as polyaromatic compounds whose chemical composition and structure are dependent on their geological origin and production history, hence are regarded as complex molecules with aromatic cores and aliphatic tails that occur in the heaviest fraction of crude oil. The aggregation of asphaltenes presents a range of technical challenges to the production and processing of oil. In this work we study the behaviour of the model asphaltene-like molecule hexa-tert-butylhexa-peri-hexabenzocoronene (HTBHBC) using molecular dynamics simulation. It was found that the regular arrangement of the tert-butyl side chains prevents the formation of strongly-bound dimers by severely restricting the configurational space of the aggregation pathway. In contrast, a modified molecule with only 3 side chains is readily able to form dimers. This work therefore confirms the influence of the molecular structure of polyaromatic compounds on their aggregation mechanism, and reveals the unexpected design rules required for model systems that can mimic the behavior of asphaltenes.

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

    PubMed

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

    2016-10-05

    Natural asphaltenes are defined as polyaromatic compounds whose chemical composition and structure are dependent on their geological origin and production history, hence are regarded as complex molecules with aromatic cores and aliphatic tails that occur in the heaviest fraction of crude oil. The aggregation of asphaltenes presents a range of technical challenges to the production and processing of oil. In this work we study the behaviour of the model asphaltene-like molecule hexa-tert-butylhexa-peri-hexabenzocoronene (HTBHBC) using molecular dynamics simulation. It was found that the regular arrangement of the tert-butyl side chains prevents the formation of strongly-bound dimers by severely restricting the configurational space of the aggregation pathway. In contrast, a modified molecule with only 3 side chains is readily able to form dimers. This work therefore confirms the influence of the molecular structure of polyaromatic compounds on their aggregation mechanism, and reveals the unexpected design rules required for model systems that can mimic the behavior of asphaltenes.

  3. A model for wet aggregation of ash particles in volcanic plumes and clouds: 2. Model application

    NASA Astrophysics Data System (ADS)

    Folch, A.; Costa, A.; Durant, A.; Macedonio, G.

    2010-09-01

    The occurrence of particle aggregation has a dramatic effect on the transport and sedimentation of volcanic ash. The aggregation process is complex and can occur under different conditions and in multiple regions of the plume and in the ash cloud. In the companion paper, Costa et al. develop an aggregation model based on a fractal relationship to describe the rate particles are incorporated into ash aggregates. The model includes the effects of both magmatic and atmospheric water present in the volcanic cloud and demonstrates that the rate of aggregation depends on the characteristics of the initial particle size distribution. The aggregation model includes two parameters, the fractal exponent Df, which describes the efficiency of the aggregation process, and the aggregate settling velocity correction factor ψe, which influences the distance at which distal mass deposition maxima form. Both parameters are adjusted using features of the observed deposits. Here this aggregation model is implemented in the FALL3D volcanic ash transport model and applied to the 18 May 1980 Mount St. Helens and the 17-18 September 1992 Crater Peak eruptions. For both eruptions, the optimized values for Df (2.96-3.00) and ψe (0.27-0.33) indicate that the ash aggregates had a bulk density of 700-800 kg m-3. The model provides a higher degree of agreement than previous fully empirical aggregation models and successfully reproduces the depositional characteristics of the deposits investigated over a large range of scales, including the position and thickness of the secondary maxima.

  4. Characterization of the Canine MHC Class I DLA-88*50101 Peptide Binding Motif as a Prerequisite for Canine T Cell Immunotherapy

    PubMed Central

    Barth, Sharon M.; Schreitmüller, Christian M.; Proehl, Franziska; Oehl, Kathrin; Lumpp, Leonie M.; Kowalewski, Daniel J.; Di Marco, Moreno; Sturm, Theo; Backert, Linus; Schuster, Heiko; Stevanović, Stefan; Rammensee, Hans-Georg; Planz, Oliver

    2016-01-01

    There are limitations in pre-clinical settings using mice as a basis for clinical development in humans. In cancer, similarities exist between humans and dogs; thus, the dog patient can be a link in the transition from laboratory research on mouse models to clinical trials in humans. Knowledge of the peptides presented on MHC molecules is fundamental for the development of highly specific T cell-based immunotherapies. This information is available for human MHC molecules but is absent for the canine MHC. In the present study, we characterized the binding motif of dog leukocyte antigen (DLA) class I allele DLA-88*50101, using human C1R and K562 transfected cells expressing the DLA-88*50101 heavy chain. MHC class I immunoaffinity-purification revealed 3720 DLA-88*50101 derived peptides, which enabled the determination of major anchor positions. The characterized binding motif of DLA-88*50101 was similar to HLA-A*02:01. Peptide binding analyses on HLA-A*02:01 and DLA-88*50101 via flow cytometry showed weak binding of DLA-88*50101 derived peptides to HLA-A*02:01, and vice versa. Our results present for the first time a detailed peptide binding motif of the canine MHC class I allelic product DLA-88*50101. These data support the goal of establishing dogs as a suitable animal model for the evaluation and development of T cell-based cancer immunotherapies, benefiting both dog and human patients. PMID:27893789

  5. Aggregation-fragmentation model of robust concentration gradient formation

    NASA Astrophysics Data System (ADS)

    Saunders, Timothy E.

    2015-02-01

    Concentration gradients of signaling molecules are essential for patterning during development and they have been observed in both unicellular and multicellular systems. In subcellular systems, clustering of the signaling molecule has been observed. We develop a theoretical model of cluster-mediated concentration gradient formation based on the Becker-Döring equations of aggregation-fragmentation processes. We show that such a mechanism produces robust concentration gradients on realistic time and spatial scales so long as the process of clustering does not significantly stabilize the signaling molecule. Finally, we demonstrate that such a model is applicable to the pom1p subcellular gradient in fission yeast.

  6. Aggregation of colloidal particles modeled as a dynamical process.

    PubMed Central

    Bentz, J; Nir, S

    1981-01-01

    Aggregation kinetics of sonicated phosphatidylserine (PtdSer) vesicles in NaCl indicate that the process is fully reversible and dynamical, involving the rapid formation and dispersal of aggregates. Accordingly, the general mass action kinetic equations are analyzed with respect to the equilibrium state and the formation of higher order aggregates. For a general class of systems, the values for the mass average aggregate size at equilibrium are obtained from simple closed-form expressions. It is shown that an analysis of the aggregation equilibrium will yield estimates for the potential energy well that holds the aggregates together. A fit to the experimental data for kinetics of Na+-induced aggregation of the vesicles has been achieved by employing mass action kinetic equations that include the dissociation reactions. The threshold of NaCl concentration required for aggregation involves the clear distinction between the rate and extent of aggregation. PMID:6940176

  7. Convex aggregative modelling of infinite memory nonlinear systems

    NASA Astrophysics Data System (ADS)

    Wachel, Paweł

    2016-08-01

    The convex aggregation technique is applied for modelling general class of nonlinear systems with unknown structure and infinite memory. The finite sample size properties of the algorithm are formally established and compared to the standard least-squares counterpart of the method. The proposed algorithm demonstrates its advantages when the a-priori knowledge and the measurement data are both scarce, that is, when the information about the actual system structure is unknown or uncertain and the measurement set is small and disturbed by a noise. Numerical experiments illustrate application and practical benefits of the method for various nonlinear systems.

  8. Aggregated Residential Load Modeling Using Dynamic Bayesian Networks

    SciTech Connect

    Vlachopoulou, Maria; Chin, George; Fuller, Jason C.; Lu, Shuai

    2014-09-28

    Abstract—It is already obvious that the future power grid will have to address higher demand for power and energy, and to incorporate renewable resources of different energy generation patterns. Demand response (DR) schemes could successfully be used to manage and balance power supply and demand under operating conditions of the future power grid. To achieve that, more advanced tools for DR management of operations and planning are necessary that can estimate the available capacity from DR resources. In this research, a Dynamic Bayesian Network (DBN) is derived, trained, and tested that can model aggregated load of Heating, Ventilation, and Air Conditioning (HVAC) systems. DBNs can provide flexible and powerful tools for both operations and planing, due to their unique analytical capabilities. The DBN model accuracy and flexibility of use is demonstrated by testing the model under different operational scenarios.

  9. 32 CFR Appendix H to Part 323 - DLA Exemption Rules

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... exemptions of this system of records from the requirements of the other cited provisions. c. ID: S100.50 DLA..., continue to publish such a notice in broad generic terms as is its current practice. d. ID: S100.10...

  10. Typology of Empirical Attributes: Dissimilarity Linkage Analysis (DLA).

    ERIC Educational Resources Information Center

    Dubin, Robert; Champoux, Joseph E.

    Dissimilarity Linkage Analysis (DLA) is an extremely simple procedure for developing a typology from empirical attributes that permits the clustering of entities. First the procedure develops a taxonomy of types from empirical attributes possessed by entities in the sample. Second, the procedure assigns entities to one, and only one, type in the…

  11. Increased genetic risk or protection for canine autoimmune lymphocytic thyroiditis in Giant Schnauzers depends on DLA class II genotype.

    PubMed

    Wilbe, M; Sundberg, K; Hansen, I R; Strandberg, E; Nachreiner, R F; Hedhammar, A; Kennedy, L J; Andersson, G; Björnerfeldt, S

    2010-06-01

    Dogs represent an excellent comparative model for autoimmune thyroiditis as several dog breeds develop canine lymphocytic thyroiditis (CLT), which is clinically similar to Hashimoto's thyroiditis in human. We obtained evidence that dog leukocyte antigen (DLA) class II genotype function as either genetic risk factor that predisposes for CLT or as protective factor against the disease. Genetic diversity at their DLA-DRB1, -DQA1, and -DQB1 loci were defined and potential association to major histocompatibility complex II haplotypes and alleles was analyzed. Giant Schnauzers carrying the DLA-DRB1*01201/DQA1*00101/DQB1*00201 haplotype showed an increased risk (odds ratio of 6.5) for developing CLT. The same risk haplotype has, to date, been observed in three different breeds affected by this disease, Giant Schnauzer, Dobermann, and Labrador Retriever, indicating that it is a common genetic risk factor in a variety of breeds affected by this disease. Importantly, protection for development of the disease was found in dogs carrying the DLA-DRB1*01301/DQA1*00301/DQB1*00501 haplotype (odds ratio of 0.3).

  12. Canine DLA-79 gene: an improved typing method, identification of new alleles and its role in graft rejection and graft-versus-host disease.

    PubMed

    Venkataraman, G M; Geraghty, D; Fox, J; Graves, S S; Zellmer, E; Storer, B E; Torok-Storb, B J; Storb, R

    2013-04-01

    Developing a preclinical canine model that predicts outcomes for hematopoietic cell transplantation in humans requires a model that mimics the degree of matching between human donor and recipient major histocompatibility complex (MHC) genes. The polymorphic class I and class II genes in mammals are typically located in a single chromosome as part of the MHC complex. However, a divergent class I gene in dogs, designated dog leukocyte antigen-79 (DLA-79), is located on chromosome 18 while other MHC genes are on chromosome 12. This gene is not taken into account while DLA matching for transplantation. Though divergent, this gene shares significant similarity in sequence and exon-intron architecture with other class I genes, and is transcribed. Little is known about the polymorphisms of DLA-79 and their potential role in transplantation. This study was aimed at exploring the reason for high rate of rejection seen in DLA-matched dogs given reduced intensity conditioning, in particular, the possibility that DLA-79 allele mismatches may be the cause. We found that about 82% of 407 dogs typed were homozygous for a single, reference allele. Owing to the high prevalence of a single allele, 87 of the 108 dogs (∼80%) transplanted were matched for DLA-79 with their donor. In conclusion, we have developed an efficient method to type alleles of a divergent MHC gene in dogs and identified two new alleles. We did not find any statistical correlation between DLA-79 allele disparity and graft rejection or graft-versus-host disease, among our transplant dogs.

  13. A model for the kinetics of homotypic cellular aggregation under static conditions

    NASA Technical Reports Server (NTRS)

    Neelamegham, S.; Munn, L. L.; Zygourakis, K.; McIntire, L. V. (Principal Investigator)

    1997-01-01

    We present the formulation and testing of a mathematical model for the kinetics of homotypic cellular aggregation. The model considers cellular aggregation under no-flow conditions as a two-step process. Individual cells and cell aggregates 1) move on the tissue culture surface and 2) collide with other cells (or aggregates). These collisions lead to the formation of intercellular bonds. The aggregation kinetics are described by a system of coupled, nonlinear ordinary differential equations, and the collision frequency kernel is derived by extending Smoluchowski's colloidal flocculation theory to cell migration and aggregation on a two-dimensional surface. Our results indicate that aggregation rates strongly depend upon the motility of cells and cell aggregates, the frequency of cell-cell collisions, and the strength of intercellular bonds. Model predictions agree well with data from homotypic lymphocyte aggregation experiments using Jurkat cells activated by 33B6, an antibody to the beta 1 integrin. Since cell migration speeds and all the other model parameters can be independently measured, the aggregation model provides a quantitative methodology by which we can accurately evaluate the adhesivity and aggregation behavior of cells.

  14. Aggregation of Environmental Model Data for Decision Support

    NASA Astrophysics Data System (ADS)

    Alpert, J. C.

    2013-12-01

    Weather forecasts and warnings must be prepared and then delivered so as to reach their intended audience in good time to enable effective decision-making. An effort to mitigate these difficulties was studied at a Workshop, 'Sustaining National Meteorological Services - Strengthening WMO Regional and Global Centers' convened, June , 2013, by the World Bank, WMO and the US National Weather Service (NWS). The skill and accuracy of atmospheric forecasts from deterministic models have increased and there are now ensembles of such models that improve decisions to protect life, property and commerce. The NWS production of numerical weather prediction products result in model output from global and high resolution regional ensemble forecasts. Ensembles are constructed by changing the initial conditions to make a 'cloud' of forecasts that attempt to span the space of possible atmospheric realizations which can quantify not only the most likely forecast, but also the uncertainty. This has led to an unprecedented increase in data production and information content from higher resolution, multi-model output and secondary calculations. One difficulty is to obtain the needed subset of data required to estimate the probability of events, and report the information. The calibration required to reliably estimate the probability of events, and honing of threshold adjustments to reduce false alarms for decision makers is also needed. To meet the future needs of the ever-broadening user community and address these issues on a national and international basis, the weather service implemented the NOAA Operational Model Archive and Distribution System (NOMADS). NOMADS provides real-time and retrospective format independent access to climate, ocean and weather model data and delivers high availability content services as part of NOAA's official real time data dissemination at its new NCWCP web operations center. An important aspect of the server's abilities is to aggregate the matrix of

  15. Polarimetric Models of Circumstellar Discs Including Aggregate Dust Grains

    NASA Astrophysics Data System (ADS)

    Mohan, Mahesh

    The work conducted in this thesis examines the nature of circumstellar discs by investigating irradiance and polarization of scattered light. Two circumstellar discs are investigated. Firstly, H-band high contrast imaging data on the transitional disc of the Herbig Ae/Be star HD169142 are presented. The images were obtained through the polarimetric differential imaging (PDI) technique on the Very Large Telescope (VLT) using the adaptive optics system NACO. Our observations use longer exposure times, allowing us to examine the edges of the disc. Analysis of the observations shows distinct signs of polarization due to circumstellar material, but due to excessive saturation and adaptive optics errors further information on the disc could not be inferred. The HD169142 disc is then modelled using the 3D radiative transfer code Hyperion. Initial models were constructed using a two disc structure, however recent PDI has shown the existence of an annular gap. In addition to this the annular gap is found not to be devoid of dust. This then led to the construction of a four-component disc structure. Estimates of the mass of dust in the gap (2.10E-6 Msun) are made as well as for the planet (1.53E-5 Msun (0.016 Mjupiter)) suspected to be responsible for causing the gap. The predicted polarization was also estimated for the disc, peaking at ~14 percent. The use of realistic dust grains (ballistic aggregate particles) in Monte Carlo code is also examined. The fortran code DDSCAT is used to calculate the scattering properties for aggregates which are used to replace the spherical grain models used by the radiative transfer code Hyperion. Currently, Hyperion uses four independent elements to define the scattering matrix, therefore the use of rotational averaging and a 50/50 percent population of grains and their enantiomers were explored to reduce the number of contributing scattering elements from DDSCAT. A python script was created to extract the scattering data from the DDSCAT

  16. Analysis of sludge aggregates produced during electrocoagulation of model wastewater.

    PubMed

    Załęska-Chróst, B; Wardzyńska, R

    2016-01-01

    This paper presents the results of the study of sludge aggregates produced during electrocoagulation of model wastewater of a composition corresponding to the effluents from the cellulose and paper industry. Wastewater was electrocoagulated statically using aluminium electrodes with a current density of 31.25 A m(-2) and 62.50 A m(-2). In subsequent stages of the treatment, sludge flocs were collected, their size was studied and their floc settling velocity (30-520 μm s(-1)) and fractal dimension (D) were determined. The values of D ranged from 1.53 to 1.95 and were directly proportional to the degree of wastewater treatment. Higher values of D were determined for sludge with lower water content (after 24 hours' settling). Fractal dimension can therefore be used as an additional parameter of wastewater treatment control.

  17. A Pairwise Preferential Interaction Model for Understanding Peptide Aggregation

    PubMed Central

    Kang, Myungshim

    2010-01-01

    A pairwise preferential interaction model (PPIM), based on Kirkwood–Buff integrals, is developed to quantify and characterize the interactions between some of the functional groups commonly observed in peptides. The existing experimental data are analyzed to determine the preferential interaction (PI) parameters for different amino acid and small peptide systems in aqueous solutions. The PIs between the different functional groups present in the peptides are then isolated and quantified by assuming simple pairwise additivity. The PPIM approach provides consistent estimates for the pair interactions between the same functional groups obtained from different solute molecules. Furthermore, these interactions appear to be chemically intuitive. It is argued that this type of approach can provide valuable information concerning specific functional group correlations which could give rise to peptide aggregation. PMID:20694045

  18. Multiple discrete soluble aggregates influence polyglutamine toxicity in a Huntington’s disease model system

    PubMed Central

    Xi, Wen; Wang, Xin; Laue, Thomas M.; Denis, Clyde L.

    2016-01-01

    Huntington’s disease (HD) results from expansions of polyglutamine stretches (polyQ) in the huntingtin protein (Htt) that promote protein aggregation, neurodegeneration, and death. Since the diversity and sizes of the soluble Htt-polyQ aggregates that have been linked to cytotoxicity are unknown, we investigated soluble Htt-polyQ aggregates using analytical ultracentrifugation. Soon after induction in a yeast HD model system, non-toxic Htt-25Q and cytotoxic Htt-103Q both formed soluble aggregates 29S to 200S in size. Because current models indicate that Htt-25Q does not form soluble aggregates, reevaluation of previous studies may be necessary. Only Htt-103Q aggregation behavior changed, however, with time. At 6 hr mid-sized aggregates (33S to 84S) and large aggregates (greater than 100S) became present while at 24 hr primarily only mid-sized aggregates (20S to 80S) existed. Multiple factors that decreased cytotoxicity of Htt-103Q (changing the length of or sequences adjacent to the polyQ, altering ploidy or chaperone dosage, or deleting anti-aging factors) altered the Htt-103Q aggregation pattern in which the suite of mid-sized aggregates at 6 hr were most correlative with cytotoxicity. Hence, the amelioration of HD and other neurodegenerative diseases may require increased attention to and discrimination of the dynamic alterations in soluble aggregation processes. PMID:27721444

  19. Multiscale modeling of the thixotropic behavior of aggregating soft colloidal particle suspensions

    NASA Astrophysics Data System (ADS)

    Mwasame, Paul; Wagner, Norman; Beris, Antony

    A multiscale model is presented that incorporates microscopic information at the soft, aggregating, colloidal particle level to a macroscopic description of a thixotropic suspension with a yield stress. This is accomplished by incorporating the relevant physics describing aggregation and breakage at the particle level into a population balance microscopic framework. A moment approach is followed to allow for model coarsening and its incorporation into a macroscopic description. Furthermore, to describe the aggregate dynamics under flow, it is necessary to include an additional description of the aggregate deformation. The yielding behavior of gel networks observed in thixotropic suspensions is modeled by adapting micromechanical models of emulsions and pastes to describe aggregate deformation under flow. A key outcome of this work is the recognition of the important role of competition between orthokinetic and perikinetic aggregation on polydispersity and dynamical behavior. Comparison to rheological experiments on a model thixotropic suspension will also be presented to validate the model developed. NSF CBET 312146.

  20. A deterministic aggregate production planning model considering quality of products

    NASA Astrophysics Data System (ADS)

    Madadi, Najmeh; Yew Wong, Kuan

    2013-06-01

    Aggregate Production Planning (APP) is a medium-term planning which is concerned with the lowest-cost method of production planning to meet customers' requirements and to satisfy fluctuating demand over a planning time horizon. APP problem has been studied widely since it was introduced and formulated in 1950s. However, in several conducted studies in the APP area, most of the researchers have concentrated on some common objectives such as minimization of cost, fluctuation in the number of workers, and inventory level. Specifically, maintaining quality at the desirable level as an objective while minimizing cost has not been considered in previous studies. In this study, an attempt has been made to develop a multi-objective mixed integer linear programming model that serves those companies aiming to incur the minimum level of operational cost while maintaining quality at an acceptable level. In order to obtain the solution to the multi-objective model, the Fuzzy Goal Programming approach and max-min operator of Bellman-Zadeh were applied to the model. At the final step, IBM ILOG CPLEX Optimization Studio software was used to obtain the experimental results based on the data collected from an automotive parts manufacturing company. The results show that incorporating quality in the model imposes some costs, however a trade-off should be done between the cost resulting from producing products with higher quality and the cost that the firm may incur due to customer dissatisfaction and sale losses.

  1. Dis-aggregation of an insoluble porphyrin in a calixarene matrix: characterization of aggregate modes by extended dipole model.

    PubMed

    de Miguel, Gustavo; Martín-Romero, María T; Pedrosa, José M; Muñoz, Eulogia; Pérez-Morales, Marta; Richardson, Tim H; Camacho, Luis

    2008-03-21

    In this paper, the different aggregation modes of a water-insoluble porphyrin (EHO) mixed with an amphiphilic calix[8]arene (C8A), at the air-water interface and in Langmuir-Blodgett (LB) film form, are analyzed as a function of the mixed composition. The strategy used to control the EHO aggregation has consisted of preparing mixed thin films containing EHO and C8A, in different ratios, at the air-water interface. Therefore, the increase of the C8A molar ratio in the mixed film diminishes the aggregation of the EHO molecules, although such an effect must be exclusively related to the dilution of the porphyrin. The reflection spectra of the mixed C8A-EHO films registered at the air-water interface, show a complex Soret band exhibiting splitting, hypochromicity and broadening features. Also, during the transfer process at high surface pressure, it has been shown that the EHO molecules are ejected from the C8A monolayer and only a fraction of porphyrin is transferred to the solid support, in spite of a complete transfer for the C8A matrix. The complex structure of the reflection spectra at the air-water interface, as well as the polarization dependence of the absorption spectra for the mixed LB films, indicate the existence of four different arrangements for the EHO hosted in the C8A matrix. The aggregate formation is governed by two factors: the attraction between the porphyrin rings which minimizes their separation, and the alkyl chain interactions, that is, hydrophobic effect and/or steric hindrance which determine and restrict the possible aggregation structures. By using the extended dipole model, the assignment of the spectral peaks observed to different EHO aggregates is shown.

  2. Cellular Models of Aggregation-dependent Template-directed Proteolysis to Characterize Tau Aggregation Inhibitors for Treatment of Alzheimer Disease.

    PubMed

    Harrington, Charles R; Storey, John M D; Clunas, Scott; Harrington, Kathleen A; Horsley, David; Ishaq, Ahtsham; Kemp, Steven J; Larch, Christopher P; Marshall, Colin; Nicoll, Sarah L; Rickard, Janet E; Simpson, Michael; Sinclair, James P; Storey, Lynda J; Wischik, Claude M

    2015-04-24

    Alzheimer disease (AD) is a degenerative tauopathy characterized by aggregation of Tau protein through the repeat domain to form intraneuronal paired helical filaments (PHFs). We report two cell models in which we control the inherent toxicity of the core Tau fragment. These models demonstrate the properties of prion-like recruitment of full-length Tau into an aggregation pathway in which template-directed, endogenous truncation propagates aggregation through the core Tau binding domain. We use these in combination with dissolution of native PHFs to quantify the activity of Tau aggregation inhibitors (TAIs). We report the synthesis of novel stable crystalline leucomethylthioninium salts (LMTX®), which overcome the pharmacokinetic limitations of methylthioninium chloride. LMTX®, as either a dihydromesylate or a dihydrobromide salt, retains TAI activity in vitro and disrupts PHFs isolated from AD brain tissues at 0.16 μM. The Ki value for intracellular TAI activity, which we have been able to determine for the first time, is 0.12 μM. These values are close to the steady state trough brain concentration of methylthioninium ion (0.18 μM) that is required to arrest progression of AD on clinical and imaging end points and the minimum brain concentration (0.13 μM) required to reverse behavioral deficits and pathology in Tau transgenic mice.

  3. Aggregate crash prediction models: introducing crash generation concept.

    PubMed

    Naderan, Ali; Shahi, Jalil

    2010-01-01

    Safety conscious planning is a new proactive approach towards understanding crashes. It requires a planning-level decision-support tool to facilitate proactive approach to assessing safety effects of alternative urban planning scenarios. The objective of this research study is to develop a series of aggregate crash prediction models (ACPM) that are consistent with the trip generation step of the conventional four-step demand models. The concept of crash generation models (CGMs) is introduced utilizing trip generation data in a generalized linear regression with the assumption of a negative binomial error structure. The relationship of crash frequencies in traffic analysis zones (TAZ) and number of trips generated by purpose is investigated. This translates into immediate checking of the impact of future trip generations on crash frequencies in comprehensive transportation-planning studies (i.e. ability to forecast crashes at each time-step trips are being forecasted). A good relation was seen between crash frequency and number of trips produced/attracted by purpose per TAZ.

  4. Electromechanical properties of smart aggregate: theoretical modeling and experimental validation

    NASA Astrophysics Data System (ADS)

    Wang, Jianjun; Kong, Qingzhao; Shi, Zhifei; Song, Gangbing

    2016-09-01

    Smart aggregate (SA), as a piezoceramic-based multi-functional device, is formed by sandwiching two lead zirconate titanate (PZT) patches with copper shielding between a pair of solid-machined cylindrical marble blocks with epoxy. Previous researches have successfully demonstrated the capability and reliability of versatile SAs to monitor the structural health of concrete structures. However, the previous works concentrated mainly on the applications of SAs in structural health monitoring; no reasonable theoretical model of SAs was proposed. In this paper, electromechanical properties of SAs were investigated using a proposed theoretical model. Based on one dimensional linear theory of piezo-elasticity, the dynamic solutions of a SA subjected to an external harmonic voltage were solved. Further, the electric impedance of the SA was computed, and the resonance and anti-resonance frequencies were calculated based on derived equations. Numerical analysis was conducted to discuss the effects of the thickness of epoxy layer and the dimension of PZT patch on the fundamental resonance and anti-resonance frequencies as well as the corresponding electromechanical coupling factor. The dynamic solutions based on the proposed theoretical model were further experimentally verified with two SA samples. The fundamental resonance and anti-resonance frequencies of SAs show good agreements in both theoretical and experimental results. The presented analysis and results contribute to the overall understanding of SA properties and help to optimize the working frequencies of SAs in structural health monitoring of civil structures.

  5. Population balance modeling of the conidial aggregation of Aspergillus niger.

    PubMed

    Lin, P-J; Grimm, L H; Wulkow, M; Hempel, D C; Krull, R

    2008-02-01

    Numerous biotechnological production processes are based on the submerse cultivation of filamentous fungi. Process design, however, is often hampered by the complex growth pattern of these organisms. In the morphologic development of coagulating filamentous fungi, like Aspergillus niger, conidial aggregation is the first step of filamentous morphogenesis. For a proper description of this phenomenon it is necessary to characterize conidial populations. Kinetic studies performed with an in-line particle size analyzer suggested that two distinct aggregation steps have to be considered. The first step of conidial aggregation starts immediately after inoculation. Both the rate constants of formation and disintegration of aggregates have been determined by measuring the concentration of conidia at the beginning of the cultivation and the concentration of particles at steady state during the first hours of cultivation. In contrast to the first aggregation step, where the collision of conidia is presumed to be responsible for the process, the second aggregation step is thought to be initiated by germination of conidia. Growing hyphae provide additional surface for the attachment of non- germinated conidia, which leads to a strong decrease in particle concentration. The specific hyphal length growth rate and the ratio of particle concentration to the growing adhesion hyphal surface are decisive matters of the second aggregation step. Both aggregation steps can be described by population dynamics and simulated using the program package PARSIVAL (PARticle SIze eVALution) for the treatment of general particle population balances.

  6. Financial Reporting of DLA-Owned Bulk Petroleum Products

    DTIC Science & Technology

    2007-11-02

    Defense Fuel Sites. The 511 fuel sites managed 864 line items that were reflected in the DLA Financial Inventory Account ( FIA ) subsidiary ledger...Financial Management Functional Area. Objective: Reengineer DoD business practices. Goal: Standardize, reduce, clarify, and reissue financial and...the Chief Financial Officers Act of 1990, as amended by the Federal Financial Management Act of 1994. This is the fifth in a series of reports on the

  7. Convectively Aggregated Structures Across a Hierarchy of Models

    NASA Astrophysics Data System (ADS)

    Silvers, Levi; Dipankar, Anurag; Hohenegger, Cathy

    2015-04-01

    Convective clouds are among the most interesting and poorest understood atmospheric phenomena. This study explores the interaction between deep convection and the lower troposphere with a focus on the coupling of deep convection to the lower tropospheric clouds, water vapor, and relative humidity. We are particularly interested in the controlling factors of the cloud amount and cloud size at cloud base across various model set-ups. In particular we seek to determine how the generation of large convective structures depends on the characteristics of the lower troposphere and parameterization choices. Our experiments are analyzed by comparing the mean state, the probability distribution functions of particular quantities, and snapshots in time of the spatial distribution of cloud related fields. It is shown that the formation of aggregated convective structures depends on the different model setups. Experiments performed using an NWP model (ICON-NWP) and two cloud-resolving models (ICON-LES and UCLA-LES) are compared. The ICOsahedral Nonhydrostatic (ICON) model is used to provide a unified modeling framework in which both the NWP and CRM versions use the same dynamical core but different physics packages. This allows for a fair comparison between the GCM and CRM and leads to a better understanding of both. To check the robustness of the CRM results we also compare the ICON experiments with the UCLA-LES model. The initial analysis looks at the ICON-NWP and both CRM experiments with a uniform domain size of (1800 km)2 and doubly periodic boundary conditions to determine some of the fundamental differences between the models. The NWP experiment has an effective resolution of 13.5 km while the CRM's have resolutions in the range of 5 km. We run the NWP experiments with the full suit of physics parameterizations as well as with the convection turned off. Further sensitivity studies are then made to isolate some of the key characteristics of the convection in each model

  8. Bacterial colonization and extinction on marine aggregates: stochastic model of species presence and abundance

    PubMed Central

    Kramer, Andrew M; Lyons, M Maille; Dobbs, Fred C; Drake, John M

    2013-01-01

    Organic aggregates provide a favorable habitat for aquatic microbes, are efficiently filtered by shellfish, and may play a major role in the dynamics of aquatic pathogens. Quantifying this role requires understanding how pathogen abundance in the water and aggregate size interact to determine the presence and abundance of pathogen cells on individual aggregates. We build upon current understanding of the dynamics of bacteria and bacterial grazers on aggregates to develop a model for the dynamics of a bacterial pathogen species. The model accounts for the importance of stochasticity and the balance between colonization and extinction. Simulation results suggest that while colonization increases linearly with background density and aggregate size, extinction rates are expected to be nonlinear on small aggregates in a low background density of the pathogen. Under these conditions, we predict lower probabilities of pathogen presence and reduced abundance on aggregates compared with predictions based solely on colonization. These results suggest that the importance of aggregates to the dynamics of aquatic bacterial pathogens may be dependent on the interaction between aggregate size and background pathogen density, and that these interactions are strongly influenced by ecological interactions and pathogen traits. The model provides testable predictions and can be a useful tool for exploring how species-specific differences in pathogen traits may alter the effect of aggregates on disease transmission. PMID:24340173

  9. Condensation versus diffusion. A spatial-scale-independent theory of aggregate structures in edible oils: applications to model systems and commercial shortenings studied via rheology and USAXS

    NASA Astrophysics Data System (ADS)

    Pink, David A.; Peyronel, Fernanda; Quinn, Bonnie; Singh, Pratham; Marangoni, Alejandro G.

    2015-09-01

    Understanding how solid fats structures come about in edible oils and quantifying their structures is of fundamental importance in developing edible oils with pre-selected characteristics. We considered the great range of fractal dimensions, from 1.91 to 2.90, reported from rheological measurements. We point out that, if the structures arise via DLA/RLA or DLCA/RLCA, as has been established using ultra small angle x-ray scattering (USAXS), we would expect fractal dimensions in the range ~1.7 to 2.1, and ~2.5 or ~3.0. We present new data for commercial fats and show that the fractal dimensions deduced lie outside these values. We have developed a model in which competition between two processes can lead to the range of fractal dimensions observed. The two processes are (i) the rate at which the solid fat particles are created as the temperature is decreased, and (ii) the rate at which these particles diffuse, thereby meeting and forming aggregates. We assumed that aggregation can take place essentially isotropically and we identified two characteristic times: a time characterizing the rate of creation of solid fats, {τ\\text{create}}(T)\\equiv 1/{{R}S}(T) , where {{R}S}(T) is the rate of solid condensation (cm3 s-1), and the diffusion time of solid fats, {τ\\text{diff}}≤ft(T,{{c}S}\\right)=< {{r}2}> /6{D}≤ft(T,{{c}S}\\right) , where {D}≤ft(T,{{c}S}\\right) is their diffusion coefficient and < {{r}2}> is the typical average distance that fats must move in order to aggregate. The intent of this model is to show that a simple process can lead to a wide range of fractal dimensions. We showed that in the limit of very fast solid creation, {τ\\text{create}}\\ll {τ\\text{diff}} the fractal dimension is predicted to be that of DLCA, ~1.7, relaxing to that of RLCA, 2.0-2.1, and that in the limit of very slow solid creation, {τ\\text{create}}\\gg {τ\\text{diff}} , the fractal dimension is predicted to be that obtained via DLA, ~2.5, relaxing to that of RLA, 3

  10. Aggregation work at polydisperse micellization: Ideal solution and ``dressed micelle'' models comparing to molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Burov, S. V.; Shchekin, A. K.

    2010-12-01

    General thermodynamic relations for the work of polydisperse micelle formation in the model of ideal solution of molecular aggregates in nonionic surfactant solution and the model of "dressed micelles" in ionic solution have been considered. In particular, the dependence of the aggregation work on the total concentration of nonionic surfactant has been analyzed. The analogous dependence for the work of formation of ionic aggregates has been examined with regard to existence of two variables of a state of an ionic aggregate, the aggregation numbers of surface active ions and counterions. To verify the thermodynamic models, the molecular dynamics simulations of micellization in nonionic and ionic surfactant solutions at two total surfactant concentrations have been performed. It was shown that for nonionic surfactants, even at relatively high total surfactant concentrations, the shape and behavior of the work of polydisperse micelle formation found within the model of the ideal solution at different total surfactant concentrations agrees fairly well with the numerical experiment. For ionic surfactant solutions, the numerical results indicate a strong screening of ionic aggregates by the bound counterions. This fact as well as independence of the coefficient in the law of mass action for ionic aggregates on total surfactant concentration and predictable behavior of the "waterfall" lines of surfaces of the aggregation work upholds the model of "dressed" ionic aggregates.

  11. Modeling the competition between aggregation and self-assembly during virus-like particle processing.

    PubMed

    Ding, Yong; Chuan, Yap Pang; He, Lizhong; Middelberg, Anton P J

    2010-10-15

    Understanding and controlling aggregation is an essential aspect in the development of pharmaceutical proteins to improve product yield, potency and quality consistency. Even a minute quantity of aggregates may be reactogenic and can render the final product unusable. Self-assembly processing of virus-like particles (VLPs) is an efficient method to quicken the delivery of safe and efficacious vaccines to the market at low cost. VLP production, as with the manufacture of many biotherapeutics, is susceptible to aggregation, which may be minimized through the use of accurate and practical mathematical models. However, existing models for virus assembly are idealized, and do not predict the non-native aggregation behavior of self-assembling viral subunits in a tractable nor useful way. Here we present a mechanistic mathematical model describing VLP self-assembly that accounts for partitioning of reactive subunits between the correct and aggregation pathways. Our results show that unproductive aggregation causes up to 38% product loss by competing favorably with the productive nucleation of self-assembling subunits, therefore limiting the availability of nuclei for subsequent capsid growth. The protein subunit aggregation reaction exhibits an apparent second-order concentration dependence, suggesting a dimerization-controlled agglomeration pathway. Despite the plethora of possible assembly intermediates and aggregation pathways, protein aggregation behavior may be predicted by a relatively simple yet realistic model. More importantly, we have shown that our bioengineering model is amenable to different reactor formats, thus opening the way to rational scale-up strategies for products that comprise biomolecular assemblies.

  12. Proteins in aggregates functionally impact multiple neurodegenerative disease models by forming proteasome-blocking complexes

    PubMed Central

    Ayyadevara, Srinivas; Balasubramaniam, Meenakshisundaram; Gao, Yuan; Yu, Li-Rong; Alla, Ramani; Shmookler Reis, Robert

    2015-01-01

    Age-dependent neurodegenerative diseases progressively form aggregates containing both shared components (e.g., TDP-43, phosphorylated tau) and proteins specific to each disease. We investigated whether diverse neuropathies might have additional aggregation-prone proteins in common, discoverable by proteomics. Caenorhabditis elegans expressing unc-54p/Q40::YFP, a model of polyglutamine array diseases such as Huntington's, accrues aggregates in muscle 2–6 days posthatch. These foci, isolated on antibody-coupled magnetic beads, were characterized by high-resolution mass spectrometry. Three Q40::YFP-associated proteins were inferred to promote aggregation and cytotoxicity, traits reduced or delayed by their RNA interference knockdown. These RNAi treatments also retarded aggregation/cytotoxicity in Alzheimer's disease models, nematodes with muscle or pan-neuronal Aβ1–42 expression and behavioral phenotypes. The most abundant aggregated proteins are glutamine/asparagine-rich, favoring hydrophobic interactions with other random-coil domains. A particularly potent modulator of aggregation, CRAM-1/HYPK, contributed < 1% of protein aggregate peptides, yet its knockdown reduced Q40::YFP aggregates 72–86% (P < 10−6). In worms expressing Aβ1–42, knockdown of cram-1 reduced β-amyloid 60% (P < 0.002) and slowed age-dependent paralysis > 30% (P < 10−6). In wild-type worms, cram-1 knockdown reduced aggregation and extended lifespan, but impaired early reproduction. Protection against seeded aggregates requires proteasome function, implying that normal CRAM-1 levels promote aggregation by interfering with proteasomal degradation of misfolded proteins. Molecular dynamic modeling predicts spontaneous and stable interactions of CRAM-1 (or human orthologs) with ubiquitin, and we verified that CRAM-1 reduces degradation of a tagged-ubiquitin reporter. We propose that CRAM-1 exemplifies a class of primitive chaperones that are initially protective and highly

  13. Model aggregation: a building-block approach to creating large macromolecular regulatory networks

    PubMed Central

    Randhawa, Ranjit; Shaffer, Clifford A.; Tyson, John J.

    2009-01-01

    Motivation: Models of regulatory networks become more difficult to construct and understand as they grow in size and complexity. Modelers naturally build large models from smaller components that each represent subsets of reactions within the larger network. To assist modelers in this process, we present model aggregation, which defines models in terms of components that are designed for the purpose of being combined. Results: We have implemented a model editor that incorporates model aggregation, and we suggest supporting extensions to the Systems Biology Markup Language (SBML) Level 3. We illustrate aggregation with a model of the eukaryotic cell cycle ‘engine’ created from smaller pieces. Availability: Java implementations are available in the JigCell Aggregation Connector. See http://jigcell.biol.vt.edu. Contact: shaffer@vt.edu PMID:19880372

  14. Mechanisms of m-cresol induced protein aggregation studied using a model protein cytochrome c†

    PubMed Central

    Singh, Surinder M.; Hutchings, Regina L.; Mallela, Krishna M.G.

    2014-01-01

    Multi-dose protein formulations require an effective antimicrobial preservative (AP) to inhibit microbial growth during long-term storage of unused formulations. m-cresol is one such AP, but has been shown to cause protein aggregation. However, the fundamental physical mechanisms underlying such AP-induced protein aggregation are not understood. In this study, we used a model protein cytochrome c to identify the protein unfolding that triggers protein aggregation. m-cresol induced cytochrome c aggregation at preservative concentrations that are commonly used to inhibit microbial growth. Addition of m-cresol decreased the temperature at which the protein aggregated and increased the aggregation rate. However, m-cresol did not perturb the tertiary or secondary structure of cytochrome c. Instead, it populated an “invisible” partially unfolded intermediate where a local protein region around the methionine residue at position 80 was unfolded. Stabilizing the Met80 region drastically decreased the protein aggregation, which conclusively shows that this local protein region acts as an aggregation “hot-spot”. Based on these results, we propose that APs induce protein aggregation by partial rather than global unfolding. Because of the availability of site-specific probes to monitor different levels of protein unfolding, cytochrome c provided a unique advantage in characterizing the partial protein unfolding that triggers protein aggregation. PMID:21229618

  15. Dispersion in DLA metallicities and deuterium abundances

    NASA Astrophysics Data System (ADS)

    Dvorkin, Irina; Silk, Joseph; Vangioni, Elisabeth; Petitjean, Patrick; Olive, Keith A.

    2017-03-01

    Recent chemical abundance measurements of damped Lyman-alpha absorbers (DLAs) revealed a large intrinsic scatter in their metallicities. We discuss a semi-analytic model that was specifically designed to study this scatter by tracing the chemical evolution of the interstellar matter in small regions of the Universe with different mean density, from over- to underdense regions. It is shown that different histories of structure formation in these regions are reflected in the chemical properties of the proto-galaxies. We also address deuterium abundance measurements, which constitute a complementary probe of the star formation and infall histories.

  16. VizieR Online Data Catalog: SDSS DLA and absorber quasar samples (Murphy+, 2016)

    NASA Astrophysics Data System (ADS)

    Murphy, M. T.; Bernet, M. L.

    2016-07-01

    Using spectral slope fits of the SDSS DR7 quasar spectra, and the DLA/sub-DLA identifications of Noterdaeme et al. (2009, Cat. J/A+A/505/1087), we found that the 774 selected quasars with a single foreground DLA are significantly (3.2σ) redder, on average, than carefully selected control groups drawn from a sample of ~7000 quasars without foreground DLAs. (4 data files).

  17. Embryonic Mutant Huntingtin Aggregate Formation in Mouse Models of Huntington’s Disease

    PubMed Central

    Osmand, Alexander P.; Bichell, Terry Jo.; Bowman, Aaron B.; Bates, Gillian P.

    2016-01-01

    The role of aggregate formation in the pathophysiology of Huntington’s disease (HD) remains uncertain. However, the temporal appearance of aggregates tends to correlate with the onset of symptoms and the numbers of neuropil aggregates correlate with the progression of clinical disease. Using highly sensitive immunohistochemical methods we have detected the appearance of diffuse aggregates during embryonic development in the R6/2 and YAC128 mouse models of HD. These are initially seen in developing axonal tracts and appear to spread throughout the cerebrum in the early neonate. PMID:27886014

  18. AVAILABLE MICRO-ACTIVITY DATA AND THEIR APPLICABILITY TO AGGREGATE EXPOSURE MODELING

    EPA Science Inventory

    Several human exposure models have been developed in recent years to address children's aggregate and cumulative exposures to pesticides under the Food Quality Protection Act of 1996. These models estimate children's exposures via all significant routes and pathways including ...

  19. Model simulations of particle aggregation effect on colloid exchange between streams and streambeds.

    PubMed

    Areepitak, Trachu; Ren, Jianhong

    2011-07-01

    Colloids found in natural streams have large reactive surface areas, which makes them significant absorbents and carriers for pollutants. Stream-subsurface exchange plays a critical role in regulating the transport of colloids and contaminants in natural streams. Previous process-based multiphase exchange models were developed without consideration of colloid-colloid interaction. However, many studies have indicated that aggregation is a significant process and needs to be considered in stream process analysis. Herein, a new colloid exchange model was developed by including particle aggregation in addition to colloid settling and filtration. Self-preserving size distribution concepts and classical aggregation theory were employed to model the aggregation process. Model simulations indicate that under conditions of low filtration and high degree of particle-particle interaction, aggregation could either decrease or increase the amount of colloids retained in streambeds, depending on the initial particle size. Thus, two possible cases may occur including enhanced colloid deposition and facilitated colloid transport. Also, when the aggregation rate is high and filtration increases, more particles are retained by bed sediments due to filtration, and fewer are aggregated, which reduces the extent of aggregation effect on colloid deposition. The work presented here will contribute to a better understanding and prediction of colloid transport phenomena in natural streams.

  20. Reduced-Order Modeling of Aggregated Thermostatic Loads With Demand Response

    SciTech Connect

    Zhang, Wei; Lian, Jianming; Chang, Chin-Yao; Kalsi, Karanjit; Sun, Yannan

    2012-12-12

    Demand Response is playing an increasingly important role in smart grid control strategies. Modeling the behavior of populations of appliances under demand response is especially important to evaluate the effectiveness of these demand response programs. In this paper, an aggregated model is proposed for a class of Thermostatically Controlled Loads (TCLs). The model efficiently includes statistical information of the population, systematically deals with heterogeneity, and accounts for a second-order effect necessary to accurately capture the transient dynamics in the collective response. However, an accurate characterization of the collective dynamics however requires the aggregate model to have a high state space dimension. Most of the existing model reduction techniques require the stability of the underlying system which does not hold for the proposed aggregated model. In this work, a novel model reduction approach is developed for the proposed aggregated model, which can significantly reduce its complexity with small performance loss. The original and the reducedorder aggregated models are validated against simulations of thousands of detailed building models using GridLAB-D, which is a realistic open source distribution simulation software. Index Terms – demand response, aggregated model, ancillary

  1. Using Human iPSC-Derived Neurons to Model TAU Aggregation.

    PubMed

    Verheyen, An; Diels, Annick; Dijkmans, Joyce; Oyelami, Tutu; Meneghello, Giulia; Mertens, Liesbeth; Versweyveld, Sofie; Borgers, Marianne; Buist, Arjan; Peeters, Pieter; Cik, Miroslav

    2015-01-01

    Alzheimer's disease and frontotemporal dementia are amongst the most common forms of dementia characterized by the formation and deposition of abnormal TAU in the brain. In order to develop a translational human TAU aggregation model suitable for screening, we transduced TAU harboring the pro-aggregating P301L mutation into control hiPSC-derived neural progenitor cells followed by differentiation into cortical neurons. TAU aggregation and phosphorylation was quantified using AlphaLISA technology. Although no spontaneous aggregation was observed upon expressing TAU-P301L in neurons, seeding with preformed aggregates consisting of the TAU-microtubule binding repeat domain triggered robust TAU aggregation and hyperphosphorylation already after 2 weeks, without affecting general cell health. To validate our model, activity of two autophagy inducers was tested. Both rapamycin and trehalose significantly reduced TAU aggregation levels suggesting that iPSC-derived neurons allow for the generation of a biologically relevant human Tauopathy model, highly suitable to screen for compounds that modulate TAU aggregation.

  2. Using Human iPSC-Derived Neurons to Model TAU Aggregation

    PubMed Central

    Verheyen, An; Diels, Annick; Dijkmans, Joyce; Oyelami, Tutu; Meneghello, Giulia; Mertens, Liesbeth; Versweyveld, Sofie; Borgers, Marianne; Buist, Arjan; Peeters, Pieter; Cik, Miroslav

    2015-01-01

    Alzheimer’s disease and frontotemporal dementia are amongst the most common forms of dementia characterized by the formation and deposition of abnormal TAU in the brain. In order to develop a translational human TAU aggregation model suitable for screening, we transduced TAU harboring the pro-aggregating P301L mutation into control hiPSC-derived neural progenitor cells followed by differentiation into cortical neurons. TAU aggregation and phosphorylation was quantified using AlphaLISA technology. Although no spontaneous aggregation was observed upon expressing TAU-P301L in neurons, seeding with preformed aggregates consisting of the TAU-microtubule binding repeat domain triggered robust TAU aggregation and hyperphosphorylation already after 2 weeks, without affecting general cell health. To validate our model, activity of two autophagy inducers was tested. Both rapamycin and trehalose significantly reduced TAU aggregation levels suggesting that iPSC-derived neurons allow for the generation of a biologically relevant human Tauopathy model, highly suitable to screen for compounds that modulate TAU aggregation. PMID:26720731

  3. Integrating service-life modeling and life-cycle assessment for recycled-aggregate concrete

    NASA Astrophysics Data System (ADS)

    Bergman, Todd Lee

    The development and implementation of one-dimensional (a) analytical and (b) numerical service-life models for chloride-induced corrosion of reinforced concrete containing both recycled-aggregates and supplementary cementitious materials (SCMs) are presented in this work. Both the analytical and numerical models account for initial chloride contamination levels due to previous applications. The effects of aggregate type (e.g., virgin, recycled aggregate, recycled mortar), aggregate replacement ratio, severity of chloride contamination levels, severity of in-service chloride exposure, reinforcement cover depth, SCM type (e.g., fly ash, slag, slice fume, metakaolin), and SCM replacement ratio on the expected service life of recycled-aggregate reinforced concrete were investigated. Results illustrated trends between concrete mixes and life cycle costs, which were employed to make conclusions on the trade-offs presented by cost, sustainability, and service life.

  4. Aggregation of polymer-grafted nanoparticles in good solvents: A hierarchical modeling method

    NASA Astrophysics Data System (ADS)

    Cheng, Lisheng; Cao, Dapeng

    2011-09-01

    Brownian dynamics simulations are carried out to study the aggregation behavior of polymer-grafted nanoparticles (NPs) in good solvents by using the coarse-grained model derived from the all-atom force field, according to the hierarchical modeling strategy, and here PEG-grafted gold nanoparticles (GNPs) were taken as an example. Generally, grafting PEG to the surface of GNPs is to protect them from aggregation in the solution. However, our results reveal that PEG-grafted GNPs may also aggregate when concentration increases. Our simulations indicate that there exists a critical aggregating concentration (CAC), beyond which the PEG-grafted GNPs will aggregate. We further check the effects of grafting density and the length of grafted chains on the aggregation behavior of the grafted GNPs, and find that there exists an optimized length of grafted chain, at which the system has the maximal CAC. Furthermore, the aggregate size of self-assembled mesostructures formed by the grafted GNPs increases with the concentration. Interestingly, it is observed that the aggregation favors to form linear gold nanowires rather than compact gold nanoclusters, and the corresponding mechanism is also addressed. It is expected that this work would provide useful information for the fabrication of metal nanowires and the surface modification of metal nanoparticles.

  5. Compression-based aggregation model for medical web services.

    PubMed

    Al-Shammary, Dhiah; Khalil, Ibrahim

    2010-01-01

    Many organizations such as hospitals have adopted Cloud Web services in applying their network services to avoid investing heavily computing infrastructure. SOAP (Simple Object Access Protocol) is the basic communication protocol of Cloud Web services that is XML based protocol. Generally,Web services often suffer congestions and bottlenecks as a result of the high network traffic that is caused by the large XML overhead size. At the same time, the massive load on Cloud Web services in terms of the large demand of client requests has resulted in the same problem. In this paper, two XML-aware aggregation techniques that are based on exploiting the compression concepts are proposed in order to aggregate the medical Web messages and achieve higher message size reduction.

  6. Antiferromagnetic model of aggregation of a magnetic fluid

    SciTech Connect

    Morozov, K.I.

    1987-07-01

    Reversible aggregation of ferromagnetic particles of a magnetic fluid (MF) in an external magnetic field has been observed in a number of experimental studies. In this work the aggregation of MF is interpreted as a separation into paramagnetic and antiferromagnetic phases. A comparative analysis of the thermodynamic stability of antiferromagnetic (droplike) and ferromagnetic (needlelike) agglomerates is carried out. It is shown that in the absence of an applied field the former are thermodynamically more advantageous than the latter; the critical field of the antiferromagnetic-ferromagnetic phase transition is found, the critical values of the concentration of the MF, the temperature, and the osmotic pressure, determining the onset of the separation of the MF into regions with high and low particle concentration, are calculated.

  7. Mucin aggregation from a rod-like meso-scale model

    NASA Astrophysics Data System (ADS)

    Moreno, Nicolas; Perilla, Jairo E.; Colina, Coray M.; Lísal, Martin

    2015-05-01

    Dissipative particle dynamics, a meso-scale particle-based model, was used to study the aggregation of mucins in aqueous solutions. Concentration, strength of the mucin-water interactions, as well as the effects of size, shape, and composition of the model molecules were studied. Model proteins were represented as rod-like objects formed by coarse-grained beads. In the first model, only one type of beads formed the mucin. It was found that all the surfaces were available to form aggregates and the conformation of the aggregates was a function of the strength of the mucin-water interaction. With this model, the number of aggregates was unaffected by the initial position of the mucins in the simulation box, except for the lowest mucin concentration. In a more refined mucin model, two kinds of beads were used in the molecule in order to represent the existence of cysteine-like terminal groups in the actual molecule. With this new scheme, aggregation took place by the interaction of the terminal groups between model molecules. The kinetic analysis of the evolution of the number of aggregates with time was also studied for both mucin models.

  8. Erythrocyte: A systems model of the control of aggregation and deformability.

    PubMed

    Bazanovas, Antonina N; Evstifeev, Aleksandr I; Khaiboullina, Svetlana F; Sadreev, Ildar I; Skorinkin, Andrey I; Kotov, Nikolay V

    2015-05-01

    Human erythrocytes are highly specialized enucleate cells that are involved in providing efficient gas transport. Erythrocytes have been extensively studied both experimentally and by mathematical modeling in recent years. However, understanding of how aggregation and deformability are regulated is limited. These properties of the erythrocyte are essential for the physiological functioning of the cell. In this work, we propose a novel mathematical model of the molecular system that controls the aggregation and deformability of the erythrocyte. This model is based on the experimental results of previously published studies. Our model suggests fundamentally new mechanisms that regulate aggregation and deformability in a latch-like manner. The results of this work could be used as a general explanation of how the erythrocytes regulate their aggregation and deformability, and are essential in understanding erythrocyte disorders and aging.

  9. Dense and sparse aggregations in complex motion: Video coupled with simulation modeling

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In censuses of aggregations composed of highly mobile animals, the link between image processing technology and simulation modeling remains relatively unexplored despite demonstrated ecological needs for abundance and density assessments. We introduce a framework that connects video censusing with ...

  10. 32 CFR Appendix A to Part 300 - Access to DLA Records

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 22060-6221, Fax: 703-767-6091, Email: hq-foia@dla.mil—Responsible for broad functional areas, such as... AFB, Ohio—Editing/routing of logistics transactions, network interoperability and eBusiness services...-5685, Email: ddc-efoia@dla.mil—Worldwide network of 25 distribution depots and nine map support...

  11. 76 FR 38117 - Notice of Intent To Prepare an Environmental Assessment Regarding DLA Energy's Mobility Fuel...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-29

    ... Mobility Fuel Purchasing Programs AGENCY: Defense Logistics Agency Energy (DLA Energy), DoD. ACTION: Notice of Intent To Prepare an Environmental Assessment Regarding DLA Energy's Mobility Fuel Purchasing... and also help facilitate the cycle of storage and deployment of fuels and other energy sources....

  12. A three-dimensional model of myxobacterial aggregation by contact-mediated interactions.

    PubMed

    Sozinova, Olga; Jiang, Yi; Kaiser, Dale; Alber, Mark

    2005-08-09

    Myxobacteria provide one of the simplest models of cell-cell interaction and organized cell movement leading to cellular differentiation. When starved, tens of thousands of cells change their movement pattern from outward spreading to inward concentration; they form aggregates that become fruiting bodies. Cells inside fruiting bodies differentiate into round, nonmotile, environmentally resistant spores. Traditionally, cell aggregation has been considered to imply chemotaxis; a long-range cell interaction. However, myxobacterial aggregation is the consequence of direct cell-contact interactions, not chemotaxis. We present here a 3D stochastic lattice-gas cellular automata model of cell aggregation based on local cell-cell contact, and no chemotaxis. We demonstrate that a 3D discrete stochastic model can simulate two stages of cell aggregation. First, a "traffic jam" forms embedded in a field of motile cells. The jam then becomes an aggregation center that accumulates more cells. We show that, at high cell density, cells stream around the traffic jam, generating a 3D hemispherical mound. Later, when the nuclear traffic jam dissolves, the aggregation center becomes a 3D ring of streaming cells.

  13. The Role of Aggregates of Therapeutic Protein Products in Immunogenicity: An Evaluation by Mathematical Modeling

    PubMed Central

    Yin, Liusong; Chen, Xiaoying; Tiwari, Abhinav; Vicini, Paolo; Hickling, Timothy P.

    2015-01-01

    Therapeutic protein products (TPP) have been widely used to treat a variety of human diseases, including cancer, hemophilia, and autoimmune diseases. However, TPP can induce unwanted immune responses that can impact both drug efficacy and patient safety. The presence of aggregates is of particular concern as they have been implicated in inducing both T cell-independent and T cell-dependent immune responses. We used mathematical modeling to evaluate several mechanisms through which aggregates of TPP could contribute to the development of immunogenicity. Modeling interactions between aggregates and B cell receptors demonstrated that aggregates are unlikely to induce T cell-independent immune responses by cross-linking B cell receptors because the amount of signal transducing complex that can form under physiologically relevant conditions is limited. We systematically evaluate the role of aggregates in inducing T cell-dependent immune responses using a recently developed multiscale mechanistic mathematical model. Our analysis indicates that aggregates could contribute to T cell-dependent immune response by inducing high affinity epitopes which may not be present in the nonaggregated TPP and/or by enhancing danger signals to break tolerance. In summary, our computational analysis is suggestive of novel insights into the mechanisms underlying aggregate-induced immunogenicity, which could be used to develop mitigation strategies. PMID:26682236

  14. An Efficient Kinetic Model for Assemblies of Amyloid Fibrils and Its Application to Polyglutamine Aggregation

    PubMed Central

    Prigent, Stéphanie; Ballesta, Annabelle; Charles, Frédérique; Lenuzza, Natacha; Gabriel, Pierre; Tine, Léon Matar; Rezaei, Human; Doumic, Marie

    2012-01-01

    Protein polymerization consists in the aggregation of single monomers into polymers that may fragment. Fibrils assembly is a key process in amyloid diseases. Up to now, protein aggregation was commonly mathematically simulated by a polymer size-structured ordinary differential equations (ODE) system, which is infinite by definition and therefore leads to high computational costs. Moreover, this Ordinary Differential Equation-based modeling approach implies biological assumptions that may be difficult to justify in the general case. For example, whereas several ordinary differential equation models use the assumption that polymerization would occur at a constant rate independently of polymer size, it cannot be applied to certain protein aggregation mechanisms. Here, we propose a novel and efficient analytical method, capable of modelling and simulating amyloid aggregation processes. This alternative approach consists of an integro-Partial Differential Equation (PDE) model of coalescence-fragmentation type that was mathematically derived from the infinite differential system by asymptotic analysis. To illustrate the efficiency of our approach, we applied it to aggregation experiments on polyglutamine polymers that are involved in Huntington’s disease. Our model demonstrates the existence of a monomeric structural intermediate acting as a nucleus and deriving from a non polymerizing monomer (). Furthermore, we compared our model to previously published works carried out in different contexts and proved its accuracy to describe other amyloid aggregation processes. PMID:23152746

  15. Spatial data aggregation for spatio-temporal individual-level models of infectious disease transmission.

    PubMed

    Deeth, Lorna E; Deardon, Rob

    2016-05-01

    A class of complex statistical models, known as individual-level models, have been effectively used to model the spread of infectious diseases. These models are often fitted within a Bayesian Markov chain Monte Carlo framework, which can have a sig nificant computational expense due to the complex nature of the likelihood function associated with this class of models. Increases in population size or duration of the modeled epidemic can contribute to this computational burden. Here, we explore the effect of reducing this computational expense by aggregating the data into spatial clusters, and therefore reducing the overall population size. Individual-level models, reparameterized to account for this aggregation effect, may then be fitted to the spatially aggregated data. The ability of two reparameterized individual-level models, when fitted to this reduced data set, to identify a covariate effect is investigated through a simulation study.

  16. Symmetries and pattern formation in hyperbolic versus parabolic models of self-organised aggregation.

    PubMed

    Buono, Pietro-Luciano; Eftimie, Raluca

    2015-10-01

    The study of self-organised collective animal behaviour, such as swarms of insects or schools of fish, has become over the last decade a very active research area in mathematical biology. Parabolic and hyperbolic models have been used intensively to describe the formation and movement of various aggregative behaviours. While both types of models can exhibit aggregation-type patterns, studies on hyperbolic models suggest that these models can display a larger variety of spatial and spatio-temporal patterns compared to their parabolic counterparts. Here we use stability, symmetry and bifurcation theory to investigate this observation more rigorously, an approach not attempted before to compare and contrast aggregation patterns in models for collective animal behaviors. To this end, we consider a class of nonlocal hyperbolic models for self-organised aggregations that incorporate various inter-individual communication mechanisms, and take the formal parabolic limit to transform them into nonlocal parabolic models. We then discuss the symmetry of these nonlocal hyperbolic and parabolic models, and the types of bifurcations present or lost when taking the parabolic limit. We show that the parabolic limit leads to a homogenisation of the inter-individual communication, and to a loss of bifurcation dynamics (in particular loss of Hopf bifurcations). This explains the less rich patterns exhibited by the nonlocal parabolic models. However, for multiple interacting populations, by breaking the population interchange symmetry of the model, one can preserve the Hopf bifurcations that lead to the formation of complex spatio-temporal patterns that describe moving aggregations.

  17. Modeling coupled nanoparticle aggregation and transport in porous media: A Lagrangian approach

    NASA Astrophysics Data System (ADS)

    Taghavy, Amir; Pennell, Kurt D.; Abriola, Linda M.

    2015-01-01

    Changes in nanoparticle size and shape due to particle-particle interactions (i.e., aggregation or agglomeration) may significantly alter particle mobility and retention in porous media. To date, however, few modeling studies have considered the coupling of transport and particle aggregation processes. The majority of particle transport models employ an Eulerian modeling framework and are, consequently, limited in the types of collisions and aggregate sizes that can be considered. In this work, a more general Lagrangian modeling framework is developed and implemented to explore coupled nanoparticle aggregation and transport processes. The model was verified through comparison of model simulations to published results of an experimental and Eulerian modeling study (Raychoudhury et al., 2012) of carboxymethyl cellulose (CMC)-modified nano-sized zero-valent iron particle (nZVI) transport and retention in water-saturated sand columns. A model sensitivity analysis reveals the influence of influent particle concentration (ca. 70 to 700 mg/L), primary particle size (10-100 nm) and pore water velocity (ca. 1-6 m/day) on particle-particle, and, consequently, particle-collector interactions. Model simulations demonstrate that, when environmental conditions promote particle-particle interactions, neglecting aggregation effects can lead to under- or over-estimation of nanoparticle mobility. Results also suggest that the extent to which higher order particle-particle collisions influence aggregation kinetics will increase with the fraction of primary particles. This work demonstrates the potential importance of time-dependent aggregation processes on nanoparticle mobility and provides a numerical model capable of capturing/describing these interactions in water-saturated porous media.

  18. In vitro model of platelet aggregation in stenotic arteries

    SciTech Connect

    Morley, D.; Santamore, W.P.

    1988-07-01

    Clinical and experimental evidence suggest a strong relationship between arterial stenosis, platelet aggregation, and subsequent thrombus formation. To facilitate the study of platelet accumulation in stenotic arteries, we developed an in vitro preparation. Arterial segments were perfused with whole citrated blood. A stenosis was created by applying an external plastic constrictor to the artery. Platelet accumulation within the stenosis was assessed by scanning electron microscopy and by radioactive counts from Indium-111 labeled platelets. Utilizing this preparation, 30 carotid arterial segments from 10 mongrel dogs were perfused at 100 mmHg for 15 min. In 10 arteries without a stenosis, scanning electron microscopy and radioactive counts demonstrated little platelet accumulation. In contrast, extensive platelet aggregation was observed in 10 arteries with stenoses. Moreover, in 10 stenotic arteries exposed to the thromboxane mimetic, U46619 (Upjohn Diagnostic Group), scanning electron microscopy and radioactive counts demonstrated a significant increase in platelet deposition. Conversely, we demonstrated a dimunition of platelet accumulation in stenosed arterial segments exposed to the prostacyclin analogue platelet inhibitor, Iloprost. The in vitro preparation allows precise control of hemodynamic variables and makes it possible to perform multiple tests on segments of the same vessel from the same animal.

  19. Singular patterns for an aggregation model with a confining potential

    NASA Astrophysics Data System (ADS)

    Kolokolnikov, Theodore; Huang, Yanghong; Pavlovski, Mark

    2013-10-01

    We consider the aggregation equation with an attractive-repulsive force law. Recent studies (Kolokolnikov et al. (2011) [22]; von Brecht et al. (2012) [23]; Balague et al. (2013) [15]) have demonstrated that this system exhibits a very rich solution structure, including steady states consisting of rings, spots, annuli, N-fold symmetries, soccer-ball patterns etc. We show that many of these patterns can be understood as singular perturbations off lower-dimensional equilibrium states. For example, an annulus is a bifurcation from a ring; soccer-ball patterns bifurcate off solutions that consist of delta-point concentrations. We apply asymptotic methods to classify the form and stability of many of these patterns. To characterize spot solutions, a class of “semi-linear” aggregation problems is derived, where the repulsion is described by a nonlinear term and the attraction is linear but non-symmetric. For a special class of perturbations that consists of a Newtonian repulsion, the spot shape is shown to be an ellipse whose precise dimensions are determined via a complex variable method. For annular shapes, their width and radial density profile are described using perturbation techniques.

  20. Archean Earth Atmosphere Fractal Haze Aggregates: Light Scattering Calculations and the Faint Young Sun Paradox

    NASA Astrophysics Data System (ADS)

    Boness, D. A.; Terrell-Martinez, B.

    2010-12-01

    As part of an ongoing undergraduate research project of light scattering calculations involving fractal carbonaceous soot aggregates relevant to current anthropogenic and natural sources in Earth's atmosphere, we have read with interest a recent paper [E.T. Wolf and O.B Toon,Science 328, 1266 (2010)] claiming that the Faint Young Sun paradox discussed four decades ago by Carl Sagan and others can be resolved without invoking heavy CO2 concentrations as a greenhouse gas warming the early Earth enough to sustain liquid water and hence allow the origin of life. Wolf and Toon report that a Titan-like Archean Earth haze, with a fractal haze aggregate nature due to nitrogen-methane photochemistry at high altitudes, should block enough UV light to protect the warming greenhouse gas NH3 while allowing enough visible light to reach the surface of the Earth. To test this hypothesis, we have employed a rigorous T-Matrix arbitrary-particle light scattering technique, to avoid the simplifications inherent in Mie-sphere scattering, on haze fractal aggregates at UV and visible wavelenths of incident light. We generate these model aggregates using diffusion-limited cluster aggregation (DLCA) algorithms, which much more closely fit actual haze fractal aggregates than do diffusion-limited aggregation (DLA) algorithms.

  1. Observations and modelling of microphysical variability, aggregation and sedimentation in tropical anvil cirrus outflow regions

    NASA Astrophysics Data System (ADS)

    Gallagher, M. W.; Connolly, P. J.; Crawford, I.; Heymsfield, A.; Bower, K. N.; Choularton, T. W.; Allen, G.; Flynn, M. J.; Vaughan, G.; Hacker, J.

    2012-07-01

    Aircraft measurements of the microphysics of a tropical convective anvil (at temperatures ~-60 °C) forming above the Hector storm, over the Tiwi Islands, Northern Australia, have been conducted with a view to determining ice crystal aggregation efficiencies from in situ measurements. The observed microphysics have been compared to an explicit bin-microphysical model of the anvil region, which includes crystal growth by vapour diffusion and aggregation and the process of differential sedimentation. It has been found in flights made using straight and level runs perpendicular to the storm that the number of ice crystals initially decreased with distance from the storm as aggregation took place resulting in larger crystals, followed by their loss from the cloud layer due to sedimentation. The net result was that the mass (i.e. Ice Water Content) in the anvil Ci cloud decreased, but also that the average particle size (weighted by number) remained relatively constant along the length of the anvil outflow. Comparisons with the explicit microphysics model showed that the changes in the shapes of the ice crystal spectra as a function of distance from the storm could be explained by the model if the aggregation efficiency was set to values of Eagg~0.5 and higher. This result is supported by recent literature on aggregation efficiencies for complex ice particles and suggests that either the mechanism of particle interlocking is important to the aggregation process, or that other effects are occuring, such as enhancement of ice-aggregation by high electric fields that arise as a consequence of charge separation within the storm. It is noteworthy that this value of the ice crystal aggregation efficiency is much larger than values used in cloud resolving models at these temperatures, which typically use E~0.0016. These results are important to understanding how cold clouds evolve in time and for the treatment of the evolution of tropical Ci in numerical models.

  2. Acoustic absorption modeling of porous concrete considering the gradation and shape of aggregates and void ratio

    NASA Astrophysics Data System (ADS)

    Kim, H. K.; Lee, H. K.

    2010-03-01

    The results of acoustic absorption modeling of porous concrete considering the gradation and shape of aggregates and void ratio are presented. To model the void texture of porous concrete, the multi-layered micro-perforated rigid panel model considering air gaps [1,2] is adopted. The parameters used in this acoustic absorption modeling are determined by a geometrical and experimental approach considering the gradation and shape of aggregates and void ratio. The predicted acoustic absorption spectra are compared with experimental results to verify the proposed acoustic absorption modeling approach. Finally, a parametric study is conducted to investigate the influence of design factors on the acoustic absorption properties of porous concrete.

  3. Simple Model Study of Phase Transition Properties of Isolated and Aggregated Protein

    NASA Astrophysics Data System (ADS)

    Ji, Yong-Yun; Yi, Wei-Qi; Zhang, Lin-Xi

    2011-03-01

    We investigate the phase transition properties of isolated and aggregated protein by exhaustive numerical study in the confined conformation space with maximally compact lattice model. The study within the confined conformation space shows some general folding properties. Various sequences show different folding properties: two-state folding, three-state folding and prion-like folding behavior. We find that the aggregated protein holds a more evident transition than isolated one and the transition temperature is generally lower than that in isolated case.

  4. Aggregate supply and demand modeling using GIS methods for the front range urban corridor, Colorado

    NASA Astrophysics Data System (ADS)

    Karakas, Ahmet; Turner, Keith

    2004-07-01

    The combined use of allocation modeling and geographical information system (GIS) technologies for providing quantitative assessments of aggregate supply and demand is evaluated using representative data for the Front Range Urban Corridor (FRUC) in Colorado. The FRUC extends from the Colorado-Wyoming border to south of Colorado Springs, and includes Denver and the major urban growth regions of Colorado. In this area, aggregate demand is high and is increasing in response to population growth. Neighborhood opposition to the establishment of new pits and quarries and the depletion of many deposits are limiting aggregate supplies. Many sources are already covered by urban development or eliminated from production by zoning. Transport of aggregate by rail from distant resources may be required in the future. Two allocation-modeling procedures are tested in this study. Network analysis procedures provided within the ARC/INFO software, are unsatisfactory. Further aggregate allocation modeling used a model specifically designed for this task; a modified version of an existing Colorado School of Mines allocation model allows for more realistic market analyses. This study evaluated four scenarios. The entire region was evaluated with a scenario reflecting the current market and by a second scenario in which some existing suppliers were closed down and new potential suppliers were activated. The conditions within the Denver metropolitan area were studied before and after the introduction of three possible rail-to-truck aggregate distribution centers. GIS techniques are helpful in developing the required database to describe the Front Range Urban Corridor aggregate market conditions. GIS methods allow the digital representation of the regional road network, and the development of a distance matrix relating all suppliers and purchasers.

  5. Aggregation of asphaltene model compounds using a porphyrin tethered to a carboxylic acid.

    PubMed

    Schulze, Matthias; Lechner, Marc P; Stryker, Jeffrey M; Tykwinski, Rik R

    2015-07-07

    A Ni(II) porphyrin functionalized with an alkyl carboxylic acid (3) has been synthesized to model the chemical behavior of the heaviest portion of petroleum, the asphaltenes. Specifically, porphyrin 3 is used in spectroscopic studies to probe aggregation with a second asphaltene model compound containing basic nitrogen (4), designed to mimic asphaltene behavior. NMR spectroscopy documents self-association of the porphyrin and aggregation with the second model compound in solution, and a Job's plot suggests a 1 : 2 stoichiometry for compounds 3 and 4.

  6. Photoacoustic ultrasound sources from diffusion-limited aggregates

    NASA Astrophysics Data System (ADS)

    Patel, Krutik; Brubaker, Morgan; Kotlerman, Alexander; Salazar, Robert; Wolf, Eli; Weld, David M.

    2016-10-01

    Metallic diffusion-limited aggregate (DLA) films are well-known to exhibit near-perfect broadband optical absorption. We demonstrate that such films also manifest a substantial and relatively material-independent photoacoustic response, as a consequence of their random nanostructure. We theoretically and experimentally analyze the photoacoustic phenomena in DLA films and show that they can be used to create broadband air-coupled acoustic sources. These sources are inexpensive and simple to fabricate and work into the ultrasonic regime. We illustrate the device possibilities by building and testing an optically addressed acoustic phased array capable of producing virtually arbitrary acoustic intensity patterns in air.

  7. A model for wet aggregation of ash particles in volcanic plumes and clouds: 1. Theoretical formulation

    NASA Astrophysics Data System (ADS)

    Costa, Antonio; Folch, Arnau; Macedonio, Giovanni

    2010-09-01

    We develop a model to describe ash aggregates in a volcanic plume. The model is based on a solution of the classical Smoluchowski equation, obtained by introducing a similarity variable and a fractal relationship for the number of primary particles in an aggregate. The considered collision frequency function accounts for different mechanisms of aggregation, such as Brownian motion, ambient fluid shear, and differential sedimentation. Although model formulation is general, here only sticking efficiency related to the presence of water is considered. However, the different binding effect of liquid water and ice is discerned. The proposed approach represents a first compromise between the full description of the aggregation process and the need to decrease the computational time necessary for solving the full Smoluchowski equation. We also perform a parametric study on the main model parameters and estimate coagulation kernels and timescales of the aggregation process under simplified conditions of interest in volcanology. Further analyses and applications to real eruptions are presented in the companion paper by Folch et al.

  8. N-Acetyl-L-Cysteine Prevents Stress-Induced Desmin Aggregation in Cellular Models of Desminopathy

    PubMed Central

    Bailleux, Virginie; Simon, Stéphanie; Leccia, Emilie; Gausseres, Blandine; Briki, Fatma; Vicart, Patrick; Batonnet-Pichon, Sabrina

    2013-01-01

    Mutations within the human desmin gene are responsible for a subcategory of myofibrillar myopathies called desminopathies. However, a single inherited mutation can produce different phenotypes within a family, suggesting that environmental factors influence disease states. Although several mouse models have been used to investigate organ-specific desminopathies, a more general mechanistic perspective is required to advance our knowledge toward patient treatment. To improve our understanding of disease pathology, we have developed cellular models to observe desmin behaviour in early stages of disease pathology, e.g., upon formation of cytoplasmic desmin aggregates, within an isogenic background. We cloned the wildtype and three mutant desmin cDNAs using a Tet-On Advanced® expression system in C2C12 cells. Mutations were selected based on positioning within desmin and capacity to form aggregates in transient experiments, as follows: DesS46Y (head domain; low aggregation), DesD399Y (central rod domain; high aggregation), and DesS460I (tail domain; moderate aggregation). Introduction of these proteins into a C2C12 background permitted us to compare between desmin variants as well as to determine the role of external stress on aggregation. Three different types of stress, likely encountered during muscle activity, were introduced to the cell models—thermal (heat shock), redox-associated (H2O2 and cadmium chloride), and mechanical (stretching) stresses—after which aggregation was measured. Cells containing variant DesD399Y were more sensitive to stress, leading to marked cytoplasmic perinuclear aggregations. We then evaluated the capacity of biochemical compounds to prevent this aggregation, applying dexamethasone (an inducer of heat shock proteins), fisetin or N-acetyl-L-cysteine (antioxidants) before stress induction. Interestingly, N-acetyl-L-cysteine pre-treatment prevented DesD399Y aggregation during most stress. N-acetyl-L-cysteine has recently been described

  9. Modeling multivalent ligand-receptor interactions with steric constraints on configurations of cell surface receptor aggregates

    SciTech Connect

    Monine, Michael; Posner, Richard; Savage, Paul; Faeder, James; Hlavacek, William S

    2008-01-01

    Signal transduction generally involves multivalent protein-protein interactions, which can produce various protein complexes and post-translational modifications. The reaction networks that characterize these interactions tend to be so large as to challenge conventional simulation procedures. To address this challenge, a kinetic Monte Carlo (KMC) method has been developed that can take advantage of a model specification in terms of reaction rules for molecular interactions. A set of rules implicitly defines the reactions that can occur as a result of the interactions represented by the rules. With the rule-based KMC method, explicit generation of the underlying chemical reaction network implied by rules is avoided. Here, we apply and extend this method to characterize the interactions of a trivalent ligand with a bivalent cell-surface receptor. This system is also studied experimentally. We consider the following kinetic models: an equivalent-site model, an extension of this model, which takes into account steric constraints on the configurations of receptor aggregates, and finally, a model that accounts for cyclic receptor aggregates. Simulation results for the equivalent-site model are consistent with an equilibrium continuum model. Using these models, we investigate the effects of steric constraints and the formation of cyclic aggregates on the kinetics and equilibria of small and large aggregate formation and the percolation phase transition that occurs in this system.

  10. AN AGGREGATION AND EPISODE SELECTION SCHEME FOR EPA'S MODELS-3 CMAQ

    EPA Science Inventory

    The development of an episode selection and aggregation approach, designed to support distributional estimation for use with the Models-3 Community Multiscale Air Quality (CMAQ) model, is described. The approach utilized cluster analysis of the 700 hPa u and v wind field compo...

  11. High-Throughput Multiplexed Quantitation of Protein Aggregation and Cytotoxicity in a Huntington’s Disease Model

    PubMed Central

    Titus, Steven A; Southall, Noel; Marugan, Juan; Austin, Christopher P; Zheng, Wei

    2012-01-01

    A hallmark of Huntington’s disease is the presence of a large polyglutamine expansion in the first exon of the Huntingtin protein and the propensity of protein aggregation by the mutant proteins. Aberrant protein aggregation also occurs in other polyglutamine expansion disorders, as well as in other neurodegenerative diseases including Parkinson’s, Alzheimer’s, and prion diseases. However, the pathophysiological role of these aggregates in the cell death that characterizes the diseases remains unclear. Identification of small molecule probes that modulate protein aggregation and cytotoxicity caused by aggregated proteins may greatly facilitate the studies on pathogenesis of these diseases and potentially lead to development of new therapies. Based on a detergent insoluble property of the Huntingtin protein aggregates, we have developed a homogenous assay to rapidly quantitate the levels of protein aggregates in a cellular model of Huntington’s disease. The protein aggregation assay has also been multiplexed with a protease release assay for the measurement of cytotoxicity resulting from aggregated proteins in the same cells. Through a testing screen of a compound library, we have demonstrated that this multiplexed cytotoxicity and protein aggregation assay has ability to identify active compounds that prevent cell death and/or modulate protein aggregation in cells of the Huntington’s disease model. Therefore, this multiplexed screening approach is also useful for development of high-throughput screening assays for other neurodegenerative diseases involving protein aggregation. PMID:23346268

  12. Mechanisms and Kinetics of Amyloid Aggregation Investigated by a Phenomenological Coarse-Grained Model

    NASA Astrophysics Data System (ADS)

    Magno, Andrea; Pellarin, Riccardo; Caflisch, Amedeo

    Amyloid fibrils are ordered polypeptide aggregates that have been implicated in several neurodegenerative pathologies, such as Alzheimer's, Parkinson's, Huntington's, and prion diseases, [1, 2] and, more recently, also in biological functionalities. [3, 4, 5] These findings have paved the way for a wide range of experimental and computational studies aimed at understanding the details of the fibril-formation mechanism. Computer simulations using low-resolution models, which employ a simplified representation of protein geometry and energetics, have provided insights into the basic physical principles underlying protein aggregation in general [6, 7, 8] and ordered amyloid aggregation. [9, 10, 11, 12, 13, 14, 15] For example, Dokholyan and coworkers have used the Discrete Molecular Dynamics method [16, 17] to shed light on the mechanisms of protein oligomerization [18] and the conformational changes that take place in proteins before the aggregation onset. [19, 20] One challenging observation, which is difficult to observe by computer simulations, is the wide range of aggregation scenarios emerging from a variety of biophysical measurements. [21, 22] Atomistic models have been employed to study the conformational space of amyloidogenic polypeptides in the monomeric state, [23, 24, 25] the very initial steps of amyloid formation, [26, 27, 28, 29, 30, 31, 32] and the structural stability of fibril models. [33, 34, 35) However, all-atom simulations of the kinetics of fibril formation are beyond what can be done with modern computers.

  13. Allelic diversity at the DLA-88 locus in Golden Retriever and Boxer breeds is limited

    PubMed Central

    Ross, Peter; Buntzman, Adam S.; Vincent, Benjamin G.; Grover, Elise N.; Gojanovich, Gregory S.; Collins, Edward J.; Frelinger, Jeffrey A.; Hess, Paul R.

    2012-01-01

    In the dog, previous analyses of major histocompatibility complex (MHC) class I genes suggest a single polymorphic locus, Dog Leukocyte Antigen (DLA)-88. While 51 alleles have been reported, estimates of prevalence have not been made. We hypothesized that, within a breed, DLA-88 diversity would be restricted, and one or more dominant alleles could be identified. Accordingly, we determined allele usage in 47 Golden Retrievers and 39 Boxers. In each population, 10 alleles were found; 4 were shared. Seven novel alleles were identified. DLA-88*05101 and *50801 predominated in Golden Retrievers, while most Boxers carried *03401. In these breeds DLA-88 polymorphisms are limited and largely non-overlapping. The finding of highly prevalent alleles fulfills an important prerequisite for studying canine CD8+ T-cell responses. PMID:22571293

  14. Viscous anisotropy of textured olivine aggregates: 2. Micromechanical model

    NASA Astrophysics Data System (ADS)

    Hansen, Lars N.; Conrad, Clinton P.; Boneh, Yuval; Skemer, Philip; Warren, Jessica M.; Kohlstedt, David L.

    2016-10-01

    The significant viscous anisotropy that results from crystallographic alignment (texture) of olivine grains in deformed upper mantle rocks strongly influences a large variety of geodynamic processes. Our ability to explore the effects of anisotropic viscosity in simulations of these processes requires a mechanical model that can predict the magnitude of anisotropy and its evolution. Unfortunately, existing models of olivine textural evolution and viscous anisotropy are calibrated for relatively small deformations and simple strain paths, making them less general than desired for many large-scale geodynamic scenarios. Here we develop a new set of micromechanical models to describe the mechanical behavior and textural evolution of olivine through a large range of strains and complex strain histories. For the mechanical behavior, we explore two extreme scenarios, one in which each grain experiences the same stress tensor (Sachs model) and one in which each grain undergoes a strain rate as close as possible to the macroscopic strain rate (pseudo-Taylor model). For the textural evolution, we develop a new model in which the director method is used to control the rate of grain rotation and the available slip systems in olivine are used to control the axis of rotation. Only recently has enough laboratory data on the deformation of olivine become available to calibrate these models. We use these new data to conduct inversions for the best parameters to characterize both the mechanical and textural evolution models. These inversions demonstrate that the calibrated pseudo-Taylor model best reproduces the mechanical observations. Additionally, the pseudo-Taylor textural evolution model can reasonably reproduce the observed texture strength, shape, and orientation after large and complex deformations. A quantitative comparison between our calibrated models and previously published models reveals that our new models excel in predicting the magnitude of viscous anisotropy and

  15. Theoretical study on fulvic acid structure, conformation and aggregation. A molecular modelling approach.

    PubMed

    Alvarez-Puebla, R A; Valenzuela-Calahorro, C; Garrido, J J

    2006-04-01

    The ubiquitous presence of humic substances (HS), combined with their ability to provide multiple sites for chemical reaction, makes them relevant to numerous biogeochemical processes such as mineral weathering, nutrient bioavailability, and contaminant transport. The reactivity of HS depends on their functional group chemistry and microstructure, which are in turn influenced by the composition of the surrounding media. In order to help towards an understanding of structure conformations and aggregation process of HS in soils and waters and to get a better knowledge of these kinds of materials, a fulvic acid (FA) has been modelled as a function of its ionic state under different conditions. Our proposed theoretical model based on the Temple-Northeastern-Birmingham (TNB) monomer fits well with experimental observations on the solubility (dipolar moment) and electronic and vibrational spectra of FAs. The presence of water molecules has a great stabilization effect on the electrostatic energy; this effect is greater as ionized rate increases. In vacuum, the non-ionized aggregated species are more stable than monomers because of the increase in their interaction due to H-bonding and non-bonding forces. When the molecules are ionized, no aggregation process takes place. In solution, the FA concentration is a critical factor for the aggregation. The system containing two FA molecules probably did not form aggregates because its equivalent concentration was too low. When the concentration was increased, the system gave rise to the formation of aggregates. The ionic state is another critical factor in the aggregation process. The ionized FA has a higher electric negative charge, which increases the energetic barriers and inhibits the approximation of FA caused by the Brownian movement.

  16. The Effects of DLA IPG I Surcharges on DDRW End User Activity Inventory Policies

    DTIC Science & Technology

    1992-12-01

    The intent of these surcharges is to enable DLA to recapture a portion of the costs incurred in meeting IPG I time standards. Additional goals are to...in meeting IPG I time standards. Additional goals are to discourage IPG I requisitioning for frivolous reasons, and when maintenance of small retail...faced with several DLA alternatives. These choices included: (1) subjectively downgrading requisitions he believed did not meet IPG I criteria; (2

  17. DLA Information Systems Technology Integration Guide for the Fiscal Year of 1991

    DTIC Science & Technology

    1991-01-01

    AD-A231 576/ 3MAR 05 1991~DL - DL INFORMATION SYSTEMS TECHNOLOGY INTEGRATION GUIDE Apovad fm p-anbc r o; JANUARY 1991 91 2 28 011 DLA INFORMATION...SYSTEMS TECHNOLOGY INTEGRATION GUIDE for the FISCAL YEAR of 1991 TABLE OF CONTENTS A. INTRODUCTION ................ . ......... 2 B. ARCHITECTURAL... INTEGRATION GUIDE for the FISCAL YEAR of 1991 DLA INFORMATION SYSTEMS TECHNOLOGY INTEGRATION GUIDE for the FISCAL YEAR of 1991 A. INTRODUCTION. The purpose of

  18. Aggregation kinetics of graphene oxides in aqueous solutions: experiments, mechanisms, and modeling.

    PubMed

    Wu, Lei; Liu, Lin; Gao, Bin; Muñoz-Carpena, Rafael; Zhang, Ming; Chen, Hao; Zhou, Zuhao; Wang, Hao

    2013-12-10

    Although graphene oxide (GO) has been used in many applications to improve human life quality, its environmental fate and behavior are still largely unknown. In this work, a novel approach that combines experimental measurements and theoretical calculations was used to determine the aggregation kinetics of GO sheets in aqueous solutions under different chemistry conditions (e.g., cation valence and pH). Experimental data showed that both cation valence and pH showed significant effect on the aggregation of GO sheets. The measured critical coagulation concentrations were in good agreement with the predictions of the extended Schulze-Hardy rule. Ca(2+) and Mg(2+) were more effective than Na(+) in aggregating the GO sheets, which could be attributed to the cross-linking between GO sheets by the divalent cations through "bridging" the functional groups at the edges of the GO sheets. When solution pH increases, deprotonation of carboxylic groups was found to play a key role in increasing GO sheet stability and surface charge development. These results suggested that edge-to-edge and face-to-face interactions were the dominant modes of GO aggregation in the presence of divalent metal ions and H(+), respectively. A modified attachment efficiency (α) model was developed on the basis of the Maxwell approach with considerations of both primary and secondary minima. The model predictions matched the experimental measurements of the aggregation kinetics of GO sheets in aqueous solutions under all of the tested experimental conditions well.

  19. FPLUME-1.0: An integral volcanic plume model accounting for ash aggregation

    NASA Astrophysics Data System (ADS)

    Folch, A.; Costa, A.; Macedonio, G.

    2016-02-01

    Eruption source parameters (ESP) characterizing volcanic eruption plumes are crucial inputs for atmospheric tephra dispersal models, used for hazard assessment and risk mitigation. We present FPLUME-1.0, a steady-state 1-D (one-dimensional) cross-section-averaged eruption column model based on the buoyant plume theory (BPT). The model accounts for plume bending by wind, entrainment of ambient moisture, effects of water phase changes, particle fallout and re-entrainment, a new parameterization for the air entrainment coefficients and a model for wet aggregation of ash particles in the presence of liquid water or ice. In the occurrence of wet aggregation, the model predicts an effective grain size distribution depleted in fines with respect to that erupted at the vent. Given a wind profile, the model can be used to determine the column height from the eruption mass flow rate or vice versa. The ultimate goal is to improve ash cloud dispersal forecasts by better constraining the ESP (column height, eruption rate and vertical distribution of mass) and the effective particle grain size distribution resulting from eventual wet aggregation within the plume. As test cases we apply the model to the eruptive phase-B of the 4 April 1982 El Chichón volcano eruption (México) and the 6 May 2010 Eyjafjallajökull eruption phase (Iceland). The modular structure of the code facilitates the implementation in the future code versions of more quantitative ash aggregation parameterization as further observations and experiment data will be available for better constraining ash aggregation processes.

  20. FPLUME-1.0: An integral volcanic plume model accounting for ash aggregation

    NASA Astrophysics Data System (ADS)

    Folch, Arnau; Costa, Antonio; Macedonio, Giovanni

    2016-04-01

    Eruption Source Parameters (ESP) characterizing volcanic eruption plumes are crucial inputs for atmospheric tephra dispersal models, used for hazard assessment and risk mitigation. We present FPLUME-1.0, a steady-state 1D cross-section averaged eruption column model based on the Buoyant Plume Theory (BPT). The model accounts for plume bending by wind, entrainment of ambient moisture, effects of water phase changes, particle fallout and re-entrainment, a new parameterization for the air entrainment coefficients and a model for wet aggregation of ash particles in presence of liquid water or ice. In the occurrence of wet aggregation, the model predicts an "effective" grain size distribution depleted in fines with respect to that erupted at the vent. Given a wind profile, the model can be used to determine the column height from the eruption mass flow rate or vice-versa. The ultimate goal is to improve ash cloud dispersal forecasts by better constraining the ESP (column height, eruption rate and vertical distribution of mass) and the "effective" particle grain size distribution resulting from eventual wet aggregation within the plume. As test cases we apply the model to the eruptive phase-B of the 4 April 1982 El Chichón volcano eruption (México) and the 6 May 2010 Eyjafjallajökull eruption phase (Iceland). The modular structure of the code facilitates the implementation in the future code versions of more quantitative ash aggregation parameterization as further observations and experiments data will be available for better constraining ash aggregation processes.

  1. Development and extension of an aggregated scale model: Part 1 - Background to ASMITA

    NASA Astrophysics Data System (ADS)

    Townend, Ian; Wang, Zheng Bing; Stive, Marcel; Zhou, Zeng

    2016-07-01

    Whilst much attention has been given to models that describe wave, tide and sediment transport processes in sufficient detail to determine the local changes in bed level over a relatively detailed representation of the bathymetry, far less attention has been given to models that consider the problem at a much larger scale (e.g. that of geomorphological elements such as a tidal flat and tidal channel). Such aggregated or lumped models tend not to represent the processes in detail but rather capture the behaviour at the scale of interest. One such model developed using the concept of an equilibrium concentration is the Aggregated Scale Morphological Interaction between Tidal basin and Adjacent coast (ASMITA). In this paper we provide some new insights into the concepts of equilibrium, and horizontal and vertical exchange that are key components of this modelling approach. In a companion paper, we summarise a range of developments that have been undertaken to extend the original model concept, to illustrate the flexibility and power of the conceptual framework. However, adding detail progressively moves the model in the direction of the more detailed process-based models and we give some consideration to the boundary between the two. Highlights The concept of aggregating model scales is explored and the basis of the ASMITA model is outlined in detail

  2. Modeling capsid kinetics assembly from the steady state distribution of multi-sizes aggregates

    NASA Astrophysics Data System (ADS)

    Hozé, Nathanaël; Holcman, David

    2014-01-01

    The kinetics of aggregation for particles of various sizes depends on their diffusive arrival and fusion at a specific nucleation site. We present here a mean-field approximation and a stochastic jump model for aggregates at equilibrium. This approach is an alternative to the classical Smoluchowski equations that do not have a close form and are not solvable in general. We analyze these mean-field equations and obtain the kinetics of a cluster formation. Our approach provides a simplified theoretical framework to study the kinetics of viral capsid formation, such as HIV from the self-assembly of the structural proteins Gag.

  3. Theoretical study on electromagnetically induced transparency in molecular aggregate models using quantum Liouville equation method

    SciTech Connect

    Minami, Takuya; Nakano, Masayoshi

    2015-01-22

    Electromagnetically induced transparency (EIT), which is known as an efficient control method of optical absorption property, is investigated using the polarizability spectra and population dynamics obtained by solving the quantum Liouville equation. In order to clarify the intermolecular interaction effect on EIT, we examine several molecular aggregate models composed of three-state monomers with the dipole-dipole coupling. On the basis of the present results, we discuss the applicability of EIT in molecular aggregate systems to a new type of optical switch.

  4. REFINED PBPK MODEL OF AGGREGATE EXPOSURE TO METHYL TERTIARY-BUTYL ETHER

    EPA Science Inventory

    Aggregate (multiple pathway) exposures to methyl tertiary-butyl ether (MTBE) in air and water occur via dermal, inhalation, and oral routes. Previously, physiologically-based pharmacokinetic (PBPK) models have been used to quantify the kinetic behavior of MTBE and its primary met...

  5. Studying the concentration dependence of the aggregation number of a micellar model system by SANS.

    PubMed

    Amann, Matthias; Willner, Lutz; Stellbrink, Jörg; Radulescu, Aurel; Richter, Dieter

    2015-06-07

    We present a small-angle neutron scattering (SANS) structural characterization of n-alkyl-PEO polymer micelles in aqueous solution with special focus on the dependence of the micellar aggregation number on increasing concentration. The single micellar properties in the dilute region up to the overlap concentration ϕ* are determined by exploiting the well characterized unimer exchange kinetics of the model system in a freezing and diluting experiment. The micellar solutions are brought to thermodynamic equilibrium at high temperatures, where unimer exchange is fast, and are then cooled to low temperatures and diluted to concentrations in the limit of infinite dilution. At low temperatures the kinetics, and therefore the key mechanism for micellar rearrangement, is frozen on the experimental time scale, thus preserving the micellar structure in the dilution process. Information about the single micellar structure in the semidilute and concentrated region are extracted from structure factor analysis at high concentrations where the micelles order into fcc and bcc close packed lattices and the aggregation number can be calculated by geometrical arguments. This approach enables us to investigate the aggregation behavior in a wide concentration regime from dilute to 6·ϕ*, showing a constant aggregation number with concentration over a large concentration regime up to a critical concentration about three times ϕ*. When exceeding this critical concentration, the aggregation number was found to increase with increasing concentration. This behavior is compared to scaling theories for star-like polymer micelles.

  6. Biological role of bacterial inclusion bodies: a model for amyloid aggregation.

    PubMed

    García-Fruitós, Elena; Sabate, Raimon; de Groot, Natalia S; Villaverde, Antonio; Ventura, Salvador

    2011-07-01

    Inclusion bodies are insoluble protein aggregates usually found in recombinant bacteria when they are forced to produce heterologous protein species. These particles are formed by polypeptides that cross-interact through sterospecific contacts and that are steadily deposited in either the cell's cytoplasm or the periplasm. An important fraction of eukaryotic proteins form inclusion bodies in bacteria, which has posed major problems in the development of the biotechnology industry. Over the last decade, the fine dissection of the quality control system in bacteria and the recognition of the amyloid-like architecture of inclusion bodies have provided dramatic insights on the dynamic biology of these aggregates. We discuss here the relevant aspects, in the interface between cell physiology and structural biology, which make inclusion bodies unique models for the study of protein aggregation, amyloid formation and prion biology in a physiologically relevant background.

  7. Traffic Flow Management Using Aggregate Flow Models and the Development of Disaggregation Methods

    NASA Technical Reports Server (NTRS)

    Sun, Dengfeng; Sridhar, Banavar; Grabbe, Shon

    2010-01-01

    A linear time-varying aggregate traffic flow model can be used to develop Traffic Flow Management (tfm) strategies based on optimization algorithms. However, there are no methods available in the literature to translate these aggregate solutions into actions involving individual aircraft. This paper describes and implements a computationally efficient disaggregation algorithm, which converts an aggregate (flow-based) solution to a flight-specific control action. Numerical results generated by the optimization method and the disaggregation algorithm are presented and illustrated by applying them to generate TFM schedules for a typical day in the U.S. National Airspace System. The results show that the disaggregation algorithm generates control actions for individual flights while keeping the air traffic behavior very close to the optimal solution.

  8. Modeling methylene blue aggregation in acidic solution to the limits of factor analysis.

    PubMed

    Golz, Emily K; Vander Griend, Douglas A

    2013-01-15

    Methylene blue (MB(+)), a common cationic thiazine dye, aggregates in acidic solutions. Absorbance data for equilibrated solutions of the chloride salt were analyzed over a concentration range of 1.0 × 10(-3) to 2.6 × 10(-5) M, in both 0.1 M HCl and 0.1 M HNO(3). Factor analyses of the raw absorbance data sets (categorically a better choice than effective absorbance) definitively show there are at least three distinct molecular absorbers regardless of acid type. A model with monomer, dimer, and trimer works well, but extensive testing has resulted in several other good models, some with higher order aggregates and some with chloride anions. Good models were frequently indistinguishable from each other by quality of fit or reasonability of molar absorptivity curves. The modeling of simulated data sets demonstrates the cases and degrees to which signal noise in the original data obscure the true model. In particular, the more mathematically similar (less orthogonal) the molar absorptivity curves of the chemical species in a model are, the less signal noise it takes to obscure the true model from other potentially good models. Unfortunately, the molar absorptivity curves in dye aggregation systems like that of methylene blue tend to be sufficiently similar so as to lead to the obscuration of models even at the noise levels (0.0001 ABS) of typical benchtop spectrophotometers.

  9. The aggregate path coupling method for the Potts model on bipartite graph

    NASA Astrophysics Data System (ADS)

    Hernández, José C.; Kovchegov, Yevgeniy; Otto, Peter T.

    2017-02-01

    In this paper, we derive the large deviation principle for the Potts model on the complete bipartite graph Kn,n as n increases to infinity. Next, for the Potts model on Kn,n, we provide an extension of the method of aggregate path coupling that was originally developed in the work of Kovchegov, Otto, and Titus [J. Stat. Phys. 144(5), 1009-1027 (2011)] for the mean-field Blume-Capel model and in Kovchegov and Otto [J. Stat. Phys. 161(3), 553-576 (2015)] for a general mean-field setting that included the generalized Curie-Weiss-Potts model analyzed in the work of Jahnel et al. [Markov Process. Relat. Fields 20, 601-632 (2014)]. We use the aggregate path coupling method to identify and determine the threshold value βs separating the rapid and slow mixing regimes for the Glauber dynamics of the Potts model on Kn,n.

  10. Disaggregation, aggregation and spatial scaling in hydrological modelling

    NASA Astrophysics Data System (ADS)

    Becker, Alfred; Braun, Peter

    1999-04-01

    A typical feature of the land surface is its heterogeneity in terms of the spatial variability of land surface characteristics and parameters controlling physical/hydrological, biological, and other related processes. Different forms and degrees of heterogeneity need to be taken into account in hydrological modelling. The first part of the article concerns the conditions under which a disaggregation of the land surface into subareas of uniform or "quasihomogeneous" behaviour (hydrotopes or hydrological response units - HRUs) is indispensable. In a case study in northern Germany, it is shown that forests in contrast to arable land, areas with shallow groundwater in contrast to those with deep, water surfaces and sealed areas should generally be distinguished (disaggregated) in modelling, whereas internal heterogeneities within these hydrotopes can be assessed statistically, e.g., by areal distribution functions (soil water holding capacity, hydraulic conductivity, etc.). Models with hydrotope-specific parameters can be applied to calculate the "vertical" processes (fluxes, storages, etc.), and this, moreover, for hydrotopes of different area, and even for groups of distributed hydrotopes in a reference area (hydrotope classes), provided that the meteorological conditions are similar. Thus, a scaling problem does not really exist in this process domain. The primary domain for the application of scaling laws is that of lateral flows in landscapes and river basins. This is illustrated in the second part of the article, where results of a case study in Bavaria/Germany are presented and discussed. It is shown that scaling laws can be applied efficiently for the determination of the Instantaneous Unit Hydrograph (IUH) of the surface runoff system in river basins: simple scaling for basins larger than 43 km 2, and multiple scaling for smaller basins. Surprisingly, only two parameters were identified as important in the derived relations: the drainage area and, in some

  11. An empirical test of the aggregation model of coexistence and consequences for competing container-dwelling mosquitoes.

    PubMed

    Fader, Joseph E; Juliano, Steven A

    2013-02-01

    We investigated the aggregation model of coexistence as a potential mechanism explaining patterns of coexistence between container mosquitoes Aedes albopictus and Aedes aegypti in southern Florida, USA. Aedes aegypti coexists with the invasive A. albopictus in many locations despite being an inferior resource competitor under most conditions. In agreement with aggregation theory we observed significant intraspecific aggregation of A. albopictus in all six field sites sampled in southern Florida in 2009. Quantitative results suggest that larval distributions of A. albopictus across containers are sufficiently aggregated to permit persistence of the inferior competitor A. aegypti. We tested whether observed levels of A. albopictus aggregation would significantly improve A. aegypti population performance in a controlled laboratory competition experiment manipulating A. albopictus aggregation while holding mean densities constant. We quantified A. aegypti's estimated rate of population change for replicate, multi-container cohorts in response to increasing A. albopictus aggregation across the cohorts. Aedes albopictus aggregation treatments produced J statistics for aggregation that spanned the range observed in the field study. We demonstrate a positive linear relationship between intraspecific aggregation of the superior competitor A. albopictus and estimated rate of population change for cohorts of the inferior A. aegypti. Thus, aggregation of A. albopictus at levels comparable to those observed in nature appears to be sufficient to reduce significantly the competitive impact of A. albopictus on multi-container cohorts of A. aegypti, and may therefore contribute to local coexistence of these competitors.

  12. An empirical test of the aggregation model of coexistence and consequences for competing container-dwelling mosquitoes

    PubMed Central

    Fader, Joseph E.; Juliano, Steven A.

    2014-01-01

    We investigated the aggregation model of coexistence as a potential mechanism explaining patterns of coexistence between container mosquitoes Aedes albopictus and Aedes aegypti in southern Florida. Aedes aegypti coexists with the invasive A. albopictus in many locations despite being an inferior resource competitor under most conditions. In agreement with aggregation theory we observed significant intraspecific aggregation of A. albopictus in all six field sites sampled in southern Florida in 2009. Quantitative results suggest that larval distributions of A. albopictus across containers are sufficiently aggregated to permit persistence of the inferior competitor A. aegypti. We tested whether observed levels of A. albopictus aggregation would significantly improve A. aegypti population performance in a controlled laboratory competition experiment manipulating A. albopictus aggregation while holding mean densities constant. We quantified A. aegypti’s estimated rate of population change for replicate, multi-container cohorts in response to increasing A. albopictus aggregation across the cohorts. Aedes albopictus aggregation treatments produced J statistics for aggregation that spanned the range observed in the field study. We demonstrate a positive linear relationship between intraspecific aggregation of the superior competitor A. albopictus and estimated rate of population change for cohorts of the inferior A. aegypti. Thus, aggregation of A. albopictus at levels comparable to those observed in nature appears to be sufficient to reduce significantly the competitive impact of A. albopictus on multi-container cohorts of A. aegypti, and may therefore contribute to local coexistence of these competitors. PMID:23691666

  13. Interval-Valued Model Level Fuzzy Aggregation-Based Background Subtraction.

    PubMed

    Chiranjeevi, Pojala; Sengupta, Somnath

    2016-07-29

    In a recent work, the effectiveness of neighborhood supported model level fuzzy aggregation was shown under dynamic background conditions. The multi-feature fuzzy aggregation used in that approach uses real fuzzy similarity values, and is robust for low and medium-scale dynamic background conditions such as swaying vegetation, sprinkling water, etc. The technique, however, exhibited some limitations under heavily dynamic background conditions, as features have high uncertainty under such noisy conditions and these uncertainties were not captured by real fuzzy similarity values. Our proposed algorithm is particularly focused toward improving the detection under heavy dynamic background conditions by modeling uncertainties in the data by interval-valued fuzzy set. In this paper, real-valued fuzzy aggregation has been extended to interval-valued fuzzy aggregation by considering uncertainties over real similarity values. We build up a procedure to calculate the uncertainty that varies for each feature, at each pixel, and at each time instant. We adaptively determine membership values at each pixel by the Gaussian of uncertainty value instead of fixed membership values used in recent fuzzy approaches, thereby, giving importance to a feature based on its uncertainty. Interval-valued Choquet integral is evaluated using interval similarity values and the membership values in order to calculate interval-valued fuzzy similarity between model and current. Adequate qualitative and quantitative studies are carried out to illustrate the effectiveness of the proposed method in mitigating heavily dynamic background situations as compared to state-of-the-art.

  14. Competition between protein folding and aggregation: A three-dimensional lattice-model simulation

    NASA Astrophysics Data System (ADS)

    Bratko, D.; Blanch, H. W.

    2001-01-01

    Aggregation of protein molecules resulting in the loss of biological activity and the formation of insoluble deposits represents a serious problem for the biotechnology and pharmaceutical industries and in medicine. Considerable experimental and theoretical efforts are being made in order to improve our understanding of, and ability to control, the process. In the present work, we describe a Monte Carlo study of a multichain system of coarse-grained model proteins akin to lattice models developed for simulations of protein folding. The model is designed to examine the competition between intramolecular interactions leading to the native protein structure, and intermolecular association, resulting in the formation of aggregates of misfolded chains. Interactions between the segments are described by a variation of the Go potential [N. Go and H. Abe, Biopolymers 20, 1013 (1981)] that extends the recognition between attracting types of segments to pairs on distinct chains. For the particular model we adopt, the global free energy minimum of a pair of protein molecules corresponds to a dimer of native proteins. When three or more molecules interact, clusters of misfolded chains can be more stable than aggregates of native folds. A considerable fraction of native structure, however, is preserved in these cases. Rates of conformational changes rapidly decrease with the size of the protein cluster. Within the timescale accessible to computer simulations, the folding-aggregation balance is strongly affected by kinetic considerations. Both the native form and aggregates can persist in metastable states, even if conditions such as temperature or concentration favor a transition to an alternative form. Refolding yield can be affected by the presence of an additional polymer species mimicking the function of a molecular chaperone.

  15. Comparison of cross-validation and bootstrap aggregating for building a seasonal streamflow forecast model

    NASA Astrophysics Data System (ADS)

    Schick, Simon; Rössler, Ole; Weingartner, Rolf

    2016-10-01

    Based on a hindcast experiment for the period 1982-2013 in 66 sub-catchments of the Swiss Rhine, the present study compares two approaches of building a regression model for seasonal streamflow forecasting. The first approach selects a single "best guess" model, which is tested by leave-one-out cross-validation. The second approach implements the idea of bootstrap aggregating, where bootstrap replicates are employed to select several models, and out-of-bag predictions provide model testing. The target value is mean streamflow for durations of 30, 60 and 90 days, starting with the 1st and 16th day of every month. Compared to the best guess model, bootstrap aggregating reduces the mean squared error of the streamflow forecast by seven percent on average. Thus, if resampling is anyway part of the model building procedure, bootstrap aggregating seems to be a useful strategy in statistical seasonal streamflow forecasting. Since the improved accuracy comes at the cost of a less interpretable model, the approach might be best suited for pure prediction tasks, e.g. as in operational applications.

  16. Moment-Based Physical Models of Broadband Clutter due to Aggregations of Fish

    DTIC Science & Technology

    2013-09-30

    statistical models for signal- processing algorithm development. These in turn will help to develop a capability to statistically forecast the impact of...the experimental area. This expectation has been affirmed by fishery catch statistics for 2012 (PACFIN, 2013a; PACFIN, 2013b, Hicks et al., 2013...aggregations of fish based on higher-order statistical measures describable in terms of physical and system parameters. Environmentally, these models

  17. Aggregated Particle-size distributions for tephra-deposit model forecasts

    NASA Astrophysics Data System (ADS)

    Mastin, L. G.; Durant, A. J.; Van Eaton, A. R.

    2015-12-01

    The accuracy of models that forecast atmospheric transport and deposition of tephra to anticipate hazards during volcanic eruptions is limited by the fact that fine ash tends to aggregate and fall out more rapidly than the individual constituent particles. Aggregation is generally accounted for by representing fine ash as aggregates with density ρagg and a log-normal size range with median μagg and standard deviation σagg. Values of these parameters likely vary with eruption type, grain size, and atmospheric conditions. To date, no studies have examined how the values vary from one eruption or deposit to another. In this study, we used the Ash3d tephra model to simulate four deposits: 18 May 1980 Mount St. Helens, 16-17 September 1992 Crater Peak (Mount Spurr), Alaska, 17 June 1996 Ruapehu, and 23 March 2009 Mount Redoubt volcano. In 158 simulations, we systematically varied μagg (1-2.3Φ) and σagg (0.1-0.3Φ), using ellipsoidal aggregates with =600 kg m-3 and a shape factor F≡((b+c)/2a)=0.44 . We evaluated the goodness of fit using three statistical comparisons: modeled versus measured (1) mass load at individual sample locations; (2) mass load versus distance along the dispersal axis; and (3) isomass area. For all deposits, the best-fit μagg ranged narrowly between ~1.6-2.0Φ (0.33-0.25mm), despite large variations in erupted mass (0.25-50 Tg), plume height (8.5-25 km), mass fraction of fine (<0.063mm) ash (3-59%), atmospheric temperature, aggregation mechanism, and water content between these eruptions. This close agreement suggests that the aggregation process may be modeled as a discrete process that is agnostic to the eruptive style or magnitude of eruption. This result paves the way to a simple, computationally-efficient parameterization of aggregation that is suitable for use in operational deposit forecasts. Further research may indicate whether this narrow range also reflects physical constraints on processes in the evolving cloud.

  18. Finite lattice model for molecular aggregation equilibria. Boolean statistics, analytical approximations, and the macroscopic limit.

    PubMed

    Rankin, Blake M; Ben-Amotz, Dor; Widom, B

    2015-09-14

    Molecular processes, ranging from hydrophobic aggregation and protein binding to mesoscopic self-assembly, are typically driven by a delicate balance of energetic and entropic non-covalent interactions. Here, we focus on a broad class of such processes in which multiple ligands bind to a central solute molecule as a result of solute-ligand (direct) and/or ligand-ligand (cooperative) interaction energies. Previously, we described a weighted random mixing (WRM) mean-field model for such processes and compared the resulting adsorption isotherms and aggregate size distributions with exact finite lattice (FL) predictions, for lattices with up to n = 20 binding sites. Here, we compare FL predictions obtained using both Bethe-Guggenheim (BG) and WRM approximations, and find that the latter two approximations are complementary, as they are each most accurate in different aggregation regimes. Moreover, we describe a computationally efficient method for exhaustively counting nearest neighbors in FL configurations, thus making it feasible to obtain FL predictions for systems with up n = 48 binding sites, whose properties approach the thermodynamic (infinite lattice) limit. We further illustrate the applicability of our results by comparing lattice model and molecular dynamics simulation predictions pertaining to the aggregation of methane around neopentane.

  19. Aggregation of peptides in the tube model with correlated sidechain orientations

    NASA Astrophysics Data System (ADS)

    Hung, Nguyen Ba; Hoang, Trinh Xuan

    2015-06-01

    The ability of proteins and peptides to aggregate and form toxic amyloid fibrils is associated with a range of diseases including BSE (or mad cow), Alzheimer's and Parkinson's Diseases. In this study, we investigate the the role of amino acid sequence in the aggregation propensity by using a modified tube model with a new procedure for hydrophobic interaction. In this model, the amino acid sidechains are not considered explicitly, but their orientations are taken into account in the formation of hydrophobic contact. Extensive Monte Carlo simulations for systems of short peptides are carried out with the use of parallel tempering technique. Our results show that the propensity to form and the structures of the aggregates strongly depend on the amino acid sequence and the number of peptides. Some sequences may not aggregate at all at a presumable physiological temperature while other can easily form fibril-like, β-sheet struture. Our study provides an insight into the principles of how the formation of amyloid can be governed by amino acid sequence.

  20. A Fractal Model for the Capacitance of Lunar Dust and Lunar Dust Aggregates

    NASA Technical Reports Server (NTRS)

    Collier, Michael R.; Stubbs, Timothy J.; Keller, John W.; Farrell, William M.; Marshall, John; Richard, Denis Thomas

    2011-01-01

    Lunar dust grains and dust aggregates exhibit clumping, with an uneven mass distribution, as well as features that span many spatial scales. It has been observed that these aggregates display an almost fractal repetition of geometry with scale. Furthermore, lunar dust grains typically have sharp protrusions and jagged features that result from the lack of aeolian weathering (as opposed to space weathering) on the Moon. A perfectly spherical geometry, frequently used as a model for lunar dust grains, has none of these characteristics (although a sphere may be a reasonable proxy for the very smallest grains and some glasses). We present a fractal model for a lunar dust grain or aggregate of grains that reproduces (1) the irregular clumpy nature of lunar dust, (2) the presence of sharp points, and (3) dust features that span multiple scale lengths. We calculate the capacitance of the fractal lunar dust analytically assuming fixed dust mass (i.e. volume) for an arbitrary number of fractal levels and compare the capacitance to that of a non-fractal object with the same volume, surface area, and characteristic width. The fractal capacitance is larger than that of the equivalent non-fractal object suggesting that for a given potential, electrostatic forces on lunar dust grains and aggregates are greater than one might infer from assuming dust grains are sphericaL Consequently, electrostatic transport of lunar dust grains, for example lofting, appears more plausible than might be inferred by calculations based on less realistic assumptions about dust shape and associated capacitance.

  1. An NMR study of macromolecular aggregation in a model polymer-surfactant solution

    NASA Astrophysics Data System (ADS)

    Barhoum, Suliman; Yethiraj, Anand

    2010-01-01

    A model complex-forming nonionic polymer-anionic surfactant system in aqueous solution has been studied at different surfactant concentrations. Using pulsed-field-gradient diffusion NMR spectroscopy, we obtain the self-diffusion coefficients of poly(ethylene glycol) (PEO) and sodium dodecyl sulfate (SDS) simultaneously and as a function of SDS concentration. In addition, we obtain NMR relaxation rates and chemical shifts as a function of SDS concentration. Within the context of a simple model, our experimental results yield the onset of aggregation of SDS on PEO chains (CAC=3.5 mM), a crossover concentration (C2=60 mM) which signals a sharp change in relaxation behavior, as well as an increase in free surfactant concentration and a critical concentration (Cm=145 mM) which signals a distinct change in diffusion behavior and a crossover to a solution containing free micelles. Cm also marks the concentration above which obstruction effects are definitely important. In addition, we obtain the concentration of SDS in monomeric form and in the form of free micelles, as well as the average number of SDS molecules in a PEO-SDS aggregate (NAggr). Taken together, our results suggests continuous changes in the aggregation phenomenon over much of the concentration but with three distinct concentrations that signal changes in the nature of the aggregates.

  2. A European model and case studies for aggregate exposure assessment of pesticides.

    PubMed

    Kennedy, Marc C; Glass, C Richard; Bokkers, Bas; Hart, Andy D M; Hamey, Paul Y; Kruisselbrink, Johannes W; de Boer, Waldo J; van der Voet, Hilko; Garthwaite, David G; van Klaveren, Jacob D

    2015-05-01

    Exposures to plant protection products (PPPs) are assessed using risk analysis methods to protect public health. Traditionally, single sources, such as food or individual occupational sources, have been addressed. In reality, individuals can be exposed simultaneously to multiple sources. Improved regulation therefore requires the development of new tools for estimating the population distribution of exposures aggregated within an individual. A new aggregate model is described, which allows individual users to include as much, or as little, information as is available or relevant for their particular scenario. Depending on the inputs provided by the user, the outputs can range from simple deterministic values through to probabilistic analyses including characterisations of variability and uncertainty. Exposures can be calculated for multiple compounds, routes and sources of exposure. The aggregate model links to the cumulative dietary exposure model developed in parallel and is implemented in the web-based software tool MCRA. Case studies are presented to illustrate the potential of this model, with inputs drawn from existing European data sources and models. These cover exposures to UK arable spray operators, Italian vineyard spray operators, Netherlands users of a consumer spray and UK bystanders/residents. The model could also be adapted to handle non-PPP compounds.

  3. DEVELOPMENT OF AN AGGREGATION AND EPISODE SELECTION SCHEME TO SUPPORT THE MODELS-3 COMMUNITY MULTISCALE AIR QUALITY MODEL

    EPA Science Inventory

    The development of an episode selection and aggregation approach, designed to support distributional estimation of use with the Models-3 Community Multiscale Air Quality (CMAQ) model, is described. The approach utilized cluster analysis of the 700-hPa east-west and north-south...

  4. The Aggregate Representation of Terrestrial Land Covers Within Global Climate Models (GCM)

    NASA Technical Reports Server (NTRS)

    Shuttleworth, W. James; Sorooshian, Soroosh

    1996-01-01

    This project had four initial objectives: (1) to create a realistic coupled surface-atmosphere model to investigate the aggregate description of heterogeneous surfaces; (2) to develop a simple heuristic model of surface-atmosphere interactions; (3) using the above models, to test aggregation rules for a variety of realistic cover and meteorological conditions; and (4) to reconcile biosphere-atmosphere transfer scheme (BATS) land covers with those that can be recognized from space; Our progress in meeting these objectives can be summarized as follows. Objective 1: The first objective was achieved in the first year of the project by coupling the Biosphere-Atmosphere Transfer Scheme (BATS) with a proven two-dimensional model of the atmospheric boundary layer. The resulting model, BATS-ABL, is described in detail in a Masters thesis and reported in a paper in the Journal of Hydrology Objective 2: The potential value of the heuristic model was re-evaluated early in the project and a decision was made to focus subsequent research around modeling studies with the BATS-ABL model. The value of using such coupled surface-atmosphere models in this research area was further confirmed by the success of the Tucson Aggregation Workshop. Objective 3: There was excellent progress in using the BATS-ABL model to test aggregation rules for a variety of realistic covers. The foci of attention have been the site of the First International Satellite Land Surface Climatology Project Field Experiment (FIFE) in Kansas and one of the study sites of the Anglo-Brazilian Amazonian Climate Observational Study (ABRACOS) near the city of Manaus, Amazonas, Brazil. These two sites were selected because of the ready availability of relevant field data to validate and initiate the BATS-ABL model. The results of these tests are given in a Masters thesis, and reported in two papers. Objective 4: Progress far exceeded original expectations not only in reconciling BATS land covers with those that can be

  5. Aggregated Modeling and Control of Air Conditioning Loads for Demand Response

    SciTech Connect

    Zhang, Wei; Lian, Jianming; Chang, Chin-Yao; Kalsi, Karanjit

    2013-06-21

    Demand response is playing an increasingly important role in the efficient and reliable operation of the electric grid. Modeling the dynamic behavior of a large population of responsive loads is especially important to evaluate the effectiveness of various demand response strategies. In this paper, a highly-accurate aggregated model is developed for a population of air conditioning loads. The model effectively includes statistical information of the population, systematically deals with load heterogeneity, and accounts for second-order dynamics necessary to accurately capture the transient dynamics in the collective response. Based on the model, a novel aggregated control strategy is designed for the load population under realistic conditions. The proposed controller is fully responsive and achieves the control objective without sacrificing end-use performance. The proposed aggregated modeling and control strategies are validated through realistic simulations using GridLAB-D. Extensive simulation results indicate that the proposed approach can effectively manage a large number of air conditioning systems to provide various demand response services, such as frequency regulation and peak load reduction.

  6. Model-driven experimental evaluation of struvite nucleation, growth and aggregation kinetics.

    PubMed

    Galbraith, S C; Schneider, P A; Flood, A E

    2014-06-01

    Nutrient stewardship is emerging as an issue of global importance, which will drive the development of nutrient recovery in the near to medium future. This will impact wastewater treatment practices, environmental protection, sustainable agriculture and global food security. A modelling framework for precipitation-based nutrient recovery systems has been developed, incorporating non-ideal solution thermodynamics, a dynamic mass balance and a dynamic population balance to track the development of the precipitating particles. The mechanisms of crystal nucleation and growth and, importantly, aggregation are considered. A novel approach to the population balance embeds the nucleation rate into the model, enabling direct regression of its kinetic parameters. The case study chosen for the modelling framework is that of struvite precipitation, given its wide interest and commercial promise as one possible nutrient recovery pathway. Power law kinetic parameters for nucleation, crystal growth and particle aggregation rates were regressed from an ensemble data set generated from 14 laboratory seeded batch experiments using synthetic solutions. These experiments were highly repeatable, giving confidence to the regressed parameter values. The model successfully describes the dynamic responses of solution pH, the evolving particle size distribution subject to nucleation, growth and aggregation effects and the aqueous magnesium concentration in the liquid phase. The proposed modelling framework could well be extended to other, more complex systems, leading to an improved understanding and commensurately greater confidence in the design, operation and optimisation of large-scale nutrient recovery processes from complex effluents.

  7. Structural five-fold symmetry in the fractal morphology of diffusion-limited aggregates

    NASA Astrophysics Data System (ADS)

    Arneodo, A.; Argoul, F.; Muzy, J. F.; Tabard, M.

    1992-09-01

    The statistical self-similarity of the geometry of diffusion-limited aggregates and the multifractal nature of the growth probability distribution on the surface of the growing clusters are investigated using the wavelet transform. This study reveals the existence of a predominant structural five-fold symmetry in the internal frozen region as well as in the active outer region of the interface. This observation is corroborated by a statistical analysis of the screening effects that govern diffusion-limited aggregation (DLA) growth in linear and sector-shaped cells. The existence of this symmetry is likely to be a clue to a hierarchichal fractal ordering. We report on the discovery of Fibonacci sequences in the inner extinct region of large mass off-lattice DLA clusters, with a branching ratio which converges asymptotically to the golden mean. We suggest an interpretation of the DLA morphology as a “quasifractal” counterpart of the well-ordered snowflake fractal architecture.

  8. Modeling disorder in polymer aggregates: The optical spectroscopy of regioregular poly(3-hexylthiophene) thin films

    NASA Astrophysics Data System (ADS)

    Spano, Frank C.

    2005-06-01

    Absorption and emission in polymer aggregates is studied theoretically, taking into account excitonic (intermolecular) coupling, exciton-phonon (EP) coupling, and disorder, all treated on equal footing within a generalized Holstein Hamiltonian with numerically generated eigenmodes and energies. The disorder is modeled as a Gaussian distribution of molecular transition frequency offsets of width σ and spatial correlation length l0. Both herringbone (HB) and lamellar aggregate morphologies are considered. The emission spectral line shape is shown to undergo marked changes in response to increasing disorder, with the intensity of the ac-polarized 0-0 emission peak generally increasing relative to the replica intensities (0-1,0-2,…) as σ increases and/or as l0 decreases. This is contrary to the behavior of the b-polarized component of the 0-0 intensity, which, in HB aggregates, decreases with increasing disorder. Comparisons are made to analogous trends in oligomer aggregates. Analytical results are obtained in the strong EP coupling regime appropriate for conjugated polymers while treating the disorder perturbatively. A method for uniquely determining σ and l0 from the emission and absorption spectra is presented. Applications are made to absorption and low-temperature emission in thin films of regioregular poly(3-hexylthiophene), with excellent agreement between theory and experiment obtained for a spatial correlation length of only 3-4 molecules.

  9. Protein carbonylation, protein aggregation and neuronal cell death in a murine model of multiple sclerosis

    NASA Astrophysics Data System (ADS)

    Dasgupta, Anushka

    Many studies have suggested that oxidative stress plays an important role in the pathophysiology of both multiple sclerosis (MS) and its animal model experimental autoimmune encephalomyelitis (EAE). Yet, the mechanism by which oxidative stress leads to tissue damage in these disorders is unclear. Recent work from our laboratory has revealed that protein carbonylation, a major oxidative modification caused by severe and/or chronic oxidative stress conditions, is elevated in MS and EAE. Furthermore, protein carbonylation has been shown to alter protein structure leading to misfolding/aggregation. These findings prompted me to hypothesize that carbonylated proteins, formed as a consequence of oxidative stress and/or decreased proteasomal activity, promote protein aggregation to mediate neuronal apoptosis in vitro and in EAE. To test this novel hypothesis, I first characterized protein carbonylation, protein aggregation and apoptosis along the spinal cord during the course of myelin-oligodendrocyte glycoprotein (MOG)35-55 peptide-induced EAE in C57BL/6 mice [Chapter 2]. The results show that carbonylated proteins accumulate throughout the course of the disease, albeit by different mechanisms: increased oxidative stress in acute EAE and decreased proteasomal activity in chronic EAE. I discovered not only that there is a temporal correlation between protein carbonylation and apoptosis but also that carbonyl levels are significantly higher in apoptotic cells. A high number of juxta-nuclear and cytoplasmic protein aggregates containing the majority of the oxidized proteins are also present during the course of EAE, which seems to be due to reduced autophagy. In chapter 3, I show that when gluthathione levels are reduced to those in EAE spinal cord, both neuron-like PC12 (nPC12) cells and primary neuronal cultures accumulate carbonylated proteins and undergo cell death (both by necrosis and apoptosis). Immunocytochemical and biochemical studies also revealed a temporal

  10. Direct Observation of Aggregative Nanoparticle Growth: Kinetic Modeling of the Size Distribution and Growth Rate

    SciTech Connect

    Woehl, Taylor J.; Park, Chiwoo; Evans, James E.; Arslan, Ilke; Ristenpart, William D.; Browning, Nigel D.

    2014-01-08

    Direct observations of solution-phase nanoparticle growth using in situ liquid transmission electron microscopy (TEM) have demonstrated the importance of “non-classical” growth mechanisms, such as aggregation and coalescence, on the growth and final morphology of nanocrystals at the atomic and single nanoparticle scales. To date, groups have quantitatively interpreted the mean growth rate of nanoparticles in terms of the Lifshitz-Slyozov-Wagner (LSW) model for Ostwald ripening, but less attention has been paid to modeling the corresponding particle size distribution. Here we use in situ fluid stage scanning TEM to demonstrate that silver nanoparticles grow by a length-scale dependent mechanism, where individual nanoparticles grow by monomer attachment but ensemble-scale growth is dominated by aggregation. Although our observed mean nanoparticle growth rate is consistent with the LSW model, we show that the corresponding particle size distribution is broader and more symmetric than predicted by LSW. Following direct observations of aggregation, we interpret the ensemble-scale growth using Smoluchowski kinetics and demonstrate that the Smoluchowski model quantitatively captures the mean growth rate and particle size distribution.

  11. A linearization approach for the model-based analysis of combined aggregate and individual patient data.

    PubMed

    Ravva, Patanjali; Karlsson, Mats O; French, Jonathan L

    2014-04-30

    The application of model-based meta-analysis in drug development has gained prominence recently, particularly for characterizing dose-response relationships and quantifying treatment effect sizes of competitor drugs. The models are typically nonlinear in nature and involve covariates to explain the heterogeneity in summary-level literature (or aggregate data (AD)). Inferring individual patient-level relationships from these nonlinear meta-analysis models leads to aggregation bias. Individual patient-level data (IPD) are indeed required to characterize patient-level relationships but too often this information is limited. Since combined analyses of AD and IPD allow advantage of the information they share to be taken, the models developed for AD must be derived from IPD models; in the case of linear models, the solution is a closed form, while for nonlinear models, closed form solutions do not exist. Here, we propose a linearization method based on a second order Taylor series approximation for fitting models to AD alone or combined AD and IPD. The application of this method is illustrated by an analysis of a continuous landmark endpoint, i.e., change from baseline in HbA1c at week 12, from 18 clinical trials evaluating the effects of DPP-4 inhibitors on hyperglycemia in diabetic patients. The performance of this method is demonstrated by a simulation study where the effects of varying the degree of nonlinearity and of heterogeneity in covariates (as assessed by the ratio of between-trial to within-trial variability) were studied. A dose-response relationship using an Emax model with linear and nonlinear effects of covariates on the emax parameter was used to simulate data. The simulation results showed that when an IPD model is simply used for modeling AD, the bias in the emax parameter estimate increased noticeably with an increasing degree of nonlinearity in the model, with respect to covariates. When using an appropriately derived AD model, the linearization

  12. An interacting particle system modelling aggregation behavior: from individuals to populations.

    PubMed

    Morale, Daniela; Capasso, Vincenzo; Oelschläger, Karl

    2005-01-01

    In this paper we investigate the stochastic modelling of a spatially structured biological population subject to social interaction. The biological motivation comes from the analysis of field experiments on a species of ants which exhibits a clear tendency to aggregate, still avoiding overcrowding. The model we propose here provides an explanation of this experimental behavior in terms of "long-ranged" aggregation and "short-ranged" repulsion mechanisms among individuals, in addition to an individual random dispersal described by a Brownian motion. Further, based on a "law of large numbers", we discuss the convergence, for large N, of a system of stochastic differential equations describing the evolution of N individuals (Lagrangian approach) to a deterministic integro-differential equation describing the evolution of the mean-field spatial density of the population (Eulerian approach).

  13. Reduction of calcium release site models via fast/slow analysis and iterative aggregation/disaggregation.

    PubMed

    Hao, Yan; Kemper, Peter; Smith, Gregory D

    2009-09-01

    Mathematical models of calcium release sites derived from Markov chain models of intracellular calcium channels exhibit collective gating reminiscent of the experimentally observed phenomenon of calcium puffs and sparks. Such models often take the form of stochastic automata networks in which the transition probabilities of each channel depend on the local calcium concentration and thus the state of the other channels. In order to overcome the state-space explosion that occurs in such compositionally defined calcium release site models, we have implemented several automated procedures for model reduction using fast/slow analysis. After categorizing rate constants in the single channel model as either fast or slow, groups of states in the expanded release site model that are connected by fast transitions are lumped, and transition rates between reduced states are chosen consistent with the conditional probability distribution among states within each group. For small problems these conditional probability distributions can be numerically calculated from the full model without approximation. For large problems the conditional probability distributions can be approximated without the construction of the full model by assuming rapid mixing of states connected by fast transitions. Alternatively, iterative aggregation/disaggregation may be employed to obtain reduced calcium release site models in a memory-efficient fashion. Benchmarking of several different iterative aggregation/disaggregation-based fast/slow reduction schemes establishes the effectiveness of automated calcium release site reduction utilizing the Koury-McAllister-Stewart method.

  14. Predictive response surface model for heat-induced rheological changes and aggregation of whey protein concentrate.

    PubMed

    Alvarez, Pedro A; Emond, Charles; Gomaa, Ahmed; Remondetto, Gabriel E; Subirade, Muriel

    2015-02-01

    Whey proteins are now far more than a by-product of cheese processing. In the last 2 decades, food manufacturers have developed them as ingredients, with the dairy industry remaining as a major user. For many applications, whey proteins are modified (denatured) to alter their structure and functional properties. The objective of this research was to study the influence of 85 to 100 °C, with protein concentration of 8% to 12%, and treatment times of 5 to 30 min, while measuring rheological properties (storage modulus, loss modulus, and complex viscosity) and aggregation (intermolecular beta-sheet formation) in dispersions of whey protein concentrate (WPC). A Box-Behnken Response Surface Methodology modeled the heat denaturation of liquid sweet WPC at 3 variables and 3 levels. The model revealed a very significant fit for viscoelastic properties, and a lesser fit for protein aggregation, at temperatures not previously studied. An exponential increase of rheological parameters was governed by protein concentration and temperature, while a modest linear relationship of aggregation was governed by temperature. Models such as these can serve as valuable guides to the ingredient and dairy industries to develop target products, as whey is a major ingredient in many functional foods.

  15. Changes of traffic characteristics after large-scale aggregation in 3Tnet: modeling, analysis, and evaluation

    NASA Astrophysics Data System (ADS)

    Yuan, Chi; Huang, Junbin; Li, Zhengbin; He, Yongqi; Xu, Anshi

    2007-11-01

    Understanding network traffic behavior is essential for all aspects of network design and operation, e.g. component design, protocol design, provisioning, operations, administration and maintenance (OAM). A careful study of traffic behavior can lead to improvements in underlying protocols to attain greater efficiencies and higher performance. Many researches have shown that traffic in Ethernet and other networks, either in local or wide area networks, exhibit properties of self-similarity. Several empirical studies on network traffic indicate that this traffic is self-similar in nature. However, the network modeling methods used in current networks have been primarily designed and analyzed under the assumption of the traditional Poisson arrival process. These "Poisson-like" models suggest that the network traffic is smooth, which is inherently unable to capture the self-similar characteristic of traffic. In this paper, after introduce the high performance broadband information network (3Tnet) of China, an aggregation model at access convergence router (ACR) is proposed and analyzed in 3Tnet. We studied the impact of large-scale aggregation applied at the edge of 3Tnet in terms of the self-similarity level observed at the output traffic in presence of self-similar input traffic. Two formulas were presented to describe the changes of Hurst parameter. Using OPNET software simulator, changes of traffic characteristics after large-scale aggregation in 3Tnet was extensive studied. The theoretic analysis results were consistent with the simulation results.

  16. Development and extension of an aggregated scale model: Part 2 — Extensions to ASMITA

    NASA Astrophysics Data System (ADS)

    Townend, Ian; Wang, Zheng Bing; Stive, Marcel; Zhou, Zeng

    2016-10-01

    Whilst much attention has been given to models that describe wave, tide and sediment transport processes in sufficient detail to determine the local changes in bed level over a relatively detailed representation of the bathymetry, far less attention has been given to models that consider the problem at a much larger scale (e.g. that of geomorphological elements such as a tidal flat and tidal channel). Such aggregated or lumped models tend not to represent the processes in detail but rather capture the behaviour at the scale of interest. One such model developed using the concept of an equilibrium concentration is the Aggregated Scale Morphological Interaction between Tidal basin and Adjacent coast (ASMITA). In a companion paper (Part 1), we detail the original model and provide some new insights into the concepts of equilibrium, and horizontal and vertical exchange that are key components of this modelling approach. In this paper, we summarise a range of developments that have been undertaken to extend the original model concept, to illustrate the flexibility and power of the conceptual framework. However, adding detail progressively moves the model in the direction of the more detailed process-based models and we give some consideration to the boundary between the two.

  17. A stochastic, Lagrangian model of sinking biogenic aggregates in the ocean (SLAMS 1.0): model formulation, validation and sensitivity

    NASA Astrophysics Data System (ADS)

    Jokulsdottir, Tinna; Archer, David

    2016-04-01

    We present a new mechanistic model, stochastic, Lagrangian aggregate model of sinking particles (SLAMS) for the biological pump in the ocean, which tracks the evolution of individual particles as they aggregate, disaggregate, sink, and are altered by chemical and biological processes. SLAMS considers the impacts of ballasting by mineral phases, binding of aggregates by transparent exopolymer particles (TEP), zooplankton grazing and the fractal geometry (porosity) of the aggregates. Parameterizations for age-dependent organic carbon (orgC) degradation kinetics, and disaggregation driven by zooplankton grazing and TEP degradation, are motivated by observed particle fluxes and size spectra throughout the water column. The model is able to explain observed variations in orgC export efficiency and rain ratio from the euphotic zone and to the sea floor as driven by sea surface temperature and the primary production rate and seasonality of primary production. The model provides a new mechanistic framework with which to predict future changes on the flux attenuation of orgC in response to climate change forcing.

  18. Modelling urban growth patterns

    NASA Astrophysics Data System (ADS)

    Makse, Hernán A.; Havlin, Shlomo; Stanley, H. Eugene

    1995-10-01

    CITIES grow in a way that might be expected to resemble the growth of two-dimensional aggregates of particles, and this has led to recent attempts1á¤-3 to model urban growth using ideas from the statistical physics of clusters. In particular, the model of diffusion-limited aggregation4,5 (DLA) has been invoked to rationalize the apparently fractal nature of urban morphologies1. The DLA model predicts that there should exist only one large fractal cluster, which is almost perfectly screened from incoming á¤~development unitsᤙ (representing, for example, people, capital or resources), so that almost all of the cluster growth takes place at the tips of the clusterᤙs branches. Here we show that an alternative model, in which development units are correlated rather than being added to the cluster at random, is better able to reproduce the observed morphology of cities and the area distribution of sub-clusters (á¤~towns') in an urban system, and can also describe urban growth dynamics. Our physical model, which corresponds to the correlated percolation model6á¤-8 in the presence of a density gradient9, is motivated by the fact that in urban areas development attracts further development. The model offers the possibility of predicting the global properties (such as scaling behaviour) of urban morphologies.

  19. Adjusting particle-size distributions to account for aggregation in tephra-deposit model forecasts

    NASA Astrophysics Data System (ADS)

    Mastin, Larry G.; Van Eaton, Alexa R.; Durant, Adam J.

    2016-07-01

    Volcanic ash transport and dispersion (VATD) models are used to forecast tephra deposition during volcanic eruptions. Model accuracy is limited by the fact that fine-ash aggregates (clumps into clusters), thus altering patterns of deposition. In most models this is accounted for by ad hoc changes to model input, representing fine ash as aggregates with density ρagg, and a log-normal size distribution with median μagg and standard deviation σagg. Optimal values may vary between eruptions. To test the variance, we used the Ash3d tephra model to simulate four deposits: 18 May 1980 Mount St. Helens; 16-17 September 1992 Crater Peak (Mount Spurr); 17 June 1996 Ruapehu; and 23 March 2009 Mount Redoubt. In 192 simulations, we systematically varied μagg and σagg, holding ρagg constant at 600 kg m-3. We evaluated the fit using three indices that compare modeled versus measured (1) mass load at sample locations; (2) mass load versus distance along the dispersal axis; and (3) isomass area. For all deposits, under these inputs, the best-fit value of μagg ranged narrowly between ˜ 2.3 and 2.7φ (0.20-0.15 mm), despite large variations in erupted mass (0.25-50 Tg), plume height (8.5-25 km), mass fraction of fine ( < 0.063 mm) ash (3-59 %), atmospheric temperature, and water content between these eruptions. This close agreement suggests that aggregation may be treated as a discrete process that is insensitive to eruptive style or magnitude. This result offers the potential for a simple, computationally efficient parameterization scheme for use in operational model forecasts. Further research may indicate whether this narrow range also reflects physical constraints on processes in the evolving cloud.

  20. Aggregation of LoD 1 building models as an optimization problem

    NASA Astrophysics Data System (ADS)

    Guercke, R.; Götzelmann, T.; Brenner, C.; Sester, M.

    3D city models offered by digital map providers typically consist of several thousands or even millions of individual buildings. Those buildings are usually generated in an automated fashion from high resolution cadastral and remote sensing data and can be very detailed. However, not in every application such a high degree of detail is desirable. One way to remove complexity is to aggregate individual buildings, simplify the ground plan and assign an appropriate average building height. This task is computationally complex because it includes the combinatorial optimization problem of determining which subset of the original set of buildings should best be aggregated to meet the demands of an application. In this article, we introduce approaches to express different aspects of the aggregation of LoD 1 building models in the form of Mixed Integer Programming (MIP) problems. The advantage of this approach is that for linear (and some quadratic) MIP problems, sophisticated software exists to find exact solutions (global optima) with reasonable effort. We also propose two different heuristic approaches based on the region growing strategy and evaluate their potential for optimization by comparing their performance to a MIP-based approach.

  1. A coarse grained protein model with internal degrees of freedom. Application to α-synuclein aggregation

    NASA Astrophysics Data System (ADS)

    Ilie, Ioana M.; den Otter, Wouter K.; Briels, Wim J.

    2016-02-01

    Particles in simulations are traditionally endowed with fixed interactions. While this is appropriate for particles representing atoms or molecules, objects with significant internal dynamics—like sequences of amino acids or even an entire protein—are poorly modelled by invariable particles. We develop a highly coarse grained polymorph patchy particle with the ultimate aim of simulating proteins as chains of particles at the secondary structure level. Conformational changes, e.g., a transition between disordered and β-sheet states, are accommodated by internal coordinates that determine the shape and interaction characteristics of the particles. The internal coordinates, as well as the particle positions and orientations, are propagated by Brownian Dynamics in response to their local environment. As an example of the potential offered by polymorph particles, we model the amyloidogenic intrinsically disordered protein α-synuclein, involved in Parkinson's disease, as a single particle with two internal states. The simulations yield oligomers of particles in the disordered state and fibrils of particles in the "misfolded" cross-β-sheet state. The aggregation dynamics is complex, as aggregates can form by a direct nucleation-and-growth mechanism and by two-step-nucleation through conversions between the two cluster types. The aggregation dynamics is complex, with fibrils formed by direct nucleation-and-growth, by two-step-nucleation through the conversion of an oligomer and by auto-catalysis of this conversion.

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

    PubMed

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

    2015-07-14

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

  3. Local-aggregate modeling for big data via distributed optimization: Applications to neuroimaging.

    PubMed

    Hu, Yue; Allen, Genevera I

    2015-12-01

    Technological advances have led to a proliferation of structured big data that have matrix-valued covariates. We are specifically motivated to build predictive models for multi-subject neuroimaging data based on each subject's brain imaging scans. This is an ultra-high-dimensional problem that consists of a matrix of covariates (brain locations by time points) for each subject; few methods currently exist to fit supervised models directly to this tensor data. We propose a novel modeling and algorithmic strategy to apply generalized linear models (GLMs) to this massive tensor data in which one set of variables is associated with locations. Our method begins by fitting GLMs to each location separately, and then builds an ensemble by blending information across locations through regularization with what we term an aggregating penalty. Our so called, Local-Aggregate Model, can be fit in a completely distributed manner over the locations using an Alternating Direction Method of Multipliers (ADMM) strategy, and thus greatly reduces the computational burden. Furthermore, we propose to select the appropriate model through a novel sequence of faster algorithmic solutions that is similar to regularization paths. We will demonstrate both the computational and predictive modeling advantages of our methods via simulations and an EEG classification problem.

  4. Cluster growth modeling of plateau erosion

    NASA Technical Reports Server (NTRS)

    Stark, Colin P.

    1994-01-01

    The pattern of erosion of a plateau along an escarpment may be modeled usng cluster growth techniques, recently popularized in models of drainage network evolution. If erosion on the scarp takes place in discrete events at rates subject to local substrate strength, the whole range of behavior is described by a combination of three cluster growth mechanisms: invasion percolation, Eden growth and diffusion-limited aggregation (DLA). These model the relative importance of preexisting substrate strength, background weathering, and seepage weathering and erosion respectively. The rate of seepage processes is determined by the efflux of groundwater at the plateau margin, which in turn is determined by the pressure field in the plateau aquifer. If this process acted alone, it would produce erosion patterns in the form of Laplacian fractals, with groundwater recharge from a distant source, or Poissionian fractals, with groundwater recharge uniform over the plateau. DLA is used to mimic the Laplacian or Poissonian potential field and the corresponding seepage growth process. The scaling structure of clusters grown by pure DLA, invasion percolation, or Eden growth is well known; this study presents a model which combines all three growth mechanisms for the first time. Mixed growth processes create clusters with different scaling properties and morphologies over distinct length scale ranges, and this is demonstrable in natural examples of plateau erosion.

  5. An ultrastructural analysis of endothelial change paralleling platelet aggregation in a light/dye model of microvascular insult.

    PubMed Central

    Povlishock, J. T.; Rosenblum, W. I.; Sholley, M. M.; Wei, E. P.

    1983-01-01

    Those microvascular endothelial events that parallel the evolution of platelet aggregation were evaluated in a well-controlled animal model. Cat pial microvessels were observed through a cranial window while local platelet aggregation was produced by intravenous injection of sodium fluorescein and simultaneous exposure of the pial vessels to light from a filtered mercury lamp that excited the fluorescein. The vessels were fixed in situ when the in vivo observations of a preselected vessel indicated early, intermediate, or advanced aggregation in that vessel. The preselected vessel was then harvested for ultrastructural study together with adjacent vessels from the illuminated field. These vessels and appropriate controls were compared in semiserial thin sections. The onset of platelet aggregation in both venules and arterioles was accompanied by focal endothelial lucency, vacuole formation, luminal membrane rupture, and swelling of the nuclear envelope. These changes were not found in control material. With intermediate aggregation these changes were more common, while with advanced aggregation these abnormalities occurred together with focal endothelial denudation. Thus, in this model denudation occurred only with advanced aggregation and was not a prerequisite for aggregation. Images Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Figure 9 Figure 10 Figure 11 Figure 12 PMID:6824062

  6. Bayesian regression models for the estimation of net cost of disease using aggregate data.

    PubMed

    Mitsakakis, Nicholas; Tomlinson, George

    2015-01-23

    Estimation of net costs attributed to a disease or other health condition is very important for health economists and policy makers. Skewness and heteroscedasticity are well-known characteristics for cost data, making linear models generally inappropriate and dictating the use of other types of models, such as gamma regression. Additional hurdles emerge when individual level data are not available. In this paper, we consider the latter case were data are only available at the aggregate level, containing means and standard deviations for different strata defined by a number of demographic and clinical factors. We summarize a number of methods that can be used for this estimation, and we propose a Bayesian approach that utilizes the sample stratum specific standard deviations as stochastic. We investigate the performance of two linear mixed models, comparing them with two proposed gamma regression mixed models, to analyze simulated data generated by gamma and log-normal distributions. Our proposed Bayesian approach seems to have significant advantages for net cost estimation when only aggregate data are available. The implemented gamma models do not seem to offer the expected benefits over the linear models; however, further investigation and refinement is needed.

  7. Hyperbolic and kinetic models for self-organized biological aggregations and movement: a brief review.

    PubMed

    Eftimie, Raluca

    2012-07-01

    We briefly review hyperbolic and kinetic models for self-organized biological aggregations and traffic-like movement. We begin with the simplest models described by an advection-reaction equation in one spatial dimension. We then increase the complexity of models in steps. To this end, we begin investigating local hyperbolic systems of conservation laws with constant velocity. Next, we proceed to investigate local hyperbolic systems with density-dependent speed, systems that consider population dynamics (i.e., birth and death processes), and nonlocal hyperbolic systems. We conclude by discussing kinetic models in two spatial dimensions and their limiting hyperbolic models. This structural approach allows us to discuss the complexity of the biological problems investigated, and the necessity for deriving complex mathematical models that would explain the observed spatial and spatiotemporal group patterns.

  8. FUS/TLS acts as an aggregation-dependent modifier of polyglutamine disease model mice

    PubMed Central

    Kino, Yoshihiro; Washizu, Chika; Kurosawa, Masaru; Yamada, Mizuki; Doi, Hiroshi; Takumi, Toru; Adachi, Hiroaki; Katsuno, Masahisa; Sobue, Gen; Hicks, Geoffrey G.; Hattori, Nobutaka; Shimogori, Tomomi; Nukina, Nobuyuki

    2016-01-01

    FUS/TLS is an RNA/DNA-binding protein associated with neurodegenerative diseases including amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Previously, we found that a prion-like domain in the N-terminus of FUS/TLS mediates co-aggregation between FUS/TLS and mutant huntingtin, the gene product of Huntington’s disease (HD). Here, we show that heterozygous knockout of FUS/TLS worsened the phenotypes of model mice of (HD, but not spinal and bulbar muscular atrophy (SBMA). This difference was correlated with the degree of pathological association between disease proteins and FUS/TLS. Co-aggregation between FUS/TLS and mutant huntingtin resulted in the depletion of free FUS/TLS protein in HD mice that was detected as a monomer in SDS-PAGE analysis. Recently, we found that FUS/TLS paralogs, TAF15 and EWS, were up-regulated in homozygous FUS/TLS knockout mice. These two proteins were up-regulated in both HD and FUS/TLS heterozygote mice, and were further elevated in HD-TLS+/− double mutant mice, consistent with the functional impairment of FUS/TLS. These results suggest that FUS/TLS sequestration by co-aggregation is a rate-limiting factor of disease phenotypes of HD and that inclusions may have an adverse aspect, rather than being simply benign or protective. In addition, our results highlight inclusions as repositories of potential modifiers of neurodegeneration. PMID:27739513

  9. Phase and sedimentation behavior of oil (octane) dispersions in the presence of model mineral aggregates.

    PubMed

    Gupta, Anju; Sender, Maximilian; Fields, Sarah; Bothun, Geoffrey D

    2014-10-15

    Adsorption of suspended particles to the interface of surfactant-dispersed oil droplets can alter emulsion phase and sedimentation behavior. This work examines the effects of model mineral aggregates (silica nanoparticle aggregates or SNAs) on the behavior of oil (octane)-water emulsions prepared using sodium bis(2-ethylhexyl) sulfosuccinate (DOSS). Experiments were conducted at different SNA hydrophobicities in deionized and synthetic seawater (SSW), and at 0.5mM and 2.5mM DOSS. SNAs were characterized by thermogravimetric analysis (TGA) and dynamic light scattering (DLS), and the emulsions were examined by optical and cryogenic scanning electron microscopy. In deionized water, oil-in-water emulsions were formed with DOSS and the SNAs did not adhere to the droplets or alter emulsion behavior. In SSW, water-in-oil emulsions were formed with DOSS and SNA-DOSS binding through cation bridging led to phase inversion to oil-in-water emulsions. Droplet oil-mineral aggregates (OMAs) were observed for hydrophilic SNAs, while hydrophobic SNAs yielded quickly sedimenting agglomerated OMAs.

  10. DTE Energy Technologies With Detroit Edison Co. and Kinectrics Inc.: Distributed Resources Aggregation Modeling and Field Configuration Testing

    SciTech Connect

    Not Available

    2003-10-01

    Summarizes the work of DTE Energy Technologies, Detroit Edison, and Kinectrics, under contract to DOE's Distribution and Interconnection R&D, to develop distributed resources aggregation modeling and field configuration testing.

  11. Concrete modelling for expertise of structures affected by alkali aggregate reaction

    SciTech Connect

    Grimal, E.; Sellier, A.; Multon, S.; Le Pape, Y.; Bourdarot, E.

    2010-04-15

    Alkali aggregate reaction (AAR) affects numerous civil engineering structures and causes irreversible expansion and cracking. In order to control the safety level and the maintenance cost of its hydraulic dams, Electricite de France (EDF) must reach better comprehension and better prediction of the expansion phenomena. For this purpose, EDF has developed a numerical model based on the finite element method in order to assess the mechanical behaviour of damaged structures. The model takes the following phenomena into account: concrete creep, the stress induced by the formation of AAR gel and the mechanical damage. A rheological model was developed to assess the coupling between the different phenomena (creep, AAR and anisotropic damage). Experimental results were used to test the model. The results show the capability of the model to predict the experimental behaviour of beams subjected to AAR. In order to obtain such prediction, it is necessary to take all the phenomena occurring in the concrete into consideration.

  12. 75 FR 43944 - Membership of the Defense Logistics Agency (DLA) Senior Executive Service (SES) Performance...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-27

    ... Defense Logistics Agency Membership of the Defense Logistics Agency (DLA) Senior Executive Service (SES... 16, 2010. ADDRESSES: Defense Logistics Agency, 8725 John J. Kingman Road, Suite 2533, Fort Belvoir... Resources (J-14), Defense Logistics Agency, (703) 767-6447. SUPPLEMENTARY INFORMATION: In accordance with...

  13. 78 FR 64493 - Juneau Hydropower, Inc.; Notice of Subsequent Draft License Application (DLA) and Draft...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-29

    ... Energy Regulatory Commission Juneau Hydropower, Inc.; Notice of Subsequent Draft License Application (DLA..., 2013. d. Applicant: Juneau Hydropower, Inc. e. Name of Project: Sweetheart Lake Hydroelectric Project.... Applicant Contact: Duff Mitchell, Business Manager, Juneau Hydropower, Inc., P.O. Box 22775, Juneau,...

  14. The color excess of quasars with intervening DLA systems. Analysis of the SDSS data release five

    NASA Astrophysics Data System (ADS)

    Vladilo, G.; Prochaska, J. X.; Wolfe, A. M.

    2008-02-01

    We analyzed the spectroscopic and photometric database of the 5th data release of the Sloan Digital Sky Survey (SDSS) to search for evidence of the quasar reddening produced by dust embedded in intervening damped Ly α (DLA) systems. From a list of 5164 quasars in the interval of emission redshift 2.25 ≤ ze ≤ 3.5 and SDSS spectra with signal-to-noise ratio SNR ⪆ 4, we built up an “absorption sample” of 248 QSOs with a single DLA system in the interval of absorption redshift 2.2 < za ≤ 3.5 and a “pool” of 1959 control QSOs without DLA systems or strong metal systems. For each QSO of the absorption sample we extracted from the pool a subset of control QSOs that are closest in redshift and magnitude. The mean color of this subset was used as a zero point to measure the “deviation from the mean color” of individual DLA-QSOs, Δ_i. The colors were measured using “BEST” ugriz SDSS imaging data. The mean color excess of the absorption sample, < E >, was estimated by averaging the individual color deviations Δ_i. We find < E(r-z) > = 27 (± 9)×10-3 mag and < E(g-z) > = 54 (± 12)×10-3 mag. These values are representative of the reddening of DLA systems at za ≈ 2.7 in SDSS QSOs with limiting magnitude r ≃ 20.2. The detection of the mean reddening is confirmed by several statistical tests. Analysis of the results suggests an origin of the reddening in dust embedded in the DLA systems, with an SMC-type extinction curve. By converting the reddening into rest-frame extinction, we derive a mean dust-to-gas ratio < AV / N(H I) > ≈ 2 to 4×10-23 mag cm^2. This value is ≃-1.25 dex lower than the mean dust-to-gas ratio of the Milky Way, in line with the lower level of metallicity in the present DLA sample. Full Tables [see full textsee full text] and [see full textsee full text] are only available in electronic form at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsweb.u-strasbg.fr/cgi-bin/qcat?J/A+A/478/701

  15. A-DROP: A predictive model for the formation of oil particle aggregates (OPAs)

    USGS Publications Warehouse

    Zhao, Lin; Boufadel, Michel C.; Geng, Xiaolong; Lee, Kenneth; King, Thomas; Robinson, Brian; Fitzpatrick, Faith A.

    2016-01-01

    Oil–particle interactions play a major role in removal of free oil from the water column. We present a new conceptual–numerical model, A-DROP, to predict oil amount trapped in oil–particle aggregates. A new conceptual formulation of oil–particle coagulation efficiency is introduced to account for the effects of oil stabilization by particles, particle hydrophobicity, and oil–particle size ratio on OPA formation. A-DROP was able to closely reproduce the oil trapping efficiency reported in experimental studies. The model was then used to simulate the OPA formation in a typical nearshore environment. Modeling results indicate that the increase of particle concentration in the swash zone would speed up the oil–particle interaction process; but the oil amount trapped in OPAs did not correspond to the increase of particle concentration. The developed A-DROP model could become an important tool in understanding the natural removal of oil and developing oil spill countermeasures by means of oil–particle aggregation.

  16. Thermodynamical model of mixed aggregation of ligands with caffeine in aqueous solution. Part II.

    PubMed

    Zdunek, M; Piosik, J; Kapuscinski, J

    2000-02-14

    A statistical-thermodynamical model of mixed association in which one component's self-association is unlimited while the second component does not self-aggregate is described. The model was tested with 4',6-diamidino-2-phenyl-indole-dihydrochloride (DAPI) and ethidium bromide (EB) using light absorption spectroscopy and calorimetry. The system is controlled by two parameters, which represent self-aggregation 'neighborhood' association constant KCC and mixed 'neighborhood' association constant KAC. Calculated, using this model, KAC = 58.2 +/- 1 M-1, KAC = 64.6 +/- 2 M-1 for DAPI and EB, respectively, are in good agreement with known values of stacking interactions. The titration microcalorimetric measurement of DAPI-CAF interaction delta H = -11.1 +/- 0.4 kcal/mol is also consistent with this type of reaction. The structures of the stacking complexes were also confirmed by semi-empirical molecular modeling in the presence of water. The data indicate that CAF forms stacking complexes with DAPI and EB, thus effectively lowering the concentration of the free ligands in the solution, and therefore, CAF can be used to modulate aromatic compound activity.

  17. Bayesian model aggregation for ensemble-based estimates of protein pKa values

    SciTech Connect

    Gosink, Luke J.; Hogan, Emilie A.; Pulsipher, Trenton C.; Baker, Nathan A.

    2014-03-01

    This paper investigates an ensemble-based technique called Bayesian Model Averaging (BMA) to improve the performance of protein amino acid p$K_a$ predictions. Structure-based p$K_a$ calculations play an important role in the mechanistic interpretation of protein structure and are also used to determine a wide range of protein properties. A diverse set of methods currently exist for p$K_a$ prediction, ranging from empirical statistical models to {\\it ab initio} quantum mechanical approaches. However, each of these methods are based on a set of assumptions that have inherent bias and sensitivities that can effect a model's accuracy and generalizability for p$K_a$ prediction in complicated biomolecular systems. We use BMA to combine eleven diverse prediction methods that each estimate pKa values of amino acids in staphylococcal nuclease. These methods are based on work conducted for the pKa Cooperative and the pKa measurements are based on experimental work conducted by the Garc{\\'i}a-Moreno lab. Our study demonstrates that the aggregated estimate obtained from BMA outperforms all individual prediction methods in our cross-validation study with improvements from 40-70\\% over other method classes. This work illustrates a new possible mechanism for improving the accuracy of p$K_a$ prediction and lays the foundation for future work on aggregate models that balance computational cost with prediction accuracy.

  18. Viscoplastic Modeling of MgSiO3 Perovskite and Periclase Aggregates

    NASA Astrophysics Data System (ADS)

    Zepeda-Alarcon, E.; Lebensohn, R.; Kaercher, P. M.; Wenk, H. R.

    2014-12-01

    Plasticity and the subsequent development of crystallographic preferred orientation (CPO) in mantle minerals is important for understanding dynamic processes in the mantle, e.g. the interpretation of seismic anisotropy as a result of CPO developed by mantle convection. Furthermore, plastic behavior of multi-phase polycrystals is still not well understood. A polycrystal plasticity code (VPFFT) with an n-site approach is used to model the development of CPO in a hard magnesium silicate perovskite and a soft periclase aggregate under an applied strain, given certain combinations of active slip systems. Special attention is put to the influence of microstructure and phase hardness contrast on CPO. Preliminary results show that in the case where periclase is surrounding the hard perovskite phase, the deformation concentrates on the soft periclase but the perovskite still develops an appreciable and amount of CPO, in agreement with experimental data. These polycrystal plasticity models are compared to diamond anvil cell experiments in the radial geometry (rDAC) where CPO is recorded as azimuthal variations of intensity along Debye rings in a diffraction pattern. Two different starting materials, enstatite+periclase and olivine, are used for the nucleation of the perovskite and periclase aggregate, microstructures are expected to differ between the two starting materials due to nucleation differences. Preliminary results show that perovskite develops a (001) texture and periclase a stronger (001) maxima. The comparison of VPFFT results with rDAC experiments gives and idea of the relative activities of the various slip systems in this aggregate and help to constrain seismic and geophysical modeling of the lower mantle.

  19. Electrostatically-controlled protein adsorption onto lipid bilayer: modeling adsorbate aggregation behavior.

    PubMed

    Trusova, Valeriya M; Gorbenko, Galyna P

    2008-03-01

    Using adsorption models based on scaled particle (SPT) and double layer theories the electrostatically-controlled protein adsorption onto membrane surface has been simulated for non-associating and self-associating ligands. The binding isotherms of monomeric and oligomeric protein species have been calculated over a range of variable parameters including lipid and protein concentrations, protein and membrane charges, pH and ionic strength. Adsorption behavior of monomers appeared to be the most sensitive to the changes in the protein aggregation state. The hallmarks of the protein oligomerization are identified. The practical guides for optimal design of binding experiments focused on obtaining proofs of protein self-association are suggested.

  20. Modeling and Control of Aggregated Air Conditioning Loads Under Realistic Conditions

    SciTech Connect

    Chang, Chin-Yao; Zhang, Wei; Lian, Jianming; Kalsi, Karanjit

    2013-02-24

    Demand-side control is playing an increasingly important role in smart grid control strategies. Modeling the dynamical behavior of a large population of appliances is especially important to evaluate the effectiveness of various load control strategies. In this paper, a high accuracy aggregated model is first developed for a population of HVAC units. The model efficiently includes statistical information of the population, systematically deals with heterogeneity, and accounts for a second-order effect necessary to accurately capture the transient dynamics in the collective response. Furthermore, the model takes into account the lockout effect of the compressor in order to represent the dynamics of the system under control more accurately. Then, a novel closed loop load control strategy is designed to track a desired demand curve and to ensure a stable and smooth response.

  1. Computer Modeling of Electrostatic Aggregation of Granular Materials in Planetary and Astrophysical Settings

    NASA Technical Reports Server (NTRS)

    Marshall, J.; Sauke, T.

    1999-01-01

    Electrostatic forces strongly influence the behavior of granular materials in both dispersed (cloud) systems and semi-packed systems. These forces can cause aggregation or dispersion of particles and are important in a variety of astrophysical and planetary settings. There are also many industrial and commercial settings where granular matter and electrostatics become partners for both good and bad. This partnership is important for human exploration on Mars where dust adheres to suits, machines, and habitats. Long-range Coulombic (electrostatic) forces, as opposed to contact-induced dipoles and van der Waals attractions, are generally regarded as resulting from net charge. We have proposed that in addition to net charge interactions, randomly distributed charge carriers on grains will result in a dipole moment regardless of any net charge. If grains are unconfined, or fluidized, they will rotate so that the dipole always induces attraction between grains. Aggregates are readily formed, and Coulombic polarity resulting from the dipole produces end-to-end stacking of grains to form filamentary aggregates. This has been demonstrated in USML experiments on Space Shuttle where microgravity facilitated the unmasking of static forces. It has also been demonstrated in a computer model using grains with charge carriers of both sign. Model results very closely resembled micro-g results with actual sand grains. Further computer modeling of the aggregation process has been conducted to improve our understanding of the aggregation process, and to provide a predictive tool for microgravity experiments slated for Space Station. These experiments will attempt to prove the dipole concept as outlined above. We have considerably enhanced the original computer model: refinements to the algorithm have improved the fidelity of grain behavior during grain contact, special attention has been paid to simulation time steps to enable establishment of a meaningful, quantitative time axis

  2. Computer Modeling of Electrostatic Aggregation of Granular Materials in Planetary and Astrophysical Settings

    NASA Astrophysics Data System (ADS)

    Marshall, J.; Sauke, T.

    1999-09-01

    Electrostatic forces strongly influence the behavior of granular materials in both dispersed (cloud) systems and semi-packed systems. These forces can cause aggregation or dispersion of particles and are important in a variety of astrophysical and planetary settings. There are also many industrial and commercial settings where granular matter and electrostatics become partners for both good and bad. This partnership is important for human exploration on Mars where dust adheres to suits, machines, and habitats. Long-range Coulombic (electrostatic) forces, as opposed to contact-induced dipoles and van der Waals attractions, are generally regarded as resulting from net charge. We have proposed that in addition to net charge interactions, randomly distributed charge carriers on grains will result in a dipole moment regardless of any net charge. If grains are unconfined, or fluidized, they will rotate so that the dipole always induces attraction between grains. Aggregates are readily formed, and Coulombic polarity resulting from the dipole produces end-to-end stacking of grains to form filamentary aggregates. This has been demonstrated in USML experiments on Space Shuttle where microgravity facilitated the unmasking of static forces. It has also been demonstrated in a computer model using grains with charge carriers of both sign. Model results very closely resembled micro-g results with actual sand grains. Further computer modeling of the aggregation process has been conducted to improve our understanding of the aggregation process, and to provide a predictive tool for microgravity experiments slated for Space Station. These experiments will attempt to prove the dipole concept as outlined above. We have considerably enhanced the original computer model: refinements to the algorithm have improved the fidelity of grain behavior during grain contact, special attention has been paid to simulation time steps to enable establishment of a meaningful, quantitative time axis

  3. Effect of mutation on aggregation propensity in homology model structures of syntaxin-3 from Homo sapiens.

    PubMed

    Maheshwari, Amutha Selvaraj; Rajesh, Durairaj; Padmanabhan, Parasuraman; Archunan, Govindaraju

    2014-10-01

    Perception of molecular mechanism would provide potent additional knowledge on mammalian membrane proteins involved in causing diseases. In human, syntaxin-3 (STX3) is a significant apical targeting protein in the epithelial membrane and in exocytosis process; it also acts as a vesicle transporter by cellular receptor in neutrophils, which is crucial for protein trafficking event. Structurally, syntaxin-3 has hydrophobic domain at carboxyl terminus that directs itself to intra-cellular compartments. In addition, the experimental structure of STX3 is not available and no mutational study has been carried out with natural variants of proteins. Moreover, there is no evidence so far for the natural variant Val286 of STX3 causing any diseases. Hence, in the present study, analyses of residue-based properties of the homology model STX3 were carried out along with mutations at carboxyl terminus of STX3 by implementing protein engineering and in silico approaches. The model structure of STX3 was constructed adopting Modeller v9.11 and the aggregation propensity was analyzed with BioLuminate tool. The results showed that there was reduction in aggregation propensity with point mutation at Val286, instead of Ile, resulting into increasing the structural stability of STX3. In conclusion, the Ccap exposed residue would be a suitable position for further mutational studies, particularly with Val286 of STX3 in human. This approach could gainfully be applied to STX3 for efficient drug designing which would be a valuable target in the cancer treatment.

  4. A thermodynamic and kinetic model for paste–aggregate interactions and the alkali–silica reaction

    SciTech Connect

    Guthrie, George D. Carey, J. William

    2015-10-15

    A new conceptual model is developed for ASR formation based on geochemical principles tied to aqueous speciation, silica solubility, kinetically controlled mineral dissolution, and diffusion. ASR development is driven largely by pH and silica gradients that establish geochemical microenvironments between paste and aggregate, with gradients the strongest within the aggregate adjacent to the paste boundary (i.e., where ASR initially forms). Super-saturation of magadiite and okenite (crystalline ASR surrogates) occurs in the zone defined by gradients in pH, dissolved silica, Na{sup +}, and Ca{sup 2} {sup +}. This model provides a thermodynamic rather than kinetic explanation of why quartz generally behaves differently from amorphous silica: quartz solubility does not produce sufficiently high concentrations of H{sub 4}SiO{sub 4} to super-saturate magadiite, whereas amorphous silica does. The model also explains why pozzolans do not generate ASR: their fine-grained character precludes formation of chemical gradients. Finally, these gradients have interesting implications beyond the development of ASR, creating unique biogeochemical environments.

  5. Computational modeling of chemotactic signaling and aggregation of microglia around implantation site during deep brain stimulation

    NASA Astrophysics Data System (ADS)

    Silchenko, A. N.; Tass, P. A.

    2013-10-01

    It is well established that prolonged electrical stimulation of brain tissue causes massive release of ATP in the extracellular space. The released ATP and the products of its hydrolysis, such as ADP and adenosine, become the main elements mediating chemotactic sensitivity and motility of microglial cells via subsequent activation of P2Y2,12 as well as A3A and A2A adenosine receptors. The size of the sheath around the electrode formed by the microglial cells is an important criterion for the optimization of the parameters of electrical current delivered to brain tissue. Here, we study a purinergic signaling pathway underlying the chemotactic motion of microglia towards the implanted electrode during deep brain stimulation. We present a computational model describing formation of a stable aggregate around the implantation site due to the joint chemo-attractive action of ATP and ADP together with a mixed influence of extracellular adenosine. The model was built in accordance with the classical Keller-Segel approach and includes an equation for the cells' density as well as equations describing the hydrolysis of extracellular ATP via successive reaction steps ATP →ADP →AMP →adenosine. The results of our modeling allowed us to reveal the dependence of the width of the encapsulating layer around the electrode on the amount of ATP released due to permanent electrical stimulation. The dependences of the aggregates' size on the parameter governing the nonlinearity of interaction between extracellular adenosine and adenosine receptors are also analyzed.

  6. Reaction limited aggregation in surfactant-mediated epitaxy

    NASA Astrophysics Data System (ADS)

    Wu, Jing; Liu, Bang-Gui; Zhang, Zhenyu; Wang, E. G.

    2000-05-01

    A theoretical model for reaction limited aggregation (RLA) is introduced to study the effect of a monolayer of surfactant on the formation of two-dimensional islands in heteroepitaxial and homoepitaxial growth. In this model the basic atomic processes are considered as follows. A stable island consists of the adatoms that have exchanged positions with the surfactant atoms beneath them. Movable active adatoms may (a) diffuse on the surfactant terrace, (b) exchange positions with the surfactant atoms beneath them and become island seeds (seed exchange), or (c) stick to stable islands and become stuck but still active adatoms. The rate-limiting step for the formation of a stable island is the seed exchange. Furthermore, a stuck but still active adatom must overcome a sizable potential-energy barrier to exchange positions with the surfactant atom beneath it and become a member of the stable island (aided exchange). The seed exchange process can occur with an adatom or collectively with an addimer. In the case of dimer exchange, the diffusing adatoms on the surfactant terrace can meet and (after exchanging) form stable dimers, which can then become island seeds. Systematic kinetic Monte Carlo simulations and rate-equation analysis of the model are carried out. The key finding of these simulations is that a counterintuitive fractal-to-compact island shape transition can be induced either by increasing deposition flux or by decreasing growth temperature. This major qualitative conclusion is valid for both the monomer and the dimer seed exchanges and for two different substrate lattices (square and triangular, respectively), although there are some quantitative differences in the flux and temperature dependence of the island density. The shape transition observed is contrary to the prediction of the classic diffusion-limited aggregation (DLA) theory, but in excellent qualitative agreement with recent experiments. In rationalizing the main finding, it is crucial to realize

  7. Modelling cell movement, cell differentiation, cell sorting and proportion regulation in Dictyostelium discoideum aggregations.

    PubMed

    Pineda, M; Weijer, C J; Eftimie, R

    2015-04-07

    Understanding the mechanisms that control tissue morphogenesis and homeostasis is a central goal not only in developmental biology but also has great relevance for our understanding of various diseases, including cancer. A model organism that is widely used to study the control of tissue morphogenesis and proportioning is the Dictyostelium discoideum. While there are mathematical models describing the role of chemotactic cell motility in the Dictyostelium assembly and morphogenesis of multicellular tissues, as well as models addressing possible mechanisms of proportion regulation, there are no models incorporating both these key aspects of development. In this paper, we introduce a 1D hyperbolic model to investigate the role of two morphogens, DIF and cAMP, on cell movement, cell sorting, cell-type differentiation and proportioning in Dictyostelium discoideum. First, we use the non-spatial version of the model to study cell-type transdifferentiation. We perform a steady-state analysis of it and show that, depending on the shape of the differentiation rate functions, multiple steady-state solutions may occur. Then we incorporate spatial dynamics into the model, and investigate the transdifferentiation and spatial positioning of cells inside the newly formed structures, following the removal of prestalk or prespore regions of a Dictyostelium slug. We show that in isolated prespore fragments, a tipped mound-like aggregate can be formed after a transdifferentiation from prespore to prestalk cells and following the sorting of prestalk cells to the centre of the aggregate. For isolated prestalk fragments, we show the formation of a slug-like structure containing the usual anterior-posterior pattern of prestalk and prespore cells.

  8. Adjusting particle-size distributions to account for aggregation in tephra-deposit model forecasts

    USGS Publications Warehouse

    Mastin, Larry G.; Van Eaton, Alexa; Durant, A.J.

    2016-01-01

    Volcanic ash transport and dispersion (VATD) models are used to forecast tephra deposition during volcanic eruptions. Model accuracy is limited by the fact that fine-ash aggregates (clumps into clusters), thus altering patterns of deposition. In most models this is accounted for by ad hoc changes to model input, representing fine ash as aggregates with density ρagg, and a log-normal size distribution with median μagg and standard deviation σagg. Optimal values may vary between eruptions. To test the variance, we used the Ash3d tephra model to simulate four deposits: 18 May 1980 Mount St. Helens; 16–17 September 1992 Crater Peak (Mount Spurr); 17 June 1996 Ruapehu; and 23 March 2009 Mount Redoubt. In 192 simulations, we systematically varied μagg and σagg, holding ρagg constant at 600 kg m−3. We evaluated the fit using three indices that compare modeled versus measured (1) mass load at sample locations; (2) mass load versus distance along the dispersal axis; and (3) isomass area. For all deposits, under these inputs, the best-fit value of μagg ranged narrowly between  ∼  2.3 and 2.7φ (0.20–0.15 mm), despite large variations in erupted mass (0.25–50 Tg), plume height (8.5–25 km), mass fraction of fine ( <  0.063 mm) ash (3–59 %), atmospheric temperature, and water content between these eruptions. This close agreement suggests that aggregation may be treated as a discrete process that is insensitive to eruptive style or magnitude. This result offers the potential for a simple, computationally efficient parameterization scheme for use in operational model forecasts. Further research may indicate whether this narrow range also reflects physical constraints on processes in the evolving cloud.

  9. Analysis of the Route-Based Aggregate Model for Strategic Air Traffic Control

    NASA Astrophysics Data System (ADS)

    De Los Santos Bernad, Victor

    Because of the vital importance of the National Airspace System (NAS) and its diagnosed growth over the next years, the planning and prediction at a strategic phase of the Traffic Flow Management (TFM) proves to be a difficult task but a useful tool to reduce the airspace congestion. Research has led to the creation of several models in order to address this challenge. Because of the complexity of the problem, the Eulerian (aggregate) approach may be the best to reduce the dimension and complexity of the problem, whilst maintaining accuracy. This study analyzes one of the latest aggregate models created, the Route-Based Aggregate Model (RBAM), and compares it to the Large-Capacity Cell Transmission Model (CTM(L)) and the Link Transmission Model (LTM). These three models share some similarities such as the non-existence of diverging nodes or, in the case of the CTM(L), the condition of submitting all the airplanes in a cell to the next cell after one time-stepBut there are also big differences which make them different enough to coexist. For example, the RBAM can be used without the need of historical data in order to model the NAS, only the information of the upcoming flight plans. Also, the RBAM is designed to base its controls from a ground perspective, allowing ground rerouting and ground delay. An explanation on how to implement the RBAM in Matlab can be found in this project, explaining the peculiarities of the translation of the cost function constraints into a Linear Programming (LP) problem, with several examples that show how the solution to the LP problem distributes the delays between ground delays and ground reroutings. Because the cost of a ground rerouting is different from the cost of a ground delay because of the extra fuel expense that the rerouting may cause (assuming always that the original route is shorter), a proper weighting of both controls is found, considering different variables such as the cost of the fuel or the cost of overtime parking

  10. Synthesis and Aggregation Behavior of Chiral Naphthoquinoline Petroporphyrin Asphaltene Model Compounds.

    PubMed

    Schulze, Matthias; Scherer, Alexander; Hampel, Frank; Stryker, Jeffrey M; Tykwinski, Rik R

    2016-03-01

    The synthesis of structurally relevant compounds that model the chemical behavior and supramolecular aggregation of the asphaltenes, the most polar and metal-rich fraction of heavy petroleum, has been extended to include fusions of important petroleum biomarkers. The synthetic protocol features a multicomponent reaction to form a dyad composed of a fused steroidal naphthoquinoline, followed by a pyrrole cyclocondensation reaction to incorporate the dyad into a chiral triad containing a Ni(II) -porphyrin substituent. This synthetic protocol has been used to prepare large molecules that represent both "continental" and "archipelago" models of asphaltene composition. The steroid-naphthoquinoline-porphyrin triads have been studied by UV/Vis and circular dichroism (CD) spectroscopies, and the results suggest that the naphthoquinoline core, a tetrahydro[4]helicene, adopts a helical conformation, producing a CD signal electronically related to the characteristic Soret absorption band of the porphyrin subunit. Finally, supramolecular aspects of asphaltene aggregation have been examined on a molecular level through analysis of axial coordination of pyridine to the Ni-porphyrin. The relative affinity of pyridine for binding to the Ni center of the porphyrin is evaluated by comparing binding propensities in a series of sterically differentiated substituted porphyrins.

  11. Influence of hydro-meteorological data spatial aggregation on streamflow modelling

    NASA Astrophysics Data System (ADS)

    Girons Lopez, Marc; Seibert, Jan

    2016-10-01

    Data availability is important for virtually any purpose in hydrology. While some parts of the world continue to be under-monitored, other areas are experiencing an increased availability of high-resolution data. The use of the highest available resolution has always been preferred and many efforts have been made to maximize the information content of data and thus improve its predictive power and reduce the costs of maintenance of hydrometric sensor networks. In the light of ever-increasing data resolution, however, it is important to assess the added value of using the highest resolution available. In this study we present an assessment of the relative importance of hydro-meteorological data resolution for hydrological modelling. We used a case study with high-resolution data availability to investigate the influence of using models calibrated with different levels of spatially aggregated meteorological input data to estimate streamflow for different periods and at different locations. We found site specific variations, but model parameterizations calibrated using sub-catchment specific meteorological input data tended to produce better streamflow estimates, with model efficiency values being up to 0.35 efficiency units higher than those calibrated with catchment averaged meteorological data. We also found that basin characteristics other than catchment area have little effect on the performance of model parameterizations applied in different locations than the calibration site. Finally, we found that using an increased number of discharge data locations has a larger impact on model calibration efficiency than using spatially specific meteorological data. The results of this study contribute to improve the knowledge on assessing data needs for water management in terms of adequate data type and level of spatial aggregation.

  12. Modelling and Laboratory Studies on the Adhesion Fatigue Performance for Thin-Film Asphalt and Aggregate System

    PubMed Central

    Wang, Dongsheng; Feng, Decheng

    2014-01-01

    Adhesion between asphalt and aggregate plays an important role in the performance of asphalt mixtures. A low-frequency adhesion fatigue test was proposed in this paper to study the effect of environment on the asphalt-aggregate adhesion system. The stress-based fatigue model had been utilized to describe the fatigue behavior of thin-film asphalt and aggregate system. The factors influencing the adhesion fatigue performance were also investigated. Experiment results show that asphalt has more important effect on the adhesion performance comparing with aggregate. Basalt, which is regarded as hydrophobic aggregates with low silica content, has better adhesion performance to asphalt binder when compared with granite. The effects of aging on the adhesion fatigue performance are different for PG64-22 and rubber asphalt. Long-term aging is found to reduce the adhesion fatigue lives for rubber asphalt and aggregate system, while the effect of long-term aging for aggregate and PG64-22 binder system is positive. Generally the increased stress amplitude and test temperature could induce greater damage and lead to less fatigue lives for adhesion test system. PMID:25054187

  13. Modelling and laboratory studies on the adhesion fatigue performance for thin-film asphalt and aggregate system.

    PubMed

    Wang, Dongsheng; Yi, Junyan; Feng, Decheng

    2014-01-01

    Adhesion between asphalt and aggregate plays an important role in the performance of asphalt mixtures. A low-frequency adhesion fatigue test was proposed in this paper to study the effect of environment on the asphalt-aggregate adhesion system. The stress-based fatigue model had been utilized to describe the fatigue behavior of thin-film asphalt and aggregate system. The factors influencing the adhesion fatigue performance were also investigated. Experiment results show that asphalt has more important effect on the adhesion performance comparing with aggregate. Basalt, which is regarded as hydrophobic aggregates with low silica content, has better adhesion performance to asphalt binder when compared with granite. The effects of aging on the adhesion fatigue performance are different for PG64-22 and rubber asphalt. Long-term aging is found to reduce the adhesion fatigue lives for rubber asphalt and aggregate system, while the effect of long-term aging for aggregate and PG64-22 binder system is positive. Generally the increased stress amplitude and test temperature could induce greater damage and lead to less fatigue lives for adhesion test system.

  14. Velocity-metallicity correlation for high-z DLA galaxies: evidence of a mass-metallicity relation?

    NASA Astrophysics Data System (ADS)

    Ledoux, C.; Petitjean, P.; Fynbo, J. P. U.; Møller, P.; Srianand, R.

    2006-10-01

    We used our database of VLT-UVES quasar spectra to build up a sample of 70 Damped Lyman-α (DLA) or strong sub-DLA systems with total neutral hydrogen column densities of log N(H i)⪆ 20 and redshifts in the range 1.7DLA metallicity and line profile velocity width, which is detected at the 6.1σ significance level. This confirms the trend previously observed in a much smaller sample by Wolfe & Prochaska (1998). The best-fit linear relation is [X/H]=1.55(± 0.12)logΔ V -4.33(± 0.23), with Δ V expressed in km s-1. The slope of the DLA velocity-metallicity relation is the same within uncertainties between the higher (z_abs>2.43) and the lower (z_abs≤ 2.43) redshift halves of our sample. However, the two populations of systems are statistically different. There is a strong redshift evolution in the sense that the median metallicity and median velocity width increase with decreasing redshift. We argue that the existence of a DLA velocity-metallicity correlation, over more than a factor of 100 spread in metallicity, is probably the consequence of an underlying mass-metallicity relation for the galaxies responsible for DLA absorption lines. Assuming a simple linear scaling of the galaxy luminosity with the mass of the dark-matter halo, we find that the slope of the DLA velocity-metallicity relation is consistent with that of the luminosity-metallicity relation derived for local galaxies. If the galaxy dynamical mass is indeed the dominant factor setting up the observed DLA velocity-metallicity correlation, then the DLA systems exhibiting the lowest metallicities among the DLA population should, on average, be associated with galaxies of lower masses (e.g., gas-rich dwarf galaxies). In turn

  15. Fractal structure and the dynamics of aggregation of synthetic melanin in low pH aqueous solutions

    SciTech Connect

    Huang, J.S.; Sung, J.; Eisner, M.; Moss, S.C.; Gallas, J.

    1989-01-01

    We have used static and dynamic light scattering to study the dynamics of aggregation of synthetic melanin, an amorphous biopolymeric substance, in low pH aqueous solution. We have found that, depending on the final pH value of the solutions, there existed two regimes of the aggregation kinetics, one corresponding to diffusion limited aggregation (DLA), and the other corresponding to reaction limited aggregation (RLA). The precipitates formed in these two regimes can be characterized by fractal structures. We have found fractal dimensions of d/sub f/ = 1.8 for the DLA clusters and d/sub f/ = 2.2 for the RLA clusters. These results agree well with the proposed limits of the fractal dimensions of the gold aggregates formed in aqueous solutions by Weitz et al.

  16. The fractal structure and the dynamics of aggregation of synthetic melanin in low pH aqueous solutions

    NASA Astrophysics Data System (ADS)

    Huang, J. S.; Sung, J.; Eisner, M.; Moss, S. C.; Gallas, J.

    1989-01-01

    We have used static and dynamic light scattering to study the dynamics of aggregation of synthetic melanin, an amorphous biopolymeric substance, in low pH aqueous solution. We have found that, depending on the final pH value of the solutions, there existed two regimes of the aggregation kinetics, one corresponding to diffusion limited aggregation (DLA), and the other corresponding to reaction limited aggregation (RLA). The precipitates formed in these two regimes can be characterized by fractal structures. We have found fractal dimensions of df =1.8 for the DLA clusters and df =2.2 for the RLA clusters. These results agree well with the proposed limits of the fractal dimensions of the gold aggregates formed in aqueous solutions by Weitz et al.

  17. Thermodynamics of Protein Aggregation

    NASA Astrophysics Data System (ADS)

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

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

  18. Changes in speed distribution: Applying aggregated safety effect models to individual vehicle speeds.

    PubMed

    Vadeby, Anna; Forsman, Åsa

    2017-03-31

    This study investigated the effect of applying two aggregated models (the Power model and the Exponential model) to individual vehicle speeds instead of mean speeds. This is of particular interest when the measure introduced affects different parts of the speed distribution differently. The aim was to examine how the estimated overall risk was affected when assuming the models are valid on an individual vehicle level. Speed data from two applications of speed measurements were used in the study: an evaluation of movable speed cameras and a national evaluation of new speed limits in Sweden. The results showed that when applied on individual vehicle speed level compared with aggregated level, there was essentially no difference between these for the Power model in the case of injury accidents. However, for fatalities the difference was greater, especially for roads with new cameras where those driving fastest reduced their speed the most. For the case with new speed limits, the individual approach estimated a somewhat smaller effect, reflecting that changes in the 15th percentile (P15) were somewhat larger than changes in P85 in this case. For the Exponential model there was also a clear, although small, difference between applying the model to mean speed changes and individual vehicle speed changes when speed cameras were used. This applied both for injury accidents and fatalities. There were also larger effects for the Exponential model than for the Power model, especially for injury accidents. In conclusion, applying the Power or Exponential model to individual vehicle speeds is an alternative that provides reasonable results in relation to the original Power and Exponential models, but more research is needed to clarify the shape of the individual risk curve. It is not surprising that the impact on severe traffic crashes was larger in situations where those driving fastest reduced their speed the most. Further investigations on use of the Power and/or the

  19. Aggregated Modeling of Thermostatic Loads in Demand Response: A Systems and Control Perspective

    SciTech Connect

    Kalsi, Karanjit; Chassin, Forrest S.; Chassin, David P.

    2011-12-12

    Demand response is playing an increasingly important role in smart grid research and technologies being examined in recently undertaken demonstration projects. The behavior of load as it is affected by various load control strategies is important to understanding the degree to which different classes of end-use load can contribute to demand response programs at various times. This paper focuses on developing aggregated models for a homogeneous population of thermostatically controlled loads. The different types of loads considered in this paper include, but are not limited to, water heaters and HVAC units. The effects of demand response and user over-ride on the load population dynamics are investigated. The controllability of the developed lumped models is validated which forms the basis for designing different control strategies.

  20. Serotonergic signalling suppresses ataxin 3 aggregation and neurotoxicity in animal models of Machado-Joseph disease.

    PubMed

    Teixeira-Castro, Andreia; Jalles, Ana; Esteves, Sofia; Kang, Soosung; da Silva Santos, Liliana; Silva-Fernandes, Anabela; Neto, Mário F; Brielmann, Renée M; Bessa, Carlos; Duarte-Silva, Sara; Miranda, Adriana; Oliveira, Stéphanie; Neves-Carvalho, Andreia; Bessa, João; Summavielle, Teresa; Silverman, Richard B; Oliveira, Pedro; Morimoto, Richard I; Maciel, Patrícia

    2015-11-01

    Polyglutamine diseases are a class of dominantly inherited neurodegenerative disorders for which there is no effective treatment. Here we provide evidence that activation of serotonergic signalling is beneficial in animal models of Machado-Joseph disease. We identified citalopram, a selective serotonin reuptake inhibitor, in a small molecule screen of FDA-approved drugs that rescued neuronal dysfunction and reduced aggregation using a Caenorhabditis elegans model of mutant ataxin 3-induced neurotoxicity. MOD-5, the C. elegans orthologue of the serotonin transporter and cellular target of citalopram, and the serotonin receptors SER-1 and SER-4 were strong genetic modifiers of ataxin 3 neurotoxicity and necessary for therapeutic efficacy. Moreover, chronic treatment of CMVMJD135 mice with citalopram significantly reduced ataxin 3 neuronal inclusions and astrogliosis, rescued diminished body weight and strikingly ameliorated motor symptoms. These results suggest that small molecule modulation of serotonergic signalling represents a promising therapeutic target for Machado-Joseph disease.

  1. Serotonergic signalling suppresses ataxin 3 aggregation and neurotoxicity in animal models of Machado-Joseph disease

    PubMed Central

    Teixeira-Castro, Andreia; Kang, Soosung; da Silva Santos, Liliana; Silva-Fernandes, Anabela; Neto, Mário F.; Brielmann, Renée M.; Bessa, Carlos; Duarte-Silva, Sara; Miranda, Adriana; Oliveira, Stéphanie; Neves-Carvalho, Andreia; Bessa, João; Summavielle, Teresa; Silverman, Richard B.; Oliveira, Pedro; Morimoto, Richard I.

    2015-01-01

    Polyglutamine diseases are a class of dominantly inherited neurodegenerative disorders for which there is no effective treatment. Here we provide evidence that activation of serotonergic signalling is beneficial in animal models of Machado-Joseph disease. We identified citalopram, a selective serotonin reuptake inhibitor, in a small molecule screen of FDA-approved drugs that rescued neuronal dysfunction and reduced aggregation using a Caenorhabditis elegans model of mutant ataxin 3-induced neurotoxicity. MOD-5, the C. elegans orthologue of the serotonin transporter and cellular target of citalopram, and the serotonin receptors SER-1 and SER-4 were strong genetic modifiers of ataxin 3 neurotoxicity and necessary for therapeutic efficacy. Moreover, chronic treatment of CMVMJD135 mice with citalopram significantly reduced ataxin 3 neuronal inclusions and astrogliosis, rescued diminished body weight and strikingly ameliorated motor symptoms. These results suggest that small molecule modulation of serotonergic signalling represents a promising therapeutic target for Machado-Joseph disease. PMID:26373603

  2. Effective short-range Coulomb correction to model the aggregation behavior of ionic surfactants

    NASA Astrophysics Data System (ADS)

    Burgos-Mármol, J. Javier; Solans, Conxita; Patti, Alessandro

    2016-06-01

    We present a short-range correction to the Coulomb potential to investigate the aggregation of amphiphilic molecules in aqueous solutions. The proposed modification allows to quantitatively reproduce the distribution of counterions above the critical micelle concentration (CMC) or, equivalently, the degree of ionization, α, of the micellar clusters. In particular, our theoretical framework has been applied to unveil the behavior of the cationic surfactant C24H49N2O2+ CH3SO4-, which offers a wide range of applications in the thriving and growing personal care market. A reliable and unambiguous estimation of α is essential to correctly understand many crucial features of the micellar solutions, such as their viscoelastic behavior and transport properties, in order to provide sound formulations for the above mentioned personal care solutions. We have validated our theory by performing extensive lattice Monte Carlo simulations, which show an excellent agreement with experimental observations. More specifically, our coarse-grained model is able to reproduce and predict the complex morphology of the micelles observed at equilibrium. Additionally, our simulation results disclose the existence of a transition from a monodisperse to a bidisperse size distribution of aggregates, unveiling the intriguing existence of a second CMC.

  3. Effective short-range Coulomb correction to model the aggregation behavior of ionic surfactants.

    PubMed

    Burgos-Mármol, J Javier; Solans, Conxita; Patti, Alessandro

    2016-06-21

    We present a short-range correction to the Coulomb potential to investigate the aggregation of amphiphilic molecules in aqueous solutions. The proposed modification allows to quantitatively reproduce the distribution of counterions above the critical micelle concentration (CMC) or, equivalently, the degree of ionization, α, of the micellar clusters. In particular, our theoretical framework has been applied to unveil the behavior of the cationic surfactant C24H49N2O2 (+) CH3SO4 (-), which offers a wide range of applications in the thriving and growing personal care market. A reliable and unambiguous estimation of α is essential to correctly understand many crucial features of the micellar solutions, such as their viscoelastic behavior and transport properties, in order to provide sound formulations for the above mentioned personal care solutions. We have validated our theory by performing extensive lattice Monte Carlo simulations, which show an excellent agreement with experimental observations. More specifically, our coarse-grained model is able to reproduce and predict the complex morphology of the micelles observed at equilibrium. Additionally, our simulation results disclose the existence of a transition from a monodisperse to a bidisperse size distribution of aggregates, unveiling the intriguing existence of a second CMC.

  4. Modeling of multi-exciton transient absorption spectra of protochlorophyllide aggregates in aqueous solution.

    PubMed

    Sytina, Olga A; Novoderezhkin, Vladimir I; van Grondelle, Rienk; Groot, Marie Louise

    2011-11-03

    Protochlorophyllide (Pchlide) is a natural porphyrin, a precursor of chlorophyll, synthesized by plants for its photosynthetic apparatus. The pigment spontaneously forms aggregates when dissolved in neat water solution. We present here calculations of the transient absorption spectra and its comprising components (ground-state bleach, stimulated emission, and excited-state absorption) for a strongly excitonically coupled linear chain of four Pchlide chromophores, using exciton theory with phenomenological Gaussian line shapes and without energetic disorder. A refined multiexciton model that includes static disorder is applied to fit the experimental power-dependent transient absorption spectra of aqueous protochlorophyllide and the kinetics for delay times up to 20 ps after photoexcitation. We show that population up to the 4-exciton manifold is sufficient to explain the pronounced saturation of the bleaching and the shape changes in the instantaneous, t = 0.2 ps transient spectra when the pulse energy is increased from 10 to 430 nJ per pulse. The decay of the multiexciton manifold is relatively slow and is preceded by a spectroscopically distinct process. We suggest that the exciton states in the Pchlide aggregates are mixed with charge-transfer states (CTS) and that the population and repopulation of the CTS coupled to the exciton states explains the relatively slow decay of the multiexciton manifold. The relevance of our results to the optical properties and dynamics of natural photosynthetic complexes and the possible physical origin of CTS formation are discussed.

  5. A new Caenorhabditis elegans model of human huntingtin 513 aggregation and toxicity in body wall muscles

    PubMed Central

    Lee, Amy L.; Ung, Hailey M.; Sands, L. Paul

    2017-01-01

    Expanded polyglutamine repeats in different proteins are the known determinants of at least nine progressive neurodegenerative disorders whose symptoms include cognitive and motor impairment that worsen as patients age. One such disorder is Huntington’s Disease (HD) that is caused by a polyglutamine expansion in the human huntingtin protein (htt). The polyglutamine expansion destabilizes htt leading to protein misfolding, which in turn triggers neurodegeneration and the disruption of energy metabolism in muscle cells. However, the molecular mechanisms that underlie htt proteotoxicity have been somewhat elusive, and the muscle phenotypes have not been well studied. To generate tools to elucidate the basis for muscle dysfunction, we engineered Caenorhabditis elegans to express a disease-associated 513 amino acid fragment of human htt in body wall muscle cells. We show that this htt fragment aggregates in C. elegans in a polyglutamine length-dependent manner and is toxic. Toxicity manifests as motor impairment and a shortened lifespan. Compared to previous models, the data suggest that the protein context in which a polyglutamine tract is embedded alters aggregation propensity and toxicity, likely by affecting interactions with the muscle cell environment. PMID:28282438

  6. Modeling conception as an aggregated Bernoulli outcome with latent variables via the EM algorithm.

    PubMed

    Zhou, H; Weinberg, C R

    1996-09-01

    We describe a general method for analyzing aggregated Bernoulli outcomes. The research is motivated by an epidemiological reproductive study where the outcome was whether pregnancy was detected in a woman's particular menstrual cycle and the Bernoulli "trials" corresponded to days with intercourse during the cycle. Each cycle is either "viable" or not, i.e., is or is not susceptible to conception. We develop an EM algorithm approach to maximizing the observed-data pseudo-likelihood, based on a set of unobservable latent outcomes linked to the specific days with intercourse. This method is flexible in that it allows one to model effect of covariates on the susceptibility factor and on the latent outcomes. Application of the method to fertility studies enables one to investigate covariates with a long-term or transient effect on the daily conception probability. A complication is that most couples contribute more than one cycle in a prospective study. A generalized estimating equation approach adjusts for the dependency among outcomes within individual couples. The method can be applied in any setting where dependency among Bernoulli trials is induced by a susceptibility factor and the trial outcomes are only observable in the aggregate.

  7. Impacts of input parameter spatial aggregation on an agricultural nonpoint source pollution model

    NASA Astrophysics Data System (ADS)

    FitzHugh, T. W.; Mackay, D. S.

    2000-09-01

    The accuracy of agricultural nonpoint source pollution models depends in part on how well model input parameters describe the relevant characteristics of the watershed. The spatial extent of input parameter aggregation has previously been shown to have a substantial impact on model output. This study investigates this problem using the Soil and Water Assessment Tool (SWAT), a distributed-parameter agricultural nonpoint source pollution model. The primary question addressed here is: how does the size or number of subwatersheds used to partition the watershed affect model output, and what are the processes responsible for model behavior? SWAT was run on the Pheasant Branch watershed in Dane County, WI, using eight watershed delineations, each with a different number of subwatersheds. Model runs were conducted for the period 1990-1996. Streamflow and outlet sediment predictions were not seriously affected by changes in subwatershed size. The lack of change in outlet sediment is due to the transport-limited nature of the Pheasant Branch watershed and the stable transport capacity of the lower part of the channel network. This research identifies the importance of channel parameters in determining the behavior of SWAT's outlet sediment predictions. Sediment generation estimates do change substantially, dropping by 44% between the coarsest and the finest watershed delineations. This change is primarily due to the sensitivity of the runoff term in the Modified Universal Soil Loss Equation to the area of hydrologic response units (HRUs). This sensitivity likely occurs because SWAT was implemented in this study with a very detailed set of HRUs. In order to provide some insight on the scaling behavior of the model two indexes were derived using the mathematics of the model. The indexes predicted SWAT scaling behavior from the data inputs without a need for running the model. Such indexes could be useful for model users by providing a direct way to evaluate alternative models

  8. Mathematical model and numerical method for studying platelet adhesion and aggregation during blood clotting

    SciTech Connect

    Fogelson, A.L.

    1984-10-01

    The repair of small blood vessels and the pathological growth of internal blood clots involve the formation of platelet aggregates adhering to portions of the vessel wall. Our microscopic model represents blood by a suspension of discrete massless platelets in a viscous incompressible fluid. Platelets are initially noncohesive; however, if stimulated by an above-threshold concentration of the chemical ADP or by contact with the adhesive injured region of the vessel wall, they become cohesive and secrete more ADP into the fluid. Cohesion between platelets and adhesion of a platelet to the injured wall are modeled by creating elastic links. Repulsive forces prevent a platelet from coming too close to another platelet or to the wall. The forces affect the fluid motion in the neighborhood of an aggregate. The platelets and secreted ADP both move by fluid advection and diffusion. The equations of the model are studied numerically in two dimensions. The platelet forces are calculated implicitly by minimizing a nonlinear energy function. Our minimization scheme merges Gill and Murray's (Math. Programming 7 (1974), 311) modified Newton's method with elements of the Yale sparse matix package. The stream-function formulation of the Stokes' equations for the fluid motion under the influence of platelet forces is solved using Bjorstad's biharmonic solver (''Numerical Solution of the Biharmonic Equation,'' Ph.D. Thesis, Stanford University, 1980). The ADP transport equation is solved with an alternating-direction implicit scheme. A linked-list data structure is introduced to keep track of changing platelet states and changing configurations of interplatelet links.

  9. Markovian and Non-Markovian Protein Sequence Evolution: Aggregated Markov Process Models

    PubMed Central

    Kosiol, Carolin; Goldman, Nick

    2011-01-01

    Over the years, there have been claims that evolution proceeds according to systematically different processes over different timescales and that protein evolution behaves in a non-Markovian manner. On the other hand, Markov models are fundamental to many applications in evolutionary studies. Apparent non-Markovian or time-dependent behavior has been attributed to influence of the genetic code at short timescales and dominance of physicochemical properties of the amino acids at long timescales. However, any long time period is simply the accumulation of many short time periods, and it remains unclear why evolution should appear to act systematically differently across the range of timescales studied. We show that the observed time-dependent behavior can be explained qualitatively by modeling protein sequence evolution as an aggregated Markov process (AMP): a time-homogeneous Markovian substitution model observed only at the level of the amino acids encoded by the protein-coding DNA sequence. The study of AMPs sheds new light on the relationship between amino acid-level and codon-level models of sequence evolution, and our results suggest that protein evolution should be modeled at the codon level rather than using amino acid substitution models. PMID:21718704

  10. Sampling Plan Development in Support of DLA’s Quality Assurance Laboratory Testing Program

    DTIC Science & Technology

    1991-09-01

    Objective 2 states "Develop and implement initiatives for continuously improving the quality of products and services delivered to our customers." Task 6 of... of products provided to the military services, Defense Logistics Agency (DLA) embarked on a comprehensive plan *° for enhancing its Quality Assurance...technically sound and appropriate for supporting the DoDIG’s Audit recommendation for laboratory testing. xi I. INTRODUCTION In its quest to improve the quality

  11. Weapon-System-Oriented Supply Management at DLA: Relating Inventory Investment to Readiness

    DTIC Science & Technology

    1993-03-01

    effect on Air Force readiness to all the Military Departments, and we validate and deepen earlier findings on opportunities for DLA improvements. As in...consumable LRU effects on weapon-system readiness are greater than "awaiting parts" effects .) "* Consumable LRUs are not numerous in comparison to the...suboptimizing effect of safety level constraints. "* Grouping items differently when system calculations are performed. The first three ideas are related

  12. Additive Manufacturing: Which DLA-Managed Legacy Parts are Potential AM Candidates

    DTIC Science & Technology

    2016-07-01

    part is a CSI, the failure of which can result in loss of life)  End item application environment (for example, some polymers are sensi- tive to...decision support process can be automated and provided as a web-based application to DoD personnel. We include a set of functional require- ments for...or capability and to identify the necessary interfaces; and  which DLA activity or organization will pay for development, implemen- tation

  13. Demand Forecasting: DLA’S Aviation Supply Chain High Value Products

    DTIC Science & Technology

    2015-04-09

    pbofbp= = = Demand Forecasting: DLA’S Aviation Supply Chain High Value Products 9 April, 2015 LCDR Mordocai Kiflu, USN LCDR Carlos Lopez, USN...APR 2015 2. REPORT TYPE 3. DATES COVERED 00-00-2015 to 00-00-2015 4. TITLE AND SUBTITLE Demand Forecasting: DLA’S Aviation Supply Chain High...both achieve target service levels and quantify the risk of stock-outs in the DLA aviation supply chain. This vision culminated in a simple process

  14. Followup Audit: DLA Officials Took Appropriate Actions to Address Concerns With Repair Parts for the High Mobility Multipurpose Wheeled Vehicle

    DTIC Science & Technology

    2016-04-29

    Followup Audit : DLA Officials Took Appropriate Actions to Address Concerns With Repair Parts for the High Mobility Multipurpose Wheeled Vehicle A P R I L...Results in Brief Followup Audit : DLA Officials Took Appropriate Actions to Address Concerns With Repair Parts for the High Mobility Multipurpose Wheeled...and Maritime Paid Too Much for High Mobility Multipurpose Wheeled Vehicle Repair Parts,” (HMMWV) was issued on April 4, 2014. The audit

  15. QUANTIFYING AGGREGATE CHLORPYRIFOS EXPOSURE AND DOSE TO CHILDREN USING A PHYSICALLY-BASED TWO-STAGE MONTE CARLO PROBABILISTIC MODEL

    EPA Science Inventory

    To help address the Food Quality Protection Act of 1996, a physically-based, two-stage Monte Carlo probabilistic model has been developed to quantify and analyze aggregate exposure and dose to pesticides via multiple routes and pathways. To illustrate model capabilities and ide...

  16. Accelerated Human Mutant Tau Aggregation by Knocking Out Murine Tau in a Transgenic Mouse Model

    PubMed Central

    Ando, Kunie; Leroy, Karelle; Héraud, Céline; Yilmaz, Zehra; Authelet, Michèle; Suain, Valèrie; De Decker, Robert; Brion, Jean-Pierre

    2011-01-01

    Many models of human tauopathies have been generated in mice by expression of a human mutant tau with maintained expression of mouse endogenous tau. Because murine tau might interfere with the toxic effects of human mutant tau, we generated a model in which a pathogenic human tau protein is expressed in the absence of wild-type tau protein, with the aim of facilitating the study of the pathogenic role of the mutant tau and to reproduce more faithfully a human tauopathy. The Tg30 line is a tau transgenic mouse model overexpressing human 1N4R double-mutant tau (P301S and G272V) that develops Alzheimer's disease-like neurofibrillary tangles in an age-dependent manner. By crossing Tg30 mice with mice invalidated for their endogenous tau gene, we obtained Tg30xtau−/− mice that express only exogenous human double-mutant 1N4R tau. Although Tg30xtau−/− mice express less tau protein compared with Tg30, they exhibit signs of decreased survival, increased proportion of sarkosyl-insoluble tau in the brain and in the spinal cord, increased number of Gallyas-positive neurofibrillary tangles in the hippocampus, increased number of inclusions in the spinal cord, and a more severe motor phenotype. Deletion of murine tau accelerated tau aggregation during aging of this mutant tau transgenic model, suggesting that murine tau could interfere with the development of tau pathology in transgenic models of human tauopathies. PMID:21281813

  17. Model of myosin node aggregation into a contractile ring: the effect of local alignment

    NASA Astrophysics Data System (ADS)

    Ojkic, Nikola; Wu, Jian-Qiu; Vavylonis, Dimitrios

    2011-09-01

    Actomyosin bundles frequently form through aggregation of membrane-bound myosin clusters. One such example is the formation of the contractile ring in fission yeast from a broad band of cortical nodes. Nodes are macromolecular complexes containing several dozens of myosin-II molecules and a few formin dimers. The condensation of a broad band of nodes into the contractile ring has been previously described by a search, capture, pull and release (SCPR) model. In SCPR, a random search process mediated by actin filaments nucleated by formins leads to transient actomyosin connections among nodes that pull one another into a ring. The SCPR model reproduces the transport of nodes over long distances and predicts observed clump-formation instabilities in mutants. However, the model does not generate transient linear elements and meshwork structures as observed in some wild-type and mutant cells during ring assembly. As a minimal model of node alignment, we added short-range aligning forces to the SCPR model representing currently unresolved mechanisms that may involve structural components, cross-linking and bundling proteins. We studied the effect of the local node alignment mechanism on ring formation numerically. We varied the new parameters and found viable rings for a realistic range of values. Morphologically, transient structures that form during ring assembly resemble those observed in experiments with wild-type and cdc25-22 cells. Our work supports a hierarchical process of ring self-organization involving components drawn together from distant parts of the cell followed by progressive stabilization.

  18. DLA-Based Strategies for Cloning Insertion Mutants: Cloning the gl4 Locus of Maize Using Mu Transposon Tagged Alleles

    PubMed Central

    Liu, Sanzhen; Dietrich, Charles R.; Schnable, Patrick S.

    2009-01-01

    Digestion–ligation–amplification (DLA), a novel adaptor-mediated PCR-based method that uses a single-stranded oligo as the adaptor, was developed to overcome difficulties of amplifying unknown sequences flanking known DNA sequences in large genomes. DLA specifically overcomes the problems associated with existing methods for amplifying genomic sequences flanking Mu transposons, including high levels of nonspecific amplification. Two DLA-based strategies, MuClone and DLA-454, were developed to isolate Mu-tagged alleles. MuClone allows for the amplification of subsets of the numerous Mu transposons in the genome, using unique three-nucleotide tags at the 3′ ends of primers, simplifying the identification of flanking sequences that cosegregate with mutant phenotypes caused by Mu insertions. DLA-454, which combines DLA with 454 pyrosequencing, permits the efficient cloning of genes for which multiple independent insertion alleles are available without the need to develop segregating populations. The utility of each approach was validated by independently cloning the gl4 (glossy4) gene. Mutants of gl4 lack the normal accumulation of epicuticular waxes. The gl4 gene is a homolog of the Arabidopsis CUT1 gene, which encodes a condensing enzyme involved in the synthesis of very-long-chain fatty acids, which are precursors of epicuticular waxes. PMID:19805815

  19. Stability analysis of 4-species Aβ aggregation model: A novel approach to obtaining physically meaningful rate constants.

    PubMed

    Ghag, G; Ghosh, P; Mauro, A; Rangachari, V; Vaidya, A

    2013-11-01

    Protein misfolding and concomitant aggregation towards amyloid formation is the underlying biochemical commonality among a wide range of human pathologies. Amyloid formation involves the conversion of proteins from their native monomeric states (intrinsically disordered or globular) to well-organized, fibrillar aggregates in a nucleation-dependent manner. Understanding the mechanism of aggregation is important not only to gain better insight into amyloid pathology but also to simulate and predict molecular pathways. One of the main impediments in doing so is the stochastic nature of interactions that impedes thorough experimental characterization and the development of meaningful insights. In this study, we have utilized a well-known intermediate state along the amyloid-β peptide aggregation pathway called protofibrils as a model system to investigate the molecular mechanisms by which they form fibrils using stability and perturbation analysis. Investigation of protofibril aggregation mechanism limits both the number of species to be modeled (monomers, and protofibrils), as well as the reactions to two (elongation by monomer addition, and protofibril-protofibril lateral association). Our new model is a reduced order four species model grounded in mass action kinetics. Our prior study required 3200 reactions, which makes determining the reaction parameters prohibitively difficult. Using this model, along with a linear perturbation argument, we rigorously determine stable ranges of rate constants for the reactions and ensure they are physically meaningful. This was accomplished by finding the ranges in which the perturbations dieout in a five-parameter sweep, which includes the monomer and protofibril equilibrium concentrations and three of the rate constants. The results presented are a proof-of-concept method in determining meaningful rate constants that can be used as a bonafide way for determining accurate rate constants for other models involving complex

  20. Large-Scale Patterns in a Minimal Cognitive Flocking Model: Incidental Leaders, Nematic Patterns, and Aggregates

    NASA Astrophysics Data System (ADS)

    Barberis, Lucas; Peruani, Fernando

    2016-12-01

    We study a minimal cognitive flocking model, which assumes that the moving entities navigate using the available instantaneous visual information exclusively. The model consists of active particles, with no memory, that interact by a short-ranged, position-based, attractive force, which acts inside a vision cone (VC), and lack velocity-velocity alignment. We show that this active system can exhibit—due to the VC that breaks Newton's third law—various complex, large-scale, self-organized patterns. Depending on parameter values, we observe the emergence of aggregates or millinglike patterns, the formation of moving—locally polar—files with particles at the front of these structures acting as effective leaders, and the self-organization of particles into macroscopic nematic structures leading to long-ranged nematic order. Combining simulations and nonlinear field equations, we show that position-based active models, as the one analyzed here, represent a new class of active systems fundamentally different from other active systems, including velocity-alignment-based flocking systems. The reported results are of prime importance in the study, interpretation, and modeling of collective motion patterns in living and nonliving active systems.

  1. Large-Scale Patterns in a Minimal Cognitive Flocking Model: Incidental Leaders, Nematic Patterns, and Aggregates.

    PubMed

    Barberis, Lucas; Peruani, Fernando

    2016-12-09

    We study a minimal cognitive flocking model, which assumes that the moving entities navigate using the available instantaneous visual information exclusively. The model consists of active particles, with no memory, that interact by a short-ranged, position-based, attractive force, which acts inside a vision cone (VC), and lack velocity-velocity alignment. We show that this active system can exhibit-due to the VC that breaks Newton's third law-various complex, large-scale, self-organized patterns. Depending on parameter values, we observe the emergence of aggregates or millinglike patterns, the formation of moving-locally polar-files with particles at the front of these structures acting as effective leaders, and the self-organization of particles into macroscopic nematic structures leading to long-ranged nematic order. Combining simulations and nonlinear field equations, we show that position-based active models, as the one analyzed here, represent a new class of active systems fundamentally different from other active systems, including velocity-alignment-based flocking systems. The reported results are of prime importance in the study, interpretation, and modeling of collective motion patterns in living and nonliving active systems.

  2. Microwave fields have little effect on α-synuclein aggregation in a Caenorhabditis elegans model of Parkinson's disease.

    PubMed

    de Pomerai, David I; Iqbal, Nooria; Lafayette, Ivan; Nagarajan, Archana; Kaviani Moghadam, Mehri; Fineberg, April; Reader, Tom; Greedy, Steve; Smartt, Chris; Thomas, David W P

    2016-02-01

    Potential health effects of radiofrequency (RF) radiation from mobile phones arouse widespread public concern. RF fields from handheld devices near the brain might trigger or aggravate brain tumors or neurodegenerative diseases such as Parkinson's disease (PD). Aggregation of neural α-synuclein (S) is central to PD pathophysiology, and invertebrate models expressing human S have helped elucidate factors affecting the aggregation process. We have recently developed a transgenic strain of Caenorhabditis elegans carrying two S constructs: SC tagged with cyan (C) blue fluorescent protein (CFP), and SV with the Venus (V) variant of yellow fluorescent protein (YFP). During S aggregation in these SC+SV worms, CFP, and YFP tags are brought close enough to allow Foerster Resonance Energy Transfer (FRET). As a positive control, S aggregation was promoted at low Hg(2+) concentrations, whereas higher concentrations activated stress-response genes. Using two different exposure systems described previously, we tested whether RF fields (1.0 GHz CW, 0.002-0.02 W kg(-1); 1.8 GHz CW or GSM, 1.8 W kg(-1)) could influence S aggregation in SC+SV worms. YFP fluorescence in similar SV-only worms provided internal controls, which should show opposite changes due to FRET quenching during S aggregation. No statistically significant changes were observed over several independent runs at 2.5, 24, or 96 h. Although our worm model is sensitive to chemical promoters of aggregation, no similar effects were attributable to RF exposures.

  3. Fitting bevacizumab aggregation kinetic data with the Finke-Watzky two-step model: Effect of thermal and mechanical stress.

    PubMed

    Oliva, Alexis; Llabrés, Matías; Fariña, José B

    2015-09-18

    Size exclusion chromatography with light scattering detection (SEC-MALLS) was assessed as a means to characterize the type of bevacizumab aggregates that form under mechanical and thermal stress, quantitatively monitoring the aggregation kinetics. The analytical method was monitored and verified during routine use at two levels: (1) the "pre-study" validation shows that the method is specific, linear, accurate, precise, robust and stability indicating; (2) the "in-study" validation was verified by inserting quality control samples and the use of control charts, indicating that the analytical method is in statistical control and stable. The aggregation kinetics data were interpreted using a modified Lumry-Eyring model, but the quality of the fit can be considered poor (R(2)>0.96), especially at higher temperatures. This indicates that the order of the reaction could not be reliably determined, suggesting a different degradation mechanism. The kinetic data set also fit the minimalistic Finke-Watzky (F-W) 2-step model, with an excellent quality of fit (R(2)>0.99), yielding the first quantitative rate constant for the steps of nucleation and growth in bevacizumab aggregation. The bevacizumab pharmaceutical preparation contains (initially) dimers, approximately 1.6% of bevacizumab total concentration, and the effect on aggregation kinetics of seeding was analyzed using the F-W 2-step model assuming [B]0≠0 (for the seeded case). The results suggested that the seeding had no impact on aggregation kinetics. Furthermore, the Arrhenius equation cannot be used to extrapolate the shelf-life since no linear temperature dependence of the rate constant was found within the temperature range. Although the real-time stability data provides the basis for determining the product shelf-life, predictive methodologies such as Vogel-Tammann-Fulcher (VFT) or the Arrhenius approach can be misleading and result in overestimates of the product shelf-life. However, they can be successfully

  4. A new method for modeling thermo-mechanical behaviors of polycrystalline aggregates

    NASA Astrophysics Data System (ADS)

    Tian, Xia; Cui, JunZhi; Li, BoWen

    2012-11-01

    We present in this paper a numerical algorithm that couples the atomistic and continuum models for the thermal-mechanical coupled problem of polycrystalline aggregates. The key point is that the conservation laws should be satisfied for both the atomistic and continuum models at the microscale. Compared with the traditional methods which construct the constitutive equations of the grain interiors and grain boundaries by continuum mechanics, our model calculates the continuum fluxes through molecular dynamics simulations, provided that the atomistic simulations are consistent with the local microstate of the system. For the grain interiors without defects, central schemes are available for solving the conservation laws and the constitutive parameters can be obtained via molecular dynamics simulations. For the grain boundary structures, the front tracking method is employed because the solutions of the conservation equations are discontinuous near the defects. Firstly, appropriate control volumes are chosen at both sides of the interface, then the finite volume method is applied to solve the continuum equations in each control volume. Fluxes near both sides of the interface are calculated via atomistic simulations. Therefore, all thermo-mechanical information can be obtained.

  5. Modelling the polarization properties of Comet 1P/Halley using a mixture of compact and aggregate particles

    NASA Astrophysics Data System (ADS)

    Das, H. S.; Paul, D.; Suklabaidya, A.; Sen, A. K.

    2011-09-01

    Both the in situ measurement of Comet 1P/Halley and the Stardust-returned samples of Comet Wild 2 showed the presence of a mixture of compact and aggregate particles, with both silicates and organic refractory being in the composition of the cometary dust. Results obtained recently from the Stardust mission suggest that the overall ratio of compact to aggregate particles is 65:35 (or 13:7) for Comet 81P/Wild 2. In the present work, we propose a model that considers cometary dust as a mixture of compact and aggregate particles, with a composition of silicate and organic. We consider compact particles as spheroidal particles and aggregates as both ballistic cluster-cluster aggregate (BCCA) and ballistic agglomeration with two migrations (BAM2) aggregate with a certain size distribution. The mixing ratio of compact to aggregate particles is taken to be 13:7. For modelling Comet 1P/Halley, the power-law size distribution n(a) ˜a-2.6, obtained from a re-analysis of the Giotto spacecraft data, for both compact and aggregate particles, is used. We consider a mixture of BAM2 and BCCA aggregates with a lower cut-off size of about 0.20 μ m and an upper cut-off of about 1 μ m. We also consider a mixture of prolate, spherical and oblate compact particles with an axial ratio (E) of 0.8-1.2 where a lower cut-off size of about 0.1 μ m and an upper cut-off of about 10 μ m are considered. Using a T-matrix code for polydisperse spheroids (0.1 μ m ≤a≤ 10 μ m) and superposition T-matrix code for aggregates (0.2 μ m ≤av≤ 1 μ m), the average simulated polarization curves are generated, which can best fit the observed polarization data at the four wavelengths: λ= 0.365, 0.485, 0.670 and 0.684 μ m. The suitable mixing percentages of aggregates obtained from the present modelling are 50 per cent BAM2 and 50 per cent BCCA particles, and the silicate-to-organic mixing percentages are 78 per cent silicate and 22 per cent organic, in terms of volume. The present model

  6. Regional Demand Models for Water-Based Recreation: Combining Aggregate and Individual-Level Choice Data

    EPA Science Inventory

    Estimating the effect of changes in water quality on non-market values for recreation involves estimating a change in aggregate consumer surplus. This aggregate value typically involves estimating both a per-person, per-trip change in willingness to pay, as well as defining the m...

  7. Processing of IgA aggregates in a rat model of chronic liver disease.

    PubMed

    Amore, A; Roccatello, D; Picciotto, G; Emancipator, S N; Ropolo, R; Cacace, G; Suriani, A; Gianoglio, B; Sena, L M; Cirina, P; Mazzucco, G; Alfieri, V; Piccoli, G; Coppo, R; De Filippi, P G

    1997-08-01

    . Similar results were obtained in control rats injected with aggregated IgG; i.e., MTT values were more prolonged in rats given whiskey or LD diet than normally nourished rats (P < 0.01). The lipotrope-deficient diet and the chronic alcohol abuse per se seem to lead to critical changes in hepatic uptake and catabolism of both an IgA and an IgG aggregate, which could account in turn for the reported appearance of renal immunoglobulin deposits in this experimental model. Due to the comparable delay in removal of IgA and IgG probes in equally nourished animals, additional factors are likely to be involved in the prominent deposition of IgA.

  8. Protein aggregation in food models: effect of. gamma. -irradiation and lipid oxidation

    SciTech Connect

    Delincee, H.; Paul, P.

    1981-09-01

    Myoglobin and serum albumin have been irradiated in aqueous solution in the presence of varying amounts of carbohydrates and lipids, and the yield of protein aggregates has been determined by gel filtration. With myoglobin the formation of aggregates evolving from the reaction with oxidizing lipids was observed, which was not found for serum albumin. The production of protein-lipid complexes, in which lipid material was occluded in the high-molecular aggregates by physical forces was demonstrated. Gel filtration and gel electrophoresis, both in the presence of SDS, and thin-layer isoelectric focusing revealed distinct structural differenes between the protein aggregates induced by irradiation and the aggregates formed by interaction with oxidizing lipids.

  9. A mechanistic model of tau amyloid aggregation based on direct observation of oligomers

    NASA Astrophysics Data System (ADS)

    Shammas, Sarah L.; Garcia, Gonzalo A.; Kumar, Satish; Kjaergaard, Magnus; Horrocks, Mathew H.; Shivji, Nadia; Mandelkow, Eva; Knowles, Tuomas P. J.; Mandelkow, Eckhard; Klenerman, David

    2015-04-01

    Protein aggregation plays a key role in neurodegenerative disease, giving rise to small oligomers that may become cytotoxic to cells. The fundamental microscopic reactions taking place during aggregation, and their rate constants, have been difficult to determine due to lack of suitable methods to identify and follow the low concentration of oligomers over time. Here we use single-molecule fluorescence to study the aggregation of the repeat domain of tau (K18), and two mutant forms linked with familial frontotemporal dementia, the deletion mutant ΔK280 and the point mutant P301L. Our kinetic analysis reveals that aggregation proceeds via monomeric assembly into small oligomers, and a subsequent slow structural conversion step before fibril formation. Using this approach, we have been able to quantitatively determine how these mutations alter the aggregation energy landscape.

  10. Monte Carlo simulation for morphology of nanoparticles and particle size distributions: comparison of the cluster-cluster aggregation model with the sectional method

    NASA Astrophysics Data System (ADS)

    Ono, Kiminori; Matsukawa, Yoshiya; Saito, Yasuhiro; Matsushita, Yohsuke; Aoki, Hideyuki; Era, Koki; Aoki, Takayuki; Yamaguchi, Togo

    2015-06-01

    This study presents the validity and ability of an aggregate mean free path cluster-cluster aggregation (AMP-CCA) model, which is a direct Monte Carlo simulation, to predict the aggregate morphology with diameters form about 15-200 nm by comparing the particle size distributions (PSDs) with the results of the previous stochastic approach. The PSDs calculated by the AMP-CCA model with the calculated aggregate as a coalesced spherical particle are in reasonable agreement with the results of the previous stochastic model regardless of the initial number concentration of particles. The shape analysis using two methods, perimeter fractal dimension and the shape categories, has demonstrated that the aggregate structures become complex with increasing the initial number concentration of particles. The AMP-CCA model provides a useful tool to calculate the aggregate morphology and PSD with reasonable accuracy.

  11. Release of major elements from recycled concrete aggregates and geochemical modelling

    SciTech Connect

    Engelsen, Christian J. Sloot, Hans A. van der; Wibetoe, Grethe; Petkovic, Gordana; Stoltenberg-Hansson, Erik; Lund, Walter

    2009-05-15

    The pH dependent leaching characteristics were assessed for different types of recycled concrete aggregates, including real construction debris and crushed fresh concrete samples prepared in laboratory. Carbonation effects were identified from the characteristic pH dependent leaching patterns for the major constituents Al, Ca, Fe, Mg, Si and SO{sub 4}{sup 2-}. The original particle size ranges were different for the samples investigated and this factor influenced the cement paste content in the samples which in turn controlled the leachable contents. Cement paste contents for concrete samples with fine particle size fractions (0-4 mm) were found to be higher than the originally present amount in the hardened concrete. Geochemical speciation modelling was applied over the entire pH range using the speciation and transport modelling framework ORCHESTRA, for which mineral saturation, solution speciation and sorption processes can be calculated based on equilibrium models and thermodynamic data. The simulated equilibrium concentrations by this model agreed well with the respective measured concentrations. The main differences between the fresh and aged materials were quantified, described and predicted by the ORCHESTRA. Solubility controlling mineral phase assemblages were calculated by the model as function of pH. Cement hydrate phases such as calcium silicate hydrate, calcium aluminate hydrate (AFm and AFt) and hydrogarnet were predominating at the material pH. The concentration of carboaluminates was found to be strongly dependent on the available carbonates in the samples. As the pH was decreased these phases decomposed to more soluble species or precipitates were formed including iron- and aluminium hydroxides, wairakite and amorphous silica. In the most acid region most phases dissolved, and the major elements were approaching maximum leachability, which was determined by the amount of cement paste.

  12. The Use of Multiple Regression Models to Determine if Conjoint Analysis Should Be Conducted on Aggregate Data.

    ERIC Educational Resources Information Center

    Fraas, John W.; Newman, Isadore

    1996-01-01

    In a conjoint-analysis consumer-preference study, researchers must determine whether the product factor estimates, which measure consumer preferences, should be calculated and interpreted for each respondent or collectively. Multiple regression models can determine whether to aggregate data by examining factor-respondent interaction effects. This…

  13. Brain Aggregates: An Effective In Vitro Cell Culture System Modeling Neurodegenerative Diseases

    PubMed Central

    Kalume, Franck; Pitstick, Rose; Oehler, Abby; Carlson, George; DeArmond, Stephen J.

    2016-01-01

    Drug discovery for neurodegenerative diseases is particularly challenging because of the discrepancies in drug effects between in vitro and in vivo studies. These discrepancies occur in part because current cell culture systems used for drug screening have many limitations. First, few cell culture systems accurately model human aging or neurodegenerative diseases. Second, drug efficacy may differ between dividing and stationary cells, the latter resembling nondividing neurons in the CNS. Brain aggregates (BrnAggs) derived from embryonic day 15 gestation mouse embryos may represent neuropathogenic processes in prion disease and reflect in vivo drug efficacy. Here, we report a new method for the production of BrnAggs suitable for drug screening and suggest that BrnAggs can model additional neurological diseases such as tauopathies. We also report a functional assay with BrnAggs by measuring electrophysiological activities. Our data suggest that BrnAggs could serve as an effective in vitro cell culture system for drug discovery for neurodegenerative diseases. PMID:26851378

  14. Synthetic Quorum Sensing and Induced Aggregation in Model Microcapsule Colonies with Repressilator Feedback

    NASA Astrophysics Data System (ADS)

    Shum, Henry; Yashin, Victor; Balazs, Anna

    We model a system of synthetic microcapsules that communicate chemically by releasing nanoparticles or signaling molecules. These signaling species bind to receptors on the shells of capsules and modulate the target shell's permeability, thereby controlling nanoparticle release from the target capsule. Using the repressilator regulatory network motif, whereby three species suppress the production of the next in a cyclic fashion, we show that large amplitude oscillations in nanoparticle release can emerge when many capsules are close together. This exemplifies quorum sensing, which is the ability of cells to gauge their population density and collectively initiate a new behavior once a critical density is reached. We present a physically realizable model in which the oscillations exhibited in crowded populations induce aggregation of the microcapsules, mimicking complex biological behavior of the slime mold Dictyostelium discoideum with only simple, synthetic components. We also show that the clusters can be dispersed and reformed repeatedly and controllably by addition of chemical stimuli, demonstrating possible applications in creating reconfigurable or programmable materials.

  15. New roles of glycosaminoglycans in α-synuclein aggregation in a cellular model of Parkinson disease.

    PubMed

    Lehri-Boufala, Sonia; Ouidja, Mohand-Ouidir; Barbier-Chassefière, Véronique; Hénault, Emilie; Raisman-Vozari, Rita; Garrigue-Antar, Laure; Papy-Garcia, Dulce; Morin, Christophe

    2015-01-01

    The causes of Parkinson disease (PD) remain mysterious, although some evidence supports mitochondrial dysfunctions and α-synuclein accumulation in Lewy bodies as major events. The abnormal accumulation of α-synuclein has been associated with a deficiency in the ubiquitin-proteasome system and the autophagy-lysosomal pathway. Cathepsin D (cathD), the major lysosomal protease responsible of α-synuclein degradation was described to be up-regulated in PD model. As glycosaminoglycans (GAGs) regulate cathD activity, and have been recently suggested to participate in PD physiopathology, we investigated their role in α-synuclein accumulation by their intracellular regulation of cathD activity. In a classical neuroblastoma cell model of PD induced by MPP+, the genetic expression of GAGs-biosynthetic enzymes was modified, leading to an increase of GAGs amounts whereas intracellular level of α-synuclein increased. The absence of sulfated GAGs increased intracellular cathD activity and limited α-synuclein accumulation. GAGs effects on cathD further suggested that specific sequences or sulfation patterns could be responsible for this regulation. The present study identifies, for the first time, GAGs as new regulators of the lysosome degradation pathway, regulating cathD activity and affecting two main biological processes, α-synuclein aggregation and apoptosis. Finally, this opens new insights into intracellular GAGs functions and new fields of investigation for glycobiological approaches in PD and neurobiology.

  16. New Roles of Glycosaminoglycans in α-Synuclein Aggregation in a Cellular Model of Parkinson Disease

    PubMed Central

    Lehri-Boufala, Sonia; Ouidja, Mohand-Ouidir; Barbier-Chassefière, Véronique; Hénault, Emilie; Raisman-Vozari, Rita; Garrigue-Antar, Laure; Papy-Garcia, Dulce; Morin, Christophe

    2015-01-01

    The causes of Parkinson disease (PD) remain mysterious, although some evidence supports mitochondrial dysfunctions and α-synuclein accumulation in Lewy bodies as major events. The abnormal accumulation of α-synuclein has been associated with a deficiency in the ubiquitin-proteasome system and the autophagy-lysosomal pathway. Cathepsin D (cathD), the major lysosomal protease responsible of α-synuclein degradation was described to be up-regulated in PD model. As glycosaminoglycans (GAGs) regulate cathD activity, and have been recently suggested to participate in PD physiopathology, we investigated their role in α-synuclein accumulation by their intracellular regulation of cathD activity. In a classical neuroblastoma cell model of PD induced by MPP+, the genetic expression of GAGs-biosynthetic enzymes was modified, leading to an increase of GAGs amounts whereas intracellular level of α-synuclein increased. The absence of sulfated GAGs increased intracellular cathD activity and limited α-synuclein accumulation. GAGs effects on cathD further suggested that specific sequences or sulfation patterns could be responsible for this regulation. The present study identifies, for the first time, GAGs as new regulators of the lysosome degradation pathway, regulating cathD activity and affecting two main biological processes, α-synuclein aggregation and apoptosis. Finally, this opens new insights into intracellular GAGs functions and new fields of investigation for glycobiological approaches in PD and neurobiology. PMID:25617759

  17. Microleakage of accelerated mineral trioxide aggregate and Portland cement in an in vitro apexification model.

    PubMed

    Hong, Seong-Tae; Bae, Kwang-Shik; Baek, Seung-Ho; Kum, Kee-Yeon; Lee, WooCheol

    2008-01-01

    The purpose of this study was to evaluate the microleakage of accelerated mineral trioxide aggregate (MTA) and Portland cement by flow porometry analysis in an in vitro apexification model. Sixty-four single-rooted, extracted teeth were divided into 4 groups (group 1, MTA; group 2, MTA with accelerator; group 3, Portland cement; and group 4, Portland cement with accelerator). In an in vitro apexification model, MTA or Portland cement mixed with or without 10% CaCl2 was condensed to 2-mm thickness. The negative control group (n = 4) had the apical foramen sealed with epoxy resin. The maximum and mean flow pore diameters of the samples were tested by capillary flow porometry at 90 minutes and 48 hours after obturation. The addition of accelerator significantly reduced the maximum pore diameters of MTA and Portland cement at the initial setting phase. After 48 hours of obturation, the maximum and mean flow pore diameters of the accelerated samples were significantly reduced compared with the normal samples. There was no statistically significant difference in the maximum pore diameter of MTA and Portland cement between the measurements at 90 minutes and 48 hours. The results imply that the addition of accelerator into MTA or Portland cement can be useful in a one-visit apexification by reducing microleakage even in an early setting time.

  18. Antioxidant Treatment and Induction of Autophagy Cooperate to Reduce Desmin Aggregation in a Cellular Model of Desminopathy

    PubMed Central

    Cabet, Eva; Batonnet-Pichon, Sabrina; Delort, Florence; Gausserès, Blandine; Vicart, Patrick; Lilienbaum, Alain

    2015-01-01

    Desminopathies, a subgroup of myofibrillar myopathies (MFMs), the progressive muscular diseases characterized by the accumulation of granulofilamentous desmin-positive aggregates, result from mutations in the desmin gene (DES), encoding a muscle-specific intermediate filament. Desminopathies often lead to severe disability and premature death from cardiac and/or respiratory failure; no specific treatment is currently available. To identify drug-targetable pathophysiological pathways, we performed pharmacological studies in C2C12 myoblastic cells expressing mutant DES. We found that inhibition of the Rac1 pathway (a G protein signaling pathway involved in diverse cellular processes), antioxidant treatment, and stimulation of macroautophagy reduced protein aggregation by up to 75% in this model. Further, a combination of two or three of these treatments was more effective than any of them alone. These results pave the way towards the development of the first treatments for desminopathies and are potentially applicable to other muscle or brain diseases associated with abnormal protein aggregation. PMID:26333167

  19. Multiscale modeling of bacterial colonies: how pili mediate the dynamics of single cells and cellular aggregates

    NASA Astrophysics Data System (ADS)

    Pönisch, Wolfram; Weber, Christoph A.; Juckeland, Guido; Biais, Nicolas; Zaburdaev, Vasily

    2017-01-01

    Neisseria gonorrhoeae is the causative agent of one of the most common sexually transmitted diseases, gonorrhea. Over the past two decades there has been an alarming increase of reported gonorrhea cases where the bacteria were resistant to the most commonly used antibiotics thus prompting for alternative antimicrobial treatment strategies. The crucial step in this and many other bacterial infections is the formation of microcolonies, agglomerates consisting of up to several thousands of cells. The attachment and motility of cells on solid substrates as well as the cell-cell interactions are primarily mediated by type IV pili, long polymeric filaments protruding from the surface of cells. While the crucial role of pili in the assembly of microcolonies has been well recognized, the exact mechanisms of how they govern the formation and dynamics of microcolonies are still poorly understood. Here, we present a computational model of individual cells with explicit pili dynamics, force generation and pili-pili interactions. We employ the model to study a wide range of biological processes, such as the motility of individual cells on a surface, the heterogeneous cell motility within the large cell aggregates, and the merging dynamics and the self-assembly of microcolonies. The results of numerical simulations highlight the central role of pili generated forces in the formation of bacterial colonies and are in agreement with the available experimental observations. The model can quantify the behavior of multicellular bacterial colonies on biologically relevant temporal and spatial scales and can be easily adjusted to include the geometry and pili characteristics of various bacterial species. Ultimately, the combination of the microbiological experimental approach with the in silico model of bacterial colonies might provide new qualitative and quantitative insights on the development of bacterial infections and thus pave the way to new antimicrobial treatments.

  20. Extensive polymorphism and evidence of selection pressure on major histocompatibility complex DLA-DRB1, DQA1 and DQB1 class II genes in Croatian grey wolves.

    PubMed

    Arbanasić, H; Huber, Đ; Kusak, J; Gomerčić, T; Hrenović, J; Galov, A

    2013-01-01

    The genes of the major histocompatibility complex (MHC) are a key component of the mammalian immune system and have become important molecular markers for measuring fitness-related genetic variation in wildlife populations. Because of human persecution and habitat fragmentation, the grey wolf has become extinct from a large part of Western and Central Europe, and remaining populations have become isolated. In Croatia, the grey wolf population, part of the Dinaric-Balkan population, shrank nearly to extinction during the 20th century, and is now legally protected. Using the cloning-sequencing method, we investigated the genetic diversity and evolutionary history of exon 2 of MHC class II DLA-DRB1, DQA1 and DQB1 genes in 77 individuals. We identified 13 DRB1, 7 DQA1 and 11 DQB1 highly divergent alleles, and 13 DLA-DRB1/DQA1/DQB1 haplotypes. Selection analysis comparing the relative rates of non-synonymous to synonymous mutations (d(N)/d(S)) showed evidence of positive selection pressure acting on all three loci. Trans-species polymorphism was found, suggesting the existence of balancing selection. Evolutionary codon models detected considerable difference between alpha and beta chain gene selection patterns: DRB1 and DQB1 appeared to be under stronger selection pressure, while DQA1 showed signs of moderate selection. Our results suggest that, despite the recent contraction of the Croatian wolf population, genetic variability in selectively maintained immune genes has been preserved.

  1. Aggregate model of cometary dust: an application to comet Levy 1990XX

    NASA Astrophysics Data System (ADS)

    Das, H. S.; Das, S. R.; Paul, T.; Suklabaidya, A.; Sen, A. K.

    2008-09-01

    In the present work, the light-scattering properties of comet Levy 1990XX are studied through simulations using Ballistic Particle-Cluster Aggregation (BPCA) or Ballistic Cluster-Cluster Aggregation (BCCA) aggregates of up to 128 spherical monomers of different compositions (e.g. silicates, carbonaceous materials etc.) and the best-fitting theoretical polarization curve is generated using the SUPERPOSITION T-MATRIX code. The best-fitting refractive indices coming out from the present analysis show silicate behaviour when monomer radius is am = 0.12μm and provide excellent results on the maximum and negative degrees of linear polarization at a single wavelength λ = 0.485μm for BCCA aggregates.

  2. Tissue Reaction and Biocompatibility of Implanted Mineral Trioxide Aggregate with Silver Nanoparticles in a Rat Model

    PubMed Central

    Zand, Vahid; Lotfi, Mehrdad; Aghbali, Amirala; Mesgariabbasi, Mehran; Janani, Maryam; Mokhtari, Hadi; Tehranchi, Pardis; Pakdel, Seyyed Mahdi Vahid

    2016-01-01

    Introduction: Biocompatibility and antimicrobial activity of endodontic materials are of utmost importance. Considering the extensive applications of mineral trioxide aggregate (MTA) in dentistry and antimicrobial properties of silver nanoparticles, this study aimed to evaluate the subcutaneous inflammatory reaction of rat connective tissues to white MTA with and without nanosilver (NS) particles. Methods and Materials: Polyethylene tubes (1.1×8 mm) containing experimental materials (MTA and MTA+NS and empty control tubes) were implanted in subcutaneous tissues of seventy-five male rats. Animals were divided into five groups (n=15) according to the time of evaluation: group 1; after 7 days, group 2; after 15 days, group 3; after 30 days, group 4; after 60 days and group 5; after 90 days. The inflammatory reaction was graded and data was analyzed using the Kruskal-Wallis and Mann-Whitney U tests. Statistical significance was defined at 0.05. Results: Comparison of cumulative inflammatory reaction at all intervals revealed that the mean grade of inflammatory reaction to MTA, MTA+NS and control samples were 3, 2 and 2, respectively. According to the Mann-Whitney analysis there were no significant differences between MTA+NS and MTA (P=0.42). Conclusion: Incorporation of 1% nanosilver to MTA does not affect the inflammatory reaction of subcutaneous tissue in rat models. PMID:26843871

  3. A physical scaling model for aggregation and disaggregation of field-scale surface soil moisture dynamics.

    PubMed

    Ojha, Richa; Govindaraju, Rao S

    2015-07-01

    Scaling relationships are needed as measurements and desired predictions are often not available at concurrent spatial support volumes or temporal discretizations. Surface soil moisture values of interest to hydrologic studies are estimated using ground based measurement techniques or utilizing remote sensing platforms. Remote sensing based techniques estimate field-scale surface soil moisture values, but are unable to provide the local-scale soil moisture information that is obtained from local measurements. Further, obtaining field-scale surface moisture values using ground-based measurements is exhaustive and time consuming. To bridge this scale mismatch, we develop analytical expressions for surface soil moisture based on sharp-front approximation of the Richards equation and assumed log-normal distribution of the spatial surface saturated hydraulic conductivity field. Analytical expressions for field-scale evolution of surface soil moisture to rainfall events are utilized to obtain aggregated and disaggregated response of surface soil moisture evolution with knowledge of the saturated hydraulic conductivity. The utility of the analytical model is demonstrated through numerical experiments involving 3-D simulations of soil moisture and Monte-Carlo simulations for 1-D renderings-with soil moisture dynamics being represented by the Richards equation in each instance. Results show that the analytical expressions developed here show promise for a principled way of scaling surface soil moisture.

  4. A stochastic model of cell aggregation under planar flow in the dilute regime.

    PubMed

    Ganghoffer, Jean-François; Kabouya, Nadjiba; Mefti, Nacim

    2010-01-19

    Models of the adhesion of a population of cells in a plane flow are developed, considering the dilute regime. Cells considered as rigid punctual entities are virtually injected at regular times within a plane channel limited by two fixed planes. The pressure profile is supposed to be triangular (constant gradient), in accordance with the assumptions of a Poiseuille flow. The cell adherence to the channel wall is governed by the balance of forces, accounting for gravity, non-specific physical interactions, such as electrostatic effects (repulsive) and Van der Waals forces (attractive), specific adhesive forces representing the ligand-receptor interactions, and friction between cells and the fluid in the vicinity of the endothelium wall. The spatial distribution of the adhesion molecules along the wall is supposed to be a random event, accounted for by a stochastic spatial variability of the dipolar moments of those molecules, according to a Gaussian process. Experimental trends reported for the rate of aggregation of L-selectin mediated leukocytes under shear flow are in qualitative accordance with the evolution versus time of adhering cells obtained by the present simulations. The effect of the maximal injection pressure on those kinetics is assessed.

  5. Extending the PRIME Model for Protein Aggregation to All Twenty Amino Acids

    PubMed Central

    Cheon, Mookyung; Chang, Iksoo

    2010-01-01

    We extend PRIME, an intermediate-resolution protein model previously used in simulations of the aggregation of polyalanine and polyglutamine, to the description of the geometry and energetics of peptides containing all twenty amino acid residues. The 20 amino acid side chains are classified into 14 groups according to their hydrophobicity, polarity, size, charge and potential for side chain hydrogen bonding. The parameters for extended PRIME, called PRIME 20, include hydrogen-bonding energies, side-chain interaction range and energy, and excluded volume. The parameters are obtained by applying a perceptron- learning algorithm and a modified stochastic learning algorithm that optimizes the energy gap between 711 known native states from the PDB and decoy structures generated by gapless threading. The number of independent pair-interaction parameters is chosen to be small enough to be physically meaningful yet large enough to give reasonably accurate results in discriminating decoys from native structures. The most physically meaningful results are obtained with 19 energy parameters. PMID:20740494

  6. Quantitative models for aggregate: some types and examples from Oklahoma carbonate rocks

    USGS Publications Warehouse

    Bliss, James D.

    1999-01-01

    Evaluation of data for three engineering variable--absorption, bulk specific gravity, and freeze-thaw durability (350 cycles)--was made for quarries in carbonate rocks in Oklahoma that supply aggregate. It was found that lower Palrozoic carbonate rocks (Cambrian through Devonian) are likely to make a better quality aggregate than upper Paleozoic (Mississippian to Permian) carbonate rocks. In addition, freeze-thaw durability can be forecast from absorption and is exemplary for lower Paleozoic carbonate rocks.

  7. Spatially Resolved Emission of a High-redshift DLA Galaxy with the Keck/OSIRIS IFU

    NASA Astrophysics Data System (ADS)

    Jorgenson, Regina A.; Wolfe, Arthur M.

    2014-04-01

    We present the first Keck/OSIRIS infrared IFU observations of a high-redshift damped Lyα (DLA) galaxy detected in the line of sight to a background quasar. By utilizing the Laser Guide Star Adaptive Optics to reduce the quasar point-spread function to FWHM ~ 0.''15, we were able to search for and map the foreground DLA emission free from the quasar contamination. We present maps of the Hα and [O III] λλ5007, 4959 emission of DLA 2222-0946 at a redshift of z ~ 2.35. From the composite spectrum over the Hα emission region, we measure a star formation rate of 9.5 ± 1.0 M ⊙ yr-1 and a dynamical mass of M dyn = 6.1 × 109 M ⊙. The average star formation rate surface density is langΣSFRrang = 0.55 M ⊙ yr-1 kpc-2, with a central peak of 1.7 M ⊙ yr-1 kpc-2. Using the standard Kennicutt-Schmidt relation, this corresponds to a gas mass surface density of Σgas = 243 M ⊙ pc-2. Integrating over the size of the galaxy, we find a total gas mass of M gas = 4.2 × 109 M ⊙. We estimate the gas fraction of DLA 2222-0946 to be f gas ~ 40%. We detect [N II] λ6583 emission at 3σ significance with a flux corresponding to a metallicity of 75% solar. Comparing this metallicity with that derived from the low-ion absorption gas ~6 kpc away, ~30% solar, indicates possible evidence for a metallicity gradient or enriched in/outflow of gas. Kinematically, both Hα and [O III] emission show relatively constant velocity fields over the central galactic region. While we detect some red and blueshifted clumps of emission, they do not correspond with rotational signatures that support an edge-on disk interpretation. The data presented herein were obtained at the W. M. Keck Observatory, which is operated as a scientific partnership among the California Institute of Technology, the University of California and the National Aeronautics and Space Administration. The Observatory was made possible by the generous financial support of the W. M. Keck Foundation.

  8. Spatially resolved emission of a high-redshift DLA galaxy with the Keck/OSIRIS IFU

    SciTech Connect

    Jorgenson, Regina A.; Wolfe, Arthur M.

    2014-04-10

    We present the first Keck/OSIRIS infrared IFU observations of a high-redshift damped Lyα (DLA) galaxy detected in the line of sight to a background quasar. By utilizing the Laser Guide Star Adaptive Optics to reduce the quasar point-spread function to FWHM ∼ 0.''15, we were able to search for and map the foreground DLA emission free from the quasar contamination. We present maps of the Hα and [O III] λλ5007, 4959 emission of DLA 2222–0946 at a redshift of z ∼ 2.35. From the composite spectrum over the Hα emission region, we measure a star formation rate of 9.5 ± 1.0 M {sub ☉} yr{sup –1} and a dynamical mass of M {sub dyn} = 6.1 × 10{sup 9} M {sub ☉}. The average star formation rate surface density is (Σ{sub SFR}) = 0.55 M {sub ☉} yr{sup –1} kpc{sup –2}, with a central peak of 1.7 M {sub ☉} yr{sup –1} kpc{sup –2}. Using the standard Kennicutt-Schmidt relation, this corresponds to a gas mass surface density of Σ{sub gas} = 243 M {sub ☉} pc{sup –2}. Integrating over the size of the galaxy, we find a total gas mass of M {sub gas} = 4.2 × 10{sup 9} M {sub ☉}. We estimate the gas fraction of DLA 2222–0946 to be f {sub gas} ∼ 40%. We detect [N II] λ6583 emission at 3σ significance with a flux corresponding to a metallicity of 75% solar. Comparing this metallicity with that derived from the low-ion absorption gas ∼6 kpc away, ∼30% solar, indicates possible evidence for a metallicity gradient or enriched in/outflow of gas. Kinematically, both Hα and [O III] emission show relatively constant velocity fields over the central galactic region. While we detect some red and blueshifted clumps of emission, they do not correspond with rotational signatures that support an edge-on disk interpretation.

  9. Molecular Aggregate Photophysics beyond the Kasha Model: Novel Design Principles for Organic Materials.

    PubMed

    Hestand, Nicholas J; Spano, Frank C

    2017-02-21

    The transport and photophysical properties of organic molecular aggregates, films, and crystals continue to receive widespread attention, driven mainly by expanding commercial applications involving display and wearable technologies as well as the promise of efficient, large-area solar cells. The main blueprint for understanding how molecular packing impacts photophysical properties was drafted over five decades ago by Michael Kasha. Kasha showed that the Coulombic coupling between two molecules, as determined by the alignment of their transition dipoles, induces energetic shifts in the main absorption spectral peak and changes in the radiative decay rate when compared to uncoupled molecules. In H-aggregates, the transition dipole moments align "side-by-side" leading to a spectral blue-shift and suppressed radiative decay rate, while in J-aggregates, the transition dipole moments align "head-to-tail" leading to a spectral red-shift and an enhanced radiative decay rate. Although many examples of H- and J-aggregates have been discovered, there are also many "unconventional" aggregates, which are not understood within the confines of Kasha's theory. Examples include nanopillars of 7,8,15,16-tetraazaterrylene, as well as several perylene-based dyes, which exhibit so-called H- to J-aggregate transformations. Such aggregates are typically characterized by significant wave function overlap between neighboring molecular orbitals as a result of small (∼4 Å) intermolecular distances, such as those found in rylene π-stacks and oligoacene herringbone lattices. Wave function overlap facilitates charge-transfer which creates an effective short-range exciton coupling that can also induce J- or H-aggregate behavior, depending on the sign. Unlike Coulomb coupling, short-range coupling is extremely sensitive to small (sub-Å) transverse displacements between neighboring chromophores. For perylene chromophores, the sign of the short-range coupling changes several times as two

  10. Cluster-cluster aggregation with particle replication and chemotaxy: a simple model for the growth of animal cells in culture

    NASA Astrophysics Data System (ADS)

    Alves, S. G.; Martins, M. L.

    2010-09-01

    Aggregation of animal cells in culture comprises a series of motility, collision and adhesion processes of basic relevance for tissue engineering, bioseparations, oncology research and in vitro drug testing. In the present paper, a cluster-cluster aggregation model with stochastic particle replication and chemotactically driven motility is investigated as a model for the growth of animal cells in culture. The focus is on the scaling laws governing the aggregation kinetics. Our simulations reveal that in the absence of chemotaxy the mean cluster size and the total number of clusters scale in time as stretched exponentials dependent on the particle replication rate. Also, the dynamical cluster size distribution functions are represented by a scaling relation in which the scaling function involves a stretched exponential of the time. The introduction of chemoattraction among the particles leads to distribution functions decaying as power laws with exponents that decrease in time. The fractal dimensions and size distributions of the simulated clusters are qualitatively discussed in terms of those determined experimentally for several normal and tumoral cell lines growing in culture. It is shown that particle replication and chemotaxy account for the simplest cluster size distributions of cellular aggregates observed in culture.

  11. Modeling of adsorption of toxic chromium on natural and surface modified lightweight expanded clay aggregate (LECA)

    NASA Astrophysics Data System (ADS)

    Kalhori, Ebrahim Mohammadi; Yetilmezsoy, Kaan; Uygur, Nihan; Zarrabi, Mansur; Shmeis, Reham M. Abu

    2013-12-01

    Lightweight Expanded Clay Aggregate (LECA) modified with an aqueous solution of magnesium chloride MgCl2 and hydrogen peroxide H2O2 was used to remove Cr(VI) from aqueous solutions. The adsorption properties of the used adsorbents were investigated through batch studies, Scanning Electron Microscopy (SEM), X-ray Diffraction (XRD), X-ray Fluorescence Spectroscopy (XRF), and Fourier Transform Infrared (FTIR) spectroscopy. The effect created by magnesium chloride on the modification of the LECA surface was greater than that of hydrogen peroxide solution and showed a substantial increase in the specific surface area which has a value of 76.12 m2/g for magnesium chloride modified LECA while the values of 53.72 m2/g, and 11.53 m2/g were found for hydrogen peroxide modified LECA and natural LECA, respectively. The extent of surface modification with enhanced porosity in modified LECA was apparent from the recorded SEM patterns. XRD and FTIR studies of themodified LECA surface did not show any structural distortion. The adsorption kinetics was found to follow the modified Freundlich kinetic model and the equilibrium data fitted the Sips and Dubinin-Radushkevich equations better than other models. Maximum sorption capacities were found to be 198.39, 218.29 and 236.24 mg/g for natural LECA, surface modified LECA with H2O2 and surface modified LECA with MgCl2, respectively. Adsorbents were found to have only a weak effect on conductivity and turbidity of aqueous solutions. Spent natural and surface modified LECA with MgCl2 was best regenerated with HCl solution, while LECA surface modified with H2O2 was best regenerated with HNO3 concentrated solution. Thermal method showed a lower regeneration percentage for all spent adsorbents.

  12. Identification of microstructural characteristics in lightweight aggregate concretes by micromechanical modelling including the interfacial transition zone (ITZ)

    SciTech Connect

    Ke, Y.; Ortola, S.; Beaucour, A.L.; Dumontet, H.

    2010-11-15

    An approach which combines both experimental techniques and micromechanical modelling is developed in order to characterise the elastic behaviour of lightweight aggregate concretes (LWAC). More than three hundred LWAC specimens with various lightweight aggregate types (5) of several volume ratios and three different mortar matrices (normal, HP, VHP) are tested. The modelling is based on iterative homogenisation process and includes the ITZ specificities experimentally observed with scanning electron microscopy (SEM). In agreement with experimental measurements, the effects of mix design parameters as well as of the interfacial transition zone (ITZ) on concrete mechanical performances are quantitatively analysed. Confrontations with experimental results allow identifying the elastic moduli of LWA which are difficult to determine experimentally. Whereas the traditional empirical formulas are not sufficiently precise, predictions of LWAC elastic behaviours computed with the micromechanical models appear in good agreement with experimental measurements.

  13. Construction aggregates

    USGS Publications Warehouse

    Tepordei, V.V.

    1995-01-01

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

  14. Use of an aggregate exposure model to estimate consumer exposure to fragrance ingredients in personal care and cosmetic products.

    PubMed

    Safford, B; Api, A M; Barratt, C; Comiskey, D; Daly, E J; Ellis, G; McNamara, C; O'Mahony, C; Robison, S; Smith, B; Thomas, R; Tozer, S

    2015-08-01

    Ensuring the toxicological safety of fragrance ingredients used in personal care and cosmetic products is essential in product development and design, as well as in the regulatory compliance of the products. This requires an accurate estimation of consumer exposure which, in turn, requires an understanding of consumer habits and use of products. Where ingredients are used in multiple product types, it is important to take account of aggregate exposure in consumers using these products. This publication investigates the use of a newly developed probabilistic model, the Creme RIFM model, to estimate aggregate exposure to fragrance ingredients using the example of 2-phenylethanol (PEA). The output shown demonstrates the utility of the model in determining systemic and dermal exposure to fragrances from individual products, and aggregate exposure. The model provides valuable information not only for risk assessment, but also for risk management. It should be noted that data on the concentrations of PEA in products used in this article were obtained from limited sources and not the standard, industry wide surveys typically employed by the fragrance industry and are thus presented here to illustrate the output and utility of the newly developed model. They should not be considered an accurate representation of actual exposure to PEA.

  15. Erosion of dust aggregates

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  16. STakeholder-Objective Risk Model (STORM): Determining the aggregated risk of multiple contaminant hazards in groundwater well catchments

    NASA Astrophysics Data System (ADS)

    Enzenhoefer, R.; Binning, P. J.; Nowak, W.

    2015-09-01

    Risk is often defined as the product of probability, vulnerability and value. Drinking water supply from groundwater abstraction is often at risk due to multiple hazardous land use activities in the well catchment. Each hazard might or might not introduce contaminants into the subsurface at any point in time, which then affects the pumped quality upon transport through the aquifer. In such situations, estimating the overall risk is not trivial, and three key questions emerge: (1) How to aggregate the impacts from different contaminants and spill locations to an overall, cumulative impact on the value at risk? (2) How to properly account for the stochastic nature of spill events when converting the aggregated impact to a risk estimate? (3) How will the overall risk and subsequent decision making depend on stakeholder objectives, where stakeholder objectives refer to the values at risk, risk attitudes and risk metrics that can vary between stakeholders. In this study, we provide a STakeholder-Objective Risk Model (STORM) for assessing the total aggregated risk. Or concept is a quantitative, probabilistic and modular framework for simulation-based risk estimation. It rests on the source-pathway-receptor concept, mass-discharge-based aggregation of stochastically occuring spill events, accounts for uncertainties in the involved flow and transport models through Monte Carlo simulation, and can address different stakeholder objectives. We illustrate the application of STORM in a numerical test case inspired by a German drinking water catchment. As one may expect, the results depend strongly on the chosen stakeholder objectives, but they are equally sensitive to different approaches for risk aggregation across different hazards, contaminant types, and over time.

  17. Effects of internal mixing and aggregate morphology on optical properties of black carbon using a discrete dipole approximation model

    NASA Astrophysics Data System (ADS)

    Scarnato, B. V.; Vahidinia, S.; Richard, D. T.; Kirchstetter, T. W.

    2013-05-01

    According to recent studies, internal mixing of black carbon (BC) with other aerosol materials in the atmosphere alters its aggregate shape, absorption of solar radiation, and radiative forcing. These mixing state effects are not yet fully understood. In this study, we characterize the morphology and mixing state of bare BC and BC internally mixed with sodium chloride (NaCl) using electron microscopy and examine the sensitivity of optical properties to BC mixing state and aggregate morphology using a discrete dipole approximation model (DDSCAT). DDSCAT is flexible in simulating the geometry and refractive index of particle aggregates. DDSCAT predicts a higher mass absorption coefficient (MAC), lower single scattering albedo (SSA), and higher absorption Angstrom exponent (AAE) for bare BC aggregates that are lacy rather than compact. Predicted values of SSA at 550 nm range between 0.16 and 0.27 for lacy and compact aggregates, respectively, in agreement with reported experimental values of 0.25 ± 0.05. The variation in absorption with wavelength does not adhere precisely to a power law relationship over the 200 to 1000 nm range. Consequently, AAE values depend on the wavelength region over which they are computed. The MAC of BC (averaged over the 200-1000 nm range) is amplified when internally mixed with NaCl (100-300 nm in radius) by factors ranging from 1.0 for lacy BC aggregates partially immersed in NaCl to 2.2 for compact BC aggregates fully immersed in NaCl. The SSA of BC internally mixed with NaCl is higher than for bare BC and increases with the embedding in the NaCl. Internally mixed BC SSA values decrease in the 200-400 nm wavelength range, a feature also common to the optical properties of dust and organics. Linear polarization features are also predicted in DDSCAT and are dependent on particle size and morphology. This study shows that DDSCAT predicts complex morphology and mixing state dependent aerosol optical properties that have been reported

  18. Engraftment of DLA-nonidentical unrelated canine marrow after high-dose fractionated total body irradiation

    SciTech Connect

    Deeg, H.J.; Storb, R.; Shulman, H.M.; Weiden, P.L.; Graham, T.C.; Thomas, E.D.

    1982-04-01

    Marrow transplants were carried out between unrelated DLA-nonidentical dogs. Recipients were conditioned for transplantation by total body irradiation (TBI) given eigher as a single dose of 9 Gy (900 rad) or fractionated in three increments of 6 Gy (600 rad) each at intervals of 48 hr. All recipients received marrow, less than or equal to 4 x 10(8) cells/kg, and no buffy coat cells. No immunosuppression was given after grafting. All 10 dogs given single dose total body irradiation failed to show engraftment and died with marrow aplasia and infectious complications (median survival 12 days). In contrast, all 10 dogs given fractionated TBI had sustained engraftment and died with graft-versus-host disease (GVHD) and infectious complications (median survival 12.5 days). None of the dogs died from radiation-induced gastroenteritis. In conclusion, resistance to DLA-nonidentical unrelated marrow grafts can be abrogated by high-dose TBI. This technique may allow hemopoietic engraftment even after i vitro manipulation of the marrow such as lymphocyte depletion by cell separation or treatment with anti-T cell antisera.

  19. Engraftment of DLA-nonidentical unrelated canine marrow after high-dose fractionated total body irradiation

    SciTech Connect

    Deeg, H.J.; Storb, R.; Shulman, H.M.; Weiden, P.L.; Graham, T.C.; Thomas, E.D.

    1982-04-01

    Marrow transplants were carried out between unrelated DLA-nonidentical dogs. Recipients were conditioned for transplantation by total body irradiation (TBI) given either as a single dose of 9 Gy (900 rad) or fractionated in three increments of 6 Gy (600 rad) each at intervals of 48 hr. All recipients received marrow, less than or equal to to 4 X 10/sup 8/ cells/kg, and no buffy coat cells. No immunosuppression was given after grafting. All 10 dogs given single-dose total body irradiation failed to show engraftment and died with marrow aplasia and infectious complications (median survival 12 days). In contrast, all 10 dogs given fractionated TBI had sustained engraftment and died with graft-versus-host disease (GVHD) and infectious complications (median survival 12.5 days). None of the dogs died from radiation-induced gastroenteritis.In conclusion, resistance to DLA-nonidentical unrelated marrow grafts can be abrogated by high-dose TBI. This technique may allow hemopoietic engraftment even after in vitro manipulation of the marrow such as lymphocyte depletion by cell separation or treatment with anti-T cell antisera.

  20. Grid Integration of Aggregated Demand Response, Part 2: Modeling Demand Response in a Production Cost Model

    SciTech Connect

    Hummon, Marissa; Palchak, David; Denholm, Paul; Jorgenson, Jennie; Olsen, Daniel J.; Kiliccote, Sila; Matson, Nance; Sohn, Michael; Rose, Cody; Dudley, Junqiao; Goli, Sasank; Ma, Ookie

    2013-12-01

    This report is one of a series stemming from the U.S. Department of Energy (DOE) Demand Response and Energy Storage Integration Study. This study is a multi-national-laboratory effort to assess the potential value of demand response (DR) and energy storage to electricity systems with different penetration levels of variable renewable resources and to improve our understanding of associatedmarkets and institutions. This report implements DR resources in the commercial production cost model PLEXOS.

  1. Complete Phenotypic Recovery of an Alzheimer's Disease Model by a Quinone-Tryptophan Hybrid Aggregation Inhibitor

    PubMed Central

    Scherzer-Attali, Roni; Pellarin, Riccardo; Convertino, Marino; Frydman-Marom, Anat; Egoz-Matia, Nirit; Peled, Sivan; Levy-Sakin, Michal; Shalev, Deborah E.; Caflisch, Amedeo; Gazit, Ehud; Segal, Daniel

    2010-01-01

    The rational design of amyloid oligomer inhibitors is yet an unmet drug development need. Previous studies have identified the role of tryptophan in amyloid recognition, association and inhibition. Furthermore, tryptophan was ranked as the residue with highest amyloidogenic propensity. Other studies have demonstrated that quinones, specifically anthraquinones, can serve as aggregation inhibitors probably due to the dipole interaction of the quinonic ring with aromatic recognition sites within the amyloidogenic proteins. Here, using in vitro, in vivo and in silico tools we describe the synthesis and functional characterization of a rationally designed inhibitor of the Alzheimer's disease-associated β-amyloid. This compound, 1,4-naphthoquinon-2-yl-L-tryptophan (NQTrp), combines the recognition capacities of both quinone and tryptophan moieties and completely inhibited Aβ oligomerization and fibrillization, as well as the cytotoxic effect of Aβ oligomers towards cultured neuronal cell line. Furthermore, when fed to transgenic Alzheimer's disease Drosophila model it prolonged their life span and completely abolished their defective locomotion. Analysis of the brains of these flies showed a significant reduction in oligomeric species of Aβ while immuno-staining of the 3rd instar larval brains showed a significant reduction in Aβ accumulation. Computational studies, as well as NMR and CD spectroscopy provide mechanistic insight into the activity of the compound which is most likely mediated by clamping of the aromatic recognition interface in the central segment of Aβ. Our results demonstrate that interfering with the aromatic core of amyloidogenic peptides is a promising approach for inhibiting various pathogenic species associated with amyloidogenic diseases. The compound NQTrp can serve as a lead for developing a new class of disease modifying drugs for Alzheimer's disease. PMID:20559435

  2. Modelling the effect of aggregates on N2O emission from denitrification in an agricultural peat soil

    NASA Astrophysics Data System (ADS)

    Stolk, P. C.; Hendriks, R. F. A.; Jacobs, C. M. J.; Moors, E. J.; Kabat, P.

    2011-09-01

    Nitrous oxide (N2O) emissions are highly variable in time, with high peak emissions lasting a few days to several weeks and low background emissions. This temporal variability is poorly understood which hampers the simulation of daily N2O emissions. In structured soils, like clay and peat, aggregates hamper the diffusion of oxygen, which leads to anaerobic microsites in the soil, favourable for denitrification. Diffusion of N2O out of the aggregates is also hampered, which leads to delayed emissions and increased reduction of N2O to N2. In this model simulation study we investigate the effect of aggregates in soils on the N2O emissions. We present a parameterization to simulate the effects of aggregates on N2O production by denitrification and on N2O reduction. The parameterization is based on the mobile-immobile model concept. It was implemented in a field-scale hydrological-biogeochemical model combination. We compared the simulated fluxes with observed fluxes from a fertilized and drained peat soil under grass. The results of this study show that aggregates strongly affect the simulated N2O emissions: peak emissions are lower, whereas the background emissions are slightly higher. Including the effect of aggregates caused a 40% decrease in the simulated annual emissions relative to the simulations without accounting for the effects of aggregates. The new parameterization significantly improved the model performance regarding simulation of observed daily N2O fluxes; r2 and RMSE improved from 0.11 and 198 g N2O-N ha-1 d-1 to 0.41 and 40 g N2O-N ha-1 d-1, respectively. Our analyses of the model results show that aggregates have a larger impact on the reduction than on the production of N2O. Reduction of N2O is more sensitive to changes in the drivers than production of N2O and is in that sense the key to understanding N2O emissions from denitrification. The effects of changing environmental conditions on reduction of N2O relative to N2O production strongly depend on

  3. 32 CFR 621.1 - Loan of Army/Defense Logistics Agency (DLA) owned property for use at national and State...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 32 National Defense 3 2010-07-01 2010-07-01 true Loan of Army/Defense Logistics Agency (DLA) owned property for use at national and State conventions. 621.1 Section 621.1 National Defense Department of... of Army/Defense Logistics Agency (DLA) owned property for use at national and State conventions....

  4. 32 CFR 621.1 - Loan of Army/Defense Logistics Agency (DLA) owned property for use at national and State...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 32 National Defense 3 2011-07-01 2009-07-01 true Loan of Army/Defense Logistics Agency (DLA) owned... of Army/Defense Logistics Agency (DLA) owned property for use at national and State conventions. (a... supply to destination and return will be borne by the requesting organization. (v) All charges...

  5. 32 CFR 621.1 - Loan of Army/Defense Logistics Agency (DLA) owned property for use at national and State...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 32 National Defense 3 2013-07-01 2013-07-01 false Loan of Army/Defense Logistics Agency (DLA... § 621.1 Loan of Army/Defense Logistics Agency (DLA) owned property for use at national and State... supply to destination and return will be borne by the requesting organization. (v) All charges...

  6. Presynaptic Alpha-Synuclein Aggregation in a Mouse Model of Parkinson's Disease

    PubMed Central

    Spinelli, Kateri J.; Taylor, Jonathan K.; Osterberg, Valerie R.; Churchill, Madeline J.; Pollock, Eden; Moore, Cynthia; Meshul, Charles K.

    2014-01-01

    Parkinson's disease and dementia with Lewy bodies are associated with abnormal neuronal aggregation of α-synuclein. However, the mechanisms of aggregation and their relationship to disease are poorly understood. We developed an in vivo multiphoton imaging paradigm to study α-synuclein aggregation in mouse cortex with subcellular resolution. We used a green fluorescent protein-tagged human α-synuclein mouse line that has moderate overexpression levels mimicking human disease. Fluorescence recovery after photobleaching (FRAP) of labeled protein demonstrated that somatic α-synuclein existed primarily in an unbound, soluble pool. In contrast, α-synuclein in presynaptic terminals was in at least three different pools: (1) as unbound, soluble protein; (2) bound to presynaptic vesicles; and (3) as microaggregates. Serial imaging of microaggregates over 1 week demonstrated a heterogeneous population with differing α-synuclein exchange rates. The microaggregate species were resistant to proteinase K, phosphorylated at serine-129, oxidized, and associated with a decrease in the presynaptic vesicle protein synapsin and glutamate immunogold labeling. Multiphoton FRAP provided the specific binding constants for α-synuclein's binding to synaptic vesicles and its effective diffusion coefficient in the soma and axon, setting the stage for future studies targeting synuclein modifications and their effects. Our in vivo results suggest that, under moderate overexpression conditions, α-synuclein aggregates are selectively found in presynaptic terminals. PMID:24501346

  7. MACROPHAGE AGGREGATES AS BIOMARKERS OF EXPOSURE: FROM FERAL POPULATIONS TO LABORATORY MODELS

    EPA Science Inventory

    Macrophage aggregates (MAs) are structures within the spleen, kidney and sometimes liver of teleost fishes. They are believed to function much like primitive lymph nodes in that phagocytized material is transported to these areas by macrophages, for destruction, recycling or stor...

  8. Protein Colloidal Aggregation Project

    NASA Technical Reports Server (NTRS)

    Oliva-Buisson, Yvette J. (Compiler)

    2014-01-01

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

  9. Computer Model of Biopolymer Crystal Growth and Aggregation by Addition of Macromolecular Units — a Comparative Study

    NASA Astrophysics Data System (ADS)

    Siódmiak, J.; Gadomski, A.

    We discuss the results of a computer simulation of the biopolymer crystal growth and aggregation based on the 2D lattice Monte Carlo technique and the HP approximation of the biopolymers. As a modeled molecule (growth unit) we comparatively consider the previously studied non-mutant lysozyme protein, Protein Data Bank (PDB) ID: 193L, which forms, under a certain set of thermodynamic-kinetic conditions, the tetragonal crystals, and an amyloidogenic variant of the lysozyme, PDB ID: 1LYY, which is known as fibril-yielding and prone-to-aggregation agent. In our model, the site-dependent attachment, detachment and migration processes are involved. The probability of growth unit motion, attachment and detachment to/from the crystal surface are assumed to be proportional to the orientational factor representing the anisotropy of the molecule. Working within a two-dimensional representation of the truly three-dimensional process, we also argue that the crystal grows in a spiral way, whereby one or more screw dislocations on the crystal surface give rise to a terrace. We interpret the obtained results in terms of known models of crystal growth and aggregation such as B-C-F (Burton-Cabrera-Frank) dislocation driven growth and M-S (Mullins-Sekerka) instability concept, with stochastic aspects supplementing the latter. We discuss the conditions under which crystals vs non-crystalline protein aggregates appear, and how the process depends upon difference in chemical structure of the protein molecule seen as the main building block of the elementary crystal cell.

  10. Fluorescence anisotropy uncovers changes in protein packing with inclusion growth in a cellular model of polyglutamine aggregation.

    PubMed

    Bhardwaj, Vishal; Panicker, Mitradas M; Udgaonkar, Jayant B

    2014-06-10

    The aggregation of polyglutamine-rich proteins is closely linked with numerous neurodegenerative disorders. In pathological and cellular models, the appearance of protein-rich inclusions in cells acts as a read out of protein aggregation. The precise organization of aggregated protein in these inclusions and their mode of growth are still poorly understood. Here, fluorescence anisotropy-based measurements have been used to probe protein packing across inclusions of varying brightness, formed by an monomeric enhanced green fluorescent protein (mEGFP)-tagged polyglutamine model peptide in cells. High-resolution, confocal-based steady-state anisotropy measurements report a large depolarization, consistent with extensive homo-Förster (fluorescence) resonance energy transfer (FRET) between the sequestered mEGFP-tagged protein molecules. An inverse correlation of fluorescence anisotropy with intensity is seen across inclusions, which becomes emphasized when the observed fluorescence anisotropy values of inclusions are corrected for the fluorescence contribution of the diffusible protein, present within and around smaller inclusions. Homo-FRET becomes enhanced as inclusion size increases. This enhancement is confirmed by two-photon excitation-based time-resolved fluorescence anisotropy decay measurements, which also suggest that the mEGFP-tagged protein molecules are arranged in multiple ways within inclusions. Bright inclusions display faster FRET rates with a larger number of mEGFP moieties participating in homo-FRET than faint inclusions do. These results are consistent with a model in which the protein is more closely packed in the brighter inclusions. In such a possible mechanism, the higher packing density of protein molecules in brighter inclusions would suggest that inclusion growth could involve an intermolecular compaction event within the inclusion, as more monomers and aggregates are recruited into the growing inclusion.

  11. Determination of thermodynamic potentials and the aggregation number for micelles with the mass-action model by isothermal titration calorimetry: A case study on bile salts.

    PubMed

    Olesen, Niels Erik; Westh, Peter; Holm, René

    2015-09-01

    The aggregation number (n), thermodynamic potentials (ΔG, ΔH, ΔS) and critical micelle concentration (CMC) for 6 natural bile salts were determined on the basis of both original and previously published isothermal titration calorimetry (ITC) data. Different procedures to estimate parameters of micelles with ITC were compared to a mass-action model (MAM) of reaction type: n⋅S⇌Mn. This analysis can provide guidelines for future ITC studies of systems behaving in accordance with this model such as micelles and proteins that undergo self-association to oligomers. Micelles with small aggregation numbers, as those of bile salts, are interesting because such small aggregates cannot be characterized as a separate macroscopic phase and the widely applied pseudo-phase model (PPM) is inaccurate. In the present work it was demonstrated that the aggregation number of micelles was constant at low concentrations enabling determination of the thermodynamic potentials by the MAM. A correlation between the aggregation number and the heat capacity was found, which implies that the dehydrated surface area of bile salts increases with the aggregation number. This is in accordance with Tanford's principles of opposing forces where neighbouring molecules in the aggregate are better able to shield from the surrounding hydrophilic environment when the aggregation number increases.

  12. Modeling the Interaction between β-Amyloid Aggregates and Choline Acetyltransferase Activity and Its Relation with Cholinergic Dysfunction through Two-Enzyme/Two-Compartment Model

    PubMed Central

    Fgaier, Hedia; Mustafa, Ibrahim H. I.; Awad, Asmaa A. R.; Elkamel, Ali

    2015-01-01

    The effect of β-amyloid aggregates on activity of choline acetyltransferase (ChAT) which is responsible for synthesizing acetylcholine (ACh) in human brain is investigated through the two-enzyme/two-compartment (2E2C) model where the presynaptic neuron is considered as compartment 1 while both the synaptic cleft and the postsynaptic neuron are considered as compartment 2 through suggesting three different kinetic mechanisms for the inhibition effect. It is found that the incorporation of ChAT inhibition by β-amyloid aggregates into the 2E2C model is able to yield dynamic solutions for concentrations of generated β-amyloid, ACh, choline, acetate, and pH in addition to the rates of ACh synthesis and ACh hydrolysis in compartments 1 and 2. It is observed that ChAT activity needs a high concentration of β-amyloid aggregates production rate. It is found that ChAT activity is reduced significantly when neurons are exposed to high levels of β-amyloid aggregates leading to reduction in levels of ACh which is one of the most significant physiological symptoms of AD. Furthermore, the system of ACh neurocycle is dominated by the oscillatory behavior when ChAT enzyme is completely inhibited by β-amyloid. It is observed that the direct inactivation of ChAT by β-amyloid aggregates may be a probable mechanism contributing to the development of AD. PMID:26413144

  13. Effects of internal mixing and aggregate morphology on optical properties of black carbon using a discrete dipole approximation model

    NASA Astrophysics Data System (ADS)

    Scarnato, B.; Vahidinia, S.; Richard, D. T.; Kirchstetter, T. W.

    2012-10-01

    According to recent studies, internal mixing of black carbon (BC) with other aerosol materials in the atmosphere alters its aggregate shape, absorption of solar radiation, and radiative forcing. These mixing state effects are not yet fully understood. In this study, we characterize the morphology and mixing state of bare BC and BC internally mixed with sodium chloride (NaCl) using electron microscopy and examine the sensitivity of optical properties to BC mixing state and aggregate morphology using a discrete dipole approximation model (DDSCAT). DDSCAT predicts a higher mass absorption coefficient, lower single scattering albedo (SSA), and higher absorption Angstrom exponent (AAE) for bare BC aggregates that are lacy rather than compact. Predicted values of SSA at 550 nm range between 0.18 and 0.27 for lacy and compact aggregates, respectively, in agreement with reported experimental values of 0.25 ± 0.05. The variation in absorption with wavelength does not adhere precisely to a power law relationship over the 200 to 1000 nm range. Consequently, AAE values depend on the wavelength region over which they are computed. In the 300 to 550 nm range, AAE values ranged in this study from 0.70 for compact to 0.95 for lacy aggregates. The SSA of BC internally mixed with NaCl (100-300 nm in radius) is higher than for bare BC and increases with the embedding in the NaCl. Internally mixed BC SSA values decrease in the 200-400 nm wavelength range, a feature also common to the optical properties of dust and organics. Linear polarization features are also predicted in DDSCAT and are dependent on particle morphology. The bare BC (with a radius of 80 nm) presents in the linear polarization a bell shape feature, which is a characteristic of the Rayleigh regime (for particles smaller than the wavelength of incident radiation). When BC is internally mixed with NaCl (100-300 nm in radius), strong depolarization features for near-VIS incident radiation are evident, such as a decrease

  14. Optical spectroscopy and system-bath interactions in molecular aggregates with full configuration interaction Frenkel exciton model

    NASA Astrophysics Data System (ADS)

    Seibt, Joachim; Sláma, Vladislav; Mančal, Tomáš

    2016-12-01

    Standard application of the Frenkel exciton model neglects resonance coupling between collective molecular aggregate states with different number of excitations. These inter-band coupling terms are, however, of the same magnitude as the intra-band coupling between singly excited states. We systematically derive the Frenkel exciton model from quantum chemical considerations, and identify it as a variant of the configuration interaction method. We discuss all non-negligible couplings between collective aggregate states, and provide compact formulae for their calculation. We calculate absorption spectra of molecular aggregate of carotenoids and identify significant band shifts as a result of inter-band coupling. The presence of inter-band coupling terms requires renormalization of the system-bath coupling with respect to standard formulation, but renormalization effects are found to be weak. We present detailed discussion of molecular dimer and calculate its time-resolved two-dimensional Fourier transformed spectra to find weak but noticeable effects of peak amplitude redistribution due to inter-band coupling.

  15. Mathematical modeling of electro-rotation spectra of small particles in liquid solutions: application to human erythrocyte aggregates.

    PubMed

    Zehe, A; Ramírez, A; Starostenko, O

    2004-02-01

    Electro-rotation can be used to determine the dielectric properties of cells, as well as to observe dynamic changes in both dielectric and morphological properties. Suspended biological cells and particles respond to alternating-field polarization by moving, deforming or rotating. While in linearly polarized alternating fields the particles are oriented along their axis of highest polarizability, in circularly polarized fields the axis of lowest polarizability aligns perpendicular to the plane of field rotation. Ellipsoidal models for cells are frequently applied, which include, beside sphere-shaped cells, also the limiting cases of rods and disks. Human erythrocyte cells, due to their particular shape, hardly resemble an ellipsoid. The additional effect of rouleaux formation with different numbers of aggregations suggests a model of circular cylinders of variable length. In the present study, the induced dipole moment of short cylinders was calculated and applied to rouleaux of human erythrocytes, which move freely in a suspending conductive medium under the effect of a rotating external field. Electro-rotation torque spectra are calculated for such aggregations of different length. Both the maximum rotation speeds and the peak frequencies of the torque are found to depend clearly on the size of the rouleaux. While the rotation speed grows with rouleaux length, the field frequency nu(p) is lowest for the largest cell aggregations where the torque shows a maximum.

  16. Importance of aggregation and small ice crystals in cirrus clouds, based on observations and an ice particle growth model

    NASA Technical Reports Server (NTRS)

    Mitchell, David L.; Chai, Steven K.; Dong, Yayi; Arnott, W. Patrick; Hallett, John

    1993-01-01

    The 1 November 1986 FIRE I case study was used to test an ice particle growth model which predicts bimodal size spectra in cirrus clouds. The model was developed from an analytically based model which predicts the height evolution of monomodal ice particle size spectra from the measured ice water content (IWC). Size spectra from the monomodal model are represented by a gamma distribution, N(D) = N(sub o)D(exp nu)exp(-lambda D), where D = ice particle maximum dimension. The slope parameter, lambda, and the parameter N(sub o) are predicted from the IWC through the growth processes of vapor diffusion and aggregation. The model formulation is analytical, computationally efficient, and well suited for incorporation into larger models. The monomodal model has been validated against two other cirrus cloud case studies. From the monomodal size spectra, the size distributions which determine concentrations of ice particles less than about 150 mu m are predicted.

  17. Modeling Soil Carbon Dynamics in Northern Forests: Effects of Spatial and Temporal Aggregation of Climatic Input Data.

    PubMed

    Dalsgaard, Lise; Astrup, Rasmus; Antón-Fernández, Clara; Borgen, Signe Kynding; Breidenbach, Johannes; Lange, Holger; Lehtonen, Aleksi; Liski, Jari

    2016-01-01

    Boreal forests contain 30% of the global forest carbon with the majority residing in soils. While challenging to quantify, soil carbon changes comprise a significant, and potentially increasing, part of the terrestrial carbon cycle. Thus, their estimation is important when designing forest-based climate change mitigation strategies and soil carbon change estimates are required for the reporting of greenhouse gas emissions. Organic matter decomposition varies with climate in complex nonlinear ways, rendering data aggregation nontrivial. Here, we explored the effects of temporal and spatial aggregation of climatic and litter input data on regional estimates of soil organic carbon stocks and changes for upland forests. We used the soil carbon and decomposition model Yasso07 with input from the Norwegian National Forest Inventory (11275 plots, 1960-2012). Estimates were produced at three spatial and three temporal scales. Results showed that a national level average soil carbon stock estimate varied by 10% depending on the applied spatial and temporal scale of aggregation. Higher stocks were found when applying plot-level input compared to country-level input and when long-term climate was used as compared to annual or 5-year mean values. A national level estimate for soil carbon change was similar across spatial scales, but was considerably (60-70%) lower when applying annual or 5-year mean climate compared to long-term mean climate reflecting the recent climatic changes in Norway. This was particularly evident for the forest-dominated districts in the southeastern and central parts of Norway and in the far north. We concluded that the sensitivity of model estimates to spatial aggregation will depend on the region of interest. Further, that using long-term climate averages during periods with strong climatic trends results in large differences in soil carbon estimates. The largest differences in this study were observed in central and northern regions with strongly

  18. Modeling Soil Carbon Dynamics in Northern Forests: Effects of Spatial and Temporal Aggregation of Climatic Input Data

    PubMed Central

    Dalsgaard, Lise; Astrup, Rasmus; Antón-Fernández, Clara; Borgen, Signe Kynding; Breidenbach, Johannes; Lange, Holger; Lehtonen, Aleksi; Liski, Jari

    2016-01-01

    Boreal forests contain 30% of the global forest carbon with the majority residing in soils. While challenging to quantify, soil carbon changes comprise a significant, and potentially increasing, part of the terrestrial carbon cycle. Thus, their estimation is important when designing forest-based climate change mitigation strategies and soil carbon change estimates are required for the reporting of greenhouse gas emissions. Organic matter decomposition varies with climate in complex nonlinear ways, rendering data aggregation nontrivial. Here, we explored the effects of temporal and spatial aggregation of climatic and litter input data on regional estimates of soil organic carbon stocks and changes for upland forests. We used the soil carbon and decomposition model Yasso07 with input from the Norwegian National Forest Inventory (11275 plots, 1960–2012). Estimates were produced at three spatial and three temporal scales. Results showed that a national level average soil carbon stock estimate varied by 10% depending on the applied spatial and temporal scale of aggregation. Higher stocks were found when applying plot-level input compared to country-level input and when long-term climate was used as compared to annual or 5-year mean values. A national level estimate for soil carbon change was similar across spatial scales, but was considerably (60–70%) lower when applying annual or 5-year mean climate compared to long-term mean climate reflecting the recent climatic changes in Norway. This was particularly evident for the forest-dominated districts in the southeastern and central parts of Norway and in the far north. We concluded that the sensitivity of model estimates to spatial aggregation will depend on the region of interest. Further, that using long-term climate averages during periods with strong climatic trends results in large differences in soil carbon estimates. The largest differences in this study were observed in central and northern regions with

  19. Early Fuel Cell Market Deployments: ARRA and Combined (IAA, DLA, ARRA); Quarter 3 2012 Composite Data Products

    SciTech Connect

    Kurtz, J.; Wipke, K.; Sprik, S.; Ramsden, T.; Ainscough, C.; Saur, G.; Post, M.

    2013-01-01

    This report from the U.S. Department of Energy's National Renewable Energy Laboratory includes early fuel cell market composite data products for the third quarter of 2012 for American Recovery and Reinvestment Act (ARRA) and combined (IAA, DLA, ARRA) deployment projects.

  20. Early Fuel Cell Market Deployments: ARRA and Combined (IAA, DLA, ARRA): Quarter 4 2013 Composite Data Products

    SciTech Connect

    Kurtz, J.; Sprik, S.

    2014-06-01

    This report includes the composite data products (CDPs) for early fuel cell market deployments in quarter 4 of 2013. Results are presented for ARRA (projects funded by the American Recovery and Reinvestment Act of 2009 [ARRA]) and Combined (projects funded by DOE Interagency Agreements [IAA], Department of Defense Defense Logistics Agency [DLA], and ARRA).

  1. Proteins aggregation and human diseases

    NASA Astrophysics Data System (ADS)

    Hu, Chin-Kun

    2015-04-01

    Many human diseases and the death of most supercentenarians are related to protein aggregation. Neurodegenerative diseases include Alzheimer's disease (AD), Huntington's disease (HD), Parkinson's disease (PD), frontotemporallobar degeneration, etc. Such diseases are due to progressive loss of structure or function of neurons caused by protein aggregation. For example, AD is considered to be related to aggregation of Aβ40 (peptide with 40 amino acids) and Aβ42 (peptide with 42 amino acids) and HD is considered to be related to aggregation of polyQ (polyglutamine) peptides. In this paper, we briefly review our recent discovery of key factors for protein aggregation. We used a lattice model to study the aggregation rates of proteins and found that the probability for a protein sequence to appear in the conformation of the aggregated state can be used to determine the temperature at which proteins can aggregate most quickly. We used molecular dynamics and simple models of polymer chains to study relaxation and aggregation of proteins under various conditions and found that when the bending-angle dependent and torsion-angle dependent interactions are zero or very small, then protein chains tend to aggregate at lower temperatures. All atom models were used to identify a key peptide chain for the aggregation of insulin chains and to find that two polyQ chains prefer anti-parallel conformation. It is pointed out that in many cases, protein aggregation does not result from protein mis-folding. A potential drug from Chinese medicine was found for Alzheimer's disease.

  2. Radiative decay of excitons in model aggregates of {pi}-conjugated oligomers

    SciTech Connect

    Manas, E.S.; Spano, F.C.

    1998-07-01

    Spontaneous emission from exciton states in an aggregate of {pi}-conjugated oligomers is studied theoretically. Each oligomer is taken as a ring of N carbon atoms and is treated using a PPP Hamiltonian. Coulombic interactions between rings are treated to first order. The radiative decay rate {gamma} from an exciton state in an aggregate of M aligned oligomers is superradiant, being M times faster than the decay rate of an isolated oligomer exciton. Inter-oligomer interactions have little effect on the exciton size and energy when the oligomer size N is large compared to the interoligomer spacing. However, when N is small, both the exciton size and energy are strongly affected by these interactions, leading to a markedly different N dependence for {gamma}.

  3. Alpha Synuclein Aggregation in a Neurotoxic Model of Parkinson’s Disease

    DTIC Science & Technology

    2001-08-01

    The cause of Parkinson’s disease (PD) is not known but the pattern of neurodegeneration can be replicated by the systemic administration of the neurotoxin 1-methyl-4-phenyl-tetrahydropyridine (MPTP). MPTP inhibits mitochondrial oxidative phosphorylation and causes oxidative injury leading to cell death. Neurons that degenerate in PD develop inclusions called Lewy bodies that are composed of aggregates of a synaptic protein, alpha synuclein. The purpose of this study is

  4. Aggregate dust model to study the polarization properties of comet C/1996 B2 Hyakutake

    NASA Astrophysics Data System (ADS)

    Das, Himadri Sekhar; Suklabaidya, Abinash; Majumder, Saonli Datta; Sen, Asoke Kumar

    2010-04-01

    The observed linear polarization data of comet Hyakutake are studied at wavelengths λ = 0.365 μm, λ = 0.485 μm and 0.684μm through simulations using Ballistic Particle-Cluster Aggregate and Ballistic Cluster-Cluster Aggregate aggregates of 128 spherical monomers. We first found that the size parameter of the monomer, x ~ 1.56-1.70, turned out to be the most suitable which provides the best fits to the observed dust scattering properties at three wavelengths: λ = 0.365 μm, 0.485 μm and 0.684 μm. Thus, the effective radius of the aggregate (r) lies in the range 0.45 μm <= r <= 0.49 μm at λ = 0.365 μm 0.60 μm <= r <= 0.66 μm at λ = 0.485 μm and 0.88 μm <= r <= 0.94 μm at λ = 0.684 μm. Now using superposition t-matrix code and the power-law size distribution, n(r) ~ r-3, the best-fitting values of complex refractive indices are calculated for the observed polarization data at the above three wavelengths. The best-fitting complex refractive indices (n, k) are found to be (1.745, 0.095) at λ = 0.365 μm, (1.743, 0.100) at λ = 0.485 μm and (1.695, 0.100) at λ = 0.684 μm. The refractive indices derived from the present analysis correspond to a mixture of both silicates and organics, which are in good agreement with the in situ measurement of comets by different spacecraft.

  5. Investigation of piperidine derivatives in ex vivo models of pain and platelet aggregation.

    PubMed

    Saify, Zafar Saeed; Rasheed, Huma; Mushtaq, Nousheen; Nisa, Mehrun; Haider, Shazia; Naz, Afshan; Azhar, Kaniz Fizza; Miana, Ghulam Abbas

    2012-11-01

    Piperidine derivatives are known to exhibit analgesic activities and are likely to possess the ability to block the effects of prostaglandins through inhibition of downstream signaling pathways. The present study investigated the activity of five derivatives (PD2-6) of 4-(4'-bromophenyl)-4-piperidinol (PD1), against pain and platelet aggregation mediated by the release of prostaglandins and thromboxane A2, respectively. The results showed that compound PD1 and its two phenacyl derivatives PD3 and PD5 exhibited a highly significant analgesic effect (p < 0.01), whereas PD4 and PD6 also showed significant activity. PD3, the most active analgesic compound when docked to the opioid receptor, had interactions between the oxygen of its nitro group and the amino group of ARG 573, indicating a distance of 1.2563 Å. The antiplatelet data showed that compound PD5 (4-(4'-bromo-phenyl)-4-hydroxy-1-[2-(2″,4″-dimethoxyphenyl)-2-oxo-ethyl]-piperidinium bromide) had an IC(50) = 0.06 mM, which was the most active compound, whereas PD3 was the second most active compound against platelet aggregating factor-induced aggregation with an IC(50) = 80 mM. Acetyl salicylic acid (IC(50) = 150 μM) was used as a positive control.

  6. Charged Dust Aggregate Interactions

    NASA Astrophysics Data System (ADS)

    Matthews, Lorin; Hyde, Truell

    2015-11-01

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

  7. Estimating transition rates in aggregated Markov models of ion channel gating with loops and with nearly equal dwell times

    PubMed Central

    Wagner, M.; Michalek, S.; Timmer, J.

    1999-01-01

    A typical task in the application of aggregated Markov models to ion channel data is the estimation of the transition rates between the states. Realistic models for ion channel data often have one or more loops. We show that the transition rates of a model with loops are not identifiable if the model has either equal open or closed dwell times. This non-identifiability of the transition rates also has an effect on the estimation of the transition rates for models which are not subject to the constraint of either equal open or closed dwell times. If a model with loops has nearly equal dwell times, the Hessian matrix of its likelihood function will be ill-conditioned and the standard deviations of the estimated transition rates become extraordinarily large for a number of data points which are typically recorded in experiments.

  8. Computational study of the effect of dispersion interactions on the thermochemistry of aggregation of fused polycyclic aromatic hydrocarbons as model asphaltene compounds in solution.

    PubMed

    Moreira da Costa, Leonardo; Stoyanov, Stanislav R; Gusarov, Sergey; Seidl, Peter R; Walkimar de M Carneiro, José; Kovalenko, Andriy

    2014-02-06

    Density functional theory (DFT), Møller-Plesset second-order perturbation theory (MP2), and semiempirical methods are employed for the geometry optimization and thermochemistry analysis of π-π stacked di-, tri-, tetra-, and pentamer aggregates of the fused polycyclic aromatic hydrocarbons (PAHs) naphthalene, anthracene, phenanthrene, tetracene, pyrene, and coronene as well as benzene. These aggregates (stabilized by dispersion interactions) are highly relevant to the intermolecular aggregation of asphaltenes, major components of heavy petroleum. The strength of π-π stacking interaction is evaluated with respect to the π-stacking distance and thermochemistry results, such as aggregation enthalpies, entropies, and Gibbs free energies (ΔG(298)). For both π-stacking interplanar distances and thermochemistry, the ωB97X-D functional with an augmented damped R(-6) dispersion correction term and MP2 are in the closest agreement with the highly accurate spin-component scaled MP2 (SCS-MP2) method that we selected as a reference. The ΔG(298) values indicate that the aggregation of coronene is spontaneous at 298 K and the formation of pyrene dimers occurs spontaneously at temperature lower than 250 K. Aggregates of smaller PAHs would be stable at even lower temperature. These findings are supported by X-ray crystallographic determination results showing that among the PAHs studied only coronene forms continuous stacked aggregates in single crystals, pyrene forms dimers, and smaller PAHs do not form π-π stacked aggregates. Thermochemistry analysis results show that PAHs containing more than four fused benzene rings would spontaneously form aggregates at 298 K. Also, round-shaped PAHs, such as phenanthrene and pyrene, form more stable aggregates than linear PAHs, such as anthracene and tetracene, due to decreased entropic penalty. These results are intended to help guide the synthesis of model asphaltene compounds for spectroscopic studies so as to help understand

  9. Iron is a specific cofactor for distinct oxidation- and aggregation-dependent Aβ toxicity mechanisms in a Drosophila model

    PubMed Central

    Ott, Stanislav; Dziadulewicz, Nikolas; Crowther, Damian C.

    2015-01-01

    ABSTRACT Metals, including iron, are present at high concentrations in amyloid plaques in individuals with Alzheimer's disease, where they are also thought to be cofactors in generating oxidative stress and modulating amyloid formation. In this study, we present data from several Drosophila models of neurodegenerative proteinopathies indicating that the interaction between iron and amyloid beta peptide (Aβ) is specific and is not seen for other aggregation-prone polypeptides. The interaction with iron is likely to be important in the dimerisation of Aβ and is mediated by three N-terminal histidines. Transgenic fly lines systematically expressing all combinations of His>Ala substitutions in Aβ were generated and used to study the pathological role of these residues. Developmental eye phenotypes, longevity and histological examinations indicate that the N-terminal histidines have distinct position-dependent and -independent mechanisms. The former mediate the toxic effects of metals and Aβ aggregation under non-oxidising conditions and the latter are relevant under oxidising conditions. Understanding how Aβ mediates neurotoxic effects in vivo will help to better target pathological pathways using aggregation blockers and metal-modifying agents. PMID:26035384

  10. Experimental traumatic brain injury induces rapid aggregation and oligomerization of amyloid-beta in an Alzheimer's disease mouse model.

    PubMed

    Washington, Patricia M; Morffy, Nicholas; Parsadanian, Maia; Zapple, David N; Burns, Mark P

    2014-01-01

    Soluble amyloid-beta (Aβ) oligomers are hypothesized to be the pathogenic species in Alzheimer's disease (AD), and increased levels of oligomers in the brain subsequent to traumatic brain injury (TBI) may exacerbate secondary injury pathways and underlie increased risk of developing AD in later life. To determine whether TBI causes Aβ aggregation and oligomerization in the brain, we exposed triple transgenic AD model mice to controlled cortical impact injury and measured levels of soluble, insoluble, and oligomeric Aβ by enzyme-linked immunosorbent assay (ELISA) at 1, 3, and 7 days postinjury. TBI rapidly increased levels of both soluble and insoluble Aβ40 and Aβ42 in the injured cortex at 1 day postinjury. We confirmed previous findings that identified damaged axons as a major site of Aβ accumulation using both immunohistochemistry and biochemistry. We also report that soluble Aβ oligomers were significantly increased in the injured cortex, as demonstrated by both ELISA and Western blot. Interestingly, the mouse brain is able to rapidly clear trauma-induced Aβ, with both soluble and insoluble Aβ species returning to sham levels by 7 days postinjury. In conclusion, we demonstrate that TBI causes acute accumulation and aggregation of Aβ in the brain, including the formation of low- and high-molecular-weight Aβ oligomers. The formation and aggregation of Aβ into toxic species acutely after injury may play a role in secondary injury cascades after trauma and, chronically, may contribute to increased risk of developing AD in later life.

  11. USE OF PBPK MODELS FOR ASSESSING ABSORBED DOSE AND CHE INHIBITION FROM AGGREGATE EXPOSURE OF INFANTS AND CHILDREN TO ORGANOPHOSPHORUS INSECTICIDES

    EPA Science Inventory

    A physiological pharmacokinetic (PBPK) modeling framework has been established to assess cumulative risk of dose and injury of infants and children to organophosphorus (OP) insecticides from aggregate sources and routes. Exposure inputs were drawn from all reasonable sources, pr...

  12. The effect of time-dependent macromolecular crowding on the kinetics of protein aggregation: a simple model for the onset of age-related neurodegenerative disease

    NASA Astrophysics Data System (ADS)

    Minton, Allen

    2014-08-01

    A linear increase in the concentration of "inert" macromolecules with time is incorporated into simple excluded volume models for protein condensation or fibrillation. Such models predict a long latent period during which no significant amount of protein aggregates, followed by a steep increase in the total amount of aggregate. The elapsed time at which these models predict half-conversion of model protein to aggregate varies by less than a factor of two when the intrinsic rate constant for condensation or fibril growth of the protein is varied over many orders of magnitude. It is suggested that this concept can explain why the symptoms of neurodegenerative diseases associated with the aggregation of very different proteins and peptides appear at approximately the same advanced age in humans.

  13. Small angle X-ray scattering study of meso-tetrakis (4-sulfonatophenyl) porphyrin in aqueous solution: a self-aggregation model.

    PubMed

    Gandini, S C M; Gelamo, E L; Itri, R; Tabak, M

    2003-08-01

    The aggregate morphology of meso-tetrakis(4-sulfonatophenyl) porphyrin (TPPS(4)) in aqueous solution is investigated by using small angle x-ray scattering (SAXS) technique. Measurements were performed at pH 4.0 and 9.0 to monitor the pH influence on the structural parameters of the aggregates. Radii of gyration were obtained from distance distribution functions p(r) analysis. The experimental data of TPPS(4) at pH 4.0 showed well-defined oscillations characteristic of large aggregates in contrast to the SAXS curve of 5 mM TPPS(4) at pH 9.0, where both a significant decrease in the intensity and the disappearance of the oscillation peaks suggest the dissociation of the aggregate. A 340-A long "hollow" cylinder with shell thickness of 20 A, compatible to the porphyrin molecule dimension, represents well the scattering curve of the aggregates at pH 4.0. According to the fitting parameters, 26 porphyrin molecules self-associate into a ringlike configuration in the plane of the cylinder cross-section. The total number of porphyrin molecules in the whole aggregate was also estimated as approximately 3000. The model compatible to SAXS data of a hollow cylinder with J-aggregation in the cross-section and H-aggregation (columnar stacking) between the cylinder layers is consistent with optical absorption spectroscopic data both in the literature and obtained in this work.

  14. A model of neutralization of Chlamydia trachomatis based on antibody and host cell aggregation on the elementary body surface.

    PubMed

    Wilson, D P; McElwain, D L S

    2004-02-07

    Humoral immunity is that aspect of specific immunity that is mediated by B lymphocytes and involves the neutralizing of pathogens by means of antibodies attaching to the pathogen's binding sites. Antibodies bind to and block ligand sites on the pathogen which prevents these sites from attaching to target cell receptors and so cell entry is inhibited. Many studies investigate the role of humoral immunity for protection against chlamydial challenge and they have shown that neutralization of the chlamydial body requires a large number of attached antibodies. Steric hindrance greatly influences the number of available sites that may be bound, reducing relative occupancy well below 100%. We model steric effects of antibody Fab fragment attachment indicating that they must be taken into consideration to accurately model valency, the number of available binding sites. We derive a partial differential equation for the number of antibody Fabs and host cell receptors that are aggregated to extracellular chlamydial elementary bodies. We consider steric effects in describing the size distribution of aggregates. Our theory is in good agreement with Monte Carlo simulations of binding. We use our theoretical prediction for the valency in a model for the in-host population dynamics of a chlamydial infection and we fit our model to experimental data.

  15. A spatial model to aggregate point-source and nonpoint-source water-quality data for large areas

    USGS Publications Warehouse

    White, D.A.; Smith, R.A.; Price, C.V.; Alexander, R.B.; Robinson, K.W.

    1992-01-01

    More objective and consistent methods are needed to assess water quality for large areas. A spatial model, one that capitalizes on the topologic relationships among spatial entities, to aggregate pollution sources from upstream drainage areas is described that can be implemented on land surfaces having heterogeneous water-pollution effects. An infrastructure of stream networks and drainage basins, derived from 1:250,000-scale digital-elevation models, define the hydrologic system in this spatial model. The spatial relationships between point- and nonpoint pollution sources and measurement locations are referenced to the hydrologic infrastructure with the aid of a geographic information system. A maximum-branching algorithm has been developed to simulate the effects of distance from a pollutant source to an arbitrary downstream location, a function traditionally employed in deterministic water quality models. ?? 1992.

  16. Marine aggregate dynamics

    NASA Astrophysics Data System (ADS)

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

  17. Aggregation in complex triacylglycerol oils: coarse-grained models, nanophase separation, and predicted x-ray intensities

    NASA Astrophysics Data System (ADS)

    Quinn, Bonnie; Peyronel, Fernanda; Gordon, Tyler; Marangoni, Alejandro; Hanna, Charles B.; Pink, David A.

    2014-11-01

    Triacylglycerols (TAGs) are biologically important molecules which form crystalline nanoplatelets (CNPs) and, ultimately, fat crystal networks in edible oils. Characterizing the self-assembled hierarchies of these networks is important to understanding their functionality and oil binding capacity. We have modelled CNPs in multicomponent oils and studied their aggregation. The oil comprises (a) a liquid componentt, and (b) components which phase separately on a nano-scale (nano-phase separation) to coat the surfaces of the CNPs impenetrably, either isotropically or anisotropically, with either liquid-like coatings or crystallites, forming a coating of thickness Δ. We modelled three cases: (i) liquid-liquid nano-phase separation, (ii) solid-liquid nano-phase separation, with CNPs coated isotropically, and (iii) CNPs coated anisotropically. The models were applied to mixes of tristearin and triolein with fully hydrogenated canola oil, shea butter with high oleic sunflower oil, and cotton seed oil. We performed Monte Carlo simulations, computed structure functions and concluded: (1) three regimes arose: (a) thin coating regime, Δ \\lt 0.0701 u (b) transition regime, 0.0701 u≤slant Δ ≤slant 0.0916 u and (c) thick coating regime, Δ \\gt 0.0916 u . (arbitrary units, u) (2) The thin coating regime exhibits 1D TAGwoods, which aggregate, via DLCA/RLCA, into fractal structures which are uniformly distributed in space. (3) In the thick coating regime, for an isotropic coating, TAGwoods are not formed and coated CNPs will not aggregate but will be uniformly distributed in space. For anisotropic coating, TAGwoods can be formed and might form 1D strings but will not form DLCA/RLCA clusters. (4) The regimes are, approximately: thin coating, 0\\lt Δ \\lt 7.0 \\text{nm} transition regime, 7.0\\ltΔ \\lt 9.2 \\text{nm} and thick coating, Δ \\gt 9.2 \\text{nm} (5) The minimum minority TAG concentration required to undergo nano-phase separation is, approximately, 0.29% (thin

  18. Aggregation in complex triacylglycerol oils: coarse-grained models, nanophase separation, and predicted x-ray intensities.

    PubMed

    Quinn, Bonnie; Peyronel, Fernanda; Gordon, Tyler; Marangoni, Alejandro; Hanna, Charles B; Pink, David A

    2014-11-19

    Triacylglycerols (TAGs) are biologically important molecules which form crystalline nanoplatelets (CNPs) and, ultimately, fat crystal networks in edible oils. Characterizing the self-assembled hierarchies of these networks is important to understanding their functionality and oil binding capacity. We have modelled CNPs in multicomponent oils and studied their aggregation. The oil comprises (a) a liquid component, and (b) components which phase separately on a nano-scale (nano-phase separation) to coat the surfaces of the CNPs impenetrably, either isotropically or anisotropically, with either liquid-like coatings or crystallites, forming a coating of thickness ?. We modelled three cases: (i) liquid?liquid nano-phase separation, (ii) solid?liquid nano-phase separation, with CNPs coated isotropically, and (iii) CNPs coated anisotropically. The models were applied to mixes of tristearin and triolein with fully hydrogenated canola oil, shea butter with high oleic sunflower oil, and cotton seed oil. We performed Monte Carlo simulations, computed structure functions and concluded: (1) three regimes arose: (a) thin coating regime, Δ < 0.0701 u (b) transition regime, 0.0701 u ≤ Δ ≤ 0.0916 u and (c) thick coating regime, Δ > 0.0916 u. (arbitrary units, u) (2) The thin coating regime exhibits 1D TAGwoods, which aggregate, via DLCA/RLCA, into fractal structures which are uniformly distributed in space. (3) In the thick coating regime, for an isotropic coating, TAGwoods are not formed and coated CNPs will not aggregate but will be uniformly distributed in space. For anisotropic coating, TAGwoods can be formed and might form 1D strings but will not form DLCA/RLCA clusters. (4) The regimes are, approximately: thin coating, 0 < Δ < 7.0 nm transition regime, 7.0 < Δ < 9.2 nm and thick coating, Δ > 9.2 nm (5) The minimum minority TAG concentration required to undergo nano-phase separation is, approximately, 0.29% (thin coatings) and 0.94% (thick coatings). Minority

  19. Aggregate dust model to describe polarization properties of Comet Hale-Bopp

    NASA Astrophysics Data System (ADS)

    Das, H. S.; Das, S. R.; Sen, A. K.

    2008-11-01

    In this work, the observed linear-polarization data of Comet Hale-Bopp are studied at wavelengths λ = 0.485 and 0.684μm through simulations using Ballistic Particle-Cluster Aggregate and Ballistic Cluster-Cluster Aggregate. Using superposition T-MATRIX code, the best-fitting values of complex refractive indices are calculated which can well match the observed polarization data at the above two wavelengths. It is found from our analysis that there is not a single value of the monomer radius (am) that can simultaneously fit the observed polarization data at two wavelengths 0.485 and 0.684 μm. However, for different am in the two wavelengths, corresponding to similar size parameter of the monomer (x ~ 1.56), better fit can be achieved. The best-fitting complex refractive indices (n, k) coming out from this analysis are found to be (1.778, 0.059) at λ = 0.485μm when am = 0.12μm and (1.755, 0.080) at λ = 0.684μm when am = 0.17μm. The above values of refractive index show silicate behaviour as the values are close to amorphous olivine. Thus, it can be concluded that the silicate composition can best match the observed polarization data of Comet Hale-Bopp at λ = 0.485 and 0.684μm. Finally, the polarization properties of Comet Hale-Bopp are compared with Comet Levy 1990XX.

  20. Hypothermia-induced platelet aggregation in human blood in an in vitro model: the dominant role of blood-material interactions.

    PubMed

    Hall, Matthew W; Solen, Kenneth A

    2002-03-05

    Hypothermia-induced platelet aggregation (HIPA) with or without neutrophil involvement may cause neurologic dysfunction during hypothermic surgery. We report the use of a previously developed model to study the contributions of several surfaces, surface area, shear rate, and blood-material exposure time to HIPA. Heparinized (1.5 u/mL) human blood was quenched to 24 degrees C and passed (0.5 mL/min) through a 75-cm long 1/32" ID tubing of polyvinylchloride (PVC), polyethylene (PE), polyurethane (PU), Teflon-FEP, or heparin (Duraflo)-coated PVC. The number of aggregates was measured by a light-scattering method, and the concentration of occlusive aggregates was assessed using constant-pressure filtration (50 mmHg). No differences were seen among PVC, PE, PU, or Teflon-FEP. The heparin-coated PVC tubing produced fewer occlusive aggregates, and heparin leaching from the coating was not the cause of the decrease in occlusive aggregates. Increasing surface area increased the number of aggregates, and increasing shear rates decreased the occlusiveness of those aggregates.

  1. Vibronic coupling in molecular crystals: A Franck-Condon Herzberg-Teller model of H-aggregate fluorescence based on quantum chemical cluster calculations

    SciTech Connect

    Wykes, M. Parambil, R.; Gierschner, J.; Beljonne, D.

    2015-09-21

    Here, we present a general approach to treating vibronic coupling in molecular crystals based on atomistic simulations of large clusters. Such clusters comprise model aggregates treated at the quantum chemical level embedded within a realistic environment treated at the molecular mechanics level. As we calculate ground and excited state equilibrium geometries and vibrational modes of model aggregates, our approach is able to capture effects arising from coupling to intermolecular degrees of freedom, absent from existing models relying on geometries and normal modes of single molecules. Using the geometries and vibrational modes of clusters, we are able to simulate the fluorescence spectra of aggregates for which the lowest excited state bears negligible oscillator strength (as is the case, e.g., ideal H-aggregates) by including both Franck-Condon (FC) and Herzberg-Teller (HT) vibronic transitions. The latter terms allow the adiabatic excited state of the cluster to couple with vibrations in a perturbative fashion via derivatives of the transition dipole moment along nuclear coordinates. While vibronic coupling simulations employing FC and HT terms are well established for single-molecules, to our knowledge this is the first time they are applied to molecular aggregates. Here, we apply this approach to the simulation of the low-temperature fluorescence spectrum of para-distyrylbenzene single-crystal H-aggregates and draw comparisons with coarse-grained Frenkel-Holstein approaches previously extensively applied to such systems.

  2. Vibronic coupling in molecular crystals: A Franck-Condon Herzberg-Teller model of H-aggregate fluorescence based on quantum chemical cluster calculations.

    PubMed

    Wykes, M; Parambil, R; Beljonne, D; Gierschner, J

    2015-09-21

    Here, we present a general approach to treating vibronic coupling in molecular crystals based on atomistic simulations of large clusters. Such clusters comprise model aggregates treated at the quantum chemical level embedded within a realistic environment treated at the molecular mechanics level. As we calculate ground and excited state equilibrium geometries and vibrational modes of model aggregates, our approach is able to capture effects arising from coupling to intermolecular degrees of freedom, absent from existing models relying on geometries and normal modes of single molecules. Using the geometries and vibrational modes of clusters, we are able to simulate the fluorescence spectra of aggregates for which the lowest excited state bears negligible oscillator strength (as is the case, e.g., ideal H-aggregates) by including both Franck-Condon (FC) and Herzberg-Teller (HT) vibronic transitions. The latter terms allow the adiabatic excited state of the cluster to couple with vibrations in a perturbative fashion via derivatives of the transition dipole moment along nuclear coordinates. While vibronic coupling simulations employing FC and HT terms are well established for single-molecules, to our knowledge this is the first time they are applied to molecular aggregates. Here, we apply this approach to the simulation of the low-temperature fluorescence spectrum of para-distyrylbenzene single-crystal H-aggregates and draw comparisons with coarse-grained Frenkel-Holstein approaches previously extensively applied to such systems.

  3. Vibronic coupling in molecular crystals: A Franck-Condon Herzberg-Teller model of H-aggregate fluorescence based on quantum chemical cluster calculations

    NASA Astrophysics Data System (ADS)

    Wykes, M.; Parambil, R.; Beljonne, D.; Gierschner, J.

    2015-09-01

    Here, we present a general approach to treating vibronic coupling in molecular crystals based on atomistic simulations of large clusters. Such clusters comprise model aggregates treated at the quantum chemical level embedded within a realistic environment treated at the molecular mechanics level. As we calculate ground and excited state equilibrium geometries and vibrational modes of model aggregates, our approach is able to capture effects arising from coupling to intermolecular degrees of freedom, absent from existing models relying on geometries and normal modes of single molecules. Using the geometries and vibrational modes of clusters, we are able to simulate the fluorescence spectra of aggregates for which the lowest excited state bears negligible oscillator strength (as is the case, e.g., ideal H-aggregates) by including both Franck-Condon (FC) and Herzberg-Teller (HT) vibronic transitions. The latter terms allow the adiabatic excited state of the cluster to couple with vibrations in a perturbative fashion via derivatives of the transition dipole moment along nuclear coordinates. While vibronic coupling simulations employing FC and HT terms are well established for single-molecules, to our knowledge this is the first time they are applied to molecular aggregates. Here, we apply this approach to the simulation of the low-temperature fluorescence spectrum of para-distyrylbenzene single-crystal H-aggregates and draw comparisons with coarse-grained Frenkel-Holstein approaches previously extensively applied to such systems.

  4. A particle-based model to simulate the micromechanics of single-plant parenchyma cells and aggregates

    NASA Astrophysics Data System (ADS)

    Van Liedekerke, P.; Ghysels, P.; Tijskens, E.; Samaey, G.; Smeedts, B.; Roose, D.; Ramon, H.

    2010-06-01

    This paper is concerned with addressing how plant tissue mechanics is related to the micromechanics of cells. To this end, we propose a mesh-free particle method to simulate the mechanics of both individual plant cells (parenchyma) and cell aggregates in response to external stresses. The model considers two important features in the plant cell: (1) the cell protoplasm, the interior liquid phase inducing hydrodynamic phenomena, and (2) the cell wall material, a viscoelastic solid material that contains the protoplasm. In this particle framework, the cell fluid is modeled by smoothed particle hydrodynamics (SPH), a mesh-free method typically used to address problems with gas and fluid dynamics. In the solid phase (cell wall) on the other hand, the particles are connected by pairwise interactions holding them together and preventing the fluid to penetrate the cell wall. The cell wall hydraulic conductivity (permeability) is built in as well through the SPH formulation. Although this model is also meant to be able to deal with dynamic and even violent situations (leading to cell wall rupture or cell-cell debonding), we have concentrated on quasi-static conditions. The results of single-cell compression simulations show that the conclusions found by analytical models and experiments can be reproduced at least qualitatively. Relaxation tests revealed that plant cells have short relaxation times (1 µs-10 µs) compared to mammalian cells. Simulations performed on cell aggregates indicated an influence of the cellular organization to the tissue response, as was also observed in experiments done on tissues with a similar structure.

  5. A particle-based model to simulate the micromechanics of single-plant parenchyma cells and aggregates.

    PubMed

    Van Liedekerke, P; Ghysels, P; Tijskens, E; Samaey, G; Smeedts, B; Roose, D; Ramon, H

    2010-05-26

    This paper is concerned with addressing how plant tissue mechanics is related to the micromechanics of cells. To this end, we propose a mesh-free particle method to simulate the mechanics of both individual plant cells (parenchyma) and cell aggregates in response to external stresses. The model considers two important features in the plant cell: (1) the cell protoplasm, the interior liquid phase inducing hydrodynamic phenomena, and (2) the cell wall material, a viscoelastic solid material that contains the protoplasm. In this particle framework, the cell fluid is modeled by smoothed particle hydrodynamics (SPH), a mesh-free method typically used to address problems with gas and fluid dynamics. In the solid phase (cell wall) on the other hand, the particles are connected by pairwise interactions holding them together and preventing the fluid to penetrate the cell wall. The cell wall hydraulic conductivity (permeability) is built in as well through the SPH formulation. Although this model is also meant to be able to deal with dynamic and even violent situations (leading to cell wall rupture or cell-cell debonding), we have concentrated on quasi-static conditions. The results of single-cell compression simulations show that the conclusions found by analytical models and experiments can be reproduced at least qualitatively. Relaxation tests revealed that plant cells have short relaxation times (1 micros-10 micros) compared to mammalian cells. Simulations performed on cell aggregates indicated an influence of the cellular organization to the tissue response, as was also observed in experiments done on tissues with a similar structure.

  6. SIRT1 modulates aggregation and toxicity through deacetylation of the androgen receptor in cell models of SBMA.

    PubMed

    Montie, Heather L; Pestell, Richard G; Merry, Diane E

    2011-11-30

    Posttranslational protein modifications can play a major role in disease pathogenesis; phosphorylation, sumoylation, and acetylation modulate the toxicity of a variety of proteotoxic proteins. The androgen receptor (AR) is substantially modified, in response to hormone binding, by phosphorylation, sumoylation, and acetylation; these modifications might thus contribute to DHT-dependent polyglutamine (polyQ)-expanded AR proteotoxicity in spinal and bulbar muscular atrophy (SBMA). SIRT1, a nuclear protein and deacetylase of the AR, is neuroprotective in many neurodegenerative disease models. Our studies reveal that SIRT1 also offers protection against polyQ-expanded AR by deacetylating the AR at lysines 630/632/633. This finding suggested that nuclear AR acetylation plays a role in the aberrant metabolism and toxicity of polyQ-expanded AR. Subsequent studies revealed that the polyQ-expanded AR is hyperacetylated and that pharmacologic reduction of acetylation reduces mutant AR aggregation. Moreover, genetic mutation to inhibit polyQ-expanded AR acetylation of lysines 630/632/633 substantially decreased its aggregation and completely abrogated its toxicity in cell lines and motor neurons. Our studies also reveal one means by which the AR acetylation state likely modifies polyQ-expanded AR metabolism and toxicity, through its effect on DHT-dependent AR stabilization. Overall, our findings reveal a neuroprotective function of SIRT1 that operates through its deacetylation of polyQ-expanded AR and highlight the potential of both SIRT1 and AR acetylation as powerful therapeutic targets in SBMA.

  7. Construction aggregates

    USGS Publications Warehouse

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

    2007-01-01

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

  8. Construction aggregates

    USGS Publications Warehouse

    Tepordei, V.V.

    1996-01-01

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

  9. Polarimetric radar observation of ice crystals and aggregates: Backscattering modeling of signatures from C to Ka band

    NASA Astrophysics Data System (ADS)

    Botta, G.; Montopoli, M.; Marzano, F. S.

    2009-04-01

    Hydrometeor classification using polarimetric Doppler weather radar is based on the characteristic polarimetric signature for each hydrometeor class. This signature can be obtained by either experimental campaigns or by proper electromagnetic modelling. Both approaches have advantages and drawbacks: the experimental approach is not easy to conduct as it requires co-located measurements of a weather radar with in-situ sampler (usually installed aboard an aircraft); moreover, it is generally strictly related to the measurement configuration (e.g., frequency, range) it is performed. Of course, experimental campaigns are needed for definitive validation, but the modelling approach exhibits a high flexibility in terms of system and meteorological parameters very well suited for retrieval algorithm design. On the other hand, a model approach is heavily dependent on the model capability to represent hydrometeor volumes in a realistic way. Within the electromagnetic scattering modelling of hydrometeor radar response, a well known technique to simulate the radar backscattering from an ensemble of particle is based on the T-matrix algorithm (Kim, 2006). The T-matrix model is based on the equivalence principle and can ensure numerical convergence for a small set of canonical shapes such as ellipsoids. These shapes are useful to represent raindrops and vertically-oriented small crystals, but are largely unrealistic when dealing with ice aggregates and crystals. In this work we use a different approach to the scattering modelling that fits well for classes like ice crystals and aggregates of different shapes and sizes: the discrete dipole approximation (DDA). The DDA model lets us simulate almost any kind of particle under the hypothesis it can be approximated as a three dimensional array of dipoles that generate the scattering field (the wavelength should be large compared to the distance between dipoles). The DDA code used is DDSCAT, developed by Draine and Flatau (2004

  10. Data aggregation issues in the application of the mobile emissions factor model. Final report, October 1993-January 1994

    SciTech Connect

    1995-08-01

    The appropriate level of spatial and temporal data aggregation for highway vehicle emissions analyses is one of several important analytical questions that has received considerable interest following passage of the Clean Air Act Amendments (CAAA) of 1990. The primary purpose of this report is to examine the effects on vehicular emissions that result from using different levels of spatial and temporal data disaggregation of actual travel data from three representative urban areas. The work also contributes to three important additional objectives that are of widespread current interest: The effects on total estimated vehicular emissions of using successive versions of the mobile model; an assessment of the Clean Air Act`s mandated Federal policies in reducing future year emissions; and specific MOBILE input variables that should be modified in developing a spatially and temporally disaggregated emissions estimate.

  11. Testing a cumulative and aggregate exposure model using biomonitoring studies and dietary records for Italian vineyard spray operators.

    PubMed

    Kennedy, Marc C; Glass, C Richard; Fustinoni, Silvia; Moretto, Angelo; Mandic-Rajcevic, Stefan; Riso, Patrizia; Turrini, Aida; van der Voet, Hilko; Hetmanski, Michel T; Fussell, Richard J; van Klaveren, Jacob D

    2015-05-01

    The need for improved tools to estimate the cumulative and aggregate exposure to compounds such as plant protection products (PPPs) is recognised in the EU Regulation 1107/2009. A new model has been developed to estimate the exposure within a population to single compounds or compounds within a Cumulative Action Group, considering dietary and non-dietary sources and multiple exposure routes. To test the model a field study was carried out in Italy with operators applying tebuconazole fungicides, with measurements of dermal exposure collected. Whole urine samples were collected and analysed to provide values for the absorbed dose of tebuconazole, with duplicate diet samples collected and analysed as a measure of dietary exposures. The model provided predicted values of exposure for combined dietary and non-dietary routes of exposures which were compared to the measured absorbed dose values based on urinary analysis. The model outputs provided mean daily exposure values of 1.77 (± 1.96) µg a.s./kg BW which are comparable to measured mean values from the biomonitoring field study of 1.73 (± 1.31) µg a.s./kg BW. To supplement the limited measurement data available, comparisons against other models were also made and found to be comparable.

  12. Investigation of Aggregates as a Model for Titan's Aerosols Using Microwave Analog Experiments and Radiative Transfer Theory

    NASA Astrophysics Data System (ADS)

    Thomas-Osip, J. E.; Gustafson, B. Å. S.

    1996-09-01

    It has been suggested that the aerosols in the atmosphere of Titan have an aggregate morphology (Bar-Nun et al., 1988: West and Smith, 1991). Previous studies were based on formulations of the Discrete Dipole Approximation to calculate the single scattering properties of such aggregates. These studies were limited in the size of the individual spheres and total size of the aggregate. We present microwave to light analog scattering measurements and radiative transfer calculations for aggregates of 250-500 individual spheres near the Raleigh size limit in a plane parallel atmosphere. The advantages of using microwave analog experiments include the possibility of investigating a broad range of particle sizes and morphologies.

  13. Evidence of Discrete Scale Invariance in DLA and Time-to-Failure by Canonical Averaging

    NASA Astrophysics Data System (ADS)

    Johansen, A.; Sornette, D.

    Discrete scale invariance, which corresponds to a partial breaking of the scaling symmetry, is reflected in the existence of a hierarchy of characteristic scales l0,l0λ,l0λ2,…, where λ is a preferred scaling ratio and l0 a microscopic cut-off. Signatures of discrete scale invariance have recently been found in a variety of systems ranging from rupture, earthquakes, Laplacian growth phenomena, "animals" in percolation to financial market crashes. We believe it to be a quite general, albeit subtle phenomenon. Indeed, the practical problem in uncovering an underlying discrete scale invariance is that standard ensemble averaging procedures destroy it as if it was pure noise. This is due to the fact, that while λ only depends on the underlying physics, l0 on the contrary is realization-dependent. Here, we adapt and implement a novel so-called "canonical" averaging scheme which re-sets the l0 of different realizations to approximately the same value. The method is based on the determination of a realization-dependent effective critical point obtained from, e.g., a maximum susceptibility criterion. We demonstrate the method on diffusion limited aggregation and a model of rupture.

  14. Fractal aggregates in Titan's atmosphere

    NASA Astrophysics Data System (ADS)

    Cabane, M.; Rannou, P.; Chassefiere, E.; Israel, G.

    1993-04-01

    The cluster structure of Titan's atmosphere was modeled by using an Eulerian microphysical model with the specific formulation of microphysical laws applying to fractal particles. The growth of aggregates in the settling phase was treated by introducing the fractal dimension as a parameter of the model. The model was used to obtain a vertical distribution of size and number density of the aggregates for different production altitudes. Results confirm previous estimates of the formation altitude of photochemical aerosols. The vertical profile of the effective radius of aggregates was calculated as a function of the visible optical depth.

  15. Aggregate modeling of fast-acting demand response and control under real-time pricing

    DOE PAGES

    Chassin, David P.; Rondeau, Daniel

    2016-08-24

    This paper develops and assesses the performance of a short-term demand response (DR) model for utility load control with applications to resource planning and control design. Long term response models tend to underestimate short-term demand response when induced by prices. This has two important consequences. First, planning studies tend to undervalue DR and often overlook its benefits in utility demand management program development. Second, when DR is not overlooked, the open-loop DR control gain estimate may be too low. This can result in overuse of load resources, control instability and excessive price volatility. Our objective is therefore to develop amore » more accurate and better performing short-term demand response model. We construct the model from first principles about the nature of thermostatic load control and show that the resulting formulation corresponds exactly to the Random Utility Model employed in economics to study consumer choice. The model is tested against empirical data collected from field demonstration projects and is shown to perform better than alternative models commonly used to forecast demand in normal operating conditions. Finally, the results suggest that (1) existing utility tariffs appear to be inadequate to incentivize demand response, particularly in the presence of high renewables, and (2) existing load control systems run the risk of becoming unstable if utilities close the loop on real-time prices.« less

  16. Aggregate modeling of fast-acting demand response and control under real-time pricing

    SciTech Connect

    Chassin, David P.; Rondeau, Daniel

    2016-08-24

    This paper develops and assesses the performance of a short-term demand response (DR) model for utility load control with applications to resource planning and control design. Long term response models tend to underestimate short-term demand response when induced by prices. This has two important consequences. First, planning studies tend to undervalue DR and often overlook its benefits in utility demand management program development. Second, when DR is not overlooked, the open-loop DR control gain estimate may be too low. This can result in overuse of load resources, control instability and excessive price volatility. Our objective is therefore to develop a more accurate and better performing short-term demand response model. We construct the model from first principles about the nature of thermostatic load control and show that the resulting formulation corresponds exactly to the Random Utility Model employed in economics to study consumer choice. The model is tested against empirical data collected from field demonstration projects and is shown to perform better than alternative models commonly used to forecast demand in normal operating conditions. Finally, the results suggest that (1) existing utility tariffs appear to be inadequate to incentivize demand response, particularly in the presence of high renewables, and (2) existing load control systems run the risk of becoming unstable if utilities close the loop on real-time prices.

  17. Correlated aggregate model of self-healing in dye-doped polymers

    NASA Astrophysics Data System (ADS)

    Kuzyk, Mark G.; Ramini, Shiva

    2012-10-01

    Self healing of chromophores in a dye-doped polymer after photodegradation is a counterintuitive process based on the nearly universal observation that molecular damage is a thermodynamically irreversible process. We propose a new simple model of this phenomenon that takes into account all observations, including the effects of concentration, temperature, and bystander states. Critical to this model are correlations between chromophores, perhaps mediated by the polymer, which actively favors the undamaged species in analogy to Bose-Einstein condensation. We use this model to predict the behavior of decay and recovery experiments as measured with amplified spontaneous emission and absorption spectroscopy.

  18. Formal description of aggregates of a generalised model of interaction processes in computer networks

    SciTech Connect

    Ratsin, Yu.V.

    1984-01-01

    The realisation using PL/1 of a formal description of a set of interaction process functions in computer networks using the language of discrete parallel processes is described. The formal description is intended for conducting computer modelling experiments. 4 references.

  19. Metamodeling Techniques to Aid in the Aggregation Process of Large Hierarchical Simulation Models

    DTIC Science & Technology

    2008-08-01

    reduce the lower-level model complexity by removing, combining, or approximating model parameters or variables at a less detailed level and thereby...function approximations . The pattern recognition task as a metamodeling tool for this research will be on prediction problems since these are the most...behavior of computer simulations for over forty years. Parametric polynomial response surface approximations have been the most popular technique used

  20. Can inducible resistance in plants cause herbivore aggregations? Spatial patterns in an inducible plant/herbivore model.

    PubMed

    Anderson, Kurt E; Inouye, Brian D; Underwood, Nora

    2015-10-01

    Many theories regarding the evolution of inducible resistance in plants have an implicit spatial component, but most relevant population dynamic studies ignore spatial dynamics. We examined a spatially explicit model of plant inducible resistance and herbivore population dynamics to explore how realistic features of resistance and herbivore responses influence spatial patterning. Both transient and persistent spatial patterns developed in all models examined, where patterns manifested as wave-like aggregations of herbivores and variation in induction levels. Patterns arose when herbivores moved away from highly induced plants, there was a lag between damage and deployment of induced resistance, and the relationship between herbivore density and strength of the induction response had a sigmoid shape. These mechanisms influenced pattern formation regardless of the assumed functional relationship between resistance and herbivore recruitment and mortality. However, in models where induction affected herbivore mortality, large-scale herbivore population cycles driven by the mortality response often co-occurred with smaller scale spatial patterns driven by herbivore movement. When the mortality effect dominated, however, spatial pattern formation was completely replaced by spatially synchronized herbivore population cycles. Our results present a new type of ecological pattern formation driven by induced trait variation, consumer behavior, and time delays that has broad implications for the community and evolutionary ecology of plant defenses.

  1. Practical Differences Among Aggregate-Level Conditional Status Metrics: From Median Student Growth Percentiles to Value-Added Models

    ERIC Educational Resources Information Center

    Castellano, Katherine E.; Ho, Andrew D.

    2015-01-01

    Aggregate-level conditional status metrics (ACSMs) describe the status of a group by referencing current performance to expectations given past scores. This article provides a framework for these metrics, classifying them by aggregation function (mean or median), regression approach (linear mean and nonlinear quantile), and the scale that supports…

  2. Continuum models of cohesive stochastic swarms: The effect of motility on aggregation patterns

    NASA Astrophysics Data System (ADS)

    Hughes, Barry D.; Fellner, Klemens

    2013-10-01

    Mathematical models of swarms of moving agents with non-local interactions have many applications and have been the subject of considerable recent interest. For modest numbers of agents, cellular automata or related algorithms can be used to study such systems, but in the present work, instead of considering discrete agents, we discuss a class of one-dimensional continuum models, in which the agents possess a density ρ(x,t) at location x at time t. The agents are subject to a stochastic motility mechanism and to a global cohesive inter-agent force. The motility mechanisms covered include classical diffusion, nonlinear diffusion (which may be used to model, in a phenomenological way, volume exclusion or other short-range local interactions), and a family of linear redistribution operators related to fractional diffusion equations. A variety of exact analytic results are discussed, including equilibrium solutions and criteria for unimodality of equilibrium distributions, full time-dependent solutions, and transitions between asymptotic collapse and asymptotic escape. We address the behaviour of the system for diffusive motility in the low-diffusivity limit for both smooth and singular interaction potentials and show how this elucidates puzzling behaviour in fully deterministic non-local particle interaction models. We conclude with speculative remarks about extensions and applications of the models.

  3. An aggregate accident model based on pooled, regional time-series data.

    PubMed

    Fridstrøm, L; Ingebrigtsen, S

    1991-10-01

    The determinants of personal injury road accidents and their severity are studied by means of generalized Poisson regression models estimated on the basis of combined cross-section/time-series data. Monthly data have been assembled for 18 Norwegian counties (every county but one), covering the period from January 1974 until December 1986. A rather wide range of potential explanatory factors are taken into account, including road use (exposure), weather, daylight, traffic density, road investment and maintenance expenditure, accident reporting routines, vehicle inspection, law enforcement, seat belt usage, proportion of inexperienced drivers, and alcohol sales. Separate probability models are estimated for the number of personal injury accidents, fatal accidents, injury victims, death victims, car occupants injured, and bicyclists and pedestrians injured. The fraction of personal injury accidents that are fatal is interpreted as an average severity measure and studied by means of a binomial logit model.

  4. Aggregation dynamics of rigid polyelectrolytes

    NASA Astrophysics Data System (ADS)

    Tom, Anvy Moly; Rajesh, R.; Vemparala, Satyavani

    2016-01-01

    Similarly charged polyelectrolytes are known to attract each other and aggregate into bundles when the charge density of the polymers exceeds a critical value that depends on the valency of the counterions. The dynamics of aggregation of such rigid polyelectrolytes are studied using large scale molecular dynamics simulations. We find that the morphology of the aggregates depends on the value of the charge density of the polymers. For values close to the critical value, the shape of the aggregates is cylindrical with height equal to the length of a single polyelectrolyte chain. However, for larger values of charge, the linear extent of the aggregates increases as more and more polymers aggregate. In both the cases, we show that the number of aggregates decrease with time as power laws with exponents that are not numerically distinguishable from each other and are independent of charge density of the polymers, valency of the counterions, density, and length of the polyelectrolyte chain. We model the aggregation dynamics using the Smoluchowski coagulation equation with kernels determined from the molecular dynamics simulations and justify the numerically obtained value of the exponent. Our results suggest that once counterions condense, effective interactions between polyelectrolyte chains short-ranged and the aggregation of polyelectrolytes are diffusion-limited.

  5. SOURCE AGGREGATION IN STABLE ISOTOPE MIXING MODELS: LUMP IT OR LEAVE IT?

    EPA Science Inventory

    A common situation when stable isotope mixing models are used to estimate source contributions to a mixture is that there are too many sources to allow a unique solution. To resolve this problem one option is to combine sources with similar signatures such that the number of sou...

  6. Role of streams in myxobacteria aggregate formation

    NASA Astrophysics Data System (ADS)

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

    2004-10-01

    Cell contact, movement and directionality are important factors in biological development (morphogenesis), and myxobacteria are a model system for studying cell-cell interaction and cell organization preceding differentiation. When starved, thousands of myxobacteria cells align, stream and form aggregates which later develop into round, non-motile spores. Canonically, cell aggregation has been attributed to attractive chemotaxis, a long range interaction, but there is growing evidence that myxobacteria organization depends on contact-mediated cell-cell communication. We present a discrete stochastic model based on contact-mediated signaling that suggests an explanation for the initialization of early aggregates, aggregation dynamics and final aggregate distribution. Our model qualitatively reproduces the unique structures of myxobacteria aggregates and detailed stages which occur during myxobacteria aggregation: first, aggregates initialize in random positions and cells join aggregates by random walk; second, cells redistribute by moving within transient streams connecting aggregates. Streams play a critical role in final aggregate size distribution by redistributing cells among fewer, larger aggregates. The mechanism by which streams redistribute cells depends on aggregate sizes and is enhanced by noise. Our model predicts that with increased internal noise, more streams would form and streams would last longer. Simulation results suggest a series of new experiments.

  7. Flow-driven instabilities during aggregation and pattern formation of Dictyostelium Discoideum: Experiments and modeling

    NASA Astrophysics Data System (ADS)

    Gholami, Azam; Steinbock, Oliver; Zykov, Vladimir; Bodenschatz, Eberhard

    2013-03-01

    We report the first experimental verification of the Differential Flow Induced Chemical Instability (DIFICI) in a signaling chemotactic biological population, where a differential flow induces traveling waves in the signaling pattern. The traveling wave speed was observed to be proportional to the flow velocity while the wave period was 7 min, which is comparable to that of starved Dictyostelium cells. Analysis and numerical simulations of the Goldbeter model show that the resulting DIFICI wave patterns appear in the oscillatory regime. In the experiments, we observe that the DIFICI wave pattern disappears after 4-5 h of starvation. We extrapolated the Goldbeter model to the experimental situation. This suggests that the dynamics switches from the oscillatory to the excitable regime as the DIFICI waves disappear in the experiment.

  8. Integrated modeling approach for fate and transport of submerged oil and oil-particle aggregates in a freshwater riverine environment

    USGS Publications Warehouse

    Fitzpatrick, Faith A.; Johnson, Rex; Zhu, Zhenduo; Waterman, David; McCulloch, Richard D.; Hayter, Earl; Garcia, Marcelo H.; Boufadel, Michel C.; Dekker, Timothy; Hassan, Jacob S.; Soong, David T.; Hoard, Christopher J.; Lee, Kenneth

    2016-01-01

    The Enbridge Line 6B pipeline release of diluted bitumen into the Kalamazoo River downstream of Marshall, Michigan, U.S.A., in July 2010 was one of the largest oil spills into freshwater in North American history. A portion of the oil interacted with river sediment and submerged requiring the development and implementation of new approaches for detection and recovery of oil mixed with river sediment. Hydrodynamic and sediment transport modeling became an integral part of containment and recovery operations for decision support about the potential fate and migration of submerged oil and oiled sediment. Three models were developed for the U.S. Environmental Protection Agency to cover a range of spatial scales of interest to onsite operations. Two-dimensional (2D) hydrodynamic and sediment transport models from the Environmental Fluid Dynamics Code and the sediment bed model SEDZLJ1 were used to simulate potential resuspension, migration, and deposition of submerged oil and oiled sediment along a 38-mile reach of the Kalamazoo River affected by the oil from Marshall to Kalamazoo. An algorithm was added to SEDZLJ to represent three additional particle size classes of oilparticle aggregates (OPAs) with a range of sizes, specific gravities, and settling velocities. Field and laboratory experiments and flume tests were done to support the numerical modeling of OPAs. A three-dimensional hydrodynamic model was developed to simulate hydrodynamics and OPA tracking through Morrow Lake, the most downstream impoundment. This model incorporated wind and dam operations into high and low flow, lake drawdown, and containment simulations. Finally, a 2D unstructured grid model, HydroSed2D, was used to simulate flows and sediment transport along 1- to 2-mile segments of the Kalamazoo River around islands and through side channels and backwater areas that are particularly prone to submerged oil deposition.Integrated models could be developed quickly due to the availability of

  9. Situational Force Scoring: Accounting for Combined Arms Effects in Aggregate Combat Models

    DTIC Science & Technology

    1992-01-01

    Army War College Model, Historical Evaluation and Research Organization (HERO), November 1982. -21- and Monti Callero . An important alternative approach...i ii l .... .... .. .. . ... • • •,, o , •,: , o •. .. : -.. . ............. .. . . . . 4-d, ,,i , b .:h l•. i...Slift" •[)’• II.-•DA$1-....... .... O ’ . .l .... ......... l .. . . .. t ieY 5•$6.6-11 Iaq -s# w D 1-LO01 i op Fig. D.4--Surviving Armor and Infantry

  10. Evaluation of dynamically downscaled extreme temperature using a spatially-aggregated generalized extreme value (GEV) model

    NASA Astrophysics Data System (ADS)

    Wang, Jiali; Han, Yuefeng; Stein, Michael L.; Kotamarthi, Veerabhadra R.; Huang, Whitney K.

    2016-11-01

    The weather research and forecast (WRF) model downscaling skill in extreme maximum daily temperature is evaluated by using the generalized extreme value (GEV) distribution. While the GEV distribution has been used extensively in climatology and meteorology for estimating probabilities of extreme events, accurately estimating GEV parameters based on data from a single pixel can be difficult, even with fairly long data records. This work proposes a simple method assuming that the shape parameter, the most difficult of the three parameters to estimate, does not vary over a relatively large region. This approach is applied to evaluate 31-year WRF-downscaled extreme maximum temperature through comparison with North American regional reanalysis (NARR) data. Uncertainty in GEV parameter estimates and the statistical significance in the differences of estimates between WRF and NARR are accounted for by conducting a novel bootstrap procedure that makes no assumption of temporal or spatial independence within a year, which is especially important for climate data. Despite certain biases over parts of the United States, overall, WRF shows good agreement with NARR in the spatial pattern and magnitudes of GEV parameter estimates. Both WRF and NARR show a significant increase in extreme maximum temperature over the southern Great Plains and southeastern United States in January and over the western United States in July. The GEV model shows clear benefits from the regionally constant shape parameter assumption, for example, leading to estimates of the location and scale parameters of the model that show coherent spatial patterns.

  11. A Conceptual Approach to Assimilating Remote Sensing Data to Improve Soil Moisture Profile Estimates in a Surface Flux/Hydrology Model. 2; Aggregation

    NASA Technical Reports Server (NTRS)

    Schamschula, Marius; Crosson, William L.; Inguva, Ramarao; Yates, Thomas; Laymen, Charles A.; Caulfield, John

    1998-01-01

    This is a follow up on the preceding presentation by Crosson. The grid size for remote microwave measurements is much coarser than the hydrological model computational grids. To validate the hydrological models with measurements we propose mechanisms to aggregate the hydrological model outputs for soil moisture to allow comparison with measurements. Weighted neighborhood averaging methods are proposed to facilitate the comparison. We will also discuss such complications as misalignment, rotation and other distortions introduced by a generalized sensor image.

  12. Effectiveness of daily living abilities (DLA) as a tool for evaluating vocational competencies: study of non-disabled workers aged 45 and over.

    PubMed

    Kikuchi, E; Murakami, K

    1995-05-01

    A questionnaire survey was conducted on 28-55 items of daily living abilities (DLA) linked to 13 basic vocational competencies such as memory, learning, planning, judgement, muscular power and concentration covering a total of 505 non-disabled blue collar male workers aged 45 and over. Results of the survey were as follows, (1) The 457 subjects were grouped into five groups ranging from normal to unsound groups according to the degree of DLA; (2) The reduction of DLA has directionality to two factors, memory and muscular power; (3) DLA provide clues for aging; (4) Among basic vocational competencies, muscular power showed the highest performance with a small standard deviation, while concentration scored low points with a large standard deviation (p < .05); (5) No age difference was found in planning ability, coordination, muscular power, physical tolerance, manual dexterity, and sense of equilibrium, while subjects aged 65 or over showed significantly low figures for learning ability, agility and concentration (p < .05); Since the findings showed various characteristics of vocational competencies and the aging process precisely in blue collar workers aged 45 and over, we assumed that the DLA survey is one of the alternatives for evaluating workers vocational competencies.

  13. An acridine derivative, [4,5-bis{(N-carboxy methyl imidazolium)methyl}acridine] dibromide, shows anti-TDP-43 aggregation effect in ALS disease models

    PubMed Central

    Prasad, Archana; Raju, Gembali; Sivalingam, Vishwanath; Girdhar, Amandeep; Verma, Meenakshi; Vats, Abhishek; Taneja, Vibha; Prabusankar, Ganesan; Patel, Basant K.

    2016-01-01

    Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease associated with aggregation of TAR DNA-binding protein-43 (TDP-43) in neuronal cells and manifests as motor neuron dysfunction & muscle atrophy. The carboxyl-terminal prion-like domain of TDP-43 can aggregate in vitro into toxic β-sheet rich amyloid-like structures. So far, treatment options for ALS are very limited and Riluzole, which targets glutamate receptors, is the only but highly ineffective drug. Therefore, great interest exists in developing molecules for ALS treatment. Here, we have examined certain derivatives of acridine containing same side chains at position 4 & 5, for inhibitory potential against TDP-43 aggregation. Among several acridine derivatives examined, AIM4, which contains polar carboxyl groups in the side arms, significantly reduces TDP-43-YFP aggregation in the powerful yeast model cell and also abolishes in vitro amyloid-like aggregation of carboxyl terminal domain of TDP-43, as observed by AFM imaging. Thus, AIM4 can be a lead molecule potentiating further therapeutic research for ALS. PMID:28000730

  14. Evaluation of membrane models and their composition for islet amyloid polypeptide-membrane aggregation.

    PubMed

    Caillon, Lucie; Lequin, Olivier; Khemtémourian, Lucie

    2013-09-01

    Human islet amyloid polypeptide (IAPP) forms amyloid fibrils in the pancreatic islets of patients suffering from type 2 diabetes mellitus (T2DM). The formation of IAPP fibrils has been shown to cause membrane damage which most likely is responsible for the death of pancreatic islet β-cells during the pathogenesis of T2DM. Several studies have demonstrated a clear interaction between IAPP and lipid membranes. However the effect of different lipid compositions and of various membrane mimetics (including micelles, bicelles, SUV and LUV) on fibril formation kinetics and fibril morphology has not yet systematically been analysed. Here we report that the interaction of IAPP with various membrane models promoted different processes of fibril formation. Our data reveal that in SDS and DPC micelles, IAPP adopts a stable α-helical structure for several days, suggesting that the micelle models may stabilize monomeric or small oligomeric species of IAPP. In contrast, zwitterionic DMPC/DHPC bicelles and DOPC SUV accelerate the fibril formation compared to zwitterionic DOPC LUV, indicating that the size of the membrane model and its curvature influence the fibrillation process. Negatively charged membranes decrease the lag-time of the fibril formation kinetics while phosphatidylethanolamine and cholesterol have an opposite effect, probably due to the modulation of the physical properties of the membrane and/or due to direct interactions with IAPP within the membrane core. Finally, our results show that the modulation of lipid composition influences not only the growth of fibrils at the membrane surface but also the interactions of β-sheet oligomers with membranes.

  15. The impacts of climate change on energy: An aggregate expenditure model for the US

    SciTech Connect

    Morrison, W.; Mendelsohn, R.

    1998-09-01

    This paper develops a theoretical model to measure the climate change impacts to the energy sector. Welfare effects are approximately equal to the resulting change in expenditures on energy and buildings. Using micro data on individuals and firms across the United States, energy expenditures are regressed on climate and other control variables to estimate both short-run and long-run climate response functions. The analysis suggests that energy expenditures have a quadratic U-shaped relationship with respect to temperature. Future warming of 2 C is predicted to cause annual damages of about $6 billion but increases of 5 C would increase damages to almost $30 billion.

  16. Coherent modelling switch between pointwise and distributed representations of cell aggregates.

    PubMed

    Colombi, A; Scianna, M; Preziosi, L

    2017-03-01

    Biological systems are typically formed by different cell phenotypes, characterized by specific biophysical properties and behaviors. Moreover, cells are able to undergo differentiation or phenotypic transitions upon internal or external stimuli. In order to take these phenomena into account, we here propose a modelling framework in which cells can be described either as pointwise/concentrated particles or as distributed masses, according to their biological determinants. A set of suitable rules then defines a coherent procedure to switch between the two mathematical representations. The theoretical environment describing cell transition is then enriched by including cell migratory dynamics and duplication/apoptotic processes, as well as the kinetics of selected diffusing chemicals influencing the system evolution. Finally, biologically relevant numerical realizations are presented: in particular, they deal with the growth of a tumor spheroid and with the initial differentiation stages of the formation of the zebrafish posterior lateral line. Both phenomena mainly rely on cell phenotypic transition and differentiated behaviour, thereby constituting biological systems particularly suitable to assess the advantages of the proposed model.

  17. Aggregation Processes on Networks: Deterministic Equations, Stochastic Model and Numerical Simulation

    SciTech Connect

    Guias, Flavius

    2008-09-01

    We introduce an infinite system of equations modeling the time evolution of the growth process of a network. The nodes are characterized by their degree k(set-membership sign)N and a fitness parameter f(set-membership sign)[0,h]. Every new node which emerges becomes a fitness f' according to a given distribution P and attaches to an existing node with fitness f and degree k at rate fA{sub k}, where A{sub k} are positive coefficients, growing sub-linearly in k. If the parameter f takes only one value, the dynamics of this process can be described by a variant of the Becker-Doering equations, where the l growth of the size of clusters of size k occurs only with increment 1. In contrast l to the established Becker-Doering equations, the system considered here is nonconservative, since mass (i.e. links) is continuously added. Nevertheless, it has the property of linearity, which is a natural consequence of the process which is being modeled. The purpose of this paper is to construct a solution of the system based on a stochastic approximation algorithm, which allows also a numerical simulation in order to get insight into its qualitative behaviour. In particular we show analytically and numerically the property of Bose-Einstein condensation, which was observed in the literature on random graphs and which can be described as an emergence of a huge cluster which captures a macroscopic fraction of the total link density.

  18. Pattern, growth, and aging in aggregation kinetics of a Vicsek-like active matter model

    NASA Astrophysics Data System (ADS)

    Das, Subir K.

    2017-01-01

    Via molecular dynamics simulations, we study kinetics in a Vicsek-like phase-separating active matter model. Quantitative results, for isotropic bicontinuous pattern, are presented on the structure, growth, and aging. These are obtained via the two-point equal-time density-density correlation function, the average domain length, and the two-time density autocorrelation function. Both the correlation functions exhibit basic scaling properties, implying self-similarity in the pattern dynamics, for which the average domain size exhibits a power-law growth in time. The equal-time correlation has a short distance behavior that provides reasonable agreement between the corresponding structure factor tail and the Porod law. The autocorrelation decay is a power-law in the average domain size. Apart from these basic similarities, the overall quantitative behavior of the above-mentioned observables is found to be vastly different from those of the corresponding passive limit of the model which also undergoes phase separation. The functional forms of these have been quantified. An exceptionally rapid growth in the active system occurs due to fast coherent motion of the particles, mean-squared-displacements of which exhibit multiple scaling regimes, including a long time ballistic one.

  19. Modeling statistics and kinetics of the natural aggregation structures and processes with the solution of generalized logistic equation

    NASA Astrophysics Data System (ADS)

    Maslov, Lev A.; Chebotarev, Vladimir I.

    2017-02-01

    The generalized logistic equation is proposed to model kinetics and statistics of natural processes such as earthquakes, forest fires, floods, landslides, and many others. This equation has the form dN(A)/dA = s dot (1-N(A)) dot N(A)q dot A-α, q>0q>0 and A>0A>0 is the size of an element of a structure, and α≥0. The equation contains two exponents α and q taking into account two important properties of elements of a system: their fractal geometry, and their ability to interact either to enhance or to damp the process of aggregation. The function N(A)N(A) can be understood as an approximation to the number of elements the size of which is less than AA. The function dN(A)/dAdN(A)/dA where N(A)N(A) is the general solution of this equation for q=1 is a product of an increasing bounded function and power-law function with stretched exponential cut-off. The relation with Tsallis non-extensive statistics is demonstrated by solving the generalized logistic equation for q>0q>0. In the case 0models super-additive, and the case q>1q>1 it models sub-additive structures. The Gutenberg-Richter (G-R) formula results from interpretation of empirical data as a straight line in the area of stretched exponent with small α. The solution is applied for modeling distribution of foreshocks and aftershocks in the regions of Napa Valley 2014, and Sumatra 2004 earthquakes fitting the observed data well, both qualitatively and quantitatively.

  20. Using three-dimensional protein structure to model protein aggregation: Collagen fibrillogenesis in vitro

    NASA Astrophysics Data System (ADS)

    Anderson, Darren; Graovac, Ivan; Rainey, Jan; Goh, M. Cynthia

    2004-03-01

    Collagen is the most prevalent protein in mammals. In vitro, it self-assembles into a variety of fibrillar constructs which depend on solution conditions. These assembly processes are still not understood in a thorough manner, in part because of the lack of a three-dimensional structure of the rather large monomer ( 3000 amino acids). Using a statistically-based reduced-rotamer representation alongside a triple-helical backbone parameterization, we have created a 3-D collagen model, and examined the location of charges as a function of pH. Using this representation, we propose a mechanism of assembly that accounts for the morphology (observed using atomic force microscopy) of the most common fibrillar construct. Furthermore, we demonstrate that the experimentally observed effects of pH and ionic strength on the assembly process can be related to the three-dimensional structure of the monomer.

  1. A Lumry-Eyring Nucleated-Polymerization (LENP) Model of Protein Aggregation Kinetics 2. Competing Growth via Condensation- and Chain-Polymerization

    PubMed Central

    Li, Yi; Roberts, Christopher J.

    2009-01-01

    The Lumry-Eyring with nucleated-polymerization (LENP) model from part 1 (Andrews and Roberts, J. Phys. Chem. B 2007, 111, 7897 7913) is expanded to explicitly account for kinetic contributions from aggregate-aggregate condensation polymerization. Experimentally accessible quantities described by the resulting model include monomer mass fraction (m), weight-average molecular weight (Mw), and ratio of Mw to number-average molecular weight (Mn) as a function of time (t). Analysis of global model behavior illustrates ways to identify which steps in the overall aggregation process are kinetically important, based on the qualitative behavior of m, Mw, and Mw/Mn vs. t, and based on whether bulk phase separation or precipitation occurs. For cases in which all aggregates remain soluble, moment equations are provided that permit straightforward numerical regression of experimental data to give separate time scales or inverse rate coefficients for nucleation and for growth by chain and condensation polymerization. Analysis of simulated data indicates that it may be possible to neglect condensation reactions if only early-time data are considered, and also highlights difficulties in conclusively distinguishing between alternative mechanisms of condensation even when kinetics are monitored with both m and wM. PMID:19368365

  2. A model for micellar aggregates of a bile salt: crystal structure of sodium taurodeoxycholate monohydrate.

    PubMed

    Campanelli, A R; Candeloro De Sanctis, S; Giglio, E; Scaramuzza, L

    1987-05-01

    Crystals of sodium taurodeoxycholate monohydrate, NaC26H44NO6S X H2O, are trigonal, space group P3(1), with a = 18.393(1), c = 7.097(1)A, V = 2079.3(5)A3, and Z = 3. The structure was solved by direct methods and Fourier techniques and refined by full-matrix least-squares calculations. The final R index is 0.051. The side chair of the anion displays an approximate folded-back conformation. The cyclopentane ring assumes an intermediate conformation between the half-chain and the beta-envelope. The sodium ion shows a distorted octahedral coordination with six oxygen atoms, giving rise to ion-ion and ion-dipole interactions. The molecules form helices, characterized by threefold screw axes, with a radius of about 16 A. The helices are packed in such a way as to be embedded in each other as cog-wheels. The helix found in this crystal structure will be used as a model and checked in the study of the micellar solutions of sodium taurodeoxycholate, following the same strategy satisfactorily employed in the case of sodium deoxycholate.

  3. Soluble tau species, not neurofibrillary aggregates, disrupt neural system integration in a tau transgenic model.

    PubMed

    Fox, Leora M; William, Christopher M; Adamowicz, David H; Pitstick, Rose; Carlson, George A; Spires-Jones, Tara L; Hyman, Bradley T

    2011-07-01

    Neurofibrillary tangles are a feature of Alzheimer disease and other tauopathies, and although they are generally believed to be markers of neuronal pathology, there is little evidence evaluating whether tangles directly impact neuronal function. To investigate the response of cells in hippocampal circuits to complex behavioral stimuli, we used an environmental enrichment paradigm to induce expression of an immediate-early gene, Arc, in the rTg4510 mouse model of tauopathy. These mice reversibly overexpress P301L tau and exhibit substantial neurofibrillary tangle deposition, neuronal loss, and memory deficits. Using fluorescent in situ hybridization to detect Arc messenger RNA, we found that rTg4510 mice have impaired hippocampal Arc expression both without stimulation and in response to environmental enrichment; this likely reflects the combination of functional impairments of existing neurons and loss of neurons. However, tangle-bearing cells were at least as likely as non-tangle-bearing neurons to exhibit Arc expression in response to enrichment. Transgene suppression with doxycycline for 6 weeks resulted in increased percentages of Arc-positive cells in rTg4510 brains compared with untreated transgenics, restoring enrichment-induced Arc messenger RNA levels to that of wild-type controls despite the continued presence of neurofibrillary pathology. We interpret these data to indicate that soluble tau contributes to impairment of hippocampal function, although tangles do not preclude neurons from responding in a functional circuit.

  4. Electrochemical deposition of layered copper thin films based on the diffusion limited aggregation

    NASA Astrophysics Data System (ADS)

    Wei, Chenhuinan; Wu, Guoxing; Yang, Sanjun; Liu, Qiming

    2016-10-01

    In this work layered copper films with smooth surface were successfully fabricated onto ITO substrate by electrochemical deposition (ECD) and the thickness of the films was nearly 60 nm. The resulting films were characterized by SEM, TEM, AFM, XPS, and XRD. We have investigated the effects of potential and the concentration of additives and found that 2D dendritic-like growth process leaded the formation of films. A suitable growth mechanism based on diffusion limited aggregation (DLA) mechanism for the copper films formation is presented, which are meaningful for further designing homogeneous and functional films.

  5. Electrochemical deposition of layered copper thin films based on the diffusion limited aggregation

    PubMed Central

    Wei, Chenhuinan; Wu, Guoxing; Yang, Sanjun; Liu, Qiming

    2016-01-01

    In this work layered copper films with smooth surface were successfully fabricated onto ITO substrate by electrochemical deposition (ECD) and the thickness of the films was nearly 60 nm. The resulting films were characterized by SEM, TEM, AFM, XPS, and XRD. We have investigated the effects of potential and the concentration of additives and found that 2D dendritic-like growth process leaded the formation of films. A suitable growth mechanism based on diffusion limited aggregation (DLA) mechanism for the copper films formation is presented, which are meaningful for further designing homogeneous and functional films. PMID:27734900

  6. Sealing properties of mineral trioxide aggregate orthograde apical plugs and root fillings in an in vitro apexification model.

    PubMed

    Martin, Rebecca L; Monticelli, Francesca; Brackett, William W; Loushine, Robert J; Rockman, Roy A; Ferrari, Marco; Pashley, David H; Tay, Franklin R

    2007-03-01

    One-visit mineral trioxide aggregate (MTA) apexification is gaining in popularity over the use of calcium hydroxide barriers. This study examined the sealing properties of two MTA apexification procedures using an in vitro apexification model. White MTA was introduced into instrumented single-rooted canals with standardized artificially created open apices to form 3- to 5-mm-thick orthograde apical plugs or complete orthograde fillings of the root segments. The remaining canal spaces in the former group were backfilled with thermoplasticized gutta-percha without a sealer. A Flodec fluid filtration device was used to record fluid flow across filled root canals at 48 hours and after 4 weeks of immersion in phosphate-buffered saline (PBS). Although MTA root fillings exhibited a better seal than MTA apical plugs at 48 hours, seals of these two groups were not significantly different after 4 weeks. Interaction of MTA with PBS may result in apatite deposition that improves the seal of MTA apical plugs with time.

  7. Impact of flavouring substances on the aggregation behaviour of dissolved barley β-glucans in a model beer.

    PubMed

    Kupetz, M; Sacher, B; Becker, T

    2016-06-05

    Structural polymers such as cereal β-glucan may cause various processing problems in beverage industry depending on concentration, molar size distribution and agglomeration behaviour. In this context, influences of the beer volatiles dodecanoic acid, octyl butanoate, ethyl decanoate and decyl acetate on molar mass and radii of barley β-glucan were investigated in ethanolic (4% w/w) model solution. After addition of 100mg/l ethyl decanoate and decyl acetate to the β-glucan solution, a wider-ranging molar mass distribution could be observed by means of asymmetric field-flow-fractionation. Due to agglomeration, average molar mass of β-glucan standard (MW=6.8×10(6)g/mol) increased by 2×10(6)g/mol (P<0.05) in solution containing decyl acetate. Furthermore, a significant growth (P<0.05) from 86 to 102 nm in gyration radius was measured. The obtained results elucidate the importance of fatty acid derived flavouring substance composition in beer regarding the aggregation behaviour of β-glucan.

  8. Impact of high cholesterol in a Parkinson's disease model: Prevention of lysosomal leakage versus stimulation of α-synuclein aggregation.

    PubMed

    Eriksson, Ida; Nath, Sangeeta; Bornefall, Per; Giraldo, Ana Maria Villamil; Öllinger, Karin

    2017-01-16

    Parkinson's disease is characterized by accumulation of intraneuronal cytoplasmic inclusions, Lewy bodies, which mainly consist of aggregated α-synuclein. Controversies exist as to whether high blood cholesterol is a risk factor for the development of the disease and whether statin treatment could have a protective effect. Using a model system of BE(2)-M17 neuroblastoma cells treated with the neurotoxin 1-methyl-4-phenylpyridinium (MPP(+)), we found that MPP(+)-induced cell death was accompanied by cholesterol accumulation in a lysosomal-like pattern in pre-apoptotic cells. To study the effects of lysosomal cholesterol accumulation, we increased lysosomal cholesterol through pre-treatment with U18666A and found delayed leakage of lysosomal contents into the cytosol, which reduced cell death. This suggests that increased lysosomal cholesterol is a stress response mechanism to protect lysosomal membrane integrity in response to early apoptotic stress. However, high cholesterol also stimulated the accumulation of α-synuclein. Treatment with the cholesterol-lowering drug lovastatin reduced MPP(+)-induced cell death by inhibiting the production of reactive oxygen species, but did not prevent lysosomal cholesterol increase nor affect α-synuclein accumulation. Our study indicates a dual role of high cholesterol in Parkinson's disease, in which it acts both as a protector against lysosomal membrane permeabilization and as a stimulator of α-synuclein accumulation.

  9. Placing Local Aggregations in a Larger-Scale Context: Hierarchical Modeling of Black-Footed Albatross Dispersion

    PubMed Central

    Jahncke, J.; Hyrenbach, K. D.

    2016-01-01

    At-sea surveys facilitate the study of the distribution and abundance of marine birds along standardized transects, in relation to changes in the local environmental conditions and large-scale oceanographic forcing. We analyzed the form and the intensity of black-footed albatross (Phoebastria nigripes: BFAL) spatial dispersion off central California, using five years (2004–2008) of vessel-based surveys of seven replicated survey lines. We related BFAL patchiness to local, regional and basin-wide oceanographic variability using two complementary approaches: a hypothesis-based model and an exploratory analysis. The former tested the strength and sign of hypothesized BFAL responses to environmental variability, within a hierarchical atmosphere—ocean context. The latter explored BFAL cross-correlations with atmospheric / oceanographic variables. While albatross dispersion was not significantly explained by the hierarchical model, the exploratory analysis revealed that aggregations were influenced by static (latitude, depth) and dynamic (wind speed, upwelling) environmental variables. Moreover, the largest BFAL patches occurred along the survey lines with the highest densities, and in association with shallow banks. In turn, the highest BFAL densities occurred during periods of negative Pacific Decadal Oscillation index values and low atmospheric pressure. The exploratory analyses suggest that BFAL dispersion is influenced by basin-wide, regional-scale and local environmental variability. Furthermore, the hypothesis-based model highlights that BFAL do not respond to oceanographic variability in a hierarchical fashion. Instead, their distributions shift more strongly in response to large-scale ocean—atmosphere forcing. Thus, interpreting local changes in BFAL abundance and dispersion requires considering diverse environmental forcing operating at multiple scales. PMID:27124491

  10. Modeling FtsZ ring formation in the bacterial cell—anisotropic aggregation via mutual interactions of polymer rods

    NASA Astrophysics Data System (ADS)

    Fischer-Friedrich, Elisabeth; Gov, Nir

    2011-04-01

    The cytoskeletal protein FtsZ polymerizes to a ring structure (Z ring) at the inner cytoplasmic membrane that marks the future division site and scaffolds the division machinery in many bacterial species. FtsZ is known to polymerize in the presence of GTP into single-stranded protofilaments. In vivo, FtsZ polymers become associated with the cytoplasmic membrane via interaction with the membrane-binding proteins FtsA and ZipA. The FtsZ ring structure is highly dynamic and undergoes constantly polymerization and depolymerization processes and exchange with the cytoplasmic pool. In this theoretical study, we consider a scenario of Z ring self-organization via self-enhanced attachment of FtsZ polymers due to end-to-end interactions and lateral interactions of FtsZ polymers on the membrane. With the assumption of exclusively circumferential polymer orientations, we derive coarse-grained equations for the dynamics of the pool of cytoplasmic and membrane-bound FtsZ. To capture stochastic effects expected in the system due to low particle numbers, we simulate our computational model using a Gillespie-type algorithm. We obtain ring- and arc-shaped aggregations of FtsZ polymers on the membrane as a function of monomer numbers in the cell. In particular, our model predicts the number of FtsZ rings forming in the cell as a function of cell geometry and FtsZ concentration. We also calculate the time of FtsZ ring localization to the midplane in the presence of Min oscillations. Finally, we demonstrate that the assumptions and results of our model are confirmed by 3D reconstructions of fluorescently-labeled FtsZ structures in E. coli that we obtained.

  11. Modeling the frequency dependence (5-120 MHz) of ultrasound backscattering by red cell aggregates in shear flow at a normal hematocrit

    NASA Astrophysics Data System (ADS)

    Fontaine, Isabelle; Cloutier, Guy

    2003-05-01

    The frequency dependence of the ultrasound signal backscattered by blood in shear flow was studied using a simulation model. The ultrasound backscattered signal was computed with a linear model that considers the characteristics of the ultrasound system and tissue acoustic properties. The tissue scattering properties were related to the position and shape of the red blood cells (RBCs). A 2D microrheological model simulated the RBC dynamics in a Couette shear flow system. This iterative model, described earlier [Biophys. J. 82, 1696-1710 (2002)], integrates the hydrodynamic effect of the flow, as well as adhesive and repulsive forces between RBCs. RBC aggregation was simulated at 40% hematocrit and shear rates of 0.05-2 s-1. The RBC aggregate sizes ranged, on average, from 3.3 RBCs at 2 s-1 to 33.5 cells at 0.05 s-1. The ultrasound backscattered power was studied at frequencies between 5-120 MHz and insonification angles between 0-180°. At frequencies below approximately 30 MHz, the ultrasound backscattered power increased as the shear rate was decreased and the size of the aggregates was raised. A totally different scattering behavior was noted above 30 MHz. Typical spectral slopes of the backscattered power (log-log scale) between 5-25 MHz equaled 3.8, whereas slopes down to 0.6 were measured at 0.05 s-1, between 40-60 MHz. The ultrasound backscattered power was shown to be angle dependent at low frequencies (5-25 MHz). The anisotropy persisted at high frequencies (>25 MHz) for small aggregates (at 2 s-1). In conclusion, this study sheds some light on the blood backscattering behavior with an emphasis on the non-Rayleigh regime. Additional experimental studies may be necessary to validate the simulation results, and to fully understand the relation between the ultrasound backscattered power, level of RBC aggregation, shear rate, frequency, and insonification angle.

  12. Glyceraldehyde 3-phosphate dehydrogenase augments the intercellular transmission and toxicity of polyglutamine aggregates in a cell model of Huntington disease.

    PubMed

    Mikhaylova, Elena R; Lazarev, Vladimir F; Nikotina, Alina D; Margulis, Boris A; Guzhova, Irina V

    2016-03-01

    The common feature of Huntington disease is the accumulation of oligomers or aggregates of mutant huntingtin protein (mHTT), which causes the death of a subset of striatal neuronal populations. The cytotoxic species can leave neurons and migrate to other groups of cells penetrating and damaging them in a prion-like manner. We hypothesized that the glycolytic enzyme glyceraldehyde 3-phosphate dehydrogenase (GAPDH), previously shown to elevate the aggregation of mHTT, is associated with an increased efficiency of intercellular propagation of mHTT. GAPDH, on its own or together with polyglutamine species, was shown to be released into the extracellular milieu mainly from dying cells as assessed by a novel enzyme immunoassay, western blotting, and ultrafiltration. The conditioned medium of cells with growing GAPDH-polyQ aggregates was toxic to naïve cells, whereas depletion of the aggregates from the medium lowered this cytotoxicity. The GAPDH component of the aggregates was found to increase their toxicity by two-fold in comparison with polyQ alone. Furthermore, GAPDH-polyQ complexes were shown to penetrate acceptor cells and to increase the capacity of polyQ to prionize its intracellular homolog containing a repeat of 25 glutamine residues. Finally, inhibitors of intracellular transport showed that polyQ-GAPDH complexes, as well as GAPDH itself, penetrated cells using clathrin-mediated endocytosis. This suggested a pivotal role of the enzyme in the intercellular transmission of Huntington disease pathogenicity. In conclusion, GAPDH occurring in complexes with polyglutamine strengthens the prion-like activity and toxicity of the migrating aggregates. Aggregating polygluatmine tracts were shown to release from the cells over-expressing mutant huntingtin in a complex with glyceraldehyde 3-phosphate dehydrogenase (GAPDH). The enzyme enhances the intracellular transport of aggregates to healthy cells, prionization of normal cellular proteins and finally cell death, thus

  13. Breed differences in development of anti-insulin antibodies in diabetic dogs and investigation of the role of dog leukocyte antigen (DLA) genes.

    PubMed

    Holder, Angela L; Kennedy, Lorna J; Ollier, William E R; Catchpole, Brian

    2015-10-15

    Administration of insulin for treatment of diabetes mellitus in dogs can stimulate an immune response, with a proportion of animals developing anti-insulin antibodies (AIA). For an IgG antibody response to occur, this would require B cell presentation of insulin peptides by major histocompatibility complex (MHC) class II molecules, encoded by dog leukocyte antigen (DLA) genes, in order to receive T-cell help for class switching. DLA genes are highly polymorphic in the dog population and vary from breed to breed. The aim of the present study was to evaluate AIA reactivity in diabetic dogs of different breeds and to investigate whether DLA genes influence AIA status. Indirect ELISA was used to determine serological reactivity to insulin in diabetic dogs, treated with either a porcine or bovine insulin preparation. DLA haplotypes for diabetic dogs were determined by sequence-based typing of DLA-DRB1, -DQA1 and -DQB1 loci. Significantly greater insulin reactivity was seen in treated diabetic dogs (n=942) compared with non-diabetic dogs (n=100). Relatively few newly diagnosed diabetic dogs (3/109) were found to be AIA positive, although this provides evidence that insulin autoantibodies might be involved in the pathogenesis of the disease in some cases. Of the diabetic dogs treated with a bovine insulin preparation, 52.3% (182/348) were AIA positive, compared with 12.6% (75/594) of dogs treated with a porcine insulin preparation, suggesting that bovine insulin is more immunogenic. Breeds such as dachshund, Cairn terrier, miniature schnauzer and Tibetan terrier were more likely to develop AIA, whereas cocker spaniels were less likely to develop AIA, compared with crossbreed dogs. In diabetic dogs, DLA haplotype DRB1*0015--DQA1*006--DQB1*023 was associated with being AIA positive, whereas the haplotype DLA-DRB1*006--DQA1*005--DQB1*007 showed an association with being AIA negative. These research findings suggest that DLA genes influence AIA responses in treated diabetic

  14. Histocompatibility studies in a closely bred colony of dogs. V. Mechanisms of cellular adaptation in long-term DL-A identical radiation chimeras

    PubMed Central

    1975-01-01

    20 Cooperstown beagles of known DL-A genotypes (B" dogs) were exposed to supralethal total body irradiation and received a bone marrow allograft from a DL-A identical donor (A" dog); the resulting chimeras have survived uneventfully for 882, 1466 days, with no evidence of secondary disease, and have been tolerant to kidney and skin allografts obtained from the donor of marrow. Treatment of "A" dogs with serum obtained from their long-term "B" chimeras had no significant effect upon the ability of the recipients to reject "B" skin allografts... PMID:1097570

  15. Information diffusion, Facebook clusters, and the simplicial model of social aggregation: a computational simulation of simplicial diffusers for community health interventions.

    PubMed

    Kee, Kerk F; Sparks, Lisa; Struppa, Daniele C; Mannucci, Mirco A; Damiano, Alberto

    2016-01-01

    By integrating the simplicial model of social aggregation with existing research on opinion leadership and diffusion networks, this article introduces the constructs of simplicial diffusers (mathematically defined as nodes embedded in simplexes; a simplex is a socially bonded cluster) and simplicial diffusing sets (mathematically defined as minimal covers of a simplicial complex; a simplicial complex is a social aggregation in which socially bonded clusters are embedded) to propose a strategic approach for information diffusion of cancer screenings as a health intervention on Facebook for community cancer prevention and control. This approach is novel in its incorporation of interpersonally bonded clusters, culturally distinct subgroups, and different united social entities that coexist within a larger community into a computational simulation to select sets of simplicial diffusers with the highest degree of information diffusion for health intervention dissemination. The unique contributions of the article also include seven propositions and five algorithmic steps for computationally modeling the simplicial model with Facebook data.

  16. A Computer-Assisted 3D Model for Analyzing the Aggregation of Tumorigenic Cells Reveals Specialized Behaviors and Unique Cell Types that Facilitate Aggregate Coalescence

    PubMed Central

    Scherer, Amanda; Kuhl, Spencer; Wessels, Deborah; Lusche, Daniel F.; Hanson, Brett; Ambrose, Joseph; Voss, Edward; Fletcher, Emily; Goldman, Charles; Soll, David R.

    2015-01-01

    We have developed a 4D computer-assisted reconstruction and motion analysis system, J3D-DIAS 4.1, and applied it to the reconstruction and motion analysis of tumorigenic cells in a 3D matrix. The system is unique in that it is fast, high-resolution, acquires optical sections using DIC microscopy (hence there is no associated photoxicity), and is capable of long-term 4D reconstruction. Specifically, a z-series at 5 μm increments can be acquired in less than a minute on tissue samples embedded in a 1.5 mm thick 3D Matrigel matrix. Reconstruction can be repeated at intervals as short as every minute and continued for 30 days or longer. Images are converted to mathematical representations from which quantitative parameters can be derived. Application of this system to cancer cells from established lines and fresh tumor tissue has revealed unique behaviors and cell types not present in non-tumorigenic lines. We report here that cells from tumorigenic lines and tumors undergo rapid coalescence in 3D, mediated by specific cell types that we have named “facilitators” and “probes.” A third cell type, the “dervish”, is capable of rapid movement through the gel and does not adhere to it. These cell types have never before been described. Our data suggest that tumorigenesis in vitro is a developmental process involving coalescence facilitated by specialized cells that culminates in large hollow spheres with complex architecture. The unique effects of select monoclonal antibodies on these processes demonstrate the usefulness of the model for analyzing the mechanisms of anti-cancer drugs. PMID:25790299

  17. Inhibition of alpha-synuclein aggregation by multifunctional dopamine agonists assessed by a novel in vitro assay and an in vivo Drosophila synucleinopathy model

    PubMed Central

    Yedlapudi, Deepthi; Joshi, Gnanada S.; Luo, Dan; Todi, Sokol V.; Dutta, Aloke K.

    2016-01-01

    Aggregation of alpha synuclein (α-syn) leading to dopaminergic neuronal death has been recognized as one of the main pathogenic factors in the initiation and progression of Parkinson’s disease (PD). Consequently, α-syn has been targeted for the development of therapeutics for PD. We have developed a novel assay to screen compounds with α-syn modulating properties by mimicking recent findings from in vivo animal studies involving intrastriatal administration of pre-formed fibrils in mice, resulting in increased α-syn pathology accompanying the formation of Lewy-body (LB) type inclusions. We found that in vitro generated α-syn pre-formed fibrils induce seeding of α-syn monomers to produce aggregates in a dose-and time-dependent manner under static conditions in vitro. These aggregates were toxic towards rat pheochromocytoma cells (PC12). Our novel multifunctional dopamine agonists D-519 and D-520 exhibited significant neuroprotection in this assay, while their parent molecules did not. The neuroprotective properties of our compounds were further evaluated in a Drosophila model of synucleinopathy. Both of our compounds showed protective properties in fly eyes against the toxicity caused by α-syn. Thus, our in vitro results on modulation of aggregation and toxicity of α-syn by our novel assay were further validated with the in vivo experiments. PMID:27917933

  18. Simulation of J-aggregate microcavity photoluminescence

    NASA Astrophysics Data System (ADS)

    Michetti, Paolo; La Rocca, Giuseppe C.

    2008-05-01

    We have developed a model in order to account for the photoexcitation dynamics of J-aggregate films and strongly coupled J-aggregate microcavities. The J aggregates are described as a disordered Frenkel exciton system in which relaxation occurs due to the presence of a thermal bath of molecular vibrations. The correspondence between the photophysics in J-aggregate films and that in J-aggregate microcavities is obtained by introducing a model polariton wave function mixing cavity photon modes and J-aggregate super-radiant excitons. With the same description of the material properties, we have calculated both absorption and luminescence spectra for the J-aggregate film and the photoluminescence of strongly coupled organic microcavities. The model is able to account for the fast relaxation dynamics in organic microcavities following nonresonant pumping and explains the temperature dependence of the ratio between the upper polariton and the lower polariton luminescence.

  19. Evaluating aggregate effects of rare and common variants in the 1000 Genomes Project exon sequencing data using latent variable structural equation modeling.

    PubMed

    Nock, Nl; Zhang, Lx

    2011-11-29

    Methods that can evaluate aggregate effects of rare and common variants are limited. Therefore, we applied a two-stage approach to evaluate aggregate gene effects in the 1000 Genomes Project data, which contain 24,487 single-nucleotide polymorphisms (SNPs) in 697 unrelated individuals from 7 populations. In stage 1, we identified potentially interesting genes (PIGs) as those having at least one SNP meeting Bonferroni correction using univariate, multiple regression models. In stage 2, we evaluate aggregate PIG effects on trait, Q1, by modeling each gene as a latent construct, which is defined by multiple common and rare variants, using the multivariate statistical framework of structural equation modeling (SEM). In stage 1, we found that PIGs varied markedly between a randomly selected replicate (replicate 137) and 100 other replicates, with the exception of FLT1. In stage 1, collapsing rare variants decreased false positives but increased false negatives. In stage 2, we developed a good-fitting SEM model that included all nine genes simulated to affect Q1 (FLT1, KDR, ARNT, ELAV4, FLT4, HIF1A, HIF3A, VEGFA, VEGFC) and found that FLT1 had the largest effect on Q1 (βstd = 0.33 ± 0.05). Using replicate 137 estimates as population values, we found that the mean relative bias in the parameters (loadings, paths, residuals) and their standard errors across 100 replicates was on average, less than 5%. Our latent variable SEM approach provides a viable framework for modeling aggregate effects of rare and common variants in multiple genes, but more elegant methods are needed in stage 1 to minimize type I and type II error.

  20. Aggregate exposure modelling of zinc pyrithione in rinse-off personal cleansing products using a person-orientated approach with market share refinement.

    PubMed

    Tozer, Sarah A; Kelly, Seamus; O'Mahony, Cian; Daly, E J; Nash, J F

    2015-09-01

    Realistic estimates of chemical aggregate exposure are needed to ensure consumer safety. As exposure estimates are a critical part of the equation used to calculate acceptable "safe levels" and conduct quantitative risk assessments, methods are needed to produce realistic exposure estimations. To this end, a probabilistic aggregate exposure model was developed to estimate consumer exposure from several rinse off personal cleansing products containing the anti-dandruff preservative zinc pyrithione. The model incorporates large habits and practices surveys, containing data on frequency of use, amount applied, co-use along with market share, and combines these data at the level of the individual based on subject demographics to better estimate exposure. The daily-applied exposure (i.e., amount applied to the skin) was 3.79 mg/kg/day for the 95th percentile consumer. The estimated internal dose for the 95th percentile exposure ranged from 0.01-1.29 μg/kg/day after accounting for retention following rinsing and dermal penetration of ZnPt. This probabilistic aggregate exposure model can be used in the human safety assessment of ingredients in multiple rinse-off technologies (e.g., shampoo, bar soap, body wash, and liquid hand soap). In addition, this model may be used in other situations where refined exposure assessment is required to support a chemical risk assessment.

  1. Data Aggregation, Curation and Modeling Approaches to Deliver Prediction Models to Support Computational Toxicology at the EPA (ACS Fall meeting)

    EPA Science Inventory

    The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program develops and utilizes QSAR modeling approaches across a broad range of applications. In terms of physical chemistry we have a particular interest in the prediction of basic physicochemical parameters ...

  2. Latent heat induced rotation limited aggregation in 2D ice nanocrystals

    NASA Astrophysics Data System (ADS)

    Bampoulis, Pantelis; Siekman, Martin H.; Kooij, E. Stefan; Lohse, Detlef; Zandvliet, Harold J. W.; Poelsema, Bene

    2015-07-01

    The basic science responsible for the fascinating shapes of ice crystals and snowflakes is still not understood. Insufficient knowledge of the interaction potentials and the lack of relevant experimental access to the growth process are to blame for this failure. Here, we study the growth of fractal nanostructures in a two-dimensional (2D) system, intercalated between mica and graphene. Based on our scanning tunneling spectroscopy data, we provide compelling evidence that these fractals are 2D ice. They grow while they are in material contact with the atmosphere at 20 °C and without significant thermal contact to the ambient. The growth is studied in situ, in real time and space at the nanoscale. We find that the growing 2D ice nanocrystals assume a fractal shape, which is conventionally attributed to Diffusion Limited Aggregation (DLA). However, DLA requires a low mass density mother phase, in contrast to the actual currently present high mass density mother phase. Latent heat effects and consequent transport of heat and molecules are found to be key ingredients for understanding the evolution of the snow (ice) flakes. We conclude that not the local availability of water molecules (DLA), but rather them having the locally required orientation is the key factor for incorporation into the 2D ice nanocrystal. In combination with the transport of latent heat, we attribute the evolution of fractal 2D ice nanocrystals to local temperature dependent rotation limited aggregation. The ice growth occurs under extreme supersaturation, i.e., the conditions closely resemble the natural ones for the growth of complex 2D snow (ice) flakes and we consider our findings crucial for solving the "perennial" snow (ice) flake enigma.

  3. Gel-Entrapped Staphylococcus aureus Bacteria as Models of Biofilm Infection Exhibit Growth in Dense Aggregates, Oxygen Limitation, Antibiotic Tolerance, and Heterogeneous Gene Expression

    PubMed Central

    Pabst, Breana; Pitts, Betsey; Lauchnor, Ellen

    2016-01-01

    An experimental model that mimicked the structure and characteristics of in vivo biofilm infections, such as those occurring in the lung or in dermal wounds where no biomaterial surface is present, was developed. In these infections, microbial biofilm forms as cell aggregates interspersed in a layer of mucus or host matrix material. This structure was modeled by filling glass capillary tubes with an agarose gel that had been seeded with Staphylococcus aureus bacteria and then incubating the gel biofilm in medium for up to 30 h. Confocal microscopy showed that the bacteria formed in discrete pockets distributed throughout the gel matrix. These aggregates enlarged over time and also developed a size gradient, with the clusters being larger near the nutrient- and oxygen-supplied interface and smaller at greater depths. Bacteria entrapped in gels for 24 h grew slowly (specific growth rate, 0.06 h−1) and were much less susceptible to oxacillin, minocycline, or ciprofloxacin than planktonic cells. Microelectrode measurements showed that the oxygen concentration decreased with depth into the gel biofilm, falling to values less than 3% of air saturation at depths of 500 μm. An anaerobiosis-responsive green fluorescent protein reporter gene for lactate dehydrogenase was induced in the region of the gel where the measured oxygen concentrations were low, confirming biologically relevant hypoxia. These results show that the gel biofilm model captures key features of biofilm infection in mucus or compromised tissue: formation of dense, distinct aggregates, reduced specific growth rates, local hypoxia, and antibiotic tolerance. PMID:27503656

  4. Allogenic forcing of autogenic processes: inferences from an aggregated process-based model of fluvio-deltaic systems

    NASA Astrophysics Data System (ADS)

    Karamitopoulos, P.; Weltje, G.; Dalman, R.

    2011-12-01

    Spatial and temporal variability of sediment storage in fluvio-deltaic sedimentary systems is controlled by the interplay of allogenic and autogenic processes. In order to investigate the effects of this interplay on the resulting stratigraphy at varying spatio-temporal scales, we carried out a series of numerical experiments using an aggregated process-based model of fluvio-deltaic systems (SIMCLAST), which combines diffusive and advective transport with sub-grid channel stability algorithms in the fluvial domain. New distributary channels occur by avulsions under conditions of local superelevation or through bifurcations due to mouth bar deposition. A series of numerical experiments were performed under forcing by glacio-eustatic sealevel cycles in the order of 100 kyr. Initial conditions of all experiments are represented by classic continental-margin topography with a shelf break. In this scenario, erosional features (canyons) are developed when sea level falls below the shelf break. Sediment supply and liquid discharge remain constant throughout the experiments. In order to characterize the topographic variability during the experiments, we used a difference measure obtained by summation of local changes in net sediment accumulation rates across the entire model domain. Long-term average variability (10 kyr resolution) correlates strongly with the allogenic sea-level signal. The long-term variability reaches a maximum around the time interval corresponding to isochronous maximum flooding surfaces, when retrogradation gives way to a new episode of progradation. Long-term mean variability is lowest during periods of sea-level fall, when incision restricts sediment dispersal. Increasing the time resolution of our difference measure allows recognition of numerous small peaks which correspond to local changes in sediment accumulation rates induced by autogenic processes (avulsions and bifurcations). The amplitudes of these peaks are related to the rate of change of

  5. Enhanced Efficacy of Human Brain-Derived Neural Stem Cells by Transplantation of Cell Aggregates in a Rat Model of Parkinson's Disease

    PubMed Central

    Shin, Eun Sil; Hwang, Onyou; Hwang, Yu-Shik; Suh, Jun-Kyo Francis; Chun, Young Il

    2014-01-01

    Objective Neural tissue transplantation has been a promising strategy for the treatment of Parkinson's disease (PD). However, transplantation has the disadvantages of low-cell survival and/or development of dyskinesia. Transplantation of cell aggregates has the potential to overcome these problems, because the cells can extend their axons into the host brain and establish synaptic connections with host neurons. In this present study, aggregates of human brain-derived neural stem cells (HB-NSC) were transplanted into a PD animal model and compared to previous report on transplantation of single-cell suspensions. Methods Rats received an injection of 6-OHDA into the right medial forebrain bundle to generate the PD model and followed by injections of PBS only, or HB-NSC aggregates in PBS into the ipsilateral striatum. Behavioral tests, multitracer (2-deoxy-2-[18F]-fluoro-D-glucose ([18F]-FDG) and [18F]-N-(3-fluoropropyl)-2-carbomethoxy-3-(4-iodophenyl)nortropane ([18F]-FP-CIT) microPET scans, as well as immunohistochemical (IHC) and immunofluorescent (IF) staining were conducted to evaluate the results. Results The stepping test showed significant improvement of contralateral forelimb control in the HB-NSC group from 6-10 weeks compared to the control group (p<0.05). [18F]-FP-CIT microPET at 10 weeks posttransplantation demonstrated a significant increase in uptake in the HB-NSC group compared to pretransplantation (p<0.05). In IHC and IF staining, tyrosine hydroxylase and human β2 microglobulin (a human cell marker) positive cells were visualized at the transplant site. Conclusion These results suggest that the HB-NSC aggregates can survive in the striatum and exert therapeutic effects in a PD model by secreting dopamine. PMID:25535514

  6. The common inhaled anesthetic isoflurane increases aggregation of huntingtin and alters calcium homeostasis in a cell model of Huntington's disease

    SciTech Connect

    Wang Qiujun; Liang Ge; Yang Hui; Wang Shouping; Eckenhoff, Maryellen F.; Wei Huafeng

    2011-02-01

    Isoflurane is known to increase {beta}-amyloid aggregation and neuronal damage. We hypothesized that isoflurane will have similar effects on the polyglutamine huntingtin protein and will cause alterations in intracellular calcium homeostasis. We tested this hypothesis in striatal cells from the expanded glutamine huntingtin knock-in mouse (STHdh{sup Q111/Q111}) and wild type (STHdh{sup Q7/Q7}) striatal neurons. The primary cultured neurons were exposed for 24 h to equipotent concentrations of isoflurane, sevoflurane, and desflurane in the presence or absence of extracellular calcium and with or without xestospongin C, a potent endoplasmic reticulum inositol 1,4,5-trisphosphate (InsP{sub 3}) receptor antagonist. Aggregation of huntingtin protein, cell viability, and calcium concentrations were measured. Isoflurane, sevoflurane, and desflurane all increased the aggregation of huntingtin in STHdh{sup Q111/Q111} cells, with isoflurane having the largest effect. Isoflurane induced greater calcium release from the ER and relatively more cell damage in the STHdh{sup Q111/Q111} huntingtin cells than in the wild type STHdh{sup Q7/Q7} striatal cells. However, sevoflurane and desflurane caused less calcium release from the ER and less cell damage. Xestospongin C inhibited the isoflurane-induced calcium release from the ER, aggregation of huntingtin, and cell damage in the STHdh{sup Q111/Q111} cells. In summary, the Q111 form of huntingtin increases the vulnerability of striatal neurons to isoflurane neurotoxicity through combined actions on the ER IP{sub 3} receptors. Calcium release from the ER contributes to the anesthetic induced huntingtin aggregation in STHdh{sup Q111/Q111} striatal cells.

  7. In vitro generation of three-dimensional substrate-adherent embryonic stem cell-derived neural aggregates for application in animal models of neurological disorders.

    PubMed

    Hargus, Gunnar; Cui, Yi-Fang; Dihné, Marcel; Bernreuther, Christian; Schachner, Melitta

    2012-05-01

    In vitro-differentiated embryonic stem (ES) cells comprise a useful source for cell replacement therapy, but the efficiency and safety of a translational approach are highly dependent on optimized protocols for directed differentiation of ES cells into the desired cell types in vitro. Furthermore, the transplantation of three-dimensional ES cell-derived structures instead of a single-cell suspension may improve graft survival and function by providing a beneficial microenvironment for implanted cells. To this end, we have developed a new method to efficiently differentiate mouse ES cells into neural aggregates that consist predominantly (>90%) of postmitotic neurons, neural progenitor cells, and radial glia-like cells. When transplanted into the excitotoxically lesioned striatum of adult mice, these substrate-adherent embryonic stem cell-derived neural aggregates (SENAs) showed significant advantages over transplanted single-cell suspensions of ES cell-derived neural cells, including improved survival of GABAergic neurons, increased cell migration, and significantly decreased risk of teratoma formation. Furthermore, SENAs mediated functional improvement after transplantation into animal models of Parkinson's disease and spinal cord injury. This unit describes in detail how SENAs are efficiently derived from mouse ES cells in vitro and how SENAs are isolated for transplantation. Furthermore, methods are presented for successful implantation of SENAs into animal models of Huntington's disease, Parkinson's disease, and spinal cord injury to study the effects of stem cell-derived neural aggregates in a disease context in vivo.

  8. The probabilistic aggregate consumer exposure model (PACEM): validation and comparison to a lower-tier assessment for the cyclic siloxane D5.

    PubMed

    Dudzina, Tatsiana; Delmaar, Christiaan J E; Biesterbos, Jacqueline W H; Bakker, Martine I; Bokkers, Bas G H; Scheepers, Paul T J; van Engelen, Jacqueline G M; Hungerbuehler, Konrad; von Goetz, Natalie

    2015-06-01

    Current practice of chemical risk assessment for consumer product ingredients still rarely exercises the aggregation of multi-source exposure. However, focusing on a single dominant source/pathway combination may lead to a significant underestimation of the risk for substances present in numerous consumer products, which often are used simultaneously. Moreover, in most cases complex multi-route exposure scenarios also need to be accounted for. This paper introduces and evaluates the performance of the Probabilistic Aggregate Consumer Exposure Model (PACEM) applied in the context of a tiered approach to exposure assessment for ingredients in cosmetics and personal care products (C&PCPs) using decamethylcyclopentasiloxane (D5) as a worked example. It is demonstrated that PACEM predicts a more realistic, but still conservative aggregate exposure within the Dutch adult population when compared to a deterministic point estimate obtained in a lower tier screening assessment. An overall validation of PACEM is performed by quantitatively relating and comparing its estimates to currently available human biomonitoring and environmental sampling data. Moderate (by maximum one order of magnitude) overestimation of exposure is observed due to a justified conservatism built into the model structure, resulting in the tool being suitable for risk assessment.

  9. The model of amyloid aggregation of Escherichia coli RNA polymerase σ70 subunit based on AFM data and in vitro assays.

    PubMed

    Koroleva, Olga N; Dubrovin, Evgeniy V; Khodak, Yu A; Kuzmina, Natalia V; Yaminsky, Igor V; Drutsa, Valeriy L

    2013-07-01

    To propose a model for recently described amyloid aggregation of E.coli RNA polymerase σ(70) subunit, we have investigated the role of its N-terminal region. For this purpose, three mutant variants of protein with deletions Δ1-73, Δ1-100 and Δ74-100 were constructed and studied in a series of in vitro assays and using atomic force microscopy (AFM). Specifically, all RNA polymerase holoenzymes, reconstituted with the use of mutant σ subunits, have shown reduced affinity for promoter-containing DNA and reduced activity in run-off transcription experiments (compared to that of WT species), thus substantiating the modern concept on the modulatory role of N-terminus in formation of open complex and transcription initiation. The ability of mutant proteins to form amyloid-like structures has been investigated using AFM, which revealed the increased propensity of mutant proteins to form rodlike aggregates with the effect being more pronounced for the mutant with the deletion Δ1-73 (10 fold increase). σ(70) subunit aggregation ability has shown complex dependence on the ionic surrounding, which we explain by Debye screening effect and the change of the internal state of the protein. Basing on the obtained data, we propose the model of amyloid fibril formation by σ(70) subunit, implying the involvement of N-terminal region according to the domain swapping mechanism.

  10. Application of linear pH gradients for the modeling of ion exchange chromatography: Separation of monoclonal antibody monomer from aggregates.

    PubMed

    Kluters, Simon; Wittkopp, Felix; Jöhnck, Matthias; Frech, Christian

    2016-02-01

    The mobile phase pH is a key parameter of every ion exchange chromatography process. However, mechanistic insights into the pH influence on the ion exchange chromatography equilibrium are rare. This work describes a mechanistic model capturing salt and pH influence in ion exchange chromatography. The pH dependence of the characteristic protein charge and the equilibrium constant is introduced to the steric mass action model based on a protein net charge model considering the number of amino acids interacting with the stationary phase. This allows the description of the adsorption equilibrium of the chromatographed proteins as a function of pH. The model parameters were determined for a monoclonal antibody monomer, dimer, and a higher aggregated species based on a manageable set of pH gradient experiments. Without further modification of the model parameters the transfer to salt gradient elution at fixed pH is demonstrated. A lumped rate model was used to predict the separation of the monoclonal antibody monomer/aggregate mixture in pH gradient elution and for a pH step elution procedure-also at increased protein loadings up to 48 g/L packed resin. The presented model combines both salt and pH influence and may be useful for the development and deeper understanding of an ion exchange chromatography separation.

  11. Toxicity assessment of aggregated/agglomerated cerium oxide nanoparticles in an in vitro 3D airway model: the influence of mucociliary clearance.

    PubMed

    Frieke Kuper, C; Gröllers-Mulderij, Mariska; Maarschalkerweerd, Thérèse; Meulendijks, Nicole M M; Reus, Astrid; van Acker, Frédérique; Zondervan-van den Beuken, Esther K; Wouters, Mariëlle E L; Bijlsma, Sabina; Kooter, Ingeborg M

    2015-03-01

    We investigated the toxicity of aggregated nanoparticles of cerium oxide (CeO2) using an in vitro 3D human bronchial epithelial model that included a mucociliary apparatus (MucilAir™). CeO2 was dispersed in saline and applied to the apical surface of the model. CeO2 did not induce distinct effects in the model, whereas it did in BEAS-2B and A549 cell cultures. The absence of effects of CeO2 was not because of the model's insensitivity. Nanoparticles of zinc oxide (ZnO) elicited positive responses in the toxicological assays. Respiratory mucus (0.1% and 1%) added to dispersions increased aggregation/agglomeration to such an extent that most CeO2 sedimented within a few minutes. Also, the mucociliary apparatus of the model removed CeO2 from the central part of the apical surface to the borders. This 'clearance' may have prevented the majority of CeO2 from reaching the epithelial cells. Chemical analysis of cerium in the basal tissue culture medium showed only minimal translocation of cerium across the 3D barrier. In conclusion, mucociliary defence appeared to prevent CeO2 reaching the respiratory epithelial cells in this 3D in vitro model. This model and approach can be used to study compounds of specific toxicological concern in airway defence mechanisms in vitro.

  12. Conflation and aggregation of spatial data improve predictive models for species with limited habitats: a case of the threatened yellow-billed cuckoo in Arizona, USA

    USGS Publications Warehouse

    Villarreal, Miguel L.; Van Riper, Charles; Petrakis, Roy E.

    2013-01-01

    Riparian vegetation provides important wildlife habitat in the Southwestern United States, but limited distributions and spatial complexity often leads to inaccurate representation in maps used to guide conservation. We test the use of data conflation and aggregation on multiple vegetation/land-cover maps to improve the accuracy of habitat models for the threatened western yellow-billed cuckoo (Coccyzus americanus occidentalis). We used species observations (n = 479) from a state-wide survey to develop habitat models from 1) three vegetation/land-cover maps produced at different geographic scales ranging from state to national, and 2) new aggregate maps defined by the spatial agreement of cover types, which were defined as high (agreement = all data sets), moderate (agreement ≥ 2), and low (no agreement required). Model accuracies, predicted habitat locations, and total area of predicted habitat varied considerably, illustrating the effects of input data quality on habitat predictions and resulting potential impacts on conservation planning. Habitat models based on aggregated and conflated data were more accurate and had higher model sensitivity than original vegetation/land-cover, but this accuracy came at the cost of reduced geographic extent of predicted habitat. Using the highest performing models, we assessed cuckoo habitat preference and distribution in Arizona and found that major watersheds containing high-probably habitat are fragmented by a wide swath of low-probability habitat. Focus on riparian restoration in these areas could provide more breeding habitat for the threatened cuckoo, offset potential future habitat losses in adjacent watershed, and increase regional connectivity for other threatened vertebrates that also use riparian corridors.

  13. Structure of Viral Aggregates

    NASA Astrophysics Data System (ADS)

    Barr, Stephen; Luijten, Erik

    2010-03-01

    The aggregation of virus particles is a particular form of colloidal self-assembly, since viruses of a give type are monodisperse and have identical, anisotropic surface charge distributions. In small-angle X-ray scattering experiments, the Qbeta virus was found to organize in different crystal structures in the presence of divalent salt and non-adsorbing polymer. Since a simple isotropic potential cannot explain the occurrence of all observed phases, we employ computer simulations to investigate how the surface charge distribution affects the virus interactions. Using a detailed model of the virus particle, we find an asymmetric ion distribution around the virus which gives rise to the different phases observed.

  14. Mathematical modelling of physical and chemical processes of coal combustion in chamber furnaces of boiler aggregates based on the package of applied programs FIRE 3D

    NASA Astrophysics Data System (ADS)

    Gil, A. V.; Starchenko, A. V.

    2012-09-01

    The furnace processes of the combustion of poly-fraction high-ashes Ekibastuz coal in the furnace chamber of the boiler aggregate PK-39 and of the combustion of highly humid brown Berezov's coal in the furnace of the BKZ-210-140 boiler are investigated by mathematical modeling using the package of applied programs FIRE 3D [1-3]. Results of the numerical modeling of the processes of aerodynamics, heat exchange, and combustion in the furnace volume and their comparison with the results of nature tests are presented.

  15. Integrated Information Support System (IISS). Volume 5. Common Data Model Subsystem. Part 29. Data Aggregators Product Specification.

    DTIC Science & Technology

    1985-11-01

    Role Boeing Military Aircraft Reviewer. Company (EMAC) D. Appleton Company Responsible for IDEF support, (DACOM) state-of-the-art literature search...SRTCDR SORTING THE COMMON DATA RECORD TRMSRT TERMINATE THE SORTING 3-12 Milt X - PS 620141320 1 November 1985 DATA AGGREGATORS Module List Module Name...OF THE RECORD "INPUT-FILE". REVISED 15 APR 1985 MODIFIED 2 MAY 1985 MODIFIED 9 MAY 1985 ARGUMENTS: INPUT-FILE - RECRD TEMP-FILE-NAME - DSPLY [ X (30

  16. Aqueous extract of Glycyrrhiza inflata inhibits aggregation by upregulating PPARGC1A and NFE2L2-ARE pathways in cell models of spinocerebellar ataxia 3.

    PubMed

    Chen, Chiung-Mei; Weng, Yu-Ting; Chen, Wan-Ling; Lin, Te-Hsien; Chao, Chih-Ying; Lin, Chih-Hsin; Chen, I-Cheng; Lee, Li-Ching; Lin, Hsuan-Yuan; Wu, Yih-Ru; Chen, Yi-Chun; Chang, Kuo-Hsuan; Tang, Hsiang-Yu; Cheng, Mei-Ling; Lee-Chen, Guey-Jen; Lin, Jung-Yaw

    2014-06-01

    Spinocerebellar ataxia (SCA) types 1, 2, 3, 6, 7, and 17 and dentatorubropallidoluysian atrophy, as well as Huntington disease, are a group of neurodegenerative disorders caused by a CAG triplet-repeat expansion encoding a long polyglutamine (polyQ) tract in the respective mutant proteins. The cytoplasmic and nuclear aggregate formation, a pathological hallmark of polyQ diseases, is probably the initial process triggering the subsequent pathological events. Compromised oxidative stress defense capacity and mitochondrial dysfunction have emerged as contributing factors to the pathogenesis of polyQ diseases. The roots of licorice (Glycyrrhiza species) have long been used as an herbal medicine. In this study, we demonstrate the aggregate-inhibitory effect of Glycyrrhiza inflata herb extract and its constituents licochalcone A and ammonium glycyrrhizinate (AMGZ) in both 293 and SH-SY5Y ATXN3/Q75 cells, SCA3 cell models. The reporter assay showed that G. inflata herb extract, licochalcone A, and AMGZ could enhance the promoter activity of peroxisome proliferator-activated receptor γ, coactivator 1α (PPARGC1A), a known regulator of mitochondrial biogenesis and antioxidative response genes. G. inflata extract, licochalcone A, and AMGZ upregulated PPARGC1A expression and its downstream target genes, SOD2 and CYCS, in the 293 ATXN3/Q75 cell model. The expression of nuclear factor erythroid 2-related factor 2 (NFE2L2), the principal transcription factor that binds to antioxidant-responsive elements (AREs) to promote ARE-dependent gene expression when the cells respond to oxidative stress, and its downstream genes, HMOX1, NQO1, GCLC, and GSTP1, was also increased by G. inflata herb extract, licochalcone A, and AMGZ. Knockdown of PPARGC1A increased aggregates in ATXN3/Q75 cells and also attenuated the aggregate-inhibiting effect of the tested compounds. G. inflata extract and its constituents significantly elevated GSH/GSSG ratio and reduced reactive oxidative species in

  17. Experimental investigations on aggregate-aggregate collisions in the early solar nebula

    NASA Astrophysics Data System (ADS)

    Blum, Jürgen; Münch, Michael

    1993-11-01

    An experimental setup has been devised to study the low-velocity aggregate-aggregate collisions that play a role in determining aggregate sizes in the preplanetary nebula; both central and grazing collisions are in this way studied for both ZrSiO4 and Aerosil 200. Fragment-mass distributions for catastrophic collisions between equal-sized aggregates are extrapolated according to several assumptions of the simple fragmentation model chosen. The model predicts a complete disintegration of the ZrSiO4 equal-size aggregates.

  18. Effect of cysteine on lowering protein aggregation and subsequent hardening of whey protein isolate (WPI) protein bars in WPI/buffer model systems.

    PubMed

    Zhu, Dan; Labuza, Theodore P

    2010-07-14

    Whey protein isolate (WPI) bar hardening without and with cysteine (Cys) or N-ethylmaleimide (NEM) was investigated in model systems (WPI/buffer = 6:4, by weight, pH 6.8, a(w) approximately 0.97) in an accelerated shelf-life test (ASLT) at 45 degrees C over a period of up to 35 days. The formation of insoluble aggregates as determined by solubility and the structural rearrangement of WPI protein aggregates as observed by SEM were responsible for the WPI bars' hardening. As corroborated by electrophoresis analysis, both beta-lactoglobulin (beta-lg) and alpha-lactalbumin (alpha-la) were involved in the formation of aggregates via the thiol-disulfide interchange reaction and/or noncovalent interactions. The former force dominated the bar hardening at an earlier stage, whereas the latter force played a role for the long-term hardening. In comparison with the control bar without Cys, the thiol-disulfide interchange reaction was significantly reduced by Cys (WPI/Cys = 0.05), increased by Cys (WPI/Cys = 0.25), and inhibited by NEM (WPI/NEM = 2). Therefore, bar hardening was significantly delayed by Cys (WPI/Cys = 0.05) and NEM but accelerated by Cys (WPI/Cys = 0.25).

  19. Estimation of electrokinetic and hydrodynamic global properties of relevant amyloid-beta peptides through the modeling of their effective electrophoretic mobilities and analysis of their propensities to aggregation.

    PubMed

    Deiber, Julio A; Piaggio, Maria V; Peirotti, Marta B

    2014-09-01

    Neuronal activity loss may be due to toxicity caused by amyloid-beta peptides forming soluble oligomers. Here amyloid-beta peptides (1-42, 1-40, 1-39, 1-38, and 1-37) are characterized through the modeling of their experimental effective electrophoretic mobilities determined by a capillary zone electrophoresis method as reported in the literature. The resulting electrokinetic and hydrodynamic global properties are used to evaluate amyloid-beta peptide propensities to aggregation through pair particles interaction potentials and Brownian aggregation kinetic theories. Two background electrolytes are considered at 25°C, one for pH 9 and ionic strength I = 40 mM (aggregation is inhibited through NH4OH) the other for pH 10 and I = 100 mM (without NH4OH). Physical explanations of peptide oligomerization mechanisms are provided. The effect of hydration, electrostatic, and dispersion forces in the amyloidogenic process of amyloid-beta peptides (1-40 and 1-42) are quantitatively presented. The interplay among effective charge number, hydration, and conformation of chains is described. It is shown that amyloid-beta peptides (1-40 and 1-42) at pH 10, I = 100 mM and 25°C, may form soluble oligomers, mainly of order 2 and 4, after an incubation of 48 h, which at higher times evolve and end up in complex structures (protofibrils and fibrils) found in plaques associated with Alzheimer's disease.

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

    PubMed

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

    2006-03-01

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

  1. Reconstructing the fractal dimension of granular aggregates from light intensity spectra.

    PubMed

    Tang, Fiona H M; Maggi, Federico

    2015-12-21

    There has been growing interest in using the fractal dimension to study the hierarchical structures of soft materials after realising that fractality is an important property of natural and engineered materials. This work presents a method to quantify the internal architecture and the space-filling capacity of granular fractal aggregates by reconstructing the three-dimensional capacity dimension from their two-dimensional optical projections. Use is made of the light intensity of the two-dimensional aggregate images to describe the aggregate surface asperities (quantified by the perimeter-based fractal dimension) and the internal architecture (quantified by the capacity dimension) within a mathematical framework. This method was tested on control aggregates of diffusion-limited (DLA), cluster-cluster (CCA) and self-correlated (SCA) types, stereolithographically-fabricated aggregates, and experimentally-acquired natural sedimentary aggregates. Statistics of the reconstructed capacity dimension featured correlation coefficients R ≥ 98%, residuals NRMSE ≤ 10% and percent errors PE ≤ 4% as compared to controls, and improved earlier approaches by up to 50%.

  2. Large-scale microfluidics providing high-resolution and high-throughput screening of Caenorhabditis elegans poly-glutamine aggregation model

    PubMed Central

    Mondal, Sudip; Hegarty, Evan; Martin, Chris; Gökçe, Sertan Kutal; Ghorashian, Navid; Ben-Yakar, Adela

    2016-01-01

    Next generation drug screening could benefit greatly from in vivo studies, using small animal models such as Caenorhabditis elegans for hit identification and lead optimization. Current in vivo assays can operate either at low throughput with high resolution or with low resolution at high throughput. To enable both high-throughput and high-resolution imaging of C. elegans, we developed an automated microfluidic platform. This platform can image 15 z-stacks of ∼4,000 C. elegans from 96 different populations using a large-scale chip with a micron resolution in 16 min. Using this platform, we screened ∼100,000 animals of the poly-glutamine aggregation model on 25 chips. We tested the efficacy of ∼1,000 FDA-approved drugs in improving the aggregation phenotype of the model and identified four confirmed hits. This robust platform now enables high-content screening of various C. elegans disease models at the speed and cost of in vitro cell-based assays. PMID:27725672

  3. Large-scale microfluidics providing high-resolution and high-throughput screening of Caenorhabditis elegans poly-glutamine aggregation model

    NASA Astrophysics Data System (ADS)

    Mondal, Sudip; Hegarty, Evan; Martin, Chris; Gökçe, Sertan Kutal; Ghorashian, Navid; Ben-Yakar, Adela

    2016-10-01

    Next generation drug screening could benefit greatly from in vivo studies, using small animal models such as Caenorhabditis elegans for hit identification and lead optimization. Current in vivo assays can operate either at low throughput with high resolution or with low resolution at high throughput. To enable both high-throughput and high-resolution imaging of C. elegans, we developed an automated microfluidic platform. This platform can image 15 z-stacks of ~4,000 C. elegans from 96 different populations using a large-scale chip with a micron resolution in 16 min. Using this platform, we screened ~100,000 animals of the poly-glutamine aggregation model on 25 chips. We tested the efficacy of ~1,000 FDA-approved drugs in improving the aggregation phenotype of the model and identified four confirmed hits. This robust platform now enables high-content screening of various C. elegans disease models at the speed and cost of in vitro cell-based assays.

  4. Influence of internal spatial aggregation procedures of the SWAT model on the modelling of the rainfall runoff processes in the Dyle catchment at 2 different scales.

    NASA Astrophysics Data System (ADS)

    Romanowicz, A. A.; Vanclooster, M.; Rounsevell, M.; La Jeunesse, I.

    2003-04-01

    The sensitivity of the surface hydrological component of the spatially distributed hydrological model SWAT [1]( ARCVIEVTM version) to internal spatial aggregation procedures was tested for the Dyle catchment and for its subcatchment of the Thyle (Belgium). For this analysis, use was made of the generalised soil association map at the scale of 1:500.000 [3], and the land use map created in an earlier study [2]. Uncalibrated simulations were performed for both catchments using the same input and parameterisation, changing only the catchment size and thereby the creation of the Hydrological Response Units (HRU) , its distribution within the catchments and its parametrisation.. The results suggest that the SWAT model is very sensitive to the internal procedures defining the HRU size and distributions and also to the way how soil and land use are assigned to the HRU (using either the dominant or multiple class option). This also suggests that the use of the same underlying input data but for different catchment sizes will affect modelling performance. Internal GIS functions transform the basic soil and land use data prior to hydrological modelling. This will complicate the upscaling of hydrological processes by means of the SWAT model. Acknowledgements This research was carried out within the framework of the EU Mulino project (contract no. EVK1-2000-22089). The authors would also like to acknowledge the developers of the AvSwat interface. Reference [1]Arnold, J.G., Engel, B.A., Srinivasan, R., 1993, Continuous-time, grid cell watershed model. Proc.of the 18-19 June 1993 Conf. Spokane, Washington, 267-278 [2] Comité National de Géographie, Carte pédologique ( d’association des soil) de la Belgique ou 1:500 000 [3] Romanowicz, A. A., Vanclooster, M., Rounsevell, M. and La Jeunesse, I., Sensitivity of the SWAT model to soil parameterisation with different land use input maps: a case study of the Thyle catchment in Belgium [in preparation] [3] Van Orshoven, J

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

    NASA Astrophysics Data System (ADS)

    Pieterse, G.; Vermeulen, A.

    2005-12-01

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

  6. Conditions for self-consistent aggregation by chemotactic particles

    NASA Astrophysics Data System (ADS)

    Inoue, Masayo; Kaneko, Kunihiko

    2008-04-01

    We have numerically studied chemotactic aggregation of microorganisms by introducing a model consisting of elements with intracellular dynamics, random walks with a state-dependent turnover rate, and secretion of attractant. Three phases with and without aggregation, as well as partial aggregation, were obtained as to the diffusion and degradation rates of the attractant, and conditions for cellular aggregation were analyzed. The size of aggregated clusters was shown to be independent of cell density, as is consistent with experiment.

  7. Aggregates in the Temporal Query Language TQuel,

    DTIC Science & Technology

    1987-07-27

    makes it possible to define both standard and unique aggregates in a rigorous way. Ceri and Gottlob present 43 prVPW t TW WRJR V P P V * a translation...from a subset of SQL that includes aggregates into relational algebra, thereby defining an operational semantics for SQL aggregates [Ceri & Gottlob ...Zvi, J. The Time Relational Model. Ph). Diss. Computer Science Department, UCLA, 1982. (Ceri & Gotlob 19851 Ceri, S. and G. Gottlob . Translating SQL

  8. Role of Multicellular Aggregates in Biofilm Formation

    PubMed Central

    Kragh, Kasper N.; Hutchison, Jaime B.; Melaugh, Gavin; Rodesney, Chris; Roberts, Aled E. L.; Irie, Yasuhiko; Jensen, Peter Ø.; Diggle, Stephen P.; Allen, Rosalind J.

    2016-01-01

    ABSTRACT In traditional models of in vitro biofilm development, individual bacterial cells seed a surface, multiply, and mature into multicellular, three-dimensional structures. Much research has been devoted to elucidating the mechanisms governing the initial attachment of single cells to surfaces. However, in natural environments and during infection, bacterial cells tend to clump as multicellular aggregates, and biofilms can also slough off aggregates as a part of the dispersal process. This makes it likely that biofilms are often seeded by aggregates and single cells, yet how these aggregates impact biofilm initiation and development is not known. Here we use a combination of experimental and computational approaches to determine the relative fitness of single cells and preformed aggregates during early development of Pseudomonas aeruginosa biofilms. We find that the relative fitness of aggregates depends markedly on the density of surrounding single cells, i.e., the level of competition for growth resources. When competition between aggregates and single cells is low, an aggregate has a growth disadvantage because the aggregate interior has poor access to growth resources. However, if competition is high, aggregates exhibit higher fitness, because extending vertically above the surface gives cells at the top of aggregates better access to growth resources. Other advantages of seeding by aggregates, such as earlier switching to a biofilm-like phenotype and enhanced resilience toward antibiotics and immune response, may add to this ecological benefit. Our findings suggest that current models of biofilm formation should be reconsidered to incorporate the role of aggregates in biofilm initiation. PMID:27006463

  9. On mean type aggregation.

    PubMed

    Yager, R R

    1996-01-01

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

  10. Structure and kinetics of shear aggregation in turbulent flows. I. Early stage of aggregation.

    PubMed

    Bäbler, Matthäus U; Moussa, Amgad S; Soos, Miroslav; Morbidelli, Massimo

    2010-08-17

    Aggregation of rigid colloidal particles leads to fractal-like structures that are characterized by a fractal dimension d(f) which is a key parameter for describing aggregation processes. This is particularly true in shear aggregation where d(f) strongly influences aggregation kinetics. Direct measurement of d(f) in the early stages of shear aggregation is however difficult, as the aggregates are small and few in number. An alternative method for determining d(f) is to use an aggregation model that when fitted to the time evolution of the cluster mass distribution allows for estimating d(f). Here, we explore three such models, two of which are based on an effective collision sphere and one which directly incorporates the permeable structure of the aggregates, and we apply them for interpreting the initial aggregate growth measured experimentally in a turbulent stirred tank reactor. For the latter, three polystyrene latexes were used that differed only in the size of the primary particles (d(p) = 420, 600, and 810 nm). It was found that all three models describe initial aggregation kinetics reasonably well using, however, substantially different values for d(f). To discriminate among the models, we therefore also studied the regrowth of preformed aggregates where d(f) was experimentally accessible. It was found that only the model that directly incorporates the permeable structure of the aggregates is able to predict correctly this second type of experiments. Applying this model to the initial aggregation kinetics, we conclude that the actual initial fractal dimension is d(f) = 2.07 +/- 0.04 as found from this model.

  11. Why patchy diffusion-limited aggregation belongs to the directed-percolation universality class

    NASA Astrophysics Data System (ADS)

    Kartha, Moses J.; Banpurkar, Arun G.

    2016-12-01

    We present a possible link between nonequilibrium phase transition observed in patchy diffusion-limited aggregation (DLA) [M. J. Kartha and A. Sayeed, Phys. Lett. A 380, 2791 (2016), 10.1016/j.physleta.2016.06.036] and directed bond percolation (DP). A system of directed percolation with patchy particles (patchy DP) in which the bond connectivity is established depending on patch size p is analyzed. It is observed that patchy DP starting from a single seed shows a nonequilibrium phase transition. Below a critical value of the patch size pc, the system reaches an absorbing state above which is a fluctuating active state as observed in the DP system. The value of this nonuniversal parameter pc is observed to be slightly higher than the value observed in patchy DLA. Close to the critical value, the order parameter P (∞ ) ˜(p-pc) β where β =0.272 ±0.010 , which is consistent with the directed-percolation universality class. Therefore the intrinsic nature of patchy DP is responsible for the phase transition in patchy DLA. This study reveals that the estimated critical value of patch size pc=0.806 25 ±0.000 20 in patchy DP is different from the critical bond probability pc=0.6447 in the DP system. This elucidates that the bond probability in DP is not equivalent to the patch probability of a particular site. Our work also gives an insight into the problem related with formation of an extended network of pentagon subunits in connection with the virus capsid.

  12. Investigating the mechanisms leading to protein aggregation

    NASA Astrophysics Data System (ADS)

    McNamara, Ruth; McManus, Jennifer J.

    2014-03-01

    The formation of protein aggregates is a feature of several diseases and is a problem during the manufacture of biopharmaceutical and protein based food products. During processing, stability may become compromised leading to the condensation of proteins to form non-native aggregates. The aim of this work is to induce aggregation on model proteins by the imposition of a particular stress to evaluate the extent of aggregation and to assess the degree of structural change to the protein. Aggregation of two proteins, lysozyme and bovine serum albumin has been induced by several mechanisms. Using various techniques (electrophoresis, HPLC, spectroscopic analysis, and microscopic techniques) both the level of aggregation extent of protein unfolding has been investigated for a range of solution conditions. Our results show that the amount of aggregation depends strongly on the mechanism by which non-native aggregation proceeds, and within each mechanism, solution conditions are an important factor. With the exception of aggregation by self-association (which is concentration dependent), the appearance of aggregation is driven by structural changes induced by the applied stress (heat, chemical denaturant, oxidation or contact with a surface). Author would like to acknowledge support from Science Foundation Ireland (SFI), National University of Maynooth John and Pat Hume Scholarship.

  13. Basin infilling of a schematic 1D estuary using two different approaches: an aggregate diffusive type model and a processed based model.

    NASA Astrophysics Data System (ADS)

    Laginha Silva, Patricia; Martins, Flávio A.; Boski, Tomász; Sampath, Dissanayake M. R.

    2010-05-01

    processes. In this viewpoint the system is broken down into its fundamental components and processes and the model is build up by selecting the important processes regardless of its time and space scale. This viewpoint was only possible to pursue in the recent years due to improvement in system knowledge and computer power (Paola, 2000). The primary aim of this paper is to demonstrate that it is possible to simulate the evolution of the sediment river bed, traditionally studied with synthetic models, with a process-based hydrodynamic, sediment transport and morphodynamic model, solving explicitly the mass and momentum conservation equations. With this objective, a comparison between two mathematical models for alluvial rivers is made to simulate the evolution of the sediment river bed of a conceptual 1D embayment for periods in the order of a thousand years: the traditional synthetic basin infilling aggregate diffusive type model based on the diffusion equation (Paola, 2000), used in the "synthesist" viewpoint and the process-based model MOHID (Miranda et al., 2000). The simulation of the sediment river bed evolution achieved by the process-based model MOHID is very similar to those obtained by the diffusive type model, but more complete due to the complexity of the process-based model. In the MOHID results it is possible to observe a more comprehensive and realistic results because this type of model include processes that is impossible to a synthetic model to describe. At last the combined effect of tide, sea level rise and river discharges was investigated in the process based model. These effects cannot be simulated using the diffusive type model. The results demonstrate the feasibility of using process based models to perform studies in scales of 10000 years. This is an advance relative to the use of synthetic models, enabling the use of variable forcing. REFERENCES • Briggs, L.I. and Pollack, H.N., 1967. Digital model of evaporate sedimentation. Science, 155, 453

  14. RAGG - R EPISODIC AGGREGATION PACKAGE

    EPA Science Inventory

    The RAGG package is an R implementation of the CMAQ episodic model aggregation method developed by Constella Group and the Environmental Protection Agency. RAGG is a tool to provide climatological seasonal and annual deposition of sulphur and nitrogen for multimedia management. ...

  15. Aggregated Recommendation through Random Forests

    PubMed Central

    2014-01-01

    Aggregated recommendation refers to the process of suggesting one kind of items to a group of users. Compared to user-oriented or item-oriented approaches, it is more general and, therefore, more appropriate for cold-start recommendation. In this paper, we propose a random forest approach to create aggregated recommender systems. The approach is used to predict the rating of a group of users to a kind of items. In the preprocessing stage, we merge user, item, and rating information to construct an aggregated decision table, where rating information serves as the decision attribute. We also model the data conversion process corresponding to the new user, new item, and both new problems. In the training stage, a forest is built for the aggregated training set, where each leaf is assigned a distribution of discrete rating. In the testing stage, we present four predicting approaches to compute evaluation values based on the distribution of each tree. Experiments results on the well-known MovieLens dataset show that the aggregated approach maintains an acceptable level of accuracy. PMID:25180204

  16. Elevated Hapln2 Expression Contributes to Protein Aggregation and Neurodegeneration in an Animal Model of Parkinson's Disease

    PubMed Central

    Wang, Qinqin; Zhou, Qinbo; Zhang, Shuzhen; Shao, Wei; Yin, Yanqing; Li, Yandong; Hou, Jincan; Zhang, Xinhua; Guo, Yongshun; Wang, Xiaomin; Gu, Xiaosong; Zhou, Jiawei

    2016-01-01

    Parkinson's disease (PD), the second most common age-associated progressive neurodegenerative disorder, is characterized by the loss of dopaminergic (DA) neurons in the substantia nigra pars compacta (SN). The pathogenesis of PD and the mechanisms underlying the degeneration of DA neurons are still not fully understood. Our previous quantitative proteomics study revealed that hyaluronan and proteoglycan binding link protein 2 (Hapln2) is one of differentially expressed proteins in the substantia nigra tissues from PD patients and healthy control subjects. However, the potential role of Hapln2 in PD pathogenesis remains elusive. In the present study, we characterized the expression pattern of Hapln2. In situ hybridization revealed that Hapln2 mRNA was widely expressed in adult rat brain with high abundance in the substantia nigra. Immunoblotting showed that expression levels of Hapln2 were markedly upregulated in the substantia nigra of either human subjects with Parkinson's disease compared with healthy control. Likewise, there were profound increases in Hapln2 expression in neurotoxin 6-hydroxydopamine-treated rat. Overexpression of Hapln2 in vitro increased vulnerability of MES23.5 cells, a dopaminergic cell line, to 6-hydroxydopamine. Moreover, Hapln2 overexpression led to the formation of cytoplasmic aggregates which were co-localized with ubiquitin and E3 ligases including Parkin, Gp78, and Hrd1 in vitro. Endogenous α-synuclein was also localized in Hapln2-containing aggregates and ablation of Hapln2 led to a marked decrease of α-synuclein in insoluble fraction compared with control. Thus, Hapln2 is identified as a novel factor contributing to neurodegeneration in PD. Our data provides new insights into the cellular mechanism underlying the pathogenesis in PD. PMID:27601993

  17. Quantifying aggregation dynamics during Myxococcus xanthus development.

    PubMed

    Zhang, Haiyang; Angus, Stuart; Tran, Michael; Xie, Chunyan; Igoshin, Oleg A; Welch, Roy D

    2011-10-01

    Under starvation conditions, a swarm of Myxococcus xanthus cells will undergo development, a multicellular process culminating in the formation of many aggregates called fruiting bodies, each of which contains up to 100,000 spores. The mechanics of symmetry breaking and the self-organization of cells into fruiting bodies is an active area of research. Here we use microcinematography and automated image processing to quantify several transient features of developmental dynamics. An analysis of experimental data indicates that aggregation reaches its steady state in a highly nonmonotonic fashion. The number of aggregates rapidly peaks at a value 2- to 3-fold higher than the final value and then decreases before reaching a steady state. The time dependence of aggregate size is also nonmonotonic, but to a lesser extent: average aggregate size increases from the onset of aggregation to between 10 and 15 h and then gradually decreases thereafter. During this process, the distribution of aggregates transitions from a nearly random state early in development to a more ordered state later in development. A comparison of experimental results to a mathematical model based on the traffic jam hypothesis indicates that the model fails to reproduce these dynamic features of aggregation, even though it accurately describes its final outcome. The dynamic features of M. xanthus aggregation uncovered in this study impose severe constraints on its underlying mechanisms.

  18. Equilibrium structure of ferrofluid aggregates.

    PubMed

    Yoon, Mina; Tománek, David

    2010-11-17

    We study the equilibrium structure of large but finite aggregates of magnetic dipoles, representing a colloidal suspension of magnetite particles in a ferrofluid. With increasing system size, the structural motif evolves from chains and rings to multi-chain and multi-ring assemblies. Very large systems form single- and multi-wall coils, tubes and scrolls. These structural changes result from a competition between various energy terms, which can be approximated analytically within a continuum model. We also study the effect of external parameters such as magnetic field on the relative stability of these structures. Our results may give insight into experimental data obtained during solidification of ferrofluid aggregates at temperatures where thermal fluctuations become negligible in comparison to inter-particle interactions. These data may also help to experimentally control the aggregation of magnetic particles.

  19. Equilibrium structure of ferrofluid aggregates

    SciTech Connect

    Yoon, Mina; Tomanek, David

    2010-01-01

    We study the equilibrium structure of large but finite aggregates of magnetic dipoles, representing a colloidal suspension of magnetite particles in a ferrofluid. With increasing system size, the structural motif evolves from chains and rings to multi-chain and multi-ring assemblies. Very large systems form single- and multi-wall coils, tubes and scrolls. These structural changes result from a competition between various energy terms, which can be approximated analytically within a continuum model. We also study the effect of external parameters such as magnetic field on the relative stability of these structures. Our results may give insight into experimental data obtained during solidification of ferrofluid aggregates at temperatures where thermal fluctuations become negligible in comparison to inter-particle interactions. These data may also help to experimentally control the aggregation of magnetic particles.

  20. Aggregate growth in a protoplanetary disk

    NASA Astrophysics Data System (ADS)

    Xiang, Chuchu; Carballido, Augusto; Matthews, Lorin; Hyde, Truell

    2017-01-01

    We present a method to model the growth of neutral and charged dusts in a turbulent protoplanetary disk, and analyze their collision probabilities. Coagulation of dust aggregates plays an important role in the formation of planets and is of key importance to the evolution of protoplanetary disks. In our method, the temporal evolution of the dusts is followed by Monte Carlo algorithm, and the inter-particle interactions are calculated by Aggregate_Builder (AB), which is a code used to model the collision process of aggregates. First an aggregate library is built and all the aggregates are binned according to their sizes. In each iteration, the collision rate for aggregates from any two bins are computed, which determines the time it takes for the next collision to happen and which two aggregates are selected for collision. Then the AB codes are used to calculate the interaction of the two aggregates. The relative velocity between the two aggregates is the vector sum of Brownian velocity and the turbulent velocity. The latter is calculated by ATHENA, which is a grid-based code for astrophysical magnetohydrodynamics. In each iteration, it’s determined whether the two aggregates hit or miss. In the case of hit, it either sticks or bounces as determined by the critical velocity. As a result, the neutral aggregates are more porous than the charged ones. For a certain size of incoming aggregates, the neutral ones have a higher collision probability than the charged ones. Also, similarly-sized aggregates have lower collision probabilities than aggregates with large size dispersions. This research enables us to determine which physical properties have a greater impact on the collision rate. By tracing the dust size distribution, we can identify the stage when they settle out to the mid-plane and how long it takes to develop to that stage. In the hit-stick regime, our results are consistent with the experiments which shows that when the velocity is smaller than the

  1. Self-Consistent Non-Stationary Theory of Multipactor in DLA Structures

    SciTech Connect

    Sinitsyn, O. V.; Nusinovich, G. S.; Antonsen, T. M.; Kishek, R.

    2009-01-22

    In this paper a non-stationary self-consistent theoretical model of multipactor in dielectric loaded accelerator structures is proposed. In comparison with our previous work, the effects of the cylindricity are included. The corresponding numerical implementation of the model is described and some simulation results are shown.

  2. Bacteriological studies of blood, tissue fluid, lymph and lymph nodes in patients with acute dermatolymphangioadenitis (DLA) in course of 'filarial' lymphedema.

    PubMed

    Olszewski, W L; Jamal, S; Manokaran, G; Pani, S; Kumaraswami, V; Kubicka, U; Lukomska, B; Tripathi, F M; Swoboda, E; Meisel-Mikolajczyk, F; Stelmach, E; Zaleska, M

    1999-10-15

    Filarial lymphedema is complicated by frequent episodes of dermatolymphangioadenitis (DLA). Severe systemic symptoms during attacks of DLA resemble those of septicemia. The question we asked was whether bacterial isolates can be found in the peripheral blood of patients during the episodes of DLA. Out of 100 patients referred to us with 'filarial' lymphedema 14 displayed acute and five subacute symptoms of DLA. All were on admission blood microfilariae negative but had a positive test in the past. Blood bacterial isolates were found in nine cases, four acute (21%) and five subacute (26%). In 10 acute cases blood cultures were found negative. Six blood isolates belonged to Bacilli, four to Cocci and one was Sarcina. To identify the sites of origin of bacterial dissemination, swabs taken from the calf skin biopsy wounds and tissue fluid, lymph and lymph node specimens were cultured. Swabs from the calf skin biopsy wound contained isolates in nine (47%) cases. They were Bacilli in nine, Cocci in three, Acinetobacter and Erwinia in two cases. Tissue fluid was collected from 10 patients and contained Bacilli in four (40%) and Staphylococci in three (30%). Lymph was drained in four patients and contained isolates in all samples (100%). They were Staphylococcus epidermis, xylosus and aureus, Acinetobacter, Bacillus subtilis and Sarcina. Three lymph nodes were biopsied and contained Staphylococcus chromogenes, xylosus, Enterococcus and Bacillus cereus. In six cases the same phenotypically defined species of bacteria were found in blood and limb tissues or fluids. In the 'control' group of patients with lymphedema without acute or subacute changes all blood cultures were negative. Interestingly, swabs from biopsy wound of these patients contained isolates in 80%, tissue fluid in 68%, lymph in 70% and lymph nodes in 58% of cases. In healthy controls, tissue fluid did not contain bacteria, and lymph isolates were found only in 12% of cases. This study demonstrates that

  3. Retiring the Short-Run Aggregate Supply Curve

    ERIC Educational Resources Information Center

    Elwood, S. Kirk

    2010-01-01

    The author argues that the aggregate demand/aggregate supply (AD/AS) model is significantly improved--although certainly not perfected--by trimming it of the short-run aggregate supply (SRAS) curve. Problems with the SRAS curve are shown first for the AD/AS model that casts the AD curve as identifying the equilibrium level of output associated…

  4. Injury Profile SIMulator, a Qualitative Aggregative Modelling Framework to Predict Crop Injury Profile as a Function of Cropping Practices, and the Abiotic and Biotic Environment. I. Conceptual Bases

    PubMed Central

    Aubertot, Jean-Noël; Robin, Marie-Hélène

    2013-01-01

    The limitation of damage caused by pests (plant pathogens, weeds, and animal pests) in any agricultural crop requires integrated management strategies. Although significant efforts have been made to i) develop, and to a lesser extent ii) combine genetic, biological, cultural, physical and chemical control methods in Integrated Pest Management (IPM) strategies (vertical integration), there is a need for tools to help manage Injury Profiles (horizontal integration). Farmers design cropping systems according to their goals, knowledge, cognition and perception of socio-economic and technological drivers as well as their physical, biological, and chemical environment. In return, a given cropping system, in a given production situation will exhibit a unique injury profile, defined as a dynamic vector of the main injuries affecting the crop. This simple description of agroecosystems has been used to develop IPSIM (Injury Profile SIMulator), a modelling framework to predict injury profiles as a function of cropping practices, abiotic and biotic environment. Due to the tremendous complexity of agroecosystems, a simple holistic aggregative approach was chosen instead of attempting to couple detailed models. This paper describes the conceptual bases of IPSIM, an aggregative hierarchical framework and a method to help specify IPSIM for a given crop. A companion paper presents a proof of concept of the proposed approach for a single disease of a major crop (eyespot on wheat). In the future, IPSIM could be used as a tool to help design ex-ante IPM strategies at the field scale if coupled with a damage sub-model, and a multicriteria sub-model that assesses the social, environmental, and economic performances of simulated agroecosystems. In addition, IPSIM could also be used to help make diagnoses on commercial fields. It is important to point out that the presented concepts are not crop- or pest-specific and that IPSIM can be used on any crop. PMID:24019908

  5. A Spectroscopic Study of the Aggregation State of the Human Antimicrobial Peptide LL-37 in Bacterial versus Host Cell Model Membranes.

    PubMed

    Bonucci, Alessio; Caldaroni, Elena; Balducci, Enrico; Pogni, Rebecca

    2015-11-17

    The LL-37 antimicrobial peptide is the only cathelicidin peptide found in humans that has antimicrobial and immunomodulatory properties. Because it exerts also chemotactic and angiogenetic activity, LL-37 is involved in promoting wound healing, reducing inflammation, and strengthening the host immune response. The key to the effectiveness of antimicrobial peptides (AMPs) lies in the different compositions of bacterial versus host cell membranes. In this context, antimicrobial peptide LL-37 and two variants were studied in the presence of model membranes with different lipid compositions and charges. The investigation was performed using an experimental strategy that combines the site-directed spin labeling-electron paramagnetic resonance technique with circular dichroism and fluorescence emission spectroscopies. LL-37 interacts with negatively charged membranes forming a stable aggregate, which can likely produce toroidal pores until the amount of bound peptide exceeds a critical concentration. At the same time, we have clearly detected an aggregate with a higher oligomeric degree for interaction of LL-37 with neutral membranes. These data confirm the absence of cell selectivity of the peptide and a more complex role in stimulating host cells.

  6. Two-dimensional growth of germanium under a diffusion limited aggregation environment

    NASA Astrophysics Data System (ADS)

    Lee, Jaejun; Kim, Sung Wook; Park, Youn Ho; Park, Jeong Min; Kim, Yeon Joo; Park, Sangwon; Yang, Jeen Moon; Choi, Heon-Jin

    2017-01-01

    The discovery of graphene has triggered immense interest in two-dimensional (2D) nanomaterials. However, the 2D growth of several layerstructured crystals such as graphene, MoS2, and black phosphorus is difficult and limited. Here, we report the gas-phase 2D growth of germanium (Ge) with a cubic structure to form Ge nanosheets (GeNSs) using the chemical vapor deposition method. Our investigation revealed that a diffusion limited aggregation (DLA) environment is essential for the 2D growth of Ge that induces a dendritic growth in the <110> direction and suppresses the growth in the [111] direction. The growth behavior was similar to the 2D growth of silicon reported previously. Thus, it can be concluded that a DLA environment is essential for the 2D growth of cubic structured materials. The electron density and mobility of GeNSs were found to be 1.3 × 1015 cm-3 and 792 cm2/Vs, respectively, and their resistivity varied with the intensity of light. [Figure not available: see fulltext.

  7. Single molecule force spectroscopy of asphaltene aggregates.

    PubMed

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

    2007-05-22

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

  8. Histocompatibility studies in a closely bred colony of dogs. 3. Genetic definition of the DL-A system of canine histocompatibility, with particular reference to the comparative immunogenicity of the major transplantable organs.

    PubMed

    Dausset, J; Rapaport, F T; Cannon, F D; Ferrebee, J W

    1971-11-01

    The segregation of the canine DL-A leukocyte group antigen(s) b, c, d, e, f, g, h, k, l, and m has been traced in 141 consecutive matings in the Cooperstown Colony of beagles. All of the leukocyte antigen(s) were regularly transmitted en bloc from parent to offspring, with no instance of independent segregation. A total of 23 haplotypes, including six different DL-A antigen patterns (gl, bkhfm, bkcd, e, be, fgl) was observed. 31 different DL-A phenotypes were observed in a population of 100 mongrel dogs. A number of statistically significant positive and negative associations between individual DL-A antigenic components occurred in this population. The results support the concept of the DL-A system as a complex immunogenetic system governed by a single region (or locus) of an autosomal pair of chromosomes. Studies of skin, kidney, heart, and liver allografts in the Cooperstown Colony indicated that the longest allograft survivals occur under genetically and serologically defined conditions of donor-recipient DL-A compatibility. Skin and renal allografts generally behaved in parallel fashion, while cardiac allografts survived for longer periods of time (MST = 47.1 days) than kidneys (MST = 28.1 days) or skin (MST = 25.1 days) under conditions of DL-A identity. Heart transplants were rejected at a more rapid rate than kidney, however, in DL-A-incompatible donor-recipient combinations. Liver transplants were accorded the longest survival time (MST = 76.2 days) under conditions of DL-A identity, but were rejected at a rapid rate (MST = 5 days) in DL-A-incompatible nonlittermate donor-recipient pairs. The results provide further evidence that the DL-A system is the principal system of histocompatibility in the canine species. The differences in survival of different organs under similar conditions of donor-recipient DL-A compatibility suggest, however, the existence of a number of unknown variables which may also be capable of significantly affecting allograft behavior.

  9. Mesoscale Simulation of Asphaltene Aggregation.

    PubMed

    Wang, Jiang; Ferguson, Andrew L

    2016-08-18

    Asphaltenes constitute a heavy aromatic crude oil fraction with a propensity to aggregate and precipitate out of solution during petroleum processing. Aggregation is thought to proceed according to the Yen-Mullins hierarchy, but the molecular mechanisms underlying mesoscopic assembly remain poorly understood. By combining coarse-grained molecular models parametrized using all-atom data with high-performance GPU hardware, we have performed molecular dynamics simulations of the aggregation of hundreds of asphaltenes over microsecond time scales. Our simulations reveal a hierarchical self-assembly mechanism consistent with the Yen-Mullins model, but the details are sensitive and depend on asphaltene chemistry and environment. At low concentrations asphaltenes exist predominantly as dispersed monomers. Upon increasing concentration, we first observe parallel stacking into 1D rod-like nanoaggregates, followed by the formation of clusters of nanoaggregates associated by offset, T-shaped, and edge-edge stacking. Asphaltenes possessing long aliphatic side chains cannot form nanoaggregate clusters due to steric repulsions between their aliphatic coronae. At very high concentrations, we observe a porous percolating network of rod-like nanoaggregates suspended in a sea of interpenetrating aliphatic side chains with a fractal dimension of ∼2. The lifetime of the rod-like aggregates is described by an exponential distribution reflecting a dynamic equilibrium between coagulation and fragmentation.

  10. Oil-Price Shocks: Beyond Standard Aggregate Demand/Aggregate Supply Analysis.

    ERIC Educational Resources Information Center

    Elwood, S. Kirk

    2001-01-01

    Explores the problems of portraying oil-price shocks using the aggregate demand/aggregate supply model. Presents a simple modification of the model that differentiates between production and absorption of goods, which enables it to better reflect the effects of oil-price shocks on open economies. (RLH)

  11. Live Cell Characterization of DNA Aggregation Delivered through Lipofection

    PubMed Central

    Mieruszynski, Stephen; Briggs, Candida; Digman, Michelle A.; Gratton, Enrico; Jones, Mark R

    2015-01-01

    DNA trafficking phenomena, such as information on where and to what extent DNA aggregation occurs, have yet to be fully characterised in the live cell. Here we characterise the aggregation of DNA when delivered through lipofection by applying the Number and Brightness (N&B) approach. The N&B analysis demonstrates extensive aggregation throughout the live cell with DNA clusters in the extremity of the cell and peri-nuclear areas. Once within the nucleus aggregation had decreased 3-fold. In addition, we show that increasing serum concentration of cell media results in greater cytoplasmic aggregation. Further, the effects of the DNA fragment size on aggregation was explored, where larger DNA constructs exhibited less aggregation. This study demonstrates the first quantification of DNA aggregation when delivered through lipofection in live cells. In addition, this study has presents a model for alternative uses of this imaging approach, which was originally developed to study protein oligomerization and aggregation. PMID:26013547

  12. Marine particle aggregate breakup in turbulent flows

    NASA Astrophysics Data System (ADS)

    Rau, Matthew; Ackleson, Steven; Smith, Geoffrey

    2016-11-01

    The dynamics of marine particle aggregate formation and breakup due to turbulence is studied experimentally. Aggregates of clay particles, initially in a quiescent aggregation tank, are subjected to fully developed turbulent pipe flow at Reynolds numbers of up to 25,000. This flow arrangement simulates the exposure of marine aggregates in coastal waters to a sudden turbulent event. Particle size distributions are measured by in-situ sampling of the small-angle forward volume scattering function and the volume concentration of the suspended particulate matter is quantified through light attenuation measurements. Results are compared to measurements conducted under laminar and turbulent flow conditions. At low shear rates, larger sized particles indicate that aggregation initially governs the particle dynamics. Breakup is observed when large aggregates are exposed to the highest levels of shear in the experiment. Models describing the aggregation and breakup rates of marine particles due to turbulence are evaluated with the population balance equation and results from the simulation and experiment are compared. Additional model development will more accurately describe aggregation dynamics for remote sensing applications in turbulent marine environments.

  13. Protein aggregation in salt solutions

    PubMed Central

    Kastelic, Miha; Kalyuzhnyi, Yurij V.; Hribar-Lee, Barbara; Dill, Ken A.; Vlachy, Vojko

    2015-01-01

    Protein aggregation is broadly important in diseases and in formulations of biological drugs. Here, we develop a theoretical model for reversible protein–protein aggregation in salt solutions. We treat proteins as hard spheres having square-well-energy binding sites, using Wertheim’s thermodynamic perturbation theory. The necessary condition required for such modeling to be realistic is that proteins in solution during the experiment remain in their compact form. Within this limitation our model gives accurate liquid–liquid coexistence curves for lysozyme and γ IIIa-crystallin solutions in respective buffers. It provides good fits to the cloud-point curves of lysozyme in buffer–salt mixtures as a function of the type and concentration of salt. It than predicts full coexistence curves, osmotic compressibilities, and second virial coefficients under such conditions. This treatment may also be relevant to protein crystallization. PMID:25964322

  14. Flow Partitioning in Fully Saturated Soil Aggregates

    SciTech Connect

    Yang, Xiaofan; Richmond, Marshall C.; Scheibe, Timothy D.; Perkins, William A.; Resat, Haluk

    2014-03-30

    Microbes play an important role in facilitating organic matter decomposition in soils, which is a major component of the global carbon cycle. Microbial dynamics are intimately coupled to environmental transport processes, which control access to labile organic matter and other nutrients that are needed for the growth and maintenance of microorganisms. Transport of soluble nutrients in the soil system is arguably most strongly impacted by preferential flow pathways in the soil. Since the physical structure of soils can be characterized as being formed from constituent micro aggregates which contain internal porosity, one pressing question is the partitioning of the flow among the “inter-aggregate” and “intra-aggregate” pores and how this may impact overall solute transport within heterogeneous soil structures. The answer to this question is particularly important in evaluating assumptions to be used in developing upscaled simulations based on highly-resolved mechanistic models. We constructed a number of diverse multi-aggregate structures with different packing ratios by stacking micro-aggregates containing internal pores and varying the size and shape of inter-aggregate pore spacing between them. We then performed pore-scale flow simulations using computational fluid dynamics methods to determine the flow patterns in these aggregate-of-aggregates structures and computed the partitioning of the flow through intra- and inter-aggregate pores as a function of the spacing between the aggregates. The results of these numerical experiments demonstrate that soluble nutrients are largely transported via flows through inter-aggregate pores. Although this result is consistent with intuition, we have also been able to quantify the relative flow capacity of the two domains under various conditions. For example, in our simulations, the flow capacity through the aggregates (intra-aggregate flow) was less than 2% of the total flow when the spacing between the aggregates

  15. Aggregations in Flatworms.

    ERIC Educational Resources Information Center

    Liffen, C. L.; Hunter, M.

    1980-01-01

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

  16. Unbonded Aggregate Surface Roads

    DTIC Science & Technology

    2006-12-01

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

  17. Biological Control of the Chagas Disease Vector Triatoma infestans with the Entomopathogenic Fungus Beauveria bassiana Combined with an Aggregation Cue: Field, Laboratory and Mathematical Modeling Assessment

    PubMed Central

    Forlani, Lucas; Pedrini, Nicolás; Girotti, Juan R.; Mijailovsky, Sergio J.; Cardozo, Rubén M.; Gentile, Alberto G.; Hernández-Suárez, Carlos M.; Rabinovich, Jorge E.; Juárez, M. Patricia

    2015-01-01

    Background Current Chagas disease vector control strategies, based on chemical insecticide spraying, are growingly threatened by the emergence of pyrethroid-resistant Triatoma infestans populations in the Gran Chaco region of South America. Methodology and findings We have already shown that the entomopathogenic fungus Beauveria bassiana has the ability to breach the insect cuticle and is effective both against pyrethroid-susceptible and pyrethroid-resistant T. infestans, in laboratory as well as field assays. It is also known that T. infestans cuticle lipids play a major role as contact aggregation pheromones. We estimated the effectiveness of pheromone-based infection boxes containing B. bassiana spores to kill indoor bugs, and its effect on the vector population dynamics. Laboratory assays were performed to estimate the effect of fungal infection on female reproductive parameters. The effect of insect exuviae as an aggregation signal in the performance of the infection boxes was estimated both in the laboratory and in the field. We developed a stage-specific matrix model of T. infestans to describe the fungal infection effects on insect population dynamics, and to analyze the performance of the biopesticide device in vector biological control. Conclusions The pheromone-containing infective box is a promising new tool against indoor populations of this Chagas disease vector, with the number of boxes per house being the main driver of the reduction of the total domestic bug population. This ecologically safe approach is the first proven alternative to chemical insecticides in the control of T. infestans. The advantageous reduction in vector population by delayed-action fungal biopesticides in a contained environment is here shown supported by mathematical modeling. PMID:25969989

  18. Directional sensing and streaming in Dictyostelium aggregation

    NASA Astrophysics Data System (ADS)

    Almeida, Sofia; Dilão, Rui

    2016-05-01

    We merge the Kessler-Levine simple discrete model for Dictyostelium cyclic adenosine monophosphate (cAMP) production and diffusion with the Dilão-Hauser directional sensing aggregation mechanism. The resulting compound model describes all the known transient patterns that emerge during Dictyostelium aggregation, which include the spontaneous formation of cAMP self-sustained target and spiral waves and streaming. We show that the streaming patterns depend on the speed of the amoebae, on the relaxation time for the production of cAMP, on the cAMP degradation rate, and on directional sensing. Moreover, we show that different signaling centers emerge during Dictyostelium aggregation.

  19. GPP Webinar: The Power of Aggregated Purchasing

    EPA Pesticide Factsheets

    Green Power Partnership webinar examining the use of an aggregated model for renewable energy purchases which can lead to significant energy, environmental and financial benefits by addressing administrative cost barriers and leveraging the shared purchasi

  20. Multicandidate Elections: Aggregate Uncertainty in the Laboratory*

    PubMed Central

    Bouton, Laurent; Castanheira, Micael; Llorente-Saguer, Aniol

    2015-01-01

    The rational-voter model is often criticized on the grounds that two of its central predictions (the paradox of voting and Duverger’s Law) are at odds with reality. Recent theoretical advances suggest that these empirically unsound predictions might be an artifact of an (arguably unrealistic) assumption: the absence of aggregate uncertainty about the distribution of preferences in the electorate. In this paper, we propose direct empirical evidence of the effect of aggregate uncertainty in multicandidate elections. Adopting a theory-based experimental approach, we explore whether aggregate uncertainty indeed favors the emergence of non-Duverger’s law equilibria in plurality elections. Our experimental results support the main theoretical predictions: sincere voting is a predominant strategy under aggregate uncertainty, whereas without aggregate uncertainty, voters massively coordinate their votes behind one candidate, who wins almost surely. PMID:28298811

  1. A Novel In Vitro CypD-Mediated p53 Aggregation Assay Suggests a Model for Mitochondrial Permeability Transition by Chaperone Systems.

    PubMed

    Lebedev, Ivan; Nemajerova, Alice; Foda, Zachariah H; Kornaj, Maja; Tong, Michael; Moll, Ute M; Seeliger, Markus A

    2016-10-09

    Tissue necrosis as a consequence of ischemia-reperfusion injury and oxidative damage is a leading cause of permanent disability and death worldwide. The complete mechanism by which cells undergo necrosis upon oxidative stress is not understood. In response to an oxidative insult, wild-type p53 has been implicated as a central regulatory component of the mitochondrial permeability transition (mPT), triggering necrosis. This process is associated with cellular stabilization and translocation of p53 into the mitochondrial matrix. Here, we probe the mechanism by which p53 activates the key mPT regulator cyclophilin D (CypD). We explore the involvement of Trap1, an Hsp90-related mitochondrial matrix protein and a member of the mitochondrial unfolded protein response, and its ability to suppress mPT in a p53-dependent manner. Our study finds that catalytically active CypD causes strong aggregation of wild-type p53 protein (both full-length and isolated DNA-binding domain) into amyloid-type fibrils in vitro. The responsible CypD residues for this activity were mapped by NMR to the active site amino acids R55, F60, F113, and W121. The data also present a new proline isomerization assay for CypD by monitoring the aggregation of p53 as an indicator of CypD activity. Moreover, we find that the inhibition of Trap1 by the mitochondria-specific HSP90 ATPase antagonist Gamitrinib strongly sensitizes primary mouse embryonic fibroblasts to mPT and permeability transition pore opening in a p53- and CypD-dependent manner. We propose a mechanism by which the influx of unfolded p53 into the mitochondrial matrix in response to oxidative stress indirectly activates the normally inhibited CypD by displacing it from Trap1 complexes. This activates CypD's isomerase activity. Liberated CypD then isomerizes multiple proteins including p53 (causing p53 aggregation) and the structural components of the mPTP pore, inducing pore opening. This working model can now be tested in the future.

  2. Silver nanoparticles coated with natural polysaccharides as models to study AgNP aggregation kinetics using UV-Visible spectrophotometry upon discharge in complex environments.

    PubMed

    Lodeiro, Pablo; Achterberg, Eric P; Pampín, Joaquín; Affatati, Alice; El-Shahawi, Mohammed S

    2016-01-01

    This study provides quantitative information on the aggregation and dissolution behaviour of silver nanoparticles (AgNPs) upon discharge in fresh and sea waters, represented here as NaCl solutions of increasing ionic strength (up to 1M) and natural fjord waters. Natural polysaccharides, sodium alginate (ALG) and gum Arabic (GA), were used as coatings to stabilize the AgNPs and the compounds acted as models to study AgNP aggregation kinetics. The DLVO theory was used to quantitatively describe the interactions between the AgNPs. The stability of AgNPs was established using UV-Visible spectrophotometry, including unique information collected during the first seconds of the aggregaton process. Alginate coating resulted in a moderate stabilization of AgNPs in terms of critical coagulation concentration (~82mM NaCl) and a low dissolution of <10% total Ag in NaCl solutions up to 1M. Gum Arabic coated AgNPs were more strongly stabilized, with ~7-30% size increase up to 77mM NaCl, but only when the silver ion content initially present in solution was low (<10% total Ag). The ALG and GA coated AgNPs showed a strongly enhanced stability in natural fjord waters (ca. 5h required to reduce the area of the surface plasmon resonance band (SPRB) by two fold) compared with NaCl at an equivalent ionic strength (1-2min period for a two fold SPRB reduction). This is ascribed to a stabilizing effect from dissolved organic matter present in natural fjord waters. Interestingly, for AgNP-GA solutions with 40% of total silver present as unreacted silver ions in the NP stock solution, fast aggregation kinetics were observed in NaCl solutions (SPRB area was reduced by ca. 50% within 40-150min), with even more rapid removal in fjord waters, attributed to the high amount of silver-chloride charged species, that interact with the NP coating and/or organic matter and reduce the NPs stabilization.

  3. Aggregate structure, morphology and the effect of aggregation mechanisms on viscosity at elevated protein concentrations.

    PubMed

    Barnett, Gregory V; Qi, Wei; Amin, Samiul; Neil Lewis, E; Roberts, Christopher J

    2015-12-01

    Non-native aggregation is a common issue in a number of degenerative diseases and during manufacturing of protein-based therapeutics. There is a growing interest to monitor protein stability at intermediate to high protein concentrations, which are required for therapeutic dosing of subcutaneous injections. An understanding of the impact of protein structural changes and interactions on the protein aggregation mechanisms and resulting aggregate size and morphology may lead to improved strategies to reduce aggregation and solution viscosity. This report investigates non-native aggregation of a model protein, α-chymotrypsinogen, under accelerated conditions at elevated protein concentrations. Far-UV circular dichroism and Raman scattering show structural changes during aggregation. Size exclusion chromatography and laser light scattering are used to monitor the progression of aggregate growth and monomer loss. Monomer loss is concomitant with increased β-sheet structures as monomers are added to aggregates, which illustrate a transition from a native monomeric state to an aggregate state. Aggregates grow predominantly through monomer-addition, resulting in a semi-flexible polymer morphology. Analysis of aggregation growth kinetics shows that pH strongly affects the characteristic timescales for nucleation (τn) and growth (τg), while the initial protein concentration has only minor effects on τn or τg. Low-shear viscosity measurements follow a common scaling relationship between average aggregate molecular weight (Mw(agg)) and concentration (σ), which is consistent with semi-dilute polymer-solution theory. The results establish a link between aggregate growth mechanisms, which couple Mw(agg) and σ, to increases in solution viscosity even at these intermediate protein concentrations (less than 3w/v %).

  4. Aggregate and the environment

    USGS Publications Warehouse

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

    2004-01-01

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

  5. Aggregation of Heterogeneously Charged Colloids.

    PubMed

    Dempster, Joshua M; Olvera de la Cruz, Monica

    2016-06-28

    Patchy colloids are attractive as programmable building blocks for metamaterials. Inverse patchy colloids, in which a charged surface is decorated with patches of the opposite charge, are additionally noteworthy as models for heterogeneously charged biological materials such as proteins. We study the phases and aggregation behavior of a single charged patch in an oppositely charged colloid with a single-site model. This single-patch inverse patchy colloid model shows a large number of phases when varying patch size. For large patch sizes we find ferroelectric crystals, while small patch sizes produce cross-linked gels. Intermediate values produce monodisperse clusters and unusual worm structures that preserve finite ratios of area to volume. The polarization observed at large patch sizes is robust under extreme disorder in patch size and shape. We examine phase-temperature dependence and coexistence curves and find that large patch sizes produce polarized liquids, in contrast to mean-field predictions. Finally, we introduce small numbers of unpatched charged colloids. These can either suppress or encourage aggregation depending on their concentration and the size of the patches on the patched colloids. These effects can be exploited to control aggregation and to measure effective patch size.

  6. Safety assessment of dangerous goods transport enterprise based on the relative entropy aggregation in group decision making model.

    PubMed

    Wu, Jun; Li, Chengbing; Huo, Yueying

    2014-01-01

    Safety of dangerous goods transport is directly related to the operation safety of dangerous goods transport enterprise. Aiming at the problem of the high accident rate and large harm in dangerous goods logistics transportation, this paper took the group decision making problem based on integration and coordination thought into a multiagent multiobjective group decision making problem; a secondary decision model was established and applied to the safety assessment of dangerous goods transport enterprise. First of all, we used dynamic multivalue background and entropy theory building the first level multiobjective decision model. Secondly, experts were to empower according to the principle of clustering analysis, and combining with the relative entropy theory to establish a secondary rally optimization model based on relative entropy in group decision making, and discuss the solution of the model. Then, after investigation and analysis, we establish the dangerous goods transport enterprise safety evaluation index system. Finally, case analysis to five dangerous goods transport enterprises in the Inner Mongolia Autonomous Region validates the feasibility and effectiveness of this model for dangerous goods transport enterprise recognition, which provides vital decision making basis for recognizing the dangerous goods transport enterprises.

  7. Aggregation and Averaging.

    ERIC Educational Resources Information Center

    Siegel, Irving H.

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

  8. Orthogonal flexible Rydberg aggregates

    NASA Astrophysics Data System (ADS)

    Leonhardt, K.; Wüster, S.; Rost, J. M.

    2016-02-01

    We study the link between atomic motion and exciton transport in flexible Rydberg aggregates, assemblies of highly excited light alkali-metal atoms, for which motion due to dipole-dipole interaction becomes relevant. In two one-dimensional atom chains crossing at a right angle adiabatic exciton transport is affected by a conical intersection of excitonic energy surfaces, which induces controllable nonadiabatic effects. A joint exciton-motion pulse that is initially governed by a single energy surface is coherently split into two modes after crossing the intersection. The modes induce strongly different atomic motion, leading to clear signatures of nonadiabatic effects in atomic density profiles. We have shown how this scenario can be exploited as an exciton switch, controlling direction and coherence properties of the joint pulse on the second of the chains [K. Leonhardt et al., Phys. Rev. Lett. 113, 223001 (2014), 10.1103/PhysRevLett.113.223001]. In this article we discuss the underlying complex dynamics in detail, characterize the switch, and derive our isotropic interaction model from a realistic anisotropic one with the addition of a magnetic bias field.

  9. Comparison of Four Probabilistic Models (CARES, Calendex, ConsEspo, SHEDS) to Estimate Aggregate Residential Exposures to Pesticides

    EPA Science Inventory

    Two deterministic models (US EPA’s Office of Pesticide Programs Residential Standard Operating Procedures (OPP Residential SOPs) and Draft Protocol for Measuring Children’s Non-Occupational Exposure to Pesticides by all Relevant Pathways (Draft Protocol)) and four probabilistic mo...

  10. Effects of Asphaltene Aggregation in Model Heptane-Toluene Mixtures on Stability of Water-in-Oil Emulsions

    PubMed

    McLean; Kilpatrick

    1997-12-01

    As part of an ongoing investigation into the stability of water-in-crude oil emulsions, model oils have been utilized to further probe the effects of crude solvency as well as specific resin-asphaltene interactions on emulsion stability. These model oils were constructed by dissolving varying amounts of resins and/or asphaltenes in a mixture of heptane and toluene. The resins and asphaltenes used in this study were isolated from four different crude types-Arab Berri (AB), Arab Heavy (AH), Alaska North Slope (ANS), and San Joaquin Valley (SJV)-and characterized in a previous study using heptane precipitation of the asphaltenes followed by an extrographic separation of the resins from silica gel. Asphaltenes dissolved in heptol at concentrations of just 0.5% were shown to generate emulsions which were even more stable than those generated from their respective whole crude oils. Some types of resins (e.g., from AH and SJV) also demonstrated an ability to stabilize emulsions although these resin-stabilized emulsions were considerably less stable than those prepared with asphaltenes. The primary factors governing the stability of these model emulsions were the aromaticity of the crude medium (as controlled by the heptane:toluene ratio), the concentration of asphaltenes, and the availability of solvating resins in the oil (i.e., the resin/asphaltene or R/A ratio). The model emulsions were the most stable when the crude medium was 30-40% toluene and in many cases at small R/A ratios (i.e., R/A model oils also played a role in determining the resultant emulsion stability which indicates the importance of specific resin-asphaltene interactions. The interfacially active components that stabilized these model systems were the most polar and/or condensed

  11. Impact of Thermostats on Folding and Aggregation Properties of Peptides Using the Optimized Potential for Efficient Structure Prediction Coarse-Grained Model.

    PubMed

    Spill, Yannick G; Pasquali, Samuela; Derreumaux, Philippe

    2011-05-10

    The simulation of amyloid fibril formation is impossible if one takes into account all chemical details of the amino acids and their detailed interactions with the solvent. We investigate the folding and aggregation of two model peptides using the optimized potential for efficient structure prediction (OPEP) coarse-grained model and replica exchange molecular dynamics (REMD) simulations coupled with either the Langevin or the Berendsen thermostat. For both the monomer of blocked penta-alanine and the trimer of the 25-35 fragment of the Alzheimer's amyloid β protein, we find little variations in the equilibrium structures and heat capacity curves using the two thermostats. Despite this high similarity, we detect significant differences in the populations of the dominant conformations at low temperatures, whereas the configurational distributions remain the same in proximity of the melting temperature. Aβ25-35 trimers at 300 K have an averaged β-sheet content of 12% and are primarily characterized by fully disordered peptides or a small curved two-stranded β-sheet stabilized by a disordered peptide. In addition, OPEP molecular dynamics simulations of Aβ25-35 hexamers at 300 K with a small curved six-stranded antiparallel β-sheet do not show any extension of the β-sheet content. These data support the idea that the mechanism of Aβ25-35 amyloid formation does not result from a high fraction of extended β-sheet-rich trimers and hexamers.

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

    PubMed

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

    2016-01-01

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

  13. [Search for chaperon-like anticataract drugs, the antiaggregants of lens crystallins. Communication. 1. Chaperon-like activity of N-acetyl carnosine dipeptide: in vitro study on a model of ultraviolet-induced aggregation of betaL-crystallin].

    PubMed

    Muranov, K O; Dizhevskaia, A K; Boldyrev, A A; Karpova, O E; Sheremet, N L; Polunin, G S; Avetisov, S E; Ostrovskiĭ, M A

    2008-01-01

    Aggregation ofcrystallins, the lens proteins, is one of the basic stages of cataract formation. Among the protein aggregation models used to study the molecular mechanisms of the initial stages of lenticular opacity, UV-induced aggregation of betaL-crystallin is most close to the in vivo conditions. The carnosine derivative N-acetyl carnosine has been shown to be effective in inhibiting the UV-induced aggregation of betaL-crystallin. Examination of the accumulation kinetics of carbonyl groups in betaL-crystallin under UV irradiation has indicated that neither carnosine nor N-acetyl carnosine fails to affect this parameter--an indicator of oxidative protein damage. By taking into account also the fact that N-acetyl carnosine is not an antioxidant, it can be believed that the molecular mechanism of action of this compound on UV-induced aggregation of betaL is unassociated with its antioxidative properties. The authors hypothesize that the molecular chaperon-like properties similar to those of alpha-crystallin underlie the mechanism of action of the acetyl derivative carnosine. The prospects for searching anticataract agents of a new chaperon-like class are discussed.

  14. Nanoscale Ionic Aggregate Morphology in Zwitterionic Copolymers

    NASA Astrophysics Data System (ADS)

    Choi, Jae-Hong; Huyck, Rebecca; Salas-de La Cruz, David; Long, Timothy E.; Winey, Karen I.

    2009-03-01

    The morphology of two different zwitterionic copolymers, poly(sulfobetaine methacrylate-ran-butyl acrylate), and poly(sulfobetaine methacrylamide-ran-butyl acrylate) are investigated as a function of the mol % content of SBMA (7 and 9 mol %) and SBMAm (6, 10 and 13 mol %), respectively. In both copolymers, X-ray scattering results show a new structure in the material arising from ionic aggregates. The sizes of the ionic aggregates are obtained through the scattering model. The sizes of the ionic aggregates increase as the ion content increases. The application of scanning transmission electron microscopy to the study of ionomer morphology has enabled direct, model-independent visualization of the ionic aggregates. The correlation between X-ray scattering results and the real space imaging for morphology of these zwitterionic copolymers will be presented.

  15. Early stages of salmon calcitonin aggregation: effect induced by ageing and oxidation processes in water and in the presence of model membranes.

    PubMed

    Gaudiano, Maria Cristina; Colone, Marisa; Bombelli, Cecilia; Chistolini, Pietro; Valvo, Luisa; Diociaiuti, Marco

    2005-06-30

    The natural ageing- and hydrogen peroxide-induced aggregation of salmon calcitonin were studied in water and in the presence of dipalmitoylphosphatidylcholine (DPPC) liposomes. The early stages of the aggregation process at low protein concentration were investigated by means of Circular Dichroism spectroscopy (CD) and conventional and immunogold labelling Transmission Electron Microscopy (TEM). In buffered water solution, salmon calcitonin showed a two-stage conformational variation related to fibril formation and phase-separation of larger aggregates. A first stage, characterised by small conformational changes but a decrease in dichroic band intensity, was followed by a second stage, 6 days after, leading to higher conformational variations and aggregations. Salmon calcitonin showed a distinct modification in the secondary structure and aggregate morphology in the presence of hydrogen peroxide with respect to natural ageing, indicating that the two aggregation processes (natural and chemical-induced) followed a distinct mechanism. The oxidised forms of the peptide were separated by liquid chromatography. The same study was performed in the presence of DPPC liposomes. The results obtained by conventional and immunogold labelling TEM evidenced that salmon calcitonin in buffered water solution essentially does not enter the liposomes but forms around them a fibril network characterised by the same conformational changes after 6 days. The oxidised sample in the presence of liposomes showed a "fibrils hank", separated from liposomes. The presence of liposomes did not affect either the aggregation or the conformational modifications yet observed by TEM and CD in water solution.

  16. Modeling Stromatolite Growth Under Oscillatory Flows

    NASA Astrophysics Data System (ADS)

    Patel, H. J.; Gong, J.; Tice, M. M.

    2014-12-01

    Stromatolite growth models based on diffusion limited aggregation (DLA) has been fairly successful at producing features commonly recognized in stromatolitic structures in the rock record. These models generally require slow mixing of solutes at time scales comparable to the growth of organisms and largely ignore fluid erosions. Recent research on microbial mats suggests that fluid flow might have a dominant control on the formation, deformation and erosion of surface microbial structures, raising the possibility that different styles of fluid flow may influence the morphology of stromatolites. Many stromatolites formed in relatively high energy, shallow water environments under oscillatory currents driven by wind-induced waves. In order to investigate the potential role of oscillatory flows in shaping stromatolites, we are constructing a numerical model of stromatolite growth parameterized by flume experiments with cyanobacterial biofilms. The model explicitly incorporates reaction-diffusion processes, surface deformation and erosion, biomass growth, sedimentation and mineral precipitation. A Lattice-Boltzmann numerical scheme was applied to the reaction-diffusion equations in order to boost computational efficiency. A basic finite element method was employed to compute surface deformation and erosion. Growth of biomass, sedimentation and carbonate precipitation was based on a modified discrete cellular automata scheme. This model will be used to test an alternative hypothesis for the formation of stromatolites in higher energy, shallow and oscillatory flow environments.

  17. Fibronectin Aggregation and Assembly

    PubMed Central

    Ohashi, Tomoo; Erickson, Harold P.

    2011-01-01

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