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Sample records for aggregation dla model

  1. The research on Virtual Plants Growth Based on DLA Model

    NASA Astrophysics Data System (ADS)

    Zou, YunLan; Chai, Bencheng

    This article summarizes the separated Evolutionary Algorithm in fractal algorithm of Diffusion Limited Aggregation model (i.e. DLA model) and put forward the virtual plant growth realization in computer based on DLA model. The method is carried out in the VB6.0 environment to achieve and verify the plant growth based on DLA model.

  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. PMID:25790463

  3. 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

  4. Pore Level Modeling of Immiscible Drainage: Validation in the Invasion Percolation and DLA Limits

    SciTech Connect

    Ferer, M.V.; Bromhal, G.S.; Smith, D.H.

    2003-03-01

    Motivated by a wide-range of applications from ground water remediation to carbon dioxide sequestration and by difficulties in reconciling experiments with previous modeling, we have developed a pore-level model of two-phase flow in porous media. We have attempted to make our model as physical and as reliable as possible, incorporating both capillary effects and viscous effects. After a detailed discussion of the model, we validate it in the very different limits of zero capillary number and zero-viscosity ratio. Invasion percolation (IP) models the flow in the limit of zero capillary number; results from our model show detailed agreement with results from IP, for small capillary numbers. Diffusion limited aggregation (DLA) models the flow in the limit of zero-viscosity ratio; flow patterns from our model have the same fractal dimension as patterns from DLA for small viscosity ratios.

  5. Conformal approach to cylindrical DLA

    NASA Astrophysics Data System (ADS)

    Taloni, A.; Caglioti, E.; Loreto, V.; Pietronero, L.

    2006-09-01

    We extend the conformal mapping approach elaborated for the radial diffusion limited aggregation model (DLA) to cylindrical geometry. We introduce in particular a complex function which allows a cylindrical cluster to be grown using as an intermediate step a radial aggregate. The aggregate grown exhibits the same self-affine features as the original cylindrical DLA. The specific choice of the transformation allows us to study the relationship between the radial and the cylindrical geometry. In particular the cylindrical aggregate can be seen as a radial aggregate with particles of size increasing with the radius. On the other hand, the radial aggregate can be seen as a cylindrical aggregate with particles of size decreasing with the height. This framework, which shifts the point of view from the geometry to the size of the particles, can open the way to more quantitative studies on the relationship between radial and cylindrical DLA.

  6. Finite size effect of harmonic measure estimation in a DLA model: Variable size of probe particles

    NASA Astrophysics Data System (ADS)

    Menshutin, Anton Yu.; Shchur, Lev N.; Vinokour, Valery M.

    2008-11-01

    A finite size effect in the probing of the harmonic measure in simulation of diffusion-limited aggregation (DLA) growth is investigated. We introduce a variable size of probe particles, to estimate harmonic measure and extract the fractal dimension of DLA clusters taking two limits, of vanishingly small probe particle size and of infinitely large size of a DLA cluster. We generate 1000 DLA clusters consisting of 50 million particles each, using an off-lattice killing-free algorithm developed in the early work. The introduced method leads to unprecedented accuracy in the estimation of the fractal dimension. We discuss the variation of the probability distribution function with the size of probing particles.

  7. 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.

  8. Diffusion Limited Aggregation: Algorithm optimization revisited

    NASA Astrophysics Data System (ADS)

    Braga, F. L.; Ribeiro, M. S.

    2011-08-01

    The Diffusion Limited Aggregation (DLA) model developed by Witten and Sander in 1978 is useful in modeling a large class of growth phenomena with local dependence. Besides its simplicity this aggregation model has a complex behavior that can be observed at the patterns generated. We propose on this work a brief review of some important proprieties of this model and present an algorithm to simulate a DLA aggregates that simpler and efficient compared to others found in the literature.

  9. Modeling realistic breast lesions using diffusion limited aggregation

    NASA Astrophysics Data System (ADS)

    Rashidnasab, Alaleh; Elangovan, Premkumar; Dance, David R.; Young, Kenneth C.; Diaz, Oliver; Wells, Kevin

    2012-03-01

    Synthesizing the appearance of malignant masses and inserting these into digital mammograms can be used as part of a wider framework for investigating the radiological detection task in X-ray mammography. However, the randomness associated with cell division within cancerous masses and the associated complex morphology challenges the realism of the modeling process. In this paper, Diffusion Limited Aggregation (DLA), a type of fractal growth process is proposed and utilized for modeling breast lesions. Masses of different sizes, shapes and densities were grown by controlling DLA growth parameters either prior to growth, or dynamically updating these during growth. A validation study was conducted by presenting 30 real and 30 simulated masses in a random order to a team of radiologists. The results from the validation study suggest that the observers found it difficult to differentiate between the real and simulated lesions.

  10. 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.

    2016-09-01

    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 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 AGB stars and Type II SNe, destruction and accretion (gas condensation in clouds). We then apply our model to Damped Lyman-α systems which are believed to be dwarf irregulars, as witnessed by their abundance patterns. Our main conclusions are: 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 Damped Lyman-α 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 nano-particles.

  11. Scaling in the Diffusion Limited Aggregation Model

    NASA Astrophysics Data System (ADS)

    Menshutin, Anton

    2012-01-01

    We present a self-consistent picture of diffusion limited aggregation (DLA) growth based on the assumption that the probability density P(r,N) for the next particle to be attached within the distance r to the center of the cluster is expressible in the scale-invariant form P[r/Rdep(N)]. It follows from this assumption that there is no multiscaling issue in DLA and there is only a single fractal dimension D for all length scales. We check our assumption self-consistently by calculating the particle-density distribution with a measured P(r/Rdep) function on an ensemble with 1000 clusters of 5×107 particles each. We also show that a nontrivial multiscaling function D(x) can be obtained only when small clusters (N<10000) are used to calculate D(x). Hence, multiscaling is a finite-size effect and is not intrinsic to DLA.

  12. Abnormal Stability in Growth of Diffusion-Limited Aggregation

    NASA Astrophysics Data System (ADS)

    Ohta, Shonosuke

    2009-01-01

    An abnormal and unsteady growth of an isotropic cluster in diffusion-limited aggregation (DLA) is observed in stability analyses. Macroscopic fluctuation due to the delay of transition from a dendritic tip to a tip-splitting growth induces the anisotropy of DLA. An asymptotic deformation factor \\varepsilon∞ = 0.0888 is obtained from large DLA clusters. A symmetric oval model proposed from the dual-stability growth of DLA gives an asymptotic fractal dimension of 1.7112 using \\varepsilon∞. The correspondence of this model to the box dimension is excellent.

  13. Scaling in the diffusion limited aggregation model.

    PubMed

    Menshutin, Anton

    2012-01-01

    We present a self-consistent picture of diffusion limited aggregation (DLA) growth based on the assumption that the probability density P(r,N) for the next particle to be attached within the distance r to the center of the cluster is expressible in the scale-invariant form P[r/R{dep}(N)]. It follows from this assumption that there is no multiscaling issue in DLA and there is only a single fractal dimension D for all length scales. We check our assumption self-consistently by calculating the particle-density distribution with a measured P(r/R{dep}) function on an ensemble with 1000 clusters of 5×10{7} particles each. We also show that a nontrivial multiscaling function D(x) can be obtained only when small clusters (N<10 000) are used to calculate D(x). Hence, multiscaling is a finite-size effect and is not intrinsic to DLA. PMID:22304265

  14. Mean-field diffusion-limited aggregation: a "density" model for viscous fingering phenomena.

    PubMed

    Bogoyavlenskiy, V A

    2001-12-01

    We explore a universal "density" formalism to describe nonequilibrium growth processes, specifically, the immiscible viscous fingering in Hele-Shaw cells (usually referred to as the Saffman-Taylor problem). For that we develop an alternative approach to the viscous fingering phenomena, whose basic concepts have been recently published in a Rapid Communication [Phys. Rev. E 63, 045305(R) (2001)]. This approach uses the diffusion-limited aggregation (DLA) paradigm as a core: we introduce a mean-field DLA generalization in stochastic and deterministic formulations. The stochastic model, a quasicontinuum DLA, simulates Monte Carlo patterns, which demonstrate a striking resemblance to natural Hele-Shaw fingers and, for steady-state growth regimes, follow precisely the Saffman-Taylor analytical solutions in channel and sector configurations. The relevant deterministic theory, a complete set of differential equations for a time development of density fields, is derived from that stochastic model. As a principal conclusion, we prove an asymptotic equivalency of both the stochastic and deterministic mean-field DLA formulations to the classic Saffman-Taylor hydrodynamics in terms of an interface evolution. PMID:11736272

  15. 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.

    2016-10-01

    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 SNII feedback prescription, the Haardt & Madau (2012) ultra-violet 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 (of relevance for the abundance of Sulfur II), are also considered in the analysis. It is found that a) for L˜L⋆ galaxies (at z=2.58), about 10% of the sight-lines through the galaxies at impact parameter b=16.2 kpc will display a Sulfur II column density of N({SII)} ≥ 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 (SFR) peaks near the value actually observed for the DLA galaxy counterpart of 27^{+20}_{-9} {M_⊙}/yr. The probability that the SFR lies in the range 10-100 M⊙/yr is found to be 0.65-0.80 for a very broad range of assumptions about the z=2.58 galaxy luminosity function. Hence, the main result is that extreme galaxies are not required to match the high impact parameter and high metallicity DLA. In fact, very good agreement between the theoretical predictions and the observed properties of the proposed DLA galaxy counterpart is found. It is argued, that the bulk of the α-elements, like Sulfur, traced by the high metal column density, b=16.2 kpc absorption lines, have been produced by

  16. A diffusion-limited aggregation model for the evolution of drainage networks

    NASA Technical Reports Server (NTRS)

    Masek, Jeffrey G.; Turcotte, Donald L.

    1993-01-01

    We propose a modified diffusion-limited aggregation (DLA) model for the evolution of fluvial drainage networks. Random walkers are introduced randomly on a grid, and each two-dimensional random walk proceeds until the walker finds a drainage network on which to accrete. This model for headward growth of drainage networks generates drainage patterns remarkably similar to actual drainages. The model also predicts statistical features which agree with actual networks, including the frequency-order (bifurcation) ratio (R(sub b) = 3.98) and the stream length-order (R(sub r) = 2.09). Using the definition of network fractal dimension D = log R(sub b)/log R(sub r), we find that our DLA model gives D = 1.87, near the observed range of D approximately equal to 1.80 - 1.85.

  17. Nanoparticle aggregation: principles and modeling.

    PubMed

    Zhang, Wen

    2014-01-01

    The high surface area to volume ratio of nanoparticles usually results in highly reactive and colloidal instability compared to their bulk counterparts. Aggregation as well as many other transformations (e.g., dissolution) in the environment may alter the physiochemical properties, reactivity, fate, transport, and biological interactions (e.g., bioavailability and uptake) of nanoparticles. The unique properties pertinent to nanoparticles, such as shape, size, surface characteristics, composition, and electronic structures, greatly challenge the ability of colloid science to understand nanoparticle aggregation and its environmental impacts. This review briefly introduces fundamentals about aggregation, fractal dimensions, classic and extended Derjaguin-Landau-Verwey-Overbeak (DLVO) theories, aggregation kinetic modeling, experimental measurements, followed by detailed discussions on the major factors on aggregation and subsequent effects on nanomaterial transport and reactivity.

  18. Diffusion limited aggregation of particles with different sizes: Fractal dimension change by anisotropic growth

    NASA Astrophysics Data System (ADS)

    Braga, F. L.; Mattos, O. A.; Amorin, V. S.; Souza, A. B.

    2015-07-01

    Clusters formation models have been extensively studied in literature, and one of the main task of this research area is the analysis of the particle aggregation processes. Some work support that the main characteristics of this processes are strictly correlated to the cluster morphology, for example in DLA. It is expected that in the DLA clusters formation with particles containing different sizes the modification of the aggregation processes can be responsible for changes in the DLA morphology. The present article is going to analyze the formation of DLA clusters of particles with different sizes and show that the aggregates obtained by this approach generate an angle selection mechanism on dendritic growth that influences the shielding effect of the DLA edge and affect the fractal dimension of the clusters.

  19. 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. PMID:16196793

  20. Average Shape of Transport-Limited Aggregates

    NASA Astrophysics Data System (ADS)

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

    2005-08-01

    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.

  1. A Numerical Study for the Relationship between Natural Manganese Dendrites and DLA Patterns

    NASA Astrophysics Data System (ADS)

    Ozbey, Tugba; Bayirli, Mehmet

    2016-03-01

    The formation mechanisms and the origin of manganese dendrites on the magnesite ore have been under discussion. The growth process of the manganese dendrites is statistically studied by comparing them to aggregations obtained according to the diffusion limited aggregation (DLA) model via Monte Carlo simulations. In this case, ten manganese dendrite patterns changing from the least dense to the densest aggregations on the surface are separately selected to determine the relationship between real and simulated patterns. The sticking parameter is ranged from 0.05≤t≤1. The density-density correlation functions C(r) (their critical exponent A), fractal dimension Df, critical exponent α, and critical exponent β pertaining to the root mean square (rms) thickness have been computed for both the ten manganese dendrites and the simulated aggregations representing them. The results indicate that manganese dendrites may be determined with the general DLA model. Analyses of manganese dendrites, both scaling and simulations, suggest the growth mechanism for the macroscopic expression of crystalline anisotropy for the dendritic patterns. These results are in good agreement with the values in other literature and can be helpful in comparing natural and simulated aggregations (both dendritic and compact deposits).

  2. Inhomogeneous diffusion-limited aggregation

    NASA Technical Reports Server (NTRS)

    Selinger, Robin Blumberg; Nittmann, Johann; Stanley, H. E.

    1989-01-01

    It is demonstrated here that inhomogeneous diffusion-limited aggregation (DLA) model can be used to simulate viscous fingering in a medium with inhomogeneous permeability and homogeneous porosity. The medium consists of a pipe-pore square-lattice network in which all pores have equal volume and the pipes have negligible volume. It is shown that fluctuations in a DLA-based growth process may be tuned by noise reduction, and that fluctuations in the velocity of the moving interface are multiplicative in form.

  3. Model for the growth of electrodeposited ferromagnetic aggregates under an in-plane magnetic field.

    PubMed

    Cronemberger, C; Sampaio, L C; Guimarães, A P; Molho, P

    2010-02-01

    The quasi-two-dimensional deposition of ferromagnetic materials by electrochemical process under the influence of a magnetic field applied in the plane of the growth leads to a surprising symmetry breaking in the dendritic structures found. The reasons for these features are still not completely understood. The original dense circular envelope becomes rectangular, as well as the sparse figures have their shapes elongated. This paper reports the results of a diffusion-limited aggregation (DLA) -like simulation. The model proposed here, a modification of the original DLA model, can deal with ferromagnetic particles under the influence of an electric field and the dipolar interactions between particles, submitted to an applied magnetic field in the plane of growth of such structures. The results were produced varying the applied magnetic field and the magnetic moment of the particles and show that the balance between these interactions is an important mechanisms that can be responsible for the changes in shape of the aggregates observed in the experiments. PMID:20365564

  4. Model for the growth of electrodeposited ferromagnetic aggregates under an in-plane magnetic field

    NASA Astrophysics Data System (ADS)

    Cronemberger, C.; Sampaio, L. C.; Guimarães, A. P.; Molho, P.

    2010-02-01

    The quasi-two-dimensional deposition of ferromagnetic materials by electrochemical process under the influence of a magnetic field applied in the plane of the growth leads to a surprising symmetry breaking in the dendritic structures found. The reasons for these features are still not completely understood. The original dense circular envelope becomes rectangular, as well as the sparse figures have their shapes elongated. This paper reports the results of a diffusion-limited aggregation (DLA) -like simulation. The model proposed here, a modification of the original DLA model, can deal with ferromagnetic particles under the influence of an electric field and the dipolar interactions between particles, submitted to an applied magnetic field in the plane of growth of such structures. The results were produced varying the applied magnetic field and the magnetic moment of the particles and show that the balance between these interactions is an important mechanisms that can be responsible for the changes in shape of the aggregates observed in the experiments.

  5. 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.

  6. Exponential Clogging Time for a One Dimensional DLA

    NASA Astrophysics Data System (ADS)

    Benjamini, Itai; Hoffman, Christopher

    2008-06-01

    In this paper a simple DLA type model is analyzed. In (Benjamini and Yadin in Commun. Math. Phys. 279:187-223, [2008]) the standard DLA model from (Witten and Sander in Phys. Rev. B 27:5686-5697, [1983]) was considered on a cylinder and the arm growing phenomena was established, provided that the section of the cylinder has sufficiently fast mixing rate. When considering DLA on a cylinder it is natural to ask how many particles it takes to clog the cylinder, e.g. modeling clogging of arteries. In this note we formulate a very simple DLA clogging model and establish an exponential lower bound on the number of particles arriving before clogging appears. In particular we possibly shed some light on why it takes so long to reach the bypass operation.

  7. 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…

  8. 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.

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

    PubMed

    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. PMID:26367320

  10. Attracted diffusion-limited aggregation.

    PubMed

    Rahbari, S H Ebrahimnazhad; Saberi, A A

    2012-07-01

    In this paper we present results of extensive Monte Carlo simulations of diffusion-limited aggregation (DLA) with a seed placed on an attractive plane as a simple model in connection with the electrical double layers. We compute the fractal dimension of the aggregated patterns as a function of the attraction strength α. For the patterns grown in both two and three dimensions, the fractal dimension shows a significant dependence on the attraction strength for small values of α and approaches that of the ordinary two-dimensional (2D) DLA in the limit of large α. For the nonattracting case with α = 1, our results in three dimensions reproduce the patterns of 3D ordinary DLA, while in two dimensions our model leads to the formation of a compact cluster with dimension 2. For intermediate α, the 3D clusters have a quasi-2D structure with a fractal dimension very close to that of the ordinary 2D DLA. This allows one to control the morphology of a growing cluster by tuning a single external parameter α. PMID:23005417

  11. Attracted diffusion-limited aggregation

    NASA Astrophysics Data System (ADS)

    Rahbari, S. H. Ebrahimnazhad; Saberi, A. A.

    2012-07-01

    In this paper we present results of extensive Monte Carlo simulations of diffusion-limited aggregation (DLA) with a seed placed on an attractive plane as a simple model in connection with the electrical double layers. We compute the fractal dimension of the aggregated patterns as a function of the attraction strength α. For the patterns grown in both two and three dimensions, the fractal dimension shows a significant dependence on the attraction strength for small values of α and approaches that of the ordinary two-dimensional (2D) DLA in the limit of large α. For the nonattracting case with α=1, our results in three dimensions reproduce the patterns of 3D ordinary DLA, while in two dimensions our model leads to the formation of a compact cluster with dimension 2. For intermediate α, the 3D clusters have a quasi-2D structure with a fractal dimension very close to that of the ordinary 2D DLA. This allows one to control the morphology of a growing cluster by tuning a single external parameter α.

  12. Lacunarity and multifractal analysis of the large DLA mass distribution

    NASA Astrophysics Data System (ADS)

    Rodriguez-Romo, Suemi; Sosa-Herrera, Antonio

    2013-08-01

    We show the methodology used to analyze fractal and mass-multifractal properties of very large Diffusion-Limited Aggregation (DLA) clusters with a maximum of 109 particles for 2D aggregates and 108 particles for 3D clusters, to support our main result; the scaling behavior obtained by our experimental results corresponds to the expected performance of monofractal objects. In order to estimate lacunarity measures for large DLA clusters, we develop a variant of the gliding-box algorithm which reduces the computer time needed to obtain experimental results. We show how our mass multifractal data have a tendency to present monofractal behavior for the mass distribution of the cases presented in this paper in the limit of very large clusters. Lacunarity analysis shows, provided we study small clusters mass distributions, data which might be interpreted as two different values of fractal dimensions while the cluster grows; however, this effect tends to vanish when the cluster size increases further, in such a way that monofractality is achieved. The outcomes of this paper lead us to conclude that the previously reported mass multifractality behavior (Vicsek et al., 1990 [13]) detected for DLA clusters is a consequence of finite size effects and floating point precision limitations and not an intrinsic feature of the phenomena, since the scaling behavior of our DLA clusters space corresponds to monofractal objects, being this situation remarkably noticeable in the limit of very large clusters.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. Aggregated models for integrated distillation systems

    SciTech Connect

    Caballero, J.A.; Grossmann, I.E.

    1999-06-01

    In this work the authors present an aggregated representation for distillation columns that can be used in the synthesis of separation sequences with heat integration. A new aggregated model is first presented for the stripping and rectifying sections of individual distillation columns. This model is based on mass balances and equilibrium feasibility, expressed in terms of flows, inlet concentrations, and recoveries. The energy balance can then be decoupled from the mass balance, and the utilities can be calculated for each separation task. The proposed model is applied to three different superstructures: state task network, state equipment network, and an intermediate representation. The proposed model yields a lower bound to the vapor flow or to the total cost of the utilities. Performance of the different superstructure representations in terms of robustness and computational time is illustrated with several examples.

  18. 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.

  19. 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.

  20. Test of multiscaling in a diffusion-limited-aggregation model using an off-lattice killing-free algorithm

    NASA Astrophysics Data System (ADS)

    Menshutin, Anton Yu.; Shchur, Lev N.

    2006-01-01

    We test the multiscaling issue of diffusion-limited-aggregation (DLA) clusters using a modified algorithm. This algorithm eliminates killing the particles at the death circle. Instead, we return them to the birth circle at a random relative angle taken from the evaluated distribution. In addition, we use a two-level hierarchical memory model that allows using large steps in conjunction with an off-lattice realization of the model. Our algorithm still seems to stay in the framework of the original DLA model. We present an accurate estimate of the fractal dimensions based on the data for a hundred clusters with 50 million particles each. We find that multiscaling cannot be ruled out. We also find that the fractal dimension is a weak self-averaging quantity. In addition, the fractal dimension, if calculated using the harmonic measure, is a nonmonotonic function of the cluster radius. We argue that the controversies in the data interpretation can be due to the weak self-averaging and the influence of intrinsic noise.

  1. A cognitive model for aggregating people's rankings.

    PubMed

    Lee, Michael D; Steyvers, Mark; Miller, Brent

    2014-01-01

    We develop a cognitive modeling approach, motivated by classic theories of knowledge representation and judgment from psychology, for combining people's rankings of items. The model makes simple assumptions about how individual differences in knowledge lead to observed ranking data in behavioral tasks. We implement the cognitive model as a Bayesian graphical model, and use computational sampling to infer an aggregate ranking and measures of the individual expertise. Applications of the model to 23 data sets, dealing with general knowledge and prediction tasks, show that the model performs well in producing an aggregate ranking that is often close to the ground truth and, as in the "wisdom of the crowd" effect, usually performs better than most of individuals. We also present some evidence that the model outperforms the traditional statistical Borda count method, and that the model is able to infer people's relative expertise surprisingly well without knowing the ground truth. We discuss the advantages of the cognitive modeling approach to combining ranking data, and in wisdom of the crowd research generally, as well as highlighting a number of potential directions for future model development.

  2. 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.

  3. 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.

  4. 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.

  5. Aggregation kinetics in a model colloidal suspension

    SciTech Connect

    Bastea, S

    2005-08-08

    The authors present molecular dynamics simulations of aggregation kinetics in a colloidal suspension modeled as a highly asymmetric binary mixture. Starting from a configuration with largely uncorrelated colloidal particles the system relaxes by coagulation-fragmentation dynamics to a structured state of low-dimensionality clusters with an exponential size distribution. The results show that short range repulsive interactions alone can give rise to so-called cluster phases. For the present model and probably other, more common colloids, the observed clusters appear to be equilibrium phase fluctuations induced by the entropic inter-colloidal attractions.

  6. 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

  7. 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. PMID:25970184

  8. Bias-free simulation of diffusion-limited aggregation on a square lattice

    NASA Astrophysics Data System (ADS)

    Loh, Yen Lee

    We identify sources of systematic error in traditional simulations of the Witten-Sander model of diffusion-limited aggregation (DLA) on a square lattice. Based on semi-analytic solutions of the walk-to-line and walk-to-square first-passage problems, we develop an algorithm that reduces the simulation bias to below 10-12. We grow clusters of 108 particles on 65536 × 65536 lattices. We verify that lattice DLA clusters inevitably grow into anisotropic shapes, dictated by the anisotropy of the aggregation process. We verify that the fractal dimension evolves from the continuum DLA value, D = 1 . 71 , for small disk-shaped clusters, towards Kesten's bound of D = 3 / 2 for highly anisotropic clusters with long protruding arms.

  9. Simulating aggregate dynamics in ocean biogeochemical models

    NASA Astrophysics Data System (ADS)

    Jackson, George A.; Burd, Adrian B.

    2015-04-01

    The dynamics of elements in the water column is complex, depending on multiple biological and physical processes operating at very different physical scales. Coagulation of particulate material is important for transforming particles and moving them in the water column. Mechanistic models of coagulation processes provide a means to predict these processes, help interpret observations, and provide insight into the processes occurring. However, most model applications have focused on describing simple marine systems and mechanisms. We argue that further model development, in close collaboration with field and experimental scientists, is required in order to extend the models to describe the large-scale elemental distributions and interactions being studied as part of GEOTRACES. Models that provide a fundamental description of trace element-particle interactions are required as are experimental tests of the mechanisms involved and the predictions arising from models. However, a comparison between simple and complicated models of aggregation and trace metal provides a means for understanding the implications of simplifying assumptions and providing guidance as to which simplifications are needed.

  10. 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.

  11. Interplay of model ingredients affecting aggregate shape plasticity in diffusion-limited aggregation.

    PubMed

    Duarte-Neto, P; Stošić, T; Stošić, B; Lessa, R; Milošević, M V

    2014-07-01

    We analyze the combined effect of three ingredients of an aggregation model--surface tension, particle flow and particle source--representing typical characteristics of many aggregation growth processes in nature. Through extensive numerical experiments and for different underlying lattice structures we demonstrate that the location of incoming particles and their preferential direction of flow can significantly affect the resulting general shape of the aggregate, while the surface tension controls the surface roughness. Combining all three ingredients increases the aggregate shape plasticity, yielding a wider spectrum of shapes as compared to earlier works that analyzed these ingredients separately. Our results indicate that the considered combination of effects is fundamental for modeling the polymorphic growth of a wide variety of structures in confined geometries and/or in the presence of external fields, such as rocks, crystals, corals, and biominerals. PMID:25122308

  12. 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

  13. 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. PMID:26549812

  14. Modeling Protein Aggregate Assembly and Structure

    NASA Astrophysics Data System (ADS)

    Guo, Jun-tao; Hall, Carol K.; Xu, Ying; Wetzel, Ronald

    One might say that "protein science" got its start in the domestic arts, built around the abilities of proteins to aggregate in response to environmental stresses such as heating (boiled eggs), heating and cooling (gelatin), and pH (cheese). Characterization of proteins in the late nineteenth century likewise focused on the ability of proteins to precipitate in response to certain salts and to aggregate in response to heating. Investigations by Chick and Martin (Chick and Martin, 1910) showed that the inactivating response of proteins to heat or solvent treatment is a two-step process involving separate denaturation and precipitation steps. Monitoring the coagulation and flocculation responses of proteins to heat and other stresses remained a major approach to understanding protein structure for decades, with solubility, or susceptibility to aggregation, serving as a kind of benchmark against which results of other methods, such as viscosity, chemical susceptibility, immune activity, crystallizability, and susceptibility to proteolysis, were compared (Mirsky and Pauling, 1936;Wu, 1931). Toward the middle of the last century, protein aggregation studies were largely left behind, as improved methods allowed elucidation of the primary sequence of proteins, reversible unfolding studies, and ultimately high-resolution structures. Curiously, the field of protein science, and in particular protein folding, is now gravitating back to a closer look at protein aggregation and protein aggregates. Unfortunately, the means developed during the second half of the twentieth century for studying native, globular proteins have not proved immediately amenable to the study of aggregate structures. Great progress is being made, however, to modify classical methods, including NMR and X-ray diffraction, as well as to develop newer techniques, that together should continue to expand our picture of aggregate structure (Kheterpal and Wetzel, 2006; Wetzel, 1999).

  15. An extended fractal growth regime in the diffusion limited aggregation including edge diffusion

    NASA Astrophysics Data System (ADS)

    Ghosh, Aritra; Batabyal, R.; Das, G. P.; Dev, B. N.

    2016-01-01

    We have investigated on-lattice diffusion limited aggregation (DLA) involving edge diffusion and compared the results with the standard DLA model. For both cases, we observe the existence of a crossover from the fractal to the compact regime as a function of sticking coefficient. However, our modified DLA model including edge diffusion shows an extended fractal growth regime like an earlier theoretical result using realistic growth models and physical parameters [Zhang et al., Phys. Rev. Lett. 73 (1994) 1829]. While the results of Zhang et al. showed the existence of the extended fractal growth regime only on triangular but not on square lattices, we find its existence on the square lattice. There is experimental evidence of this growth regime on a square lattice. The standard DLA model cannot characterize fractal morphology as the fractal dimension (Hausdorff dimension, DH) is insensitive to morphology. It also predicts DH = DP (the perimeter dimension). For the usual fractal structures, observed in growth experiments on surfaces, the perimeter dimension can differ significantly (DH ≠ DP) depending on the morphology. Our modified DLA model shows minor sensitivity to this difference.

  16. Interplay of model ingredients affecting aggregate shape plasticity in diffusion-limited aggregation

    NASA Astrophysics Data System (ADS)

    Duarte-Neto, P.; Stošić, T.; Stošić, B.; Lessa, R.; Milošević, M. V.

    2014-07-01

    We analyze the combined effect of three ingredients of an aggregation model—surface tension, particle flow and particle source—representing typical characteristics of many aggregation growth processes in nature. Through extensive numerical experiments and for different underlying lattice structures we demonstrate that the location of incoming particles and their preferential direction of flow can significantly affect the resulting general shape of the aggregate, while the surface tension controls the surface roughness. Combining all three ingredients increases the aggregate shape plasticity, yielding a wider spectrum of shapes as compared to earlier works that analyzed these ingredients separately. Our results indicate that the considered combination of effects is fundamental for modeling the polymorphic growth of a wide variety of structures in confined geometries and/or in the presence of external fields, such as rocks, crystals, corals, and biominerals.

  17. 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:...

  18. 3D simulation of the Cluster-Cluster Aggregation model

    NASA Astrophysics Data System (ADS)

    Li, Chao; Xiong, Hailing

    2014-12-01

    We write a program to implement the Cluster-Cluster Aggregation (CCA) model with java programming language. By using the simulation program, the fractal aggregation growth process can be displayed dynamically in the form of a three-dimensional (3D) figure. Meanwhile, the related kinetics data of aggregation simulation can be also recorded dynamically. Compared to the traditional programs, the program has better real-time performance and is more helpful to observe the fractal growth process, which contributes to the scientific study in fractal aggregation. Besides, because of adopting java programming language, the program has very good cross-platform performance.

  19. 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...

  20. 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.

  1. Effect of the Viscosity of Silicone Oil on the Aggregation Behavior of C:F Clusters on a Silicone Oil Liquid Substrate

    NASA Astrophysics Data System (ADS)

    Deng, Yan-Hong; Ye, Chao; Yuan, Yuan; Liu, Hui-Min; Cui, Jin

    2011-04-01

    We investigate the effect of silicone oil viscosity on the aggregation behavior of C:F clusters deposited on silicone oil liquid substrates with viscous coefficients of 100, 350 and 500mm2/s by C4F8 dual-frequency capacitively coupled plasma. The aggregated C:F clusters all exhibit a branch-like fractal structure. However, the fractal dimension decreases from 1.67 to 1.45 with the silicone oil viscous coefficient increasing from 100mm2/s to 500 mm2/s. Owing to the fractal dimension of 1.67 and 1.45, corresponding to the diffusion-limited-aggregation (DLA) model and the cluster-cluster-aggregation (CCA) model respectively, the results show that the increase of silicone oil viscosity can lead to the change of C:F clusters aggregating on a silicone oil liquid substrate from DLA to CCA growth.

  2. 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.

  3. Crossover from capillary fingering to viscous fingering for immiscible unstable flow:Experiment and modeling.

    PubMed

    Ferer, M; Ji, Chuang; Bromhal, Grant S; Cook, Joshua; Ahmadi, Goodarz; Smith, Duane H

    2004-01-01

    Invasion percolation with trapping (IPT) and diffusion-limited aggregation (DLA) are simple fractal models, which are known to describe two-phase flow in porous media at well defined, but unphysical limits of the fluid properties and flow conditions. A decade ago, Fernandez, Rangel, and Rivero predicted a crossover from IPT (capillary fingering) to DLA (viscous fingering) for the injection of a zero-viscosity fluid as the injection velocity was increased from zero. [Phys. Rev. Lett. 67, 2958 (1991)

  4. 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.

  5. A computational model of chemotaxis-based cell aggregation.

    PubMed

    Eyiyurekli, Manolya; Manley, Prakash; Lelkes, Peter I; Breen, David E

    2008-09-01

    We present a computational model that successfully captures the cell behaviors that play important roles in 2-D cell aggregation. A virtual cell in our model is designed as an independent, discrete unit with a set of parameters and actions. Each cell is defined by its location, size, rates of chemoattractant emission and response, age, life cycle stage, proliferation rate and number of attached cells. All cells are capable of emitting and sensing a chemoattractant chemical, moving, attaching to other cells, dividing, aging and dying. We validated and fine-tuned our in silico model by comparing simulated 24-h aggregation experiments with data derived from in vitro experiments using PC12 pheochromocytoma cells. Quantitative comparisons of the aggregate size distributions from the two experiments are produced using the Earth Mover's Distance (EMD) metric. We compared the two size distributions produced after 24 h of in vitro cell aggregation and the corresponding computer simulated process. Iteratively modifying the model's parameter values and measuring the difference between the in silico and in vitro results allow us to determine the optimal values that produce simulated aggregation outcomes closely matched to the PC12 experiments. Simulation results demonstrate the ability of the model to recreate large-scale aggregation behaviors seen in live cell experiments.

  6. An agent-based mathematical model about carp aggregation

    NASA Astrophysics Data System (ADS)

    Liang, Yu; Wu, Chao

    2005-05-01

    This work presents an agent-based mathematical model to simulate the aggregation of carp, a harmful fish in North America. The referred mathematical model is derived from the following assumptions: (1) instead of the consensus among every carps involved in the aggregation, the aggregation of carp is completely a random and spontaneous physical behavior of numerous of independent carp; (2) carp aggregation is a collective effect of inter-carp and carp-environment interaction; (3) the inter-carp interaction can be derived from the statistical analytics about large-scale observed data. The proposed mathematical model is mainly based on empirical inter-carp force field, whose effect is featured with repulsion, parallel orientation, attraction, out-of-perception zone, and blind. Based on above mathematical model, the aggregation behavior of carp is formulated and preliminary simulation results about the aggregation of small number of carps within simple environment are provided. Further experiment-based validation about the mathematical model will be made in our future work.

  7. 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.

  8. 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).

  9. 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. PMID:27566773

  10. 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.

  11. Fractal model of consolidation of weakly aggregated colloidal dispersions

    NASA Astrophysics Data System (ADS)

    Potanin, A. A.; Russel, W. B.

    1996-04-01

    A microrheological model for the consolidation of aggregated colloidal dispersion is presented. Interparticle forces are responsible for the formation of the fractal-like network of particles chains. Aggregation is supposed to be weak in that the chains are gradually created and annihilated. In the framework of this model a constitutive equation is proposed which includes linear dependence of the normal stress upon consolidation rate at low stresses and yieldlike behavior as the stress reaches critical value. Our constitutive equation thus generalizes earlier models based on the compressive yield stress concept by taking into account the deformation in the low-compression limit (analog to the Newtonian flow in the low-shear limit). The constitutive equation is employed to calculate numerically concentration profiles of consolidating samples in better agreement with the experimental data for weakly aggregated alumina dispersions.

  12. An improved collision efficiency model for particle aggregation

    NASA Astrophysics Data System (ADS)

    Olsen, Aaron; Franks, George; Biggs, Simon; Jameson, Graeme J.

    2006-11-01

    A generalized geometric model is presented which describes the collision efficiency factor of aggregation (the probability of a binary particle or aggregate collision resulting in adhesion) for systems comprised of two oppositely charged species. Application of the general model to specific systems requires calculation of the area of each species available for collision with a second species. This is in contrast to previous models developed for polymer-particle flocculation that are based on the fractional surface coverage of adsorbed polymer. The difference between these approaches is suggested as an explanation for previously observed discrepancies between theory and observation. In the current work the specific case of oppositely charged nondeformable spherical particles (heteroaggregation) is quantitatively addressed. The optimum concentration of oppositely charged particles for rapid aggregation (maximum collision efficiency) as a function of relative particle size is calculated and an excellent correlation is found with data taken from literature.

  13. An improved collision efficiency model for particle aggregation.

    PubMed

    Olsen, Aaron; Franks, George; Biggs, Simon; Jameson, Graeme J

    2006-11-14

    A generalized geometric model is presented which describes the collision efficiency factor of aggregation (the probability of a binary particle or aggregate collision resulting in adhesion) for systems comprised of two oppositely charged species. Application of the general model to specific systems requires calculation of the area of each species available for collision with a second species. This is in contrast to previous models developed for polymer-particle flocculation that are based on the fractional surface coverage of adsorbed polymer. The difference between these approaches is suggested as an explanation for previously observed discrepancies between theory and observation. In the current work the specific case of oppositely charged nondeformable spherical particles (heteroaggregation) is quantitatively addressed. The optimum concentration of oppositely charged particles for rapid aggregation (maximum collision efficiency) as a function of relative particle size is calculated and an excellent correlation is found with data taken from literature. PMID:17115794

  14. 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.

  15. Modelling parasite aggregation: disentangling statistical and ecological approaches.

    PubMed

    Yakob, Laith; Soares Magalhães, Ricardo J; Gray, Darren J; Milinovich, Gabriel; Wardrop, Nicola; Dunning, Rebecca; Barendregt, Jan; Bieri, Franziska; Williams, Gail M; Clements, Archie C A

    2014-05-01

    The overdispersion in macroparasite infection intensity among host populations is commonly simulated using a constant negative binomial aggregation parameter. We describe an alternative to utilising the negative binomial approach and demonstrate important disparities in intervention efficacy projections that can come about from opting for pattern-fitting models that are not process-explicit. We present model output in the context of the epidemiology and control of soil-transmitted helminths due to the significant public health burden imposed by these parasites, but our methods are applicable to other infections with demonstrable aggregation in parasite numbers among hosts.

  16. 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

  17. 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.

  18. 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.

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

    PubMed

    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

  20. 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.

  1. Scattering and propagation of terahertz pulses in random soot aggregate systems

    NASA Astrophysics Data System (ADS)

    Li, Hai-Ying; Wu, Zhen-Sen; Bai, Lu; Li, Zheng-Jun

    2014-05-01

    Scattering and propagation of terahertz pulses in random soot aggregate systems are studied by using the generalized multi-particle Mie-solution (GMM) and the pulse propagation theory. Soot aggregates are obtained by the diffusion-limited aggregation (DLA) model. For a soot aggregate in soot aggregate systems, scattering characteristics are analyzed by using the GMM. Scattering intensities versus scattering angles are given. The effects of different positions of the aggregate on the scattering intensities, scattering cross sections, extinction cross sections, and absorption cross sections are computed and compared. Based on pulse propagation in random media, the transmission of terahertz pulses in random soot aggregate systems is determined by the two-frequency mutual coherence function. Numerical simulations and analysis are given for terahertz pulses (0.7956 THz).

  2. 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

  3. Three-dimensional Myoblast Aggregates--Effects of Modeled Microgravity

    NASA Technical Reports Server (NTRS)

    Byerly, Diane; Sognier, M. A.; Marquette, M. L.

    2006-01-01

    The overall objective of these studies is to elucidate the molecular and cellular alterations that contribute to muscle atrophy in astronauts caused by exposure to microgravity conditions in space. To accomplish this, a three-dimensional model test system was developed using mouse myoblast cells (C2C12). Myoblast cells were grown as three-dimensional aggregates (without scaffolding or other solid support structures) in both modeled microgravity (Rotary Cell Culture System, Synthecon, Inc.) and at unit gravity in coated Petri dishes. Evaluation of H&E stained thin sections of the aggregates revealed the absence of any necrosis. Confocal microscopy evaluations of cells stained with the Live/Dead assay (Molecular Probes) confirmed that viable cells were present throughout the aggregates with an average of only three dead cells observed per aggregate. Preliminary results from gene array analysis (Affymetrix chip U74Av2) showed that approximately 14% of the genes were down regulated (decreased more than 3 fold) and 4% were upregulated in cells exposed to modeled microgravity for 12 hours compared to unit gravity controls. Additional studies using fluorescent phallacidin revealed a decrease in F-actin in the cells exposed to modeled microgravity compared to unit gravity. Myoblast cells grown as aggregates in modeled microgravity exhibited spontaneous differentiation into syncitia while no differentiation was seen in the unit gravity controls. These studies show that 1)the model test system developed is suitable for assessing cellular and molecular alterations in myoblasts; 2) gene expression alterations occur rapidly (within 12 hours) following exposure to modeled microgravity; and 3) modeled microgravity conditions stimulated myoblast cell differentiation. Achieving a greater understanding of the molecular alterations leading to muscle atrophy will eventually enable the development of cell-based countermeasures, which may be valuable for treatment of muscle diseases on

  4. 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+.

  5. Multiscale modelling of nucleosome core particle aggregation.

    PubMed

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

    2015-02-18

    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 (CoHex(3+)) 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 CoHex(3+). 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, spermidine(3+).

  6. Anisotropic diffusion limited aggregation in three dimensions: universality and nonuniversality.

    PubMed

    Goold, Nicholas R; Somfai, Ellák; Ball, Robin C

    2005-09-01

    We explore the macroscopic consequences of lattice anisotropy for diffusion limited aggregation (DLA) in three dimensions. Simple cubic and bcc lattice growths are shown to approach universal asymptotic states in a coherent fashion, and the approach is accelerated by the use of noise reduction. These states are strikingly anisotropic dendrites with a rich hierarchy of structure. For growth on an fcc lattice, our data suggest at least two stable fixed points of anisotropy, one matching the bcc case. Hexagonal growths, favoring six planar and two polar directions, appear to approach a line of asymptotic states with continuously tunable polar anisotropy. The more planar of these growths visually resembles real snowflake morphologies. Our simulations use a new and dimension-independent implementation of the DLA model. The algorithm maintains a hierarchy of sphere coverings of the growth, supporting efficient random walks onto the growth by spherical moves. Anisotropy was introduced by restricting growth to certain preferred directions. PMID:16241431

  7. Anisotropic diffusion limited aggregation in three dimensions: Universality and nonuniversality

    NASA Astrophysics Data System (ADS)

    Goold, Nicholas R.; Somfai, Ellák; Ball, Robin C.

    2005-09-01

    We explore the macroscopic consequences of lattice anisotropy for diffusion limited aggregation (DLA) in three dimensions. Simple cubic and bcc lattice growths are shown to approach universal asymptotic states in a coherent fashion, and the approach is accelerated by the use of noise reduction. These states are strikingly anisotropic dendrites with a rich hierarchy of structure. For growth on an fcc lattice, our data suggest at least two stable fixed points of anisotropy, one matching the bcc case. Hexagonal growths, favoring six planar and two polar directions, appear to approach a line of asymptotic states with continuously tunable polar anisotropy. The more planar of these growths visually resembles real snowflake morphologies. Our simulations use a new and dimension-independent implementation of the DLA model. The algorithm maintains a hierarchy of sphere coverings of the growth, supporting efficient random walks onto the growth by spherical moves. Anisotropy was introduced by restricting growth to certain preferred directions.

  8. Sticky Particles: Modeling Rigid Aggregates in Dense Planetary Rings

    NASA Astrophysics Data System (ADS)

    Perrine, Randall P.; Richardson, D. C.; Scheeres, D. J.

    2008-09-01

    We present progress on our study of planetary ring dynamics. We use local N-body simulations to examine small patches of dense rings in which self-gravity and mutual collisions dominate the dynamics of the ring material. We use the numerical code pkdgrav to model the motions of 105-7 ring particles, using a sliding patch model with modified periodic boundary conditions. The exact nature of planetary ring particles is not well understood. If covered in a frost-like layer, such irregular surfaces may allow for weak cohesion between colliding particles. Thus we have recently added new functionality to our model, allowing "sticky particles” to lock into rigid aggregates while in a rotating reference frame. This capability allows particles to adhere to one another, forming irregularly shaped aggregates that move as rigid bodies. (The bonds between particles can subsequently break, given sufficient stress.) These aggregates have greater strength than gravitationally bound "rubble piles,” and are thus able to grow larger and survive longer under similar stresses. This new functionality allows us to explore planetary ring properties and dynamics in a new way, by self-consistently forming (and destroying) non-spherical aggregates and moonlets via cohesive forces, while in a rotating frame, subjected to planetary tides. (We are not aware of any similar implementations in other existing models.) These improvements allow us to study the many effects that particle aggregation may have on the rings, such as overall ring structure; wake formation; equilibrium properties of non-spherical particles, like pitch angle, orientation, shape, size distribution, and spin; and the surface properties of the ring material. We present test cases and the latest results from this new model. This work is supported by a NASA Earth and Space Science Fellowship.

  9. 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.

  10. Individual based and mean-field modeling of direct aggregation

    PubMed Central

    Burger, Martin; Haškovec, Jan; Wolfram, Marie-Therese

    2013-01-01

    We introduce two models of biological aggregation, based on randomly moving particles with individual stochasticity depending on the perceived average population density in their neighborhood. In the first-order model the location of each individual is subject to a density-dependent random walk, while in the second-order model the density-dependent random walk acts on the velocity variable, together with a density-dependent damping term. The main novelty of our models is that we do not assume any explicit aggregative force acting on the individuals; instead, aggregation is obtained exclusively by reducing the individual stochasticity in response to higher perceived density. We formally derive the corresponding mean-field limits, leading to nonlocal degenerate diffusions. Then, we carry out the mathematical analysis of the first-order model, in particular, we prove the existence of weak solutions and show that it allows for measure-valued steady states. We also perform linear stability analysis and identify conditions for pattern formation. Moreover, we discuss the role of the nonlocality for well-posedness of the first-order model. Finally, we present results of numerical simulations for both the first- and second-order model on the individual-based and continuum levels of description. PMID:24926113

  11. 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

  12. Balancing aggregation and smoothing errors in inverse models

    DOE PAGES

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

    2015-01-13

    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

  13. 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.

  14. 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. PMID:24376691

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

    PubMed

    Ebrahimi, Ali; Or, Dani

    2016-09-01

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

  17. 2011 Dielectric Laser Acceleration Workshop (DLA2011)

    SciTech Connect

    Bermel, Peter; Byer, Robert L.; Colby, Eric R.; Cowan, Benjamin M.; Dawson, Jay; England, R.Joel; Noble, Robert J.; Qi, Ming-Hao; Yoder, Rodney B.; /Manhattanville Coll., Purchase

    2012-04-17

    The first ICFA Mini-workshop on Dielectric Laser Accelerators was held on September 15-16, 2011 at SLAC National Accelerator Laboratory. We present the results of the Workshop, and discuss the main conclusions of the Accelerator Applications, Photonics, and Laser Technologies working groups. Over 50 participants from 4 countries participated, discussing the state of the art in photonic structures, laser science, and nanofabrication as it pertains to laser-driven particle acceleration in dielectric structures. Applications of this new and promising acceleration concept to discovery science and industrial, medical, and basic energy sciences were explored. The DLA community is presently focused on making demonstrations of high gradient acceleration and a compatible attosecond injector source - two critical steps towards realizing the potential of this technology.

  18. Exact dynamics of a class of aggregation models

    NASA Astrophysics Data System (ADS)

    Majumdar, Satya N.; Sire, Clément

    1993-11-01

    The dynamics of a class of aggregation models proposed by Takayasu and co-workers are solved exactly in one dimension and in the mean field limit. These models describe the aggregation of positive and negative charges. In one dimension, we find the dynamical cluster-size exponents z=3/2 and zc=3/4 when the average flux of injected charges is nonzero and zero, respectively. We also find the crossover exponent near the transition to be φ=4/3. Within mean field theory, we find these exponents to be z=2, zc=1, and φ=1. Assuming dynamic scaling, we show that in any dimension, these exponents are related to one single static exponent.

  19. Neighborhood Supported Model Level Fuzzy Aggregation for Moving Object Segmentation.

    PubMed

    Chiranjeevi, Pojala; Sengupta, Somnath

    2014-02-01

    We propose a new algorithm for moving object detection in the presence of challenging dynamic background conditions. We use a set of fuzzy aggregated multifeature similarity measures applied on multiple models corresponding to multimodal backgrounds. The algorithm is enriched with a neighborhood-supported model initialization strategy for faster convergence. A model level fuzzy aggregation measure driven background model maintenance ensures more robustness. Similarity functions are evaluated between the corresponding elements of the current feature vector and the model feature vectors. Concepts from Sugeno and Choquet integrals are incorporated in our algorithm to compute fuzzy similarities from the ordered similarity function values for each model. Model updating and the foreground/background classification decision is based on the set of fuzzy integrals. Our proposed algorithm is shown to outperform other multi-model background subtraction algorithms. The proposed approach completely avoids explicit offline training to initialize background model and can be initialized with moving objects also. The feature space uses a combination of intensity and statistical texture features for better object localization and robustness. Our qualitative and quantitative studies illustrate the mitigation of varieties of challenging situations by our approach. PMID:24235250

  20. Thermodynamically reversible generalization of diffusion limited aggregation.

    PubMed

    D'Souza, R M; Margolus, N H

    1999-07-01

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

  1. A new example of the diffusion-limited aggregation: Ni-Cu film patterns

    NASA Astrophysics Data System (ADS)

    Kockar, Hakan; Bayirli, Mehmet; Alper, Mursel

    2010-02-01

    The mechanism of the growth of the dendrites in the Ni-Cu films is studied by comparing them with the aggregates obtained by Monte Carlo (MC) simulations according to the diffusion-limited aggregation (DLA) model. The films were grown by electrodeposition. The structural analysis of the films carried out using the x-ray diffraction showed that the films have a face-centered cubic structure. Scanning electron microscope (SEM) was used for morphological observations and the film compositions were determined by energy dispersive x-ray spectroscopy. The observed SEM images are compared with the patterns obtained by MC simulations according to DLA model in which the sticking probability, P between the particles is used as a parameter. For all samples between the least and the densest aggregates in the films, the critical exponents of the density-density correlation functions, α were within the interval 0.160 ± 0.005-0.124 ± 0.006, and the fractal dimensions, Df, varies from 1.825 ± 0.006 to 1.809 ± 0.008 according to the method of two-point correlation function. These values are also verified by the mass-radius method. The pattern with α and Df within these intervals was obtained by MC simulations to DLA model while the sticking probability, P was within the interval from 0.35 to 0.40 obtained by varying P (1-0.001). The results showed that the DLA model in this binary system is a possible mechanism for the formation of the ramified pattern of Ni-Cu within the Ni-rich base part of the Ni-Cu films due to the diffusive characteristics of Cu.

  2. 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.

  3. Wax crystallization and aggregation in a model crude oil

    NASA Astrophysics Data System (ADS)

    Vignati, Emanuele; Piazza, Roberto; Visintin, Ruben F. G.; Lapasin, Romano; D'Antona, Paolo; Lockhart, Thomas P.

    2005-11-01

    The high-molecular-weight paraffinic ('wax') fraction separates from crude oils at low temperatures, a process that can lead to a sol-gel transition when the mass of wax solids exceeds 1-2%. Attractive interactions between the micron-size wax solids suspended in the non-polar medium have been suggested to be responsible for gel formation. The present study reports an optically transparent model oil system, based on a mixture of linear and branched paraffins. Rheological measurements and optical microscopy show that the model system reproduces essential features of crude oil gels. Small-angle light scattering studies conducted at temperatures intermediate between the cloud point (58 °C) and sol-gel transition (39 °C) show that phase separation and wax solid aggregation are rapid processes, leading to the formation of dynamically arrested structures well above the sol-gel transition determined rheologically. Analysis of gravity settling effects has provided a rough estimate for the yield stress of the wax particle network formed (greater than 0.7 Pa at 45 °C and 0.07 Pa at 55 °C). Clusters formed by the aggregated wax solids possess a fractal dimension of about 1.8, consistent with diffusion-limited cluster-cluster aggregation.

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

    PubMed

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

    2016-10-01

    Natural asphaltenes are defined as polyaromatic compounds whose chemical composition and structure are dependent on their geological origin and production history, hence are regarded as complex molecules with aromatic cores and aliphatic tails that occur in the heaviest fraction of crude oil. The aggregation of asphaltenes presents a range of technical challenges to the production and processing of oil. In this work we study the behaviour of the model asphaltene-like molecule hexa-tert-butylhexa-peri-hexabenzocoronene (HTBHBC) using molecular dynamics simulation. It was found that the regular arrangement of the tert-butyl side chains prevents the formation of strongly-bound dimers by severely restricting the configurational space of the aggregation pathway. In contrast, a modified molecule with only 3 side chains is readily able to form dimers. This work therefore confirms the influence of the molecular structure of polyaromatic compounds on their aggregation mechanism, and reveals the unexpected design rules required for model systems that can mimic the behavior of asphaltenes. PMID:27465036

  5. 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. 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.

  7. Development of a Ferroelectric Based Tunable DLA Structure

    NASA Astrophysics Data System (ADS)

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

    2009-01-01

    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 μm thickness and dielectric constant of 450-550. The frequency shift by temperature variation of the cylindrical Ka-band tunable DLA of 14 MHz/° K has been demonstrated leading to an overall DLA structure frequency tuning range of 140-280 MHz with 10-20° 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.

  8. Aggregate input-output models of neuronal populations.

    PubMed

    Saxena, Shreya; Schieber, Marc H; Thakor, Nitish V; Sarma, Sridevi V

    2012-07-01

    An extraordinary amount of electrophysiological data has been collected from various brain nuclei to help us understand how neural activity in one region influences another region. In this paper, we exploit the point process modeling (PPM) framework and describe a method for constructing aggregate input-output (IO) stochastic models that predict spiking activity of a population of neurons in the "output" region as a function of the spiking activity of a population of neurons in the "input" region. We first build PPMs of each output neuron as a function of all input neurons, and then cluster the output neurons using the model parameters. Output neurons that lie within the same cluster have the same functional dependence on the input neurons. We first applied our method to simulated data, and successfully uncovered the predetermined relationship between the two regions. We then applied our method to experimental data to understand the input-output relationship between motor cortical neurons and 1) somatosensory and 2) premotor cortical neurons during a behavioral task. Our aggregate IO models highlighted interesting physiological dependences including relative effects of inhibition/excitation from input neurons and extrinsic factors on output neurons.

  9. 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.

  10. Influence of particle size on diffusion-limited aggregation.

    PubMed

    Tan, Z J; Zou, X W; Zhang, W B; Jin, Z Z

    1999-11-01

    The influence of particle size on diffusion-limited aggregation (DLA) has been investigated by computer simulations. For DLA clusters consisting of two kinds of particles with different sizes, when large particles are in the minority, the patterns of clusters appear asymmetrical and nonuniform, and their fractal dimensions D(f) increase compared with one-component DLA. With increasing size of large particles, D(f) increases. This increase can be attributed to two reasons: one is that large particles become new growth centers; the other is the big masses of large particles. As the concentration ratio x(n) of large particles increases, D(f) will reach a maximum value D(f(m)) and then decrease. When x(n) exceeds a certain value, the morphology and D(f) of the two-component DLA clusters are similar to those of one-component DLA clusters. PMID:11970534

  11. 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.

  12. A population balance equation model of aggregation dynamics in Taxus suspension cell cultures.

    PubMed

    Kolewe, Martin E; Roberts, Susan C; Henson, Michael A

    2012-02-01

    The nature of plant cells to grow as multicellular aggregates in suspension culture has profound effects on bioprocess performance. Recent advances in the measurement of plant cell aggregate size allow for routine process monitoring of this property. We have exploited this capability to develop a conceptual model to describe changes in the aggregate size distribution that are observed over the course of a Taxus cell suspension batch culture. We utilized the population balance equation framework to describe plant cell aggregates as a particulate system, accounting for the relevant phenomenological processes underlying aggregation, such as growth and breakage. We compared model predictions to experimental data to select appropriate kernel functions, and found that larger aggregates had a higher breakage rate, biomass was partitioned asymmetrically following a breakage event, and aggregates grew exponentially. Our model was then validated against several datasets with different initial aggregate size distributions and was able to quantitatively predict changes in total biomass and mean aggregate size, as well as actual size distributions. We proposed a breakage mechanism where a fraction of biomass was lost upon each breakage event, and demonstrated that even though smaller aggregates have been shown to produce more paclitaxel, an optimum breakage rate was predicted for maximum paclitaxel accumulation. We believe this is the first model to use a segregated, corpuscular approach to describe changes in the size distribution of plant cell aggregates, and represents an important first step in the design of rational strategies to control aggregation and optimize process performance.

  13. Phase transition in diffusion limited aggregation with patchy particles in two dimensions

    NASA Astrophysics Data System (ADS)

    Kartha, Moses J.; Sayeed, Ahmed

    2016-08-01

    The influence of patchy interactions on diffusion-limited aggregation (DLA) has been investigated by computer simulations. In this model, the adsorption of the particle is irreversible, but the adsorption occurs only when the 'sticky patch' makes contact with the sticky patch of a previously adsorbed particle. As we vary the patch size, growth rate of the cluster decreases, and below a well-defined critical patch size, pc the steady state growth rate goes to zero. The system reaches an absorbing phase producing a non-equilibrium continuous phase transition. The order parameter close to the critical value of the patch size shows a power law behavior ρ (∞) ∼(p -pc) β, where β = 0.2840. We have found that the value of the critical exponent convincingly shows that this transition in patchy DLA belongs to the directed percolation universality class.

  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. 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.

  16. 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

  17. 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. PMID:26744947

  18. Modeling aggregation of dust monomers in low gravity environments

    NASA Astrophysics Data System (ADS)

    Doyon, Julien; Rioux, Claude

    The modeling of aggregation phenomena in microgravity is of paramount relevance to the understanding of the formation of planets. Relevant experiments have been carried out at a ground based laboratory and on aircraft providing low gravity during parabolic flight.1 Other possible environments are rockets, shuttles and the international space station. Numerical simulation of aggregation can provide us a tool to understand the formal and the-oretical background of the phenomena. The comparison between low gravity experiment and modeling prediction may confirm a theory. Also, experiments that are hard to perform can be simulated on computers allowing a vast choice of physical properties. Simulations to date have been constrained to ensembles of 100 to 1000 monomers.2 We have been able to extend such numbers to 10 000 monomers and the final goal is about 100 000 monomers, where gravitational effects become relevant yielding spheroidal systems of particles (planetesimals and planetoids). Simulations made are assumed to be diffusion processes where colliding particles will stick together with a certain probability. Future work shall include other interactions like electrostatic or magnetic forces. Recent results are to be shown at the meeting. I acknowledge the support from the ELIPS program (jointly between Canadian and European space agencies). The guidance of Prof. Slobodrian is warmly thanked. References. 1. R.J. Slobodrian, C. Rioux and J.-C. Leclerc, Microgravity Research and Aplications in Phys-ical Sciences and Biotechnology, Proceedings of the First International Symposium, Sorrento, Italy (2000) ESA SP-454, p.779-786. and Refs. therein. 2. P. Deladurantaye, C Rioux and R.J Slobodrian, Chaos, Solitons Fractals , (1997), pp. 1693-1708. Carl Robert and Eric Litvak, Software " Fractal", private communication.

  19. 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

  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. Diffusion-Limited Aggregation with Polygon Particles

    NASA Astrophysics Data System (ADS)

    Deng, Li; Wang, Yan-Ting; Ou-Yang, Zhong-Can

    2012-12-01

    Diffusion-limited aggregation (DLA) assumes that particles perform pure random walk at a finite temperature and aggregate when they come close enough and stick together. Although it is well known that DLA in two dimensions results in a ramified fractal structure, how the particle shape influences the formed morphology is still unclear. In this work, we perform the off-lattice two-dimensional DLA simulations with different particle shapes of triangle, quadrangle, pentagon, hexagon, and octagon, respectively, and compare with the results for circular particles. Our results indicate that different particle shapes only change the local structure, but have no effects on the global structure of the formed fractal cluster. The local compactness decreases as the number of polygon edges increases.

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

    PubMed

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

    2008-03-21

    In this paper, the different aggregation modes of a water-insoluble porphyrin (EHO) mixed with an amphiphilic calix[8]arene (C8A), at the air-water interface and in Langmuir-Blodgett (LB) film form, are analyzed as a function of the mixed composition. The strategy used to control the EHO aggregation has consisted of preparing mixed thin films containing EHO and C8A, in different ratios, at the air-water interface. Therefore, the increase of the C8A molar ratio in the mixed film diminishes the aggregation of the EHO molecules, although such an effect must be exclusively related to the dilution of the porphyrin. The reflection spectra of the mixed C8A-EHO films registered at the air-water interface, show a complex Soret band exhibiting splitting, hypochromicity and broadening features. Also, during the transfer process at high surface pressure, it has been shown that the EHO molecules are ejected from the C8A monolayer and only a fraction of porphyrin is transferred to the solid support, in spite of a complete transfer for the C8A matrix. The complex structure of the reflection spectra at the air-water interface, as well as the polarization dependence of the absorption spectra for the mixed LB films, indicate the existence of four different arrangements for the EHO hosted in the C8A matrix. The aggregate formation is governed by two factors: the attraction between the porphyrin rings which minimizes their separation, and the alkyl chain interactions, that is, hydrophobic effect and/or steric hindrance which determine and restrict the possible aggregation structures. By using the extended dipole model, the assignment of the spectral peaks observed to different EHO aggregates is shown. PMID:18327313

  3. 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.

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

    PubMed Central

    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.

    2015-01-01

    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. PMID:25759392

  5. 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.

  6. 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

  7. 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

  8. 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…

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

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... PROGRAM DEFENSE LOGISTICS AGENCY PRIVACY PROGRAM Pt. 323, App. H Appendix H to Part 323—DLA Exemption... systems of records maintained by the Defense Logistics Agency will be exempt from the requirements of 5 U... entered into this system, the Defense Logistics Agency claims the same exemptions for the records...

  10. 32 CFR Appendix H to Part 323 - DLA Exemption Rules

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 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 will.... b. ID: S500.20 (Specific exemption). 1. System name: Defense Logistics Agency Criminal...

  11. 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

    ...) Performance Review Board (PRB) AGENCY: DLA. ACTION: Notice of membership--2010 DLA PRB. SUMMARY: This notice announces the appointment of members to the DLA SES Performance Review Board (PRB). The publication of PRB composition is required by 5 U.S.C. 4314(c)(4). The PRB provides fair and impartial review of SES...

  12. Multifractal analysis of the branch structure of diffusion-limited aggregates

    NASA Astrophysics Data System (ADS)

    Hanan, W. G.; Heffernan, D. M.

    2012-02-01

    We examine the branch structure of radial diffusion-limited aggregation (DLA) clusters for evidence of multifractality. The lacunarity of DLA clusters is measured and the generalized dimensions D(q) of their mass distribution is estimated using the sandbox method. We find that the global n-fold symmetry of the aggregates can induce anomalous scaling behavior into these measurements. However, negating the effects of this symmetry, standard scaling is recovered.

  13. Multifractal analysis of the branch structure of diffusion-limited aggregates.

    PubMed

    Hanan, W G; Heffernan, D M

    2012-02-01

    We examine the branch structure of radial diffusion-limited aggregation (DLA) clusters for evidence of multifractality. The lacunarity of DLA clusters is measured and the generalized dimensions D(q) of their mass distribution is estimated using the sandbox method. We find that the global n-fold symmetry of the aggregates can induce anomalous scaling behavior into these measurements. However, negating the effects of this symmetry, standard scaling is recovered. PMID:22463212

  14. Multifractal analysis of the branch structure of diffusion-limited aggregates.

    PubMed

    Hanan, W G; Heffernan, D M

    2012-02-01

    We examine the branch structure of radial diffusion-limited aggregation (DLA) clusters for evidence of multifractality. The lacunarity of DLA clusters is measured and the generalized dimensions D(q) of their mass distribution is estimated using the sandbox method. We find that the global n-fold symmetry of the aggregates can induce anomalous scaling behavior into these measurements. However, negating the effects of this symmetry, standard scaling is recovered.

  15. Rainfall variability effects on aggregate crop model predictions

    NASA Astrophysics Data System (ADS)

    Dzotsi, Kofikuma Adzewoda

    Crop production operates in a highly heterogeneous environment. Space-time variability in weather and spatial heterogeneity in soil and management generate variability in crop yield. While it is practically unfeasible to thoroughly sample the variability of the crop environment, quantification of the associated uncertainties in crop performance can provide vital information for decision-making. The present study used rainfall data collected in southwestern Georgia at scales ranging from 1 km to 60 km to assess the effect of weather variability (in particular rainfall) on crop predictions aggregated over soil and management variations. The simple SALUS (System Approach to Land Use Sustainability) crop model was integrated in DSSAT (Decision Support System for Agrotechnology Transfer) then parameterized and tested for maize, peanut and cotton for use in obtaining the crop predictions. Analysis of the rainfall data indicated that variability in storm characteristics depends upon the season. Winter rainfall was more correlated at a mean distance of 54 km between locations than summer rainfall was at a mean distance of 3 km. The pairwise correlation between locations decreased with distance faster in the summer than in the winter. This rainfall variability translated into crop yield variability in the study area (about 3100 km²). It was found that weather variability explained 60% and 49% of maize yield variability respectively in 2010 and 2011 when heterogeneity in weather, soil, cultivar and planting dates were accounted for simultaneously. Uncertainties in crop predictions due to rainfall spatial uncertainty decreased as the number of sites where weather data were collected increased. Expressed in terms of maize yield coefficient of variation, this uncertainty decreased exponentially from 27% to approximately 4% at a sampling density of 20 weather locations. Based on 30 years of generated weather data, it was concluded that the general form of the relationship

  16. 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

  17. Model discrimination and mechanistic interpretation of kinetic data in protein aggregation studies.

    PubMed

    Bernacki, Joseph P; Murphy, Regina M

    2009-04-01

    Given the importance of protein aggregation in amyloid diseases and in the manufacture of protein pharmaceuticals, there has been increased interest in measuring and modeling the kinetics of protein aggregation. Several groups have analyzed aggregation data quantitatively, typically measuring aggregation kinetics by following the loss of protein monomer over time and invoking a nucleated growth mechanism. Such analysis has led to mechanistic conclusions about the size and nature of the nucleus, the aggregation pathway, and/or the physicochemical properties of aggregation-prone proteins. We have examined some of the difficulties that arise when extracting mechanistic meaning from monomer-loss kinetic data. Using literature data on the aggregation of polyglutamine, a mutant beta-clam protein, and protein L, we determined parameter values for 18 different kinetic models. We developed a statistical model discrimination method to analyze protein aggregation data in light of competing mechanisms; a key feature of the method is that it penalizes overparameterization. We show that, for typical monomer-loss kinetic data, multiple models provide equivalent fits, making mechanistic determination impossible. We also define the type and quality of experimental data needed to make more definitive conclusions about the mechanism of aggregation. Specifically, we demonstrate how direct measurement of fibril size provides robust discrimination. PMID:19348769

  18. Joint translog model of energy aggregation and industrial demand for energy in US manufacturing

    SciTech Connect

    Taheri, A.A.

    1987-01-01

    This study builds on the work of Berndt and Christensen (1973b), Hudson and Jorgenson (1974), and Fuss (1977) by extending the (solo) price-aggregation model to incorporate the joint price/quantity aggregation of energy inputs, using the recently developed translog (Christensen et al., 1973) as (homothetic) aggregator models. The procedure represents the first step in a two-step optimization, which holds under the assumption of (homothetic) weak-separability, and generates aggregates that are internally consistent and first-step optimal. The two models are integrated via the theory of duality, and estimated indirectly by joint estimation of a complete system of derived fuel-share equations. One major advantage of this joint estimation is that, the complete system yields parameter estimates that are more efficient than those obtained by the (solo) price-aggregation model. It also leads to more-robust estimated models based on the same body of data. While the internally consistent energy aggregates have important applications in aggregate energy research, the aggregation model also provides an econometric model for empirical investigation of interfuel substitution responses in the US manufacturing.

  19. Anisotropic diffusion-limited aggregation.

    PubMed

    Popescu, M N; Hentschel, H G E; Family, F

    2004-06-01

    Using stochastic conformal mappings, we study the effects of anisotropic perturbations on diffusion-limited aggregation (DLA) in two dimensions. The harmonic measure of the growth probability for DLA can be conformally mapped onto a constant measure on a unit circle. Here we map m preferred directions for growth to a distribution on the unit circle, which is a periodic function with m peaks in [-pi,pi) such that the angular width sigma of the peak defines the "strength" of anisotropy kappa= sigma(-1) along any of the m chosen directions. The two parameters (m,kappa) map out a parameter space of perturbations that allows a continuous transition from DLA (for small enough kappa ) to m needlelike fingers as kappa--> infinity. We show that at fixed m the effective fractal dimension of the clusters D(m,kappa) obtained from mass-radius scaling decreases with increasing kappa from D(DLA) approximately 1.71 to a value bounded from below by D(min) = 3 / 2. Scaling arguments suggest a specific form for the dependence of the fractal dimension D(m,kappa) on kappa for large kappa which compares favorably with numerical results. PMID:15244564

  20. Diffusion-limited aggregation on curved surfaces

    NASA Astrophysics Data System (ADS)

    Choi, J.; Crowdy, D.; Bazant, M. Z.

    2010-08-01

    We develop a general theory of transport-limited aggregation phenomena occurring on curved surfaces, based on stochastic iterated conformal maps and conformal projections to the complex plane. To illustrate the theory, we use stereographic projections to simulate diffusion-limited aggregation (DLA) on surfaces of constant Gaussian curvature, including the sphere (K>0) and the pseudo-sphere (K<0), which approximate "bumps" and "saddles" in smooth surfaces, respectively. Although the curvature affects the global morphology of the aggregates, the fractal dimension (in the curved metric) is remarkably insensitive to curvature, as long as the particle size is much smaller than the radius of curvature. We conjecture that all aggregates grown by conformally invariant transport on curved surfaces have the same fractal dimension as DLA in the plane. Our simulations suggest, however, that the multifractal dimensions increase from hyperbolic (K<0) to elliptic (K>0) geometry, which we attribute to curvature-dependent screening of tip branching.

  1. 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

  2. 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 ...

  3. 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.

  4. 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. PMID:21627165

  5. 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

  6. 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

  7. The effect of surfactant and solid phase concentration on drug aggregates in model aerosol propellent suspensions.

    PubMed

    Bower, C; Washington, C; Purewal, T S

    1996-04-01

    The effect of increasing solid phase concentration on the morphology and flocculation rate of model aerosol suspensions has been investigated. Suspensions of micronized salbutamol sulphate and lactose in trichlorotrifluoroethane (P113) were studied under conditions of increasing shear stress. By use of image analysis techniques, measurement of aggregate size, fractal dimension and rate of aggregation was performed. The effect of the surfactant sorbitan monooleate on morphology and flocculation rate was also studied. Increased solid phase concentration caused an increase in the rate of aggregation and average aggregate size at a given value of shear stress. Surfactant addition retarded the aggregation rate, and caused a shift from a diffusion-limited cluster aggregation to a reaction-limited cluster aggregation mechanism. The aggregate profiles showed a corresponding change from rugged and crenellated without surfactant, to increasingly smooth and Euclidian with increasing surfactant concentration. The morphological changes were characterized by a decrease in the average boundary fractal dimension which also correlated well with the corresponding reduction in aggregation rate.

  8. Linear relationship statistics in diffusion limited aggregation

    NASA Astrophysics Data System (ADS)

    Saberi, Abbas Ali

    2009-11-01

    We show that various surface parameters in two-dimensional diffusion limited aggregation (DLA) grow linearly with the number of particles. We find the ratio of the average length of the perimeter and the accessible perimeter of a DLA cluster together with its external perimeters to the cluster size, and define a microscopic schematic procedure for attachment of an incident new particle to the cluster. We measure the fractal dimension of the red sites (i.e., the sites such that cutting each of them splits the cluster) as equal to that of the DLA cluster. It is also shown that the average number of dead sites and the average number of red sites have linear relationships with the cluster size.

  9. Is it really possible to grow isotropic on-lattice diffusion-limited aggregates?

    NASA Astrophysics Data System (ADS)

    Alves, S. G.; Ferreira, S. C., Jr.

    2006-03-01

    In a recent paper (Bogoyavlenskiy V A 2002 J. Phys. A: Math. Gen. 35 2533), an algorithm aiming to generate isotropic clusters of the on-lattice diffusion-limited aggregation (DLA) model was proposed. The procedure consists of aggregation probabilities proportional to the squared number of occupied sites (k2). In the present work, we analysed this algorithm using the noise reduced version of the DLA model and large-scale simulations. In the noiseless limit, instead of isotropic patterns, a 45° (30°) rotation in the anisotropy directions of the clusters grown on square (triangular) lattices was observed. A generalized algorithm, in which the aggregation probability is proportional to kν, was proposed. The exponent ν has a nonuniversal critical value νc, for which the patterns generated in the noiseless limit exhibit the original (axial) anisotropy for ν < νc and the rotated one (diagonal) for ν > νc. The values νc = 1.395 ± 0.005 and νc = 0.82 ± 0.01 were found for square and triangular lattices, respectively. Moreover, large-scale simulations show that there is a nontrivial relation between the noise reduction and anisotropy direction. The case ν = 2 (Bogoyavlenskiy's rule) is an example where the patterns exhibit the axial anisotropy for small and the diagonal one for large noise reduction.

  10. 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.

  11. Flocculation of hematite with polyacrylic acid: Fractal structures in the reaction- and diffusion-limited aggregation regimes

    SciTech Connect

    Ferretti, R.; Zhang, J.; Buffle, J.

    1998-12-15

    The structure of hematite aggregates in the presence of fairly monodisperse polyacrylic acid (PAA) with two different molecular weights (M{sub w} = 1.36 {times} 10{sup 6}, M{sub w}/M{sub n} = 1.53; M{sub w} = 3.69 {times} 10{sup 4}, M{sub w}/M{sub n} = 1.60) was studied using static light scattering (SLS). The fractal dimensions were calculated from the scattering exponents, after taking into account the finite size of aggregates, using exponential and Gaussian cutoff functions. Three flocculation regimes, namely, pre-DLA, DLA (diffusion-limited aggregation), and post-DLA, were defined based on the polymer concentration. In the DLA regime, fractal dimension values, D{sub f} = 1.84 {+-} 0.02 and 1.73 {+-} 0.02, were obtained using exponential and Gaussian cutoff functions, respectively. A fractal dimension of approximately 2.0 was found, as expected, in the pre-DLA regime (at PAA concentrations lower than the optimal dosage for a DLA regime) where the flocculation rate was reaction limited. In contrast, in the post-DLA regime, the flocculation was slow but the structure of aggregates was as tenuous as in the DLA regime with a fractal dimension D{sub f} {approx} 1.8. Moreover, for all three regimes, the D{sub f} values were independent of the molecular weights of PAA. The lower fractal dimension in post-DLA was probably due to the increased concentration of polymer chains between adjacent particles in aggregates. The steric hindrance favored tip-to-tip aggregation, leading to a more tenuous structure.

  12. Evaluation of a DLA-79 allele associated with multiple immune-mediated diseases in dogs.

    PubMed

    Friedenberg, Steven G; Buhrman, Greg; Chdid, Lhoucine; Olby, Natasha J; Olivry, Thierry; Guillaumin, Julien; O'Toole, Theresa; Goggs, Robert; Kennedy, Lorna J; Rose, Robert B; Meurs, Kathryn M

    2016-03-01

    Immune-mediated diseases are common and life-threatening disorders in dogs. Many canine immune-mediated diseases have strong breed predispositions and are believed to be inherited. However, the genetic mutations that cause these diseases are mostly unknown. As many immune-mediated diseases in humans share polymorphisms among a common set of genes, we conducted a candidate gene study of 15 of these genes across four immune-mediated diseases (immune-mediated hemolytic anemia, immune-mediated thrombocytopenia, immune-mediated polyarthritis (IMPA), and atopic dermatitis) in 195 affected and 206 unaffected dogs to assess whether causative or predictive polymorphisms might exist in similar genes in dogs. We demonstrate a strong association (Fisher's exact p = 0.0004 for allelic association, p = 0.0035 for genotypic association) between two polymorphic positions (10 bp apart) in exon 2 of one allele in DLA-79, DLA-79*001:02, and multiple immune-mediated diseases. The frequency of this allele was significantly higher in dogs with immune-mediated disease than in control dogs (0.21 vs. 0.12) and ranged from 0.28 in dogs with IMPA to 0.15 in dogs with atopic dermatitis. This allele has two non-synonymous substitutions (compared with the reference allele, DLA-79*001:01), resulting in F33L and N37D amino acid changes. These mutations occur in the peptide-binding pocket of the protein, and based upon our computational modeling studies, are likely to affect critical interactions with the peptide N-terminus. Further studies are warranted to confirm these findings more broadly and to determine the specific mechanism by which the identified variants alter canine immune system function.

  13. Population balance modelling of particle flocculation with attention to aggregate restructuring and permeability.

    PubMed

    Jeldres, Ricardo I; Concha, Fernando; Toledo, Pedro G

    2015-10-01

    A population balance model based on a detailed literature review is used to describe coagulation and flocculation kinetics as well as the time evolution of aggregate size distribution in a turbulent shear flow simultaneously with the breakage and restructuring of aggregates. The fractal nature and permeability of the aggregates and their evolution with time are also part of the model. Restructuring is absent in coagulation with soluble salts, but is present in flocculation caused by large polyelectrolyte molecules; in the latter, aggregates never reach a steady-state size, but a size that decreases gradually through particle and polymer rearrangement. The model is tested against available experimental data for monodisperse polystyrene particles coagulated with hydrated aluminium sulphate at different shear rates, and precipitated calcium carbonate flocculated with a cationic polyelectrolyte of very high molecular weight at different flocculant dosages. The numerical solution of the model requires adjusting three parameters, i.e, maximum collision efficiency (αmax), critical force needed for the breakage of the aggregates (B) and rate of aggregate restructuring (γ), which are obtained from minimising the difference between experimental data and model predictions. The model studied for the two very different systems shows excellent agreement with experimental flocculation kinetics and a reasonably good fit for aggregate size distributions. The model is most sensitive to the fragmentation rate through parameter B, somewhat less to the collision efficiency through parameter αmax and little to γ. When the aggregates undergo restructuring, properties such as permeability, breakage rate and collision rate change considerably over time. When the aggregates are permeable, the collision frequency is significantly smaller than when they are impervious. PMID:26253811

  14. 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. PMID:21097152

  15. NUMERICAL MODELING OF THE COAGULATION AND POROSITY EVOLUTION OF DUST AGGREGATES

    SciTech Connect

    Okuzumi, Satoshi; Sakagami, Masa-aki; Tanaka, Hidekazu

    2009-12-20

    Porosity evolution of dust aggregates is crucial in understanding dust evolution in protoplanetary disks. In this study, we present useful tools to study the coagulation and porosity evolution of dust aggregates. First, we present a new numerical method for simulating dust coagulation and porosity evolution as an extension of the conventional Smoluchowski equation. This method follows the evolution of the mean porosity for each aggregate mass simultaneously with the evolution of the mass distribution function. This method reproduces the results of previous Monte Carlo simulations with much less computational expense. Second, we propose a new collision model for porous dust aggregates on the basis of our N-body experiments on aggregate collisions. As the first step, we focus on 'hit-and-stick' collisions, which involve neither compression nor fragmentation of aggregates. We first obtain empirical data on porosity changes between the classical limits of ballistic cluster-cluster and particle-cluster aggregation. Using the data, we construct a recipe for the porosity change due to general hit-and-stick collisions as well as formulae for the aerodynamical and collisional cross sections. Our collision model is thus more realistic than a previous model of Ormel et al. based on the classical aggregation limits only. Simple coagulation simulations using the extended Smoluchowski method show that our collision model explains the fractal dimensions of porous aggregates observed in a full N-body simulation and a laboratory experiment. By contrast, similar simulations using the collision model of Ormel et al. result in much less porous aggregates, meaning that this model underestimates the porosity increase upon unequal-sized collisions. Besides, we discover that aggregates at the high-mass end of the distribution can have a considerably small aerodynamical cross section per unit mass compared with aggregates of lower masses. This occurs when aggregates drift under uniform

  16. Numerical Modeling of the Coagulation and Porosity Evolution of Dust Aggregates

    NASA Astrophysics Data System (ADS)

    Okuzumi, Satoshi; Tanaka, Hidekazu; Sakagami, Masa-aki

    2009-12-01

    Porosity evolution of dust aggregates is crucial in understanding dust evolution in protoplanetary disks. In this study, we present useful tools to study the coagulation and porosity evolution of dust aggregates. First, we present a new numerical method for simulating dust coagulation and porosity evolution as an extension of the conventional Smoluchowski equation. This method follows the evolution of the mean porosity for each aggregate mass simultaneously with the evolution of the mass distribution function. This method reproduces the results of previous Monte Carlo simulations with much less computational expense. Second, we propose a new collision model for porous dust aggregates on the basis of our N-body experiments on aggregate collisions. As the first step, we focus on "hit-and-stick" collisions, which involve neither compression nor fragmentation of aggregates. We first obtain empirical data on porosity changes between the classical limits of ballistic cluster-cluster and particle-cluster aggregation. Using the data, we construct a recipe for the porosity change due to general hit-and-stick collisions as well as formulae for the aerodynamical and collisional cross sections. Our collision model is thus more realistic than a previous model of Ormel et al. based on the classical aggregation limits only. Simple coagulation simulations using the extended Smoluchowski method show that our collision model explains the fractal dimensions of porous aggregates observed in a full N-body simulation and a laboratory experiment. By contrast, similar simulations using the collision model of Ormel et al. result in much less porous aggregates, meaning that this model underestimates the porosity increase upon unequal-sized collisions. Besides, we discover that aggregates at the high-mass end of the distribution can have a considerably small aerodynamical cross section per unit mass compared with aggregates of lower masses. This occurs when aggregates drift under uniform

  17. 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.

  18. 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 ...

  19. A qualitative model for aggregation and diffusion of β-amyloid in Alzheimer's disease.

    PubMed

    Achdou, Yves; Franchi, Bruno; Marcello, Norina; Tesi, Maria Carla

    2013-12-01

    In this paper we present a mathematical model for the aggregation and diffusion of Aβ amyloid in the brain affected by Alzheimer's disease, at the early stage of the disease. The model is based on a classical discrete Smoluchowski aggregation equation modified to take diffusion into account. We also describe a numerical scheme and discuss the results of the simulations in the light of the recent biomedical literature.

  20. Ganoderma lucidum total triterpenes attenuate DLA induced ascites and EAC induced solid tumours in Swiss albino mice.

    PubMed

    Smina, T P; Mathew, J; Janardhanan, K K

    2016-01-01

    G. lucidum total triterpenes were assessed for its apoptosis-inducing and anti-tumour activities. The ability of the total triterpenes to induce apoptosis was evaluated in Dalton's lymphoma ascites (DLA) and Ehrlich's ascites carcinoma (EAC) cell lines. Total triterpenes were found to be highly cytotoxic to DLA and EAC cell lines with IC50 values 5 ± 0.32 and 7.9 ± 0.2 µg/ml respectively. Total triterpenes induced apoptosis in both cell lines which is evident from the DNA fragmentation assay. Anti-tumour activity was accessed using DLA induced solid and EAC induced ascites tumour models in Swiss albino mice. Administration of 10, 50 and 100 mg/kg b. wt. total triterpenes showed 11.86, 27.27 and 40.57% increase in life span of animals in ascites tumour model. Treatment with 10, 50 and 100 mg/kg b. wt. total triterpenes exhibited 76.86, 85.01 and 91.03% inhibition in tumour volume and 67.96, 72.38 and 77.90% inhibition in tumour weight respectively in the solid tumour model. The study reveals the significant dose-dependent anti-tumour activity of total triterpenes in both models. Total triterpenes were more active against the solid tumour than the ascites tumour. The anti-oxidant potential and ability to induce cell-specific apoptosis could be contributing to its anti-tumour activities. PMID:27188870

  1. Simple off-lattice model to study the folding and aggregation of peptides

    NASA Astrophysics Data System (ADS)

    Combe, Nicolas; Frenkel, Daan

    We present a numerical study of a new protein model. This off-lattice model takes into account both the hydrogen bonds and the amino-acid interactions. It reproduces the folding of a small protein (peptide): morphological analysis of the conformations at low temperature shows two well-known substructures α-helix and β-sheet depending on the chosen sequence. The folding pathway in the scope of this model is studied through a free-energy analysis. We then study the aggregation of proteins. Proteins in the aggregate are mainly bound via hydrogen bonds. Performing a free-energy analysis we show that the addition of a peptide to such an aggregate is not favourable. We qualitatively reproduce the abnormal aggregation of proteins in prion diseases.

  2. Random aggregation models for the formation and evolution of coding and non-coding DNA

    NASA Astrophysics Data System (ADS)

    Provata, A.

    A random aggregation model with influx is proposed for the formation of the non-coding DNA regions via random co-aggregation and influx of biological macromolecules such as viruses, parasite DNA, and replication segments. The constant mixing (transpositions) and influx drives the system in an out-of-equilibrium steady state characterised by a power law size distribution. The model predicts the long range distributions found in the noncoding eucaryotic DNA and explains the observed correlations. For the formation of coding DNA a random closed aggregation model is proposed which predicts short range coding size distributions. The closed aggregation process drives the system in an almost “frozen” stable state which is robust to external perturbations and which is characterised by well defined space and time scales, as observed in coding sequences.

  3. 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.

  4. 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.

  5. 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.

  6. 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).

  7. Aggregated α-Synuclein Increases SOD1 Oligomerization in a Mouse Model of Amyotrophic Lateral Sclerosis.

    PubMed

    Koch, Yvonne; Helferich, Anika M; Steinacker, Petra; Oeckl, Patrick; Walther, Paul; Weishaupt, Jochen H; Danzer, Karin M; Otto, Markus

    2016-08-01

    Aggregation of misfolded disease-related proteins is a hallmark of neurodegenerative diseases. Aggregate propagation accompanying disease progression has been demonstrated for different proteins (eg, for α-synuclein). Additional evidence supports aggregate cross-seeding activity for α-synuclein. For mutated superoxide dismutase 1 (SOD1), which causes familial amyotrophic lateral sclerosis (ALS), self-propagation of aggregation and cell-to-cell transmission have been demonstrated in vitro. However, there is a prominent lack of in vivo data concerning aggregation and cross-aggregation processes of SOD1. We analyzed the effect of α-synuclein and SOD1 seeds in cell culture using protein fragment complementation assay and intracerebral injection of α-synuclein and SOD1 seeds into SOD1(G93A) transgenic ALS mice. Survival of injected mice was determined, and SOD1 aggregates in the facial nuclei were quantified during disease course. We found that α-synuclein preformed fibrils increased the oligomerization rate of SOD1 in vivo and in vitro, whereas aggregated SOD1 did not exert any effect in both experimental setups. Notably, survival of ALS mice was not changed after inoculation of preformed fibrils. We conclude that misfolded α-synuclein can increase SOD1 aggregation and suppose that α-synuclein seeds are transported from the temporal cortex to the facial nuclei. However, unlike other proteins, the further enhancement of a self-aggregation process by additional SOD1 could not be confirmed in our models.

  8. 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.

  9. 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.

  10. Impact of climate aggregation over different scales on regional NPP modelling

    NASA Astrophysics Data System (ADS)

    Kuhnert, Matthias

    2016-04-01

    Model input data aggregation methods and data aggregation across spatial scales affect various model outputs, e.g. Net Primary Productivity (NPP). The scale at which data is collected is of great importance. In ecosystem modelling studies we often see soil and climate data collected at coarse scale being used in models to predict ecosystem responses e.g. NPP in dependency of these parameters at finer scale. Outputs of these models are impacted by the way the data is aggregated or dis-aggregated to the spatial scale. Up to know there are very few studies which quantified the impact of scaling on the simulation results. In this study, we quantify the impact of climate data aggregation using five different resolutions, to simulate NPP by 11 different crop and biogeochemical models for the same study area. The aggregation effect is investigated for wheat and maize cropping systems in the state of North Rhine-Westphalia, Germany. The simulation results are analysed for NPP averaged over growing seasons of a 30 year period at different spatial resolutions as well as for annual NPP during growing season. While there is only a minor impact of input data aggregation on NPP on 30 year averages, the annual data show differences in NPP up to 9.4 % and 13.6 % between the different resolutions for wheat and maize, respectively. The scale effect differ between the models and shows higher impacts for extreme years. This is tested by selecting years with extreme dry conditions based on a drought index, which showed stronger scale effects of up to 12.8 % and 15.5 % for wheat and maize, respectively.

  11. Morphological transition between diffusion-limited and ballistic aggregation growth patterns.

    PubMed

    Ferreira, S C; Alves, S G; Brito, A Faissal; Moreira, J G

    2005-05-01

    In this work, the transition between diffusion-limited (DLA) and ballistic aggregation (BA) models was reconsidered using a model in which biased random walks simulate the particle trajectories. The bias is controlled by a parameter lambda, which assumes the value lambda=0 (1) for the ballistic (diffusion-limited) aggregation model. Patterns growing from a single seed were considered. In order to simulate large clusters, an efficient algorithm was developed. For lambda (not equal to) 0 , the patterns are fractal on small length scales, but homogeneous on large ones. We evaluated the mean density of particles (-)rho in the region defined by a circle of radius r centered at the initial seed. As a function of r, (-)rho reaches the asymptotic value rho(0)(lambda) following a power law (-)rho = rho(0) +Ar(-gamma) with a universal exponent gamma=0.46 (2) , independent of lambda . The asymptotic value has the behavior rho(0) approximately |1-lambda|(beta) , where beta=0.26 (1) . The characteristic crossover length that determines the transition from DLA- to BA-like scaling regimes is given by xi approximately |1-lambda|(-nu) , where nu=0.61 (1) , while the cluster mass at the crossover follows a power law M(xi) approximately |1-lambda(-alpha) , where alpha=0.97 (2) . We deduce the scaling relations beta=nugamma and beta=2nu-alpha between these exponents. PMID:16089530

  12. On a Competitive Model of Laplacian Growth

    NASA Astrophysics Data System (ADS)

    Loutsenko, Igor; Yermolayeva, Oksana; Zinsmeister, Michel

    2011-11-01

    We introduce a competitive model of Laplacian growth in both stochastic and deterministic versions. This defines two different aggregation laws with probabilities λ and 1- λ. The parameter λ varying from 0 to 1 is used to weight a ratio between the inner and outer harmonic measures that leads to a competition between the Eden-like process and the DLA solved with site-sticking conditions. We perform numerical and qualitative analysis of the competitive growth.

  13. Stationary growth and unique invariant harmonic measure of cylindrical diffusion limited aggregation.

    PubMed

    Marchetti, Riccardo; Taloni, Alessandro; Caglioti, Emanuele; Loreto, Vittorio; Pietronero, Luciano

    2012-08-10

    We prove that the harmonic measure is stationary, unique, and invariant on the interface of diffusion limited aggregation (DLA) growing on a cylinder surface. We provide a detailed theoretical analysis puzzling together multiscaling, multifractality, and conformal invariance, supported by extensive numerical simulations of clusters built using conformal mappings and on a lattice. The growth properties of the active and frozen zones are clearly elucidated. We show that the unique scaling exponent characterizing the stationary growth is the DLA fractal dimension. PMID:23006279

  14. Stationary Growth and Unique Invariant Harmonic Measure of Cylindrical Diffusion Limited Aggregation

    NASA Astrophysics Data System (ADS)

    Marchetti, Riccardo; Taloni, Alessandro; Caglioti, Emanuele; Loreto, Vittorio; Pietronero, Luciano

    2012-08-01

    We prove that the harmonic measure is stationary, unique, and invariant on the interface of diffusion limited aggregation (DLA) growing on a cylinder surface. We provide a detailed theoretical analysis puzzling together multiscaling, multifractality, and conformal invariance, supported by extensive numerical simulations of clusters built using conformal mappings and on a lattice. The growth properties of the active and frozen zones are clearly elucidated. We show that the unique scaling exponent characterizing the stationary growth is the DLA fractal dimension.

  15. A desolvation model for trifluoroethanol-induced aggregation of enhanced green fluorescent protein.

    PubMed

    Anderson, Valerie L; Webb, Watt W

    2012-02-22

    Studies of amyloid disease-associated proteins in aqueous solutions containing 2,2,2-trifluoroethanol (TFE) have shown that the formation of structural intermediates is often correlated with enhanced protein aggregation. Here, enhanced green fluorescent protein (EGFP) is used as a model protein system to investigate the causal relationship between TFE-induced structural transitions and aggregation. Using circular dichroism spectroscopy, light scattering measurements, and transmission electron microscopy imaging, we demonstrate that population of a partially α-helical, monomeric intermediate is roughly correlated with the growth of β-sheet-rich, flexible fibrils for acid-denatured EGFP. By fitting our circular dichroism data to a model in which TFE-water mixtures are assumed to be ideal solutions, we show that increasing entropic costs of protein solvation in TFE-water mixtures may both cause the population of the intermediate state and increase aggregate production. Tertiary structure and electrostatic repulsion also impede aggregation. We conclude that initiation of EGFP aggregation in TFE likely involves overcoming of multiple protective factors, rather than stabilization of aggregation-prone structural elements.

  16. Percolation model for growth rates of aggregates and its application for business firm growth

    NASA Astrophysics Data System (ADS)

    Fu, Dongfeng; Buldyrev, Sergey V.; Salinger, Michael A.; Stanley, H. Eugene

    2006-09-01

    Motivated by recent empirical studies of business firm growth, we develop a dynamic percolation model which captures some of the features of the economical system—i.e., merging and splitting of business firms—represented as aggregates on a d -dimensional lattice. We find the steady-state distribution of the aggregate size and explore how this distribution depends on the model parameters. We find that at the critical threshold, the standard deviation of the aggregate growth rates, σ , increases with aggregate size S as σ˜Sβ , where β can be explained in terms of the connectedness length exponent ν and the fractal dimension df , with β=1/(2νdf)≈0.20 for d=2 and 0.125 for d→∞ . The distributions of aggregate growth rates have a sharp peak at the center and pronounced wings extending over many standard deviations, giving the distribution a tent-shape form—the Laplace distribution. The distributions for different aggregate sizes scaled by their standard deviations collapse onto the same curve.

  17. 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.

  18. The implication of input data aggregation on upscaling of soil organic carbon changes - a case study with CENTURY model

    NASA Astrophysics Data System (ADS)

    Grosz, Balázs; Dechow, Rene; Ewert, Frank; Gaiser, Thomas; Hoffmann, Holger; Zhao, Gang

    2015-04-01

    Soil organic carbon models which have been extensively tested and calibrated for field scale applications in the past are now increasingly used for larger scale estimations. In large scale applications, recent data availability and limited computational capacity requires adequate aggregation of the model input and model initialization. Method and level of driver aggregation in up scaling studies are sources of uncertainty and might bias the aggregated model outcome. The suitability of up scaled model results using aggregated driving data depends on both the sensitivity of the model on these model drivers and the scale of interest describing the desired aggregation level of the model output. The implications of driver aggregation schemes have been examined in a scaling exercise within the joint research project MACSUR (Modelling European Agriculture with Climate Change for Food Security). In this study, meteorological driving data and data on soil properties on several aggregation levels have been used to calculate the soil organic carbon change of agricultural land use in North Rhine-Westphalia with the bio-geo-chemical model CENTURY. The model couples processes determining crop growth, soil organic matter and nutrient dynamics. In the aggregation study meteorological data and soil properties from a NUTS 2 region in Germany (North Rhine-Westphalia) from 1980 to 2010 were prepared on 6 aggregation levels corresponding to grid cells in 1x1km, 10x10km, 25x25km, 50x50km, 100x100km resolution and spatial means on federate state level. Upscaling exercises have been conducted by combining several aggregation levels of soil properties and weather data. Results show that the aggregation of meteorological data has little impact on modeled soil organic carbon changes although model uncertainty increases slightly with decreasing scale of interest from NUTS 2 (federal state) level to smaller grid cell size. Contrary, the aggregation of soil properties result in high uncertainty

  19. 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.

  20. Determination of critical nucleation number for a single nucleation amyloid-β aggregation model

    PubMed Central

    Ghosh, Preetam; Vaidya, Ashwin; Kumar, Amit; Rangachari, Vijayaraghavan

    2016-01-01

    Aggregates of amyloid-β (Aβ) peptide are known to be the key pathological agents in Alzheimer disease (AD). Aβ aggregates to form large, insoluble fibrils that deposit as senile plaques in AD brains. The process of aggregation is nucleation–dependent in which the formation of a nucleus is the rate–limiting step, and controls the physiochemical fate of the aggregates formed. Therefore, understanding the properties of nucleus and pre-nucleation events will be significant in reducing the existing knowledge–gap in AD pathogenesis. In this report, we have determined the plausible range of critical nucleation number (n*), the number of monomers associated within the nucleus for a homogenous aggregation model with single unique nucleation event, by two independent methods: A reduced-order stability analysis and ordinary differential equation based numerical analysis, supported by experimental biophysics. The results establish that the most likely range of n* is between 7 and 14 and within, this range, n* = 12 closely supports the experimental data. These numbers are in agreement with those previously reported, and importantly, the report establishes a new modeling framework using two independent approaches towards a convergent solution in modeling complex aggregation reactions. Our model also suggests that the formation of large protofibrils is dependent on the nature of n*, further supporting the idea that pre-nucleation events are significant in controlling the fate of larger aggregates formed. This report has re-opened an old problem with a new perspective and holds promise towards revealing the molecular events in amyloid pathologies in the future. PMID:26774039

  1. Induced growth of dendrite gold nanostructure by controlling self-assembly aggregation dynamics.

    PubMed

    Abdellatif, M H; Abdelrasoul, G N; Scarpellini, A; Marras, S; Diaspro, A

    2015-11-15

    Self-assembly of gold nanoparticles (AuNPs) is an important growth mode for fabricating functional materials. In this work we report a dendrite structure formed by slowing down the aggregation dynamics of AuNPs self-assembly. The obtained results show that the aggregation dynamics is dominated by the Reaction Limited Aggregation Model (RLA) more than the Diffusion Limited Aggregation Model (DLA). In which the repulsion due to electrostatic forces is dominant by the Van Der Walls attraction forces, and low sticking probability of nanoparticles. The aggregation dynamics of AuNPs can be slowed down if the water evaporation of the drop casted colloidal AuNPs on a quartz substrate is slowed. Slowing down the evaporation allows electrostatic repulsion forces to decrease gradually. At certain point, the attraction forces become higher than the electrostatic repulsion and hence cluster aggregation take place slowly. The slow aggregation dynamics allows the nanoparticles to sample all possible orientation in the sticking site, searching for the lowest energy configuration. The size distribution of the nanoparticles in liquid is confirmed using dynamic light scattering based on Stokes-Einstein equation for diffusion coefficient in water. X-ray and photoluminescence (PL) spectra of the sample after aggregation showed a shift which is related to the aggregation compared with non-aggregated colloidal nanoparticles in the solution. The study shows that dendrite self similar structure can be formed by slowing down the aggregation dynamics of nanoparticles as a result of minimizing the Helmholtz free surface energy of the system. PMID:26233557

  2. 32 CFR Appendix A to Part 1285 - Gaining Access to DLA Records

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    .... DLA Systems Automation Center, Attn: DSAC-E, P.O. Box 1605, Columbus, OH 43216-5002. DLA... Center, Attn: DCSC-WXA, 3990 E. Broad Street, Columbus, OH 43216-5000. Defense Electronics Supply Center, Attn: DESC-WXA, 1507 Wilmington Pike, Dayton, OH 45444-5252. Defense Fuel Supply Center, Attn:...

  3. Predictive model for diffusion-limited aggregation kinetics of nanocolloids under high concentration.

    PubMed

    Lattuada, Marco

    2012-01-12

    Smoluchowski's equation for the rate of aggregation of colloidal particles under diffusion-limited conditions has set the basis for the interpretation of kinetics of aggregation phenomena. Nevertheless, its use is limited to sufficiently dilute conditions. In this work we propose a correction to Smoluchowski's equation by using a result derived by Richards ( J. Phys. Chem. 1986 , 85 , 3520 ) within the framework of trapping theory. This corrected aggregation kernel, which accounts for concentration dependence effects, has been implemented in a population-balance equations scheme and used to model the aggregation kinetics of colloidal particles undergoing diffusion-limited aggregation under concentrated conditions (up to a particle volume fraction of 30%). The predictions of population balance calculations have been validated by means of Brownian dynamic simulations. It was found that the corrected kernel can very well reproduce the results from Brownian dynamic simulations for all concentration values investigated, and is also able to accurately predict the time required by a suspension to reach the gel point. On the other hand, classical Smoluchowski's theory substantially underpredicts the rate of aggregation as well as the onset of gelation, with deviations becoming progressively more severe as the particle volume fraction increases. PMID:22148884

  4. 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...

  5. 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.

  6. A Colloidal Description of Intermolecular Interactions Driving Fibril-Fibril Aggregation of a Model Amphiphilic Peptide.

    PubMed

    Owczarz, Marta; Motta, Anna C; Morbidelli, Massimo; Arosio, Paolo

    2015-07-14

    We apply a kinetic analysis platform to study the intermolecular interactions underlying the colloidal stability of dispersions of charged amyloid fibrils consisting of a model amphiphilic peptide (RADA 16-I). In contrast to the aggregation mechanisms observed in the large majority of proteins and peptides, where several elementary reactions involving both monomers and fibrils are present simultaneously, the system selected in this work allows the specific investigation of the fibril-fibril aggregation process. We examine the intermolecular interactions driving the aggregation reaction at pH 2.0 by changing the buffer composition in terms of salt concentration, type of ion as well as type and concentration of organic solvent. The aggregation kinetics are followed by dynamic light scattering, and the experimental data are simulated by Smoluchowski population balance equations, which allow to estimate the energy barrier between two colliding fibrils in terms of the Fuchs stability ratio (W). When normalized on a dimensionless time weighted on the Fuchs stability ratio, the aggregation profiles under a broad range of conditions collapse on a single master curve, indicating that the buffer composition modifies the aggregation kinetics without affecting the aggregation mechanism. Our results show that the aggregation process does not occur under diffusion-limited conditions. Rather, the reaction rate is limited by the presence of an activation energy barrier that is largely dominated by electrostatic repulsive interactions. Such interactions could be reduced by increasing the concentration of salt, which induces charge screening, or the concentration of organic solvent, which affects the dielectric constant. It is remarkable that the dependence of the activation energy on the ionic strength can be described quantitatively in terms of charge screening effects in the frame of the DLVO theory, although specific anion and cation effects are also observed. While anion

  7. Small molecules preventing GAPDH aggregation are therapeutically applicable in cell and rat models of oxidative stress.

    PubMed

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

    2016-03-01

    Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is one of the most abundant targets of the oxidative stress. Oxidation of the enzyme causes its inactivation and the formation of intermolecular disulfide bonds, and leads to the accumulation of GAPDH aggregates and ultimately to cell death. The aim of this work was to reveal the ability of chemicals to break the described above pathologic linkage by inhibiting GAPDH aggregation. Using the model of oxidative stress based on SK-N-SH human neuroblastoma cells treated with hydrogen peroxide, we found that lentivirus-mediated down- or up-regulation of GAPDH content caused inhibition or enhancement of the protein aggregation and respectively reduced or increased the level of cell death. To reveal substances that are able to inhibit GAPDH aggregation, we developed a special assay based on dot ultrafiltration using the collection of small molecules of plant origin. In the first round of screening, five compounds were found to possess anti-aggregation activity as established by ultrafiltration and dynamic light scattering; some of the substances efficiently inhibited GAPDH aggregation in nanomolar concentrations. The ability of the compounds to bind GAPDH molecules was proved by the drug affinity responsive target stability assay, molecular docking and differential scanning calorimetry. Results of experiments with SK-N-SH human neuroblastoma treated with hydrogen peroxide show that two substances, RX409 and RX426, lowered the degree of GAPDH aggregation and reduced cell death by 30%. Oxidative injury was emulated in vivo by injecting of malonic acid into the rat brain, and we showed that the treatment with RX409 or RX426 inhibited GAPDH-mediated aggregation in the brain, reduced areas of the injury as proved by magnetic resonance imaging, and augmented the behavioral status of the rats as established by the "beam walking" test. In conclusion, the data show that two GAPDH binders could be therapeutically relevant in the

  8. Physical mechanisms controlling the initiation of convective self-aggregation in a General Circulation Model

    NASA Astrophysics Data System (ADS)

    Coppin, David; Bony, Sandrine

    2015-12-01

    Cloud-resolving models have shown that under certain conditions, the Radiative-Convective Equilibrium (RCE) could become unstable and lead to the spontaneous organization of the atmosphere into dry and wet areas, and the aggregation of convection. In this study, we show that this "self-aggregation" behavior also occurs in nonrotating RCE simulations performed with the IPSL-CM5A-LR General Circulation Model (GCM), and that it exhibits a strong dependence on sea surface temperature (SST). We investigate the physical mechanisms that control the initiation of self-aggregation in this model, and their dependence on temperature. At low SSTs, the onset of self-aggregation is primarily controlled by the coupling between low-cloud radiative effects and shallow circulations and the formation of "radiatively driven cold pools" in areas devoid of deep convection, while at high SSTs it is primarily controlled by the coupling between surface fluxes and circulation within convective areas. At intermediate temperatures, the occurrence of self-aggregation is less spontaneous and depends on initial conditions, but it can arise through a combination of both mechanisms. Through their coupling to circulation and surface fluxes, the radiative effects of low-level clouds play a critical role in both initiation mechanisms, and the sensitivity of boundary layer clouds to surface temperature explains to a large extent the temperature dependence of convective self-aggregation. At any SST, the presence of cloud-radiative effects in the free troposphere is necessary to the initiation, growth, and maintenance of convective aggregation.

  9. 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

  10. 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.

  11. Modeling fusion of cellular aggregates in biofabrication using phase field theories.

    PubMed

    Yang, Xiaofeng; Mironov, Vladimir; Wang, Qi

    2012-06-21

    A mathematical model based on the phase field formulation is developed to study fusion of cellular aggregates/clusters. In a novel biofabrication process known as bioprinting (Mironov et al., 2009a), live multicellular aggregates/clusters are used to make tissue or organ constructs via the layer-by-layer deposition technique, in which the printed bio-constructs are embedded in hydrogels rich in maturogens and placed in bioreactors to undergo the fusion process of self-assembly, maturation, and differentiation to form the desired functional tissue or organ products. We formulate the mathematical model to study the morphological development of the printed bio-constructs during fusion by exploring the chemical-mechanical interaction among the cellular aggregates involved. Specifically, we treat the cellular aggregates and the surrounding hydrogels as two immiscible complex fluids in the time scale comparable to cellular aggregate fusion and then develop an effective mean-field potential that incorporates the long-range, attractive interaction between cells as well as the short-range, repulsive interaction due to immiscibility between the cell and the hydrogel. We then implement the model using a high order spectral method to simulate the making of a set of tissues/organs in simple yet fundamental geometries like a ring, a sheet of tissues, and a Y-shaped, bifurcating vascular junction by the layer-by-layer deposition of spheroidal cellular clusters in the bioprinting technology.

  12. Molecular mechanisms of protein aggregation from global fitting of kinetic models.

    PubMed

    Meisl, Georg; Kirkegaard, Julius B; Arosio, Paolo; Michaels, Thomas C T; Vendruscolo, Michele; Dobson, Christopher M; Linse, Sara; Knowles, Tuomas P J

    2016-02-01

    The elucidation of the molecular mechanisms by which soluble proteins convert into their amyloid forms is a fundamental prerequisite for understanding and controlling disorders that are linked to protein aggregation, such as Alzheimer's and Parkinson's diseases. However, because of the complexity associated with aggregation reaction networks, the analysis of kinetic data of protein aggregation to obtain the underlying mechanisms represents a complex task. Here we describe a framework, using quantitative kinetic assays and global fitting, to determine and to verify a molecular mechanism for aggregation reactions that is compatible with experimental kinetic data. We implement this approach in a web-based software, AmyloFit. Our procedure starts from the results of kinetic experiments that measure the concentration of aggregate mass as a function of time. We illustrate the approach with results from the aggregation of the β-amyloid (Aβ) peptides measured using thioflavin T, but the method is suitable for data from any similar kinetic experiment measuring the accumulation of aggregate mass as a function of time; the input data are in the form of a tab-separated text file. We also outline general experimental strategies and practical considerations for obtaining kinetic data of sufficient quality to draw detailed mechanistic conclusions, and the procedure starts with instructions for extensive data quality control. For the core part of the analysis, we provide an online platform (http://www.amylofit.ch.cam.ac.uk) that enables robust global analysis of kinetic data without the need for extensive programming or detailed mathematical knowledge. The software automates repetitive tasks and guides users through the key steps of kinetic analysis: determination of constraints to be placed on the aggregation mechanism based on the concentration dependence of the aggregation reaction, choosing from several fundamental models describing assembly into linear aggregates and

  13. alpha-Synuclein fission yeast model: concentration-dependent aggregation without plasma membrane localization or toxicity.

    PubMed

    Brandis, Katrina A; Holmes, Isaac F; England, Samantha J; Sharma, Nijee; Kukreja, Lokesh; DebBurman, Shubhik K

    2006-01-01

    Despite fission yeast's history of modeling salient cellular processes, it has not yet been used to model human neurodegeneration-linked protein misfolding. Because alpha-synuclein misfolding and aggregation are linked to Parkinson's disease (PD), here, we report a fission yeast (Schizosaccharomyces pombe) model that evaluates alpha-synuclein misfolding, aggregation, and toxicity and compare these properties with those recently characterized in budding yeast (Saccharomyces cerevisiae). Wild-type alpha-synuclein and three mutants (A30P, A53T, and A30P/A53T) were expressed with thiamine-repressible promoters (using vectors of increasing promoter strength: pNMT81, pNMT41, and pNMT1) to test directly in living cells the nucleation polymerization hypothesis for alpha-synuclein misfolding and aggregation. In support of the hypothesis, wild-type and A53T alpha-synuclein formed prominent intracellular cytoplasmic inclusions within fission yeast cells in a concentration- and time-dependent manner, whereas A30P and A30P/A53T remained diffuse throughout the cytoplasm. A53T alpha-synuclein formed aggregates faster than wild-type alpha-synuclein and at a lower alpha-synuclein concentration. Unexpectedly, unlike in budding yeast, wild-type and A53T alpha-synuclein did not target to the plasma membrane in fission yeast, not even at low alpha-synuclein concentrations or as a precursor step to forming aggregates. Despite alpha-synuclein's extensive aggregation, it was surprisingly nontoxic to fission yeast. Future genetic dissection might yield molecular insight into this protection against toxicity. We speculate that alpha-synuclein toxicity might be linked to its membrane binding capacity. To conclude, S. pombe and S. cerevisiae model similar yet distinct aspects of alpha-synuclein biology, and both organisms shed insight into alpha-synuclein's role in PD pathogenesis.

  14. Modeling the influence of aggregation on nanoparticle transport and retention in porous media

    NASA Astrophysics Data System (ADS)

    Taghavy, A.; Pennell, K. D.; Abriola, L. M.

    2012-12-01

    A number of experimental studies relating to nanoparticle transport have observed the influence of particle-particle interactions (i.e., aggregation) on particle-soil grain interactions (i.e., deposition) in porous media. To date, however, nanoparticle transport models have neglected such particle-particle interactions. Here, a one-dimensional Lagrangian particle transport simulator is presented which couples particle transport and retention in porous media with particle-particle interactions. A random-walk particle-tracking approach is employed to simulate the transport of nanoparticles, with Smoluchowski's second-order expression for perikinetic aggregation incorporated to represent particle-particle interactions. Aggregates are treated as fractal objects to relate cluster mass to size, and a correlation developed by Tufenkji and Elimelech (2004) for single collector contact efficiency is implemented to describe time-dependent transport behavior of growing aggregates. A maximum collector capacity-based extension of colloid filtration theory was coupled with the particle straining of Bradford et al. (2003) to describe the retention of particles in the porous medium. The developed simulator is implemented in a sensitivity study to identify the most important physicochemical factors that influence aggregation and deposition of silver nanoparticles under steady flow conditions in uniform sands. Under reaction-limited conditions (i.e. an aggregation attachment efficiency of less than 1), for aggregation of particles with a primary diameter of 12nm, particle mobility (i.e. the percent elution of particles) increased with aggregation in a ca. 15 cm sand column due to a reduction in the magnitude of Brownian forces. For a substantially longer travel distance (i.e. field scale problems) or at a slower flow velocity (i.e. typical groundwater velocities), however, aggregates may become large enough for the interception, sedimentation, and/or straining processes to dominate

  15. Diffusion-limited aggregates grown on nonuniform substrates

    NASA Astrophysics Data System (ADS)

    Cornette, V.; Centres, P. M.; Ramirez-Pastor, A. J.; Nieto, F.

    2013-12-01

    In the present paper, patterns of diffusion-limited aggregation (DLA) grown on nonuniform substrates are investigated by means of Monte Carlo simulations. We consider a nonuniform substrate as the largest percolation cluster of dropped particles with different structures and forms that occupy more than a single site on the lattice. The aggregates are grown on such clusters, in the range the concentration, p, from the percolation threshold, pc up to the jamming coverage, pj. At the percolation threshold, the aggregates are asymmetrical and the branches are relatively few. However, for larger values of p, the patterns change gradually to a pure DLA. Tiny qualitative differences in this behavior are observed for different k sizes. Correspondingly, the fractal dimension of the aggregates increases as p raises in the same range pc≤p≤pj. This behavior is analyzed and discussed in the framework of the existing theoretical approaches.

  16. A conceptual model for milling formations in biological aggregates.

    PubMed

    Lukeman, Ryan; Li, Yue-Xian; Edelstein-Keshet, Leah

    2009-02-01

    Collective behavior of swarms and flocks has been studied from several perspectives, including continuous (Eulerian) and individual-based (Lagrangian) models. Here, we use the latter approach to examine a minimal model for the formation and maintenance of group structure, with specific emphasis on a simple milling pattern in which particles follow one another around a closed circular path.We explore how rules and interactions at the level of the individuals lead to this pattern at the level of the group. In contrast to many studies based on simulation results, our model is sufficiently simple that we can obtain analytical predictions. We consider a Newtonian framework with distance-dependent pairwise interaction-force. Unlike some other studies, our mill formations do not depend on domain boundaries, nor on centrally attracting force-fields or rotor chemotaxis.By focusing on a simple geometry and simple distant-dependent interactions, we characterize mill formations and derive existence conditions in terms of model parameters. An eigenvalue equation specifies stability regions based on properties of the interaction function. We explore this equation numerically, and validate the stability conclusions via simulation, showing distinct behavior inside, outside, and on the boundary of stability regions. Moving mill formations are then investigated, showing the effect of individual autonomous self-propulsion on group-level motion. The simplified framework allows us to clearly relate individual properties (via model parameters) to group-level structure. These relationships provide insight into the more complicated milling formations observed in nature, and suggest design properties of artificial schools where such rotational motion is desired. PMID:18855072

  17. 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.

  18. 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.

  19. Voronoi diagram-based spheroid model for microwave scattering of complex snow aggregates

    NASA Astrophysics Data System (ADS)

    Honeyager, Ryan; Liu, Guosheng; Nowell, Holly

    2016-02-01

    Methods to model snow aggregate scattering properties at microwave frequencies can be divided into structurally explicit and implicit techniques. Explicit techniques, such as the discrete dipole approximation (DDA), determine scattering and backscatter cross-sections assuming full knowledge of a given snow particle's structure. Such calculations are computationally expensive. Implicit techniques, such as using the T-matrix method (TMM) with optically soft spheroids, model equivalent particles with variable mass, bulk density and aspect ratio according to an effective-medium approximation. It is highly desirable that there should be a good agreement between modeled aggregate cross-sections using both methods. A Voronoi bounding-neighbor algorithm is presented in this study to determine the bulk equivalent density of complex three-dimensional snow aggregates. While mass and aspect ratio are easily parameterized quantities, attempts to parameterize the bulk density of snowflakes have usually relied on a bounding ellipsoid, which can be determined from a flake's radius of gyration, root mean square mean or simply from its maximum diameter. We compared the Voronoi algorithm against existing bounding spheroid approaches and mass-effective density relations at ten frequencies from 10.65 to 183.31 GHz, using a set of 1005 aggregates with maximum dimensions from a few hundred microns to several centimeters. When using the Voronoi-determined effective density, the asymmetry parameter, scattering, and backscatter cross-sections determined using the TMM reasonably match those for DDA-computed snow aggregates. From Ku to W-band, soft spheroids can reproduce cross-sections for aggregates up to 9 mm in maximum dimension. Volume-integrated cross-sections always agree to within 25% of DDA. As the DDA is computationally expensive, this offers a fast alternative that efficiently evaluates scattering properties at microwave frequencies.

  20. 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

  1. MODELING THE INFLUENCE OF ACTIVE SUBSLAB DEPRESSURIZATION (ASD) SYSTEMS ON AIRFLOWS IN SUBSLAB AGGREGATE BEDS

    EPA Science Inventory

    A simple model is presented that allows the pressure difference in a subslab aggregate layer to be estimated as a function of radial distance from the central suction point of an active subslab depressurization system by knowing the average size, thickness, porosity, and permeabi...

  2. 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...

  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. 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.

  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

    2015-06-01

    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. PMID:25892401

  6. 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

    2015-06-01

    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.

  7. Hydration and diffusion processes shape microbial community organization and function in model soil aggregates

    NASA Astrophysics Data System (ADS)

    Ebrahimi, Ali; Or, Dani

    2015-12-01

    The constantly changing soil hydration status affects gas and nutrient diffusion through soil pores and thus the functioning of soil microbial communities. The conditions within soil aggregates are of particular interest due to limitations to oxygen diffusion into their core, and the presence of organic carbon often acting as binding agent. We developed a model for microbial life in simulated soil aggregates comprising of 3-D angular pore network model (APNM) that mimics soil hydraulic and transport properties. Within these APNM, we introduced individual motile (flagellated) microbial cells with different physiological traits that grow, disperse, and respond to local nutrients and oxygen concentrations. The model quantifies the dynamics and spatial extent of anoxic regions that vary with hydration conditions, and their role in shaping microbial community size and activity and the spatial (self) segregation of anaerobes and aerobes. Internal carbon source and opposing diffusion directions of oxygen and carbon within an aggregate were essential to emergence of stable coexistence of aerobic and anaerobic communities (anaerobes become extinct when carbon sources are external). The model illustrates a range of hydration conditions that promote or suppress denitrification or decomposition of organic matter and thus affect soil GHG emissions. Model predictions of CO2 and N2O production rates were in good agreement with limited experimental data. These limited tests support the dynamic modeling approach whereby microbial community size, composition, and spatial arrangement emerge from internal interactions within soil aggregates. The upscaling of the results to a population of aggregates of different sizes embedded in a soil profile is underway.

  8. 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.

  9. Aggregate-Depleted Brain Fails to Induce Aβ Deposition in a Mouse Model of Alzheimer's Disease

    PubMed Central

    Duran-Aniotz, Claudia; Morales, Rodrigo; Moreno-Gonzalez, Ines; Hu, Ping Ping; Fedynyshyn, Joseph; Soto, Claudio

    2014-01-01

    Recent studies in animal models of Alzheimer's disease (AD) show that amyloid-beta (Aβ) misfolding can be transmissible; however, the mechanisms by which this process occurs have not been fully explored. The goal of this study was to analyze whether depletion of aggregates from an AD brain suppresses its in vivo “seeding” capability. Removal of aggregates was performed by using the Aggregate Specific Reagent 1 (ASR1) compound which has been previously described to specifically bind misfolded species. Our results show that pre-treatment with ASR1-coupled magnetic beads reduces the in vivo misfolding inducing capability of an AD brain extract. These findings shed light respect to the active principle responsible for the prion-like spreading of Alzheimer's amyloid pathology and open the possibility of using seeds-capturing reagents as a promising target for AD treatment. PMID:24533166

  10. Experimental and modeling study of breakage and restructuring of open and dense colloidal aggregates.

    PubMed

    Harshe, Yogesh M; Lattuada, Marco; Soos, Miroslav

    2011-05-17

    In this work we present experimental and simulation analysis of the breakage and restructuring of colloidal aggregates in dilute conditions under shear. In order to cover a broad range of hydrodynamic and interparticle forces, aggregates composed of primary particles with two sizes, d(p) = 90 and 810 nm, were generated. Moreover, to understand the dependence of breakage and restructuring on the cluster structure, aggregates grown under stagnant and turbulent conditions, having substantially different initial internal structures with fractal dimension d(f) equal to 1.7 and 2.7, respectively, were used. The aggregates were broken by exposing them to a well-defined elongational flow produced in a nozzle positioned between two syringes. To investigate the evolution of aggregate size and morphology, respectively, the mean radius of gyration, , and d(f) were monitored during the breakup process using light scattering and confocal laser scanning microscopy. It was found that the evolution of aggregates' fractal dimension during breakage is solely controlled by their initial structure and is independent of the primary particles size. Similarly, the scaling of the steady-state vs the applied hydrodynamic stress is independent of primary particle size, however, depends on the history of aggregate structure. To quantitatively explain these observations, the breakage process was modeled using stokesian dynamics simulations incorporating DLVO and contact interactions among particles. The required flow-field for these simulations was obtained from computational fluid dynamics. The complex flow pattern was simplified by considering a characteristic stream line passing through the zone with the highest hydrodynamic stress inside the nozzle, this being the most critical flow condition experienced by the clusters. As the flow-field along this streamline was found to be neither pure simple shear nor pure extensional flow, the real flow was approximated as an elongational

  11. Fast community detection based on sector edge aggregation metric model in hyperbolic space

    NASA Astrophysics Data System (ADS)

    Wang, Zuxi; Li, Qingguang; Xiong, Wei; Jin, Fengdong; Wu, Yao

    2016-06-01

    By studying the edge aggregation characteristic of nodes in hyperbolic space, Sector Edge Aggregation Metric (SEAM) model is proposed and theoretically proved in this paper. In hyperbolic disk SEAM model determines the minimum angular range of a sector which possesses the maximal edge aggregation of nodes. The set of nodes within such sector has dense internal links, which corresponds with the characteristic of community structure. Based on SEAM model, we propose a fast community detection algorithm called Greedy Optimization Modularity Algorithm (GOMA) which employs greedy optimization strategy and hyperbolic coordinates. GOMA firstly divides initial communities according to the quantitative results of sector edge aggregation given by SEAM and the nodes' hyperbolic coordinates, then based on greedy optimization strategy, only merges the two angular neighboring communities in hyperbolic disk to optimize the network modularity function, and consequently obtains high-quality community detection. The strategies of initial community partition and merger in hyperbolic space greatly improve the speed of searching the most optimal modularity. Experimental results indicate that GOMA is able to detect out high-quality community structure in synthetic and real networks, and performs better when applied to the large-scale and dense networks with strong clustering.

  12. 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.

  13. Structural modeling of dahlia-type single-walled carbon nanohorn aggregates by molecular dynamics.

    PubMed

    Hawelek, L; Brodka, A; Dore, John C; Hannon, Alex C; Iijima, S; Yudasaka, M; Ohba, T; Kaneko, K; Burian, A

    2013-09-19

    The structure of dahlia-type single-walled carbon nanohorn aggregates has been modeled by classical molecular dynamics simulations, and the validity of the model has been verified by neutron diffraction. Computer-generated models consisted of an outer part formed from single-walled carbon nanohorns with diameters of 20-50 Å and a length of 400 Å and an inner turbostratic graphite-like core with a diameter of 130 Å. The diffracted intensity and the pair correlation function computed for such a constructed model are in good agreement with the neutron diffraction experimental data. The proposed turbostratic inner core explains the occurrence of the additional (002) and (004) graphitic peaks in the diffraction pattern of the studied sample and provides information about the interior structure of the dahlia-type aggregates. PMID:23978218

  14. FPLUME-1.0: An integrated volcanic plume model accounting for ash aggregation

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

    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 cross-section averaged eruption column model based on the Buoyant Plume Theory (BPT). The model accounts for plume bent over 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).

  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. 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.

  17. 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.

  18. Aggregate formation in a model fluid with microscopic piecewise-continuous competing interactions

    NASA Astrophysics Data System (ADS)

    Cigala, G.; Costa, D.; Bomont, J.-M.; Caccamo, C.

    2015-09-01

    We use the hypernetted chain theory - complemented in a few selected cases by Monte Carlo simulations to assess its accuracy - to study a model fluid composed by hard spheres surrounded by an attractive square-well, followed by a linearly decreasing repulsive ramp. The proposed competing interaction allows us to study individually the influence of all the defining parameters on the formation of aggregates out of the homogeneous fluid, as signalled by the development of a local peak at low wavevectors in the static structure factor. We document an accurate linear scaling of the temperature whereupon aggregates develop (at constant density) as a function of both the square-well width and the height of the repulsive barrier, over a wide range of such properties; a much drastic dependence is instead observed on the repulsion range, well described by an exponential increase. We show that typical correlation distances among aggregates, in early conditions for their development, fall approximately at a constant fraction of the width of the repulsive barrier. We analyse different possibilities in which attraction or repulsion prevails in the overall balance of microscopic interaction: we document, as expected, that for sufficiently weak repulsion barriers, or sufficiently large attractive wells, the structure factor shows a trend to increase in the limit of vanishing wavevectors, heralding a standard liquid-vapour phase separation at low temperatures. At the opposite end, the development of aggregates seems to be hardly favoured, for the present model, if attraction is completely neglected.

  19. 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.

  20. 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...

  1. Site-specific updating and aggregation of Bayesian belief network models for multiple experts.

    PubMed

    Stiber, Neil A; Small, Mitchell J; Pantazidou, Marina

    2004-12-01

    A method for combining multiple expert opinions that are encoded in a Bayesian Belief Network (BBN) model is presented and applied to a problem involving the cleanup of hazardous chemicals at a site with contaminated groundwater. The method uses Bayes Rule to update each expert model with the observed evidence, then uses it again to compute posterior probability weights for each model. The weights reflect the consistency of each model with the observed evidence, allowing the aggregate model to be tailored to the particular conditions observed in the site-specific application of the risk model. The Bayesian update is easy to implement, since the likelihood for the set of evidence (observations for selected nodes of the BBN model) is readily computed by sequential execution of the BBN model. The method is demonstrated using a simple pedagogical example and subsequently applied to a groundwater contamination problem using an expert-knowledge BBN model. The BBN model in this application predicts the probability that reductive dechlorination of the contaminant trichlorethene (TCE) is occurring at a site--a critical step in the demonstration of the feasibility of monitored natural attenuation for site cleanup--given information on 14 measurable antecedent and descendant conditions. The predictions for the BBN models for 21 experts are weighted and aggregated using examples of hypothetical and actual site data. The method allows more weight for those expert models that are more reflective of the site conditions, and is shown to yield an aggregate prediction that differs from that of simple model averaging in a potentially significant manner.

  2. 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

  3. Modeling the interplay between protein and lipid aggregation in supported membranes.

    PubMed

    de Prado Salas, Pablo González; Encinar, Mario; Alonso, Alvaro; Vélez, Marisela; Tarazona, Pedro

    2015-01-01

    We present a theoretical model that deals with the complex interplay between lipid segregation and the self-aggregation of lipid-attached proteins. The model, in contrast to previous ones that consider proteins only as passive elements affecting the lipid distribution, describes the system including three terms: the dynamic interactions between protein monomers, the interactions between lipid components, and a mixed term considering protein-lipid interactions. It is used to explain experimental results performed on a well-defined system in which a self-aggregating soluble bacterial cytoskeletal protein polymerizes on a lipid bilayer containing two lipid components. All the elements considered in a previously described protein model, including torsion of the monomers within the filament, are needed to account for the observed filament shapes. The model also points out that lipid segregation can affect the length and curvature of the filaments and that the dynamic behavior of the lipids and proteins can have different time scales, giving rise to memory effects. This simple model that considers a dynamic protein assembly on a fluid and active lipid surface can be easily extended to other biologically relevant situations in which the interplay between protein and lipid aggregation is needed to fully describe the system. PMID:24968242

  4. Modeling the interplay between protein and lipid aggregation in supported membranes.

    PubMed

    de Prado Salas, Pablo González; Encinar, Mario; Alonso, Alvaro; Vélez, Marisela; Tarazona, Pedro

    2015-01-01

    We present a theoretical model that deals with the complex interplay between lipid segregation and the self-aggregation of lipid-attached proteins. The model, in contrast to previous ones that consider proteins only as passive elements affecting the lipid distribution, describes the system including three terms: the dynamic interactions between protein monomers, the interactions between lipid components, and a mixed term considering protein-lipid interactions. It is used to explain experimental results performed on a well-defined system in which a self-aggregating soluble bacterial cytoskeletal protein polymerizes on a lipid bilayer containing two lipid components. All the elements considered in a previously described protein model, including torsion of the monomers within the filament, are needed to account for the observed filament shapes. The model also points out that lipid segregation can affect the length and curvature of the filaments and that the dynamic behavior of the lipids and proteins can have different time scales, giving rise to memory effects. This simple model that considers a dynamic protein assembly on a fluid and active lipid surface can be easily extended to other biologically relevant situations in which the interplay between protein and lipid aggregation is needed to fully describe the system.

  5. Rapid formation of large aggregates during the spring bloom of Kerguelen Island: observations and model comparisons

    NASA Astrophysics Data System (ADS)

    Jouandet, M.-P.; Jackson, G. A.; Carlotti, F.; Picheral, M.; Stemmann, L.; Blain, S.

    2014-08-01

    While production of aggregates and their subsequent sinking is known to be one pathway for the downward movement of organic matter from the euphotic zone, the rapid transition from non-aggregated to aggregated particles has not been reported previously. We made one vertical profile of particle size distributions (PSD; sizes ranging from 0.052 to several millimeters in equivalent spherical diameter) at pre-bloom stage and seven vertical profiles 3 weeks later over a 48 h period at early bloom stage using the Underwater Vision Profiler during the Kerguelen Ocean and Plateau Compared Study cruise 2 (KEOPS2, October-November 2011). In these naturally iron-fertilized waters southeast of Kerguelen Island (Southern Ocean), the total particle numerical abundance increased by more than fourfold within this time period. A massive total volume increase associated with particle size distribution changes was observed over the 48 h survey, showing the rapid formation of large particles and their accumulation at the base of the mixed layer. The results of a one-dimensional particle dynamics model support coagulation as the mechanism responsible for the rapid aggregate formation and the development of the VT subsurface maxima. The comparison of VT profiles between early bloom stage and pre-bloom stage indicates an increase of particulate export below 200 m when bloom has developed. These results highlight the role of coagulation in forming large particles and triggering carbon export at the early stage of a naturally iron-fertilized bloom, while zooplankton grazing may dominate later in the season. The rapid changes observed illustrate the critical need to measure carbon export flux with high sampling temporal resolution. Our results are the first published in situ observations of the rapid accumulation of marine aggregates and their export and the general agreement of this rapid event with a model of phytoplankton growth and coagulation.

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

    PubMed

    Ross, P; Buntzman, A S; Vincent, B G; Grover, E N; Gojanovich, G S; Collins, E J; Frelinger, J A; Hess, P R

    2012-08-01

    In the dog, previous analyses of major histocompatibility complex 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

  7. A study of the association between chronic superficial keratitis and polymorphisms in the upstream regulatory regions of DLA-DRB1, DLA-DQB1 and DLA-DQA1.

    PubMed

    Barrientos, Laura S; Zapata, Gustavo; Crespi, Julian A; Posik, Diego M; Díaz, Silvina; It, Veronica; Peral-García, Pilar; Giovambattista, Guillermo

    2013-12-15

    Canine chronic superficial keratitis (CSK) is an inflammatory corneal disease that primarily occurs in German shepherd dogs (GSDs). Several studies support the hypothesis that CSK is an immune-mediated disease. To investigate the genetic factors associated with CSK development, the upstream regulatory regions (URRs) of the DLA-DRB, -DQA and -DQB genes were genotyped in 60 dogs, including 32 CSK animals. LD analysis identified two blocks (r(2)≤45), with two DLA-DRB1 and five DLA-DQB1 haplotypes. Analysis of DLA-URR alleles/haplotypes showed a significant association between DQB1*-154 [C/T] (p=0.016) and CSK, suggesting that the T variant may increase the risk for developing CSK disease (OR=3, 95% CI=1.25-7.68). When haplotype associations were performed, the URR-DQB*CATT haplotype was significantly associated with CSK (p=0.016), increasing the risk of develop this disease over two-fold (OR=3, 95%, CI=1.25-7.68). These results showed that dogs homozygous at DRB1*69 [C/T] had a risk for developing CSK disease that was over four times the risk for heterozygotes. This genetic association supports the previous clinical, histological and pharmacological studies that suggest that CSK is an immune-mediated disease, and this association could potentially be used to identify susceptible animals.

  8. A study of the association between chronic superficial keratitis and polymorphisms in the upstream regulatory regions of DLA-DRB1, DLA-DQB1 and DLA-DQA1.

    PubMed

    Barrientos, Laura S; Zapata, Gustavo; Crespi, Julian A; Posik, Diego M; Díaz, Silvina; It, Veronica; Peral-García, Pilar; Giovambattista, Guillermo

    2013-12-15

    Canine chronic superficial keratitis (CSK) is an inflammatory corneal disease that primarily occurs in German shepherd dogs (GSDs). Several studies support the hypothesis that CSK is an immune-mediated disease. To investigate the genetic factors associated with CSK development, the upstream regulatory regions (URRs) of the DLA-DRB, -DQA and -DQB genes were genotyped in 60 dogs, including 32 CSK animals. LD analysis identified two blocks (r(2)≤45), with two DLA-DRB1 and five DLA-DQB1 haplotypes. Analysis of DLA-URR alleles/haplotypes showed a significant association between DQB1*-154 [C/T] (p=0.016) and CSK, suggesting that the T variant may increase the risk for developing CSK disease (OR=3, 95% CI=1.25-7.68). When haplotype associations were performed, the URR-DQB*CATT haplotype was significantly associated with CSK (p=0.016), increasing the risk of develop this disease over two-fold (OR=3, 95%, CI=1.25-7.68). These results showed that dogs homozygous at DRB1*69 [C/T] had a risk for developing CSK disease that was over four times the risk for heterozygotes. This genetic association supports the previous clinical, histological and pharmacological studies that suggest that CSK is an immune-mediated disease, and this association could potentially be used to identify susceptible animals. PMID:24238945

  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. Detection, monitoring and modelling of alkali-aggregate reaction in Kouga Dam (South Africa)

    SciTech Connect

    Elges, H.; Lecocq, P.; Oosthuizen, C.; Geertsema, A.

    1995-12-31

    Kouga Dam (formerly Paul Sauer Dam) is a double curvature arch dam completed in 1969. The aggregates and the cement used for the construction have subsequently been proven to be alkali reactive. The results of the monitoring programme and the alkali-aggregate reaction (AAR) tests as well as the methodology developed to standardise the logging of cores for these investigations are presented. A brief description of the Finite Element Model used to approximate the AAR process in order to determine positions for in-situ stress measurements is also given. The aim with these tests is to refine the model for prediction of the long-term behaviour of the dam and to make an assessment of the possibility of raising the dam.

  12. Defense logistics agency (DLA) supplement for the environmental assesment and management (team) guide. Final report

    SciTech Connect

    Schell, D.J.

    1994-11-01

    In response to the growing number of environmental laws and regulations worldwide, the Defense Logistic Agency (DLA) has adopted an environmental compliance program that identifies compliance problems before they are cited as violations by the U.S. Environmental Protection Agency (USEPA). In 1993, the DLA developed a program to maintain compliance with all Federal, state, and local environmental regulations. The goal is to protect human health/safety and the environment. The resulting system combines Federal environmental regulations, along with good management practices and risk management information, into a series of checklists that show legal requirements and which specific items or operations to review. In fiscal year 1994, the DLA became a participant in the efforts to create a single compliance assessment manual for use by all members of the DOD. The resultant manual is The Environmental Assessment and Management (TEAM) Guide. In order to examine Army Regulations (ARs), DLA Regulations (DLARs), and DLA Manuals (DLAMs), the DLA supplement was developed to use in conjunction with the TEAM Guide.

  13. Discretized and aggregated: modeling dive depth of harbor seals from ordered categorical data with temporal autocorrelation.

    PubMed

    Higgs, Megan D; Ver Hoef, Jay M

    2012-09-01

    Ordered categorical data are pervasive in environmental and ecological data, and often arise from constraints that require discretizing a continuous variable into ordered categories. A great deal of data have been collected toward the study of marine mammal dive behavior using satellite depth recorders (SDRs), which often discretize a continuous variable such as depth. Additionally, data storage or transmission constraints may also necessitate the aggregation of data over time intervals of a specified length. The categorization and aggregation create a time series of ordered multicategory counts for each animal, which present challenges in terms of statistical modeling and practical interpretation. We describe an intuitive strategy for modeling such aggregated, ordered categorical data allowing for inference regarding the category probabilities and a measure of central tendency on the original scale of the data (e.g., meters), along with incorporation of temporal correlation and overdispersion. The strategy extends covariate-specific cutpoint models for ordinal data. We demonstrate the method in an analysis of SDR dive-depth data collected on harbor seals in Alaska. The primary goal of the analysis is to assess the relationship of covariates, such as time of day, with number of dives and maximum depth of dives. We also predict missing values and introduce novel graphical summaries of the data and results. PMID:22118495

  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. 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.

  16. Phase-field modeling of two-dimensional solute precipitation/dissolution: Solid fingers and diffusion-limited precipitation

    SciTech Connect

    Xu, Zhijie; Meakin, Paul

    2011-01-28

    Two-dimensional dendritic growth due to solute precipitation was simulated using a phase-field model reported earlier [Z. Xu and P. Meakin, J. Chem. Phys. 129, 014705 (2008)]. It was shown that diffusion-limited precipitation due to the chemical reaction at the solid-liquid interface posses similarities with diffusion-limited aggregation (DLA). The diffusion-limited precipitation is attained by setting the chemical reaction rate much larger compared to the solute diffusion to eliminate the effect of the interface growth kinetics. The phase-field simulation results were in reasonable agreement with the analytical solutions. The fractal solid fingers can be formed in the diffusion-limited precipitation and have a fractal dimension measured , close to 1.64, the fractal dimensionality of large square lattice diffusion-limited aggregation (DLA) clusters.

  17. 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.

  18. 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.

  19. Translation of two aggregated low-density lipoproteins within blood plasma: a mathematical model.

    PubMed

    Hadjinicolaou, Maria; Protopapas, Eleftherios

    2015-01-01

    Arteriosclerosis is a disease in which the artery walls get thicker and harder. Atherosclerosis is a specific form of arteriosclerosis which allows less blood to travel through the artery and increases blood pressure. Low-density lipoproteins (LDLs) and their ability to aggregate are important in atherosclerosis. In the present study we develop a mathematical model that describes the translation of two aggregated LDSs through blood plasma. We model the two aggregated LDLs as an inverted oblate spheroid and the flow as a creeping steady incompressible axisymmetric one. The mathematical tools that we used are the Kelvin inversion and the semi-separation of variables in the spheroidal coordinate systems. The stream function is given as a series expansion of even order terms of combinations of Gegenbauer functions of angular and radial dependence. The analytical solution is expected to give insight into the study of the various chemical precipitation methods used for the precipitation of lipoproteins, as this is the first step for the measurement of their concentration within blood plasma. PMID:25417024

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

    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.

  1. 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.

  2. Multi-objective calibration of a reservoir model: aggregation and non-dominated sorting approaches

    NASA Astrophysics Data System (ADS)

    Huang, Y.

    2012-12-01

    Numerical reservoir models can be helpful tools for water resource management. These models are generally calibrated against historical measurement data made in reservoirs. In this study, two methods are proposed for the multi-objective calibration of such models: aggregation and non-dominated sorting methods. Both methods use a hybrid genetic algorithm as an optimization engine and are different in fitness assignment. In the aggregation method, a weighted sum of scaled simulation errors is designed as an overall objective function to measure the fitness of solutions (i.e. parameter values). The contribution of this study to the aggregation method is the correlation analysis and its implication to the choice of weight factors. In the non-dominated sorting method, a novel method based on non-dominated sorting and the method of minimal distance is used to calculate the dummy fitness of solutions. The proposed methods are illustrated using a water quality model that was set up to simulate the water quality of Pepacton Reservoir, which is located to the north of New York City and is used for water supply of city. The study also compares the aggregation and the non-dominated sorting methods. The purpose of this comparison is not to evaluate the pros and cons between the two methods but to determine whether the parameter values, objective function values (simulation errors) and simulated results obtained are significantly different with each other. The final results (objective function values) from the two methods are good compromise between all objective functions, and none of these results are the worst for any objective function. The calibrated model provides an overall good performance and the simulated results with the calibrated parameter values match the observed data better than the un-calibrated parameters, which supports and justifies the use of multi-objective calibration. The results achieved in this study can be very useful for the calibration of water

  3. 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

  4. 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.

  5. 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.

  6. Drosophila Melanogaster as a Model System for Studies of Islet Amyloid Polypeptide Aggregation

    PubMed Central

    Schultz, Sebastian Wolfgang; Nilsson, K. Peter R.; Westermark, Gunilla Torstensdotter

    2011-01-01

    Background Recent research supports that aggregation of islet amyloid polypeptide (IAPP) leads to cell death and this makes islet amyloid a plausible cause for the reduction of beta cell mass, demonstrated in patients with type 2 diabetes. IAPP is produced by the beta cells as a prohormone, and proIAPP is processed into IAPP by the prohormone convertases PC1/3 and PC2 in the secretory granules. Little is known about the pathogenesis for islet amyloid and which intracellular mechanisms are involved in amyloidogenesis and induction of cell death. Methodology/Principal Findings We have established expression of human proIAPP (hproIAPP), human IAPP (hIAPP) and the non-amyloidogenic mouse IAPP (mIAPP) in Drosophila melanogaster, and compared survival of flies with the expression driven to different cell populations. Only flies expressing hproIAPP in neurons driven by the Gal4 driver elavC155,Gal4 showed a reduction in lifespan whereas neither expression of hIAPP or mIAPP influenced survival. Both hIAPP and hproIAPP expression caused formation of aggregates in CNS and fat body region, and these aggregates were both stained by the dyes Congo red and pFTAA, both known to detect amyloid. Also, the morphology of the highly organized protein granules that developed in the fat body of the head in hIAPP and hproIAPP expressing flies was characterized, and determined to consist of 15.8 nm thick pentagonal rod-like structures. Conclusions/Significance These findings point to a potential for Drosophila melanogaster to serve as a model system for studies of hproIAPP and hIAPP expression with subsequent aggregation and developed pathology. PMID:21695120

  7. Molecular hairpin: a possible model for inhibition of tau aggregation by tannic acid.

    PubMed

    Yao, Junliang; Gao, Xing; Sun, Wenliang; Yao, Tianming; Shi, Shuo; Ji, Liangnian

    2013-03-19

    Inhibition of anomalous aggregation of tau protein would be an attractive therapeutic target for Alzheimer's disease (AD). In this study, tannic acid (TA), a polymeric plant polyphenol, and its monomer, gallic acid (GA), were introduced as the references to afford a molecular framework that integrates tau binding properties and inhibitory effects. Using a thioflavin S fluorescence assay and electron microscopy, we demonstrated that TA could competently inhibit the in vitro aggregation of tau peptide R3, corresponding to the third repeat unit of the microtubule-binding domain, with an IC50 of 3.5 μM, while GA's inhibition was comparatively piddling (with an IC50 of 92 μM). In the isothermal titration calorimetry experiment, we found that TA could strongly bind to R3 with a large amount of heat released. Circular dichroism spectra showed TA dose-dependently suppressed the conformational transition of R3 from a random coil structure to a β-sheet structure during the aggregation process. Finally, a structural model was built using molecular docking simulation to elucidate the possible binding sites for TA on the tau peptide surface. Our results suggest that TA recognizably interacts with tau peptide by forming a hairpin binding motif, a key framework required for inhibiting tau polymerization, in addition to hydrogen bonding, hydrophilic-hydrophobic interactions, and static electrical interactions, as reported previously. The inhibitory effect of TA on human full-length tau protein (tau441) was also verified by electron microscopy. This finding hints at the possibility of TA as a leading compound of anti-AD drugs and offers a new stratagem for the rational molecular design of a tau aggregation inhibitor. PMID:23442089

  8. Kinetic model of the aggregation of alpha-synuclein provides insights into prion-like spreading.

    PubMed

    Iljina, Marija; Garcia, Gonzalo A; Horrocks, Mathew H; Tosatto, Laura; Choi, Minee L; Ganzinger, Kristina A; Abramov, Andrey Y; Gandhi, Sonia; Wood, Nicholas W; Cremades, Nunilo; Dobson, Christopher M; Knowles, Tuomas P J; Klenerman, David

    2016-03-01

    The protein alpha-synuclein (αS) self-assembles into small oligomeric species and subsequently into amyloid fibrils that accumulate and proliferate during the development of Parkinson's disease. However, the quantitative characterization of the aggregation and spreading of αS remains challenging to achieve. Previously, we identified a conformational conversion step leading from the initially formed oligomers to more compact oligomers preceding fibril formation. Here, by a combination of single-molecule fluorescence measurements and kinetic analysis, we find that the reaction in solution involves two unimolecular structural conversion steps, from the disordered to more compact oligomers and then to fibrils, which can elongate by further monomer addition. We have obtained individual rate constants for these key microscopic steps by applying a global kinetic analysis to both the decrease in the concentration of monomeric protein molecules and the increase in oligomer concentrations over a 0.5-140-µM range of αS. The resulting explicit kinetic model of αS aggregation has been used to quantitatively explore seeding the reaction by either the compact oligomers or fibrils. Our predictions reveal that, although fibrils are more effective at seeding than oligomers, very high numbers of seeds of either type, of the order of 10(4), are required to achieve efficient seeding and bypass the slow generation of aggregates through primary nucleation. Complementary cellular experiments demonstrated that two orders of magnitude lower numbers of oligomers were sufficient to generate high levels of reactive oxygen species, suggesting that effective templated seeding is likely to require both the presence of template aggregates and conditions of cellular stress. PMID:26884195

  9. Optimising Cell Aggregate Expansion in a Perfused Hollow Fibre Bioreactor via Mathematical Modelling

    PubMed Central

    Chapman, Lloyd A. C.; Shipley, Rebecca J.; Whiteley, Jonathan P.; Ellis, Marianne J.; Byrne, Helen M.; Waters, Sarah L.

    2014-01-01

    The need for efficient and controlled expansion of cell populations is paramount in tissue engineering. Hollow fibre bioreactors (HFBs) have the potential to meet this need, but only with improved understanding of how operating conditions and cell seeding strategy affect cell proliferation in the bioreactor. This study is designed to assess the effects of two key operating parameters (the flow rate of culture medium into the fibre lumen and the fluid pressure imposed at the lumen outlet), together with the cell seeding distribution, on cell population growth in a single-fibre HFB. This is achieved using mathematical modelling and numerical methods to simulate the growth of cell aggregates along the outer surface of the fibre in response to the local oxygen concentration and fluid shear stress. The oxygen delivery to the cell aggregates and the fluid shear stress increase as the flow rate and pressure imposed at the lumen outlet are increased. Although the increased oxygen delivery promotes growth, the higher fluid shear stress can lead to cell death. For a given cell type and initial aggregate distribution, the operating parameters that give the most rapid overall growth can be identified from simulations. For example, when aggregates of rat cardiomyocytes that can tolerate shear stresses of up to are evenly distributed along the fibre, the inlet flow rate and outlet pressure that maximise the overall growth rate are predicted to be in the ranges to (equivalent to to ) and to (or 15.6 psi to 15.7 psi) respectively. The combined effects of the seeding distribution and flow on the growth are also investigated and the optimal conditions for growth found to depend on the shear tolerance and oxygen demands of the cells. PMID:25157635

  10. Kinetic model of the aggregation of alpha-synuclein provides insights into prion-like spreading

    PubMed Central

    Iljina, Marija; Garcia, Gonzalo A.; Horrocks, Mathew H.; Tosatto, Laura; Choi, Minee L.; Ganzinger, Kristina A.; Abramov, Andrey Y.; Gandhi, Sonia; Wood, Nicholas W.; Cremades, Nunilo; Dobson, Christopher M.; Knowles, Tuomas P. J.; Klenerman, David

    2016-01-01

    The protein alpha-synuclein (αS) self-assembles into small oligomeric species and subsequently into amyloid fibrils that accumulate and proliferate during the development of Parkinson’s disease. However, the quantitative characterization of the aggregation and spreading of αS remains challenging to achieve. Previously, we identified a conformational conversion step leading from the initially formed oligomers to more compact oligomers preceding fibril formation. Here, by a combination of single-molecule fluorescence measurements and kinetic analysis, we find that the reaction in solution involves two unimolecular structural conversion steps, from the disordered to more compact oligomers and then to fibrils, which can elongate by further monomer addition. We have obtained individual rate constants for these key microscopic steps by applying a global kinetic analysis to both the decrease in the concentration of monomeric protein molecules and the increase in oligomer concentrations over a 0.5–140-µM range of αS. The resulting explicit kinetic model of αS aggregation has been used to quantitatively explore seeding the reaction by either the compact oligomers or fibrils. Our predictions reveal that, although fibrils are more effective at seeding than oligomers, very high numbers of seeds of either type, of the order of 104, are required to achieve efficient seeding and bypass the slow generation of aggregates through primary nucleation. Complementary cellular experiments demonstrated that two orders of magnitude lower numbers of oligomers were sufficient to generate high levels of reactive oxygen species, suggesting that effective templated seeding is likely to require both the presence of template aggregates and conditions of cellular stress. PMID:26884195

  11. Dynamic modeling of copper bioaccumulation by Mytilus edulis in the presence of humic acid aggregates.

    PubMed

    Sánchez-Marín, Paula; Aierbe, Eneko; Lorenzo, J Ignacio; Mubiana, Valentine K; Beiras, Ricardo; Blust, Ronny

    2016-09-01

    Copper (Cu) complexation by humic acids (HA) is expected to decrease Cu bioavailability for aquatic organisms as predicted by metal bioavailability models, such as the biotic ligand model (BLM). This has been confirmed for non-feeding organisms such as marine invertebrate embryos or microalgae, but for filter-feeding organisms such as the mussel Mytilus edulis, Cu bioaccumulation was higher in the presence of HA, suggesting that part of the Cu-HA complexes were available for uptake. This study shows the dynamic modeling of Cu accumulation kinetics in the gills and rest of the soft-body of M. edulis in the absence and presence of HA. Assuming that truly dissolved Cu is taken in the body via the gills following BLM premises, and including uptake of Cu-HA aggregates via the gut into the rest compartment, this two-compartmental model could successfully explain the observed bioaccumulation data. This modeling approach gives strong evidence to the hypothesis that Cu-HA aggregates can be ingested by mussels leading to Cu absorption in the digestive system. PMID:27498364

  12. Utilitarian Opacity Model for Aggregate Particles in Protoplanetary Nebulae and Exoplanet Atmospheres

    NASA Astrophysics Data System (ADS)

    Cuzzi, Jeffrey N.; Estrada, Paul R.; Davis, Sanford S.

    2014-02-01

    As small solid grains grow into larger ones in protoplanetary nebulae, or in the cloudy atmospheres of exoplanets, they generally form porous aggregates rather than solid spheres. A number of previous studies have used highly sophisticated schemes to calculate opacity models for irregular, porous particles with sizes much smaller than a wavelength. However, mere growth itself can affect the opacity of the medium in far more significant ways than the detailed compositional and/or structural differences between grain constituents once aggregate particle sizes exceed the relevant wavelengths. This physics is not new; our goal here is to provide a model that provides physical insight and is simple to use in the increasing number of protoplanetary nebula evolution and exoplanet atmosphere models appearing in recent years, yet quantitatively captures the main radiative properties of mixtures of particles of arbitrary size, porosity, and composition. The model is a simple combination of effective medium theory with small-particle closed-form expressions, combined with suitably chosen transitions to geometric optics behavior. Calculations of wavelength-dependent emission and Rosseland mean opacity are shown and compared with Mie theory. The model's fidelity is very good in all comparisons we have made except in cases involving pure metal particles or monochromatic opacities for solid particles with sizes comparable to the wavelength.

  13. Diversified Anchoring Features the Peptide Presentation of DLA-88*50801: First Structural Insight into Domestic Dog MHC Class I.

    PubMed

    Xiao, Jin; Xiang, Wangzhen; Chai, Yan; Haywood, Joel; Qi, Jianxun; Ba, Limin; Qi, Peng; Wang, Ming; Liu, Jun; Gao, George F

    2016-09-15

    Canines represent a crucial animal model for studying human diseases and organ transplantation, as well as the evolution of domestic animals. MHCs, with a central role in cellular immunity, are commonly used in the study of dog population genetics and genome evolution. However, the molecular basis for the peptide presentation of dog MHC remains largely unknown. In this study, peptide presentation by canine MHC class I DLA-88*50801 was structurally determined, revealing diversified anchoring modes of the binding peptides. Flexible and large pockets composed of both hydrophobic and hydrophilic residues can accommodate pathogen-derived peptides with diverse anchor residues, as confirmed by thermostability measurements. Furthermore, DLA-88*50801 contains an unusual α2 helix with a large coil in the TCR contact region. These results further our understanding of canine T cell immunity through peptide presentation of MHC class I and shed light on the molecular basis for vaccine development for canine infectious diseases, for example, canine distemper virus. PMID:27511732

  14. Multiscale modeling of upper mantle plasticity: From single-crystal rheology to multiphase aggregate deformation

    NASA Astrophysics Data System (ADS)

    Raterron, Paul; Detrez, Fabrice; Castelnau, Olivier; Bollinger, Caroline; Cordier, Patrick; Merkel, Sébastien

    2014-03-01

    We report a first application of an improved second-order (SO) viscoplastic self-consistent model for multiphase aggregates, applied to an olivine + diopside aggregate as analogue for a dry upper mantle peridotite deformed at 10-15 s-1 shear strain rate along a 20-Ma ocean geotherm. Beside known dislocation slip systems, this SO-model version accounts for an isotropic relaxation mechanism representing ‘diffusion-related’ creep mechanisms in olivine. Slip-system critical resolved shear stress (CRSS) are evaluated in both phases - as functions of P, T, oxygen fugacity (fO2) and strain rate - from previously reported experimental data obtained on single crystals and first-principle calculations coupled with the Peierls-Nabarro model for crystal plasticity; and the isotropic-mechanism dependence on T and P matches that of Si self-diffusion in olivine, while its relative activity is constrained by reported data. The model reproduces well the olivine and diopside lattice preferred orientations (LPO) produced experimentally and observed in naturally deformed rocks, as well as observed sensitivities of multiphase aggregate strength to the volume fraction of the hard phase (here diopside). It shows a significant weakening of olivine LPO with increasing depth, which results from the combined effects of the P-induced [1 0 0]/[0 0 1] dislocation-slip transition and the increasing activity with T of ‘diffusion-related’ creep. This work thus provides a first quantification of the respective effects of [1 0 0]/[0 0 1] slip transition and diffusion creep on the olivine LPO weakening inducing the seismic anisotropy attenuation observed in the upper mantle.

  15. 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.

  16. 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.

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

    PubMed

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

    2016-05-15

    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.

  18. 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.

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

    PubMed

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

    2016-05-15

    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. PMID:26992749

  20. Modeling of Nonlinear Aggregation for Information Fusion Systems with Outliers Based on the Choquet Integral

    PubMed Central

    Su, Kuo-Lan; Jau, You-Min; Jeng, Jin-Tsong

    2011-01-01

    Modern information fusion systems essentially associate decision-making processes with multi-sensor systems. Precise decision-making processes depend upon aggregating useful information extracted from large numbers of messages or large datasets; meanwhile, the distributed multi-sensor systems which employ several geographically separated local sensors are required to provide sufficient messages or data with similar and/or dissimilar characteristics. These kinds of information fusion techniques have been widely investigated and used for implementing several information retrieval systems. However, the results obtained from the information fusion systems vary in different situations and performing intelligent aggregation and fusion of information from a distributed multi-source, multi-sensor network is essentially an optimization problem. A flexible and versatile framework which is able to solve complex global optimization problems is a valuable alternative to traditional information fusion. Furthermore, because of the highly dynamic and volatile nature of the information flow, a swift soft computing technique is imperative to satisfy the demands and challenges. In this paper, a nonlinear aggregation based on the Choquet integral (NACI) model is considered for information fusion systems that include outliers under inherent interaction among feature attributes. The estimation of interaction coefficients for the proposed model is also performed via a modified algorithm based on particle swarm optimization with quantum-behavior (QPSO) and the high breakdown value estimator, least trimmed squares (LTS). From simulation results, the proposed MQPSO algorithm with LTS (named LTS-MQPSO) readily corrects the deviations caused by outliers and swiftly achieves convergence in estimating the parameters of the proposed NACI model for the information fusion systems with outliers. PMID:22163747

  1. Fasudil attenuates aggregation of α-synuclein in models of Parkinson's disease.

    PubMed

    Tatenhorst, Lars; Eckermann, Katrin; Dambeck, Vivian; Fonseca-Ornelas, Luis; Walle, Hagen; Lopes da Fonseca, Tomás; Koch, Jan C; Becker, Stefan; Tönges, Lars; Bähr, Mathias; Outeiro, Tiago F; Zweckstetter, Markus; Lingor, Paul

    2016-04-22

    Parkinson's disease (PD) is the most common neurodegenerative movement disorder, yet disease-modifying treatments do not currently exist. Rho-associated protein kinase (ROCK) was recently described as a novel neuroprotective target in PD. Since alpha-synuclein (α-Syn) aggregation is a major hallmark in the pathogenesis of PD, we aimed to evaluate the anti-aggregative potential of pharmacological ROCK inhibition using the isoquinoline derivative Fasudil, a small molecule inhibitor already approved for clinical use in humans. Fasudil treatment significantly reduced α-Syn aggregation in vitro in a H4 cell culture model as well as in a cell-free assay. Nuclear magnetic resonance spectroscopy analysis revealed a direct binding of Fasudil to tyrosine residues Y133 and Y136 in the C-terminal region of α-Syn. Importantly, this binding was shown to be biologically relevant using site-directed mutagenesis of these residues in the cell culture model. Furthermore, we evaluated the impact of long-term Fasudil treatment on α-Syn pathology in vivo in a transgenic mouse model overexpressing human α-Syn bearing the A53T mutation (α-Syn(A53T) mice). Fasudil treatment improved motor and cognitive functions in α-Syn(A53T) mice as determined by Catwalk(TM) gait analysis and novel object recognition (NOR), without apparent side effects. Finally, immunohistochemical analysis revealed a significant reduction of α-Syn pathology in the midbrain of α-Syn(A53T) mice after Fasudil treatment. Our results demonstrate that Fasudil, next to its effects mediated by ROCK-inhibition, directly interacts with α-Syn and attenuates α-Syn pathology. This underscores the translational potential of Fasudil as a disease-modifying drug for the treatment of PD and other synucleinopathies.

  2. 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.

  3. 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

  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. To Aggregate or Not and Potentially Better Questions for Clustered Data: The Need for Hierarchical Linear Modeling in CTE Research

    ERIC Educational Resources Information Center

    Nimon, Kim

    2012-01-01

    Using state achievement data that are openly accessible, this paper demonstrates the application of hierarchical linear modeling within the context of career technical education research. Three prominent approaches to analyzing clustered data (i.e., modeling aggregated data, modeling disaggregated data, modeling hierarchical data) are discussed…

  7. Cluster-Cluster Aggregation Calculations of Fractal Haze Particles: Titan and the Early Earth

    NASA Astrophysics Data System (ADS)

    Terrell-Martinez, Bernice; Boness, David

    2010-10-01

    The atmosphere of the Archean Earth (3.8 to 2.5 billion years ago) is thought to have been dominated by a thick hydrocarbon haze similar to that of Titan's current atmosphere. To understand radiative transport in the atmospheres of the early Earth and of Titan, it is necessary to compute light scattering in UV, visible, and IR wavelength ranges for realistic fractal aggregate hydrocarbon aerosol particles. We report preliminary work on MATLAB, True BASIC, and Fortran programs to simulate the growth of fractal aggregate aerosols through diffusion limited aggregation (DLA) and cluster-cluster aggregation (CCA) physical processes. The results of these computations are being used with a T-Matrix light scattering program to test recently published, widely-reported conclusions about the early Earth and the faint young Sun paradox [E. T. Wolf and O. B. Toon, Science 328, 1266 (2010)]. This modeling is also relevant to understanding atmospheric carbonaceous soot aerosol anthropogenic and natural effects on climate change of Earth today.

  8. 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

  9. 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.

  10. 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. PMID:25054187

  11. 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.

  12. Optimal Re-Routes and Ground Delays Using a Route-Based Aggregate Air Traffic Flow Model

    NASA Astrophysics Data System (ADS)

    Soler, Lluis

    The National Airspace System (NAS) is very complex and with a high level of uncertainty. For this reason, developing an automated conflict resolution tool at NAS level is presented as a big challenge. One way to address the problem is by using aggregate models, which can significantly reduce its dimension and complexity. Significant effort has been made to develop an air traffic aggregate model capable to effectively state and solve the problem. In this study, a Route-Based Aggregate Model is developed and tested. It consists in a modification of several existing models and overcomes some issues identified in previous aggregate models. It allows the implementation of Traffic Flow Management conventional controls, such as ground delay and rerouting. These control strategies can be used to avoid congestion conflicts based on sectors and airports capacity as well as regions affected by convective weather. The optimization problem is posed as a Linear Programming routine, which guarantees an optimal solution that minimizes the total accumulated delay required to avoid such capacity conflicts. The solutions can be directly translated into specific instructions at aircraft level, via modification of the times of departure and flight plans. The model is integrated with Future Air Traffic Management Concepts Evaluation Tool (FACET), a state of the art air traffic simulation tool, and uses its files as both input and output. This allows simulating in FACET the solution obtained from the aggregate domain. The approach is validated by applying it in three realistic scenarios at different scales. Results show that, for time horizons larger than 2 hours, the accuracy of the aggregate model is similar to other simulation tools. Also, the modified flight plans, the product of the disaggregated solution, reduce the number of capacity conflicts in the FACET simulation. Future research will study the robustness of these solutions and determine the most appropriate scenarios where to

  13. Huntingtin aggregation kinetics and their pathological role in a Drosophila Huntington's disease model.

    PubMed

    Weiss, Kurt R; Kimura, Yoko; Lee, Wyan-Ching Mimi; Littleton, J Troy

    2012-02-01

    Huntington's disease is a neurodegenerative disorder resulting from expansion of a polyglutamine tract in the Huntingtin protein. Mutant Huntingtin forms intracellular aggregates within neurons, although it is unclear whether aggregates or more soluble forms of the protein represent the pathogenic species. To examine the link between aggregation and neurodegeneration, we generated Drosophila melanogaster transgenic strains expressing fluorescently tagged human huntingtin encoding pathogenic (Q138) or nonpathogenic (Q15) proteins, allowing in vivo imaging of Huntingtin expression and aggregation in live animals. Neuronal expression of pathogenic Huntingtin leads to pharate adult lethality, accompanied by formation of large aggregates within the cytoplasm of neuronal cell bodies and neurites. Live imaging and Fluorescence Recovery After Photobleaching (FRAP) analysis of pathogenic Huntingtin demonstrated that new aggregates can form in neurons within 12 hr, while preexisting aggregates rapidly accumulate new Huntingtin protein within minutes. To examine the role of aggregates in pathology, we conducted haplo-insufficiency suppressor screens for Huntingtin-Q138 aggregation or Huntingtin-Q138-induced lethality, using deficiencies covering ~80% of the Drosophila genome. We identified two classes of interacting suppressors in our screen: those that rescue viability while decreasing Huntingtin expression and aggregation and those that rescue viability without disrupting Huntingtin aggregation. The most robust suppressors reduced both soluble and aggregated Huntingtin levels, suggesting toxicity is likely to be associated with both forms of the mutant protein in Huntington's disease.

  14. Sequence-dependent abnormal aggregation of human Tau fragment in an inducible cell model.

    PubMed

    Liu, Xiao-Ling; Hu, Ji-Ying; Hu, Meng-Yun; Zhang, Yi; Hong, Zheng-Yuan; Cheng, Xiao-Qing; Chen, Jie; Pang, Dai-Wen; Liang, Yi

    2015-08-01

    A pathological hallmark of Alzheimer disease (AD) is the accumulation of misfolded hyperphosphorylated microtubule-associated protein Tau within neurons, forming neurofibrillary tangles and leading to synaptic dysfunction and neuronal death. Here we study sequence-dependent abnormal aggregation of human fragment Tau244-372 in an inducible cell model. As evidenced by confocal laser scanning microscopy, Western blot, and immunogold electron microscopy, fibril-forming motifs are essential and sufficient for abnormal aggregation of Tau244-372 in SH-SY5Y neuroblastoma cells induced by Congo red: when its two fibril-forming segments PHF6 and PHF6* are deleted, Tau244-372 does lose its ability to form fibrils in SH-SY5Y cells, and the replacement of PHF6 and PHF6* with an unrelated amyloidogenic sequence IFQINS from human lysozyme does rescue the fibril-forming ability of Tau244-372 in SH-SY5Y cells. By contrast, insertion of a non-fibril forming peptide GGGGGG does not drive the disabled Tau244-372 to misfold in SH-SY5Y cells. Furthermore, as revealed by quantum dots based probes combined with annexin V staining, annexin V-FITC apoptosis detection assay, and immunofluorescence, fibril-forming motifs are essential and sufficient for early apoptosis of living SH-SY5Y cells induced by abnormal aggregation of Tau244-372. Our results suggest that fibril-forming motifs could be the determinants of Tau protein tending to misfold in living cells, thereby inducing neuronal apoptosis and causing the initiation and development of AD.

  15. 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.

  16. 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.

  17. Model for upper atmospheric aggregation of ash following hypervelocity impact events

    NASA Astrophysics Data System (ADS)

    Huber, Matthew; Artemieva, Natasha

    2014-05-01

    Introduction: Accretionary lapilli (AL) have been found in hypervelocity impact crater ejecta deposits and are similar to volcanically produced AL [1]. The initial conditions of ejection from an impact crater are vastly different than ejection from a volcano, particularly regarding the mass of ejecta and the velocity of ejection. Thus, some models of AL formation may not apply to impact ejecta. We propose an upper atmospheric aggregation model. A numerical model is herein described Numerical model: Re-entry is modeled using the 3D hydrocode SOVA [2], using mainly its "dusty flow" subroutines. Particles are treated as solid non-deformable; they move through the atmosphere and exchange momentum and energy. Radiative, conductive, and convective heat transfer are included. Details of the procedure may be found in [2]. Initial mass flux of ejecta, velocities, and re-entry angles are derived from crater-forming models. The power law SFD N>m~m-b is used with the exponent b of 0.8 and 0.9. The largest fragment for a given distance can be deduced from observations. The smallest fragments are ~10 µm in diameter. Results: During re-entry, particles decelerate due to drag, heating the atmosphere, and the atmospheric gas heats particles via conduction, convection, and radiative transfer. Additionally, shock waves are generated. Intensity of these processes depends on the total mass and velocity of ejecta, but also on the ejecta SFD. Particles of varying sizes were modeled. Large particles penetrate to low altitudes, maintaining temperature. Small particles decelerate at high altitudes, have elevated temperatures, and heat the atmosphere to T> 600 K. These particles can release water from pores or, in some cases, from mineral structures. Cold particles entering later may be coated by this water, permitting aggregation and pushing other particles to lower altitudes. Substantial mixing of particles at temperatures and densities suitable for AL formation remains as long as ejecta

  18. 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.

  19. Diffusion-limited aggregation with power-law pinning.

    PubMed

    Hentschel, H G E; Popescu, M N; Family, F

    2004-01-01

    Using stochastic conformal mapping techniques we study the patterns emerging from Laplacian growth with a power-law decaying threshold for growth R(-gamma)(N) (where R(N) is the radius of the N-particle cluster). For gamma>1 the growth pattern is in the same universality class as diffusion limited aggregation (DLA), while for gamma<1 the resulting patterns have a lower fractal dimension D(gamma) than a DLA cluster due to the enhancement of growth at the hot tips of the developing pattern. Our results indicate that a pinning transition occurs at gamma=1/2, significantly smaller than might be expected from the lower bound alpha(min) approximately 0.67 of multifractal spectrum of DLA. This limiting case shows that the most singular tips in the pruned cluster now correspond to those expected for a purely one-dimensional line. Using multifractal analysis, analytic expressions are established for D(gamma) both close to the breakdown of DLA universality class, i.e., gamma less, similar 1, and close to the pinning transition, i.e., gamma greater, similar 1/2. PMID:14995617

  20. 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. PMID:27334191

  1. 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.

  2. 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.

  3. A mini review: proteoglycan aggregate profiles in the Pond-Nuki dog model of osteoarthritis and in canine disuse atrophy.

    PubMed

    Howell, D S; Muller, F; Manicourt, D H

    1992-01-01

    The Pond-Nuki dog model of osteoarthritis has characteristics which seem to mimic the human disease in early stages, particularly with respect to progressive changes in the cartilage matrix. Aggregating proteoglycans were studied using novel extraction and ultracentrifugation methods designed to separate very large macromolecules. With these methods two large peaks of proteoglycan (PG) aggregates (PGA-1 and PGA-2) were separated in preparative amounts and were shown to have unequivocal differences in composition in many respects. The profiles of these peaks have been studied as a function of joint location, topographic site, cartilage layer, presence of cartilage atrophy versus osteoarthritis, as well as treatment of the animals with various agents. Both link protein (essential for forming link-protein stabilized aggregates) and hyaluronate are required to regenerate normal aggregate profiles from the deficient aggregate fractions obtained from osteoarthritic cartilage. Canine proteoglycan link-stabilized aggregates (PGA-2) are confined to the middle and deep zone of cartilage. We believe that their reduction or elimination in the Pond-Nuki model results from a disturbance or loss of functional link protein (and hyaluronate), thereby weakening the middle and deep cartilage layers.

  4. A fast and accurate implementation of tunable algorithms used for generation of fractal-like aggregate models

    NASA Astrophysics Data System (ADS)

    Skorupski, Krzysztof; Mroczka, Janusz; Wriedt, Thomas; Riefler, Norbert

    2014-06-01

    In many branches of science experiments are expensive, require specialist equipment or are very time consuming. Studying the light scattering phenomenon by fractal aggregates can serve as an example. Light scattering simulations can overcome these problems and provide us with theoretical, additional data which complete our study. For this reason a fractal-like aggregate model as well as fast aggregation codes are needed. Until now various computer models, that try to mimic the physics behind this phenomenon, have been developed. However, their implementations are mostly based on a trial-and-error procedure. Such approach is very time consuming and the morphological parameters of resulting aggregates are not exact because the postconditions (e.g. the position error) cannot be very strict. In this paper we present a very fast and accurate implementation of a tunable aggregation algorithm based on the work of Filippov et al. (2000). Randomization is reduced to its necessary minimum (our technique can be more than 1000 times faster than standard algorithms) and the position of a new particle, or a cluster, is calculated with algebraic methods. Therefore, the postconditions can be extremely strict and the resulting errors negligible (e.g. the position error can be recognized as non-existent). In our paper two different methods, which are based on the particle-cluster (PC) and the cluster-cluster (CC) aggregation processes, are presented.

  5. Probing surface characteristics of diffusion-limited-aggregation clusters with particles of variable size

    NASA Astrophysics Data System (ADS)

    Menshutin, A. Yu.; Shchur, L. N.; Vinokur, V. M.

    2007-01-01

    We develop a technique for probing the harmonic measure of a diffusion-limited-aggregation (DLA) cluster surface with variable-size particles and generate 1000 clusters with 50×106 particles using an original off-lattice killing-free algorithm. Taking, in sequence, the limit of the vanishing size of the probing particles and then sending the growing cluster size to infinity, we achieve unprecedented accuracy in determining the fractal dimension D=1.7100(2) crucial to the characterization of the geometric properties of DLA clusters.

  6. 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

  7. 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.

  8. The study of MCF-7 cell aggregates encapsulated in alginate microbeads under the modeled weightlessness

    NASA Astrophysics Data System (ADS)

    Li, Yu; Zheng, Hongxia; Tian, Weiming; Yu, Lei; Zhang, Yao; Han, Fengtong

    Assessing the risks associated with exposure to the microgravity encountered in space is essential for the success of long-term space exploration. For understanding of the effects of microgravity, either traditional 2-dimensional (2D) cell cultures of adherent cell populations or animal models were typically used. The 2D in vitro systems do not allow assessment of the dynamic effects of intercellular interactions within tissues, whereas potentially confounding factors tend to be overlooked in animal models. Therefore novel cell culture model representative of the cellular interactions and with extracellular matrix present in tissues needs to be used. Toward this overall goal, 3D cell aggregates of breast cancer cell line MCF-7 was constructed by encapsu-lating in alginate microbeads. With this model we studied the simulated microgravity effects on MCF-7 by incubating the microbeads in NASA rotary cell culture system with a rate of 15rpm.We found MCF-7 showed higher proliferation rate than that of control group character-ized by up regulation of Ki-67. Further study showed that the effect was achieved by activating the MAPK intercellular signaling pathway. The result is inconsistent with previous conclusion obtained with 2D cell culture model which indicated that 3D cell culture model maybe better for elucidating the microgravity effects.

  9. 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,...

  10. 32 CFR Appendix A to Part 1285 - Gaining Access to DLA Records

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ..., Cameron Station, Alexandria, Virginia 22304-6100 The headquarters is organized by broad functional area... nonrestricted publications may be placed through DASC-PD, Cameron Station, Alexandria, VA 22304-6130. That... Logistics Agency, Attn: HQ DLA-XAM, Cameron Station, Alexandria, VA 22304-6100. Defense Construction...

  11. 32 CFR Appendix A to Part 300 - Access to DLA Records

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    .... Broad Street, Columbus, OH 43218-3990, Fax: 614-692-4385, Email: dscc.efoia@dla.mil—Maritime and land... Services, 5450 Carlisle Pike, Bldg 9, P.O. Box 2020, Mechanicsburg, PA 17055-0788, Fax: 717-605-3999,...

  12. What can trigger the onset of Parkinson's disease - A modeling study based on a compartmental model of α-synuclein transport and aggregation in neurons.

    PubMed

    Kuznetsov, I A; Kuznetsov, A V

    2016-08-01

    The aim of this paper is to develop a minimal model describing events leading to the onset of Parkinson's disease (PD). The model accounts for α-synuclein (α-syn) production in the soma, transport toward the synapse, misfolding, and aggregation. The production and aggregation of polymeric α-syn is simulated using a minimalistic 2-step Finke-Watzky model. We utilized the developed model to analyze what changes in a healthy neuron are likely to lead to the onset of α-syn aggregation. We checked the effects of interruption of α-syn transport toward the synapse, entry of misfolded (infectious) α-syn into the somatic and synaptic compartments, increasing the rate of α-syn synthesis in the soma, and failure of α-syn degradation machinery. Our model suggests that failure of α-syn degradation machinery is probably the most likely cause for the onset of α-syn aggregation leading to PD. PMID:27211070

  13. 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...

  14. Modeling Aggregation of Ionic Surfactants Using a Smeared Charge Approximation in Dissipative Particle Dynamics Simulations.

    PubMed

    Mao, Runfang; Lee, Ming-Tsung; Vishnyakov, Aleksey; Neimark, Alexander V

    2015-09-01

    Using dissipative particle dynamics (DPD) simulations, we explore the specifics of micellization in the solutions of anionic and cationic surfactants and their mixtures. Anionic surfactant sodium dodecyl sulfate (SDS) and cationic surfactant cetyltrimethylammonium bromide (CTAB) are chosen as characteristic examples. Coarse-grained models of the surfactants are constructed and parameterized using a combination of atomistic molecular simulation and infinite dilution activity coefficient calibration. Electrostatic interactions of charged beads are treated using a smeared charge approximation: the surfactant heads and dissociated counterions are modeled as beads with charges distributed around the bead center in an implicit dielectric medium. The proposed models semiquantitatively describe self-assembly in solutions of SDS and CTAB at various surfactant concentrations and molarities of added electrolyte. In particular, the model predicts a decline in the free surfactant concentration with the increase of the total surfactant loading, as well as characteristic aggregation transitions in single-component surfactant solutions caused by the addition of salt. The calculated values of the critical micelle concentration reasonably agree with experimental observations. Modeling of catanionic SDS-CTAB mixtures show consecutive transitions to worm-like micelles and then to vesicles caused by the addition of CTAB to micellar solution of SDS. PMID:26241704

  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. Simulating extremely metal-poor gas and DLA metal content at redshift z ≃ 7

    NASA Astrophysics Data System (ADS)

    Maio, Umberto; Ciardi, Benedetta; Müller, Volker

    2013-10-01

    We present the first theoretical study of metals in damped-Lyα (DLA) systems at redshift z ≃ 7. The features of cold, primordial gas are studied by means of N-body, hydro, chemistry simulations, including atomic and molecular non-equilibrium chemistry, cooling, star formation for Population III and Population II-I regimes, stellar evolution, cosmic metal spreading according to proper yields (for He, C, O, Si, Fe, Mg, S, etc.) and lifetimes and feedback effects. Theoretical expectations are then compared to recently available constraints from DLA observations. We find that DLA galaxies at z ≃ 7 account for ˜10 per cent of the whole galaxy population and for most of the metal-poor galaxies at these epochs. About 7 per cent of these DLA galaxies contain purely pristine material and ˜34 per cent of them consist of very weakly polluted gas, being, therefore, suitable candidates as Population III sites. The remaining ˜59 per cent are enriched above ˜10-4 Z⊙. Additionally, DLA candidates appear to have: gas masses ≲ 2 × 108 M⊙; very low star formation rate, ˜ 10- 3 - 10- 2 M⊙ yr- 1 (significantly weaker than late-time counterparts); mean molecular fractions covering a fairly wide range, xmol ˜ 10- 3-10- 6; typical metallicities Z ≲ 10-3 Z⊙ and H I column densities N_{H I}≳ 3× 10^{20} cm^{-2} (in agreement with recent observations). They present no or weak correlations between their gas mass and Z, N_{H I}, or xmol; a moderate correlation between xmol and Z, linked to the ongoing molecular-driven star formation and metal pollution processes; a mild anticorrelation between N_{H I} and xmol, due to H depletion into molecules; and a chemical content that is subject to environmental dependences.

  17. Random walks, diffusion limited aggregation in a wedge, and average conformal maps.

    PubMed

    Sander, Leonard M; Somfai, Ellák

    2005-06-01

    We investigate diffusion-limited aggregation (DLA) in a wedge geometry. Arneodo and collaborators have suggested that the ensemble average of DLA cluster density should be close to the noise-free selected Saffman-Taylor finger. We show that a different, but related, ensemble average, that of the conformal maps associated with random clusters, yields a nontrivial shape which is also not far from the Saffman-Taylor finger. However, we have previously demonstrated that the same average of DLA in a channel geometry is not the Saffman-Taylor finger. This casts doubt on the idea that the average of noisy diffusion-limited growth is governed by a simple transcription of noise-free results. PMID:16035911

  18. 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

  19. Electrical load models: Obtention and application to the identification of end uses at low aggregation levels

    NASA Astrophysics Data System (ADS)

    Fuentes Moreno, Juan Alvaro

    The knowledge of the load composition has a great interest for the Utilities as well as users and researchers. In this thesis a method that tries to obtain information about the load composition has been developed. Among its main characteristics are: it is non-intrusive, it can work continuously in real time and it can be used only at a low aggregation level. The load composition is obtained by means of measuring, for each phase, the voltage and total current waveform at the secondary of a distribution transformer. After this stage has been done, the total current absorbed, per phase, is decompose into a linear combination of predicted currents of loads present in our database of single electrical loads. These single electrical loads have been previously measured in the laboratory and their behaviour, under a distoted voltage supply, modelled. The model used for these individual loads is a generalization of the crossed frequency admittance matrix, a black box type model which tries to capture the relationship between the harmonic voltages of the voltage supplied and the absorbed harmonic currents. The performance of the method has been evaluated in tests in laboratory as well as in a real application, showing that, if the individual loads are grouped into groups of loads with similar electrical behaviour, then the results obtained can be representative of these groups.

  20. 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...

  1. A predictive aggregate transport model for microfiltration of combined macromolecular solutions and poly-disperse suspensions: model development.

    PubMed

    Baruah, Gautam Lal; Belfort, Georges

    2003-01-01

    A methodology, called the aggregate transport model, is presented that can a priori predict both the pressure-independent permeation flux and yield of target species for the microfiltration of poly-disperse solutions. The model captures the phenomenon of critical shear rate. Beyond the critical shear rate (expressed as a ratio of shear rate to permeation flux), the transmission of proteins drops sharply as a result of cake classification. The widely reported benefits of operating at uniform transmembrane pressure and constant wall concentration follow from this method. The methodology is general in nature and can be used predictively to obtain an optimal balance between flux and yield of target species during the microfiltration of many commercial poly-disperse suspensions. In the accompanying paper we test this model for microfiltration of transgenic whole goat milk.

  2. 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.

  3. 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.

  4. Horton and Tokunaga self-similarity in basic models of branching, aggregation, time series

    NASA Astrophysics Data System (ADS)

    Zaliapin, I.; Kovchegov, Y.

    2012-12-01

    Hierarchical branching structures are readily seen in river and drainage networks, lightening, botanical trees, vein structure of leaves, snowflakes, and bronchial passages, to mention but a few. Empirical evidence reveals a surprising similarity among natural hierarchies of diverse origin; many of them are closely approximated by so-called self-similar trees (SSTs). A two-parametric subclass of Tokunaga SSTs plays a special role in theory and applications, as it has been shown to emerge in unprecedented variety of modeled and natural phenomena. The Tokunaga SSTs with a broad range of parameters are seen in studies of river networks, aftershock sequences, vein structure of botanical leaves, numerical analyses of diffusion limited aggregation, two dimensional site percolation, and nearest-neighbor clustering in Euclidean spaces. The omnipresence of Tokunaga self-similarity hints at the existence of universal underlying mechanisms responsible for its appearance and prompts the question: What basic probability models may generate Tokunaga self-similar trees? This paper reviews the existing results on Tokunaga self-similarity of the critical binary Galton-Watson process, also known as Shreve's random topology model or equiprobable binary tree model. We then present new analytic results that establish Horton and Tokunaga self-similarity in (i) level-set tree representation of white noise, (ii) level-set tree representation of random walk and Brownian motion, and (iii) Kingman's coalescent process. We also formulate a conjecture, based on extensive numerical experiments, about Tokunaga self-similarity for the (iv) additive and (v) multiplicative coalescents as well as (vi) fractional Brownian motion. The listed processes are among the essential building blocks in natural and computer sciences modeling. Accordingly, the results of this study may provide at least a partial explanation for the presence of Horton and Tokunaga self-similarity in observed and modeled branching

  5. Multiparticle sintering dynamics: from fractal-like aggregates to compact structures.

    PubMed

    Eggersdorfer, Max L; Kadau, Dirk; Herrmann, Hans J; Pratsinis, Sotiris E

    2011-05-17

    Multiparticle sintering is encountered in almost all high temperature processes for material synthesis (titania, silica, and nickel) and energy generation (e.g., fly ash formation) resulting in aggregates of primary particles (hard- or sinter-bonded agglomerates). This mechanism of particle growth is investigated quantitatively by mass and energy balances during viscous sintering of amorphous aerosol materials (e.g., SiO(2) and polymers) that typically have a distribution of sizes and complex morphology. This model is validated at limited cases of sintering between two (equally or unequally sized) particles, and chains of particles. The evolution of morphology, surface area and radii of gyration of multiparticle aggregates are elucidated for various sizes and initial fractal dimension. For each of these structures that had been generated by diffusion limited (DLA), cluster-cluster (DLCA), and ballistic particle-cluster agglomeration (BPCA) the surface area evolution is monitored and found to scale differently than that of the radius of gyration (moment of inertia). Expressions are proposed for the evolution of fractal dimension and the surface area of aggregates undergoing viscous sintering. These expressions are important in design of aerosol processes with population balance equations (PBE) and/or fluid dynamic simulations for material synthesis or minimization and even suppression of particle formation. PMID:21488641

  6. 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.

  7. A novel thromboxane receptor antagonist, nstpbp5185, inhibits platelet aggregation and thrombus formation in animal models.

    PubMed

    Huang, Shiu-Wen; Kuo, Heng-Lan; Hsu, Ming-Tsung; Tseng, Yufeng Jane; Lin, Shu-Wha; Kuo, Sheng-Chu; Peng, Hui-Chin; Lien, Jin-Cherng; Huang, Tur-Fu

    2016-08-01

    A novel benzimidazole derivative, nstpbp5185, was discovered through in vitro and in vivo evaluations for antiplatelet activity. Thromaboxane receptor (TP) is important in vascular physiology, haemostasis and pathophysiological thrombosis. Nstpbp5185 concentration-dependently inhibited human platelet aggregation caused by collagen, arachidonic acid and U46619. Nstpbp5185 caused a right-shift of the concentration-response curve of U46619 and competitively inhibited the binding of 3H-SQ-29548 to TP receptor expressed on HEK-293 cells, with an IC50 of 0.1 µM, indicating that nstpbp5185 is a TP antagonist. In murine thrombosis models, nstpbp5185 significantly prolonged the latent period in triggering platelet plug formation in mesenteric and FeCl3-induced thrombi formation, and increased the survival rate in pulmonary embolism model with less bleeding than aspirin. This study suggests nstpbp5185, an orally selective anti-thrombotic agent, acting through blockade of TXA2 receptor, may be efficacious for prevention or treatment of pathologic thrombosis.

  8. 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.

  9. A novel thromboxane receptor antagonist, nstpbp5185, inhibits platelet aggregation and thrombus formation in animal models.

    PubMed

    Huang, Shiu-Wen; Kuo, Heng-Lan; Hsu, Ming-Tsung; Tseng, Yufeng Jane; Lin, Shu-Wha; Kuo, Sheng-Chu; Peng, Hui-Chin; Lien, Jin-Cherng; Huang, Tur-Fu

    2016-08-01

    A novel benzimidazole derivative, nstpbp5185, was discovered through in vitro and in vivo evaluations for antiplatelet activity. Thromaboxane receptor (TP) is important in vascular physiology, haemostasis and pathophysiological thrombosis. Nstpbp5185 concentration-dependently inhibited human platelet aggregation caused by collagen, arachidonic acid and U46619. Nstpbp5185 caused a right-shift of the concentration-response curve of U46619 and competitively inhibited the binding of 3H-SQ-29548 to TP receptor expressed on HEK-293 cells, with an IC50 of 0.1 µM, indicating that nstpbp5185 is a TP antagonist. In murine thrombosis models, nstpbp5185 significantly prolonged the latent period in triggering platelet plug formation in mesenteric and FeCl3-induced thrombi formation, and increased the survival rate in pulmonary embolism model with less bleeding than aspirin. This study suggests nstpbp5185, an orally selective anti-thrombotic agent, acting through blockade of TXA2 receptor, may be efficacious for prevention or treatment of pathologic thrombosis. PMID:27173725

  10. Experimental models for identifying modifiers of polyglutamine-induced aggregation and neurodegeneration.

    PubMed

    Calamini, Barbara; Lo, Donald C; Kaltenbach, Linda S

    2013-07-01

    Huntington's disease (HD) typifies a class of inherited neurodegenerative disorders in which a CAG expansion in a single gene leads to an extended polyglutamine tract and misfolding of the expressed protein, driving cumulative neural dysfunction and degeneration. HD is invariably fatal with symptoms that include progressive neuropsychiatric and cognitive impairments, and eventual motor disability. No curative therapies yet exist for HD and related polyglutamine diseases; therefore, substantial efforts have been made in the drug discovery field to identify potential drug and drug target candidates for disease-modifying treatment. In this context, we review here a range of early-stage screening approaches based in in vitro, cellular, and invertebrate models to identify pharmacological and genetic modifiers of polyglutamine aggregation and induced neurodegeneration. In addition, emerging technologies, including high-content analysis, three-dimensional culture models, and induced pluripotent stem cells are increasingly being incorporated into drug discovery screening pipelines for protein misfolding disorders. Together, these diverse screening strategies are generating novel and exciting new probes for understanding the disease process and for furthering development of therapeutic candidates for eventual testing in the clinical setting. PMID:23700210

  11. 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.

  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. Phase-field modeling of two-dimensional solute precipitation∕dissolution: solid fingers and diffusion-limited precipitation.

    PubMed

    Xu, Zhijie; Meakin, Paul

    2011-01-28

    Two-dimensional dendritic growth due to solute precipitation was simulated using a phase-field model reported earlier [Z. Xu and P. Meakin, J. Chem. Phys. 129, 014705 (2008)]. It was shown that diffusion-limited precipitation due to the chemical reaction at the solid-liquid interface has similarities with diffusion-limited aggregation (DLA). The diffusion-limited precipitation is attained by setting the chemical reaction rate much larger compared to the solute diffusion to eliminate the effect of the interface growth kinetics. The phase-field simulation results were in reasonable agreement with the analytical solutions. The fractal solid fingers can be formed in the diffusion-limited precipitation and have a fractal dimension measured d(f)=1.68, close to 1.64, the fractal dimensionality of large square lattice DLA clusters. PMID:21280717

  14. Phase-field modeling of two-dimensional solute precipitation/dissolution: Solid fingers and diffusion-limited precipitation

    NASA Astrophysics Data System (ADS)

    Xu, Zhijie; Meakin, Paul

    2011-01-01

    Two-dimensional dendritic growth due to solute precipitation was simulated using a phase-field model reported earlier [Z. Xu and P. Meakin, J. Chem. Phys. 129, 014705 (2008)]. It was shown that diffusion-limited precipitation due to the chemical reaction at the solid-liquid interface has similarities with diffusion-limited aggregation (DLA). The diffusion-limited precipitation is attained by setting the chemical reaction rate much larger compared to the solute diffusion to eliminate the effect of the interface growth kinetics. The phase-field simulation results were in reasonable agreement with the analytical solutions. The fractal solid fingers can be formed in the diffusion-limited precipitation and have a fractal dimension measured d_f = 1.68, close to 1.64, the fractal dimensionality of large square lattice DLA clusters.

  15. Phase-field modeling of two-dimensional solute precipitation/dissolution: Solid fingers and diffusion-limited precipitation

    SciTech Connect

    Zhijie Xu; Paul Meakin

    2011-01-01

    Two-dimensional dendritic growth due to solute precipitation was simulated using a phase-field model reported earlier [Z. Xu and P. Meakin, J. Chem. Phys. 129, 014705 (2008)]. It was shown that diffusion-limited precipitation due to the chemical reaction at the solid–liquid interface has similarities with diffusion-limited aggregation (DLA). The diffusion-limited precipitation is attained by setting the chemical reaction rate much larger compared to the solute diffusion to eliminate the effect of the interface growth kinetics. The phase-field simulation results were in reasonable agreement with the analytical solutions. The fractal solid fingers can be formed in the diffusion-limited precipitation and have a fractal dimension measured df = 1.68, close to 1.64, the fractal dimensionality of large square lattice DLA clusters.

  16. Mucin-vesicle interactions in model bile: evidence for vesicle aggregation and fusion before cholesterol crystal formation.

    PubMed

    Afdhal, N H; Niu, N; Nunes, D P; Bansil, R; Cao, X X; Gantz, D; Small, D M; Offner, G D

    1995-09-01

    Nucleation of cholesterol monohydrate crystals from bile is a critical step in the formation of cholesterol gallstones. Measurement of nucleation in model bile system and the characteristics of the initial nucleus have proven elusive. In this study we have used three separate physical chemical techniques to examine vesicle aggregation and fusion, including dynamic light scattering (DLS), transmission electron microscopy (TEM), and fluorescent biochemical assays. These assays enabled us to quantify the effect of biliary proteins, such as gallbladder mucin, on vesicle fusion and aggregation. In the absence of mucin, fusion is a relatively slow process occurring over 24 hours, whereas physiological concentrations of mucin are able to accelerate almost complete fusion of vesicles within 6 hours. Vesicle fusion and aggregation as characterized by TEM result in the formation of aggregates of multilamellar vesicles and giant fusion bodies associated with a background of mucin. These mucin-vesicle aggregate bodies may represent true nuclei and precede cholesterol monohydrate crystal nucleation. In future studies, these vesicle fusion assays can be used to quantitatively examine the effect of putative pro- and anti-nucleating proteins on the earliest steps of cholesterol crystal nucleation.

  17. 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

  18. Growth of Silicon Nanosheets Under Diffusion-Limited Aggregation Environments.

    PubMed

    Lee, Jaejun; Kim, Sung Wook; Kim, Ilsoo; Seo, Dongjea; Choi, Heon-Jin

    2015-12-01

    The two-dimensional (2D) growth of cubic-structured (silicon) Si nanosheets (SiNSs) was investigated. Freestanding, single-crystalline SiNSs with a thickness of 5-20 nm were grown on various Si substrates under an atmospheric chemical vapor deposition process. Systematic investigation indicated that a diffusion-limited aggregation (DLA) environment that leads to dendritic growth in <110> directions at the initial stage is essential for 2D growth. The kinetic aspects under DLA environments that ascribe to the dendritic and 2D growth were discussed. Under the more dilute conditions made by addition of Ar to the flow of H2, the SiNSs grew epitaxially on the substrates with periodic arrangement at a specific angle depending on the orientation of the substrate. It reveals that SiNSs always grew two dimensionally with exposing (111) surfaces. That is thermodynamically favorable. PMID:26518028

  19. Growth of Silicon Nanosheets Under Diffusion-Limited Aggregation Environments

    NASA Astrophysics Data System (ADS)

    Lee, Jaejun; Kim, Sung Wook; Kim, Ilsoo; Seo, Dongjea; Choi, Heon-Jin

    2015-10-01

    The two-dimensional (2D) growth of cubic-structured (silicon) Si nanosheets (SiNSs) was investigated. Freestanding, single-crystalline SiNSs with a thickness of 5-20 nm were grown on various Si substrates under an atmospheric chemical vapor deposition process. Systematic investigation indicated that a diffusion-limited aggregation (DLA) environment that leads to dendritic growth in <110> directions at the initial stage is essential for 2D growth. The kinetic aspects under DLA environments that ascribe to the dendritic and 2D growth were discussed. Under the more dilute conditions made by addition of Ar to the flow of H2, the SiNSs grew epitaxially on the substrates with periodic arrangement at a specific angle depending on the orientation of the substrate. It reveals that SiNSs always grew two dimensionally with exposing (111) surfaces. That is thermodynamically favorable.

  20. Fractal aggregation growth and the surrounding diffusion field

    NASA Astrophysics Data System (ADS)

    Miyashita, Satoru; Saito, Yukio; Uwaha, Makio

    2005-10-01

    Silver metal trees grow and form a forest at the edge of a Cu plate in the AgNO3 water solution in a two-dimensional ( d=2) cell. The local structure of the forest is similar to that of the diffusion-limited aggregation (DLA), but the whole pattern approaches a uniform structure. Its growth dynamics is characterized by the fractal dimension Df of DLA. Time-dependence of the tip height is found to satisfy the scaling relation with the solute concentration c, and the asymptotic growth velocity V is consistent with the power law V˜c expected from the theory. The thickness ξc of the diffusion boundary layer is measured by the Michelson interferometry, and the scaling relation is also confirmed.

  1. 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

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

    NASA Astrophysics Data System (ADS)

    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.

  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. 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.

  5. A Coarse-Grained Model for Polyglutamine Aggregation Modulated by Amphipathic Flanking Sequences

    PubMed Central

    Ruff, Kiersten M.; Khan, Siddique J.; Pappu, Rohit V.

    2014-01-01

    The aggregation of proteins with expanded polyglutamine (polyQ) tracts is directly relevant to the formation of neuronal intranuclear inclusions in Huntington’s disease. In vitro studies have uncovered the effects of flanking sequences as modulators of the driving forces and mechanisms of polyQ aggregation in sequence segments associated with HD. Specifically, a seventeen-residue amphipathic stretch (N17) that is directly N-terminal to the polyQ tract in huntingtin decreases the overall solubility, destabilizes nonfibrillar aggregates, and accelerates fibril formation. Published results from atomistic simulations showed that the N17 module reduces the frequency of intermolecular association. Our reanalysis of these simulation results demonstrates that the N17 module also reduces interchain entanglements between polyQ domains. These two effects, which are observed on the smallest lengthscales, are incorporated into phenomenological pair potentials and used in coarse-grained Brownian dynamics simulations to investigate their impact on large-scale aggregation. We analyze the results from Brownian dynamics simulations using the framework of diffusion-limited cluster aggregation. When entanglements prevail, which is true in the absence of N17, small spherical clusters and large linear aggregates form on distinct timescales, in accord with in vitro experiments. Conversely, when entanglements are quenched and a barrier to intermolecular associations is introduced, both of which are attributable to N17, the timescales for forming small species and large linear aggregates become similar. Therefore, the combination of a reduction of interchain entanglements through homopolymeric polyQ and barriers to intermolecular associations appears to be sufficient for providing a minimalist phenomenological rationalization of in vitro observations regarding the effects of N17 on polyQ aggregation. PMID:25185558

  6. Tests of the pesticide root zone model and the aggregate model for transport and transformation of aldicarb, metolachlor, and bromide

    SciTech Connect

    Parrish, R.S.; Smith, C.N.; Fong, F.K.

    1992-01-01

    Mathematical models are widely used to predict leaching of pesticides and nutrients in agricultural systems. The work was conducted to investigate the predictive capability of the Pesticide Root Zone Model (PRZM) and the Aggregate Model (AGGR) for the pesticides aldicarb (2-methyl-2-(methylthio)propionaldehyde-O-(methyl-carbamoyl)oxime), metolachlor (2-chloro-N-(2-ethyl-6-methylphenyl)-N-(2-methoxy-1-methylethyl)acetamide) and for a bromide tracer. Model predictions were compared with data collected from 1984 to 1987 in the Dougherty Plain area of southwestern Georgia. Field data were used to estimate mean concentrations of pesticide and bromide residues in the soil profile on various dates after application in each of four growing seasons. Both models tended to predict rates of movement of bromide tracer compounds in excess of that observed. For metolachlor, a pesticide with a soprption-partition coefficient that is higher than for other compounds in the study, both models provided reasonably accurate predictions within the upper 30-cm zone. For the pesticide aldicarb, results were more variable.

  7. A study of the circum-galactic medium at z ˜ 0.6 using DLA-galaxies

    NASA Astrophysics Data System (ADS)

    Rahmani, Hadi; Péroux, Céline; Turnshek, David A.; Rao, Sandhya M.; Quiret, Samuel; Hamilton, Timothy S.; Kulkarni, Varsha P.; Monier, Eric M.; Zafar, Tayyaba

    2016-08-01

    We present the study of a sample of nine QSO fields, with damped-Lyα (DLA) or sub-DLA systems at z ˜ 0.6, observed with the X-Shooter spectrograph at the Very Large Telescope. By suitably positioning the X-Shooter slit based on high spatial resolution images of HST/ACS we are able to detect absorbing galaxies in 7 out of 9 fields (˜ 78% success rate) at impact parameters from 10 to 30 kpc. In 5 out of 7 fields the absorbing galaxies are confirmed via detection of multiple emission lines at the redshift of DLAs where only 1 out of 5 also emits a faint continuum. In 2 out of these 5 fields we detect a second galaxy at the DLA redshift. Extinction corrected star formation rates (SFR) of these DLA-galaxies, estimated using their Hα fluxes, are in the range 0.3-6.7 M⊙ yr-1. The emission metallicities of these five DLA-galaxies are estimated to be from 0.2 to 0.9 Z⊙. Based on the Voigt profile fits to absorption lines we find the metallicity of the absorbing neutral gas to be in a range of 0.05-0.6 Z⊙. The two remaining DLA-galaxies are quiescent galaxies with SFR < 0.4 M⊙ yr-1 (3σ) presenting continuum emission but weak or no emission lines. Using X-Shooter spectrum we estimate i-band absolute magnitude of -19.5 ± 0.2 for both these DLA-galaxies that indicates they are sub-L⋆ galaxies. Comparing our results with that of other surveys in the literature we find a possible redshift evolution of the SFR of DLA-galaxies.

  8. Partitioning the aggregation of parasites on hosts into intrinsic and extrinsic components via an extended Poisson-gamma mixture model.

    PubMed

    Calabrese, Justin M; Brunner, Jesse L; Ostfeld, Richard S

    2011-01-01

    It is well known that parasites are often highly aggregated on their hosts such that relatively few individuals host the large majority of parasites. When the parasites are vectors of infectious disease, a key consequence of this aggregation can be increased disease transmission rates. The cause of this aggregation, however, is much less clear, especially for parasites such as arthropod vectors, which generally spend only a short time on their hosts. Regression-based analyses of ticks on various hosts have focused almost exclusively on identifying the intrinsic host characteristics associated with large burdens, but these efforts have had mixed results; most host traits examined have some small influence, but none are key. An alternative approach, the Poisson-gamma mixture distribution, has often been used to describe aggregated parasite distributions in a range of host/macroparasite systems, but lacks a clear mechanistic basis. Here, we extend this framework by linking it to a general model of parasite accumulation. Then, focusing on blacklegged ticks (Ixodes scapularis) on mice (Peromyscus leucopus), we fit the extended model to the best currently available larval tick burden datasets via hierarchical Bayesian methods, and use it to explore the relative contributions of intrinsic and extrinsic factors on observed tick burdens. Our results suggest that simple bad luck-inhabiting a home range with high vector density-may play a much larger role in determining parasite burdens than is currently appreciated. PMID:22216216

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

    PubMed

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

    2015-08-10

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

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

    PubMed

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

    2015-08-10

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

  11. Analytical and modeling investigations of volume fraction of interfacial layers around ellipsoidal aggregate particles in multiphase materials

    NASA Astrophysics Data System (ADS)

    Xu, W. X.; Chen, H. S.

    2013-01-01

    The determination of the volume fraction of interfacial layers is very significant for assessing the quantitative relationship between the microstructure and macroscopic physical properties of complex multiphase materials. In this work, based on a three-phase composite structure, an approximate analytical model for the volume fraction of interfacial layers around ellipsoidal aggregate particles is presented in detail. To verify the accuracy and reliability of the derived analytical model, a numerical model is introduced by means of random packing of polydispersed ellipsoidal aggregate particles, in which the relative spatial position between an arbitrary point and an ellipsoidal particle is precisely and conveniently determined. With the analytical and numerical models applied, the dependence of the volume fraction of interfacial layers on various factors, such as the particle shape, the volume fraction and the maximum particle size of aggregates, and the thickness of the interfacial layers, is evaluated. Furthermore, the results from the analytical model and the numerical model with these factors are compared. It is found that the theoretical results are favorably consistent with the simulated results.

  12. Transition in the fractal properties from diffusion-limited aggregation to Laplacian growth via their generalization.

    PubMed

    Hentschel, H George E; Levermann, Anders; Procaccia, Itamar

    2002-07-01

    We study the fractal and multifractal properties (i.e., the generalized dimensions of the harmonic measure) of a two-parameter family of growth patterns that result from a growth model that interpolates between diffusion-limited aggregation (DLA) and Laplacian growth patterns in two dimensions. The two parameters are beta that determines the size of particles accreted to the interface, and C that measures the degree of coverage of the interface by each layer accreted to the growth pattern at every growth step. DLA and Laplacian growth are obtained at beta=0, C=0 and beta=2, C=1, respectively. The main purpose of this paper is to show that there exists a line in the beta-C phase diagram that separates fractal (D<2) from nonfractal (D=2) growth patterns. Moreover, Laplacian growth is argued to lie in the nonfractal part of the phase diagram. Some of our arguments are not rigorous, but together with the numerics they indicate this result rather strongly. We first consider the family of models obtained for beta=0, C>0, and derive for them a scaling relation D=2D(3). We then propose that this family has growth patterns for which D=2 for some C>C(cr), where C(cr) may be zero. Next we consider the whole beta-C phase diagram and define a line that separates two-dimensional growth patterns from fractal patterns with D<2. We explain that Laplacian growth lies in the region belonging to two-dimensional growth patterns, motivating the main conjecture of this paper, i.e., that Laplacian growth patterns are two dimensional. The meaning of this result is that the branches of Laplacian growth patterns have finite (and growing) area on scales much larger than any ultraviolet cutoff length. PMID:12241482

  13. 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.

  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. 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. PMID:26071898

  16. Failure of donor lymphocyte infusion to prevent graft rejection in dogs given DLA-identical marrow after 1 Gy of total body irradiation.

    PubMed

    Baron, Frédéric; Sandmaier, Brenda M; Zellmer, Eustacia; Sorror, Mohamed; Storer, Barry; Storb, Rainer

    2006-08-01

    We investigated in a preclinical canine model of hematopoietic cell transplantation (HCT) whether preemptive donor lymphocyte infusion (DLI) given 1 month after HCT could prevent late graft rejection that was the rule in historical dogs given suboptimal conditioning with 1 Gy of total body irradiation (TBI) before and immunosuppression with cyclosporine (CSP) and either mycophenolate mofetil (MMF; n = 6) or rapamycin (n = 5) after dog leukocyte antigen (DLA)-identical marrow transplantation. Nine dogs given DLA-identical marrow after 1 Gy of TBI followed by postgrafting MMF and CSP were studied. A single DLI was given 28-36 days after HCT, either with (n = 5) or without (n = 4) preceding treatment with the immunosuppressive drug pentostatin. Two of the 4 dogs given DLI only maintained stable mixed donor-host chimera beyond 30 weeks after HCT, whereas 2 rejected their grafts, on weeks 10 and 15 after HCT. One of the 5 dogs given pentostatin before DLI maintained a stable mixed donor-host chimera beyond 30 weeks, whereas 4 rejected their grafts, at weeks 8, 12, 12, and 16 after HCT. The 30-week probability of stable mixed chimerism was 33% among dogs given DLI, versus 0% among 11 historical dogs (P = .003). In conclusion, DLI was only moderately effective in preventing graft rejection in this model. Additional immunosuppression with pentostatin did not improve that outcome. The model might be useful in developing potential strategies aimed at preventing graft rejection in patients with low donor chimerism levels. PMID:16864051

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. Model calculations on the transitions between surfactant aggregates on different shapes

    SciTech Connect

    Eriksson, J.C.; Ljunggren, S. )

    1990-05-01

    In a series of papers published earlier, the authors presented theories about the formation of surfactant micelles which include detailed treatments of the mechanics, surface thermodynamics, and small system thermodynamics of spherical, rod-shaped, and disk-shaped aggregates. In the present paper, they develop a calculation scheme which yields the volume fractions of the various kinds of sodium dodecyl sulfate (SDS) micelles and also of SDS vesicles, at different solution states. The familiar hierarchy of surfactant aggregates of different shapes is generated automatically upon raising the salt concentration, i.e., without introducing any extraneous packing or geometrical constraints, and is due to the more rapid decrease of the electrostatic free energy for the less curved aggregate surfaces.

  2. Digestion-ligation-amplification (DLA): a simple genome walking method to amplify unknown sequences flanking mutator (Mu) transposons and thereby facilitate gene cloning.

    PubMed

    Liu, Sanzhen; Hsia, An-Ping; Schnable, Patrick S

    2013-01-01

    Digestion-ligation-amplification (DLA), a novel PCR-based genome walking method, was developed to amplify unknown sequences flanking known sequences of interest. DLA specifically overcomes the problems associated with amplifying genomic sequences flanking high copy number transposons in large genomes. Two DLA-based strategies, MuClone and DLA-454, were developed to isolate Mu-tagged alleles. MuClone allows for the amplification of DNA flanking 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 co-segregate with mutant phenotypes caused by Mu insertions. DLA-454, which combines DLA with 454 pyrosequencing, permits the efficient amplification and sequencing of Mu flanking regions in a high-throughput manner.

  3. Use of magnetic forces to promote stem cell aggregation during differentiation, and cartilage tissue modeling.

    PubMed

    Fayol, D; Frasca, G; Le Visage, C; Gazeau, F; Luciani, N; Wilhelm, C

    2013-05-14

    Magnetic forces induce cell condensation necessary for stem cell differentiation into cartilage and elicit the formation of a tissue-like structure: Magnetically driven fusion of aggregates assembled by micromagnets results in the formation of a continuous tissue layer containing abundant cartilage matrix. PMID:23526452

  4. 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.

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

    PubMed

    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.

  6. 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

  7. 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.

  8. 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

  9. 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. PMID:23134500

  10. A Describing Function Approach to Aggregating High-Resolution Land-Surface Data for Macroscale Hydrologic Modeling

    NASA Astrophysics Data System (ADS)

    Knowles, N.; Georgakakos, K. P.

    2002-12-01

    A new methodology is presented for development of macroscale hydrologic model percolation parameters from a spatial database of soil properties. This approach is applied to three distinct catchments within California- the Kings, American, and lower Eel river basins. Each unique vertical soil profile in these catchments is divided into an upper and a lower layer based on permeability gradients. A one-dimensional numerical unsaturated flow model is applied to each profile to yield percolation from upper to lower layers as a function of lower layer moisture deficit. A Holtan-type power law relationship is postulated to adequately represent profile percolation, with parameters estimated by curve-fitting the numerical model results. These parameters are then aggregated from the scale of the observable soil profiles to the level of the macroscale hydrologic model elements in a mass-conserving manner. In this process, the power law relationship is considered a describing function approximation to the numerical model response. To estimate parameter and flux uncertainties, a Monte Carlo approach is employed in which the soil property values are sampled randomly within the uncertainty ranges provided in the soils database or established by previous studies in the literature. The resulting ensembles of soil profiles are used in the describing function method to generate ensembles of hydrologic parameter spatial distributions for the catchments of interest. These ensembles are used as measures of hydrologic parameter uncertainty. The relationship between aggregate moisture flux and soil parameter distributions is explored, as is the dependence of mean parameter and aggregate flux values and their respective uncertainties on spatial scale. The methodology presented provides a useful means of investigating model-process observability given present-day soils databases, and a robust method for determining physically based macro-scale hydrologic parameters for subsequent

  11. An in vitro model of granuloma-like cell aggregates substantiates early host immune responses against Mycobacterium massiliense infection

    PubMed Central

    Je, Sungmo; Quan, Hailian; Na, Yirang; Cho, Sang-Nae; Kim, Bum-Joon

    2016-01-01

    ABSTRACT Mycobacterium massiliense (M. mass), belonging to the M. abscessus complex, is a rapidly growing mycobacterium that is known to cause tuberculous-like lesions in humans. To better understand the interaction between host cells and M. mass, we used a recently developed in vitro model of early granuloma-like cell aggregates composed of human peripheral blood mononuclear cells (PBMCs). PBMCs formed granuloma-like, small and rounded cell aggregates when infected by live M. mass. Microscopic examination showed monocytes and macrophages surrounded by lymphocytes, which resembled cell aggregation induced by M. tuberculosis (M. tb). M. mass-infected PBMCs exhibited higher expression levels of HLA-DR, CD86 and CD80 on macrophages, and a significant decrease in the populations of CD4+ and CD8+ T cells. Interestingly, low doses of M. mass were sufficient to infect PBMCs, while active host cell death was gradually induced with highly increased bacterial loads, reflecting host destruction and dissemination of virulent rapid-growing mycobacteria (RGM). Collectively, this in vitro model of M. mass infection improves our understanding of the interplay of host immune cells with mycobacteria, and may be useful for developing therapeutics to control bacterial pathogenesis. PMID:27489303

  12. Modeling of fractal intermediates in the self-assembly of silicatein filaments

    NASA Astrophysics Data System (ADS)

    Murr, Meredith; Thakur, Gunjan; Mezic, Igor; Morse, Daniel

    2006-03-01

    Silicateins are proteins with catalytic, structure-directing activity that are responsible for silica biosynthesis in certain sponges, Self-assembly of the silicatein monomers and oligomers was previously shown experimentally (Murr and Morse 2005) to form fibrous structures through the formation of diffusion limited, fractally patterned aggregates on the path to filament formation. We present a diffusion-limited aggregation (DLA) based model that is capable of capturing the basic properties of this self-assembly process. The Silicatein oligomer is modeled with three sites of attachment. Rules of attachment are specified that allow for specific interaction between these sites when oligomers are in proximity. The process differs from a DLA process in the following: 1) The process of aggregation is continued dynamically, i.e. the growing structures are spatially distributed and keep diffusing as they are growing 2) The molecules are oriented. Thus rotational diffusion is important. 3) The attachment can happen at more than 1 site and the strength of the active sites can be varied. We show that the self-assembled structures have a good level of similarity with the in-vitro experimental results. We quantify this by comparing the fractal dimension of the experimental data and the model output.

  13. Emergence of multicellularity in a model of cell growth, death and aggregation under size-dependent selection

    PubMed Central

    Duran-Nebreda, Salva; Solé, Ricard

    2015-01-01

    How multicellular life forms evolved from unicellular ones constitutes a major problem in our understanding of the evolution of our biosphere. A recent set of experiments involving yeast cell populations have shown that selection for faster sedimenting cells leads to the appearance of stable aggregates of cells that are able to split into smaller clusters. It was suggested that the observed evolutionary patterns could be the result of evolved programmes affecting cell death. Here, we show, using a simple model of cell–cell interactions and evolving adhesion rates, that the observed patterns in cluster size and localized mortality can be easily interpreted in terms of waste accumulation and toxicity-driven apoptosis. This simple mechanism would have played a key role in the early evolution of multicellular life forms based on both aggregative and clonal development. The potential extensions of this work and its implications for natural and synthetic multicellularity are discussed. PMID:25551152

  14. 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.

  15. 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

  16. 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

  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. 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.

  19. 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.

  20. Particle-based simulation of ellipse-shaped particle aggregation as a model for vascular network formation

    NASA Astrophysics Data System (ADS)

    Palachanis, Dimitrios; Szabó, András; Merks, Roeland M. H.

    2015-12-01

    Computational modeling is helpful for elucidating the cellular mechanisms driving biological morphogenesis. Previous simulation studies of blood vessel growth based on the cellular Potts model proposed that elongated, adhesive or mutually attractive endothelial cells suffice for the formation of blood vessel sprouts and vascular networks. Because each mathematical representation of a model introduces potential artifacts, it is important that model results are reproduced using alternative modeling paradigms. Here, we present a lattice-free, particle-based simulation of the cell elongation model of vasculogenesis. The new, particle-based simulations confirm the results obtained from the previous cellular Potts simulations. Furthermore, our current findings suggest that the emergence of order is possible with the application of a high enough attractive force or, alternatively, a longer attraction radius. The methodology will be applicable to a range of problems in morphogenesis and noisy particle aggregation in which cell shape is a key determining factor.

  1. Construction aggregates

    USGS Publications Warehouse

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

    2000-01-01

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

  2. Construction aggregates

    USGS Publications Warehouse

    Tepordei, V.V.

    1994-01-01

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

  3. Assessment of the efficacy of solutes from extremophiles on protein aggregation in cell models of Huntington's and Parkinson's diseases.

    PubMed

    Jorge, Carla D; Ventura, Rita; Maycock, Christopher; Outeiro, Tiago F; Santos, Helena; Costa, Júlia

    2011-06-01

    Protein misfolding and deposition in the brain are implicated in the etiology of numerous neurodegenerative disorders. Here, organic solutes characteristic of microorganisms adapted to hot environments, were tested on experimental cell models of Huntington's and Parkinson's diseases. Diglycerol phosphate, di-myo-inositol phosphate, mannosylglycerate, and mannosylglyceramide were not toxic to the cells, at 10 mM concentration, but caused a decrease in cell density, which suggested an effect on proliferation. In contrast, mannosyl-lactate, an artificial analogue of mannosylglycerate, had a negative impact on cell viability. Concerning protein aggregation, inclusions of mutant huntingtin were reduced in the presence of diglycerol phosphate and di-myo-inositol phosphate, increased with mannosylglycerate, while mannosyl-lactate and mannosylglyceramide had no significant effect. α-Synuclein aggregation was not affected by the solutes tested, except for di-myo-inositol phosphate that led to a slight increased percentage of cells displaying visible aggregates. These solutes might be useful in the development of therapies for protein misfolding diseases.

  4. 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

    2014-02-01

    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

  5. 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...

  6. 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.

  7. 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.

  8. 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... Defense (Continued) DEPARTMENT OF THE ARMY SUPPLIES AND EQUIPMENT LOAN AND SALE OF PROPERTY § 621.1 Loan of Army/Defense Logistics Agency (DLA) owned property for use at national and State conventions....

  9. 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... Defense (Continued) DEPARTMENT OF THE ARMY SUPPLIES AND EQUIPMENT LOAN AND SALE OF PROPERTY § 621.1 Loan of Army/Defense Logistics Agency (DLA) owned property for use at national and State conventions....

  10. 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) owned property for use at national and State conventions. 621.1 Section 621.1 National Defense... § 621.1 Loan of Army/Defense Logistics Agency (DLA) owned property for use at national and...

  11. 32 CFR 621.1 - Loan of Army/Defense Logistics Agency (DLA) owned property for use at national and State...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 32 National Defense 3 2014-07-01 2014-07-01 false Loan of Army/Defense Logistics Agency (DLA) owned property for use at national and State conventions. 621.1 Section 621.1 National Defense... § 621.1 Loan of Army/Defense Logistics Agency (DLA) owned property for use at national and...

  12. 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

  13. 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

  14. 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.

  15. 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).

  16. 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.

  17. Sir2 is induced by oxidative stress in a yeast model of Huntington disease and its activation reduces protein aggregation.

    PubMed

    Sorolla, M Alba; Nierga, Clara; Rodríguez-Colman, M José; Reverter-Branchat, Gemma; Arenas, Alicia; Tamarit, Jordi; Ros, Joaquim; Cabiscol, Elisa

    2011-06-01

    Huntington disease (HD) is a neurodegenerative disorder caused by expansion of CAG trinucleotide repeats, leading to an elongated polyglutamine sequence (polyQ) in the huntingtin protein. Misfolding of mutant polyQ proteins with expanded tracts results in aggregation, causing cytotoxicity. Oxidative stress in HD has been documented in humans as important to disease progression. Using yeast cells as a model of HD, we report that when grown at high glucose concentration, cells expressing mutant polyQ do not show apparent oxidative stress. At higher cell densities, when glucose becomes limiting and cells are metabolically shifting from fermentation to respiration, protein oxidation and catalase activity increases in relation to the length of the polyQ tract. Oxidative stress, either endogenous as a result of mutant polyQ expression or exogenously generated, increases Sir2 levels. Δ sir2 cells expressing expanded polyQ lengths show signs of oxidative stress even at the early exponential phase. In a wild-type background, isonicotinamide, a Sir2 activator, decreases mutant polyQ aggregation and the stress generated by expanded polyQ. Taken together, these results describe mutant polyQ proteins as being more toxic in respiring cells, causing oxidative stress and an increase in Sir2 levels. Activation of Sir2 would play a protective role against this toxicity. PMID:21513696

  18. Distance-decay patterns of nutrient loading at watershed scale: Regression modeling with a special spatial aggregation strategy

    NASA Astrophysics Data System (ADS)

    Zhang, Tao

    2011-05-01

    SummaryThe effect of distance-decay on nutrient flux usually plays an important role in nutrient retention from non-point sources to surface waters. However, the distance-decay effect has been inappropriately neglected in many studies that adopted regression modeling method to quantify the relationship between watershed landscape and in-stream nutrient loading level. The goal of this study was to develop non-linear regression models that better quantify the role of distance on non-point source nutrient loads in rivers by using simulation results of a spatially-explicit model applied to the watersheds in the Upper Chattahoochee River Basin, Georgia. Because a detailed spatially-explicit modeling approach typically simulates the nutrient flux across the entire watershed, it provides opportunities to examine the nutrient decay patterns at watershed scale. The simulation results confirmed that regarding the effect of flow distance on nutrient loading, the exponential decay setting in the spatially-explicit model performs well. Other heterogeneous factors including slope and soil conditions do affect the decay results but not strongly enough to change the general exponential patterns. The nutrient contribution from areas that were greater than 300 meters to the river network was negligible. It was also found that the decay rate for urban lands is lower than that for other land-covers. Based on these findings, a spatial aggregation strategy in the lateral dimension of the river network was adopted and eight non-linear regression models which explicitly addressed the effects of distance-decay were designed to estimate the nutrient annual average loads. The model validation results showed that three of them can well estimate the nutrient loads. This study shows the usage of stream-lateral-dimension aggregation strategy in addressing nutrient distance-decay patterns and developing simple regression models of nutrient loading. This study also illustrates the advantages of

  19. 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.

  20. 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.

  1. Construction aggregates

    USGS Publications Warehouse

    Tepordei, V.V.

    1993-01-01

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

  2. Marrow grafts between phenotypically DLA-identical and haploidentical unrelated dogs: additional antigens controlling engraftment are not detected by cell-mediated lympholysis

    SciTech Connect

    Deeg, H.J.; Storb, R.; Raff, R.F.; Weiden, P.L.; DeRose, S.; Thomas, E.D.

    1982-01-01

    Bone marrow transplants with low marrow cell doses (less than or equal to4 X 10/sup 8/ cells/kg) from unrelated donors were carried out in 16 dogs conditioned with 9 Gy (900 rad) of total body irradiation. No immunosuppression was given after grafting. Eleven donor-recipient pairs were phenotypically identical (group 1) for the known antigens of the canine major histocompatibility complex (DLA) and in five the donor was homozygous and the recipient heterozygous for DLA (group 2), as determined by serological histocompatibility typing and mixed leukocyte cultures including homozygous cell typing. In addition, lymphocytes from donors and recipients in group 1 were mutually nonreactive in cell-mediated lympholysis; lymphocytes from recipients in group 2 were not cytotoxic against donor cells. Eight dogs rejected their grafts and eight showed sustained engraftment; of these, four died from graft-versus-host disease. The incidence of rejection was higher than in DLA-identical littermates but lower than in DLA-nonidentical unrelated or littermate dogs. These results indicate that antigens different from the recognized alleles at DLA are involved in the control of engraftment. These antigens most likely represent the expression of unrecognized differences within DLA or are coded for by a locus different from but linked to DLA-A, B, C or D; they are not recognized in the cell-mediated lympholysis assay.

  3. Silver self aggregation in a nanodevice for enhanced Raman spectroscopy: experiments vs. simplified modeling via molecular dynamics.

    PubMed

    Babiaczyk, Wojtek Iwo; Bonella, Sara; Ciccotti, Giovanni; Coluccio, Maria Laura; Gentile, Francesco; Di Fabrizio, Enzo

    2012-04-01

    We present a study, via experiments and exploratory molecular dynamics simulations, of self aggregation in cylindrical nanostructures obtained experimentally by combining high resolution electron beam lithography with electroless silver deposition. This process is key to the fabrication of a nanolens device, where a strong surface enhancement can be exploited for Raman spectroscopy. In order to investigate the process, we introduce a simple theoretical model and compare the results of simulations with the fabricated silver nanostructures during the growth phase. Our simulations qualitatively agree with the experiments and allow a general characterization of the process at length scales smaller than those easily accessible by microscopy. We identify a geometrical parameter, the aspect ratio of the cylinder, that relates two different types of growth with different characteristics and, possibly, different Raman enhancements.

  4. Scaling exponent of the maximum growth probability in diffusion-limited aggregation.

    PubMed

    Jensen, Mogens H; Mathiesen, Joachim; Procaccia, Itamar

    2003-04-01

    An early (and influential) scaling relation in the multifractal theory of diffusion limited aggregation (DLA) is the Turkevich-Scher conjecture that relates the exponent alpha(min) that characterizes the "hottest" region of the harmonic measure and the fractal dimension D of the cluster, i.e., D=1+alpha(min). Due to lack of accurate direct measurements of both D and alpha(min), this conjecture could never be put to a serious test. Using the method of iterated conformal maps, D was recently determined as D=1.713+/-0.003. In this paper, we determine alpha(min) accurately with the result alpha(min)=0.665+/-0.004. We thus conclude that the Turkevich-Scher conjecture is incorrect for DLA. PMID:12786408

  5. Prediction of reversible IgG1 aggregation occurring in a size exclusion chromatography column is enabled through a model based approach.

    PubMed

    Ojala, Frida; Sellberg, Anton; Hansen, Thomas Budde; Hansen, Ernst Broberg; Nilsson, Bernt

    2015-09-01

    One important aspect of antibody separation being studied today is aggregation, as this not only leads to a loss in yield, but aggregates can also be hazardous if injected into the body. The aim of this study was to determine whether the methodology applied in the previous study could be used to predict the aggregation of a different batch of IgG1, and to model the aggregation occurring in a SEC column. Aggregation was found to be reversible. The equilibrium parameter was found to be 272 M(-1) and the reaction kinetic parameter 1.33 × 10(-5) s(-1) , both within the 95% confidence interval of the results obtained in the previous work. The effective diffusivities were estimated to be 1.45 × 10(-13) and 1.90 10(-14) m(2) /s for the monomers and dimers, respectively. Good agreement was found between the new model and the chromatograms obtained in the SEC experiments. The model was also able to predict the decrease of dimers due to the dilution and separation in the SEC column during long retention times.

  6. Construction aggregates

    USGS Publications Warehouse

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

    2001-01-01

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

  7. Effects of Spatial Aggregation of Soil Spatial Information on Watershed Hydrological Modeling

    NASA Astrophysics Data System (ADS)

    Li, R.; Zhu, A.; Song, X.

    2011-12-01

    Impacts of detailed soil spatial information on hydrological modeling across different spatial scales are lack of comprehensive understanding. This paper examines such effects by comparing the simulated runoffs across scales from watershed models based on two different levels of soil spatial information, 10 meter resolution soil data derived from SoLIM and the 1:24 000 scale Soil Survey Geographic (SSURGO) data base. The examination was conducted at three different spatial scales: two at different watershed size levels and one at the model minimum simulation unit level. A fully distributed hydrologic model and a semi-distributed model were used to assess the effects. The study was conducted in a 19.5 square kilometers watershed located in northwest Dane county, Wisconsin. The results showed that differences in simulated runoff at the minimum simulation unit level are large. However, the difference gradually decreases as the spatial scale of simulation units increases. For sub-basins larger than 10 square kilometers in Brewery Creek, simulated stream flows using spatially detailed soil data, SoLIM data, would not vary significantly from those using SSURGO soil data. The unique findings of this study provide an important and unified perspective on the different views reported in the literature concerning how spatial detail of the input soil data affects watershed modeling and offer a potential useful basis for selecting the level of detail of soil spatial information appropriate for watershed modeling at a given model simulation scale.

  8. Aggregate and Individual Replication Probability within an Explicit Model of the Research Process

    ERIC Educational Resources Information Center

    Miller, Jeff; Schwarz, Wolf

    2011-01-01

    We study a model of the research process in which the true effect size, the replication jitter due to changes in experimental procedure, and the statistical error of effect size measurement are all normally distributed random variables. Within this model, we analyze the probability of successfully replicating an initial experimental result by…

  9. Macropore-mesopore model of water flow through aggregated porous media

    SciTech Connect

    Fong, L.; Appelbaum, H.R.

    1980-12-01

    A combined, one-dimensional, macropore-mesopore, hydrologic model was developed for simulating water flow through soils for analysis of data related to water and chemical flow in soils. Flows within the macroporous system as well as interactive flows between macroporous and mesoporous systems were modeled. Computer subroutines were written and incorporated into the existing one-dimensional Terrestrial Ecosystem Hydrologic Model (TEHM) developed at ORNL. Simulation showed that macropore flow effects are important during heavy precipitation and are more significant in soils of comparatively low hydraulic conductivity (5 to 10 cm/d). Increased drainage and decreased lateral flow result from the addition of the macropore model. The effect was more pronounced in soils of large macroporosity. Preliminary results indicate that the model is insensitive to geometrical properties of macropores.

  10. Aggregation of Trp > Glu point mutants of human gamma-D crystallin provides a model for hereditary or UV-induced cataract.

    PubMed

    Serebryany, Eugene; Takata, Takumi; Erickson, Erika; Schafheimer, Nathaniel; Wang, Yongting; King, Jonathan A

    2016-06-01

    Numerous mutations and covalent modifications of the highly abundant, long-lived crystallins of the eye lens cause their aggregation leading to progressive opacification of the lens, cataract. The nature and biochemical mechanisms of the aggregation process are poorly understood, as neither amyloid nor native-state polymers are commonly found in opaque lenses. The βγ-crystallin fold contains four highly conserved buried tryptophans, which can be oxidized to more hydrophilic products, such as kynurenine, upon UV-B irradiation. We mimicked this class of oxidative damage using Trp→Glu point mutants of human γD-crystallin. Such substitutions may represent a model of UV-induced photodamage-introduction of a charged group into the hydrophobic core generating "denaturation from within." The effects of Trp→Glu substitutions were highly position dependent. While each was destabilizing, only the two located in the bottom of the double Greek key fold-W42E and W130E-yielded robust aggregation of partially unfolded intermediates at 37°C and pH 7. The αB-crystallin chaperone suppressed aggregation of W130E, but not W42E, indicating distinct aggregation pathways from damage in the N-terminal vs C-terminal domain. The W130E aggregates had loosely fibrillar morphology, yet were nonamyloid, noncovalent, showed little surface hydrophobicity, and formed at least 20°C below the melting temperature of the native β-sheets. These features are most consistent with domain-swapped polymerization. Aggregation of partially destabilized crystallins under physiological conditions, as occurs in this class of point mutants, could provide a simple in vitro model system for drug discovery and optimization. PMID:26991007

  11. Finite Element Modeling of Crystallographic Preferred Orientation (CPO) in Two- Phase Aggregates: Rrelevant for Anisotropy of the Earth's lower Lower Mantle

    NASA Astrophysics Data System (ADS)

    Zepeda-Alarcon, E.; Wenk, H. R.; Kasemer, M.; Dawson, P.; Carson, R.

    2015-12-01

    Deformation of lower mantle minerals has been studied experimentally in some detail, but the underlying physical processes that govern deformation are still not well understood. We have implemented the orthorhombic symmetry in the viscoplastic finite element code FEpX developed at Cornell University, making this code useful for understanding plasticity of mineral aggregates like bridgmanite (with perovskite structure) and ferropericlase, the main mineral components of the lower mantle. High pressure radial diamond anvil cell (rDAC) and large volume press (D-DIA) experiments suggest that CPO is much weaker in 2-phase aggregates compared to 1-phase aggregates. But so far this has not been modeled satisfactorily with polycrystal plasticity theory that assumes that grains deform homogeneously, such as the Taylor or self-consistent approaches. Since it is expected that local heterogeneity plays a crucial role in deformation of 2-phase aggregates, we use a finite element approach where each grain in the aggregate is composed of individual elements. The constitutive equations between stress and strain are solved for all the elements in the aggregate, taking the local environment of each element into account. The FEpX code models the mechanical behavior of a virtual polycrystal, generated by the Neper code, which deforms by dislocation slip over large strain paths. The slip systems for the orthorhombic perovskite structure have been implemented into the code and, in particular, the development of CPO due to different combinations of slip systems is examined in the 2-phase aggregate of bridgmanite and periclase. Preliminary results show that there is an important correlation between CPO of both bridgmanite and periclase with the relative volume fractions and the microstructure of the aggregate. If the soft periclase is interconnected it absorbs deformation by grain boundary sliding instead of by dislocation glide. Model results are compared with high pressure r

  12. 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.

  13. Validation of an aggregate exposure model for substances in consumer products: a case study of diethyl phthalate in personal care products

    PubMed Central

    Delmaar, Christiaan; Bokkers, Bas; ter Burg, Wouter; Schuur, Gerlienke

    2015-01-01

    As personal care products (PCPs) are used in close contact with a person, they are a major source of consumer exposure to chemical substances contained in these products. The estimation of realistic consumer exposure to substances in PCPs is currently hampered by the lack of appropriate data and methods. To estimate aggregate exposure of consumers to substances contained in PCPs, a person-oriented consumer exposure model has been developed (the Probabilistic Aggregate Consumer Exposure Model, PACEM). The model simulates daily exposure in a population based on product use data collected from a survey among the Dutch population. The model is validated by comparing diethyl phthalate (DEP) dose estimates to dose estimates based on biomonitoring data. It was found that the model's estimates compared well with the estimates based on biomonitoring data. This suggests that the person-oriented PACEM model is a practical tool for assessing realistic aggregate exposures to substances in PCPs. In the future, PACEM will be extended with use pattern data on other product groups. This will allow for assessing aggregate exposure to substances in consumer products across different product groups. PMID:25352161

  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. Multi-objective calibration of a reservoir water quality model in aggregation and non-dominated sorting approaches

    NASA Astrophysics Data System (ADS)

    Huang, Yongtai

    2014-03-01

    Numerical water quality models are developed to predict contaminant fate and transport in receiving waters such as reservoirs and lakes. They can be helpful tools for water resource management. The objective of this study is to calibrate a water quality model which was set up to simulate the water quality conditions of Pepacton Reservoir, Downsville, New York, USA, using an aggregation hybrid genetic algorithm (AHGA) and a non-dominated sorting hybrid genetic algorithm (NSHGA). Both AHGA and NSHGA use a hybrid genetic algorithm (HGA) as optimization engines but are different in fitness assignment. In the AHGA, a weighted sum of scaled simulation errors is designed as an overall objective function to measure the fitness of solutions (i.e., parameter values). In the NSHGA, a method based on non-dominated sorting and Euclidean distances is proposed to calculate the dummy fitness of solutions. In addition, this study also compares the AHGA and the NSHGA. The purpose of this comparison is to determine whether the objective function values (i.e., simulation errors) and simulated results obtained by the AHGA and the NSHGA are significantly different from each other. The results show that the objective function values from the two HGAs are good compromises between all objective functions, and the calibrated model results match the observed data reasonably well and are comparable to other studies, supporting and justifying the use of multi-objective calibration.

  16. A method of aggregating heterogeneous subgrid land cover input data for multi-scale urban parameterization within atmospheric models

    NASA Astrophysics Data System (ADS)

    Shaffer, S. R.

    2015-12-01

    A method for representing grid-scale heterogeneous development density for urban climate models from probability density functions of sub-grid resolution observed data is proposed. Derived values are evaluated in relation to normalized Shannon Entropy to provide guidance in assessing model input data. Urban fraction for dominant and mosaic urban class contributions are estimated by combining analysis of 30-meter resolution National Land Cover Database 2006 data products for continuous impervious surface area and categorical land cover. The method aims at reducing model error through improvement of urban parameterization and representation of observations employed as input data. The multi-scale variation of parameter values are demonstrated for several methods of utilizing input. The method provides multi-scale and spatial guidance for determining where parameterization schemes may be mis-representing heterogeneity of input data, along with motivation for employing mosaic techniques based upon assessment of input data. The proposed method has wider potential for geographic application, and complements data products which focus on characterizing central business districts. The method enables obtaining urban fraction dependent upon resolution and class partition scheme, based upon improved parameterization of observed data, which provides one means of influencing simulation prediction at various aggregated grid scales.

  17. 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.

  18. 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…

  19. Aggregation of wet and dry land surfaces in interception schemes for general circulation models

    SciTech Connect

    Taylor, C.

    1995-03-01

    This paper investigates the parameterization of rainfall interception by a vegetation canopy in general circulation models (GCMs). Recent land surface schemes have introduced canopy water balance equations, which include sub-grid scale rainfall variability. However, current models do not distinguish between wet and dry areas when solving the set of energy balance equations. An alternative method is set out here that solves one set of surface flux equations for the wet area and one for the dry area. The approximation of using a single surface temperature to determine the surface fluxes is shown to overestimate the wet canopy evaporation from a forest by typically 30%. When implemented in the single column version of the U.K. Meteorological Office (UKMO) GCM, this excessive evaporation leads to significant overprediction of modeled interception loss from Amazonian rain forest.

  20. 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...

  1. Quercetin mediated reduction of angiogenic markers and chaperones in DLA-induced solid tumours.

    PubMed

    Anand, Kushi; Asthana, Pallavi; Kumar, Anup; Ambasta, Rashmi K; Kumar, Pravir

    2011-01-01

    Diet-derived flavonoids, in particular quercetin, may play advantageous roles by preventing or/and inhibiting oncogenesis. Evidence suggests that quercetin can elicit various properties depending on the cell type. The aim of this study was to evaluate its effects on Dalton's lymphoma ascites (DLA) induced solid tumours and to identify the target(s) of action. We addressed this question by inducing subcutaneous solid tumours in Swiss albino mice and investigated whether the quercetin affects essential biological processes that are responsible for tumour growth, morphology, angiogenesis and apoptosis. We also studied influence on several heat shock proteins (HSPs). Our findings demonstrate that intra-tumour administration of quercetin results in decreased volume/weight. Furthermore, we demonstrate that quercetin promotes apoptosis of cancer cells by down-regulating the levels of Hsp90 and Hsp70. Depletion of these two chaperones by quercetin might result in triggering of caspase-3 in treated tumours. Moreover, it also down-regulated the expression of major key angiogenic or pro-angiogenic factors, like HIF-1α and VEGF In addition, H and E staining together with immunofluorescence of fixed tumour tissue provided evidence in support of increased cell death in quercetin-treated mice. PMID:22393949

  2. 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.

    2016-02-01

    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.

  3. An aggregate modeling and measurement approach for power estimation of through-the-wall target returns

    NASA Astrophysics Data System (ADS)

    Thajudeen, Christopher; Hoorfar, Ahmad; Ahmad, Fauzia; Dogaru, Traian

    2010-04-01

    With recent advances in both algorithm and component technologies, through-the-wall sensing and imaging is emerging as an affordable sensor technology in civilian and military settings. One of the primary objectives of through-the-wall sensing systems is to detect and identify targets of interest, such as humans and cache of weapons, enclosed in building structures. Effective approaches that achieve proper target radar cross section (RCS) registration behind walls must, in general, exploit a detailed understanding of the radar phenomenology and more specifically, knowledge of the expected strength of the radar return from targets of interest. In this paper, we investigate the effects of various wall types on the received power of the target return through the use of a combined measurement and electromagnetic modeling approach. The RCS of material-exact rifle and human models are investigated in free-space using numerical electromagnetic modeling tools. A modified radar range equation, which analytically accounts for the wall effects, including multiple reflections within a given homogeneous or layered wall, is then employed in conjunction with wideband measured parameters of various common wall types, to estimate the received power versus frequency from the aforementioned targets. The proposed technique is, in principle, applicable to both bistatic and mono-static operations.

  4. 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.

  5. APPLICATION AND EVALUATION OF AN AGGREGATE PHYSICALLY-BASED TWO-STAGE MONTE CARLO PROBABILISTIC MODEL FOR QUANTIFYING CHILDREN'S RESIDENTIAL EXPOSURE AND DOSE TO CHLORPYRIFOS

    EPA Science Inventory

    Critical voids in exposure data and models lead risk assessors to rely on conservative assumptions. Risk assessors and managers need improved tools beyond the screening level analysis to address aggregate exposures to pesticides as required by the Food Quality Protection Act o...

  6. A novel inhibitor of amyloid β (Aβ) peptide aggregation: from high throughput screening to efficacy in an animal model of Alzheimer disease.

    PubMed

    McKoy, Angela Fortner; Chen, Jermont; Schupbach, Trudi; Hecht, Michael H

    2012-11-01

    Compelling evidence indicates that aggregation of the amyloid β (Aβ) peptide is a major underlying molecular culprit in Alzheimer disease. Specifically, soluble oligomers of the 42-residue peptide (Aβ42) lead to a series of events that cause cellular dysfunction and neuronal death. Therefore, inhibiting Aβ42 aggregation may be an effective strategy for the prevention and/or treatment of disease. We describe the implementation of a high throughput screen for inhibitors of Aβ42 aggregation on a collection of 65,000 small molecules. Among several novel inhibitors isolated by the screen, compound D737 was most effective in inhibiting Aβ42 aggregation and reducing Aβ42-induced toxicity in cell culture. The protective activity of D737 was most significant in reducing the toxicity of high molecular weight oligomers of Aβ42. The ability of D737 to prevent Aβ42 aggregation protects against cellular dysfunction and reduces the production/accumulation of reactive oxygen species. Most importantly, treatment with D737 increases the life span and locomotive ability of flies in a Drosophila melanogaster model of Alzheimer disease.

  7. 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.

  8. 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.

  9. Aggregation and dendritic growth in a magnetic granular system

    NASA Astrophysics Data System (ADS)

    González-Gutiérrez, J.; Carrillo-Estrada, J. L.; Ruiz-Suárez, J. C.

    2013-12-01

    We experimentally study the aggregation of non-Brownian paramagnetic beads in a vibrofluidized system induced by an external magnetic dipole. A dendritic growth is observed in real time, particle by particle, and with the naked eye. Two aggregation stages are observed, where tip, tip-split and side-branching growths are differentiated. We found clusters morphologically similar to those generated by a diffusion limited aggregation algorithm (DLA). However, in our case, due to the finite range of the magnetic field, the clusters reach a finite size and their structures exhibit different rates of aggregation. These are revealed by the existence of two different scaling relations of the mass with the gyration radius, and the nature of the radial mass distribution function. The structures of the clusters are fractal objects with an effective mass fractal dimension of around 1.8. We found that an exponential function describes the aggregation phenomenon as a function of time. This exponential behavior is independent of the final state of the morphology (shape and length) of the agglomerates.

  10. A Fluorescence Resonance Energy Transfer Assay For Monitoring α- Synclein Aggregation in a Caenorhabditis Elegans Model For Parkinson's Disease.

    PubMed

    Nagarajan, Archana; Bodhicharla, Rakesh; Winter, Jody; Anbalagan, Charumathi; Morgan, Kevin; Searle, Mark; Nazir, Aamir; Adenle, Ademola; Fineberg, April; Brady, Declan; Vere, Kelly; Richens, Jo; O'Shea, Paul; Bell, David; de-Pomerai, David

    2015-01-01

    The aggregation of α-synuclein (Syn or S) to form insoluble fibrils is important in the pathogenesis of Parkinson's disease, but key risk factors remain ill-defined. We have developed Fluorescence Resonance Energy Transfer (FRET)-based assays for α-synuclein aggregation, using Green Fluorescent Protein variants Cerulean (C) or Venus (V), fused to each other (CV, VC) or to human synuclein (SC, SV etc). Bacterially expressed proteins were purified to homogeneity, and C-terminal fusions SC and SV largely retained their ability to aggregate in vitro. FRET signals from mixtures of SC and SV were used to monitor aggregation. These fusion genes were linked to the C. elegans unc-54 myosin promoter to generate integrated transgenic strains. Increased FRET signals, indicative of S aggregation, were observed following treatment of unc-54::SC + unc-54::SV double transgenic worms with low concentrations of mercury or chlorpyrifos, or with RNAi against hsp-70 and hip-1. Opposite changes in Yellow Fluorescent Protein (YFP) fluorescence in an unc-54::SV strain (NL5901) are likely to reflect FRET from Yellow Fluorescent Protein to aggregates of Syn fusion protein. This could provide the basis for a high throughput screening assay, which could be used for studying the effects of toxic chemicals and environmental pollutants on the aggregation of proteins such as Syn in vivo. PMID:26295817

  11. 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.

  12. Before the Endless Forms: Embodied Model of Transition from Single Cells to Aggregates to Ecosystem Engineering

    PubMed Central

    Solé, Ricard V.; Valverde, Sergi

    2013-01-01

    The emergence of complex multicellular systems and their associated developmental programs is one of the major problems of evolutionary biology. The advantages of cooperation over individuality seem well known but it is not clear yet how such increase of complexity emerged from unicellular life forms. Current multicellular systems display a complex cell-cell communication machinery, often tied to large-scale controls of body size or tissue homeostasis. Some unicellular life forms are simpler and involve groups of cells cooperating in a tissue-like fashion, as it occurs with biofilms. However, before true gene regulatory interactions were widespread and allowed for controlled changes in cell phenotypes, simple cellular colonies displaying adhesion and interacting with their environments were in place. In this context, models often ignore the physical embedding of evolving cells, thus leaving aside a key component. The potential for evolving pre-developmental patterns is a relevant issue: how far a colony of evolving cells can go? Here we study these pre-conditions for morphogenesis by using CHIMERA, a physically embodied computational model of evolving virtual organisms in a pre-Mendelian world. Starting from a population of identical, independent cells moving in a fluid, the system undergoes a series of changes, from spatial segregation, increased adhesion and the development of generalism. Eventually, a major transition occurs where a change in the flow of nutrients is triggered by a sub-population. This ecosystem engineering phenomenon leads to a subsequent separation of the ecological network into two well defined compartments. The relevance of these results for evodevo and its potential ecological triggers is discussed. PMID:23596506

  13. Measuring neuronal branching patterns using model-based approach.

    PubMed

    Luczak, Artur

    2010-01-01

    Neurons have complex branching systems which allow them to communicate with thousands of other neurons. Thus understanding neuronal geometry is clearly important for determining connectivity within the network and how this shapes neuronal function. One of the difficulties in uncovering relationships between neuronal shape and its function is the problem of quantifying complex neuronal geometry. Even by using multiple measures such as: dendritic length, distribution of segments, direction of branches, etc, a description of three dimensional neuronal embedding remains incomplete. To help alleviate this problem, here we propose a new measure, a shape diffusiveness index (SDI), to quantify spatial relations between branches at the local and global scale. It was shown that growth of neuronal trees can be modeled by using diffusion limited aggregation (DLA) process. By measuring "how easy" it is to reproduce the analyzed shape by using the DLA algorithm it can be measured how "diffusive" is that shape. Intuitively, "diffusiveness" measures how tree-like is a given shape. For example shapes like an oak tree will have high values of SDI. This measure is capturing an important feature of dendritic tree geometry, which is difficult to assess with other measures. This approach also presents a paradigm shift from well-defined deterministic measures to model-based measures, which estimate how well a model with specific properties can account for features of analyzed shape. PMID:21079752

  14. 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

  15. Placing Local Aggregations in a Larger-Scale Context: Hierarchical Modeling of Black-Footed Albatross Dispersion.

    PubMed

    Michael, P E; 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

  16. Impact of flavouring substances on the aggregation behaviour of dissolved barley β-glucans in a model beer.

    PubMed

    Kupetz, M; Sacher, B; Becker, T

    2016-06-01

    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. PMID:27083361

  17. 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

  18. Adsorption-induced colloidal aggregation

    NASA Astrophysics Data System (ADS)

    Law, B. M.; Petit, J.-M.; Beysens, D.

    1998-03-01

    Reversible colloidal aggregation in binary liquid mixtures has been studied for a number of years. As the phase separation temperature of the liquid mixture is approached the thickness of an adsorption layer around the colloidal particles increases. Beysens and coworkers have demonstrated experimentally that this adsorption layer is intimately connected with the aggregation of the colloidal particles, however, no definitive theory has been available which can explain all of the experimental observations. In this contribution we describe an extension of the Derjaguin, Landau, Verwey, and Overbeek theory of colloidal aggregation which takes into account the presence of the adsorption layer and which more realistically models the attractive dispersion interactions. This modified theory can quantitatively account for many of the observed experimental features such as the characteristics of the aggregated state, the general shape of the aggregation line, and the temperature dependence of the second virial coefficient for a lutidine-water mixture containing a small volume fraction of silica colloidal particles.

  19. Nanostructured diffusion-limited-aggregation crystal pattern formation in a reactive microemulsion system

    NASA Astrophysics Data System (ADS)

    Srivastava, Rohit; Srivastava, P. K.

    2014-03-01

    Nanostructured diffusion-limited-aggregation (DLA) crystal pattern formation in microemulsion consisting of water, styrene, cetyltrimethylammonium chloride (CTACl), potassium persulphate and an oscillating Belousov-Zhabotinsky (BZ) reactant is reported. A variety of spatiotemporal patterns like concentric wave, spatial (stripe) and chaotic patterns appear. A colloidal phase composed of numerous nano-sized particles has been observed. The solid phase nucleation has been found to occur in the colloidal phase and has been found to grow in a symmetric crystal pattern with the progress of the reaction finally exhibiting DLA structures. We show that the formation of a nanostructured DLA crystal pattern is governed by spatial structures emerging in the BZ microemulsion system. Without any spatial structure in the microemulsion system only hydrogel of high viscosity is formed. A nano-sized branched crystal pattern was formed with a particle diameter in the range of 60-100 nm, as evident by transmission electron microscope, powder x-ray diffraction and particle size analyser studies.

  20. Direct Evidence of Cold Gas in DLA 0812+32B

    NASA Astrophysics Data System (ADS)

    Jorgenson, Regina A.; Wolfe, Arthur M.; Prochaska, J. Xavier; Carswell, Robert F.

    2009-10-01

    We present the first direct evidence for cold gas in a high redshift DLA galaxy. We measured several multiplets of weak neutral carbon (C I) transitions in order to perform a curve of growth analysis. A Δ χ2 test constrains the best-fit Doppler parameter, b = 0.33+0.05 -0.04 km s-1 and log N(C I) = 13.30 ± 0.2 cm-2. This Doppler parameter constrains the kinetic temperature of the gas to T <= 78 K (T <= 115 K, 2σ). We used the associated C I fine structure lines to constrain the volume density of the gas, n(H I) ~40-200 cm-3 (2σ), resulting in a lower limit on the cloud size of approximately 0.1-1 parsec. While it is difficult to determine the metallicity of the cold component, the absence of Cr II indicates that the cold cloud suffers a high level of dust depletion. Additionally, the large amount of Lyman and Werner-band molecular hydrogen absorption (log N(H2)total = 19.88 cm-2, f _H_2 ≥ 0.06) with an excitation temperature of T ex = 46 K as determined by the rotational J = 0 and J = 1 states, is consistent with the presence of cold gas. We propose that this cloud may be gravitationally confined and may represent a transition gas phase from primarily neutral atomic gas, to a colder, denser molecular phase that will eventually host star formation.

  1. 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.

  2. 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

  3. 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 ...

  4. 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.

  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. 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.

  7. 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. PMID:26092325

  8. Accuracy of aggregate 2- and 3-component models of body composition relative to 4-component for the measurement of changes in fat mass during weight loss in overweight and obese subjects.

    PubMed

    Lara, Jose; Johnstone, Alexandra M; Wells, Jonathan; Jebb, Susan; Siervo, Mario

    2014-08-01

    The 4-component (4-C) model is the reference method to measure fat mass (FM). Simpler 2-component (2-C) models are widely used to assess FM. We hypothesised that an aggregate 2-C model may improve accuracy of FM assessment during weight loss (WL). One hundred and six overweight and obese men and women were enrolled in different WL programs (fasting, very low energy diet, low energy diet). Body density, bone mineral content, and total body water were measured. FM was calculated using 2-C, 3-C, and 4-C models. Aggregate equations for 2-C, 3-C, and 4-C models were calculated, with the aggregate 4-C model assumed as the reference method. The aggregate approach postulates that the average of the individual estimates obtained from each model is more accurate than the best single measurement. The average WL was -7.5 kg. The agreement between 3-C and 4-C models for FM change was excellent (R(2) = 0.99). The aggregate 2-C equation was more accurate than individual 2-C estimates in measuring changes in FM. The aggregate model was characterised by a lower measurement error at baseline and post-WL. The relationship between the aggregate 3-C and 4-C component models was highly linear (R(2) = 0.99), whereas a lower linearity was found for the aggregate 2-C and 4-C model (R(2) = 0.72). The aggregate 2-C model is characterised by a greater accuracy than commonly applied 2-C equations for the measurement of FM during WL in overweight and obese men and women.

  9. Morphological diagram of diffusion driven aggregate growth in plane: Competition of anisotropy and adhesion

    NASA Astrophysics Data System (ADS)

    Menshutin, A. Yu.; Shchur, L. N.

    2011-09-01

    Two-dimensional structures grown with Witten and Sander algorithm are investigated. We analyze clusters grown off-lattice and clusters grown with antenna method with N=3,4,5,6,7 and 8 allowed growth directions. With the help of variable probe particles technique we measure fractal dimension of such clusters D(N) as a function of their size N. We propose that in the thermodynamic limit of infinite cluster size the aggregates grown with high degree of anisotropy ( N=3,4,5) tend to have fractal dimension D equal to 3/2, while off-lattice aggregates and aggregates with lower anisotropy ( N>6) have D≈1.710. Noise-reduction procedure results in the change of universality class for DLA. For high enough noise-reduction value clusters with N⩾6 have fractal dimension going to 3/2 when N→∞.

  10. Measurement of Lens Protein Aggregation in Vivo Using Dynamic Light Scattering in a Guinea Pig/UVA Model for Nuclear Cataract

    PubMed Central

    Simpanya, M. Francis; Ansari, Rafat R.; Leverenz, Victor; Giblin, Frank J.

    2009-01-01

    The role of UVA radiation in the formation of human nuclear cataract is not well understood. We have previously shown that exposing guinea pigs for 5 months to a chronic low level of UVA light produces increased lens nuclear light scattering and elevated levels of protein disulfide. Here we have used the technique of dynamic light scattering (DLS) to investigate lens protein aggregation in vivo in the guinea pig/UVA model. DLS size distribution analysis conducted at the same location in the lens nucleus of control and UVA-irradiated animals showed a 28% reduction in intensity of small diameter proteins in experimental lenses compared with controls (P < 0.05). In addition, large diameter proteins in UVA-exposed lens nuclei increased five-fold in intensity compared to controls (P < 0.05). The UVA-induced increase in apparent size of lens nuclear small diameter proteins was three-fold (P < 0.01), and the size of large diameter aggregates was more than four-fold in experimental lenses compared with controls. The diameter of crystallin aggregates in the UVA-irradiated lens nucleus was estimated to be 350 nm, a size able to scatter light. No significant changes in protein size were detected in the anterior cortex of UVA-irradiated lenses. It is presumed that the presence of a UVA chromophore in the guinea pig lens (NADPH bound to zeta crystallin), as well as traces of oxygen, contributed to UVA-induced crystallin aggregation. The results indicate a potentially harmful role for UVA light in the lens nucleus. A similar process of UVA-irradiated protein aggregation may take place in the older human lens nucleus, accelerating the formation of human nuclear cataract. PMID:18627516

  11. Gel-Entrapped Staphylococcus aureus Bacteria as Models of Biofilm Infection Exhibit Growth in Dense Aggregates, Oxygen Limitation, Antibiotic Tolerance, and Heterogeneous Gene Expression.

    PubMed

    Pabst, Breana; Pitts, Betsey; Lauchnor, Ellen; Stewart, Philip S

    2016-10-01

    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

  12. Texture development during progressive deformation of hematite aggregates: Constraints from VPSC models and naturally deformed iron oxides from Minas Gerais, Brazil

    NASA Astrophysics Data System (ADS)

    Ferreira, Filippe; Lagoeiro, Leonardo; Morales, Luiz F. G.; Oliveira, Claudinei G. de; Barbosa, Paola; Ávila, Carlos; Cavalcante, Geane C. G.

    2016-09-01

    We show that naturally-deformed hematite from the Quadrilátero Ferrífero Province, Minas Gerais, Brazil, develops CPOs by dislocation creep, strongly influenced by basal plane parallel glide, even when this is not the favored slip system. Characterization of microstructure and texture, particularly intragranular misorientations, of naturally deformed hematite aggregates by EBSD allowed us to determine the importance of different slip systems, and confirm dislocation creep as the dominant deformation mechanism. Viscoplastic self-consistent (VPSC) models were constructed to constrain the slip systems required to operate for the observed CPO to develop, and its rheological implications. Changes in the CRSS ratio of hematite prism and basal slip systems and deformation regime lead to the development of distinct patterns of hematite crystallographic orientations. The basal slip-dominated simple shear model is the only one that can develop quasi-single-crystal CPO of the kind observed in highly deformed rocks from Quadrilátero Ferrífero. Comparison between naturally deformed hematite aggregates and VPSC models shows that CPO development of hematite is strongly influenced by a highly viscoplastic anisotropy through dislocation creep on hematite basal plane. Nonetheless, our results demonstrate that even the unfavorable slip systems should be regarded when the bulk rheology of mineral aggregates is evaluated.

  13. Self-Assembly and Critical Aggregation Concentration Measurements of ABA Triblock Copolymers with Varying B Block Types: Model Development, Prediction, and Validation.

    PubMed

    Aydin, Fikret; Chu, Xiaolei; Uppaladadium, Geetartha; Devore, David; Goyal, Ritu; Murthy, N Sanjeeva; Zhang, Zheng; Kohn, Joachim; Dutt, Meenakshi

    2016-04-21

    The dissipative particle dynamics (DPD) simulation technique is a coarse-grained (CG) molecular dynamics-based approach that can effectively capture the hydrodynamics of complex systems while retaining essential information about the structural properties of the molecular species. An advantageous feature of DPD is that it utilizes soft repulsive interactions between the beads, which are CG representation of groups of atoms or molecules. In this study, we used the DPD simulation technique to study the aggregation characteristics of ABA triblock copolymers in aqueous medium. Pluronic polymers (PEG-PPO-PEG) were modeled as two segments of hydrophilic beads and one segment of hydrophobic beads. Tyrosine-derived PEG5K-b-oligo(desaminotyrosyl tyrosine octyl ester-suberate)-b-PEG5K (PEG5K-oligo(DTO-SA)-PEG5K) block copolymers possess alternate rigid and flexible components along the hydrophobic oligo(DTO-SA) chain, and were modeled as two segments of hydrophilic beads and one segment of hydrophobic, alternate soft and hard beads. The formation, structure, and morphology of the initial aggregation of the polymer molecules in aqueous medium were investigated by following the aggregation dynamics. The dimensions of the aggregates predicted by the computational approach were in good agreement with corresponding results from experiments, for the Pluronic and PEG5K-oligo(DTO-SA)-PEG5K block copolymers. In addition, DPD simulations were utilized to determine the critical aggregation concentration (CAC), which was compared with corresponding results from an experimental approach. For Pluronic polymers F68, F88, F108, and F127, the computational results agreed well with experimental measurements of the CAC measurements. For PEG5K-b-oligo(DTO-SA)-b-PEG5K block polymers, the complexity in polymer structure made it difficult to directly determine their CAC values via the CG scheme. Therefore, we determined CAC values of a series of triblock copolymers with 3-8 DTO-SA units using DPD

  14. Water level measurements for modeling hydraulic properties in the 300-FF-5 and 100 Aggregate Area Operable units

    SciTech Connect

    Campbell, M.D.; McMahon, W.J.; Simpson, K.R.

    1993-04-01

    Pressure transducers connected to dataloggers were used to measure ground water and Columbia River water elevations simultaneously and hourly at 35 locations in the 300-FF-5 Operable Unit and 16 locations in the 100 Aggregate Area Operable Unit on the Hanford Site. Water temperatures were also measured at 12 of these locations. This report details the findings of these studies.

  15. 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.

  16. 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

  17. 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.

  18. 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. PMID:25448805

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

    NASA Astrophysics Data System (ADS)

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

    2008-03-01

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

  20. 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.

  1. 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

  2. Translation of energy into morphology: Simulation of stromatolite morphospace using a stochastic model

    NASA Astrophysics Data System (ADS)

    Dupraz, C.; Pattisina, R.; Verrecchia, E. P.

    2006-03-01

    Stromatolites are examples of an iterative system involving radiate accretive growth of microbial mats, biofilm and/or minerals that result from interaction between intrinsic and extrinsic factors, which progressively shape the final morphology. These interactions can neither be easily described by simple mathematical equations, nor by simple physical laws or chemical reactions. Therefore, a holistic approach that will reduce the system to a set of variables (which are combinations of natural variables) is proposed in order to create virtual morphologies which will be compared with their natural counterparts. The combination of both Diffusion Limited Aggregation (DLA) and cellular automata (CA) allows the exploration of the stromatolite morphological space and a representation of the intrinsic and extrinsic factors responsible for natural stromatolite morphogenesis. The holistic approach provides a translation in simple parameters of (1) the way that energy, nutrients and sedimentary particles reach the active surface of a future build-up, (2) how these elements are distributed and used in order to create morphology, and (3) how simple environmental parameters, such as sedimentation, can disturb morphogenesis. In addition, most Precambrian stromatolite morphologies that are impossible to produce with numerical modeling such as the Kardar-Parisi-Zhang (KPZ) equation can be simulated with the DLA-CA model and this, with a minimum set of variables.

  3. 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.

  4. Latent heat induced rotation limited aggregation in 2D ice nanocrystals.

    PubMed

    Bampoulis, Pantelis; Siekman, Martin H; Kooij, E Stefan; Lohse, Detlef; Zandvliet, Harold J W; Poelsema, Bene

    2015-07-21

    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. PMID:26203037

  5. 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.

  6. Changes in fractal dimension during aggregation.

    PubMed

    Chakraborti, Rajat K; Gardner, Kevin H; Atkinson, Joseph F; Van Benschoten, John E

    2003-02-01

    Experiments were performed to evaluate temporal changes in the fractal dimension of aggregates formed during flocculation of an initially monodisperse suspension of latex microspheres. Particle size distributions and aggregate geometrical information at different mixing times were obtained using a non-intrusive optical sampling and digital image analysis technique, under variable conditions of mixing speed, coagulant (alum) dose and particle concentration. Pixel resolution required to determine aggregate size and geometric measures including the fractal dimension is discussed and a quantitative measure of accuracy is developed. The two-dimensional fractal dimension was found to range from 1.94 to 1.48, corresponding to aggregates that are either relatively compact or loosely structured, respectively. Changes in fractal dimension are explained using a conceptual model, which describes changes in fractal dimension associated with aggregate growth and changes in aggregate structure. For aggregation of an initially monodisperse suspension, the fractal dimension was found to decrease over time in the initial stages of floc formation.

  7. 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).

  8. Scaling and multiscaling behavior of the perimeter of a diffusion-limited aggregation generated by the Hastings-Levitov method

    NASA Astrophysics Data System (ADS)

    Mohammadi, F.; Saberi, A. A.; Rouhani, S.

    2009-09-01

    In this paper, we analyze the scaling behavior of a diffusion-limited aggregation (DLA) simulated by the Hastings-Levitov method. We obtain the fractal dimension of the clusters by direct analysis of the geometrical patterns, in good agreement with one obtained from an analytical approach. We compute the two-point density correlation function and we show that, in the large-size limit, it agrees with the obtained fractal dimension. These support the statistical agreement between the patterns and DLA clusters. We also investigate the scaling properties of various length scales and their fluctuations, related to the boundary of the cluster. We find that all of the length scales do not have a simple scaling with the same correction to scaling exponent. The fractal dimension of the perimeter is obtained equal to that of the cluster. The growth exponent is computed from the evolution of the interface width equal to β = 0.557(2). We also show that the perimeter of the DLA cluster has an asymptotic multiscaling behavior.

  9. Scaling and multiscaling behavior of the perimeter of a diffusion-limited aggregation generated by the Hastings-Levitov method.

    PubMed

    Mohammadi, F; Saberi, A A; Rouhani, S

    2009-09-16

    In this paper, we analyze the scaling behavior of a diffusion-limited aggregation (DLA) simulated by the Hastings-Levitov method. We obtain the fractal dimension of the clusters by direct analysis of the geometrical patterns, in good agreement with one obtained from an analytical approach. We compute the two-point density correlation function and we show that, in the large-size limit, it agrees with the obtained fractal dimension. These support the statistical agreement between the patterns and DLA clusters. We also investigate the scaling properties of various length scales and their fluctuations, related to the boundary of the cluster. We find that all of the length scales do not have a simple scaling with the same correction to scaling exponent. The fractal dimension of the perimeter is obtained equal to that of the cluster. The growth exponent is computed from the evolution of the interface width equal to β = 0.557(2). We also show that the perimeter of the DLA cluster has an asymptotic multiscaling behavior. PMID:21832341

  10. Streaming instability of aggregating slime mold amoebae

    NASA Astrophysics Data System (ADS)

    Levine, Herbert; Reynolds, William

    1991-05-01

    We propose a new model of aggregation in the cellular slime mold D. Discoideum. Our approach couples the excitable signaling system to amoeba chemotaxis; the resultant system of equations is tractable to analytical and numerical approaches. Using our model, we derive the existence of a streaming instability for the concentric target aggregation pattern.

  11. 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.

  12. 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

  13. Simulation and assessment of realistic breast lesions using fractal growth models.

    PubMed

    Rashidnasab, A; Elangovan, P; Yip, M; Diaz, O; Dance, D R; Young, K C; Wells, K

    2013-08-21

    A new method of generating realistic three dimensional simulated breast lesions known as diffusion limited aggregation (DLA) is presented, and compared with the random walk (RW) method. Both methods of lesion simulation utilize a physics-based method for inserting these simulated lesions into 2D clinical mammogram images that takes into account the polychromatic x-ray spectrum, local glandularity and scatter. DLA and RW masses were assessed for realism via a receiver operating characteristic (ROC) study with nine observers. The study comprised 150 images of which 50 were real pathology proven mammograms, 50 were normal mammograms with RW inserted masses and 50 were normal mammograms with DLA inserted masses. The average area under the ROC curve for the DLA method was 0.55 (95% confidence interval 0.51-0.59) compared to 0.60 (95% confidence interval 0.56-0.63) for the RW method. The observer study results suggest that the DLA method produced more realistic masses with more variability in shape compared to the RW method. DLA generated lesions can overcome the lack of complexity in structure and shape in many current methods of mass simulation. PMID:23892735

  14. Simulation and assessment of realistic breast lesions using fractal growth models

    NASA Astrophysics Data System (ADS)

    Rashidnasab, A.; Elangovan, P.; Yip, M.; Diaz, O.; Dance, D. R.; Young, K. C.; Wells, K.

    2013-08-01

    A new method of generating realistic three dimensional simulated breast lesions known as diffusion limited aggregation (DLA) is presented, and compared with the random walk (RW) method. Both methods of lesion simulation utilize a physics-based method for inserting these simulated lesions into 2D clinical mammogram images that takes into account the polychromatic x-ray spectrum, local glandularity and scatter. DLA and RW masses were assessed for realism via a receiver operating characteristic (ROC) study with nine observers. The study comprised 150 images of which 50 were real pathology proven mammograms, 50 were normal mammograms with RW inserted masses and 50 were normal mammograms with DLA inserted masses. The average area under the ROC curve for the DLA method was 0.55 (95% confidence interval 0.51-0.59) compared to 0.60 (95% confidence interval 0.56-0.63) for the RW method. The observer study results suggest that the DLA method produced more realistic masses with more variability in shape compared to the RW method. DLA generated lesions can overcome the lack of complexity in structure and shape in many current methods of mass simulation.

  15. 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

  16. The JGrass-NewAge system for forecasting and managing the hydrological budgets at the basin scale: the models of flow generation, propagation, and aggregation

    NASA Astrophysics Data System (ADS)

    Formetta, G.; Mantilla, R.; Franceschi, S.; Antonello, A.; Rigon, R.

    2011-04-01

    This paper presents a discussion of the predictive capacity of the first implementation of the semi-distributed hydrological modeling system JGrass-NewAge. This model focuses on the hydrological balance of medium scale to large scale basins, and considers statistics of the processes at the hillslope scale. The whole modeling system consists of six main parts: (i) estimation of energy balance; (ii) estimation of evapotranspiration; (iii) snow modelling; (iv) estimation of runoff production; (v) aggregation and propagation of flows in channel, and (vi) description of intakes, out-takes, and reservoirs. This paper details the processes, of runoff production, and aggregation/propagation of flows on a river network. The system is based on a hillslope-link geometrical partition of the landscape, so the basic unit, where the budget is evaluated, consists of hillslopes that drain into a single associated link rather than cells or pixels. To this conceptual partition corresponds an implementation of informatics that uses vectorial features for channels, and raster data for hillslopes. Runoff production at each channel link is estimated through a combination of the Duffy (1996) model and a GIUH model for estimating residence times in hillslope. Routing in channels uses equations integrated for any channels' link, and produces discharges at any link end, for any link in the river network. The model has been tested against measured discharges according to some indexes of goodness of fit such as RMSE and Nash Sutcliffe. The characteristic ability to reproduce discharge in any point of the river network is used to infer some statistics, and notably, the scaling properties of the modeled discharge.

  17. Diffusion-limited aggregation as a markovian process: bond-sticking conditions

    PubMed

    Kol; Aharony

    2000-08-01

    Cylindrical lattice diffusion limited aggregation (DLA), with a narrow width N, is solved using a Markovian matrix method. This matrix contains the probabilities that the front moves from one configuration to another at each growth step, calculated exactly by solving the Laplace equation and using the proper normalization. The method is applied for a series of approximations, which include only a finite number of rows near the front. The matrix is then used to find the weights of the steady-state growing configurations and the rate of approaching this steady-state stage. The former are then used to find the average upward growth probability, the average steady-state density and the fractal dimensionality of the aggregate, which is extrapolated to a value near 1.64. PMID:11088734

  18. Kinetics of bacterial phospholipase C activity at micellar interfaces: effect of substrate aggregate microstructure and a model for the kinetic parameters.

    PubMed

    Singh, Jasmeet; Ranganathan, Radha; Hajdu, Joseph

    2008-12-25

    Activity at micellar interfaces of bacterial phospholipase C from Bacillus cereus on phospholipids solubilized in micelles was investigated with the goal of elucidating the role of the interface microstructure and developing further an existing kinetic model. Enzyme kinetics and physicochemical characterization of model substrate aggregates were combined, thus enabling the interpretation of kinetics in the context of the interface. Substrates were diacylphosphatidylcholine of different acyl chain lengths in the form of mixed micelles with dodecyldimethylammoniopropanesulfonate. An early kinetic model, reformulated to reflect the interfacial nature of the kinetics, was applied to the kinetic data. A better method of data treatment is proposed, use of which makes the presence of microstructure effects quite transparent. Models for enzyme-micelle binding and enzyme-lipid binding are developed, and expressions incorporating the microstructural properties are derived for the enzyme-micelle dissociation constant K(s) and the interface Michaelis-Menten constant, K(M). Use of these expressions in the interface kinetic model brings excellent agreement between the kinetic data and the model. Numerical values for the thermodynamic and kinetic parameters are determined. Enzyme-lipid binding is found to be an activated process with an acyl chain length dependent free energy of activation that decreases with micelle lipid molar fraction with a coefficient of about -15RT and correlates with the tightness of molecular packing in the substrate aggregate. Thus, the physical insight obtained includes a model for the kinetic parameters that shows that these parameters depend on the substrate concentration and acyl chain length of the lipid. Enzyme-micelle binding is indicated to be hydrophobic and solvent mediated with a dissociation constant of 1.2 mM.

  19. Taurine and platelet aggregation

    SciTech Connect

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

    1986-03-01

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

  20. A review of volcanic ash aggregation

    NASA Astrophysics Data System (ADS)

    Brown, R. J.; Bonadonna, C.; Durant, A. J.

    2012-01-01

    Most volcanic ash particles with diameters <63 μm settle from eruption clouds as particle aggregates that cumulatively have larger sizes, lower densities, and higher terminal fall velocities than individual constituent particles. Particle aggregation reduces the atmospheric residence time of fine ash, which results in a proportional increase in fine ash fallout within 10-100 s km from the volcano and a reduction in airborne fine ash mass concentrations 1000 s km from the volcano. Aggregate characteristics vary with distance from the volcano: proximal aggregates are typically larger (up to cm size) with concentric structures, while distal aggregates are typically smaller (sub-millimetre size). Particles comprising ash aggregates are bound through hydro-bonds (liquid and ice water) and electrostatic forces, and the rate of particle aggregation correlates with cloud liquid water availability. Eruption source parameters (including initial particle size distribution, erupted mass, eruption column height, cloud water content and temperature) and the eruption plume temperature lapse rate, coupled with the environmental parameters, determines the type and spatiotemporal distribution of aggregates. Field studies, lab experiments and modelling investigations have already provided important insights on the process of particle aggregation. However, new integrated observations that combine remote sensing studies of ash clouds with field measurement and sampling, and lab experiments are required to fill current gaps in knowledge surrounding the theory of ash aggregate formation.

  1. 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

  2. Generalization of the DLA process with different immiscible components by time-scale coarse graining

    NASA Astrophysics Data System (ADS)

    Postnikov, E. B.; Ryabov, A. B.; Loskutov, A.

    2007-10-01

    In the framework of the mean-field approximation we propose a new approach to the description of the growth of fractal structures which are formed as a result of the process of diffusion limited aggregation. Our approach is based on the coarse graining of the time scale which takes into account the property of discreteness of such structures. The obtained system of partial differential equations allows us to evaluate numerically the fractal dimension and the cluster density depending on the distance from the cluster center. The results are in a quite good agreement with values found by the direct numerical simulations. The proposed approach is generalized for the case of the cluster description with different immiscible particles.

  3. 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.

  4. Elevated Hapln2 Expression Contributes to Protein Aggregation and Neurodegeneration in an Animal Model of Parkinson's Disease.

    PubMed

    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

  5. 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

  6. Waves and aggregation patterns in myxobacteria

    NASA Astrophysics Data System (ADS)

    Igoshin, Oleg A.; Welch, Roy; Kaiser, Dale; Oster, George

    2004-03-01

    Under starvation conditions, a population of myxobacteria aggregates to build a fruiting body whose shape is species-specific and within which the cells sporulate. Early in this process, cells often pass through a "ripple phase" characterized by traveling linear, concentric, and spiral waves. These waves are different from the waves observed during slime mold aggregation that depend on diffusible morphogens, because myxobacteria communicate by direct contact. The difference is most dramatic when waves collide: rather than annihilating one another, myxobacterial waves appear to pass through one another unchanged. Under certain conditions, the spacing and location of the nascent fruiting bodies is determined by the wavelength and pattern of the waves. Later in fruiting body development, waves are replaced by streams of cells that circulate around small initial aggregates enlarging and rounding them. Still later, pairs of motile aggregates coalesce to form larger aggregates that develop into fruiting bodies. Here we present a mathematical model that quantitatively explains these wave and aggregation phenomena.

  7. 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. ...

  8. 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

  9. 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.

  10. Effect of alcohol aggregation on the retention factors of chiral solutes with an amylose-based sorbent: modeling and implications for the adsorption mechanism.

    PubMed

    Tsui, Hung-Wei; Franses, Elias I; Wang, Nien-Hwa Linda

    2014-02-01

    Various displacement models in the literature have been widely used for understanding the adsorption mechanisms of solutes in various chromatography systems. The models were used for describing the often-observed linear plots of the logarithms of the retention factor versus the logarithms of the polar modifier concentration CI(0). The slopes of such a plot was inferred to be equal to the number of the displaced modifier molecules upon adsorption of one solute molecule, and were generally found to be greater than 1. In this study, the retention factors of four structurally related chiral solutes, ethyl lactate (EL), methyl mandelate (MM), benzoin (B), and pantolactone (PL), were measured for the amylose tris[(S)-α-methylbenzylcarbamate] sorbent, or AS, as a function of the concentration of isopropanol (IPA) in n-hexane. With increasing IPA concentration CI(0), the slopes increase from less than 1, at a concentration range from 0.13 to 1.3M, to slightly more than 1 at higher concentrations. Such slopes cannot be explained by the conventional retention models. It was found previously for monovalent solutes that such slopes can only be explained when the aggregation of the mobile phase modifier, isopropyl alcohol, was accounted for. A new retention model is presented here, accounting for alcohol aggregation, multivalent solute adsorption, multivalent solute-alcohol complexation, alcohol adsorption, and solute intra hydrogen-bonding, which occur in these four solutes. The slope is found to be controlled by three key dimensionless groups, the fraction of the sorbent binding sites covered by IPA, the fraction of the solute molecules in complex form, and the fraction of the IPA molecules in aggregate form. The limiting slope at a very high IPA concentration is equal to the value of (x+y)/n, where x is the number of the solute-sorbent binding sites and y is the number of the alcohol molecules in the solute-alcohol complex, and n is the alcohol aggregation number. The model

  11. 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

  12. 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

    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.

  13. 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…

  14. 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.

  15. Enhancing mitochondrial calcium buffering capacity reduces aggregation of misfolded SOD1 and motor neuron cell death without extending survival in mouse models of inherited amyotrophic lateral sclerosis.

    PubMed

    Parone, Philippe A; Da Cruz, Sandrine; Han, Joo Seok; McAlonis-Downes, Melissa; Vetto, Anne P; Lee, Sandra K; Tseng, Eva; Cleveland, Don W

    2013-03-13

    Mitochondria have been proposed as targets for toxicity in amyotrophic lateral sclerosis (ALS), a progressive, fatal adult-onset neurodegenerative disorder characterized by the selective loss of motor neurons. A decrease in the capacity of spinal cord mitochondria to buffer calcium (Ca(2+)) has been observed in mice expressing ALS-linked mutants of SOD1 that develop motor neuron disease with many of the key pathological hallmarks seen in ALS patients. In mice expressing three different ALS-causing SOD1 mutants, we now test the contribution of the loss of mitochondrial Ca(2+)-buffering capacity to disease mechanism(s) by eliminating ubiquitous expression of cyclophilin D, a critical regulator of Ca(2+)-mediated opening of the mitochondrial permeability transition pore that determines mitochondrial Ca(2+) content. A chronic increase in mitochondrial buffering of Ca(2+) in the absence of cyclophilin D was maintained throughout disease course and was associated with improved mitochondrial ATP synthesis, reduced mitochondrial swelling, and retention of normal morphology. This was accompanied by an attenuation of glial activation, reduction in levels of misfolded SOD1 aggregates in the spinal cord, and a significant suppression of motor neuron death throughout disease. Despite this, muscle denervation, motor axon degeneration, and disease progression and survival were unaffected, thereby eliminating mutant SOD1-mediated loss of mitochondrial Ca(2+) buffering capacity, altered mitochondrial morphology, motor neuron death, and misfolded SOD1 aggregates, as primary contributors to disease mechanism for fatal paralysis in these models of familial ALS. PMID:23486940

  16. Mammalian ribosomal and chaperone protein RPS3A counteracts α-synuclein aggregation and toxicity in a yeast model system.

    PubMed

    De Graeve, Stijn; Marinelli, Sarah; Stolz, Frank; Hendrix, Jelle; Vandamme, Jurgen; Engelborghs, Yves; Van Dijck, Patrick; Thevelein, Johan M

    2013-11-01

    Accumulation of aggregated forms of αSyn (α-synuclein) into Lewy bodies is a known hallmark associated with neuronal cell death in Parkinson's disease. When expressed in the yeast Saccharomyces cerevisiae, αSyn interacts with the plasma membrane, forms inclusions and causes a concentration-dependent growth defect. We have used a yeast mutant, cog6Δ, which is particularly sensitive to moderate αSyn expression, for screening a mouse brain-specific cDNA library in order to identify mammalian proteins that counteract αSyn toxicity. The mouse ribosomal and chaperone protein RPS3A was identified as a suppressor of αSyn [WT (wild-type) and A53T] toxicity in yeast. We demonstrated that the 50 N-terminal amino acids are essential for this function. The yeast homologues of RPS3A were not effective in suppressing the αSyn-induced growth defect, illustrating the potential of our screening system to identify modifiers that would be missed using yeast gene overexpression as the first screening step. Co-expression of mouse RPS3A delayed the formation of αSyn-GFP inclusions in the yeast cells. The results of the present study suggest that the recently identified extraribosomal chaperonin function of RPS3A also acts on the neurodegeneration-related protein αSyn and reveal a new avenue for identifying promising candidate mammalian proteins involved in αSyn functioning.

  17. 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)

  18. 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

  19. Protein aggregation in salt solutions.

    PubMed

    Kastelic, Miha; Kalyuzhnyi, Yurij V; Hribar-Lee, Barbara; Dill, Ken A; Vlachy, Vojko

    2015-05-26

    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.

  20. Aggregations in Flatworms.

    ERIC Educational Resources Information Center

    Liffen, C. L.; Hunter, M.

    1980-01-01

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

  1. 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

  2. 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

  3. How Hot Precursor Modify Island Nucleation: A Rate-Equation Model

    NASA Astrophysics Data System (ADS)

    Morales-Cifuentes, Josue; Einstein, T. L.; Pimpinelli, Alberto

    2015-03-01

    We describe the analysis, based on rate equations, of the hot precursor model mentioned in the previous talk. Two key parameters are the competing times of ballistic monomers decaying into thermalized monomers vs. being captured by an island, which naturally define a ``thermalization'' scale for the system. We interpret the energies and dimmensionless parameters used in the model, and provide both an implicit analytic solution and a convenient asymptotic approximation. Further analysis reveals novel scaling regimes and nonmonotonic crossovers between them. To test our model, we applied it to experiments on parahexaphenyl (6P) on sputtered mica. With the resulting parameters, the curves derived from our analytic treatment account very well for the data at the 4 different temperatures. The fit shows that the high-flux regime corresponds not to ALA (attachment-limited aggregation) or HMA (hot monomer aggregation) but rather to an intermediate scaling regime related to DLA (diffusion-limited aggregation). We hope this work stimulates further experimental investigations. Work at UMD supported by NSF CHE 13-05892.

  4. Fractal dynamics of bioconvective patterns

    NASA Technical Reports Server (NTRS)

    Noever, David A.

    1991-01-01

    Biologically generated cellular patterns, sometimes called bioconvective patterns, are found to cluster into aggregates which follow fractal growth dynamics akin to diffusion-limited aggregation (DLA) models. The pattern formed is self-similar with fractal dimension of 1.66 +/-0.038. Bioconvective DLA branching results from thermal roughening which shifts the balance between ordering viscous forces and disordering cell motility and random diffusion. The phase diagram for pattern morphology includes DLA, boundary spokes, random clusters, and reverse clusters.

  5. Directional sensing and streaming in Dictyostelium aggregation.

    PubMed

    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. PMID:27300919

  6. 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.

  7. Directional sensing and streaming in Dictyostelium aggregation.

    PubMed

    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.

  8. 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.

  9. Self-Consistent Non-Stationary Theory of Multipactor in DLA Structures

    NASA Astrophysics Data System (ADS)

    Sinitsyn, O. V.; Nusinovich, G. S.; Antonsen, T. M.; Kishek, R.

    2009-01-01

    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.

  10. Competitive aggregation dynamics using phase wave signals.

    PubMed

    Sakaguchi, Hidetsugu; Maeyama, Satomi

    2014-10-21

    Coupled equations of the phase equation and the equation of cell concentration n are proposed for competitive aggregation dynamics of slime mold in two dimensions. Phase waves are used as tactic signals of aggregation in this model. Several aggregation clusters are formed initially, and target patterns appear around the localized aggregation clusters. Owing to the competition among target patterns, the number of the localized aggregation clusters decreases, and finally one dominant localized pattern survives. If the phase equation is replaced with the complex Ginzburg-Landau equation, several spiral patterns appear, and n is localized near the center of the spiral patterns. After the competition among spiral patterns, one dominant spiral survives. PMID:24956327

  11. 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.

  12. 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 %).

  13. 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.

  14. DLA Class II Alleles and Haplotypes Are Associated with Risk for and Protection from Chronic Hepatitis in the English Springer Spaniel

    PubMed Central

    Bexfield, Nicholas H.; Watson, Penny J.; Aguirre-Hernandez, Jesús; Sargan, David R.; Tiley, Laurence; Heeney, Jonathan L.; Kennedy, Lorna J.

    2012-01-01

    Chronic hepatitis (CH) is common in dogs in the United Kingdom. An increased prevalence of the disease is seen in the English Springer spaniel (ESS), and this breed suffer from a severe form with young to middle aged female dogs being predisposed. The disease shares histological features with those of human viral hepatitis, although the specific aetiological agent has not yet been identified. The aim of the current study was to investigate whether dog leucocyte antigen (DLA) class II alleles and haplotypes are associated with susceptibility/resistance to CH in the ESS. Sequence-based genotyping of the polymorphic exon 2 from DLA-DRB1, -DQA1 and -DQB1 class II loci were performed in 66 ESSs with CH and 84 healthy controls. There was a significant difference in the distribution of the protective alleles DRB1*00501 (3.0% vs. 12.0%, odds ratio [OR] = 0.23, 95% confidence interval [CI] = 0.06–0.74) and DQB1*00501 (3.8% vs. 12.0%, OR = 0.29, 95% CI = 0.09–0.85) between cases and controls. The haplotype DLA-DRB1*00501/DQA1*00301/DQB1*00501 was present in 11.9% of controls and 3.0% of cases and was significantly associated with protection against disease development (OR = 0.26, 95% CI = 0.08–0.80). There was a significant difference in the distribution of the risk alleles DRB1*00601 (14.4% vs. 6.5%, OR = 2.40, 95% CI = 1.10–5.63) and DQB1*00701 (14.4% vs. 6.5%, OR = 2.40, 95% CI = 1.10–5.63) between cases and controls. A risk haplotype (DLA-DRB1*00601/DQA1*005011/DQB1*00701) was present in 14.4% of cases and 6.5% of controls and conferred an elevated risk of developing CH with an OR of 3.13 (95% CI = 1.20–8.26). These results demonstrate that DLA class II is significantly associated with risk and protection from developing CH in ESSs. PMID:22870335

  15. 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

  16. Safety Assessment of Dangerous Goods Transport Enterprise Based on the Relative Entropy Aggregation in Group Decision Making Model

    PubMed Central

    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. PMID:25477954

  17. 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 hig