The breakup mechanism of biomolecular and colloidal aggregates in a shear flow

NASA Astrophysics Data System (ADS)

Ó Conchúir, Breanndán; Zaccone, Alessio

2014-03-01

The theory of self-assembly of colloidal particles in shear flow is incomplete. Previous analytical approaches have failed to capture the microscopic interplay between diffusion, shear and intermolecular interactions which controls the aggregates fate in shear. In this work we analytically solved the drift-diffusion equation for the breakup rate of a dimer in flow. Then applying rigidity percolation theory, we found that the lifetime of a generic cluster formed under shear is controlled by the typical lifetime of a single bond in its interior, which in turn depends on the efficiency of the stress transmitted from other bonds in the cluster. We showed that aggregate breakup is a thermally-activated process where the activation energy is controlled by the interplay between intermolecular forces and the shear drift, and where structural parameters determine whether cluster fragmentation or surface erosion prevails. In our latest work, we analyzed floppy modes and nonaffine deformations to derive a lower bound on the fractal dimension df below which aggregates are mechanically unstable, ie. for large aggregates df ~= 2.4. This theoretical framework is in quantitative agreement with experiments and can be used for population balance modeling of colloidal and protein aggregation.

Edible oil structures at low and intermediate concentrations. I. Modeling, computer simulation, and predictions for X ray scattering

NASA Astrophysics Data System (ADS)

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

2013-12-01

Triacylglycerols (TAGs) are biologically important molecules which form the recently discovered highly anisotropic crystalline nanoplatelets (CNPs) and, ultimately, the large-scale fat crystal networks in edible oils. Identifying the hierarchies of these networks and how they spontaneously self-assemble is important to understanding their functionality and oil binding capacity. We have modelled CNPs and studied how they aggregate under the assumption that all CNPs are present before aggregation begins and that their solubility in the liquid oil is very low. We represented CNPs as rigid planar arrays of spheres with diameter ≈50 nm and defined the interaction between spheres in terms of a Hamaker coefficient, A, and a binding energy, VB. We studied three cases: weak binding, |VB|/kBT ≪ 1, physically realistic binding, VB = Vd(R, Δ), so that |VB|/kBT ≈ 1, and Strong binding with |VB|/kBT ≫ 1. We divided the concentration of CNPs, ϕ, with 0≤ϕ= 10-2 (solid fat content) ≤1, into two regions: Low and intermediate concentrations with 0<ϕ<0.25 and high concentrations with 0.25 < ϕ and considered only the first case. We employed Monte Carlo computer simulation to model CNP aggregation and analyzed them using static structure functions, S(q). We found that strong binding cases formed aggregates with fractal dimension, D, 1.7≤D ≤1.8, in accord with diffusion limited cluster-cluster aggregation (DLCA) and weak binding formed aggregates with D =3, indicating a random distribution of CNPs. We found that models with physically realistic intermediate binding energies formed linear multilayer stacks of CNPs (TAGwoods) with fractal dimension D =1 for ϕ =0.06,0.13, and 0.22. TAGwood lengths were greater at lower ϕ than at higher ϕ, where some of the aggregates appeared as thick CNPs. We increased the spatial scale and modelled the TAGwoods as rigid linear arrays of spheres of diameter ≈500 nm, interacting via the attractive van der Waals interaction. We found that TAGwoods aggregated via DLCA into clusters with fractal dimension D =1.7-1.8. As the simulations were run further, TAGwoods relaxed their positions in order to maximize the attractive interaction making the process look like reaction limited cluster-cluster aggregation with the fractal dimension increasing to D =2.0-2.1. For higher concentrations of CNPs, many TAGwood clusters were formed and, because of their weak interactions, were distributed randomly with D =3.0. We summarize the hierarchy of structures and make predictions for X-ray scattering.

Photo-induced transformation process at gold clusters-semiconductor interface: Implications for the complexity of gold clusters-based photocatalysis

PubMed Central

Liu, Siqi; Xu, Yi-Jun

2016-01-01

The recent thrust in utilizing atomically precise organic ligands protected gold clusters (Au clusters) as photosensitizer coupled with semiconductors for nano-catalysts has led to the claims of improved efficiency in photocatalysis. Nonetheless, the influence of photo-stability of organic ligands protected-Au clusters at the Au/semiconductor interface on the photocatalytic properties remains rather elusive. Taking Au clusters–TiO2 composites as a prototype, we for the first time demonstrate the photo-induced transformation of small molecular-like Au clusters to larger metallic Au nanoparticles under different illumination conditions, which leads to the diverse photocatalytic reaction mechanism. This transformation process undergoes a diffusion/aggregation mechanism accompanied with the onslaught of Au clusters by active oxygen species and holes resulting from photo-excited TiO2 and Au clusters. However, such Au clusters aggregation can be efficiently inhibited by tuning reaction conditions. This work would trigger rational structural design and fine condition control of organic ligands protected-metal clusters-semiconductor composites for diverse photocatalytic applications with long-term photo-stability. PMID:26947754

Modeling fractal cities using the correlated percolation model.

NASA Astrophysics Data System (ADS)

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

1996-03-01

Cities grow in a way that might be expected to resemble the growth of two-dimensional aggregates of particles, and this has led to recent attempts to model urban growth using ideas from the statistical physics of clusters. In particular, the model of diffusion limited aggregation (DLA) has been invoked to rationalize the apparently fractal nature of urban morphologies(M. Batty and P. Longley, Fractal Cities) (Academic, San Diego, 1994). The DLA model predicts that there should exist only one large fractal cluster, which is almost perfectly screened from incoming 'development units' (representing, for example, people, capital or resources), so that almost all of the cluster growth takes place at the tips of the cluster's branches. We show that an alternative model(H. A. Makse, S. Havlin, H. E. Stanley, Nature 377), 608 (1995), in which development units are correlated rather than being added to the cluster at random, is better able to reproduce the observed morphology of cities and the area distribution of sub-clusters ('towns') in an urban system, and can also describe urban growth dynamics. Our physical model, which corresponds to the correlated percolation model in the presence of a density gradient, is motivated by the fact that in urban areas development attracts further development. The model offers the possibility of predicting the global properties (such as scaling behavior) of urban morphologies.

Density-Aware Clustering Based on Aggregated Heat Kernel and Its Transformation

DOE PAGES

Huang, Hao; Yoo, Shinjae; Yu, Dantong; ...

2015-06-01

Current spectral clustering algorithms suffer from the sensitivity to existing noise, and parameter scaling, and may not be aware of different density distributions across clusters. If these problems are left untreated, the consequent clustering results cannot accurately represent true data patterns, in particular, for complex real world datasets with heterogeneous densities. This paper aims to solve these problems by proposing a diffusion-based Aggregated Heat Kernel (AHK) to improve the clustering stability, and a Local Density Affinity Transformation (LDAT) to correct the bias originating from different cluster densities. AHK statistically\\ models the heat diffusion traces along the entire time scale, somore » it ensures robustness during clustering process, while LDAT probabilistically reveals local density of each instance and suppresses the local density bias in the affinity matrix. Our proposed framework integrates these two techniques systematically. As a result, not only does it provide an advanced noise-resisting and density-aware spectral mapping to the original dataset, but also demonstrates the stability during the processing of tuning the scaling parameter (which usually controls the range of neighborhood). Furthermore, our framework works well with the majority of similarity kernels, which ensures its applicability to many types of data and problem domains. The systematic experiments on different applications show that our proposed algorithms outperform state-of-the-art clustering algorithms for the data with heterogeneous density distributions, and achieve robust clustering performance with respect to tuning the scaling parameter and handling various levels and types of noise.« less

Amplifying and attenuating the coffee-ring effect in drying sessile nanofluid droplets

NASA Astrophysics Data System (ADS)

Crivoi, A.; Duan, Fei

2013-04-01

Experiments and simulations to promote or attenuate the “coffee-ring effect” for pinned sessile nanofluid droplets are presented. The addition of surfactant inside a water suspension of aluminum oxide nanoparticles results in coffee-ring formation after the pinned sessile droplets are fully dried on a substrate, while droplets of the same suspension without the surfactant produce a fine uniform coverage. A mathematical model based on diffusion-limited cluster-cluster aggregation has been developed to explain the observed difference in the experiments. The simulations show that the particle sticking probability is a crucial factor on the morphology of finally dried structures.

[Results of Simulation Studies

NASA Technical Reports Server (NTRS)

2003-01-01

Lattice Monte Carlo and off-lattice molecular dynamics simulations of h(sub 1)t(sub 4) and h(sub 4)t(sub l) (head/tail) amphiphile solutions have been performed as a function of surfactant concentration and temperature. The lattice and off-lattice systems exhibit quite different self-assembly behavior at equivalent thermodynamic conditions. We found that in the weakly aggregating regime (no preferred-size micelles), all models yield similar micelle size distributions at the same average aggregation number, albeit at different thermodynamic conditions (temperatures). In the strongly aggregating regime, this mapping between models (through temperature adjustment) fails, and the models exhibit qualitatively different micellization behavior. Incipient micellization in a model self-associating telechelic polymer solution results in a network with a transient elastic response that decays by a two-step relaxation: the first is due to a heterogeneous jump-diffusion process involving entrapment of end-groups within well-defined clusters and this is followed by rapid diffusion to neighboring clusters and a decay (terminal relaxation) due to cluster disintegration. The viscoelastic response of the solution manifests characteristics of a glass transition and entangled polymer network.

Reversible Self-Assembly of Glutathione-Coated Gold Nanoparticle Clusters via pH-Tunable Interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moaseri, Ehsan; Bollinger, Jonathan A.; Changalvaie, Behzad

In this study, nanoparticle (NP) clusters with diameters ranging from 20 to 100 nm are reversibly assembled from 5 nm gold (Au) primary particles coated with glutathione (GSH) in aqueous solution as a function of pH in the range of 5.4 to 3.8. As the pH is lowered, the GSH surface ligands become partially zwitterionic and form interparticle hydrogen bonds that drive the self-limited assembly of metastable clusters in <1 min. Whereas clusters up to 20 nm in size are stable against cluster–cluster aggregation for up to 1 day, clusters up to 80 nm in size can be stabilized overmore » this period via the addition of citrate to the solution in equal molarity with GSH molecules. The cluster diameter may be cycled reversibly by tuning pH to manipulate the colloidal interactions; however, modest background cluster–cluster aggregation occurs during cycling. Cluster sizes can be stabilized for at least 1 month via the addition of PEG-thiol as a grafted steric stabilizer, where PEG-grafted clusters dissociate back to starting primary NPs at pH 7 in fewer than 3 days. Whereas the presence of excess citrate has little effect on the initial size of the metastable clusters, it is necessary for both the cycling and dissociation to mediate the GSH–GSH hydrogen bonds. In conclusion, these metastable clusters exhibit significant characteristics of equilibrium self-limited assembly between primary particles and clusters on time scales where cluster–cluster aggregation is not present.« less

Reversible Self-Assembly of Glutathione-Coated Gold Nanoparticle Clusters via pH-Tunable Interactions

DOE PAGES

Moaseri, Ehsan; Bollinger, Jonathan A.; Changalvaie, Behzad; ...

2017-10-06

In this study, nanoparticle (NP) clusters with diameters ranging from 20 to 100 nm are reversibly assembled from 5 nm gold (Au) primary particles coated with glutathione (GSH) in aqueous solution as a function of pH in the range of 5.4 to 3.8. As the pH is lowered, the GSH surface ligands become partially zwitterionic and form interparticle hydrogen bonds that drive the self-limited assembly of metastable clusters in <1 min. Whereas clusters up to 20 nm in size are stable against cluster–cluster aggregation for up to 1 day, clusters up to 80 nm in size can be stabilized overmore » this period via the addition of citrate to the solution in equal molarity with GSH molecules. The cluster diameter may be cycled reversibly by tuning pH to manipulate the colloidal interactions; however, modest background cluster–cluster aggregation occurs during cycling. Cluster sizes can be stabilized for at least 1 month via the addition of PEG-thiol as a grafted steric stabilizer, where PEG-grafted clusters dissociate back to starting primary NPs at pH 7 in fewer than 3 days. Whereas the presence of excess citrate has little effect on the initial size of the metastable clusters, it is necessary for both the cycling and dissociation to mediate the GSH–GSH hydrogen bonds. In conclusion, these metastable clusters exhibit significant characteristics of equilibrium self-limited assembly between primary particles and clusters on time scales where cluster–cluster aggregation is not present.« less

A Game Theory Algorithm for Intra-Cluster Data Aggregation in a Vehicular Ad Hoc Network

PubMed Central

Chen, Yuzhong; Weng, Shining; Guo, Wenzhong; Xiong, Naixue

2016-01-01

Vehicular ad hoc networks (VANETs) have an important role in urban management and planning. The effective integration of vehicle information in VANETs is critical to traffic analysis, large-scale vehicle route planning and intelligent transportation scheduling. However, given the limitations in the precision of the output information of a single sensor and the difficulty of information sharing among various sensors in a highly dynamic VANET, effectively performing data aggregation in VANETs remains a challenge. Moreover, current studies have mainly focused on data aggregation in large-scale environments but have rarely discussed the issue of intra-cluster data aggregation in VANETs. In this study, we propose a multi-player game theory algorithm for intra-cluster data aggregation in VANETs by analyzing the competitive and cooperative relationships among sensor nodes. Several sensor-centric metrics are proposed to measure the data redundancy and stability of a cluster. We then study the utility function to achieve efficient intra-cluster data aggregation by considering both data redundancy and cluster stability. In particular, we prove the existence of a unique Nash equilibrium in the game model, and conduct extensive experiments to validate the proposed algorithm. Results demonstrate that the proposed algorithm has advantages over typical data aggregation algorithms in both accuracy and efficiency. PMID:26907272

A Game Theory Algorithm for Intra-Cluster Data Aggregation in a Vehicular Ad Hoc Network.

PubMed

Chen, Yuzhong; Weng, Shining; Guo, Wenzhong; Xiong, Naixue

2016-02-19

Vehicular ad hoc networks (VANETs) have an important role in urban management and planning. The effective integration of vehicle information in VANETs is critical to traffic analysis, large-scale vehicle route planning and intelligent transportation scheduling. However, given the limitations in the precision of the output information of a single sensor and the difficulty of information sharing among various sensors in a highly dynamic VANET, effectively performing data aggregation in VANETs remains a challenge. Moreover, current studies have mainly focused on data aggregation in large-scale environments but have rarely discussed the issue of intra-cluster data aggregation in VANETs. In this study, we propose a multi-player game theory algorithm for intra-cluster data aggregation in VANETs by analyzing the competitive and cooperative relationships among sensor nodes. Several sensor-centric metrics are proposed to measure the data redundancy and stability of a cluster. We then study the utility function to achieve efficient intra-cluster data aggregation by considering both data redundancy and cluster stability. In particular, we prove the existence of a unique Nash equilibrium in the game model, and conduct extensive experiments to validate the proposed algorithm. Results demonstrate that the proposed algorithm has advantages over typical data aggregation algorithms in both accuracy and efficiency.

Polymorphism of Lysozyme Condensates.

PubMed

Safari, Mohammad S; Byington, Michael C; Conrad, Jacinta C; Vekilov, Peter G

2017-10-05

Protein condensates play essential roles in physiological processes and pathological conditions. Recently discovered mesoscopic protein-rich clusters may act as crucial precursors for the nucleation of ordered protein solids, such as crystals, sickle hemoglobin polymers, and amyloid fibrils. These clusters challenge settled paradigms of protein condensation as the constituent protein molecules present features characteristic of both partially misfolded and native proteins. Here we employ the antimicrobial enzyme lysozyme and examine the similarities between mesoscopic clusters, amyloid structures, and disordered aggregates consisting of chemically modified protein. We show that the mesoscopic clusters are distinct from the other two classes of aggregates. Whereas cluster formation and amyloid oligomerization are both reversible, aggregation triggered by reduction of the intramolecular S-S bonds is permanent. In contrast to the amyloid structures, protein molecules in the clusters retain their enzymatic activity. Furthermore, an essential feature of the mesoscopic clusters is their constant radius of less than 50 nm. The amyloid and disordered aggregates are significantly larger and rapidly grow. These findings demonstrate that the clusters are a product of limited protein structural flexibility. In view of the role of the clusters in the nucleation of ordered protein solids, our results suggest that fine-tuning the degree of protein conformational stability is a powerful tool to control and direct the pathways of protein condensation.

Coagulation-fragmentation for a finite number of particles and application to telomere clustering in the yeast nucleus

NASA Astrophysics Data System (ADS)

Hozé, Nathanaël; Holcman, David

2012-01-01

We develop a coagulation-fragmentation model to study a system composed of a small number of stochastic objects moving in a confined domain, that can aggregate upon binding to form local clusters of arbitrary sizes. A cluster can also dissociate into two subclusters with a uniform probability. To study the statistics of clusters, we combine a Markov chain analysis with a partition number approach. Interestingly, we obtain explicit formulas for the size and the number of clusters in terms of hypergeometric functions. Finally, we apply our analysis to study the statistical physics of telomeres (ends of chromosomes) clustering in the yeast nucleus and show that the diffusion-coagulation-fragmentation process can predict the organization of telomeres.

Cluster structure of anaerobic aggregates of an expanded granular sludge bed reactor.

PubMed

Gonzalez-Gil, G; Lens, P N; Van Aelst, A; Van As, H; Versprille, A I; Lettinga, G

2001-08-01

The metabolic properties and ultrastructure of mesophilic aggregates from a full-scale expanded granular sludge bed reactor treating brewery wastewater are described. The aggregates had a very high methanogenic activity on acetate (17.19 mmol of CH(4)/g of volatile suspended solids [VSS].day or 1.1 g of CH(4) chemical oxygen demand/g of VSS.day). Fluorescent in situ hybridization using 16S rRNA probes of crushed granules showed that 70 and 30% of the cells belonged to the archaebacterial and eubacterial domains, respectively. The spherical aggregates were black but contained numerous whitish spots on their surfaces. Cross-sectioning these aggregates revealed that the white spots appeared to be white clusters embedded in a black matrix. The white clusters were found to develop simultaneously with the increase in diameter. Energy-dispersed X-ray analysis and back-scattered electron microscopy showed that the whitish clusters contained mainly organic matter and no inorganic calcium precipitates. The white clusters had a higher density than the black matrix, as evidenced by the denser cell arrangement observed by high-magnification electron microscopy and the significantly higher effective diffusion coefficient determined by nuclear magnetic resonance imaging. High-magnification electron microscopy indicated a segregation of acetate-utilizing methanogens (Methanosaeta spp.) in the white clusters from syntrophic species and hydrogenotrophic methanogens (Methanobacterium-like and Methanospirillum-like organisms) in the black matrix. A number of physical and microbial ecology reasons for the observed structure are proposed, including the advantage of segregation for high-rate degradation of syntrophic substrates.

Cluster Structure of Anaerobic Aggregates of an Expanded Granular Sludge Bed Reactor

PubMed Central

Gonzalez-Gil, G.; Lens, P. N. L.; Van Aelst, A.; Van As, H.; Versprille, A. I.; Lettinga, G.

2001-01-01

The metabolic properties and ultrastructure of mesophilic aggregates from a full-scale expanded granular sludge bed reactor treating brewery wastewater are described. The aggregates had a very high methanogenic activity on acetate (17.19 mmol of CH4/g of volatile suspended solids [VSS]·day or 1.1 g of CH4 chemical oxygen demand/g of VSS·day). Fluorescent in situ hybridization using 16S rRNA probes of crushed granules showed that 70 and 30% of the cells belonged to the archaebacterial and eubacterial domains, respectively. The spherical aggregates were black but contained numerous whitish spots on their surfaces. Cross-sectioning these aggregates revealed that the white spots appeared to be white clusters embedded in a black matrix. The white clusters were found to develop simultaneously with the increase in diameter. Energy-dispersed X-ray analysis and back-scattered electron microscopy showed that the whitish clusters contained mainly organic matter and no inorganic calcium precipitates. The white clusters had a higher density than the black matrix, as evidenced by the denser cell arrangement observed by high-magnification electron microscopy and the significantly higher effective diffusion coefficient determined by nuclear magnetic resonance imaging. High-magnification electron microscopy indicated a segregation of acetate-utilizing methanogens (Methanosaeta spp.) in the white clusters from syntrophic species and hydrogenotrophic methanogens (Methanobacterium-like and Methanospirillum-like organisms) in the black matrix. A number of physical and microbial ecology reasons for the observed structure are proposed, including the advantage of segregation for high-rate degradation of syntrophic substrates. PMID:11472948

Physical model of protein cluster positioning in growing bacteria

NASA Astrophysics Data System (ADS)

Wasnik, Vaibhav; Wang, Hui; Wingreen, Ned S.; Mukhopadhyay, Ranjan

2017-10-01

Chemotaxic receptors in bacteria form clusters at cell poles and also laterally, and this clustering plays an important role in signal transduction. These clusters were found to be periodically arranged on the surface of the bacterium Escherichia coli, independent of any known positioning mechanism. In this work we extend a model based on diffusion and aggregation to more realistic geometries and present a means based on ‘bursty’ protein production to distinguish spontaneous positioning from an independently existing positioning mechanism. We also consider the case of isotropic cellular growth and characterize the degree of order arising spontaneously. Our model could also be relevant for other examples of periodically positioned protein clusters in bacteria.

Reaction and Aggregation Dynamics of Cell Surface Receptors

NASA Astrophysics Data System (ADS)

Wang, Michelle Dong

This dissertation is composed of both theoretical and experimental studies of cell surface receptor reaction and aggregation. Project I studies the reaction rate enhancement due to surface diffusion of a bulk dissolved ligand with its membrane embedded target, using numerical calculations. The results show that the reaction rate enhancement is determined by ligand surface adsorption and desorption kinetic rates, surface and bulk diffusion coefficients, and geometry. In particular, we demonstrate that the ligand surface adsorption and desorption kinetic rates, rather than their ratio (the equilibrium constant), are important in rate enhancement. The second and third projects are studies of acetylcholine receptor clusters on cultured rat myotubes using fluorescence techniques after labeling the receptors with tetramethylrhodamine -alpha-bungarotoxin. The second project studies when and where the clusters form by making time-lapse movies. The movies are made from overlay of the pseudocolored total internal reflection fluorescence (TIRF) images of the cluster, and the schlieren images of the cell cultures. These movies are the first movies made using TIRF, and they clearly show the cluster formation from the myoblast fusion, the first appearance of clusters, and the eventual disappearance of clusters. The third project studies the fine structural features of individual clusters observed under TIRF. The features were characterized with six parameters by developing a novel fluorescence technique: spatial fluorescence autocorrelation. These parameters were then used to study the feature variations with age, and with treatments of drugs (oligomycin and carbachol). The results show little variation with age. However, drug treatment induced significant changes in some parameters. These changes were different for oligomycin and carbachol, which indicates that the two drugs may eliminate clusters through different mechanisms.

Fractal patterns formed by growth of radial viscous fingers*

NASA Astrophysics Data System (ADS)

Praud, Olivier

2004-03-01

We examine fractal patterns formed by the injection of air into oil in a thin (0.13 mm) layer contained between two cylindrical glass plates of 288 mm diameter (a Hele-Shaw cell) [1]. The resultant radially grown patterns are similar to those formed in Diffusion Limited Aggregation (DLA), but the relation between the continuum limit of DLA and continuum (Laplacian) growth remains an open question. Our viscous fingering patterns in the limit of very high pressure difference reach an asymptotic state in which they exhibit a fractal dimension of 1.70± 0.02, in good agreement with a calculation of the fractal dimension of a DLA cluster, 1.713± 0.003 [2]. The generalized dimensions are also computed and show that the observed pattern is self-similar with Dq = 1.70 for all q. Further, the probability density function of shielding angles suggests the existence of a critical angle close to 75 degrees. This result is in accord with numerical and analytical evidence of a critical angle in DLA [3]. Thus fractal viscous fingering patterns and Diffusion Limited Aggregation clusters have a similar geometrical structure. *Work conducted in collaboration with H.L. Swinney, M.G. Moore and Eran Sharon [1] E. Sharon, M. G. Moore, W. D. McCormick, and H. L. Swinney, Phys. Rev. Lett. 91, 205504 (2003). [2] B.Davidovitch et A. Levermann and I. Procaccia, Phys. Rev. E 62, 5919 (2000). [3] D. A. Kessler et al., Phys. Rev. E 57, 6913 (1998).

Formation and Growth of Stacking Fault Tetrahedra in Ni via Vacancy Aggregation Mechanism

DOE PAGES

Aidhy, Dilpuneet S.; Lu, Chenyang; Jin, Ke; ...

2015-12-29

Using molecular dynamics simulations, the formation and growth of stacking fault tetrahedra (SFT) are captured by vacancy cluster diffusion and aggregation mechanisms in Ni. The vacancytetrahedron acts as a nucleation point for SFT formation. Simulations show that perfect SFT can grow to the next size perfect SFT via a vacancy aggregation mechanism. The stopping and range of ions in matter (SRIM) calculations and transmission electron microscopy (TEM) observations reveal that SFT can form farther away from the initial cascade-event locations, indicating the operation of diffusion-based vacancy-aggregation mechanism.

Formation and Growth of Stacking Fault Tetrahedra in Ni via Vacancy Aggregation Mechanism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aidhy, Dilpuneet S.; Lu, Chenyang; Jin, Ke

Using molecular dynamics simulations, the formation and growth of stacking fault tetrahedra (SFT) are captured by vacancy cluster diffusion and aggregation mechanisms in Ni. The vacancytetrahedron acts as a nucleation point for SFT formation. Simulations show that perfect SFT can grow to the next size perfect SFT via a vacancy aggregation mechanism. The stopping and range of ions in matter (SRIM) calculations and transmission electron microscopy (TEM) observations reveal that SFT can form farther away from the initial cascade-event locations, indicating the operation of diffusion-based vacancy-aggregation mechanism.

Efficient clustering aggregation based on data fragments.

PubMed

Wu, Ou; Hu, Weiming; Maybank, Stephen J; Zhu, Mingliang; Li, Bing

2012-06-01

Clustering aggregation, known as clustering ensembles, has emerged as a powerful technique for combining different clustering results to obtain a single better clustering. Existing clustering aggregation algorithms are applied directly to data points, in what is referred to as the point-based approach. The algorithms are inefficient if the number of data points is large. We define an efficient approach for clustering aggregation based on data fragments. In this fragment-based approach, a data fragment is any subset of the data that is not split by any of the clustering results. To establish the theoretical bases of the proposed approach, we prove that clustering aggregation can be performed directly on data fragments under two widely used goodness measures for clustering aggregation taken from the literature. Three new clustering aggregation algorithms are described. The experimental results obtained using several public data sets show that the new algorithms have lower computational complexity than three well-known existing point-based clustering aggregation algorithms (Agglomerative, Furthest, and LocalSearch); nevertheless, the new algorithms do not sacrifice the accuracy.

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.

ATCA observations of the MACS-Planck Radio Halo Cluster Project. II. Radio observations of an intermediate redshift cluster sample

NASA Astrophysics Data System (ADS)

Martinez Aviles, G.; Johnston-Hollitt, M.; Ferrari, C.; Venturi, T.; Democles, J.; Dallacasa, D.; Cassano, R.; Brunetti, G.; Giacintucci, S.; Pratt, G. W.; Arnaud, M.; Aghanim, N.; Brown, S.; Douspis, M.; Hurier, J.; Intema, H. T.; Langer, M.; Macario, G.; Pointecouteau, E.

2018-04-01

Aim. A fraction of galaxy clusters host diffuse radio sources whose origins are investigated through multi-wavelength studies of cluster samples. We investigate the presence of diffuse radio emission in a sample of seven galaxy clusters in the largely unexplored intermediate redshift range (0.3 < z < 0.44). Methods: In search of diffuse emission, deep radio imaging of the clusters are presented from wide band (1.1-3.1 GHz), full resolution ( 5 arcsec) observations with the Australia Telescope Compact Array (ATCA). The visibilities were also imaged at lower resolution after point source modelling and subtraction and after a taper was applied to achieve better sensitivity to low surface brightness diffuse radio emission. In case of non-detection of diffuse sources, we set upper limits for the radio power of injected diffuse radio sources in the field of our observations. Furthermore, we discuss the dynamical state of the observed clusters based on an X-ray morphological analysis with XMM-Newton. Results: We detect a giant radio halo in PSZ2 G284.97-23.69 (z = 0.39) and a possible diffuse source in the nearly relaxed cluster PSZ2 G262.73-40.92 (z = 0.421). Our sample contains three highly disturbed massive clusters without clear traces of diffuse emission at the observed frequencies. We were able to inject modelled radio haloes with low values of total flux density to set upper detection limits; however, with our high-frequency observations we cannot exclude the presence of RH in these systems because of the sensitivity of our observations in combination with the high z of the observed clusters. The reduced images are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/611/A94

Coalescence of silver clusters by immersion in diluted HF solution

NASA Astrophysics Data System (ADS)

Milazzo, R. G.; Mio, A. M.; D'Arrigo, G.; Grimaldi, M. G.; Spinella, C.; Rimini, E.

2015-07-01

The galvanic displacement deposition of silver on H-terminated Si (100) in the time scale of seconds is instantaneous and characterized by a cluster density of 1011-1012 cm-2. The amount of deposited Ag follows a t1/2 dependence in agreement with a Cottrell diffusion limited mechanism. At the same time, during the deposition, the cluster density reduces by a factor 5. This behavior is in contrast with the assumption of immobile clusters. We show in the present work that coalescence and aggregation occur also in the samples immersed in the diluted hydrofluoric acid (HF) solution without the presence of Ag+. Clusters agglomerate according to a process of dynamic coalescence, typical of colloids, followed by atomic redistribution at the contact regions with the generation of multiple internal twins and stacking-faults. The normalized size distributions in terms of r/rmean follow also the prediction of the Smoluchowski ripening mechanism. No variation of the cluster density occurs for samples immersed in pure H2O solution. The different behavior might be associated to the strong attraction of clusters to oxide-terminated Si surface in presence of water. The silver clusters are instead weakly bound to hydrophobic H-terminated Si in presence of HF. HF causes then the detachment of clusters and a random movement on the silicon surface with mobility of about 10-13 cm2/s. Attractive interaction (probably van der Waals) among particles promotes coarsening.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ben-Naim, Eli; Krapivsky, Paul

Here we generalize the ordinary aggregation process to allow for choice. In ordinary aggregation, two random clusters merge and form a larger aggregate. In our implementation of choice, a target cluster and two candidate clusters are randomly selected and the target cluster merges with the larger of the two candidate clusters.We study the long-time asymptotic behavior and find that as in ordinary aggregation, the size density adheres to the standard scaling form. However, aggregation with choice exhibits a number of different features. First, the density of the smallest clusters exhibits anomalous scaling. Second, both the small-size and the large-size tailsmore » of the density are overpopulated, at the expense of the density of moderate-size clusters. Finally, we also study the complementary case where the smaller candidate cluster participates in the aggregation process and find an abundance of moderate clusters at the expense of small and large clusters. Additionally, we investigate aggregation processes with choice among multiple candidate clusters and a symmetric implementation where the choice is between two pairs of clusters.« less

Kinetics of Aggregation with Choice

DOE PAGES

Ben-Naim, Eli; Krapivsky, Paul

2016-12-01

Here we generalize the ordinary aggregation process to allow for choice. In ordinary aggregation, two random clusters merge and form a larger aggregate. In our implementation of choice, a target cluster and two candidate clusters are randomly selected and the target cluster merges with the larger of the two candidate clusters.We study the long-time asymptotic behavior and find that as in ordinary aggregation, the size density adheres to the standard scaling form. However, aggregation with choice exhibits a number of different features. First, the density of the smallest clusters exhibits anomalous scaling. Second, both the small-size and the large-size tailsmore » of the density are overpopulated, at the expense of the density of moderate-size clusters. Finally, we also study the complementary case where the smaller candidate cluster participates in the aggregation process and find an abundance of moderate clusters at the expense of small and large clusters. Additionally, we investigate aggregation processes with choice among multiple candidate clusters and a symmetric implementation where the choice is between two pairs of clusters.« less

Diffuse radio emission in the complex merging galaxy cluster Abell2069

NASA Astrophysics Data System (ADS)

Drabent, A.; Hoeft, M.; Pizzo, R. F.; Bonafede, A.; van Weeren, R. J.; Klein, U.

2015-03-01

Context. Galaxy clusters with signs of a recent merger in many cases show extended diffuse radio features. This emission originates from relativistic electrons that suffer synchrotron losses due to the intracluster magnetic field. The mechanisms of particle acceleration and the properties of the magnetic field are still poorly understood. Aims: We search for diffuse radio emission in galaxy clusters. Here, we study the complex galaxy cluster Abell 2069, for which X-ray observations indicate a recent merger. Methods: We investigate the cluster's radio continuum emission by deep Westerbork Synthesis Radio Telescope (WSRT) observations at 346 MHz and Giant Metrewave Radio Telescope (GMRT) observations at 322 MHz. Results: We find an extended diffuse radio feature roughly coinciding with the main component of the cluster. We classify this emission as a radio halo and estimate its lower limit flux density at 25 ± 9 mJy. Moreover, we find a second extended diffuse source located at the cluster's companion and estimate its flux density at 15 ± 2 mJy. We speculate that this is a small halo or a mini-halo. If true, this cluster is the first example of a double-halo in a single galaxy cluster.

Stacking and Branching in Self-Aggregation of Caffeine in Aqueous Solution: From the Supramolecular to Atomic Scale Clustering.

PubMed

Tavagnacco, Letizia; Gerelli, Yuri; Cesàro, Attilio; Brady, John W

2016-09-22

The dynamical and structural properties of caffeine solutions at the solubility limit have been investigated as a function of temperature by means of MD simulations, static and dynamic light scattering, and small angle neutron scattering experiments. A clear picture unambiguously supported by both experiment and simulation emerges: caffeine self-aggregation promotes the formation of two distinct types of clusters: linear aggregates of stacked molecules, formed by 2-14 caffeine molecules depending on the thermodynamic conditions and disordered branched aggregates with a size in the range 1000-3000 Å. While the first type of association is well-known to occur under room temperature conditions for both caffeine and other purine systems, such as nucleotides, the presence of the supramolecular aggregates has not been reported previously. MD simulations indicate that branched structures are formed by caffeine molecules in a T-shaped arrangement. An increase of the solubility limit (higher temperature but also higher concentration) broadens the distribution of cluster sizes, promoting the formation of stacked aggregates composed by a larger number of caffeine molecules. Surprisingly, the effect on the branched aggregates is rather limited. Their internal structure and size do not change considerably in the range of solubility limits investigated.

Brownian aggregation rate of colloid particles with several active sites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nekrasov, Vyacheslav M.; Yurkin, Maxim A.; Chernyshev, Andrei V., E-mail: chern@ns.kinetics.nsc.ru

2014-08-14

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

Scattering properties of alumina particle clusters with different radius of monomers in aerocraft plume

NASA Astrophysics Data System (ADS)

Li, Jingying; Bai, Lu; Wu, Zhensen; Guo, Lixin; Gong, Yanjun

2017-11-01

In this paper, diffusion limited aggregation (DLA) algorithm is improved to generate the alumina particle cluster with different radius of monomers in the plume. Scattering properties of these alumina clusters are solved by the multiple sphere T matrix method (MSTM). The effect of the number and radius of monomers on the scattering properties of clusters of alumina particles is discussed. The scattering properties of two types of alumina particle clusters are compared, one has different radius of monomers that follows lognormal probability distribution, another has the same radius of monomers that equals the mean of lognormal probability distribution. The result show that the scattering phase functions and linear polarization degrees of these two types of alumina particle clusters are of great differences. For the alumina clusters with different radius of monomers, the forward scatterings are bigger and the linear polarization degree has multiple peaks. Moreover, the vary of their scattering properties do not have strong correlative with the change of number of monomers. For larger booster motors, 25-38% of the plume being condensed alumina. The alumina can scatter radiation from other sources present in the plume and effect on radiation transfer characteristics of plume. In addition, the shape, size distribution and refractive index of the particles in the plume are estimated by linear polarization degree. Therefore, accurate scattering properties calculation is very important to decrease the deviation in the related research.

Diffuse x-ray scattering and transmission electron microscopy study of defects in antimony-implanted silicon

NASA Astrophysics Data System (ADS)

Takamura, Y.; Marshall, A. F.; Mehta, A.; Arthur, J.; Griffin, P. B.; Plummer, J. D.; Patel, J. R.

2004-04-01

Ion implantation followed by laser annealing has been used to create supersaturated and electrically active concentrations of antimony in silicon. Upon subsequent thermal annealing, however, these metastable dopants deactivate towards the equilibrium solubility limit. In this work, the formation of inactive antimony structures has been studied with grazing incidence diffuse x-ray scattering, and transmission electron microscopy, and the results are correlated to previous high-resolution x-ray diffraction data. We find that at a concentration of 6.0×1020 cm-3, small, incoherent clusters of radius 3-4 Å form during annealing at 900 °C. At a higher concentration of 2.2×1021 cm-3, deactivation at 600 °C occurs through the formation of small, antimony aggregates and antimony precipitates. The size of these precipitates from diffuse x-ray scattering is roughly 15 Å in radius for anneal times from 15 to 180 seconds. This value is consistent with the features observed in high-resolution and mass contrast transmission electron microscopy images. The coherent nature of the aggregates and precipitates causes the expansion of the surrounding silicon matrix as the deactivation progresses. In addition, the sensitivity of the diffuse x-ray scattering technique has allowed us to detect the presence of small clusters of radius ˜2 Å in unprocessed Czochralski silicon wafers. These defects are not observed in floating zone silicon wafers, and are tentatively attributed to thermal donors.

Clustering and heterogeneous dynamics in a kinetic Monte Carlo model of self-propelled hard disks

NASA Astrophysics Data System (ADS)

Levis, Demian; Berthier, Ludovic

2014-06-01

We introduce a kinetic Monte Carlo model for self-propelled hard disks to capture with minimal ingredients the interplay between thermal fluctuations, excluded volume, and self-propulsion in large assemblies of active particles. We analyze in detail the resulting (density, self-propulsion) nonequilibrium phase diagram over a broad range of parameters. We find that purely repulsive hard disks spontaneously aggregate into fractal clusters as self-propulsion is increased and rationalize the evolution of the average cluster size by developing a kinetic model of reversible aggregation. As density is increased, the nonequilibrium clusters percolate to form a ramified structure reminiscent of a physical gel. We show that the addition of a finite amount of noise is needed to trigger a nonequilibrium phase separation, showing that demixing in active Brownian particles results from a delicate balance between noise, interparticle interactions, and self-propulsion. We show that self-propulsion has a profound influence on the dynamics of the active fluid. We find that the diffusion constant has a nonmonotonic behavior as self-propulsion is increased at finite density and that activity produces strong deviations from Fickian diffusion that persist over large time scales and length scales, suggesting that systems of active particles generically behave as dynamically heterogeneous systems.

Transient shear viscosity of weakly aggregating polystyrene latex dispersions

NASA Astrophysics Data System (ADS)

de Rooij, R.; Potanin, A. A.; van den Ende, D.; Mellema, J.

1994-04-01

The transient behavior of the viscosity (stress growth) of a weakly aggregating polystyrene latex dispersion after a step from a high shear rate to a lower shear rate has been measured and modeled. Single particles cluster together into spherical fractal aggregates. The steady state size of these aggregates is determined by the shear stresses exerted on the latter by the flow field. The restructuring process taking place when going from a starting situation with monodisperse spherical aggregates to larger monodisperse spherical aggregates is described by the capture of primary fractal aggregates by growing aggregates until a new steady state is reached. It is assumed that the aggregation mechanism is diffusion limited. The model is valid if the radii of primary aggregates Rprim are much smaller than the radii of the growing aggregates. Fitting the model to experimental data at two volume fractions and a number of step sizes in shear rate yielded physically reasonable values of Rprim at fractal dimensions 2.1≤df≤2.2. The latter range is in good agreement with the range 2.0≤df≤2.3 obtained from steady shear results. The experimental data have also been fitted to a numerical solution of the diffusion equation for primary aggregates for a cell model with moving boundary, also yielding 2.1≤df≤2.2. The range for df found from both approaches agrees well with the range df≊2.1-2.2 determined from computer simulations on diffusion-limited aggregation including restructuring or thermal breakup after formation of bonds. Thus a simple model has been put forward which may capture the basic features of the aggregating model dispersion on a microstructural level and leads to physically acceptable parameter values.

Diffusion Monte Carlo simulations of gas phase and adsorbed D2-(H2)n clusters

NASA Astrophysics Data System (ADS)

Curotto, E.; Mella, M.

2018-03-01

We have computed ground state energies and analyzed radial distributions for several gas phase and adsorbed D2(H2)n and HD(H2)n clusters. An external model potential designed to mimic ionic adsorption sites inside porous materials is used [M. Mella and E. Curotto, J. Phys. Chem. A 121, 5005 (2017)]. The isotopic substitution lowers the ground state energies by the expected amount based on the mass differences when these are compared with the energies of the pure clusters in the gas phase. A similar impact is found for adsorbed aggregates. The dissociation energy of D2 from the adsorbed clusters is always much higher than that of H2 from both pure and doped aggregates. Radial distributions of D2 and H2 are compared for both the gas phase and adsorbed species. For the gas phase clusters, two types of hydrogen-hydrogen interactions are considered: one based on the assumption that rotations and translations are adiabatically decoupled and the other based on nonisotropic four-dimensional potential. In the gas phase clusters of sufficiently large size, we find the heavier isotopomer more likely to be near the center of mass. However, there is a considerable overlap among the radial distributions of the two species. For the adsorbed clusters, we invariably find the heavy isotope located closer to the attractive interaction source than H2, and at the periphery of the aggregate, H2 molecules being substantially excluded from the interaction with the source. This finding rationalizes the dissociation energy results. For D2-(H2)n clusters with n ≥12 , such preference leads to the desorption of D2 from the aggregate, a phenomenon driven by the minimization of the total energy that can be obtained by reducing the confinement of (H2)12. The same happens for (H2)13, indicating that such an effect may be quite general and impact on the absorption of quantum species inside porous materials.

Early-stage aggregation in three-dimensional charged granular gas.

PubMed

Singh, Chamkor; Mazza, Marco G

2018-02-01

Neutral grains made of the same dielectric material can attain considerable charges due to collisions and generate long-range interactions. We perform molecular dynamic simulations in three dimensions for a dilute, freely cooling granular gas of viscoelastic particles that exchange charges during collisions. As compared to the case of clustering of viscoelastic particles solely due to dissipation, we find that the electrostatic interactions due to collisional charging alter the characteristic size, morphology, and growth rate of the clusters. The average cluster size grows with time as a power law, whose exponent is relatively larger in the charged gas than the neutral case. The growth of the average cluster size is found to be independent of the ratio of characteristic Coulomb to kinetic energy, or equivalently, of the typical Bjerrum length. However, this ratio alters the crossover time of the growth. Both simulations and mean-field calculations based on Smoluchowski's equation suggest that a suppression of particle diffusion due to the electrostatic interactions helps in the aggregation process.

Early-stage aggregation in three-dimensional charged granular gas

NASA Astrophysics Data System (ADS)

Singh, Chamkor; Mazza, Marco G.

2018-02-01

Neutral grains made of the same dielectric material can attain considerable charges due to collisions and generate long-range interactions. We perform molecular dynamic simulations in three dimensions for a dilute, freely cooling granular gas of viscoelastic particles that exchange charges during collisions. As compared to the case of clustering of viscoelastic particles solely due to dissipation, we find that the electrostatic interactions due to collisional charging alter the characteristic size, morphology, and growth rate of the clusters. The average cluster size grows with time as a power law, whose exponent is relatively larger in the charged gas than the neutral case. The growth of the average cluster size is found to be independent of the ratio of characteristic Coulomb to kinetic energy, or equivalently, of the typical Bjerrum length. However, this ratio alters the crossover time of the growth. Both simulations and mean-field calculations based on Smoluchowski's equation suggest that a suppression of particle diffusion due to the electrostatic interactions helps in the aggregation process.

CHARGING AND COAGULATION OF DUST IN PROTOPLANETARY PLASMA ENVIRONMENTS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Matthews, L. S.; Land, V.; Hyde, T. W., E-mail: lorin_matthews@baylor.edu

2012-01-01

Combining a particle-particle, particle-cluster, and cluster-cluster agglomeration model with an aggregate charging model, the coagulation and charging of dust particles in plasma environments relevant for protoplanetary disks have been investigated, including the effect of electron depletion in high dust density environments. The results show that charged aggregates tend to grow by adding small particles and clusters to larger particles and clusters, and that cluster-cluster aggregation is significantly more effective than particle-cluster aggregation. Comparisons of the grain structure show that with increasing aggregate charge the compactness factor, {phi}{sub {sigma}}, decreases and has a narrower distribution, indicating a fluffier structure. Neutral aggregatesmore » are more compact, with larger {phi}{sub {sigma}}, and exhibit a larger variation in fluffiness. Overall, increased aggregate charge leads to larger, fluffier, and more massive aggregates.« less

Multiscale Computer Simulation of Failure in Aerogels

NASA Technical Reports Server (NTRS)

Good, Brian S.

2008-01-01

Aerogels have been of interest to the aerospace community primarily for their thermal properties, notably their low thermal conductivities. While such gels are typically fragile, recent advances in the application of conformal polymer layers to these gels has made them potentially useful as lightweight structural materials as well. We have previously performed computer simulations of aerogel thermal conductivity and tensile and compressive failure, with results that are in qualitative, and sometimes quantitative, agreement with experiment. However, recent experiments in our laboratory suggest that gels having similar densities may exhibit substantially different properties. In this work, we extend our original diffusion limited cluster aggregation (DLCA) model for gel structure to incorporate additional variation in DLCA simulation parameters, with the aim of producing DLCA clusters of similar densities that nevertheless have different fractal dimension and secondary particle coordination. We perform particle statics simulations of gel strain on these clusters, and consider the effects of differing DLCA simulation conditions, and the resultant differences in fractal dimension and coordination, on gel strain properties.

Ultra small angle x-ray scattering in complex mixtures of triacylglycerols

NASA Astrophysics Data System (ADS)

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

2014-11-01

Ultra-small angle x-ray scattering (USAXS) has been used to elucidate, in situ, the aggregation structure of unsheared model edible oils. Each system comprised one or two solid lipids and a combination of liquid lipids. The 3D nano- to micro-structures of each system were characterized. The length scale investigated, using the Bonse-Hart camera at beamline ID-15D at the Advanced Photon Source, ANL, ranged from 300 Å-10 µm. Using the Unified Fit model, level-1 analysis showed that the scatterers were 2D objects with either a smooth, a rough, or a diffuse surface. These 2D objects had an average radius of gyration Rg1 between 200-1500 Å. Level-2 analysis displayed a slope between -1 and -2. Use of the Guinier-Porod model gave s ≈ 1 thus showing that it was cylinders (TAGwoods) aggregating with fractal dimension 1 ≤ D2 ≤ 2. D2 = 1 is consistent with 1D structures formed from TAGwoods, while D2 = 2 implies that the TAGwoods had formed structures characteristic of diffusion or reaction limited cluster-cluster aggregation (DLCA/RLCA). These aggregates exhibited radii of gyration, Rg2, between 2500 and 6500 Å. Level-3 analyses showed diffuse surfaces, for most of the systems. These interpretations are in accord with theoretical models which studied crystalline nano-platelets (CNPs) coated with nano-scale layers arising from phase separation at the CNP surfaces. These layers could be due to either liquid-liquid phase separation with the CNPs coated, uniformly or non-uniformly, by a diffuse layer of TAGs, or solid-liquid phase separation with the CNPs coated by a rough layer of crystallites. A fundamental understanding of the self-organizing structures arising in these systems helps advance the characterization of fat crystal networks from nanometres to micrometres. This research can be used to design novel fat structures that use healthier fats via nano- and meso-scale structural engineering.

Reproductive pair correlations and the clustering of organisms.

PubMed

Young, W R; Roberts, A J; Stuhne, G

2001-07-19

Clustering of organisms can be a consequence of social behaviour, or of the response of individuals to chemical and physical cues. Environmental variability can also cause clustering: for example, marine turbulence transports plankton and produces chlorophyll concentration patterns in the upper ocean. Even in a homogeneous environment, nonlinear interactions between species can result in spontaneous pattern formation. Here we show that a population of independent, random-walking organisms ('brownian bugs'), reproducing by binary division and dying at constant rates, spontaneously aggregates. Using an individual-based model, we show that clusters form out of spatially homogeneous initial conditions without environmental variability, predator-prey interactions, kinesis or taxis. The clustering mechanism is reproductively driven-birth must always be adjacent to a living organism. This clustering can overwhelm diffusion and create non-poissonian correlations between pairs (parent and offspring) or organisms, leading to the emergence of patterns.

Numerical insights into the early stages of nanoscale electrodeposition: nanocluster surface diffusion and aggregative growth.

PubMed

Mamme, Mesfin Haile; Köhn, Christoph; Deconinck, Johan; Ustarroz, Jon

2018-04-19

Fundamental understanding of the early stages of electrodeposition at the nanoscale is key to address the challenges in a wide range of applications. Despite having been studied for decades, a comprehensive understanding of the whole process is still out of reach. In this work, we introduce a novel modelling approach that couples a finite element method (FEM) with a random walk algorithm, to study the early stages of nanocluster formation, aggregation and growth, during electrochemical deposition. This approach takes into account not only electrochemical kinetics and transport of active species, but also the surface diffusion and aggregation of adatoms and small nanoclusters. The simulation results reveal that the relative surface mobility of the nanoclusters compared to that of the adatoms plays a crucial role in the early growth stages. The number of clusters, their size and their size dispersion are influenced more significantly by nanocluster mobility than by the applied overpotential itself. Increasing the overpotential results in shorter induction times and leads to aggregation prevalence at shorter times. A higher mobility results in longer induction times, a delayed transition from nucleation to aggregation prevalence, and as a consequence, a larger surface coverage of smaller clusters with a smaller size dispersion. As a consequence, it is shown that a classical first-order nucleation kinetics equation cannot describe the evolution of the number of clusters with time, N(t), in potentiostatic electrodeposition. Instead, a more accurate representation of N(t) is provided. We show that an evaluation of N(t), which neglects the effect of nanocluster mobility and aggregation, can induce errors of several orders of magnitude in the determination of nucleation rate constants. These findings are extremely important towards evaluating the elementary electrodeposition processes, considering not only adatoms, but also nanoclusters as building blocks.

Optimal approximation of harmonic growth clusters by orthogonal polynomials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Teodorescu, Razvan

2008-01-01

Interface dynamics in two-dimensional systems with a maximal number of conservation laws gives an accurate theoreticaI model for many physical processes, from the hydrodynamics of immiscible, viscous flows (zero surface-tension limit of Hele-Shaw flows), to the granular dynamics of hard spheres, and even diffusion-limited aggregation. Although a complete solution for the continuum case exists, efficient approximations of the boundary evolution are very useful due to their practical applications. In this article, the approximation scheme based on orthogonal polynomials with a deformed Gaussian kernel is discussed, as well as relations to potential theory.

Multiscale Computer Simulation of Tensile and Compressive Strain in Polymer- Coated Silica Aerogels

NASA Technical Reports Server (NTRS)

Good, Brian

2009-01-01

While the low thermal conductivities of silica aerogels have made them of interest to the aerospace community as lightweight thermal insulation, the application of conformal polymer coatings to these gels increases their strength significantly, making them potentially useful as structural materials as well. In this work we perform multiscale computer simulations to investigate the tensile and compressive strain behavior of silica and polymer-coated silica aerogels. Aerogels are made up of clusters of interconnected particles of amorphous silica of less than bulk density. We simulate gel nanostructure using a Diffusion Limited Cluster Aggregation (DLCA) procedure, which produces aggregates that exhibit fractal dimensions similar to those observed in real aerogels. We have previously found that model gels obtained via DLCA exhibited stress-strain curves characteristic of the experimentally observed brittle failure. However, the strain energetics near the expected point of failure were not consistent with such failure. This shortcoming may be due to the fact that the DLCA process produces model gels that are lacking in closed-loop substructures, compared with real gels. Our model gels therefore contain an excess of dangling strands, which tend to unravel under tensile strain, producing non-brittle failure. To address this problem, we have incorporated a modification to the DLCA algorithm that specifically produces closed loops in the model gels. We obtain the strain energetics of interparticle connections via atomistic molecular statics, and abstract the collective energy of the atomic bonds into a Morse potential scaled to describe gel particle interactions. Polymer coatings are similarly described. We apply repeated small uniaxial strains to DLCA clusters, and allow relaxation of the center eighty percent of the cluster between strains. The simulations produce energetics and stress-strain curves for looped and nonlooped clusters, for a variety of densities and interaction parameters.

Effects of stomata clustering on leaf gas exchange.

PubMed

Lehmann, Peter; Or, Dani

2015-09-01

A general theoretical framework for quantifying the stomatal clustering effects on leaf gaseous diffusive conductance was developed and tested. The theory accounts for stomatal spacing and interactions among 'gaseous concentration shells'. The theory was tested using the unique measurements of Dow et al. (2014) that have shown lower leaf diffusive conductance for a genotype of Arabidopsis thaliana with clustered stomata relative to uniformly distributed stomata of similar size and density. The model accounts for gaseous diffusion: through stomatal pores; via concentration shells forming at pore apertures that vary with stomata spacing and are thus altered by clustering; and across the adjacent air boundary layer. Analytical approximations were derived and validated using a numerical model for 3D diffusion equation. Stomata clustering increases the interactions among concentration shells resulting in larger diffusive resistance that may reduce fluxes by 5-15%. A similar reduction in conductance was found for clusters formed by networks of veins. The study resolves ambiguities found in the literature concerning stomata end-corrections and stomatal shape, and provides a new stomata density threshold for diffusive interactions of overlapping vapor shells. The predicted reduction in gaseous exchange due to clustering, suggests that guard cell function is impaired, limiting stomatal aperture opening. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Mean-cluster approach indicates cell sorting time scales are determined by collective dynamics

NASA Astrophysics Data System (ADS)

Beatrici, Carine P.; de Almeida, Rita M. C.; Brunnet, Leonardo G.

2017-03-01

Cell migration is essential to cell segregation, playing a central role in tissue formation, wound healing, and tumor evolution. Considering random mixtures of two cell types, it is still not clear which cell characteristics define clustering time scales. The mass of diffusing clusters merging with one another is expected to grow as td /d +2 when the diffusion constant scales with the inverse of the cluster mass. Cell segregation experiments deviate from that behavior. Explanations for that could arise from specific microscopic mechanisms or from collective effects, typical of active matter. Here we consider a power law connecting diffusion constant and cluster mass to propose an analytic approach to model cell segregation where we explicitly take into account finite-size corrections. The results are compared with active matter model simulations and experiments available in the literature. To investigate the role played by different mechanisms we considered different hypotheses describing cell-cell interaction: differential adhesion hypothesis and different velocities hypothesis. We find that the simulations yield normal diffusion for long time intervals. Analytic and simulation results show that (i) cluster evolution clearly tends to a scaling regime, disrupted only at finite-size limits; (ii) cluster diffusion is greatly enhanced by cell collective behavior, such that for high enough tendency to follow the neighbors, cluster diffusion may become independent of cluster size; (iii) the scaling exponent for cluster growth depends only on the mass-diffusion relation, not on the detailed local segregation mechanism. These results apply for active matter systems in general and, in particular, the mechanisms found underlying the increase in cell sorting speed certainly have deep implications in biological evolution as a selection mechanism.

Ceria nanoclusters on graphene/Ru(0001): A new model catalyst system

DOE PAGES

Novotny, Z.; Netzer, F. P.; Dohnalek, Z.

2016-03-22

In this study, the growth of ceria nanoclusters on single-layer graphene on Ru(0001) has been examined, with a view towards fabricating a stable system for model catalysis studies. The surface morphology and cluster distribution as a function of oxide coverage and substrate temperature has been monitored by scanning tunneling microscopy (STM), whereas the chemical composition of the cluster deposits has been determined by Auger electron spectroscopy (AES). The ceria nanoparticles are of the CeO 2(111)-type and are anchored at the intrinsic defects of the graphene surface, resulting in a variation of the cluster densities across the macroscopic sample surface. Themore » ceria clusters on graphene display a remarkable stability against reduction in ultrahigh vacuum up to 900 K, but some sintering of clusters is observed for temperatures > 450 K. The evolution of the cluster size distribution suggests that the sintering proceeds via a Smoluchowski ripening mechanism, i.e. diffusion and aggregation of entire clusters.« less

Editors pp iii Effects of long-range magnetic interactions on DLA aggregation [rapid communication

NASA Astrophysics Data System (ADS)

Xu, Xiao-Jun; Cai, Ping-Gen; Ye, Quan-Lin; Xia, A.-Gen; Ye, Gao-Xiang

2005-04-01

An extra degree of freedom is introduced in the well-known diffusion-limited aggregation model, i.e., the growth entities are “spin” taking. The model with long-range magnetic interactions that decay as βC/rα on two-dimensional square lattices is studied for different values of α. This model leads to a wide variety of kinetic processes and morphology distribution with both the coupling energy βC and the range of the interactions, i.e., the exponent α. The simulated result of the model shows that the “quenching” of the degree of freedom on the cluster by the long-range magnetic interactions leads to branching or compactness, but, moreover, to combined geometric and physical “transitions” of the aggregations with the growth parameters.

Interpretation of light scattering and turbidity measurements in aggregated systems: effect of intra-cluster multiple-light scattering.

PubMed

Soos, Miroslav; Lattuada, Marco; Sefcik, Jan

2009-11-12

In this work we studied the effect of intracluster multiple-light scattering on the scattering properties of a population of fractal aggregates. To do so, experimental data of diffusion-limited aggregation for three polystyrene latexes with similar surface properties but different primary particle diameters (equal to 118, 420, and 810 nm) were obtained by static light scattering and by means of a spectrophotometer. In parallel, a population balance equation (PBE) model, which takes into account the effect of intracluster multiple-light scattering by solving the T-matrix and the mean-field version of T-matrix, was formulated and validated against time evolution of the root mean radius of gyration, , of the zero angle intensity of scattered light, I(0), and of the turbidity, tau. It was found that the mean-field version of the T-matrix theory is able to correctly predict the time evolution of all measured light scattering quantities for all sizes of primary particles without any adjustable parameter. The structure of the aggregates, characterized by fractal dimension, d(f), was independent of the primary particle size and equal to 1.7, which is in agreement with values found in literature. Since the mean-field version of the T-matrix theory used is rather complicated and requires advanced knowledge of cluster structure (i.e., the particle-particle correlation function), a simplified version of the light scattering model was proposed and tested. It was found that within the range of operating conditions investigated, the simplified version of the light scattering model was able to describe with reasonable accuracy the time evolution of all measured light scattering quantities of the cluster mass distribution (CMD) for all three sizes of primary particles and two values of the laser wavelength.

The stability of vacancy clusters and their effect on helium behaviors in 3C-SiC

NASA Astrophysics Data System (ADS)

Sun, Jingjing; Li, B. S.; You, Yu-Wei; Hou, Jie; Xu, Yichun; Liu, C. S.; Fang, Q. F.; Wang, Z. G.

2018-05-01

We have carried out systematical ab initio calculations to study the stability of vacancy clusters and their effect on helium behaviors in 3C-SiC. It is found that the formation energies of vacancy clusters containing only carbon vacancies are the lowest although the vacancies are not closest to each other, while the binding energies of vacancy clusters composed of both silicon and carbon vacancies in the closest neighbors to each other are the highest. Vacancy clusters can provide with free space for helium atoms to aggregate, while interstitial sites are not favorable for helium atoms to accumulate. The binding energies of vacancy clusters with helium atoms increase almost linearly with the ratio of helium to vacancy, n/m. The binding strength of vacancy cluster having the participation of the silicon vacancy with helium is relatively stronger than that without silicon vacancy. The vacancy clusters with more vacancies can trap helium atoms more tightly. With the presence of vacancy clusters in the material, the diffusivity of helium will be significantly reduced. Moreover, the three-dimension electron density is calculated to analyze the interplay of vacancy clusters with helium.

Probabilistic Analysis of Hierarchical Cluster Protocols for Wireless Sensor Networks

NASA Astrophysics Data System (ADS)

Kaj, Ingemar

Wireless sensor networks are designed to extract data from the deployment environment and combine sensing, data processing and wireless communication to provide useful information for the network users. Hundreds or thousands of small embedded units, which operate under low-energy supply and with limited access to central network control, rely on interconnecting protocols to coordinate data aggregation and transmission. Energy efficiency is crucial and it has been proposed that cluster based and distributed architectures such as LEACH are particularly suitable. We analyse the random cluster hierarchy in this protocol and provide a solution for low-energy and limited-loss optimization. Moreover, we extend these results to a multi-level version of LEACH, where clusters of nodes again self-organize to form clusters of clusters, and so on.

Suppression of vacancy cluster growth in concentrated solid solution alloys

DOE PAGES

Zhao, Shijun; Velisa, Gihan; Xue, Haizhou; ...

2016-12-13

Large vacancy clusters, such as stacking-fault tetrahedra, are detrimental vacancy-type defects in ion-irradiated structural alloys. Suppression of vacancy cluster formation and growth is highly desirable to improve the irradiation tolerance of these materials. In this paper, we demonstrate that vacancy cluster growth can be inhibited in concentrated solid solution alloys by modifying cluster migration pathways and diffusion kinetics. The alloying effects of Fe and Cr on the migration of vacancy clusters in Ni concentrated alloys are investigated by molecular dynamics simulations and ion irradiation experiment. While the diffusion coefficients of small vacancy clusters in Ni-based binary and ternary solid solutionmore » alloys are higher than in pure Ni, they become lower for large clusters. This observation suggests that large clusters can easily migrate and grow to very large sizes in pure Ni. In contrast, cluster growth is suppressed in solid solution alloys owing to the limited mobility of large vacancy clusters. Finally, the differences in cluster sizes and mobilities in Ni and in solid solution alloys are consistent with the results from ion irradiation experiments.« less

Optical characterization limits of nanoparticle aggregates at different wavelengths using approximate Bayesian computation

NASA Astrophysics Data System (ADS)

Eriçok, Ozan Burak; Ertürk, Hakan

2018-07-01

Optical characterization of nanoparticle aggregates is a complex inverse problem that can be solved by deterministic or statistical methods. Previous studies showed that there exists a different lower size limit of reliable characterization, corresponding to the wavelength of light source used. In this study, these characterization limits are determined considering a light source wavelength range changing from ultraviolet to near infrared (266-1064 nm) relying on numerical light scattering experiments. Two different measurement ensembles are considered. Collection of well separated aggregates made up of same sized particles and that of having particle size distribution. Filippov's cluster-cluster algorithm is used to generate the aggregates and the light scattering behavior is calculated by discrete dipole approximation. A likelihood-free Approximate Bayesian Computation, relying on Adaptive Population Monte Carlo method, is used for characterization. It is found that when the wavelength range of 266-1064 nm is used, successful characterization limit changes from 21-62 nm effective radius for monodisperse and polydisperse soot aggregates.

Cluster growth mechanisms in Lennard-Jones fluids: A comparison between molecular dynamics and Brownian dynamics simulations

NASA Astrophysics Data System (ADS)

Jung, Jiyun; Lee, Jumin; Kim, Jun Soo

2015-03-01

We present a simulation study on the mechanisms of a phase separation in dilute fluids of Lennard-Jones (LJ) particles as a model of self-interacting molecules. Molecular dynamics (MD) and Brownian dynamics (BD) simulations of the LJ fluids are employed to model the condensation of a liquid droplet in the vapor phase and the mesoscopic aggregation in the solution phase, respectively. With emphasis on the cluster growth at late times well beyond the nucleation stage, we find that the growth mechanisms can be qualitatively different: cluster diffusion and coalescence in the MD simulations and Ostwald ripening in the BD simulations. We also show that the rates of the cluster growth have distinct scaling behaviors during cluster growth. This work suggests that in the solution phase the random Brownian nature of the solute dynamics may lead to the Ostwald ripening that is qualitatively different from the cluster coalescence in the vapor phase.

On the interplay of point defects and Cd in non-polar ZnCdO films

NASA Astrophysics Data System (ADS)

Zubiaga, A.; Reurings, F.; Tuomisto, F.; Plazaola, F.; García, J. A.; Kuznetsov, A. Yu.; Egger, W.; Zúñiga-Pérez, J.; Muñoz-Sanjosé, V.

2013-01-01

Non-polar ZnCdO films, grown over m- and r-sapphire with a Cd concentration ranging between 0.8% and 5%, have been studied by means of slow positron annihilation spectroscopy (PAS) combined with chemical depth profiling by secondary ion mass spectroscopy and Rutherford back-scattering. Vacancy clusters and Zn vacancies with concentrations up to 1017 cm-3 and 1018 cm-3, respectively, have been measured inside the films. Secondary ion mass spectroscopy results show that most Cd stays inside the ZnCdO film but the diffused atoms can penetrate up to 1.3 μm inside the ZnO buffer. PAS results give an insight to the structure of the meta-stable ZnCdO above the thermodynamical solubility limit of 2%. A correlation between the concentration of vacancy clusters and Cd has been measured. The concentration of Zn vacancies is one order of magnitude larger than in as-grown non-polar ZnO films and the vacancy cluster are, at least partly, created by the aggregation of smaller Zn vacancy related defects. The Zn vacancy related defects and the vacancy clusters accumulate around the Cd atoms as a way to release the strain induced by the substitutional CdZn in the ZnO crystal.

Vacancy clustering and its dissociation process in electroless deposited copper films studied by monoenergetic positron beams

NASA Astrophysics Data System (ADS)

Uedono, A.; Yamashita, Y.; Tsutsui, T.; Dordi, Y.; Li, S.; Oshima, N.; Suzuki, R.

2012-05-01

Positron annihilation was used to probe vacancy-type defects in electroless deposited copper films. For as-deposited films, two different types of vacancy-type defects were found to coexist; these were identified as vacancy aggregates (V3-V4) and larger vacancy clusters (˜V10). After annealing at about 200 °C, the defects started to diffuse toward the surface and aggregate. The same tendency has been observed for sulfur only, suggesting the formation of complexes between sulfur and vacancies. The defect concentration near the Cu/barrier-metal interface was high even after annealing above 600 °C, and this was attributed to an accumulation of vacancy-impurity complexes. The observed defect reactions were attributed to suppression of the vacancy diffusion to sinks through the formation of impurity-vacancy complexes. It was shown that electroless plating has a high potential to suppress the formation of voids/hillocks caused by defect migration.

Insulin Regulates Glut4 Confinement in Plasma Membrane Clusters in Adipose Cells

PubMed Central

Lizunov, Vladimir A.; Stenkula, Karin; Troy, Aaron; Cushman, Samuel W.; Zimmerberg, Joshua

2013-01-01

Insulin-stimulated delivery of glucose transporter-4 (GLUT4) to the plasma membrane (PM) is the hallmark of glucose metabolism. In this study we examined insulin’s effects on GLUT4 organization in PM of adipose cells by direct microscopic observation of single monomers tagged with photoswitchable fluorescent protein. In the basal state, after exocytotic delivery only a fraction of GLUT4 is dispersed into the PM as monomers, while most of the GLUT4 stays at the site of fusion and forms elongated clusters (60–240 nm). GLUT4 monomers outside clusters diffuse freely and do not aggregate with other monomers. In contrast, GLUT4 molecule collision with an existing cluster can lead to immediate confinement and association with that cluster. Insulin has three effects: it shifts the fraction of dispersed GLUT4 upon delivery, it augments the dissociation of GLUT4 monomers from clusters ∼3-fold and it decreases the rate of endocytic uptake. All together these three effects of insulin shift most of the PM GLUT4 from clustered to dispersed states. GLUT4 confinement in clusters represents a novel kinetic mechanism for insulin regulation of glucose homeostasis. PMID:23520472

Insulin regulates Glut4 confinement in plasma membrane clusters in adipose cells.

PubMed

Lizunov, Vladimir A; Stenkula, Karin; Troy, Aaron; Cushman, Samuel W; Zimmerberg, Joshua

2013-01-01

Insulin-stimulated delivery of glucose transporter-4 (GLUT4) to the plasma membrane (PM) is the hallmark of glucose metabolism. In this study we examined insulin's effects on GLUT4 organization in PM of adipose cells by direct microscopic observation of single monomers tagged with photoswitchable fluorescent protein. In the basal state, after exocytotic delivery only a fraction of GLUT4 is dispersed into the PM as monomers, while most of the GLUT4 stays at the site of fusion and forms elongated clusters (60-240 nm). GLUT4 monomers outside clusters diffuse freely and do not aggregate with other monomers. In contrast, GLUT4 molecule collision with an existing cluster can lead to immediate confinement and association with that cluster. Insulin has three effects: it shifts the fraction of dispersed GLUT4 upon delivery, it augments the dissociation of GLUT4 monomers from clusters ∼3-fold and it decreases the rate of endocytic uptake. All together these three effects of insulin shift most of the PM GLUT4 from clustered to dispersed states. GLUT4 confinement in clusters represents a novel kinetic mechanism for insulin regulation of glucose homeostasis.

Hydrophobic hydration driven self-assembly of curcumin in water: Similarities to nucleation and growth under large metastability, and an analysis of water dynamics at heterogeneous surfaces

NASA Astrophysics Data System (ADS)

Hazra, Milan Kumar; Roy, Susmita; Bagchi, Biman

2014-11-01

As the beneficial effects of curcumin have often been reported to be limited to its small concentrations, we have undertaken a study to find the aggregation properties of curcumin in water by varying the number of monomers. Our molecular dynamics simulation results show that the equilibrated structure is always an aggregated state with remarkable structural rearrangements as we vary the number of curcumin monomers from 4 to 16 monomers. We find that the curcumin monomers form clusters in a very definite pattern where they tend to aggregate both in parallel and anti-parallel orientation of the phenyl rings, often seen in the formation of β-sheet in proteins. A considerable enhancement in the population of parallel alignments is observed with increasing the system size from 12 to 16 curcumin monomers. Due to the prevalence of such parallel alignment for large system size, a more closely packed cluster is formed with maximum number of hydrophobic contacts. We also follow the pathway of cluster growth, in particular the transition from the initial segregated to the final aggregated state. We find the existence of a metastable structural intermediate involving a number of intermediate-sized clusters dispersed in the solution. We have constructed a free energy landscape of aggregation where the metatsable state has been identified. The course of aggregation bears similarity to nucleation and growth in highly metastable state. The final aggregated form remains stable with the total exclusion of water from its sequestered hydrophobic core. We also investigate water structure near the cluster surface along with their orientation. We find that water molecules form a distorted tetrahedral geometry in the 1st solvation layer of the cluster, interacting rather strongly with the hydrophilic groups at the surface of the curcumin. The dynamics of such quasi-bound water molecules near the surface of curcumin cluster is considerably slower than the bulk signifying a restricted motion as often found in protein hydration layer.

Soft learning vector quantization and clustering algorithms based on ordered weighted aggregation operators.

PubMed

Karayiannis, N B

2000-01-01

This paper presents the development and investigates the properties of ordered weighted learning vector quantization (LVQ) and clustering algorithms. These algorithms are developed by using gradient descent to minimize reformulation functions based on aggregation operators. An axiomatic approach provides conditions for selecting aggregation operators that lead to admissible reformulation functions. Minimization of admissible reformulation functions based on ordered weighted aggregation operators produces a family of soft LVQ and clustering algorithms, which includes fuzzy LVQ and clustering algorithms as special cases. The proposed LVQ and clustering algorithms are used to perform segmentation of magnetic resonance (MR) images of the brain. The diagnostic value of the segmented MR images provides the basis for evaluating a variety of ordered weighted LVQ and clustering algorithms.

Polymer depletion-driven cluster aggregation and initial phase separation in charged nanosized colloids

NASA Astrophysics Data System (ADS)

Gögelein, Christoph; Nägele, Gerhard; Buitenhuis, Johan; Tuinier, Remco; Dhont, Jan K. G.

2009-05-01

We study polymer depletion-driven cluster aggregation and initial phase separation in aqueous dispersions of charge-stabilized silica spheres, where the ionic strength and polymer (dextran) concentration are systematically varied, using dynamic light scattering and visual observation. Without polymers and for increasing salt and colloid content, the dispersions become increasingly unstable against irreversible cluster formation. By adding nonadsorbing polymers, a depletion-driven attraction is induced, which lowers the stabilizing Coulomb barrier and enhances the cluster growth rate. The initial growth rate increases with increasing polymer concentration and decreases with increasing polymer molar mass. These observations can be quantitatively understood by an irreversible dimer formation theory based on the classical Derjaguin, Landau, Verwey, and Overbeek pair potential, with the depletion attraction modeled by the Asakura-Oosawa-Vrij potential. At low colloid concentration, we observe an exponential cluster growth rate for all polymer concentrations considered, indicating a reaction-limited aggregation mechanism. At sufficiently high polymer and colloid concentrations, and lower salt content, a gas-liquidlike demixing is observed initially. Later on, the system separates into a gel and fluidlike phase. The experimental time-dependent state diagram is compared to the theoretical equilibrium phase diagram obtained from a generalized free-volume theory and is discussed in terms of an initial reversible phase separation process in combination with irreversible aggregation at later times.

Polymer depletion-driven cluster aggregation and initial phase separation in charged nanosized colloids.

PubMed

Gögelein, Christoph; Nägele, Gerhard; Buitenhuis, Johan; Tuinier, Remco; Dhont, Jan K G

2009-05-28

We study polymer depletion-driven cluster aggregation and initial phase separation in aqueous dispersions of charge-stabilized silica spheres, where the ionic strength and polymer (dextran) concentration are systematically varied, using dynamic light scattering and visual observation. Without polymers and for increasing salt and colloid content, the dispersions become increasingly unstable against irreversible cluster formation. By adding nonadsorbing polymers, a depletion-driven attraction is induced, which lowers the stabilizing Coulomb barrier and enhances the cluster growth rate. The initial growth rate increases with increasing polymer concentration and decreases with increasing polymer molar mass. These observations can be quantitatively understood by an irreversible dimer formation theory based on the classical Derjaguin, Landau, Verwey, and Overbeek pair potential, with the depletion attraction modeled by the Asakura-Oosawa-Vrij potential. At low colloid concentration, we observe an exponential cluster growth rate for all polymer concentrations considered, indicating a reaction-limited aggregation mechanism. At sufficiently high polymer and colloid concentrations, and lower salt content, a gas-liquidlike demixing is observed initially. Later on, the system separates into a gel and fluidlike phase. The experimental time-dependent state diagram is compared to the theoretical equilibrium phase diagram obtained from a generalized free-volume theory and is discussed in terms of an initial reversible phase separation process in combination with irreversible aggregation at later times.

Morphological Evolution of Nanocluster Aggregates and Single Crystals in Alkaline Zinc Electrodeposition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Desai, D; Turney, DE; Anantharaman, B

2014-04-24

The morphology of Zn electrodeposits is studied on carbon-coated transmission electron microscopy grids. At low over-potentials (eta = -50 mV), the morphology develops by aggregation at two distinct length scales: similar to 5 nm diameter monocrystalline nanoclusters form similar to 50 nm diameter polycrystalline aggregates, and the aggregates form a branched network. Epitaxial (00 (0) over bar2) growth above an overpotential of vertical bar eta(c)vertical bar > 125 mV leads to the formation of hexagonal single crystals up to 2 mu m in diameter. Potentiostatic current transients were used to calculate the nucleation rate from Scharifker et al.'s model. Themore » exp(eta) dependence of the nucleation rates indicates that atomistic nucleation theory explains the nucleation process better than Volmer-Weber theory. A kinetic model is provided using the rate equations of vapor solidification to simulate the evolution of the different morphologies. On solving these equations, we show that aggregation is attributed to cluster impingement and cluster diffusion while single-crystal formation is attributed to direct attachment.« less

Growth of Ni nanoclusters on irradiated graphene: a molecular dynamics study.

PubMed

Valencia, F J; Hernandez-Vazquez, E E; Bringa, E M; Moran-Lopez, J L; Rogan, J; Gonzalez, R I; Munoz, F

2018-04-23

We studied the soft landing of Ni atoms on a previously damaged graphene sheet by means of molecular dynamics simulations. We found a monotonic decrease of the cluster frequency as a function of its size, but few big clusters comprise an appreciable fraction of the total number of Ni atoms. The aggregation of Ni atoms is also modeled by means of a simple phenomenological model. The results are in clear contrast with the case of hard or energetic landing of metal atoms, where there is a tendency to form mono-disperse metal clusters. This behavior is attributed to the high diffusion of unattached Ni atoms, together with vacancies acting as capture centers. The findings of this work show that a simple study of the energetics of the system is not enough in the soft landing regime, where it is unavoidable to also consider the growth process of metal clusters.

Porosity and Variations in Microgravity Aerogel Nano-Structures. 2; New Laser Speckle Characterization Methods

NASA Technical Reports Server (NTRS)

Hunt, A. J.; Ayers, M. R.; Sibille, L.; Smith, D. D.

2001-01-01

The transition from sol to gel is a process that is critical to the properties of engineered nanomaterials, but one with few available techniques for observing the dynamic processes occurring during the evolution of the gel network. Specifically, the observation of various cluster aggregation models, such as diffusion-limited and reaction-limited cluster growth can be quite difficult. This can be rather important as the actual aggregation model can dramatically influence the mechanical properties of gels, and is significantly affected by the presence of convective flows, or their absence in microgravity. We have developed two new non-intrusive optical methods for observing the aggregation processes within gels in real time. These make use of the dynamic behavior of laser speckle patterns produced when an intense laser source is passed through a gelling sol. The first method is a simplified time-correlation measurement, where the speckle pattern is observed using a CCD camera and information on the movement of the scattering objects is readily apparent. This approach is extremely sensitive to minute variations in the flow field as the observed speckle pattern is a diffraction-based image, and is therefore sensitive to motions within the sol on the order of the wavelength of the probing light. Additionally, this method has proven useful in determining a precise time for the gel-point, an event often difficult to measure. Monitoring the evolution of contrast within the speckle field is another method that has proven useful for studying aeration. In this case, speckle contrast is dependent upon the size (correlation length) and number of scattering centers, increasing with increasing size, and decreasing with increasing numbers. The dynamic behavior of cluster growth in gels causes both of these to change simultaneously with time, the exact rate of which is determined by the specific aggregation model involved. Actual growth processes can now be observed, and the effects of varying gravity fields on the growth processes qualitatively described. Results on preliminary ground-based measurements have been obtained.

Regime of aggregate structures and magneto-rheological characteristics of a magnetic rod-like particle suspension: Monte Carlo and Brownian dynamics simulations

NASA Astrophysics Data System (ADS)

Okada, Kazuya; Satoh, Akira

2017-09-01

In the present study, we address a suspension composed ferromagnetic rod-like particles to elucidate a regime change in the aggregate structures and the magneto-rheological characteristics. Monte Carlo simulations have been employed for investigating the aggregate structures in thermodynamic equilibrium, and Brownian dynamics simulations for magneto-rheological features in a simple shear flow. The main results obtained here are summarized as follows. For the case of thermodynamic equilibrium, the rod-like particles aggregate to form thick chain-like clusters and the neighboring clusters incline in opposite directions. If the external magnetic field is increased, the thick chain-like clusters in the magnetic field direction grow thicker by adsorbing the neighboring clusters that incline in the opposite direction. Hence, a significant phase change in the particle aggregates is not induced by an increase in the magnetic field strength. For the case of a simple shear flow, even a weak shear flow induces a significant regime change from the thick chain-like clusters of thermodynamic equilibrium into wall-like aggregates composed of short raft-like clusters. A strong external magnetic field drastically changes these aggregates into wall-like aggregates composed of thick chain-like clusters rather than the short raft-like clusters. The internal structure of these aggregates is not strongly influenced by a shear flow, and the formation of the short raft-like clusters is maintained inside the aggregates. The main contribution to the net viscosity is the viscosity component due to magnetic particle-particle interaction forces in relation to the present volumetric fraction. Hence, a larger magnetic interaction strength and also a stronger external magnetic field give rise to a larger magneto-rheological effect. However, the dependence of the viscosity on these factors is governed in a complex manner by whether or not the wall-like aggregates are composed mainly of short raft-like clusters. An increase in the shear rate functions to simply decrease the effect of the magnetic particle-particle and the particle-field interactions.

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

NASA Astrophysics Data System (ADS)

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

2010-09-01

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

Metalloid Aluminum Clusters with Fluorine

DTIC Science & Technology

2016-12-01

molecular dynamics, binding energy , siesta code, density of states, projected density of states 15. NUMBER OF PAGES 69 16. PRICE CODE 17. SECURITY...high energy density compared to explosives, but typically release this energy slowly via diffusion-limited combustion. There is recent interest in using...examine the cluster binding energy and electronic structure. Partial fluorine substitution in a prototypical aluminum-cyclopentadienyl cluster results

Superhydrophilic nanostructure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mao, Samuel S; Zormpa, Vasileia; Chen, Xiaobo

2015-05-12

An embodiment of a superhydrophilic nanostructure includes nanoparticles. The nanoparticles are formed into porous clusters. The porous clusters are formed into aggregate clusters. An embodiment of an article of manufacture includes the superhydrophilic nanostructure on a substrate. An embodiment of a method of fabricating a superhydrophilic nanostructure includes applying a solution that includes nanoparticles to a substrate. The substrate is heated to form aggregate clusters of porous clusters of the nanoparticles.

[Study of the clinical phenotype of symptomatic chronic airways disease by hierarchical cluster analysis and two-step cluster analyses].

PubMed

Ning, P; Guo, Y F; Sun, T Y; Zhang, H S; Chai, D; Li, X M

2016-09-01

To study the distinct clinical phenotype of chronic airway diseases by hierarchical cluster analysis and two-step cluster analysis. A population sample of adult patients in Donghuamen community, Dongcheng district and Qinghe community, Haidian district, Beijing from April 2012 to January 2015, who had wheeze within the last 12 months, underwent detailed investigation, including a clinical questionnaire, pulmonary function tests, total serum IgE levels, blood eosinophil level and a peak flow diary. Nine variables were chosen as evaluating parameters, including pre-salbutamol forced expired volume in one second(FEV1)/forced vital capacity(FVC) ratio, pre-salbutamol FEV1, percentage of post-salbutamol change in FEV1, residual capacity, diffusing capacity of the lung for carbon monoxide/alveolar volume adjusted for haemoglobin level, peak expiratory flow(PEF) variability, serum IgE level, cumulative tobacco cigarette consumption (pack-years) and respiratory symptoms (cough and expectoration). Subjects' different clinical phenotype by hierarchical cluster analysis and two-step cluster analysis was identified. (1) Four clusters were identified by hierarchical cluster analysis. Cluster 1 was chronic bronchitis in smokers with normal pulmonary function. Cluster 2 was chronic bronchitis or mild chronic obstructive pulmonary disease (COPD) patients with mild airflow limitation. Cluster 3 included COPD patients with heavy smoking, poor quality of life and severe airflow limitation. Cluster 4 recognized atopic patients with mild airflow limitation, elevated serum IgE and clinical features of asthma. Significant differences were revealed regarding pre-salbutamol FEV1/FVC%, pre-salbutamol FEV1% pred, post-salbutamol change in FEV1%, maximal mid-expiratory flow curve(MMEF)% pred, carbon monoxide diffusing capacity per liter of alveolar(DLCO)/(VA)% pred, residual volume(RV)% pred, total serum IgE level, smoking history (pack-years), St.George's respiratory questionnaire(SGRQ) score, acute exacerbation in the past one year, PEF variability and allergic dermatitis (P<0.05). (2) Four clusters were also identified by two-step cluster analysis as followings, cluster 1, COPD patients with moderate to severe airflow limitation; cluster 2, asthma and COPD patients with heavy smoking, airflow limitation and increased airways reversibility; cluster 3, patients having less smoking and normal pulmonary function with wheezing but no chronic cough; cluster 4, chronic bronchitis patients with normal pulmonary function and chronic cough. Significant differences were revealed regarding gender distribution, respiratory symptoms, pre-salbutamol FEV1/FVC%, pre-salbutamol FEV1% pred, post-salbutamol change in FEV1%, MMEF% pred, DLCO/VA% pred, RV% pred, PEF variability, total serum IgE level, cumulative tobacco cigarette consumption (pack-years), and SGRQ score (P<0.05). By different cluster analyses, distinct clinical phenotypes of chronic airway diseases are identified. Thus, individualized treatments may guide doctors to provide based on different phenotypes.

GDPC: Gravitation-based Density Peaks Clustering algorithm

NASA Astrophysics Data System (ADS)

Jiang, Jianhua; Hao, Dehao; Chen, Yujun; Parmar, Milan; Li, Keqin

2018-07-01

The Density Peaks Clustering algorithm, which we refer to as DPC, is a novel and efficient density-based clustering approach, and it is published in Science in 2014. The DPC has advantages of discovering clusters with varying sizes and varying densities, but has some limitations of detecting the number of clusters and identifying anomalies. We develop an enhanced algorithm with an alternative decision graph based on gravitation theory and nearby distance to identify centroids and anomalies accurately. We apply our method to some UCI and synthetic data sets. We report comparative clustering performances using F-Measure and 2-dimensional vision. We also compare our method to other clustering algorithms, such as K-Means, Affinity Propagation (AP) and DPC. We present F-Measure scores and clustering accuracies of our GDPC algorithm compared to K-Means, AP and DPC on different data sets. We show that the GDPC has the superior performance in its capability of: (1) detecting the number of clusters obviously; (2) aggregating clusters with varying sizes, varying densities efficiently; (3) identifying anomalies accurately.

ADHD latent class clusters: DSM-IV subtypes and comorbidity

PubMed Central

Elia, Josephine; Arcos-Burgos, Mauricio; Bolton, Kelly L.; Ambrosini, Paul J.; Berrettini, Wade; Muenke, Maximilian

2014-01-01

ADHD (Attention Deficit Hyperactivity Disorder) has a complex, heterogeneous phenotype only partially captured by Diagnostic and Statistical Manual of Mental Disorders (DSM-IV) criteria. In this report, latent class analyses (LCA) are used to identify ADHD phenotypes using K-SADS-IVR (Schedule for Affective Disorders & Schizophrenia for School Age Children-IV-Revised) symptoms and symptom severity data from a clinical sample of 500 ADHD subjects, ages 6–18, participating in an ADHD genetic study. Results show that LCA identified six separate ADHD clusters, some corresponding to specific DSM-IV subtypes while others included several subtypes. DSM-IV comorbid anxiety and mood disorders were generally similar across all clusters, and subjects without comorbidity did not aggregate within any one cluster. Age and gender composition also varied. These results support findings from population-based LCA studies. The six clusters provide additional homogenous groups that can be used to define ADHD phenotypes in genetic association studies. The limited age ranges aggregating in the different clusters may prove to be a particular advantage in genetic studies where candidate gene expression may vary during developmental phases. DSM-IV comorbid mood and anxiety disorders also do not appear to increase cluster heterogeneity; however, longitudinal studies that cover period of risk are needed to support this finding. PMID:19900717

Mesoscale Simulation and Machine Learning of Asphaltene Aggregation Phase Behavior and Molecular Assembly Landscapes.

PubMed

Wang, Jiang; Gayatri, Mohit A; Ferguson, Andrew L

2017-05-11

Asphaltenes constitute the heaviest fraction of the aromatic group in crude oil. Aggregation and precipitation of asphaltenes during petroleum processing costs the petroleum industry billions of dollars each year due to downtime and production inefficiencies. Asphaltene aggregation proceeds via a hierarchical self-assembly process that is well-described by the Yen-Mullins model. Nevertheless, the microscopic details of the emergent cluster morphologies and their relative stability under different processing conditions remain poorly understood. We perform coarse-grained molecular dynamics simulations of a prototypical asphaltene molecule to establish a phase diagram mapping the self-assembled morphologies as a function of temperature, pressure, and n-heptane:toluene solvent ratio informing how to control asphaltene aggregation by regulating external processing conditions. We then combine our simulations with graph matching and nonlinear manifold learning to determine low-dimensional free energy surfaces governing asphaltene self-assembly. In doing so, we introduce a variant of diffusion maps designed to handle data sets with large local density variations, and report the first application of many-body diffusion maps to molecular self-assembly to recover a pseudo-1D free energy landscape. Increasing pressure only weakly affects the landscape, serving only to destabilize the largest aggregates. Increasing temperature and toluene solvent fraction stabilizes small cluster sizes and loose bonding arrangements. Although the underlying molecular mechanisms differ, the strikingly similar effect of these variables on the free energy landscape suggests that toluene acts upon asphaltene self-assembly as an effective temperature.

A generalized electrochemical aggregative growth mechanism.

PubMed

Ustarroz, Jon; Hammons, Joshua A; Altantzis, Thomas; Hubin, Annick; Bals, Sara; Terryn, Herman

2013-08-07

The early stages of nanocrystal nucleation and growth are still an active field of research and remain unrevealed. In this work, by the combination of aberration-corrected transmission electron microscopy (TEM) and electrochemical characterization of the electrodeposition of different metals, we provide a complete reformulation of the Volmer-Weber 3D island growth mechanism, which has always been accepted to explain the early stages of metal electrodeposition and thin-film growth on low-energy substrates. We have developed a Generalized Electrochemical Aggregative Growth Mechanism which mimics the atomistic processes during the early stages of thin-film growth, by incorporating nanoclusters as building blocks. We discuss the influence of new processes such as nanocluster self-limiting growth, surface diffusion, aggregation, and coalescence on the growth mechanism and morphology of the resulting nanostructures. Self-limiting growth mechanisms hinder nanocluster growth and favor coalescence driven growth. The size of the primary nanoclusters is independent of the applied potential and deposition time. The balance between nucleation, nanocluster surface diffusion, and coalescence depends on the material and the overpotential, and influences strongly the morphology of the deposits. A small extent of coalescence leads to ultraporous dendritic structures, large surface coverage, and small particle size. Contrarily, full recrystallization leads to larger hemispherical monocrystalline islands and smaller particle density. The mechanism we propose represents a scientific breakthrough from the fundamental point of view and indicates that achieving the right balance between nucleation, self-limiting growth, cluster surface diffusion, and coalescence is essential and opens new, exciting possibilities to build up enhanced supported nanostructures using nanoclusters as building blocks.

Brief Communication: Buoyancy-Induced Differences in Soot Morphology

NASA Technical Reports Server (NTRS)

Ku, Jerry C.; Griffin, Devon W.; Greenberg, Paul S.; Roma, John

1995-01-01

Reduction or elimination of buoyancy in flames affects the dominant mechanisms driving heat transfer, burning rates and flame shape. The absence of buoyancy produces longer residence times for soot formation, clustering and oxidation. In addition, soot pathlines are strongly affected in microgravity. We recently conducted the first experiments comparing soot morphology in normal and reduced-gravity laminar gas jet diffusion flames. Thermophoretic sampling is a relatively new but well-established technique for studying the morphology of soot primaries and aggregates. Although there have been some questions about biasing that may be induced due to sampling, recent analysis by Rosner et al. showed that the sample is not biased when the system under study is operating in the continuum limit. Furthermore, even if the sampling is preferentially biased to larger aggregates, the size-invariant premise of fractal analysis should produce a correct fractal dimension.

Synchronous Firefly Algorithm for Cluster Head Selection in WSN.

PubMed

Baskaran, Madhusudhanan; Sadagopan, Chitra

2015-01-01

Wireless Sensor Network (WSN) consists of small low-cost, low-power multifunctional nodes interconnected to efficiently aggregate and transmit data to sink. Cluster-based approaches use some nodes as Cluster Heads (CHs) and organize WSNs efficiently for aggregation of data and energy saving. A CH conveys information gathered by cluster nodes and aggregates/compresses data before transmitting it to a sink. However, this additional responsibility of the node results in a higher energy drain leading to uneven network degradation. Low Energy Adaptive Clustering Hierarchy (LEACH) offsets this by probabilistically rotating cluster heads role among nodes with energy above a set threshold. CH selection in WSN is NP-Hard as optimal data aggregation with efficient energy savings cannot be solved in polynomial time. In this work, a modified firefly heuristic, synchronous firefly algorithm, is proposed to improve the network performance. Extensive simulation shows the proposed technique to perform well compared to LEACH and energy-efficient hierarchical clustering. Simulations show the effectiveness of the proposed method in decreasing the packet loss ratio by an average of 9.63% and improving the energy efficiency of the network when compared to LEACH and EEHC.

Classification Order of Surface-Confined Intermixing at Epitaxial Interface

NASA Astrophysics Data System (ADS)

Michailov, M.

The self-organization phenomena at epitaxial interface hold special attention in contemporary material science. Being relevant to the fundamental physical problem of competing, long-range and short-range atomic interactions in systems with reduced dimensionality, these phenomena have found exacting academic interest. They are also of great technological importance for their ability to bring spontaneous formation of regular nanoscale surface patterns and superlattices with exotic properties. The basic phenomenon involved in this process is surface diffusion. That is the motivation behind the present study which deals with important details of diffusion scenarios that control the fine atomic structure of epitaxial interface. Consisting surface imperfections (terraces, steps, kinks, and vacancies), the interface offers variety of barriers for surface diffusion. Therefore, the adatoms and clusters need a certain critical energy to overcome the corresponding diffusion barriers. In the most general case the critical energies can be attained by variation of the system temperature. Hence, their values define temperature limits of system energy gaps associated with different diffusion scenarios. This systematization imply classification order of surface alloying: blocked, incomplete, and complete. On that background, two diffusion problems, related to the atomic-scale surface morphology, will be discussed. The first problem deals with diffusion of atomic clusters on atomically smooth interface. On flat domains, far from terraces and steps, we analyzed the impact of size, shape, and cluster/substrate lattice misfit on the diffusion behavior of atomic clusters (islands). We found that the lattice constant of small clusters depends on the number N of building atoms at 1 < N ≤ 10. In heteroepitaxy, this effect of variable lattice constant originates from the enhanced charge transfer and the strong influence of the surface potential on cluster atomic arrangement. At constant temperature, the variation of the lattice constant leads to variable misfit which affects the island migration. The cluster/substrate commensurability influences the oscillation behavior of the diffusion coefficient caused by variation in the cluster shape. We discuss the results in a physical model that implies cluster diffusion with size-dependent cluster/substrate misfit. The second problem is devoted to diffusion phenomena in the vicinity of atomic terraces on stepped or vicinal surfaces. Here, we develop a computational model that refines important details of diffusion behavior of adatoms accounting for the energy barriers at specific atomic sites (smooth domains, terraces, and steps) located on the crystal surface. The dynamic competition between energy gained by mixing and substrate strain energy results in diffusion scenario where adatoms form alloyed islands and alloyed stripes in the vicinity of terrace edges. Being in agreement with recent experimental findings, the observed effect of stripe and island alloy formation opens up a way regular surface patterns to be configured at different atomic levels on the crystal surface. The complete surface alloying of the entire interface layer is also briefly discussed with critical analysis and classification of experimental findings and simulation data.

Unity and diversity in mixing: Stretching, diffusion, breakup, and aggregation in chaotic flows

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ottino, J.M.

1991-05-01

Experiments and theory have produced a reasonably good qualitative understanding of the evolution of chaotic mixing of passive tracers, especially in two-dimensional time-periodic flow fields. Such an understanding forms a fabric for the evolution of breakup, aggregation, and diffusion-controlled reactions in more complex flows. These systems can be viewed as a population of microstructures'' whose behavior is dictated by iterations of a chaotic flow; microstructures break, diffuse, and aggregate, causing the population to evolve in space and time. This paper presents simple physical models for such processes. Self-similarity is common to all the problems; examples arise in the context ofmore » the distribution of stretchings within chaotic flows, in the asymptotic evolution of diffusion-reaction processes at striation thickness scales, in the equilibrium distribution of drop sizes generated upon mixing of immiscible fluids, in the equations describing mean-field kinetics of coagulation, in the sequence of actions necessary for the destruction of islands in two-dimensional flow, and in the fractal structure of clusters produced upon aggregation in chaotic flows.« less

Version 4.0 of code Java for 3D simulation of the CCA model

NASA Astrophysics Data System (ADS)

Fan, Linyu; Liao, Jianwei; Zuo, Junsen; Zhang, Kebo; Li, Chao; Xiong, Hailing

2018-07-01

This paper presents a new version Java code for the three-dimensional simulation of Cluster-Cluster Aggregation (CCA) model to replace the previous version. Many redundant traverses of clusters-list in the program were totally avoided, so that the consumed simulation time is significantly reduced. In order to show the aggregation process in a more intuitive way, we have labeled different clusters with varied colors. Besides, a new function is added for outputting the particle's coordinates of aggregates in file to benefit coupling our model with other models.

Co-existence of monomers and clusters in concentrated protein solutions

NASA Astrophysics Data System (ADS)

Chinchalikar, Akshay J.; Kumar, Sugam; Aswal, V. K.; Callow, P.; Wagh, A. G.

2012-06-01

Small-angle neutron scattering (SANS) measurements have been performed on concentrated protein solutions in order to study aggregation of lysozyme molecules at different pH. The variation of correlation peak in concentration (C) dependent SANS data shows deviation from C1/3 behavior suggesting the aggregation phenomena in these systems. The aggregates or clusters coexist along with monomers with cluster fraction proportional to protein concentration. The clustering is also favored at higher pH approaching isoelectric point (pI) because of decrease in charge on the protein molecule.

Theory and modeling of particles with DNA-mediated interactions

NASA Astrophysics Data System (ADS)

Licata, Nicholas A.

In recent years significant attention has been attracted to proposals which utilize DNA for nanotechnological applications. Potential applications of these ideas range from the programmable self-assembly of colloidal crystals, to biosensors and nanoparticle based drug delivery platforms. In Chapter I we introduce the system, which generically consists of colloidal particles functionalized with specially designed DNA markers. The sequence of bases on the DNA markers determines the particle type. Due to the hybridization between complementary single-stranded DNA, specific, type-dependent interactions can be introduced between particles by choosing the appropriate DNA marker sequences. In Chapter II we develop a statistical mechanical description of the aggregation and melting behavior of particles with DNA-mediated interactions. A quantitative comparison between the theory and experiments is made by calculating the experimentally observed melting profile. In Chapter III a model is proposed to describe the dynamical departure and diffusion of particles which form reversible key-lock connections. The model predicts a crossover from localized to diffusive behavior. The random walk statistics for the particles' in plane diffusion is discussed. The lateral motion is analogous to dispersive transport in disordered semiconductors, ranging from standard diffusion with a renormalized diffusion coefficient to anomalous, subdiffusive behavior. In Chapter IV we propose a method to self-assemble nanoparticle clusters using DNA scaffolds. An optimal concentration ratio is determined for the experimental implementation of our self-assembly proposal. A natural extension is discussed in Chapter V, the programmable self-assembly of nanoparticle clusters where the desired cluster geometry is encoded using DNA-mediated interactions. We determine the probability that the system self-assembles the desired cluster geometry, and discuss the connections to jamming in granular and colloidal systems. In Chapter VI we consider a nanoparticle based drug delivery platform for targeted, cell specific chemotherapy. A key-lock model is proposed to describe the results of in-vitro experiments, and the situation in-vivo is discussed. The cooperative binding, and hence the specificity to cancerous cells, is kinetically limited. The implications for optimizing the design of nanoparticle based drug delivery platforms is discussed. In Chapter VII we present prospects for future research: the connection between DNA-mediated colloidal crystallization and jamming, and the inverse problem in self-assembly.

The single scattering properties of the aerosol particles as aggregated spheres

NASA Astrophysics Data System (ADS)

Wu, Y.; Gu, X.; Cheng, T.; Xie, D.; Yu, T.; Chen, H.; Guo, J.

2012-08-01

The light scattering and absorption properties of anthropogenic aerosol particles such as soot aggregates are complicated in the temporal and spatial distribution, which introduce uncertainty of radiative forcing on global climate change. In order to study the single scattering properties of anthorpogenic aerosol particles, the structures of these aerosols such as soot paticles and soot-containing mixtures with the sulfate or organic matter, are simulated using the parallel diffusion limited aggregation algorithm (DLA) based on the transmission electron microscope images (TEM). Then, the single scattering properties of randomly oriented aerosols, such as scattering matrix, single scattering albedo (SSA), and asymmetry parameter (AP), are computed using the superposition T-matrix method. The comparisons of the single scattering properties of these specific types of clusters with different morphological and chemical factors such as fractal parameters, aspect ratio, monomer radius, mixture mode and refractive index, indicate that these different impact factors can respectively generate the significant influences on the single scattering properties of these aerosols. The results show that aspect ratio of circumscribed shape has relatively small effect on single scattering properties, for both differences of SSA and AP are less than 0.1. However, mixture modes of soot clusters with larger sulfate particles have remarkably important effects on the scattering and absorption properties of aggregated spheres, and SSA of those soot-containing mixtures are increased in proportion to the ratio of larger weakly absorbing attachments. Therefore, these complex aerosols come from man made pollution cannot be neglected in the aerosol retrievals. The study of the single scattering properties on these kinds of aggregated spheres is important and helpful in remote sensing observations and atmospheric radiation balance computations.

Mechanisms behind overshoots in mean cluster size profiles in aggregation-breakup processes.

PubMed

Sadegh-Vaziri, Ramiar; Ludwig, Kristin; Sundmacher, Kai; Babler, Matthaus U

2018-05-26

Aggregation and breakup of small particles in stirred suspensions often shows an overshoot in the time evolution of the mean cluster size: Starting from a suspension of primary particles the mean cluster size first increases before going through a maximum beyond which a slow relaxation sets in. Such behavior was observed in various systems, including polymeric latices, inorganic colloids, asphaltenes, proteins, and, as shown by independent experiments in this work, in the flocculation of microalgae. This work aims at investigating possible mechanism to explain this phenomenon using detailed population balance modeling that incorporates refined rate models for aggregation and breakup of small particles in turbulence. Four mechanisms are considered: (1) restructuring, (2) decay of aggregate strength, (3) deposition of large clusters, and (4) primary particle aggregation where only aggregation events between clusters and primary particles are permitted. We show that all four mechanisms can lead to an overshoot in the mean size profile, while in contrast, aggregation and breakup alone lead to a monotonic, "S"-shaped size evolution profile. In order to distinguish between the different mechanisms simple protocols based on variations of the shear rate during the aggregation-breakup process are proposed. Copyright © 2018 Elsevier Inc. All rights reserved.

Characterization of the diffusion of epidermal growth factor receptor clusters by single particle tracking.

PubMed

Boggara, Mohan; Athmakuri, Krishna; Srivastava, Sunit; Cole, Richard; Kane, Ravi S

2013-02-01

A number of studies have shown that receptors of the epidermal growth factor receptor family (ErbBs) exist as higher-order oligomers (clusters) in cell membranes in addition to their monomeric and dimeric forms. Characterizing the lateral diffusion of such clusters may provide insights into their dynamics and help elucidate their functional relevance. To that end, we used single particle tracking to study the diffusion of clusters of the epidermal growth factor (EGF) receptor (EGFR; ErbB1) containing bound fluorescently-labeled ligand, EGF. EGFR clusters had a median diffusivity of 6.8×10(-11)cm(2)/s and were found to exhibit different modes of transport (immobile, simple, confined, and directed) similar to that previously reported for single EGFR molecules. Disruption of actin filaments increased the median diffusivity of EGFR clusters to 10.3×10(-11)cm(2)/s, while preserving the different modes of diffusion. Interestingly, disruption of microtubules rendered EGFR clusters nearly immobile. Our data suggests that microtubules may play an important role in the diffusion of EGFR clusters either directly or perhaps indirectly via other mechanisms. To our knowledge, this is the first report probing the effect of the cytoskeleton on the diffusion of EGFR clusters in the membranes of live cells. Copyright © 2012 Elsevier B.V. All rights reserved.

Time scales of transient enhanced diffusion: Free and clustered interstitials

NASA Astrophysics Data System (ADS)

Cowern, N. E. B.; Huizing, H. G. A.; Stolk, P. A.; Visser, C. C. G.; de Kruif, R. C. M.; Kyllesbech Larsen, K.; Privitera, V.; Nanver, L. K.; Crans, W.

1996-12-01

Transient enhanced diffusion (TED) and electrical activation after nonamorphizing Si implantations into lightly B-doped Si multilayers shows two distinct timescales, each related to a different class of interstitial defect. At 700°C, ultrafast TED occurs within the first 15 s with a B diffusivity enhancement of > 2 × 10 5. Immobile clustered B is present at low concentration levels after the ultrafast transient and persists for an extended period (˜ 10 2-10 3 s). The later phase of TED exhibits a near-constant diffusivity enhancement of ≈ 1 × 10 4, consistent with interstitial injection controlled by dissolving {113} interstitial clusters. The relative contributions of the ultrafast and regular TED regimes to the final diffusive broadening of the B profile depends on the proportion of interstitials that escape capture by {113} clusters growing within the implant damage region upon annealing. Our results explain the ultrafast TED recently observed after medium-dose B implantation. In that case there are enough B atoms to trap a large proportion of interstitials in SiB clusters, and the remaining interstitials contribute to TED without passing through an intermediate {113} defect stage. The data on the ultrafast TED pulse allows us to extract lower limits for the diffusivities of the Si interstitial ( DI > 2 × 10 -10 cm 2s -1) and the B interstitial(cy) defect ( DBi > 2 × 10 -13 cm 2s -1) at 700°C.

Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation.

PubMed

Nawrocki, Grzegorz; Wang, Po-Hung; Yu, Isseki; Sugita, Yuji; Feig, Michael

2017-12-14

For a long time, the effect of a crowded cellular environment on protein dynamics has been largely ignored. Recent experiments indicate that proteins diffuse more slowly in a living cell than in a diluted solution, and further studies suggest that the diffusion depends on the local surroundings. Here, detailed insight into how diffusion depends on protein-protein contacts is presented based on extensive all-atom molecular dynamics simulations of concentrated villin headpiece solutions. After force field adjustments in the form of increased protein-water interactions to reproduce experimental data, translational and rotational diffusion was analyzed in detail. Although internal protein dynamics remained largely unaltered, rotational diffusion was found to slow down more significantly than translational diffusion as the protein concentration increased. The decrease in diffusion is interpreted in terms of a transient formation of protein clusters. These clusters persist on sub-microsecond time scales and follow distributions that increasingly shift toward larger cluster size with increasing protein concentrations. Weighting diffusion coefficients estimated for different clusters extracted from the simulations with the distribution of clusters largely reproduces the overall observed diffusion rates, suggesting that transient cluster formation is a primary cause for a slow-down in diffusion upon crowding with other proteins.

Mobility of large clusters on a semiconductor surface: Kinetic Monte Carlo simulation results

NASA Astrophysics Data System (ADS)

M, Esen; A, T. Tüzemen; M, Ozdemir

2016-01-01

The mobility of clusters on a semiconductor surface for various values of cluster size is studied as a function of temperature by kinetic Monte Carlo method. The cluster resides on the surface of a square grid. Kinetic processes such as the diffusion of single particles on the surface, their attachment and detachment to/from clusters, diffusion of particles along cluster edges are considered. The clusters considered in this study consist of 150-6000 atoms per cluster on average. A statistical probability of motion to each direction is assigned to each particle where a particle with four nearest neighbors is assumed to be immobile. The mobility of a cluster is found from the root mean square displacement of the center of mass of the cluster as a function of time. It is found that the diffusion coefficient of clusters goes as D = A(T)Nα where N is the average number of particles in the cluster, A(T) is a temperature-dependent constant and α is a parameter with a value of about -0.64 < α < -0.75. The value of α is found to be independent of cluster sizes and temperature values (170-220 K) considered in this study. As the diffusion along the perimeter of the cluster becomes prohibitive, the exponent approaches a value of -0.5. The diffusion coefficient is found to change by one order of magnitude as a function of cluster size.

Minimal Model of Quantum Kinetic Clusters for the Energy-Transfer Network of a Light-Harvesting Protein Complex.

PubMed

Wu, Jianlan; Tang, Zhoufei; Gong, Zhihao; Cao, Jianshu; Mukamel, Shaul

2015-04-02

The energy absorbed in a light-harvesting protein complex is often transferred collectively through aggregated chromophore clusters. For population evolution of chromophores, the time-integrated effective rate matrix allows us to construct quantum kinetic clusters quantitatively and determine the reduced cluster-cluster transfer rates systematically, thus defining a minimal model of energy-transfer kinetics. For Fenna-Matthews-Olson (FMO) and light-havrvesting complex II (LCHII) monomers, quantum Markovian kinetics of clusters can accurately reproduce the overall energy-transfer process in the long-time scale. The dominant energy-transfer pathways are identified in the picture of aggregated clusters. The chromophores distributed extensively in various clusters can assist a fast and long-range energy transfer.

Gap junctions contribute to anchorage-independent clustering of breast cancer cells.

PubMed

Gava, Fabien; Rigal, Lise; Mondesert, Odile; Pesce, Elise; Ducommun, Bernard; Lobjois, Valérie

2018-02-27

Cancer cell aggregation is a key process involved in the formation of clusters of circulating tumor cells. We previously reported that cell-cell adhesion proteins, such as E-cadherin, and desmosomal proteins are involved in cell aggregation to form clusters independently of cell migration or matrix adhesion. Here, we investigated the involvement of gap junction intercellular communication (GJIC) during anchorage-independent clustering of MCF7 breast adenocarcinoma cells. We used live cell image acquisition and analysis to monitor the kinetics of MCF7 cell clustering in the presence/absence of GJIC pharmacological inhibitors and to screen a LOPAC® bioactive compound library. We also used a calcein transfer assay and flow cytometry to evaluate GJIC involvement in cancer cell clustering. We first demonstrated that functional GJIC are established in the early phase of cancer cell aggregation. We then showed that pharmacological inhibition of GJIC using tonabersat and meclofenamate delayed MCF7 cell clustering and reduced calcein transfer. We also found that brefeldin A, an inhibitor of vesicular trafficking, which we identified by screening a small compound library, and latrunculin A, an actin cytoskeleton-disrupting agent, both impaired MCF7 cell clustering and calcein transfer. Our results demonstrate that GJIC are involved from the earliest stages of anchorage-independent cancer cell aggregation. They also give insights into the regulatory mechanisms that could modulate the formation of clusters of circulating tumor cells.

Tetraspanin Tspan9 regulates platelet collagen receptor GPVI lateral diffusion and activation

PubMed Central

Haining, Elizabeth J.; Matthews, Alexandra L.; Noy, Peter J.; Romanska, Hanna M.; Harris, Helen J.; Pike, Jeremy; Morowski, Martina; Gavin, Rebecca L.; Yang, Jing; Milhiet, Pierre-Emmanuel; Berditchevski, Fedor; Nieswandt, Bernhard; Poulter, Natalie S.; Watson, Steve P.; Tomlinson, Michael G.

2017-01-01

Abstract The tetraspanins are a superfamily of four-transmembrane proteins, which regulate the trafficking, lateral diffusion and clustering of the transmembrane proteins with which they interact. We have previously shown that tetraspanin Tspan9 is expressed on platelets. Here we have characterised gene-trap mice lacking Tspan9. The mice were viable with normal platelet numbers and size. Tspan9-deficient platelets were specifically defective in aggregation and secretion induced by the platelet collagen receptor GPVI, despite normal surface GPVI expression levels. A GPVI activation defect was suggested by partially impaired GPVI-induced protein tyrosine phosphorylation. In mechanistic experiments, Tspan9 and GPVI co-immunoprecipitated and co-localised, but super-resolution imaging revealed no defects in collagen-induced GPVI clustering on Tspan9-deficient platelets. However, single particle tracking using total internal reflection fluorescence microscopy showed that GPVI lateral diffusion was reduced by approximately 50% in the absence of Tspan9. Therefore, Tspan9 plays a fine-tuning role in platelet activation by regulating GPVI membrane dynamics. PMID:28032533

Application and Limitations of Nanocasting in Metal–Organic Frameworks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Malonzo, Camille D.; Wang, Zhao; Duan, Jiaxin

Nanocasting can be a useful strategy to transfer the catalytic metal clusters in metal-organic frameworks (MOFs) to an all-inorganic support such as silica. The incorporation of silica in the MOF pores as a secondary support has the potential to extend the application of the highly tunable metal-based active sites in MOFs to high temperature catalysis. Here, we demonstrate the applicability of the nanocasting method to a range of MOFs that incorporate catalytically attractive hexazirconium, hexacerium, or pentanickel oxide-based clusters (UiO-66, (Ce)UiO-66, (Ce)UiO-67, (Ce)MOF-808, DUT-9, and In- and Ni-post-metalated NU-1000). We describe, in tutorial form, the challenges associated with nanocasting ofmore » MOFs that are related to their small pore size and to considerations of chemical and mechanical stability, and we provide approaches to overcome some of these challenges. Some of these nanocast materials feature the site-isolated clusters in a porous, thermally stable silica matrix, suitable for catalysis at high temperatures; in others, structural rearrangement of clusters or partial cluster aggregation occurs, but extensive aggregation can be mitigated by the silica skeleton introduced during nanocasting.« less

Domain and network aggregation of CdTe quantum rods within Langmuir Blodgett monolayers

NASA Astrophysics Data System (ADS)

Zimnitsky, Dmitry; Xu, Jun; Lin, Zhiqun; Tsukruk, Vladimir V.

2008-05-01

Control over the organization of quantum rods was demonstrated by changing the surface area at the air-liquid interface by means of the Langmuir-Blodgett (LB) technique. The LB isotherm of CdTe quantum rods capped with a mixture of alkylphosphines shows a transition point in the liquid-solid state, which is caused by the inter-rod reorganization. As we observed, at low surface pressure the quantum rods are assembled into round-shaped aggregates composed of a monolayer of nanorods packed in limited-size clusters with random orientation. The increase of the surface pressure leads to the rearrangement of these aggregates into elongated bundles composed of uniformly oriented nanorod clusters. Further compression results in denser packing of nanorods aggregates and in the transformation of monolayered domains into a continuous network of locally ordered quantum rods.

A Survey on the Taxonomy of Cluster-Based Routing Protocols for Homogeneous Wireless Sensor Networks

PubMed Central

Naeimi, Soroush; Ghafghazi, Hamidreza; Chow, Chee-Onn; Ishii, Hiroshi

2012-01-01

The past few years have witnessed increased interest among researchers in cluster-based protocols for homogeneous networks because of their better scalability and higher energy efficiency than other routing protocols. Given the limited capabilities of sensor nodes in terms of energy resources, processing and communication range, the cluster-based protocols should be compatible with these constraints in either the setup state or steady data transmission state. With focus on these constraints, we classify routing protocols according to their objectives and methods towards addressing the shortcomings of clustering process on each stage of cluster head selection, cluster formation, data aggregation and data communication. We summarize the techniques and methods used in these categories, while the weakness and strength of each protocol is pointed out in details. Furthermore, taxonomy of the protocols in each phase is given to provide a deeper understanding of current clustering approaches. Ultimately based on the existing research, a summary of the issues and solutions of the attributes and characteristics of clustering approaches and some open research areas in cluster-based routing protocols that can be further pursued are provided. PMID:22969350

A survey on the taxonomy of cluster-based routing protocols for homogeneous wireless sensor networks.

PubMed

Naeimi, Soroush; Ghafghazi, Hamidreza; Chow, Chee-Onn; Ishii, Hiroshi

2012-01-01

The past few years have witnessed increased interest among researchers in cluster-based protocols for homogeneous networks because of their better scalability and higher energy efficiency than other routing protocols. Given the limited capabilities of sensor nodes in terms of energy resources, processing and communication range, the cluster-based protocols should be compatible with these constraints in either the setup state or steady data transmission state. With focus on these constraints, we classify routing protocols according to their objectives and methods towards addressing the shortcomings of clustering process on each stage of cluster head selection, cluster formation, data aggregation and data communication. We summarize the techniques and methods used in these categories, while the weakness and strength of each protocol is pointed out in details. Furthermore, taxonomy of the protocols in each phase is given to provide a deeper understanding of current clustering approaches. Ultimately based on the existing research, a summary of the issues and solutions of the attributes and characteristics of clustering approaches and some open research areas in cluster-based routing protocols that can be further pursued are provided.

Synchronous Firefly Algorithm for Cluster Head Selection in WSN

PubMed Central

Baskaran, Madhusudhanan; Sadagopan, Chitra

2015-01-01

Wireless Sensor Network (WSN) consists of small low-cost, low-power multifunctional nodes interconnected to efficiently aggregate and transmit data to sink. Cluster-based approaches use some nodes as Cluster Heads (CHs) and organize WSNs efficiently for aggregation of data and energy saving. A CH conveys information gathered by cluster nodes and aggregates/compresses data before transmitting it to a sink. However, this additional responsibility of the node results in a higher energy drain leading to uneven network degradation. Low Energy Adaptive Clustering Hierarchy (LEACH) offsets this by probabilistically rotating cluster heads role among nodes with energy above a set threshold. CH selection in WSN is NP-Hard as optimal data aggregation with efficient energy savings cannot be solved in polynomial time. In this work, a modified firefly heuristic, synchronous firefly algorithm, is proposed to improve the network performance. Extensive simulation shows the proposed technique to perform well compared to LEACH and energy-efficient hierarchical clustering. Simulations show the effectiveness of the proposed method in decreasing the packet loss ratio by an average of 9.63% and improving the energy efficiency of the network when compared to LEACH and EEHC. PMID:26495431

On aggregation in CA models in biology

NASA Astrophysics Data System (ADS)

Alber, Mark S.; Kiskowski, Audi

2001-12-01

Aggregation of randomly distributed particles into clusters of aligned particles is modeled using a cellular automata (CA) approach. The CA model accounts for interactions between more than one type of particle, in which pressures for angular alignment with neighbors compete with pressures for grouping by cell type. In the case of only one particle type clusters tend to unite into one big cluster. In the case of several types of particles the dynamics of clusters is more complicated and for specific choices of parameters particle sorting occurs simultaneously with the formation of clusters of aligned particles.

Cluster-cluster aggregation kinetics and primary particle growth of soot nanoparticles in flame by light scattering and numerical simulations.

PubMed

di Stasio, Stefano; Konstandopoulos, Athanasios G; Kostoglou, Margaritis

2002-03-01

The agglomeration kinetics of growing soot generated in a diffusion atmospheric flame are here studied in situ by light scattering technique to infer cluster morphology and size (fractal dimension D(f) and radius of gyration R(g)). SEM analysis is used as a standard reference to obtain primary particle size D(P) at different residence times. The number N(P) of primary particles per aggregate and the number concentration n(A) of clusters are evaluated on the basis of the measured angular patterns of the scattered light intensity. The major finding is that the kinetics of the coagulation process that yields to the formation of chain-like aggregates by soot primary particles (size 10 to 40 nm) can be described with a constant coagulation kernel beta(c,exp)=2.37x10(-9) cm3/s (coagulation constant tau(c) approximately = 0.28 ms). This result is in nice accord with the Smoluchowski coagulation equation in the free molecular regime, and, vice versa, it is in contrast with previous studies conducted by invasive (ex situ) techniques, which claimed the evidence in flames of coagulation rates much larger than the kinetic theory predictions. Thereafter, a number of numerical simulations is implemented to compare with the experimental results on primary particle growth rate and on the process of aggregate reshaping that is observed by light scattering at later residence times. The restructuring process is conjectured to occur, for not well understood reasons, as a direct consequence of the atomic rearrangement in the solid phase carbon due to the prolonged residence time within the flame. Thus, on one side, it is shown that the numerical simulations of primary size history compare well with the values of primary size from SEM experiment with a growth rate constant of primary diameter about 1 nm/s. On the other side, the evolution of aggregate morphology is found to be predictable by the numerical simulations when the onset of a first-order "thermal" restructuring mechanism is assumed to occur in the flame at about 20 ms residence time leading to aggregates with an asymptotic fractal dimension D(f,infinity) approximately = 2.5.

Kinetics of carbon clustering in detonation of high explosives: Does theory match experiment?

NASA Astrophysics Data System (ADS)

Velizhanin, Kirill; Watkins, Erik; Dattelbaum, Dana; Gustavsen, Richard; Aslam, Tariq; Podlesak, David; Firestone, Millicent; Huber, Rachel; Ringstrand, Bryan; Willey, Trevor; Bagge-Hansen, Michael; Hodgin, Ralph; Lauderbach, Lisa; van Buuren, Tony; Sinclair, Nicholas; Rigg, Paulo; Seifert, Soenke; Gog, Thomas

2017-06-01

Chemical reactions in detonation of carbon-rich high explosives yield carbon clusters as major constituents of the products. Efforts to model carbon clustering as a diffusion-limited irreversible coagulation of carbon clusters go back to the seminal paper by Shaw and Johnson. However, first direct experimental observations of the kinetics of clustering yielded cluster growth one to two orders of magnitude slower than theoretical predictions. Multiple efforts were undertaken to test and revise the basic assumptions of the model in order to achieve better agreement with experiment. We discuss our very recent direct experimental observations of carbon clustering dynamics and demonstrate that these new results are in much better agreement with the modified Shaw-Johnson model. The implications of this much better agreement on our present understanding of detonation carbon clustering processes and possible ways to increase the agreement between theory and experiment even further are discussed.

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. Copyright © 2014 Elsevier Ltd. All rights reserved.

Rigidity of transmembrane proteins determines their cluster shape

NASA Astrophysics Data System (ADS)

Jafarinia, Hamidreza; Khoshnood, Atefeh; Jalali, Mir Abbas

2016-01-01

Protein aggregation in cell membrane is vital for the majority of biological functions. Recent experimental results suggest that transmembrane domains of proteins such as α -helices and β -sheets have different structural rigidities. We use molecular dynamics simulation of a coarse-grained model of protein-embedded lipid membranes to investigate the mechanisms of protein clustering. For a variety of protein concentrations, our simulations under thermal equilibrium conditions reveal that the structural rigidity of transmembrane domains dramatically affects interactions and changes the shape of the cluster. We have observed stable large aggregates even in the absence of hydrophobic mismatch, which has been previously proposed as the mechanism of protein aggregation. According to our results, semiflexible proteins aggregate to form two-dimensional clusters, while rigid proteins, by contrast, form one-dimensional string-like structures. By assuming two probable scenarios for the formation of a two-dimensional triangular structure, we calculate the lipid density around protein clusters and find that the difference in lipid distribution around rigid and semiflexible proteins determines the one- or two-dimensional nature of aggregates. It is found that lipids move faster around semiflexible proteins than rigid ones. The aggregation mechanism suggested in this paper can be tested by current state-of-the-art experimental facilities.

Stability of fluctuating and transient aggregates of amphiphilic solutes in aqueous binary mixtures: Studies of dimethylsulfoxide, ethanol, and tert-butyl alcohol

NASA Astrophysics Data System (ADS)

Banerjee, Saikat; Bagchi, Biman

2013-10-01

In aqueous binary mixtures, amphiphilic solutes such as dimethylsulfoxide (DMSO), ethanol, tert-butyl alcohol (TBA), etc., are known to form aggregates (or large clusters) at small to intermediate solute concentrations. These aggregates are transient in nature. Although the system remains homogeneous on macroscopic length and time scales, the microheterogeneous aggregation may profoundly affect the properties of the mixture in several distinct ways, particularly if the survival times of the aggregates are longer than density relaxation times of the binary liquid. Here we propose a theoretical scheme to quantify the lifetime and thus the stability of these microheterogeneous clusters, and apply the scheme to calculate the same for water-ethanol, water-DMSO, and water-TBA mixtures. We show that the lifetime of these clusters can range from less than a picosecond (ps) for ethanol clusters to few tens of ps for DMSO and TBA clusters. This helps explaining the absence of a strong composition dependent anomaly in water-ethanol mixtures but the presence of the same in water-DMSO and water-TBA mixtures.

NUMERICAL MODELING OF THE COAGULATION AND POROSITY EVOLUTION OF DUST AGGREGATES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Okuzumi, Satoshi; Sakagami, Masa-aki; Tanaka, Hidekazu, E-mail: satoshi.okuzumi@ax2.ecs.kyoto-u.ac.j

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 dustmore » 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 acceleration (e.g., gravity) and their collision is induced by the difference in their terminal velocities. We point out an important implication of this discovery for dust growth in protoplanetary disks.« less

Optically active red-emitting Cu nanoclusters originating from complexation and redox reaction between copper(ii) and d/l-penicillamine

NASA Astrophysics Data System (ADS)

Long, Tengfei; Guo, Yanjia; Lin, Min; Yuan, Mengke; Liu, Zhongde; Huang, Chengzhi

2016-05-01

Despite a significant surge in the number of investigations into both optically active Au and Ag nanostructures, there is currently only limited knowledge about optically active Cu nanoclusters (CuNCs) and their potential applications. Here, we have succeeded in preparing a pair of optically active red-emitting CuNCs on the basis of complexation and redox reaction between copper(ii) and penicillamine (Pen) enantiomers, in which Pen serves as both a reducing agent and a stabilizing ligand. Significantly, the CuNCs feature unique aggregation induced emission (AIE) characteristics and therefore can serve as pH stimuli-responsive functional materials. Impressively, the ligand chirality plays a dramatic role for the creation of brightly emissive CuNCs, attributed to the conformation of racemic Pen being unfavorable for the electrostatic interaction, and thus suppressing the formation of cluster aggregates. In addition, the clusters display potential toward cytoplasmic staining and labelling due to the high photoluminescence (PL) quantum yields (QYs) and remarkable cellular uptake, in spite that no chirality-dependent effects in autophagy and subcellular localization are observed in the application of chiral cluster enantiomer-based cell imaging.Despite a significant surge in the number of investigations into both optically active Au and Ag nanostructures, there is currently only limited knowledge about optically active Cu nanoclusters (CuNCs) and their potential applications. Here, we have succeeded in preparing a pair of optically active red-emitting CuNCs on the basis of complexation and redox reaction between copper(ii) and penicillamine (Pen) enantiomers, in which Pen serves as both a reducing agent and a stabilizing ligand. Significantly, the CuNCs feature unique aggregation induced emission (AIE) characteristics and therefore can serve as pH stimuli-responsive functional materials. Impressively, the ligand chirality plays a dramatic role for the creation of brightly emissive CuNCs, attributed to the conformation of racemic Pen being unfavorable for the electrostatic interaction, and thus suppressing the formation of cluster aggregates. In addition, the clusters display potential toward cytoplasmic staining and labelling due to the high photoluminescence (PL) quantum yields (QYs) and remarkable cellular uptake, in spite that no chirality-dependent effects in autophagy and subcellular localization are observed in the application of chiral cluster enantiomer-based cell imaging. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr01492e

On the radiative properties of soot aggregates part 1: Necking and overlapping

NASA Astrophysics Data System (ADS)

Yon, J.; Bescond, A.; Liu, F.

2015-09-01

There is a strong interest in accurately modelling the radiative properties of soot aggregates (also known as black carbon particles) emitted from combustion systems and fires to gain improved understanding of the role of black carbon to global warming. This study conducted a systematic investigation of the effects of overlapping and necking between neighbouring primary particles on the radiative properties of soot aggregates using the discrete dipole approximation. The degrees of overlapping and necking are quantified by the overlapping and necking parameters. Realistic soot aggregates were generated numerically by constructing overlapping and necking to fractal aggregates formed by point-touch primary particles simulated using a diffusion-limited cluster aggregation algorithm. Radiative properties (differential scattering, absorption, total scattering, specific extinction, asymmetry factor and single scattering albedo) were calculated using the experimentally measured soot refractive index over the spectral range of 266-1064 nm for 9 combinations of the overlapping and necking parameters. Overlapping and necking affect significantly the absorption and scattering properties of soot aggregates, especially in the near UV spectrum due to the enhanced multiple scattering effects within an aggregate. By using correctly modified aggregate properties (fractal dimension, prefactor, primary particle radius, and the number of primary particle) and by accounting for the effects of multiple scattering, the simple Rayleigh-Debye-Gans theory for fractal aggregates can reproduce reasonably accurate radiative properties of realistic soot aggregates.

Molecular Dynamics Study of the Solution Structure, Clustering, and Diffusion of Four Aqueous Alkanolamines.

PubMed

Melnikov, Sergey M; Stein, Matthias

2018-03-15

CO 2 sequestration from anthropogenic resources is a challenge to the design of environmental processes at a large scale. Reversible chemical absorption by amine-based solvents is one of the most efficient methods of CO 2 removal. Molecular simulation techniques are very useful tools to investigate CO 2 binding by aqueous alkanolamine molecules for further technological application. In the present work, we have performed detailed atomistic molecular dynamics simulations of aqueous solutions of three prototype amines: monoethanolamine (MEA) as a standard, 3-aminopropanol (MPA), 2-methylaminoethanol (MMEA), and 4-diethylamino-2-butanol (DEAB) as potential novel CO 2 absorptive solvents. Solvent densities, radial distribution functions, cluster size distributions, hydrogen-bonding statistics, and diffusion coefficients for a full range of mixture compositions have been obtained. The solvent densities and diffusion coefficients from simulations are in good agreement with those in the experiment. In aqueous solution, MEA, MPA, and MMEA molecules prefer to be fully solvated by water molecules, whereas DEAB molecules tend to self-aggregate. In a range from 30/70-50/50 (w/w) alkanolamine/water mixtures, they form a bicontinuous phase (both alkanolamine and water are organized in two mutually percolating clusters). Among the studied aqueous alkanolamine solutions, the diffusion coefficients decrease in the following order MEA > MPA = MMEA > DEAB. With an increase of water content, the diffusion coefficients increase for all studied alkanolamines. The presented results are a first step for process-scale simulation and provide important qualitative and quantitative information for the design and engineering of efficient new CO 2 removal processes.

Reaction Mechanism for Direct Propylene Epoxidation by Alumina-Supported Silver Aggregates. The Role of the Particle / Support Interface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cheng, Lei; Yin, Chunrong; Mehmood, Faisal

2013-11-21

Sub-nanometer Ag aggregates on alumina supports have been found to be active toward direct propylene epoxidation to propylene oxide by molecular oxygen at low temperatures, with a negligible amount of carbon dioxide formation (Science 328, p. 224, 2010). In this work, we computationally and experimentally investigate the origin of the high reactivity of the sub-nanometer Ag aggregates. Computationally, we study O 2 dissociation and propylene epoxidation on unsupported Ag 19 and Ag 20 clusters, as well as alumina-supported Ag 19. The O 2 dissociation and propylene epoxidation apparent barriers at the interface between the Ag aggregate and the alumina supportmore » are calculated to be 0.2 and 0.2~0.4 eV, respectively. These barriers are somewhat lower than those on sites away from the interface. The mechanism at the interface is similar to what was previously found for the silver trimer on alumina and can account for the high activity observed for the direct oxidation of propylene on the Ag aggregates. The barriers for oxygen dissociation on these model systems both at the interface and on the surfaces are small compared to crystalline surfaces, indicating that availability of oxygen will not be a rate limiting step for the aggregates, as in the case of the crystalline surfaces. Experimentally, we investigate Ultrananocrystalline Diamond (UNCD)-supported silver aggregates under reactive conditions of propylene partial oxidation. The UNCD-supported Ag clusters are found to be not measurably active toward propylene oxidation, in contrast to the alumina supported Ag clusters. This suggests that the lack of metal-oxide interfacial sites of the Ag-UNCD catalyst, limits the epoxidation catalytic activity. This combined computational and experimental study shows the importance of the metal-oxide interface as well as the non-crystalline nature of the alumina-supported sub-nanometer Ag aggregate catalysts for propylene epoxidation.« less

Reaction Rate of Small Diffusing Molecules on a Cylindrical Membrane

NASA Astrophysics Data System (ADS)

Straube, Ronny; Ward, Michael J.; Falcke, Martin

2007-10-01

Biomembranes consist of a lipid bi-layer into which proteins are embedded to fulfill numerous tasks in localized regions of the membrane. Often, the proteins have to reach these regions by simple diffusion. Motivated by the observation that IP3 receptor channels (IP3R) form clusters on the surface of the endoplasmic reticulum (ER) during ATP-induced calcium release, the reaction rate of small diffusing molecules on a cylindrical membrane is calculated based on the Smoluchowski approach. In this way, the cylindrical topology of the tubular ER is explicitly taken into account. The problem can be reduced to the solution of the diffusion equation on a finite cylindrical surface containing a small absorbing hole. The solution is constructed by matching appropriate `inner' and `outer' asymptotic expansions. The asymptotic results are compared with those from numerical simulations and excellent agreement is obtained. For realistic parameter sets, we find reaction rates in the range of experimentally measured clustering rates of IP3R. This supports the idea that clusters are formed by a purely diffusion limited process.

Cross-layer cluster-based energy-efficient protocol for wireless sensor networks.

PubMed

Mammu, Aboobeker Sidhik Koyamparambil; Hernandez-Jayo, Unai; Sainz, Nekane; de la Iglesia, Idoia

2015-04-09

Recent developments in electronics and wireless communications have enabled the improvement of low-power and low-cost wireless sensors networks (WSNs). One of the most important challenges in WSNs is to increase the network lifetime due to the limited energy capacity of the network nodes. Another major challenge in WSNs is the hot spots that emerge as locations under heavy traffic load. Nodes in such areas quickly drain energy resources, leading to disconnection in network services. In such an environment, cross-layer cluster-based energy-efficient algorithms (CCBE) can prolong the network lifetime and energy efficiency. CCBE is based on clustering the nodes to different hexagonal structures. A hexagonal cluster consists of cluster members (CMs) and a cluster head (CH). The CHs are selected from the CMs based on nodes near the optimal CH distance and the residual energy of the nodes. Additionally, the optimal CH distance that links to optimal energy consumption is derived. To balance the energy consumption and the traffic load in the network, the CHs are rotated among all CMs. In WSNs, energy is mostly consumed during transmission and reception. Transmission collisions can further decrease the energy efficiency. These collisions can be avoided by using a contention-free protocol during the transmission period. Additionally, the CH allocates slots to the CMs based on their residual energy to increase sleep time. Furthermore, the energy consumption of CH can be further reduced by data aggregation. In this paper, we propose a data aggregation level based on the residual energy of CH and a cost-aware decision scheme for the fusion of data. Performance results show that the CCBE scheme performs better in terms of network lifetime, energy consumption and throughput compared to low-energy adaptive clustering hierarchy (LEACH) and hybrid energy-efficient distributed clustering (HEED).

Heterogeneous gene expression signatures correspond to distinct lung pathologies and biomarkers of disease severity in idiopathic pulmonary fibrosis.

PubMed

DePianto, Daryle J; Chandriani, Sanjay; Abbas, Alexander R; Jia, Guiquan; N'Diaye, Elsa N; Caplazi, Patrick; Kauder, Steven E; Biswas, Sabyasachi; Karnik, Satyajit K; Ha, Connie; Modrusan, Zora; Matthay, Michael A; Kukreja, Jasleen; Collard, Harold R; Egen, Jackson G; Wolters, Paul J; Arron, Joseph R

2015-01-01

There is microscopic spatial and temporal heterogeneity of pathological changes in idiopathic pulmonary fibrosis (IPF) lung tissue, which may relate to heterogeneity in pathophysiological mediators of disease and clinical progression. We assessed relationships between gene expression patterns, pathological features, and systemic biomarkers to identify biomarkers that reflect the aggregate disease burden in patients with IPF. Gene expression microarrays (N=40 IPF; 8 controls) and immunohistochemical analyses (N=22 IPF; 8 controls) of lung biopsies. Clinical characterisation and blood biomarker levels of MMP3 and CXCL13 in a separate cohort of patients with IPF (N=80). 2940 genes were significantly differentially expressed between IPF and control samples (|fold change| >1.5, p<0.05). Two clusters of co-regulated genes related to bronchiolar epithelium or lymphoid aggregates exhibited substantial heterogeneity within the IPF population. Gene expression in bronchiolar and lymphoid clusters corresponded to the extent of bronchiolisation and lymphoid aggregates determined by immunohistochemistry in adjacent tissue sections. Elevated serum levels of MMP3, encoded in the bronchiolar cluster, and CXCL13, encoded in the lymphoid cluster, corresponded to disease severity and shortened survival time (p<10(-7) for MMP3 and p<10(-5) for CXCL13; Cox proportional hazards model). Microscopic pathological heterogeneity in IPF lung tissue corresponds to specific gene expression patterns related to bronchiolisation and lymphoid aggregates. MMP3 and CXCL13 are systemic biomarkers that reflect the aggregate burden of these pathological features across total lung tissue. These biomarkers may have clinical utility as prognostic and/or surrogate biomarkers of disease activity in interventional studies in IPF. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Relative dispersion of clustered drifters in a small micro-tidal estuary

NASA Astrophysics Data System (ADS)

Suara, Kabir; Chanson, Hubert; Borgas, Michael; Brown, Richard J.

2017-07-01

Small tide-dominated estuaries are affected by large scale flow structures which combine with the underlying bed generated smaller scale turbulence to significantly increase the magnitude of horizontal diffusivity. Field estimates of horizontal diffusivity and its associated scales are however rare due to limitations in instrumentation. Data from multiple deployments of low and high resolution clusters of GPS-drifters are used to examine the dynamics of a surface flow in a small micro-tidal estuary through relative dispersion analyses. During the field study, cluster diffusivity, which combines both large- and small-scale processes ranged between, 0.01 and 3.01 m2/s for spreading clusters and, -0.06 and -4.2 m2/s for contracting clusters. Pair-particle dispersion, Dp2, was scale dependent and grew as Dp2 ∼ t1.83 in streamwise and Dp2 ∼ t0.8 in cross-stream directions. At small separation scale, pair-particle (d < 0.5 m) relative diffusivity followed the Richardson's 4/3 power law and became weaker as separation scale increases. Pair-particle diffusivity was described as Kp ∼ d1.01 and Kp ∼ d0.85 in the streamwise and cross-stream directions, respectively for separation scales ranging from 0.1 to 10 m. Two methods were used to identify the mechanism responsible for dispersion within the channel. The results clearly revealed the importance of strain fields (stretching and shearing) in the spreading of particles within a small micro-tidal channel. The work provided input for modelling dispersion of passive particle in shallow micro-tidal estuaries where these were not previously experimentally studied.

Theory of Stochastic Laplacian Growth

NASA Astrophysics Data System (ADS)

Alekseev, Oleg; Mineev-Weinstein, Mark

2017-07-01

We generalize the diffusion-limited aggregation by issuing many randomly-walking particles, which stick to a cluster at the discrete time unit providing its growth. Using simple combinatorial arguments we determine probabilities of different growth scenarios and prove that the most probable evolution is governed by the deterministic Laplacian growth equation. A potential-theoretical analysis of the growth probabilities reveals connections with the tau-function of the integrable dispersionless limit of the two-dimensional Toda hierarchy, normal matrix ensembles, and the two-dimensional Dyson gas confined in a non-uniform magnetic field. We introduce the time-dependent Hamiltonian, which generates transitions between different classes of equivalence of closed curves, and prove the Hamiltonian structure of the interface dynamics. Finally, we propose a relation between probabilities of growth scenarios and the semi-classical limit of certain correlation functions of "light" exponential operators in the Liouville conformal field theory on a pseudosphere.

Influence of reactive gas admixture on transition metal cluster nucleation in a gas aggregation cluster source

NASA Astrophysics Data System (ADS)

Peter, Tilo; Polonskyi, Oleksandr; Gojdka, Björn; Mohammad Ahadi, Amir; Strunskus, Thomas; Zaporojtchenko, Vladimir; Biederman, Hynek; Faupel, Franz

2012-12-01

We quantitatively assessed the influence of reactive gases on the formation processes of transition metal clusters in a gas aggregation cluster source. A cluster source based on a 2 in. magnetron is used to study the production rate of titanium and cobalt clusters. Argon served as working gas for the DC magnetron discharge, and a small amount of reactive gas (oxygen and nitrogen) is added to promote reactive cluster formation. We found that the cluster production rate depends strongly on the reactive gas concentration for very small amounts of reactive gas (less than 0.1% of total working gas), and no cluster formation takes place in the absence of reactive species. The influence of discharge power, reactive gas concentration, and working gas pressure are investigated using a quartz micro balance in a time resolved manner. The strong influence of reactive gas is explained by a more efficient formation of nucleation seeds for metal-oxide or nitride than for pure metal.

The effect of realistic forces in finite epitaxial islands: Equilibrium structure, stability limits and substrate-induced dissociation of migrating clusters

NASA Astrophysics Data System (ADS)

Milchev, Andrey; Markov, Ivan

1985-06-01

The behaviour of finite epitaxial islands in the periodic field of the substrate is theoretically investigated. The harmonic interactions, traditionally adopted in the model of Frank and Van der Merwe, are replaced by Toda and Morse potentials and sets of difference recursion equations, governing the equilibrium properties of the system, are derived and solved numerically. It is shown that allowing for anharmonicity in the interactions in the deposit reveals several qualiatively new effects, such as: (1) The existence of substrate-induced rupture of anharmonic clusters which migrate on the substrate. It is predicted that such dissociation should be enhanced, if (a) the energy barrier for surface diffusion is increased, (b) the natural incompatibility between substrate and deposit is decreased, and (c) the size of the clusters grows. (2) A split in the misfit stability limits for pseudomorphism and for spontaneous generation of misfit dislocations with respect to the sign of the misfit. The limits corresponding to negative misfit rapidly increase while the positive misfit limits decrease (in absolute terms) with growing degree of anharmonicity. (3) A marked asymmetry in the magnitude of various properties of the clusters, such as adhesion to the substrate, activation energy for surface diffusion, mean strain, dislocation lengths, etc., with respect to the sign of the mismatch between surface and deposit.

The number and growth pattern of plasmacytoid dendritic cells vary in different types of reactive lymph nodes: an immunohistochemical study.

PubMed

Rollins-Raval, Marian A; Marafioti, Teresa; Swerdlow, Steven H; Roth, Christine G

2013-06-01

Plasmacytoid dendritic cells, which play a fundamental role in the innate immune response, are best known for their presence in hyaline-vascular Castleman disease and histiocytic necrotizing lymphadenitis. The relative number and distribution in many reactive entities as detected using more sensitive methods are uncertain, and their diagnostic implications are unknown. Immunohistochemical studies for plasmacytoid dendritic cell-associated markers CD123 and CD2AP were performed on 42 lymph nodes with hyaline-vascular Castleman disease, histiocytic necrotizing lymphadenitis, sarcoidosis, necrotizing granulomatous inflammation, viral infection, dermatopathic lymphadenopathy, autoimmune disease, and a histologic pattern compatible with toxoplasmosis. The overall plasmacytoid dendritic cell numbers and growth patterns (tight aggregates, loose aggregates/clusters, scattered single cells) were assessed. Plasmacytoid dendritic cells were present in all cases and were predominantly distributed in loose aggregates/clusters or singly. They were most numerous in granulomatous inflammation and histiocytic necrotizing lymphadenitis, whereas viral infections showed the fewest overall numbers and a predominant pattern of scattered single cells. Tight aggregates of plasmacytoid dendritic cells were most numerous in hyaline-vascular Castleman disease (100% sensitive, 68% specific). Plasmacytoid dendritic cells are not limited to a small number of reactive lymphadenopathies but are found in many reactive processes, often with a predominant pattern of loose aggregates/clusters and scattered single cells. However, tight aggregates were a characteristic feature of hyaline-vascular Castleman disease, and viral infections typically showed only few scattered cells distributed singly. Copyright © 2013 Elsevier Inc. All rights reserved.

Lifetime of Major Histocompatibility Complex Class-I Membrane Clusters Is Controlled by the Actin Cytoskeleton

PubMed Central

Lavi, Yael; Gov, Nir; Edidin, Michael; Gheber, Levi A.

2012-01-01

Lateral heterogeneity of cell membranes has been demonstrated in numerous studies showing anomalous diffusion of membrane proteins; it has been explained by models and experiments suggesting dynamic barriers to free diffusion, that temporarily confine membrane proteins into microscopic patches. This picture, however, comes short of explaining a steady-state patchy distribution of proteins, in face of the transient opening of the barriers. In our previous work we directly imaged persistent clusters of MHC-I, a type I transmembrane protein, and proposed a model of a dynamic equilibrium between proteins newly delivered to the cell surface by vesicle traffic, temporary confinement by dynamic barriers to lateral diffusion, and dispersion of the clusters by diffusion over the dynamic barriers. Our model predicted that the clusters are dynamic, appearing when an exocytic vesicle fuses with the plasma membrane and dispersing with a typical lifetime that depends on lateral diffusion and the dynamics of barriers. In a subsequent work, we showed this to be the case. Here we test another prediction of the model, and show that changing the stability of actin barriers to lateral diffusion changes cluster lifetimes. We also develop a model for the distribution of cluster lifetimes, consistent with the function of barriers to lateral diffusion in maintaining MHC-I clusters. PMID:22500754

Thermodynamics, morphology, and kinetics of early-stage self-assembly of π-conjugated oligopeptides

DOE Office of Scientific and Technical Information (OSTI.GOV)

None, None

Synthetic oligopeptides containing π-conjugated cores self-assemble novel materials with attractive electronic and photophysical properties. All-atom, explicit solvent molecular dynamics simulations of Asp-Phe-Ala-Gly-OPV3-Gly-Ala-Phe-Asp peptides were used to parameterize an implicit solvent model to simulate early-stage self-assembly. Under low-pH conditions, peptides assemble into β-sheet-like stacks with strongly favorable monomer association free energies of ΔF ≈ -25kBT. Aggregation at high-pH produces disordered aggregates destabilized by Coulombic repulsion between negatively charged Asp termini (ΔF ≈ -5kBT). In simulations of hundreds of monomers over 70 ns we observe the spontaneous formation of up to undecameric aggregates under low-pH conditions. Modeling assembly as a continuous-time Markovmore » process, we infer transition rates between different aggregate sizes and microsecond relaxation times for early-stage assembly. Our data suggests a hierarchical model of assembly in which peptides coalesce into small clusters over tens of nanoseconds followed by structural ripening and diffusion limited aggregation on longer time scales. This work provides new molecular-level understanding of early-stage assembly, and a means to study the impact of peptide sequence and aromatic core chemistry upon the thermodynamics, assembly kinetics, and morphology of the supramolecular aggregates.« less

Thermodynamics, morphology, and kinetics of early-stage self-assembly of π-conjugated oligopeptides

DOE PAGES

None, None

2016-03-22

Synthetic oligopeptides containing π-conjugated cores self-assemble novel materials with attractive electronic and photophysical properties. All-atom, explicit solvent molecular dynamics simulations of Asp-Phe-Ala-Gly-OPV3-Gly-Ala-Phe-Asp peptides were used to parameterize an implicit solvent model to simulate early-stage self-assembly. Under low-pH conditions, peptides assemble into β-sheet-like stacks with strongly favorable monomer association free energies of ΔF ≈ -25kBT. Aggregation at high-pH produces disordered aggregates destabilized by Coulombic repulsion between negatively charged Asp termini (ΔF ≈ -5kBT). In simulations of hundreds of monomers over 70 ns we observe the spontaneous formation of up to undecameric aggregates under low-pH conditions. Modeling assembly as a continuous-time Markovmore » process, we infer transition rates between different aggregate sizes and microsecond relaxation times for early-stage assembly. Our data suggests a hierarchical model of assembly in which peptides coalesce into small clusters over tens of nanoseconds followed by structural ripening and diffusion limited aggregation on longer time scales. This work provides new molecular-level understanding of early-stage assembly, and a means to study the impact of peptide sequence and aromatic core chemistry upon the thermodynamics, assembly kinetics, and morphology of the supramolecular aggregates.« less

A passive physical model for DnaK chaperoning

NASA Astrophysics Data System (ADS)

Uhl, Lionel; Dumont, Audrey; Dukan, Sam

2018-03-01

Almost all living organisms use protein chaperones with a view to preventing proteins from misfolding or aggregation either spontaneously or during cellular stress. This work uses a reaction-diffusion stochastic model to describe the dynamic localization of the Hsp70 chaperone DnaK in Escherichia coli cells during transient proteotoxic collapse characterized by the accumulation of insoluble proteins. In the model, misfolded (‘abnormal’) proteins are produced during alcoholic stress and have the propensity to aggregate with a polymerization-like kinetics. When aggregates diffuse more slowly they grow larger. According to Michaelis-Menten-type kinetics, DnaK has the propensity to bind with misfolded proteins or aggregates in order to catalyse refolding. To match experimental fluorescence microscopy data showing clusters of DnaK-GFP localized in multiple foci, the model includes spatial zones with local reduced diffusion rates to generate spontaneous assemblies of DnaK called ‘foci’. Numerical simulations of our model succeed in reproducing the kinetics of DnaK localization experimentally observed. DnaK starts from foci, moves to large aggregates during acute stress, resolves those aggregates during recovery and finally returns to its initial punctate localization pattern. Finally, we compare real biological events with hypothetical repartitions of the protein aggregates or DnaK. We then notice that DnaK action is more efficient on protein aggregates than on protein homogeneously distributed.

Effect of silver ions and clusters on the luminescence properties of Eu-doped borate glasses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiao, Qing, E-mail: jiaoqing@nbu.edu.cn; Wang, Xi; Qiu, Jianbei

2015-12-15

Highlights: • Ag{sup +} and Ag clusters are investigated in the borate glasses via ion exchange method. • The aggregation of silver ions to the clusters was controlled by the ion exchange concentration. • Eu{sup 3+}/Eu{sup 2+} ions emission was enhanced with the sensitization of the silver species. • Energy transfer process from Ag ions and Ag clusters to Eu ions is identified by the lifetime measurements. - Abstract: Silver ions and clusters were applied to Eu{sup 3+}-doped borate glasses via the Ag{sup +}–Na{sup +} ion exchange method. Eu{sup 3+}/Eu{sup 2+} ion luminescence enhancement was achieved after silver ion exchange.more » Absorption spectra showed no band at 420 nm, which indicates that silver nanoparticles can be excluded as a silver state in the glass. Silver ion aggregation into clusters during the ion exchange process may be inferred. The effect of silver ions and clusters on rare earth emissions was investigated using spectral information and lifetime measurements. Significant luminescence enhancements were observed from the energy transfer of Ag{sup +} ions and clusters to Eu{sup 3+}/Eu{sup 2+} ions, companied with the silver ions aggregated into the clusters state. The results of this research may extend the current understanding of interactions between rare-earth ions and Ag species.« less

Modeling Aggregation Processes of Lennard-Jones particles Via Stochastic Networks

NASA Astrophysics Data System (ADS)

Forman, Yakir; Cameron, Maria

2017-07-01

We model an isothermal aggregation process of particles/atoms interacting according to the Lennard-Jones pair potential by mapping the energy landscapes of each cluster size N onto stochastic networks, computing transition probabilities from the network for an N-particle cluster to the one for N+1, and connecting these networks into a single joint network. The attachment rate is a control parameter. The resulting network representing the aggregation of up to 14 particles contains 6427 vertices. It is not only time-irreversible but also reducible. To analyze its transient dynamics, we introduce the sequence of the expected initial and pre-attachment distributions and compute them for a wide range of attachment rates and three values of temperature. As a result, we find the configurations most likely to be observed in the process of aggregation for each cluster size. We examine the attachment process and conduct a structural analysis of the sets of local energy minima for every cluster size. We show that both processes taking place in the network, attachment and relaxation, lead to the dominance of icosahedral packing in small (up to 14 atom) clusters.

Thermodynamics and Kinetics of Prenucleation Clusters, Classical and Non-Classical Nucleation

PubMed Central

Zahn, Dirk

2015-01-01

Recent observations of prenucleation species and multi-stage crystal nucleation processes challenge the long-established view on the thermodynamics of crystal formation. Here, we review and generalize extensions to classical nucleation theory. Going beyond the conventional implementation as has been used for more than a century now, nucleation inhibitors, precursor clusters and non-classical nucleation processes are rationalized as well by analogous concepts based on competing interface and bulk energy terms. This is illustrated by recent examples of species formed prior to/instead of crystal nucleation and multi-step nucleation processes. Much of the discussed insights were obtained from molecular simulation using advanced sampling techniques, briefly summarized herein for both nucleation-controlled and diffusion-controlled aggregate formation. PMID:25914369

Isotropic model for cluster growth on a regular lattice

NASA Astrophysics Data System (ADS)

Yates, Christian A.; Baker, Ruth E.

2013-08-01

There exists a plethora of mathematical models for cluster growth and/or aggregation on regular lattices. Almost all suffer from inherent anisotropy caused by the regular lattice upon which they are grown. We analyze the little-known model for stochastic cluster growth on a regular lattice first introduced by Ferreira Jr. and Alves [J. Stat. Mech. Theo. & Exp.1742-546810.1088/1742-5468/2006/11/P11007 (2006) P11007], which produces circular clusters with no discernible anisotropy. We demonstrate that even in the noise-reduced limit the clusters remain circular. We adapt the model by introducing a specific rearrangement algorithm so that, rather than adding elements to the cluster from the outside (corresponding to apical growth), our model uses mitosis-like cell splitting events to increase the cluster size. We analyze the surface scaling properties of our model and compare it to the behavior of more traditional models. In “1+1” dimensions we discover and explore a new, nonmonotonic surface thickness scaling relationship which differs significantly from the Family-Vicsek scaling relationship. This suggests that, for models whose clusters do not grow through particle additions which are solely dependent on surface considerations, the traditional classification into “universality classes” may not be appropriate.

Elucidation of flow-mediated tumour cell-induced platelet aggregation using an ultrasound standing wave trap.

PubMed

Bazou, D; Santos-Martinez, M J; Medina, C; Radomski, M W

2011-04-01

Tumour cells activate and aggregate platelets [tumour cell-induced platelet aggregation (TCIPA)] and this process plays an important role in the successful metastasis of cancer cells. To date, most studies on TCIPA have been conducted under no-flow conditions. In this study, we have investigated TCIPA in real time under flow conditions, using an ultrasound standing wave trap that allows formation and levitation of cancer cell clusters in suspension, thus mimicking the conditions generated by flowing blood. Using 59M adenocarcinoma and HT1080 fibrosarcoma cells and human platelets, cancer cell cluster-platelet aggregates were imaged in real time using epi-fluorescence microscopy (F-actin) and investigated in detail using confocal microscopy (matrix metalloproteinase-2-GPIIb/IIIa co-localization) and scanning electron and helium-ion microscopy (<1 nm resolution). The release of gelatinases from aggregates was studied using zymography. We found that platelet activation and aggregation takes place on the surface of cancer cells (TCIPA), leading to time-dependent disruption of cancer cell clusters. Pharmacological modulation of TCIPA revealed that EDTA, prostacyclin, o-phenanthroline and apyrase significantly down-regulated TCIPA and, in turn, delayed cell cluster disruption, However, EGTA and aspirin were ineffective. Pharmacological inhibition of TCIPA correlated with the down-regulation of platelet activation as shown by flow-cytometry assay of platelet P-selectin. Our results show for the first time, that during TCIPA, platelet activation disrupts cancer cell clusters and this can contribute to metastasis. Thus, selective targeting of platelet aggregate-cancer cell clusters may be an important strategy to control metastasis. © 2011 The Authors. British Journal of Pharmacology © 2011 The British Pharmacological Society.

Growth properties of protoplanetary dust in a long-term microgravity experiment

NASA Astrophysics Data System (ADS)

Brisset, Julie; Kothe, Stefan; Weidling, Rene; Heisselmann, Daniel; Blum, Juergen

2014-11-01

In the very first steps of the formation of a new planetary system, dust agglomerates and grows inside the protoplanetary disk that rotates around the newly formed star. In this disk, collisions between the dust particles, induced by interactions with the surrounding gas, lead to sticking. Aggregates start growing until their sizes and relative velocities are high enough for collisions to result in bouncing or fragmentation. As part of a series of microgravity experiments aiming at the investigation of the transitions between sticking, bouncing and fragmentation of colliding dust aggregates, the Suborbital Particle and Aggregation Experiment (SPACE) was designed, built and operated both at the drop tower in Bremen (August 2011) and on the REXUS 12 suborbital rocket (March 2012). The SPACE experiment allowed for the observation of collisions between aggregates of sizes of a few 100 µm that were composed of SiO2, a commonly used protoplanetary dust analog material. At velocities below 10 cm/s, clusters composed of a high number of aggregates (more than 10^4) formed and grew to sizes of up to 5 mm. The analysis of these collisions delivered valuable input to a current dust collision model, which maps the outcome of collisions depending on the aggregate sizes and their relative velocities. The sticking probability of sub-mm-sized dust aggregates could directly be measured during the suborbital rocket flight, over a velocity range covering the transition between the sticking and bouncing regimes. In addition, the evolution of clusters formed from sub-mm-sized aggregates during the different experiments could be observed and some of their intrinsic properties derived. The measured characteristics were the cluster fractal dimensions, the tensile strength of their outer aggregate layer and the effective surface energy of their constituents. Threshold energies for cluster restructuring and fragmentation could also be determined. All these cluster properties are important input parameters for molecular dynamics or numerical simulations investigating the behavior of macroscopic clusters (>1 mm in size) in protoplanetary disks.

Modeling of mixing processes: Fluids, particulates, and powders

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ottino, J.M.; Hansen, S.

Work under this grant involves two main areas: (1) Mixing of Viscous Liquids, this first area comprising aggregation, fragmentation and dispersion, and (2) Mixing of Powders. In order to produce a coherent self-contained picture, we report primarily on results obtained under (1), and within this area, mostly on computational studies of particle aggregation in regular and chaotic flows. Numerical simulations show that the average cluster size of compact clusters grows algebraically, while the average cluster size of fractal clusters grows exponentially; companion mathematical arguments are used to describe the initial growth of average cluster size and polydispersity. It is foundmore » that when the system is well mixed and the capture radius independent of mass, the polydispersity is constant for long-times and the cluster size distribution is self-similar. Furthermore, our simulations indicate that the fractal nature of the clusters is dependent upon the mixing.« less

Synchronization as Aggregation: Cluster Kinetics of Pulse-Coupled Oscillators.

PubMed

O'Keeffe, Kevin P; Krapivsky, P L; Strogatz, Steven H

2015-08-07

We consider models of identical pulse-coupled oscillators with global interactions. Previous work showed that under certain conditions such systems always end up in sync, but did not quantify how small clusters of synchronized oscillators progressively coalesce into larger ones. Using tools from the study of aggregation phenomena, we obtain exact results for the time-dependent distribution of cluster sizes as the system evolves from disorder to synchrony.

In vitro motility evaluation of aggregated cancer cells by means of automatic image processing.

PubMed

De Hauwer, C; Darro, F; Camby, I; Kiss, R; Van Ham, P; Decaesteker, C

1999-05-01

Set up of an automatic image processing based method that enables the motility of in vitro aggregated cells to be evaluated for a number of hours. Our biological model included the PC-3 human prostate cancer cell line growing as a monolayer on the bottom of Falcon plastic dishes containing conventional culture media. Our equipment consisted of an incubator, an inverted phase contrast microscope, a Charge Coupled Device (CCD) video camera, and a computer equipped with an image processing software developed in our laboratory. This computer-assisted microscope analysis of aggregated cells enables global cluster motility to be evaluated. This analysis also enables the trajectory of each cell to be isolated and parametrized within a given cluster or, indeed, the trajectories of individual cells outside a cluster. The results show that motility inside a PC-3 cluster is not restricted to slight motion due to cluster expansion, but rather consists of a marked cell movement within the cluster. The proposed equipment enables in vitro aggregated cell motility to be studied. This method can, therefore, be used in pharmacological studies in order to select anti-motility related compounds. The compounds selected by the equipment described could then be tested in vivo as potential anti-metastatic.

Solid state and aqueous behavior of uranyl peroxide cage clusters

NASA Astrophysics Data System (ADS)

Pellegrini, Kristi Lynn

Uranyl peroxide cage clusters include a large family of more than 50 published clusters of a variety of sizes, which can incorporate various ligands including pyrophosphate and oxalate. Previous studies have reported that uranyl clusters can be used as a method to separate uranium from a solid matrix, with potential applications in reprocessing of irradiated nuclear fuel. Because of the potential applications of these novel structures in an advanced nuclear fuel cycle and their likely presence in areas of contamination, it is important to understand their behavior in both solid state and aqueous systems, including complex environments where other ions are present. In this thesis, I examine the aqueous behavior of U24Pp 12, as well as aqueous cluster systems with added mono-, di-, and trivalent cations. The resulting solutions were analyzed using dynamic light scattering and ultra-small angle X-ray scattering to evaluate the species in solution. Precipitates of these systems were analyzed using powder X-ray diffraction, X-ray fluorescence spectrometry, and Raman spectroscopy. The results of these analyses demonstrate the importance of cation size, charge, and concentration of added cations on the aqueous behavior of uranium macroions. Specifically, aggregates of various sizes and shapes form rapidly upon addition of cations, and in some cases these aggregates appear to precipitate into an X-ray amorphous material that still contains U24Pp12 clusters. In addition, I probe aggregation of U24Pp12 and U60, another uranyl peroxide cage cluster, in mixed solvent water-alcohol systems. The aggregation of uranyl clusters in water-alcohol systems is a result of hydrogen bonding with polar organic molecules and the reduction of the dielectric constant of the system. Studies of aggregation of uranyl clusters also allow for comparison between the newer uranyl polyoxometalate family and century-old transition metal polyoxometalates. To complement the solution studies of uranyl cage clusters, solid state analyses of U24Pp12 are presented, including single crystal X-ray diffraction and preliminary single crystal neutron diffraction. Solid state analyses are used to probe the complicated bonding environments between U24Pp12 and crystallized counterions, giving further insight into the importance of cluster protonation and counterions in uranyl cluster systems. The combination of solid state and solution techniques provides information about the complicated nature of uranyl peroxide nanoclusters, and insight towards future applications of clusters in the advanced nuclear fuel cycle and the environment.

Dimension dependence of clustering dynamics in models of ballistic aggregation and freely cooling granular gas

NASA Astrophysics Data System (ADS)

Paul, Subhajit; Das, Subir K.

2018-03-01

Via event-driven molecular dynamics simulations we study kinetics of clustering in assemblies of inelastic particles in various space dimensions. We consider two models, viz., the ballistic aggregation model (BAM) and the freely cooling granular gas model (GGM), for each of which we quantify the time dependence of kinetic energy and average mass of clusters (that form due to inelastic collisions). These quantities, for both the models, exhibit power-law behavior, at least in the long time limit. For the BAM, corresponding exponents exhibit strong dimension dependence and follow a hyperscaling relation. In addition, in the high packing fraction limit the behavior of these quantities become consistent with a scaling theory that predicts an inverse relation between energy and mass. On the other hand, in the case of the GGM we do not find any evidence for such a picture. In this case, even though the energy decay, irrespective of packing fraction, matches quantitatively with that for the high packing fraction picture of the BAM, it is inversely proportional to the growth of mass only in one dimension, and the growth appears to be rather insensitive to the choice of the dimension, unlike the BAM.

Atomistic modeling of dropwise condensation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sikarwar, B. S., E-mail: bssikarwar@amity.edu; Singh, P. L.; Muralidhar, K.

The basic aim of the atomistic modeling of condensation of water is to determine the size of the stable cluster and connect phenomena occurring at atomic scale to the macroscale. In this paper, a population balance model is described in terms of the rate equations to obtain the number density distribution of the resulting clusters. The residence time is taken to be large enough so that sufficient time is available for all the adatoms existing in vapor-phase to loose their latent heat and get condensed. The simulation assumes clusters of a given size to be formed from clusters of smallermore » sizes, but not by the disintegration of the larger clusters. The largest stable cluster size in the number density distribution is taken to be representative of the minimum drop radius formed in a dropwise condensation process. A numerical confirmation of this result against predictions based on a thermodynamic model has been obtained. Results show that the number density distribution is sensitive to the surface diffusion coefficient and the rate of vapor flux impinging on the substrate. The minimum drop radius increases with the diffusion coefficient and the impinging vapor flux; however, the dependence is weak. The minimum drop radius predicted from thermodynamic considerations matches the prediction of the cluster model, though the former does not take into account the effect of the surface properties on the nucleation phenomena. For a chemically passive surface, the diffusion coefficient and the residence time are dependent on the surface texture via the coefficient of friction. Thus, physical texturing provides a means of changing, within limits, the minimum drop radius. The study reveals that surface texturing at the scale of the minimum drop radius does not provide controllability of the macro-scale dropwise condensation at large timescales when a dynamic steady-state is reached.« less

Rumor Diffusion in an Interests-Based Dynamic Social Network

PubMed Central

Mao, Xinjun; Guessoum, Zahia; Zhou, Huiping

2013-01-01

To research rumor diffusion in social friend network, based on interests, a dynamic friend network is proposed, which has the characteristics of clustering and community, and a diffusion model is also proposed. With this friend network and rumor diffusion model, based on the zombie-city model, some simulation experiments to analyze the characteristics of rumor diffusion in social friend networks have been conducted. The results show some interesting observations: (1) positive information may evolve to become a rumor through the diffusion process that people may modify the information by word of mouth; (2) with the same average degree, a random social network has a smaller clustering coefficient and is more beneficial for rumor diffusion than the dynamic friend network; (3) a rumor is spread more widely in a social network with a smaller global clustering coefficient than in a social network with a larger global clustering coefficient; and (4) a network with a smaller clustering coefficient has a larger efficiency. PMID:24453911

Rumor diffusion in an interests-based dynamic social network.

PubMed

Tang, Mingsheng; Mao, Xinjun; Guessoum, Zahia; Zhou, Huiping

2013-01-01

To research rumor diffusion in social friend network, based on interests, a dynamic friend network is proposed, which has the characteristics of clustering and community, and a diffusion model is also proposed. With this friend network and rumor diffusion model, based on the zombie-city model, some simulation experiments to analyze the characteristics of rumor diffusion in social friend networks have been conducted. The results show some interesting observations: (1) positive information may evolve to become a rumor through the diffusion process that people may modify the information by word of mouth; (2) with the same average degree, a random social network has a smaller clustering coefficient and is more beneficial for rumor diffusion than the dynamic friend network; (3) a rumor is spread more widely in a social network with a smaller global clustering coefficient than in a social network with a larger global clustering coefficient; and (4) a network with a smaller clustering coefficient has a larger efficiency.

The development of structure in the expanding universe

NASA Technical Reports Server (NTRS)

Silk, J.; White, S. D.

1978-01-01

A model for clustering in an expanding universe is developed based on an application of the coagulation equation to the collision and aggregation of bound condensations. While the growth rate of clustering is determined by the rate at which density fluctuations reach the nonlinear regime and therefore depends on the initial fluctuation spectrum, the mass spectrum rapidly approaches a self-similar limiting form. This form is determined by the tidal processes which lead to the merging of condensations, and is not dependent on initial conditions.

A smart checkpointing scheme for improving the reliability of clustering routing protocols.

PubMed

Min, Hong; Jung, Jinman; Kim, Bongjae; Cho, Yookun; Heo, Junyoung; Yi, Sangho; Hong, Jiman

2010-01-01

In wireless sensor networks, system architectures and applications are designed to consider both resource constraints and scalability, because such networks are composed of numerous sensor nodes with various sensors and actuators, small memories, low-power microprocessors, radio modules, and batteries. Clustering routing protocols based on data aggregation schemes aimed at minimizing packet numbers have been proposed to meet these requirements. In clustering routing protocols, the cluster head plays an important role. The cluster head collects data from its member nodes and aggregates the collected data. To improve reliability and reduce recovery latency, we propose a checkpointing scheme for the cluster head. In the proposed scheme, backup nodes monitor and checkpoint the current state of the cluster head periodically. We also derive the checkpointing interval that maximizes reliability while using the same amount of energy consumed by clustering routing protocols that operate without checkpointing. Experimental comparisons with existing non-checkpointing schemes show that our scheme reduces both energy consumption and recovery latency.

Significant Transient Mobility of Platinum Clusters via a Hot Precursor State on the Alumina Surface.

PubMed

Beniya, Atsushi; Hirata, Hirohito; Watanabe, Yoshihide

2016-11-17

Relaxation dynamics of hot metal clusters on oxide surfaces play a crucial role in a variety of physical and chemical processes. However, their transient mobility has not been investigated as much as other systems such as atoms and molecules on metal surfaces due to experimental difficulties. To study the role of the transient mobility of clusters on the oxide surface, we investigated the initial adsorption process of size-selected Pt clusters on a thin Al 2 O 3 film. Soft-landing the size-selected clusters while suppressing the thermal migration resulted in the transient migration controlling the initial adsorption states as an isolated and aggregated cluster, as revealed using scanning tunneling microscopy. We demonstrate that transient migration significantly contributes to the initial cluster adsorption process; the cross section for aggregation is seven times larger than the expected value from geometrical considerations, indicating that metal clusters are highly mobile during a energy dissipation process on the oxide surface.

A Smart Checkpointing Scheme for Improving the Reliability of Clustering Routing Protocols

PubMed Central

Min, Hong; Jung, Jinman; Kim, Bongjae; Cho, Yookun; Heo, Junyoung; Yi, Sangho; Hong, Jiman

2010-01-01

In wireless sensor networks, system architectures and applications are designed to consider both resource constraints and scalability, because such networks are composed of numerous sensor nodes with various sensors and actuators, small memories, low-power microprocessors, radio modules, and batteries. Clustering routing protocols based on data aggregation schemes aimed at minimizing packet numbers have been proposed to meet these requirements. In clustering routing protocols, the cluster head plays an important role. The cluster head collects data from its member nodes and aggregates the collected data. To improve reliability and reduce recovery latency, we propose a checkpointing scheme for the cluster head. In the proposed scheme, backup nodes monitor and checkpoint the current state of the cluster head periodically. We also derive the checkpointing interval that maximizes reliability while using the same amount of energy consumed by clustering routing protocols that operate without checkpointing. Experimental comparisons with existing non-checkpointing schemes show that our scheme reduces both energy consumption and recovery latency. PMID:22163389

Distributed shared memory for roaming large volumes.

PubMed

Castanié, Laurent; Mion, Christophe; Cavin, Xavier; Lévy, Bruno

2006-01-01

We present a cluster-based volume rendering system for roaming very large volumes. This system allows to move a gigabyte-sized probe inside a total volume of several tens or hundreds of gigabytes in real-time. While the size of the probe is limited by the total amount of texture memory on the cluster, the size of the total data set has no theoretical limit. The cluster is used as a distributed graphics processing unit that both aggregates graphics power and graphics memory. A hardware-accelerated volume renderer runs in parallel on the cluster nodes and the final image compositing is implemented using a pipelined sort-last rendering algorithm. Meanwhile, volume bricking and volume paging allow efficient data caching. On each rendering node, a distributed hierarchical cache system implements a global software-based distributed shared memory on the cluster. In case of a cache miss, this system first checks page residency on the other cluster nodes instead of directly accessing local disks. Using two Gigabit Ethernet network interfaces per node, we accelerate data fetching by a factor of 4 compared to directly accessing local disks. The system also implements asynchronous disk access and texture loading, which makes it possible to overlap data loading, volume slicing and rendering for optimal volume roaming.

Dynamic Evolution Model Based on Social Network Services

NASA Astrophysics Data System (ADS)

Xiong, Xi; Gou, Zhi-Jian; Zhang, Shi-Bin; Zhao, Wen

2013-11-01

Based on the analysis of evolutionary characteristics of public opinion in social networking services (SNS), in the paper we propose a dynamic evolution model, in which opinions are coupled with topology. This model shows the clustering phenomenon of opinions in dynamic network evolution. The simulation results show that the model can fit the data from a social network site. The dynamic evolution of networks accelerates the opinion, separation and aggregation. The scale and the number of clusters are influenced by confidence limit and rewiring probability. Dynamic changes of the topology reduce the number of isolated nodes, while the increased confidence limit allows nodes to communicate more sufficiently. The two effects make the distribution of opinion more neutral. The dynamic evolution of networks generates central clusters with high connectivity and high betweenness, which make it difficult to control public opinions in SNS.

Detecting cancer clusters in a regional population with local cluster tests and Bayesian smoothing methods: a simulation study

PubMed Central

2013-01-01

Background There is a rising public and political demand for prospective cancer cluster monitoring. But there is little empirical evidence on the performance of established cluster detection tests under conditions of small and heterogeneous sample sizes and varying spatial scales, such as are the case for most existing population-based cancer registries. Therefore this simulation study aims to evaluate different cluster detection methods, implemented in the open soure environment R, in their ability to identify clusters of lung cancer using real-life data from an epidemiological cancer registry in Germany. Methods Risk surfaces were constructed with two different spatial cluster types, representing a relative risk of RR = 2.0 or of RR = 4.0, in relation to the overall background incidence of lung cancer, separately for men and women. Lung cancer cases were sampled from this risk surface as geocodes using an inhomogeneous Poisson process. The realisations of the cancer cases were analysed within small spatial (census tracts, N = 1983) and within aggregated large spatial scales (communities, N = 78). Subsequently, they were submitted to the cluster detection methods. The test accuracy for cluster location was determined in terms of detection rates (DR), false-positive (FP) rates and positive predictive values. The Bayesian smoothing models were evaluated using ROC curves. Results With moderate risk increase (RR = 2.0), local cluster tests showed better DR (for both spatial aggregation scales > 0.90) and lower FP rates (both < 0.05) than the Bayesian smoothing methods. When the cluster RR was raised four-fold, the local cluster tests showed better DR with lower FPs only for the small spatial scale. At a large spatial scale, the Bayesian smoothing methods, especially those implementing a spatial neighbourhood, showed a substantially lower FP rate than the cluster tests. However, the risk increases at this scale were mostly diluted by data aggregation. Conclusion High resolution spatial scales seem more appropriate as data base for cancer cluster testing and monitoring than the commonly used aggregated scales. We suggest the development of a two-stage approach that combines methods with high detection rates as a first-line screening with methods of higher predictive ability at the second stage. PMID:24314148

Secure data aggregation in wireless sensor networks using homomorphic encryption

NASA Astrophysics Data System (ADS)

Kumar, Manish; Verma, Shekhar; Lata, Kusum

2015-04-01

In a Wireless Sensor Network (WSN), aggregation exploits the correlation between spatially and temporally proximate sensor data to reduce the total data volume to be transmitted to the sink. Mobile agents (MAs) fit into this paradigm, and data can be aggregated and collected by an MA from different sensor nodes using context specific codes. The MA-based data collection suffers due to large size of a typical WSN and is prone to security problems. In this article, homomorphic encryption in a clustered WSN has been proposed for secure and efficient data collection using MAs. The nodes keep encrypted data that are given to an MA for data aggregation tasks. The MA performs all the data aggregation operations upon encrypted data as it migrates between nodes in a tree-like structure in which the nodes are leafs and the cluster head is the root of the tree. It returns and deposits the encrypted aggregated data to the cluster head after traversing through all the intra cluster nodes over a shortest path route. The homomorphic encryption and aggregation processing in encrypted domain makes the data collection process secure. Simulation results confirm the effectiveness of the proposed secure data aggregation mechanism. In addition to security, MA-based mechanism leads to lesser delay and bandwidth requirements.

When clusters collide: constraints on antimatter on the largest scales

DOE Office of Scientific and Technical Information (OSTI.GOV)

Steigman, Gary, E-mail: steigman@mps.ohio-state.edu

2008-10-15

Observations have ruled out the presence of significant amounts of antimatter in the Universe on scales ranging from the solar system, to the Galaxy, to groups and clusters of galaxies, and even to distances comparable to the scale of the present horizon. Except for the model-dependent constraints on the largest scales, the most significant upper limits to diffuse antimatter in the Universe are those on the {approx}Mpc scale of clusters of galaxies provided by the EGRET upper bounds to annihilation gamma rays from galaxy clusters whose intracluster gas is revealed through its x-ray emission. On the scale of individual clustersmore » of galaxies the upper bounds to the fraction of mixed matter and antimatter for the 55 clusters from a flux-limited x-ray survey range from 5 Multiplication-Sign 10{sup -9} to <1 Multiplication-Sign 10{sup -6}, strongly suggesting that individual clusters of galaxies are made entirely of matter or of antimatter. X-ray and gamma-ray observations of colliding clusters of galaxies, such as the Bullet Cluster, permit these constraints to be extended to even larger scales. If the observations of the Bullet Cluster, where the upper bound to the antimatter fraction is found to be <3 Multiplication-Sign 10{sup -6}, can be generalized to other colliding clusters of galaxies, cosmologically significant amounts of antimatter will be excluded on scales of order {approx}20 Mpc (M{approx}5 Multiplication-Sign 10{sup 15}M{sub sun})« less

Data-driven cluster reinforcement and visualization in sparsely-matched self-organizing maps.

PubMed

Manukyan, Narine; Eppstein, Margaret J; Rizzo, Donna M

2012-05-01

A self-organizing map (SOM) is a self-organized projection of high-dimensional data onto a typically 2-dimensional (2-D) feature map, wherein vector similarity is implicitly translated into topological closeness in the 2-D projection. However, when there are more neurons than input patterns, it can be challenging to interpret the results, due to diffuse cluster boundaries and limitations of current methods for displaying interneuron distances. In this brief, we introduce a new cluster reinforcement (CR) phase for sparsely-matched SOMs. The CR phase amplifies within-cluster similarity in an unsupervised, data-driven manner. Discontinuities in the resulting map correspond to between-cluster distances and are stored in a boundary (B) matrix. We describe a new hierarchical visualization of cluster boundaries displayed directly on feature maps, which requires no further clustering beyond what was implicitly accomplished during self-organization in SOM training. We use a synthetic benchmark problem and previously published microbial community profile data to demonstrate the benefits of the proposed methods.

Phosphorus-defect interactions during thermal annealing of ion implanted silicon

NASA Astrophysics Data System (ADS)

Keys, Patrick Henry

Ion implantation of dopant atoms into silicon generates nonequilibrium levels of crystal defects that can lead to the detrimental effects of transient enhanced diffusion (TED), incomplete dopant activation, and p-n junction leakage. In order to control these effects, it is vital to have a clear understanding of dopant-defect interactions and develop models that account for these interactions. This research focuses on experimentally investigating and modeling the clustering of phosphorus dopant atoms with silicon interstitials. Damage recovery of 40keV Si+ implants in phosphorus doped wells is experimentally analyzed. The effects of background phosphorus concentration, self implant dose, and anneal temperature are investigated. Phosphorus concentrations ranging from 2.0 x 1017 to 4.0 x 1019 cm-3 and Si+ doses ranging from 5.0 x 1013 cm-2 to 2.0 x 1014 cm-2 are studied during 650-800°C anneals. A dramatic reduction in the number of interstitials bound in {311} defects with increasing phosphorus background concentration is observed. It is suggested that the reduction of interstitials in {311} defects at high phosphorus concentrations is due to the formation of phosphorus-interstitial clusters (PICs). The critical concentration for clustering (approximately 1.0 x 1019 cm-3 at 750°C) is strongly temperature dependent and in close agreement with the kink concentration of phosphorus diffusion. Information gained from these "well experiments" is applied to the study of direct phosphorus implantation. An experimental study is conducted on 40keV phosphorus implanted to a dose of 1.0 x 1014 cm-2 during 650-800°C anneals. Electrically inactive PICs are shown to form at concentrations below the solid solubility limit due to high interstitial supersaturations. Data useful for developing a model to accurately predict phosphorus diffusion under nonequilibrium conditions are extracted from the experimental results. A cluster-mediated diffusion model is developed using the Florida Object Oriented Process Simulator (FLOOPS). The nucleation of defects is controlled by the diffusion-limited competition for excess interstitials between PICs and {311} clusters. The release of interstitials is driven by cluster dissolution. Modeling results show a strong correlation to those experimentally observed over a wide temporal and thermal domain using a single set of parameters. Improvements in process simulator accuracy are demonstrated with respect to dopant activation, TED, and dose loss.

Constraints on the dark matter neutralinos from the radio emissions of galaxy clusters

NASA Astrophysics Data System (ADS)

Kiew, Ching-Yee; Hwang, Chorng-Yuan; Zainal Abibin, Zamri

2017-05-01

By assuming the dark matter to be composed of neutralinos, we used the detection of upper limit on diffuse radio emission in a sample of galaxy clusters to put constraint on the properties of neutralinos. We showed the upper limit constraint on <σv>-mχ space with neutralino annihilation through b\\bar{b} and μ+μ- channels. The best constraint is from the galaxy clusters A2199 and A1367. We showed the uncertainty due to the density profile and cluster magnetic field. The largest uncertainty comes from the uncertainty in dark matter spatial distribution. We also investigated the constraints on minimal Supergravity (mSUGRA) and minimal supersymmetric standard model (MSSM) parameter space by scanning the parameters using the darksusy package. By using the current radio observation, we managed to exclude 40 combinations of mSUGRA parameters. On the other hand, 573 combinations of MSSM parameters can be excluded by current observation.

Confinement and diffusion time-scales of CR hadrons in AGN-inflated bubbles

NASA Astrophysics Data System (ADS)

Prokhorov, D. A.; Churazov, E. M.

2017-09-01

While rich clusters are powerful sources of X-rays, γ-ray emission from these large cosmic structures has not been detected yet. X-ray radiative energy losses in the central regions of relaxed galaxy clusters are so strong that one needs to consider special sources of energy, likely active galactic nucleus (AGN) feedback, to suppress catastrophic cooling of the gas. We consider a model of AGN feedback that postulates that the AGN supplies the energy to the gas by inflating bubbles of relativistic plasma, whose energy content is dominated by cosmic-ray (CR) hadrons. If most of these hadrons can quickly escape the bubbles, then collisions of CRs with thermal protons in the intracluster medium (ICM) should lead to strong γ-ray emission, unless fast diffusion of CRs removes them from the cluster. Therefore, the lack of detections with modern γ-ray telescopes sets limits on the confinement time of CR hadrons in bubbles and CR diffusive propagation in the ICM.

Influence of cell shape, inhomogeneities and diffusion barriers in cell polarization models

NASA Astrophysics Data System (ADS)

Giese, Wolfgang; Eigel, Martin; Westerheide, Sebastian; Engwer, Christian; Klipp, Edda

2015-12-01

In silico experiments bear the potential for further understanding of biological transport processes by allowing a systematic modification of any spatial property and providing immediate simulation results. Cell polarization and spatial reorganization of membrane proteins are fundamental for cell division, chemotaxis and morphogenesis. We chose the yeast Saccharomyces cerevisiae as an exemplary model system which entails the shuttling of small Rho GTPases such as Cdc42 and Rho, between an active membrane-bound form and an inactive cytosolic form. We used partial differential equations to describe the membrane-cytosol shuttling of proteins. In this study, a consistent extension of a class of 1D reaction-diffusion systems into higher space dimensions is suggested. The membrane is modeled as a thin layer to allow for lateral diffusion and the cytosol is modeled as an enclosed volume. Two well-known polarization mechanisms were considered. One shows the classical Turing-instability patterns, the other exhibits wave-pinning dynamics. For both models, we investigated how cell shape and diffusion barriers like septin structures or bud scars influence the formation of signaling molecule clusters and subsequent polarization. An extensive set of in silico experiments with different modeling hypotheses illustrated the dependence of cell polarization models on local membrane curvature, cell size and inhomogeneities on the membrane and in the cytosol. In particular, the results of our computer simulations suggested that for both mechanisms, local diffusion barriers on the membrane facilitate Rho GTPase aggregation, while diffusion barriers in the cytosol and cell protrusions limit spontaneous molecule aggregations of active Rho GTPase locally.

Ensemble Clustering using Semidefinite Programming with Applications

PubMed Central

Singh, Vikas; Mukherjee, Lopamudra; Peng, Jiming; Xu, Jinhui

2011-01-01

In this paper, we study the ensemble clustering problem, where the input is in the form of multiple clustering solutions. The goal of ensemble clustering algorithms is to aggregate the solutions into one solution that maximizes the agreement in the input ensemble. We obtain several new results for this problem. Specifically, we show that the notion of agreement under such circumstances can be better captured using a 2D string encoding rather than a voting strategy, which is common among existing approaches. Our optimization proceeds by first constructing a non-linear objective function which is then transformed into a 0–1 Semidefinite program (SDP) using novel convexification techniques. This model can be subsequently relaxed to a polynomial time solvable SDP. In addition to the theoretical contributions, our experimental results on standard machine learning and synthetic datasets show that this approach leads to improvements not only in terms of the proposed agreement measure but also the existing agreement measures based on voting strategies. In addition, we identify several new application scenarios for this problem. These include combining multiple image segmentations and generating tissue maps from multiple-channel Diffusion Tensor brain images to identify the underlying structure of the brain. PMID:21927539

Ensemble Clustering using Semidefinite Programming with Applications.

PubMed

Singh, Vikas; Mukherjee, Lopamudra; Peng, Jiming; Xu, Jinhui

2010-05-01

In this paper, we study the ensemble clustering problem, where the input is in the form of multiple clustering solutions. The goal of ensemble clustering algorithms is to aggregate the solutions into one solution that maximizes the agreement in the input ensemble. We obtain several new results for this problem. Specifically, we show that the notion of agreement under such circumstances can be better captured using a 2D string encoding rather than a voting strategy, which is common among existing approaches. Our optimization proceeds by first constructing a non-linear objective function which is then transformed into a 0-1 Semidefinite program (SDP) using novel convexification techniques. This model can be subsequently relaxed to a polynomial time solvable SDP. In addition to the theoretical contributions, our experimental results on standard machine learning and synthetic datasets show that this approach leads to improvements not only in terms of the proposed agreement measure but also the existing agreement measures based on voting strategies. In addition, we identify several new application scenarios for this problem. These include combining multiple image segmentations and generating tissue maps from multiple-channel Diffusion Tensor brain images to identify the underlying structure of the brain.

Understanding the presence of vacancy clusters in ZnO from a kinetic perspective

NASA Astrophysics Data System (ADS)

Bang, Junhyeok; Kim, Youg-Sung; Park, C. H.; Gao, F.; Zhang, S. B.

2014-06-01

Vacancy clusters have been observed in ZnO by positron-annihilation spectroscopy (PAS), but detailed mechanisms are unclear. This is because the clustering happens in non-equilibrium conditions, for which theoretical method has not been well established. Combining first-principles calculation and kinetic Monte Carlo simulation, we determine the roles of non-equilibrium kinetics on the vacancies clustering. We find that clustering starts with the formation of Zn and O vacancy pairs (VZn - Vo), which further grow by attracting additional mono-vacancies. At this stage, vacancy diffusivity becomes crucial: due to the larger diffusivity of VZn compared to VO, more VZn-abundant clusters are formed than VO-abundant clusters. The large dissociation energy barriers, e.g., over 2.5 eV for (VZn - Vo), suggest that, once formed, it is difficult for the clusters to dissociate. By promoting mono-vacancy diffusion, thermal annealing will increase the size of the clusters. As the PAS is insensitive to VO donor defects, our results suggest an interpretation of the experimental data that could not have been made without the in-depth calculations.

Modeling the Movement of Homicide by Type to Inform Public Health Prevention Efforts.

PubMed

Zeoli, April M; Grady, Sue; Pizarro, Jesenia M; Melde, Chris

2015-10-01

We modeled the spatiotemporal movement of hotspot clusters of homicide by motive in Newark, New Jersey, to investigate whether different homicide types have different patterns of clustering and movement. We obtained homicide data from the Newark Police Department Homicide Unit's investigative files from 1997 through 2007 (n = 560). We geocoded the address at which each homicide victim was found and recorded the date of and the motive for the homicide. We used cluster detection software to model the spatiotemporal movement of statistically significant homicide clusters by motive, using census tract and month of occurrence as the spatial and temporal units of analysis. Gang-motivated homicides showed evidence of clustering and diffusion through Newark. Additionally, gang-motivated homicide clusters overlapped to a degree with revenge and drug-motivated homicide clusters. Escalating dispute and nonintimate familial homicides clustered; however, there was no evidence of diffusion. Intimate partner and robbery homicides did not cluster. By tracking how homicide types diffuse through communities and determining which places have ongoing or emerging homicide problems by type, we can better inform the deployment of prevention and intervention efforts.

Investigation of defect clusters in ion-irradiated Ni and NiCo using diffuse X-ray scattering and electron microscopy

DOE PAGES

Olsen, Raina J.; Jin, Ke; Lu, Chenyang; ...

2015-11-23

The nature of defect clusters in Ni and Nimore » $$_{50}$$Co$$_{50}$$ (NiCo) irradiated at room temperature with 2–16 MeV Ni ions is studied using asymptotic diffuse X-ray scattering and transmission electron microscopy (TEM). Analysis of the scattering data provides separate size distributions for vacancy and interstitial type defect clusters, showing that both types of defect clusters have a smaller size and higher density in NiCo than in Ni. Diffuse scattering results show good quantitative agreement with TEM results for cluster sizes greater than 4 nm diameter, but find that the majority of vacancy clusters are under 2 nm in NiCo, which, if not detected, would lead to the conclusion that defect density was actually lower in the alloy. Interstitial dislocation loops and stacking fault tetrahedra are identified by TEM. Lastly comparison of diffuse scattering lineshapes to those calculated for dislocation loops and SFTs indicates that most of the vacancy clusters are SFTs.« less

Rate laws of the self-induced aggregation kinetics of Brownian particles

NASA Astrophysics Data System (ADS)

Mondal, Shrabani; Sen, Monoj Kumar; Baura, Alendu; Bag, Bidhan Chandra

2016-03-01

In this paper we have studied the self induced aggregation kinetics of Brownian particles in the presence of both multiplicative and additive noises. In addition to the drift due to the self aggregation process, the environment may induce a drift term in the presence of a multiplicative noise. Then there would be an interplay between the two drift terms. It may account qualitatively the appearance of the different laws of aggregation process. At low strength of white multiplicative noise, the cluster number decreases as a Gaussian function of time. If the noise strength becomes appreciably large then the variation of cluster number with time is fitted well by the mono exponentially decaying function of time. For additive noise driven case, the decrease of cluster number can be described by the power law. But in case of multiplicative colored driven process, cluster number decays multi exponentially. However, we have explored how the rate constant (in the mono exponentially cluster number decaying case) depends on strength of interference of the noises and their intensity. We have also explored how the structure factor at long time depends on the strength of the cross correlation (CC) between the additive and the multiplicative noises.

Stable dissipative optical vortex clusters by inhomogeneous effective diffusion.

PubMed

Li, Huishan; Lai, Shiquan; Qui, Yunli; Zhu, Xing; Xie, Jianing; Mihalache, Dumitru; He, Yingji

2017-10-30

We numerically show the generation of robust vortex clusters embedded in a two-dimensional beam propagating in a dissipative medium described by the generic cubic-quintic complex Ginzburg-Landau equation with an inhomogeneous effective diffusion term, which is asymmetrical in the two transverse directions and periodically modulated in the longitudinal direction. We show the generation of stable optical vortex clusters for different values of the winding number (topological charge) of the input optical beam. We have found that the number of individual vortex solitons that form the robust vortex cluster is equal to the winding number of the input beam. We have obtained the relationships between the amplitudes and oscillation periods of the inhomogeneous effective diffusion and the cubic gain and diffusion (viscosity) parameters, which depict the regions of existence and stability of vortex clusters. The obtained results offer a method to form robust vortex clusters embedded in two-dimensional optical beams, and we envisage potential applications in the area of structured light.

Computer simulations of dendrimer-polyelectrolyte complexes.

PubMed

Pandav, Gunja; Ganesan, Venkat

2014-08-28

We carry out a systematic analysis of static properties of the clusters formed by complexation between charged dendrimers and linear polyelectrolyte (LPE) chains in a dilute solution under good solvent conditions. We use single chain in mean-field simulations and analyze the structure of the clusters through radial distribution functions of the dendrimer, cluster size, and charge distributions. The effects of LPE length, charge ratio between LPE and dendrimer, the influence of salt concentration, and the dendrimer generation number are examined. Systems with short LPEs showed a reduced propensity for aggregation with dendrimers, leading to formation of smaller clusters. In contrast, larger dendrimers and longer LPEs lead to larger clusters with significant bridging. Increasing salt concentration was seen to reduce aggregation between dendrimers as a result of screening of electrostatic interactions. Generally, maximum complexation was observed in systems with an equal amount of net dendrimer and LPE charges, whereas either excess LPE or dendrimer concentrations resulted in reduced clustering between dendrimers.

Comparative Study of Broadband Photometry Relations for Ultra-Diffuse and Normal Galaxies in the Coma Cluster

NASA Astrophysics Data System (ADS)

Stone, Maria Babakhanyan

Ultra-diffuse galaxies are a novel type of galaxies discovered first in the Coma cluster. These objects are characterized simultaneously by large sizes and by very low counts of constituent stars. Conflicting theories have been proposed to explain how these large diffuse galaxies could have survived in the harsh environment of clusters. To date, thousands of these new galaxies have been identified in cluster environments. However, further studies are required to understand their relationship to the known giant and dwarf classes of galaxies. The purpose of this study is to compare the trends of inner and outer populations of normal members of the Coma cluster and ultra-diffuse galaxies in color-magnitude space. The present work used several astronomical catalogs to identify the member galaxies based on the coordinates of their positions and to extract available colors and magnitudes. We obtained correlations to convert colors and magnitudes from different systems into the common Sloan Digital Sky Survey system to facilitate the comparative analysis. We showed the quantitative relations describing the color-magnitude trends of galaxies in the core and the outskirts of the cluster. We confirmed that the inner and outer populations of ultra-diffuse galaxies exhibit an offset similar to the normal red sequence galaxies. We presented an initial assessment of stellar population ages and metallicities which correspond to the obtained color offsets. We surveyed the available images of the cluster for outliers, merger candidates, and candidate ultra-diffuse galaxies. We conclude that ultra-diffuse galaxies are an important part of the Coma cluster evolutionary history and future work is needed especially in obtaining spectroscopic data of a larger number of these dim galaxies.

Oxygen transport in off-stoichiometric uranium dioxide mediated by defect clustering dynamics

DOE PAGES

Yu, Jianguo; Bai, Xian -Ming; El-Azab, Anter; ...

2015-03-05

In this study, oxygen transport is central to many properties of oxides such as stoichiometric changes, phase transformation and ionic conductivity. In this paper, we report a mechanism for oxygen transport in uranium dioxide (UO 2) in which the kinetics is mediated by defect clustering dynamics. In particular, the kinetic Monte Carlo (KMC) method has been used to investigate the kinetics of oxygen transport in UO 2 under the condition of creation and annihilation of oxygen vacancies and interstitials as well as oxygen interstitial clustering, with variable offstoichiometry and temperature conditions. It is found that in hypo-stoichiometric UO 2-x, oxygenmore » transport is well described by the vacancy diffusion mechanism while in hyper-stoichiometric UO 2+x, oxygen interstitial cluster diffusion contributes significantly to oxygen transport kinetics, particularly at high temperatures and high off-stoichiometry levels. It is also found that diinterstitial clusters and single interstitials play dominant roles in oxygen diffusion while other larger clusters have negligible contributions. However, the formation, coalescence and dissociation of these larger clusters indirectly affects the overall oxygen diffusion due to their interactions with mono and di-interstitials, thus providing a explanation of the experimental observation of saturation or even drop of oxygen diffusivity at high off-stoichiometry.« less

Optical amplification of photothermal therapy with gold nanoparticles and nanoclusters

NASA Astrophysics Data System (ADS)

Khlebtsov, Boris; Zharov, Vladimir; Melnikov, Andrei; Tuchin, Valery; Khlebtsov, Nikolai

2006-10-01

Recently, several groups (Anderson, Halas, Zharov, and their co-workers, 2003; El-Sayed and co-workers, 2006) demonstrated, through pioneering results, the great potential of photothermal (PT) therapy for the selective treatment of cancer cells, bacteria, viruses, and DNA targeted with gold nanospheres, nanoshells, nanorods, and nanosphere clusters. However, the current understanding of the relationship between the nanoparticle/cluster parameters (size, shape, particle/cluster structure, etc) and the efficiency of PT therapy is limited. Here, we report theoretical simulations aimed at finding the optimal single-particle and cluster structures to achieve its maximal absorption, which is crucial for PT therapeutic effects. To characterize the optical amplification in laser-induced thermal effects, we introduce relevant parameters such as the ratio of the absorption cross section to the gold mass of a single-particle structure and absorption amplification, defined as the ratio of cluster absorption to the total absorption of non-interacting particles. We consider the absorption efficiency of single nanoparticles (gold spheres, rods, and silica/gold nanoshells), linear chains, 2D lattice arrays, 3D random volume clusters, and the random aggregated N-particle ensembles on the outer surface of a larger dielectric sphere, which mimic aggregation of nanosphere bioconjugates on or within cancer cells. The cluster particles are bare or biopolymer-coated gold nanospheres. The light absorption of cluster structures is studied by using the generalized multiparticle Mie solution and the T-matrix method. The gold nanoshells with (silica core diameter)/(gold shell thickness) parameters of (50-100)/(3-8) nm and nanorods with minor/major sizes of (15-20)/(50-70) nm are shown to be more efficient PT labels and sensitizers than the equivolume solid single gold spheres. In the case of nanosphere clusters, the interparticle separations and the short linear-chain fragments are the main structural parameters determining the absorption efficiency and its spectral shifting to the red. Although we have not found a noticeable dependence of absorption amplification on the cluster sphere size, 20-40 nm particles are found to be most effective, in accordance with our experimental observations. The long-wavelength absorption efficiency of random clusters increases with the cluster particle number N at small N and reveals a saturation behaviour at N>20.

Price Formation Based on Particle-Cluster Aggregation

NASA Astrophysics Data System (ADS)

Wang, Shijun; Zhang, Changshui

In the present work, we propose a microscopic model of financial markets based on particle-cluster aggregation on a two-dimensional small-world information network in order to simulate the dynamics of the stock markets. "Stylized facts" of the financial market time series, such as fat-tail distribution of returns, volatility clustering and multifractality, are observed in the model. The results of the model agree with empirical data taken from historical records of the daily closures of the NYSE composite index.

Structural disorder in the decagonal Al-Co-Ni. II. Modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kobas, Miroslav; Weber, Thomas; Steurer, Walter

2005-06-01

The hydrodynamic theory of phasonic and phononic disorder is applied successfully to describe the short-range disordered structure of a decagonal Al{sub 71.5}Co{sub 14.6}Ni{sub 13.9} quasicrystal (Edagawa phase, superstructure type I). Moreover, model calculations demonstrate that the main features of diffuse scattering can be equally well described by phasonic disorder and fivefold orientational disorder of clusters. The calculations allow us to distinguish the different cluster types published so far and the best agreement with experimental data could be achieved with the mirror-symmetric Abe cluster. Modeling of phason diffuse scattering associated with the S1 and S2 superstructure reflections indicate disorder of superclusters.more » The former show basically intercluster correlations inside quasiperiodic layers, while the latter exhibit intra- and inter-cluster correlations, both between adjacent and inside quasiperiodic layers. The feasibility, potential, and limits of the Patterson method in combination with the punch-and-fill method employed is shown on the example of a phasonic disordered rhombic Penrose tiling. A variation of the elastic constants does not change qualitatively the way phasonic disorder is realized in the local quasicrystalline structure. For the same model system it is also shown that phasonic fluctuations of the atomic surfaces yield average clusters in the cut space, which correspond to fivefold orientationally disordered clusters.« less

First passage times in homogeneous nucleation: Dependence on the total number of particles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yvinec, Romain; Bernard, Samuel; Pujo-Menjouet, Laurent

2016-01-21

Motivated by nucleation and molecular aggregation in physical, chemical, and biological settings, we present an extension to a thorough analysis of the stochastic self-assembly of a fixed number of identical particles in a finite volume. We study the statistics of times required for maximal clusters to be completed, starting from a pure-monomeric particle configuration. For finite volumes, we extend previous analytical approaches to the case of arbitrary size-dependent aggregation and fragmentation kinetic rates. For larger volumes, we develop a scaling framework to study the first assembly time behavior as a function of the total quantity of particles. We find thatmore » the mean time to first completion of a maximum-sized cluster may have a surprisingly weak dependence on the total number of particles. We highlight how higher statistics (variance, distribution) of the first passage time may nevertheless help to infer key parameters, such as the size of the maximum cluster. Finally, we present a framework to quantify formation of macroscopic sized clusters, which are (asymptotically) very unlikely and occur as a large deviation phenomenon from the mean-field limit. We argue that this framework is suitable to describe phase transition phenomena, as inherent infrequent stochastic processes, in contrast to classical nucleation theory.« less

First passage times in homogeneous nucleation: Dependence on the total number of particles

NASA Astrophysics Data System (ADS)

Yvinec, Romain; Bernard, Samuel; Hingant, Erwan; Pujo-Menjouet, Laurent

2016-01-01

Motivated by nucleation and molecular aggregation in physical, chemical, and biological settings, we present an extension to a thorough analysis of the stochastic self-assembly of a fixed number of identical particles in a finite volume. We study the statistics of times required for maximal clusters to be completed, starting from a pure-monomeric particle configuration. For finite volumes, we extend previous analytical approaches to the case of arbitrary size-dependent aggregation and fragmentation kinetic rates. For larger volumes, we develop a scaling framework to study the first assembly time behavior as a function of the total quantity of particles. We find that the mean time to first completion of a maximum-sized cluster may have a surprisingly weak dependence on the total number of particles. We highlight how higher statistics (variance, distribution) of the first passage time may nevertheless help to infer key parameters, such as the size of the maximum cluster. Finally, we present a framework to quantify formation of macroscopic sized clusters, which are (asymptotically) very unlikely and occur as a large deviation phenomenon from the mean-field limit. We argue that this framework is suitable to describe phase transition phenomena, as inherent infrequent stochastic processes, in contrast to classical nucleation theory.

Genuine non-self-averaging and ultraslow convergence in gelation.

PubMed

Cho, Y S; Mazza, M G; Kahng, B; Nagler, J

2016-08-01

In irreversible aggregation processes droplets or polymers of microscopic size successively coalesce until a large cluster of macroscopic scale forms. This gelation transition is widely believed to be self-averaging, meaning that the order parameter (the relative size of the largest connected cluster) attains well-defined values upon ensemble averaging with no sample-to-sample fluctuations in the thermodynamic limit. Here, we report on anomalous gelation transition types. Depending on the growth rate of the largest clusters, the gelation transition can show very diverse patterns as a function of the control parameter, which includes multiple stochastic discontinuous transitions, genuine non-self-averaging and ultraslow convergence of the transition point. Our framework may be helpful in understanding and controlling gelation.

Pattern formation in a model for mountain pine beetle dispersal: linking model predictions to data.

PubMed

Strohm, S; Tyson, R C; Powell, J A

2013-10-01

Pattern formation occurs in a wide range of biological systems. This pattern formation can occur in mathematical models because of diffusion-driven instability or due to the interaction between reaction, diffusion, and chemotaxis. In this paper, we investigate the spatial pattern formation of attack clusters in a system for Mountain Pine Beetle. The pattern formation (aggregation) of the Mountain Pine Beetle in order to attack susceptible trees is crucial for their survival and reproduction. We use a reaction-diffusion equation with chemotaxis to model the interaction between Mountain Pine Beetle, Mountain Pine Beetle pheromones, and susceptible trees. Mathematical analysis is utilized to discover the spacing in-between beetle attacks on the susceptible landscape. The model predictions are verified by analysing aerial detection survey data of Mountain Pine Beetle Attack from the Sawtooth National Recreation Area. We find that the distance between Mountain Pine Beetle attack clusters predicted by our model closely corresponds to the observed attack data in the Sawtooth National Recreation Area. These results clarify the spatial mechanisms controlling the transition from incipient to epidemic populations and may lead to control measures which protect forests from Mountain Pine Beetle outbreak.

Modeling the Movement of Homicide by Type to Inform Public Health Prevention Efforts

PubMed Central

Grady, Sue; Pizarro, Jesenia M.; Melde, Chris

2015-01-01

Objectives. We modeled the spatiotemporal movement of hotspot clusters of homicide by motive in Newark, New Jersey, to investigate whether different homicide types have different patterns of clustering and movement. Methods. We obtained homicide data from the Newark Police Department Homicide Unit’s investigative files from 1997 through 2007 (n = 560). We geocoded the address at which each homicide victim was found and recorded the date of and the motive for the homicide. We used cluster detection software to model the spatiotemporal movement of statistically significant homicide clusters by motive, using census tract and month of occurrence as the spatial and temporal units of analysis. Results. Gang-motivated homicides showed evidence of clustering and diffusion through Newark. Additionally, gang-motivated homicide clusters overlapped to a degree with revenge and drug-motivated homicide clusters. Escalating dispute and nonintimate familial homicides clustered; however, there was no evidence of diffusion. Intimate partner and robbery homicides did not cluster. Conclusions. By tracking how homicide types diffuse through communities and determining which places have ongoing or emerging homicide problems by type, we can better inform the deployment of prevention and intervention efforts. PMID:26270315

Hierarchical clustering method for improved prostate cancer imaging in diffuse optical tomography

NASA Astrophysics Data System (ADS)

Kavuri, Venkaiah C.; Liu, Hanli

2013-03-01

We investigate the feasibility of trans-rectal near infrared (NIR) based diffuse optical tomography (DOT) for early detection of prostate cancer using a transrectal ultrasound (TRUS) compatible imaging probe. For this purpose, we designed a TRUS-compatible, NIR-based image system (780nm), in which the photo diodes were placed on the trans-rectal probe. DC signals were recorded and used for estimating the absorption coefficient. We validated the system using laboratory phantoms. For further improvement, we also developed a hierarchical clustering method (HCM) to improve the accuracy of image reconstruction with limited prior information. We demonstrated the method using computer simulations laboratory phantom experiments.

Effect of Dust Coagulation Dynamics on the Geometry of Aggregates

NASA Technical Reports Server (NTRS)

Nakamura, R.

1996-01-01

Master equation gives a more fundamental description of stochastic coagulation processes rather than popular Smoluchowski's equation. In order to examine the effect of the dynamics on the geometry of resulting aggregates, we study Master equation with a rigorous Monte Carlo algorithm. It is found that Cluster-Cluster aggregation model is a good approximation of orderly growth and the aggregates have fluffy structures with a fractal dimension approx. 2. A scaling analysis of Smoluchowski's equation also supports this conclusion.

On Defect Cluster Aggregation and Non-Reducibilty in Tin-Doped Indium Oxide

NASA Astrophysics Data System (ADS)

Warschkow, Oliver; Ellis, Donald E.; Gonzalez, Gabriela; Mason, Thomas O.

2003-03-01

The conductivity of tin-doped indium oxide (ITO), a transparent conductor, is critically dependent on the amount of tin-doping and oxygen partial pressure during preparation and annealing. Frank and Kostlin (Appl. Phys. A 27 (1982) 197-206) rationalized the carrier concentration dependence by postulating the formation of two types of neutral defect clusters at medium tin-doping levels: "Reducible" and "non-reducible" defect clusters; so named to indicate their ability to create carriers under reduction. According to Frank and Kostlin, both are composed of a single oxygen interstitial and two tin atoms substituting for indium, positioned in non-nearest and nearest coordination, respectively. This present work, seeking to distinguish reducible and non-reducible clusters by use of an atomistic model, finds only a weak correlation of oxygen interstitial binding energies with the relative positioning of dopants. Instead, the number of tin-dopants in the vicinity of the interstitial has a much larger effect on how strongly it is bound, a simple consequence of Coulomb interactions. We postulate that oxygen interstitials become non-reducible when clustered with three or more Sn_In. This occurs at higher doping levels as reducible clusters aggregate and share tin atoms. A simple probabilistic model, estimating the average number of clusters so aggregated, provides a qualitatively correct description of the carrier density in reduced ITO as a function of Sn doping level.

Diffusion Of Mass In Evaporating Multicomponent Drops

NASA Technical Reports Server (NTRS)

Bellan, Josette; Harstad, Kenneth G.

1992-01-01

Report summarizes study of diffusion of mass and related phenomena occurring in evaporation of dense and dilute clusters of drops of multicomponent liquids intended to represent fuels as oil, kerosene, and gasoline. Cluster represented by simplified mathematical model, including global conservation equations for entire cluster and conditions on boundary between cluster and ambient gas. Differential equations of model integrated numerically. One of series of reports by same authors discussing evaporation and combustion of sprayed liquid fuels.

Collective behavior in two-dimensional biological systems: Receptor clustering and beta-sheet aggregation

NASA Astrophysics Data System (ADS)

Guo, Chinlin

We studied two particular biomedical systems which exhibit collective molecular behavior. One is clustering of tumor necrosis factor receptor I (TNFR1), and another is β-sheet folding and aggregation. Receptor clustering has been shown to be a crucial step in many signaling events but its biological meaning has not been adequately addressed. Here, via a simple lattice model, we show how cells use this clustering machinery to enhance sensitivity as well as robustness. On the other hand, intracellular deposition of aggregated protein rich in β-sheet is a prominent cytopathological feature of most neurodegenerative diseases. How this aggregation occurs and how it responds to therapy is not completely understood. Here, we started from a reconstruction of the H-bond potential and carry out a full investigation of β-sheet thermodynamics as well as kinetics. We show that β-sheet aggregation is most likely due to molecular stacking and found that the minimal length of an aggregate mutant polymer corresponds well with the number observed in adult Huntington's disease. We have also shown that molecular agents such as dendrimers might fail at high-dose therapy; instead, a potential therapy strategy is to block β-turn formation. Our predictions can be used for future experimental tests and clinical trials.

Aggregation and Gelation of Aromatic Polyamides with Parallel and Anti-parallel Alignment of Molecular Dipole Along the Backbone

NASA Astrophysics Data System (ADS)

Zhu, Dan; Shang, Jing; Ye, Xiaodong; Shen, Jian

2016-12-01

The understanding of macromolecular structures and interactions is important but difficult, due to the facts that a macromolecules are of versatile conformations and aggregate states, which vary with environmental conditions and histories. In this work two polyamides with parallel or anti-parallel dipoles along the linear backbone, named as ABAB (parallel) and AABB (anti-parallel) have been studied. By using a combination of methods, the phase behaviors of the polymers during the aggregate and gelation, i.e., the forming or dissociation processes of nuclei and fibril, cluster of fibrils, and cluster-cluster aggregation have been revealed. Such abundant phase behaviors are dominated by the inter-chain interactions, including dispersion, polarity and hydrogen bonding, and correlatd with the solubility parameters of solvents, the temperature, and the polymer concentration. The results of X-ray diffraction and fast-mode dielectric relaxation indicate that AABB possesses more rigid conformation than ABAB, and because of that AABB aggregates are of long fibers while ABAB is of hairy fibril clusters, the gelation concentration in toluene is 1 w/v% for AABB, lower than the 3 w/v% for ABAB.

Inhibition of Protein Aggregation: Supramolecular Assemblies of Arginine Hold the Key

PubMed Central

Das, Utpal; Hariprasad, Gururao; Ethayathulla, Abdul S.; Manral, Pallavi; Das, Taposh K.; Pasha, Santosh; Mann, Anita; Ganguli, Munia; Verma, Amit K.; Bhat, Rajiv; Chandrayan, Sanjeev Kumar; Ahmed, Shubbir; Sharma, Sujata; Kaur, Punit; Singh, Tej P.; Srinivasan, Alagiri

2007-01-01

Background Aggregation of unfolded proteins occurs mainly through the exposed hydrophobic surfaces. Any mechanism of inhibition of this aggregation should explain the prevention of these hydrophobic interactions. Though arginine is prevalently used as an aggregation suppressor, its mechanism of action is not clearly understood. We propose a mechanism based on the hydrophobic interactions of arginine. Methodology We have analyzed arginine solution for its hydrotropic effect by pyrene solubility and the presence of hydrophobic environment by 1-anilino-8-naphthalene sulfonic acid fluorescence. Mass spectroscopic analyses show that arginine forms molecular clusters in the gas phase and the cluster composition is dependent on the solution conditions. Light scattering studies indicate that arginine exists as clusters in solution. In the presence of arginine, the reverse phase chromatographic elution profile of Alzheimer's amyloid beta 1-42 (Aβ1-42) peptide is modified. Changes in the hydrodynamic volume of Aβ1-42 in the presence of arginine measured by size exclusion chromatography show that arginine binds to Aβ1-42. Arginine increases the solubility of Aβ1-42 peptide in aqueous medium. It decreases the aggregation of Aβ1-42 as observed by atomic force microscopy. Conclusions Based on our experimental results we propose that molecular clusters of arginine in aqueous solutions display a hydrophobic surface by the alignment of its three methylene groups. The hydrophobic surfaces present on the proteins interact with the hydrophobic surface presented by the arginine clusters. The masking of hydrophobic surface inhibits protein-protein aggregation. This mechanism is also responsible for the hydrotropic effect of arginine on various compounds. It is also explained why other amino acids fail to inhibit the protein aggregation. PMID:18000547

Matilda: A mass filtered nanocluster source

NASA Astrophysics Data System (ADS)

Kwon, Gihan

Cluster science provides a good model system for the study of the size dependence of electronic properties, chemical reactivity, as well as magnetic properties of materials. One of the main interests in cluster science is the nanoscale understanding of chemical reactions and selectivity in catalysis. Therefore, a new cluster system was constructed to study catalysts for applications in renewable energy. Matilda, a nanocluster source, consists of a cluster source and a Retarding Field Analyzer (RFA). A moveable AJA A310 Series 1"-diameter magnetron sputtering gun enclosed in a water cooled aggregation tube served as the cluster source. A silver coin was used for the sputtering target. The sputtering pressure in the aggregation tube was controlled, ranging from 0.07 to 1torr, using a mass flow controller. The mean cluster size was found to be a function of relative partial pressure (He/Ar), sputtering power, and aggregation length. The kinetic energy distribution of ionized clusters was measured with the RFA. The maximum ion energy distribution was 2.9 eV/atom at a zero pressure ratio. At high Ar flow rates, the mean cluster size was 20 ˜ 80nm, and at a 9.5 partial pressure ratio, the mean cluster size was reduced to 1.6nm. Our results showed that the He gas pressure can be optimized to reduce the cluster size variations. Results from SIMION, which is an electron optics simulation package, supported the basic function of an RFA, a three-element lens and the magnetic sector mass filter. These simulated results agreed with experimental data. For the size selection experiment, the channeltron electron multiplier collected ionized cluster signal at different positions during Ag deposition on a TEM grid for four and half hours. The cluster signal was high at the position for neutral clusters, which was not bent by a magnetic field, and the signal decreased rapidly far away from the neutral cluster region. For cluster separation according to mass to charge ratio in a magnetic sector mass filter, the ion energy of the cluster and its distribution must be precisely controlled by acceleration or deceleration. To verify the size separation, a high resolution microscope was required. Matilda provided narrow particle sized distribution from atomic scale to 4nm in size with different pressure ratio without additional mass filter. It is very economical way to produce relatively narrow particle size distribution.

Exact solutions for mass-dependent irreversible aggregations.

PubMed

Son, Seung-Woo; Christensen, Claire; Bizhani, Golnoosh; Grassberger, Peter; Paczuski, Maya

2011-10-01

We consider the mass-dependent aggregation process (k+1)X→X, given a fixed number of unit mass particles in the initial state. One cluster is chosen proportional to its mass and is merged into one, either with k neighbors in one dimension, or--in the well-mixed case--with k other clusters picked randomly. We find the same combinatorial exact solutions for the probability to find any given configuration of particles on a ring or line, and in the well-mixed case. The mass distribution of a single cluster exhibits scaling laws and the finite-size scaling form is given. The relation to the classical sum kernel of irreversible aggregation is discussed.

Multiple relaxations of the cluster surface diffusion in a homoepitaxial SrTiO3 layer

NASA Astrophysics Data System (ADS)

Woo, Chang-Su; Chu, Kanghyun; Song, Jong-Hyun; Yang, Chan-Ho

2018-03-01

We examine the surface diffusion process of adatomic clusters on a (001)-oriented SrTiO3 single crystal using reflection high energy electron diffraction (RHEED). We find that the recovery curve of the RHEED intensity acquired after a homoepitaxial half-layer growth can be accurately fit into a double exponential function, indicating the existence of two dominant relaxation mechanisms. The characteristic relaxation times at selected growth temperatures are investigated to determine the diffusion activation barriers of 0.67 eV and 0.91 eV, respectively. The Monte Carlo simulation of the cluster hopping model suggests that the decrease in the number of dimeric and trimeric clusters during surface diffusion is the origin of the observed relaxation phenomena.

Nucleation and growth of Ag on Sb-terminated Ge( 1 0 0 )

NASA Astrophysics Data System (ADS)

Chan, L. H.; Altman, E. I.

2002-06-01

The effect of Sb on Ag growth on Ge(1 0 0) was characterized using scanning tunneling microscopy, low energy electron diffraction, and Auger electron spectroscopy. Silver was found to immediately form three-dimensional clusters on the Sb-covered surface over the entire temperature range studied (320-570 K), thus the growth was Volmer-Weber. Regardless of the deposition conditions, there was no evidence that Sb segregated to the Ag surface, despite Sb having a lower surface tension than either Ag or Ge. The failure of Sb to segregate to the surface could be understood in terms of the much stronger interaction between Sb and Ge versus Ag and Ge creating a driving force to maintain an Sb-Ge interface. Silver nucleation on Sb/Ge(1 0 0) was characterized by measuring the Ag cluster density as a function of deposition rate. The results revealed that the cluster density was nearly independent of the deposition rate below 420 K, indicating that heterogeneous nucleation at defects in the Sb-terminated surface competed with homogeneous nucleation. At higher temperatures, the defects were less effective in trapping diffusing Ag atoms and the dependence of the cluster density on deposition rate suggested a critical size of at least two. For temperatures above 420 K, the Ag diffusion barrier plus the dissociation energy of the critical cluster was estimated by measuring the cluster density as a function of temperature; the results suggested a value of 0.84±0.1 eV which is significantly higher than values reported for Ag nucleation on Sb-free surfaces. In comparison to the bare Ge surface, Ag formed a higher density of smaller, lower clusters when Sb was present. Below 420 K the higher cluster density could be attributed to nucleation at defects in the Sb layer while at higher temperatures the high diffusion barrier restricted the cluster size and density. Although Sb does not act as a surfactant in this system since it does not continuously float to the surface and the growth is not layer-by-layer, adding Sb was found to be useful in limiting the Ag cluster size and height which led to smoother, more continuous Ag films and in preventing the formation of metastable Ag-Ge surface alloys.

Occurrence of Radio Minihalos in a Mass-Limited Sample of Galaxy Clusters

NASA Technical Reports Server (NTRS)

Giacintucci, Simona; Markevitch, Maxim; Cassano, Rossella; Venturi, Tiziana; Clarke, Tracy E.; Brunetti, Gianfranco

2017-01-01

We investigate the occurrence of radio minihalos-diffuse radio sources of unknown origin observed in the cores of some galaxy clusters-in a statistical sample of 58 clusters drawn from the Planck Sunyaev-Zeldovich cluster catalog using a mass cut (M(sub 500) greater than 6 x 10(exp 14) solar mass). We supplement our statistical sample with a similarly sized nonstatistical sample mostly consisting of clusters in the ACCEPT X-ray catalog with suitable X-ray and radio data, which includes lower-mass clusters. Where necessary (for nine clusters), we reanalyzed the Very Large Array archival radio data to determine whether a minihalo is present. Our total sample includes all 28 currently known and recently discovered radio minihalos, including six candidates. We classify clusters as cool-core or non-cool-core according to the value of the specific entropy floor in the cluster center, rederived or newly derived from the Chandra X-ray density and temperature profiles where necessary (for 27 clusters). Contrary to the common wisdom that minihalos are rare, we find that almost all cool cores-at least 12 out of 15 (80%)-in our complete sample of massive clusters exhibit minihalos. The supplementary sample shows that the occurrence of minihalos may be lower in lower-mass cool-core clusters. No minihalos are found in non-cool cores or "warm cores." These findings will help test theories of the origin of minihalos and provide information on the physical processes and energetics of the cluster cores.

High-Performance and Traditional Multicrystalline Silicon: Comparing Gettering Responses and Lifetime-Limiting Defects

DOE Office of Scientific and Technical Information (OSTI.GOV)

Castellanos, Sergio; Ekstrom, Kai E.; Autruffe, Antoine

2016-05-01

In recent years, high-performance multicrystalline silicon (HPMC-Si) has emerged as an attractive alternative to traditional ingot-based multicrystalline silicon (mc-Si), with a similar cost structure but improved cell performance. Herein, we evaluate the gettering response of traditional mc-Si and HPMC-Si. Microanalytical techniques demonstrate that HPMC-Si and mc-Si share similar lifetime-limiting defect types but have different relative concentrations and distributions. HPMC-Si shows a substantial lifetime improvement after P-gettering compared with mc-Si, chiefly because of lower area fraction of dislocation-rich clusters. In both materials, the dislocation clusters and grain boundaries were associated with relatively higher interstitial iron point-defect concentrations after diffusion, which ismore » suggestive of dissolving metal-impurity precipitates. The relatively fewer dislocation clusters in HPMC-Si are shown to exhibit similar characteristics to those found in mc-Si. Given similar governing principles, a proxy to determine relative recombination activity of dislocation clusters developed for mc-Si is successfully transferred to HPMC-Si.« less

Toward an empirical definition of pediatric PTSD: the phenomenology of PTSD symptoms in youth.

PubMed

Carrion, Victor G; Weems, Carl F; Ray, Rebecca; Reiss, Allan L

2002-02-01

To examine the frequency and intensity of posttraumatic stress disorder (PTSD) symptoms and their relation to clinical impairment, to examine the requirement of meeting all DSM-IV symptom cluster criteria (i.e., criteria B, C, D), and to examine the aggregation of PTSD symptom clusters across developmental stages. Fifty-nine children between the ages of 7 and 14 years with a history of trauma and PTSD symptoms were assessed with the Clinician-Administered PTSD Scale for Children and Adolescents. Data support the utility of distinguishing between the frequency and the intensity of symptoms in the investigation of the phenomenology of pediatric PTSD. Children fulfilling requirements for two symptom clusters did not differ significantly from children meeting all three cluster criteria with regard to impairment and distress. Reexperience (cluster B) showed increased aggregation with avoidance and numbing (cluster C) and hyperarousal (cluster D) in the later stages of puberty. Frequency and intensity of symptoms may both contribute to the phenomenology of pediatric PTSD. Children with subthreshold criteria for PTSD demonstrate substantial functional impairment and distress.

Self-aggregation in scaled principal component space

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ding, Chris H.Q.; He, Xiaofeng; Zha, Hongyuan

2001-10-05

Automatic grouping of voluminous data into meaningful structures is a challenging task frequently encountered in broad areas of science, engineering and information processing. These data clustering tasks are frequently performed in Euclidean space or a subspace chosen from principal component analysis (PCA). Here we describe a space obtained by a nonlinear scaling of PCA in which data objects self-aggregate automatically into clusters. Projection into this space gives sharp distinctions among clusters. Gene expression profiles of cancer tissue subtypes, Web hyperlink structure and Internet newsgroups are analyzed to illustrate interesting properties of the space.

Effect of centrifugation on dynamic susceptibility of magnetic fluids

NASA Astrophysics Data System (ADS)

Pshenichnikov, Alexander; Lebedev, Alexander; Lakhtina, Ekaterina; Kuznetsov, Andrey

2017-06-01

The dispersive composition, dynamic susceptibility and spectrum of times of magnetization relaxation for six samples of magnetic fluid obtained by centrifuging two base colloidal solutions of the magnetite in kerosene was investigated experimentally. The base solutions differed by the concentration of the magnetic phase and the width of the particle size distribution. The procedure of cluster analysis allowing one to estimate the characteristic sizes of aggregates with uncompensated magnetic moments was described. The results of the magnetogranulometric and cluster analyses were discussed. It was shown that centrifugation has a strong effect on the physical properties of the separated fractions, which is related to the spatial redistribution of particles and multi-particle aggregates. The presence of aggregates in magnetic fluids is interpreted as the main reason of low-frequency (0.1-10 kHz) dispersion of the dynamic susceptibility. The obtained results count in favor of using centrifugation as an effective means of changing the dynamic susceptibility over wide limits and obtaining fluids with the specified type of susceptibility dispersion.

Simulating the minimum core for hydrophobic collapse in globular proteins.

PubMed Central

Tsai, J.; Gerstein, M.; Levitt, M.

1997-01-01

To investigate the nature of hydrophobic collapse considered to be the driving force in protein folding, we have simulated aqueous solutions of two model hydrophobic solutes, methane and isobutylene. Using a novel methodology for determining contacts, we can precisely follow hydrophobic aggregation as it proceeds through three stages: dispersed, transition, and collapsed. Theoretical modeling of the cluster formation observed by simulation indicates that this aggregation is cooperative and that the simulations favor the formation of a single cluster midway through the transition stage. This defines a minimum solute hydrophobic core volume. We compare this with protein hydrophobic core volumes determined from solved crystal structures. Our analysis shows that the solute core volume roughly estimates the minimum core size required for independent hydrophobic stabilization of a protein and defines a limiting concentration of nonpolar residues that can cause hydrophobic collapse. These results suggest that the physical forces driving aggregation of hydrophobic molecules in water is indeed responsible for protein folding. PMID:9416609

Relativistic inverse Compton scattering of photons from the early universe.

PubMed

Malu, Siddharth; Datta, Abhirup; Colafrancesco, Sergio; Marchegiani, Paolo; Subrahmanyan, Ravi; Narasimha, D; Wieringa, Mark H

2017-12-05

Electrons at relativistic speeds, diffusing in magnetic fields, cause copious emission at radio frequencies in both clusters of galaxies and radio galaxies through non-thermal radiation emission called synchrotron. However, the total power radiated through this mechanism is ill constrained, as the lower limit of the electron energy distribution, or low-energy cutoffs, for radio emission in galaxy clusters and radio galaxies, have not yet been determined. This lower limit, parametrized by the lower limit of the electron momentum - p min - is critical for estimating the total energetics of non-thermal electrons produced by cluster mergers or injected by radio galaxy jets, which impacts the formation of large-scale structure in the universe, as well as the evolution of local structures inside galaxy clusters. The total pressure due to the relativistic, non-thermal population of electrons can be measured using the Sunyaev-Zel'dovich Effect, and is critically dependent on p min , making the measurement of this non-thermal pressure a promising technique to estimate the electron low-energy cutoff. We present here the first unambiguous detection of this Sunyaev-Zel'dovich Effect for a non-thermal population of electrons in a radio galaxy jet/lobe, located at a significant distance away from the center of the Bullet cluster of galaxies.

Detection of a Double Relic in the Torpedo Cluster: SPT-CL J0245-5302

NASA Astrophysics Data System (ADS)

Zheng, Q.; Johnston-Hollitt, M.; Duchesne, S. W.; Li, W. T.

2018-06-01

The Torpedo cluster, SPT-CL J0245-5302 (S0295) is a massive, merging cluster at a redshift of z = 0.300, which exhibits a strikingly similar morphology to the Bullet cluster 1E 0657-55.8 (z = 0.296), including a classic bow shock in the cluster's intra-cluster medium revealed by Chandra X-ray observations. We present Australia Telescope Compact Array data centred at 2.1 GHz and Murchison Widefield Array data at frequencies between 72 MHz and 231 MHz which we use to study the properties of the cluster. We characterise a number of discrete and diffuse radio sources in the cluster, including the detection of two previously unknown radio relics on the cluster periphery. The average spectral index of the diffuse emission between 70 MHz and 3.1 GHz is α =-1.63_{-0.10}^{+0.10} and a radio-derived Mach number for the shock in the west of the cluster is calculated as M = 2.04. The Torpedo cluster is thus a double relic system at moderate redshift.

A comparison between observed and analytical velocity dispersion profiles of 20 nearby galaxy clusters

NASA Astrophysics Data System (ADS)

Khan, Mohammad S.; Abdullah, Mohamed H.; Ali, Gamal B.

2014-05-01

We derive analytical expression for the velocity dispersion of galaxy clusters, using the statistical mechanical approach. We compare the observed velocity dispersion profiles for 20 nearby ( z≤0.1) galaxy clusters with the analytical ones. It is interesting to find that the analytical results closely match with the observed velocity dispersion profiles only if the presence of the diffuse matter in clusters is taken into consideration. This takes us to introduce a new approach to detect the ratio of diffuse mass, M diff , within a galaxy cluster. For the present sample, the ratio f= M diff / M, where M the cluster's total mass is found to has an average value of 45±12 %. This leads us to the result that nearly 45 % of the cluster mass is impeded outside the galaxies, while around 55 % of the cluster mass is settled in the galaxies.

Low-velocity collision behaviour of clusters composed of sub-millimetre sized dust aggregates

NASA Astrophysics Data System (ADS)

Brisset, J.; Heißelmann, D.; Kothe, S.; Weidling, R.; Blum, J.

2017-07-01

Context. The experiment results presented apply to the very first stages of planet formation, when small dust aggregates collide in the protoplanetary disc and grow into bigger clusters. In 2011, before flying on the REXUS 12 suborbital rocket in 2012, the Suborbital Particle and Aggregation Experiment (SPACE) performed drop tower flights. We present the results of this first microgravity campaign. Aims: The experiments presented aim to measure the outcome of collisions between sub-mm sized protoplanetary dust aggregate analogues. We also observed the clusters formed from these aggregates and their collision behaviour. Methods: The experiments were performed at the drop tower in Bremen. The protoplanetary dust analogue materials were micrometre-sized monodisperse and polydisperse SiO2 particles prepared into aggregates with sizes between 120 μm and 250 μm. One of the dust samples contained aggregates that were previously compacted through repeated bouncing. During three flights of 9 s of microgravity each, individual collisions between aggregates and the formation of clusters of up to a few millimetres in size were observed. In addition, the collisions of clusters with the experiment cell walls leading to compaction or fragmentation were recorded. Results: We observed collisions amongst dust aggregates and collisions between dust clusters and the cell aluminium walls at speeds ranging from about 0.1 cm s-1 to 20 cm s-1. The velocities at which sticking occurred ranged from 0.18 to 5.0 cm s-1 for aggregates composed of monodisperse dust, with an average value of 2.1 ± 0.9 cm s-1 for reduced masses ranging from 1.2 × 10-6 to 1.8 × 10-3 g with an average value of 2.2+16-2.1 × 10-4 g. The velocities at which bouncing occurred ranged from 1.9 to 11.9 cm s-1 for the same aggregates with an average of 5.9 ± 3.2 cm s-1 for reduced masses ranging from 2.1 × 10-6 to 2.4 × 10-4 with an average of 7.8 ± 2.4 × 10-5 g. The velocities at which fragmentation occurred ranged from 4.9 to 23.8 cm s-1 for the same aggregates with an average of 10.1 ± 3.2 cm s-1 for reduced masses ranging from 1.2 × 10-5 to 1.2 × 10-3 with an average value of 4.2 ± 2.4 × 10-4 g. From the restructuring and fragmentation of clusters composed of dust aggregates colliding with the aluminium cell walls, we derived a collision recipe for dust aggregates ( 100 μm) following the model of Dominik & Tielens (1997, ApJ, 480, 647) developed for microscopic particles. We measured a critical rolling energy of 1.8 ± 0.9 × 10-13 J and a critical breaking energy of 3.5 ± 1.5 × 10-13 J for 100 μm-sized non-compacted aggregates. A movie associated to Fig. 3 is available at http://www.aanda.org

The peculiar cluster MACS J0417.5-1154 in the C and X-bands

NASA Astrophysics Data System (ADS)

Sandhu, Pritpal; Malu, Siddharth; Raja, Ramij; Datta, Abhirup

2018-06-01

We present 5.5 and 9.0 GHz Australia Telescope Compact Array (ATCA) observations of the cluster MACSJ0417.5-1154, one of the most massive galaxy clusters and one of the brightest in X-ray in the Massive Cluster Survey (MACS). We estimate diffuse emission at 5.5 and 9.0 GHz from our ATCA observations, and compare the results with the 235 MHz and 610 MHz GMRT observations and 1575 MHz VLA observations. We also estimate the diffuse emission at low frequencies from existing GLEAM survey data (using the MWA telescope (http://www.mwatelescope.org)), and find that the steepening reported in earlier studies may have been an artefact of underestimates of diffuse emission at low frequencies. High-frequency radio observations of galaxy cluster mergers therefore provide an important complement to low-frequency observations, not only for a probing the `on' and `off' state of radio halos in these mergers, but also to constrain energetics of cluster mergers. We comment on the future directions that further studies of this cluster can take.

Effects of lateral diffusion on morphology and dynamics of a microscopic lattice-gas model of pulsed electrodeposition.

PubMed

Frank, Stefan; Roberts, Daniel E; Rikvold, Per Arne

2005-02-08

The influence of nearest-neighbor diffusion on the decay of a metastable low-coverage phase (monolayer adsorption) in a square lattice-gas model of electrochemical metal deposition is investigated by kinetic Monte Carlo simulations. The phase-transformation dynamics are compared to the well-established Kolmogorov-Johnson-Mehl-Avrami theory. The phase transformation is accelerated by diffusion, but remains in accord with the theory for continuous nucleation up to moderate diffusion rates. At very high diffusion rates the phase-transformation kinetic shows a crossover to instantaneous nucleation. Then, the probability of medium-sized clusters is reduced in favor of large clusters. Upon reversal of the supersaturation, the adsorbate desorbs, but large clusters still tend to grow during the initial stages of desorption. Calculation of the free energy of subcritical clusters by enumeration of lattice animals yields a quasiequilibrium distribution which is in reasonable agreement with the simulation results. This is an improvement relative to classical droplet theory, which fails to describe the distributions, since the macroscopic surface tension is a bad approximation for small clusters.

A DISTANT RADIO MINI-HALO IN THE PHOENIX GALAXY CLUSTER

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van Weeren, R. J.; Andrade-Santos, F.; Forman, W. R.

We report the discovery of extended radio emission in the Phoenix cluster (SPT-CL J2344-4243, z = 0.596) with the Giant Metrewave Radio Telescope (GMRT) at 610 MHz. The diffuse emission extends over a region of at least 400-500 kpc and surrounds the central radio source of the Brightest Cluster Galaxy, but does not appear to be directly associated with it. We classify the diffuse emission as a radio mini-halo, making it the currently most distant mini-halo known. Radio mini-halos have been explained by synchrotron emitting particles re-accelerated via turbulence, possibly induced by gas sloshing generated from a minor merger event. Chandra observationsmore » show a non-concentric X-ray surface brightness distribution, which is consistent with this sloshing interpretation. The mini-halo has a flux density of 17 ± 5 mJy, resulting in a 1.4 GHz radio power of (10.4 ± 3.5) × 10{sup 24} W Hz{sup –1}. The combined cluster emission, which includes the central compact radio source, is also detected in a shallow GMRT 156 MHz observation and together with the 610 MHz data we compute a spectral index of –0.84 ± 0.12 for the overall cluster radio emission. Given that mini-halos typically have steeper radio spectra than cluster radio galaxies, this spectral index should be taken as an upper limit for the mini-halo.« less

Automating the expert consensus paradigm for robust lung tissue classification

NASA Astrophysics Data System (ADS)

Rajagopalan, Srinivasan; Karwoski, Ronald A.; Raghunath, Sushravya; Bartholmai, Brian J.; Robb, Richard A.

2012-03-01

Clinicians confirm the efficacy of dynamic multidisciplinary interactions in diagnosing Lung disease/wellness from CT scans. However, routine clinical practice cannot readily accomodate such interactions. Current schemes for automating lung tissue classification are based on a single elusive disease differentiating metric; this undermines their reliability in routine diagnosis. We propose a computational workflow that uses a collection (#: 15) of probability density functions (pdf)-based similarity metrics to automatically cluster pattern-specific (#patterns: 5) volumes of interest (#VOI: 976) extracted from the lung CT scans of 14 patients. The resultant clusters are refined for intra-partition compactness and subsequently aggregated into a super cluster using a cluster ensemble technique. The super clusters were validated against the consensus agreement of four clinical experts. The aggregations correlated strongly with expert consensus. By effectively mimicking the expertise of physicians, the proposed workflow could make automation of lung tissue classification a clinical reality.

Infrared Spectroscopy of Naphthalene Aggregation and Cluster Formation in Argon Matrices

NASA Technical Reports Server (NTRS)

Roser, J. E.; Allamondola, L. J.

2011-01-01

Fourier-transform mid-infrared absorption spectra of mixed argon/naphthalene matrices at 5 K are shown with ratios of argon-to-naphthalene that vary from 1000 to 0. These spectra show the changes as naphthalene clustering and aggregation occurs, with moderate spectral shifts affecting the C-H vibrational modes and relatively small or no shifts to the C-C and C-C-C vibrational modes. The possible contribution of homogeneous naphthalene clusters to the interstellar unidentified infrared bands is discussed. The contribution of polycyclic aromatic hydrocarbon (PAH) clusters to the 7.7 micron emission plateau and the blue shading of the 12.7 micron emission band are identified as promising candidates for future research. In addition, since PAH clusters are model components of Jupiter and Titan's atmospheres, the information presented here may also be applicable to the spectroscopy of these objects.

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…

Clustering on Magnesium Surfaces - Formation and Diffusion Energies.

PubMed

Chu, Haijian; Huang, Hanchen; Wang, Jian

2017-07-12

The formation and diffusion energies of atomic clusters on Mg surfaces determine the surface roughness and formation of faulted structure, which in turn affect the mechanical deformation of Mg. This paper reports first principles density function theory (DFT) based quantum mechanics calculation results of atomic clustering on the low energy surfaces {0001} and [Formula: see text]. In parallel, molecular statics calculations serve to test the validity of two interatomic potentials and to extend the scope of the DFT studies. On a {0001} surface, a compact cluster consisting of few than three atoms energetically prefers a face-centered-cubic stacking, to serve as a nucleus of stacking fault. On a [Formula: see text], clusters of any size always prefer hexagonal-close-packed stacking. Adatom diffusion on surface [Formula: see text] is high anisotropic while isotropic on surface (0001). Three-dimensional Ehrlich-Schwoebel barriers converge as the step height is three atomic layers or thicker. Adatom diffusion along steps is via hopping mechanism, and that down steps is via exchange mechanism.

Galaxy collisions as a mechanism of ultra diffuse galaxy (UDG) formation

NASA Astrophysics Data System (ADS)

Baushev, A. N.

2018-04-01

We suggest a possible mechanism of ultra diffuse galaxy formation: the UDGs may occur as a result of a central collision of galaxies. If the galaxies are young and contain a lot of gas, the collision may kick all the gas off the systems and thus strongly suppress any further star formation. As a result, the galaxies now have a very low surface brightness and other properties typical of the ultra diffuse galaxies. We use the Coma cluster (where numerous UDGs were recently discovered) to test the efficiency of the process. The mechanism works very well and can transform a significant fraction of the cluster population into ultra diffuse galaxies. The UDGs formed by the process concentrate towards the center of the cluster, and their globular cluster systems remain undamaged, in accordance with observational results. The projected surface density of UDGs in the cluster may help us to recognize the mechanism of UDG formation, or clarify relative contributions of several possible competitive mechanisms at work.

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

PubMed Central

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

2016-01-01

The presumptive altered dynamics of transient molecular interactions in vivo contributing to neurodegenerative diseases have remained elusive. Here, using single-molecule localization microscopy, we show that disease-inducing Huntingtin (mHtt) protein fragments display three distinct dynamic states in living cells – 1) fast diffusion, 2) dynamic clustering and 3) stable aggregation. Large, stable aggregates of mHtt exclude chromatin and form 'sticky' decoy traps that impede target search processes of key regulators involved in neurological disorders. Functional domain mapping based on super-resolution imaging reveals an unexpected role of aromatic amino acids in promoting protein-mHtt aggregate interactions. Genome-wide expression analysis and numerical simulation experiments suggest mHtt aggregates reduce transcription factor target site sampling frequency and impair critical gene expression programs in striatal neurons. Together, our results provide insights into how mHtt dynamically forms aggregates and disrupts the finely-balanced gene control mechanisms in neuronal cells. DOI: http://dx.doi.org/10.7554/eLife.17056.001 PMID:27484239

There is a need for new systemic sclerosis subset criteria. A content analytic approach.

PubMed

Johnson, S R; Soowamber, M L; Fransen, J; Khanna, D; Van Den Hoogen, F; Baron, M; Matucci-Cerinic, M; Denton, C P; Medsger, T A; Carreira, P E; Riemekasten, G; Distler, J; Gabrielli, A; Steen, V; Chung, L; Silver, R; Varga, J; Müller-Ladner, U; Vonk, M C; Walker, U A; Wollheim, F A; Herrick, A; Furst, D E; Czirjak, L; Kowal-Bielecka, O; Del Galdo, F; Cutolo, M; Hunzelmann, N; Murray, C D; Foeldvari, I; Mouthon, L; Damjanov, N; Kahaleh, B; Frech, T; Assassi, S; Saketkoo, L A; Pope, J E

2018-01-01

Systemic sclerosis (SSc) is heterogenous. The objectives of this study were to evaluate the purpose, strengths and limitations of existing SSc subset criteria, and identify ideas among experts about subsets. We conducted semi-structured interviews with randomly sampled international SSc experts. The interview transcripts underwent an iterative process with text deconstructed to single thought units until a saturated conceptual framework with coding was achieved and respondent occurrence tabulated. Serial cross-referential analyses of clusters were developed. Thirty experts from 13 countries were included; 67% were male, 63% were from Europe and 37% from North America; median experience of 22.5 years, with a median of 55 new SSc patients annually. Three thematic clusters regarding subsetting were identified: research and communication; management; and prognosis (prediction of internal organ involvement, survival). The strength of the limited/diffuse system was its ease of use, however 10% stated this system had marginal value. Shortcomings of the diffuse/limited classification were the risk of misclassification, predictions/generalizations did not always hold true, and that the elbow or knee threshold was arbitrary. Eighty-seven percent use more than 2 subsets including: SSc sine scleroderma, overlap conditions, antibody-determined subsets, speed of progression, and age of onset (juvenile, elderly). We have synthesized an international view of the construct of SSc subsets in the modern era. We found a number of factors underlying the construct of SSc subsets. Considerations for the next phase include rate of change and hierarchal clustering (e.g. limited/diffuse, then by antibodies).

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wykes, M., E-mail: mikewykes@gmail.com; Parambil, R.; Gierschner, J.

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 fluorescencemore » 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.« less

Elucidation of flow-mediated tumour cell-induced platelet aggregation using an ultrasound standing wave trap

PubMed Central

Bazou, D; Santos-Martinez, MJ; Medina, C; Radomski, MW

2011-01-01

BACKGROUND AND PURPOSE Tumour cells activate and aggregate platelets [tumour cell-induced platelet aggregation (TCIPA)] and this process plays an important role in the successful metastasis of cancer cells. To date, most studies on TCIPA have been conducted under no-flow conditions. In this study, we have investigated TCIPA in real time under flow conditions, using an ultrasound standing wave trap that allows formation and levitation of cancer cell clusters in suspension, thus mimicking the conditions generated by flowing blood. EXPERIMENTAL APPROACH Using 59M adenocarcinoma and HT1080 fibrosarcoma cells and human platelets, cancer cell cluster–platelet aggregates were imaged in real time using epi-fluorescence microscopy (F-actin) and investigated in detail using confocal microscopy (matrix metalloproteinase-2-GPIIb/IIIa co-localization) and scanning electron and helium-ion microscopy (<1 nm resolution). The release of gelatinases from aggregates was studied using zymography. KEY RESULTS We found that platelet activation and aggregation takes place on the surface of cancer cells (TCIPA), leading to time-dependent disruption of cancer cell clusters. Pharmacological modulation of TCIPA revealed that EDTA, prostacyclin, o-phenanthroline and apyrase significantly down-regulated TCIPA and, in turn, delayed cell cluster disruption, However, EGTA and aspirin were ineffective. Pharmacological inhibition of TCIPA correlated with the down-regulation of platelet activation as shown by flow-cytometry assay of platelet P-selectin. CONCLUSION AND IMPLICATIONS Our results show for the first time, that during TCIPA, platelet activation disrupts cancer cell clusters and this can contribute to metastasis. Thus, selective targeting of platelet aggregate–cancer cell clusters may be an important strategy to control metastasis. PMID:21182493

Social aggregation as a cooperative game

NASA Astrophysics Data System (ADS)

Vilone, Daniele; Guazzini, Andrea

2011-07-01

A new approach for the description of phenomena of social aggregation is suggested. On the basis of psychological concepts (as for instance social norms and cultural coordinates), we deduce a general mechanism for social aggregation in which different clusters of individuals can merge according to cooperation among the agents. In their turn, the agents can cooperate or defect according to the clusters' distribution inside the system. The fitness of an individual increases with the size of its cluster, but decreases with the work the individual had to do in order to join it. In order to test the reliability of such a new approach, we introduce a couple of simple toy models with the features illustrated above. We see, from this preliminary study, how cooperation is the most convenient strategy only in the presence of very large clusters, while on the other hand it is not necessary to have one hundred percent of cooperators for reaching a totally ordered configuration with only one megacluster filling the whole system.

The interplay between star formation and the nuclear environment of our Galaxy: deep X-ray observations of the Galactic centre Arches and Quintuplet clusters

NASA Astrophysics Data System (ADS)

Wang, Q. Daniel; Dong, Hui; Lang, Cornelia

2006-09-01

The Galactic centre (GC) provides a unique laboratory for a detailed examination of the interplay between massive star formation and the nuclear environment of our Galaxy. Here, we present a 100-ks Chandra Advanced CCD Imaging Spectrometer (ACIS) observation of the Arches and Quintuplet star clusters. We also report on a complementary mapping of the dense molecular gas near the Arches cluster made with the Owens Valley Millimeter Array. We present a catalogue of 244 point-like X-ray sources detected in the observation. Their number-flux relation indicates an overpopulation of relatively bright X-ray sources, which are apparently associated with the clusters. The sources in the core of the Arches and Quintuplet clusters are most likely extreme colliding wind massive star binaries. The diffuse X-ray emission from the core of the Arches cluster has a spectrum showing a 6.7-keV emission line and a surface intensity profile declining steeply with radius, indicating an origin in a cluster wind. In the outer regions near the Arches cluster, the overall diffuse X-ray enhancement demonstrates a bow shock morphology and is prominent in the Fe Kα 6.4-keV line emission with an equivalent width of ~1.4 keV. Much of this enhancement may result from an ongoing collision between the cluster and the adjacent molecular cloud, which have a relative velocity >~120km-1. The older and less-compact Quintuplet cluster contains much weaker X-ray sources and diffuse emission, probably originating from low-mass stellar objects as well as a cluster wind. However, the overall population of these objects, constrained by the observed total diffuse X-ray luminosities, is substantially smaller than expected for both clusters, if they have normal Miller & Scalo initial mass functions. This deficiency of low-mass objects may be a manifestation of the unique star formation environment of the GC, where high-velocity cloud-cloud and cloud-cluster collisions are frequent.

Diffuse light and building history of the galaxy cluster Abell 2667

NASA Astrophysics Data System (ADS)

Covone, G.; Adami, C.; Durret, F.; Kneib, J.-P.; Lima Neto, G. B.; Slezak, E.

2006-12-01

Aims.We searched for diffuse intracluster light in the galaxy cluster Abell 2667 (z=0.233) from HST images in three broad band-filters. Methods: .We applied an iterative multi-scale wavelet analysis and reconstruction technique to these images, which allows to subtract stars and galaxies from the original images. Results: .We detect a zone of diffuse emission southwest of the cluster center (DS1) and a second faint object (ComDif) within DS1. Another diffuse source (DS2) may be detected at lower confidence level northeast of the center. These sources of diffuse light contribute to 10-15% of the total visible light in the cluster. Whether they are independent entities or part of the very elliptical external envelope of the central galaxy remains unclear. Deep VLT VIMOS integral field spectroscopy reveals a faint continuum at the positions of DS1 and ComDif but do not allow a redshift to be computed, so we conclude if these sources are part of the central galaxy or not. A hierarchical substructure detection method reveals the presence of several galaxy pairs and groups defining a similar direction to the one drawn by the DS1 - central galaxy - DS2 axis. The analysis of archive XMM-Newton and Chandra observations shows X-ray emission elongated in the same direction. The X-ray temperature map shows the presence of a cool core, a broad cool zone stretching from north to south, and hotter regions towards the northeast, southwest, and northwest. This might suggest shock fronts along these directions produced by infalling material, even if uncertainties remain quite large on the temperature determination far from the center. Conclusions: .These various data are consistent with a picture in which diffuse sources are concentrations of tidal debris and harassed matter expelled from infalling galaxies by tidal stripping and undergoing an accretion process onto the central cluster galaxy; as such, they are expected to be found along the main infall directions. Note, however, that the limited signal to noise of the various data and the apparent lack of large numbers of well-defined independent tidal tails, besides the one named ComDif, preclude definitive conclusions on this scenario.

Familial aggregation of suicide explained by cluster B traits: a three-group family study of suicide controlling for major depressive disorder.

PubMed

McGirr, Alexander; Alda, Martin; Séguin, Monique; Cabot, Sophie; Lesage, Alain; Turecki, Gustavo

2009-10-01

There is substantial evidence suggesting that suicide aggregates in families. However, the extent of overlap between the liability to suicide and psychiatric disorders, particularly major depressive disorder, remains an important issue. Similarly, factors that account for the familial transmission of suicidal behavior remain unclear. Thus, through direct and blind assessment of first-degree relatives, the authors conducted a family study of suicide by examining three proband groups: probands who committed suicide in the context of major depressive disorder, living depressed probands with no history of suicidal behavior, and psychiatrically normal community comparison probands. Participants were 718 first-degree relatives from 120 families: 296 relatives of 51 depressed probands who committed suicide, 185 relatives of 34 nonsuicidal depressed probands, and 237 relatives of 35 community comparison subjects. Psychopathology, suicidal behavior, and behavioral measures were assessed via interviews. The relatives of probands who committed suicide had higher levels of suicidal behavior (10.8%) than the relatives of nonsuicidal depressed probands (6.5%) and community comparison probands (3.4%). Testing cluster B traits as intermediate phenotypes of suicide showed that the relatives of depressed probands who committed suicide had elevated levels of cluster B traits; familial predisposition to suicide was associated with increased levels of cluster B traits; cluster B traits demonstrated familial aggregation and were associated with suicide attempts among relatives; and cluster B traits mediated, at least in part, the relationship between familial predisposition and suicide attempts among relatives. Analyses were repeated for severity of attempts, where cluster B traits also met criteria for endophenotypes of suicide. Familial transmission of suicide and major depression, while partially overlapping, are distinct. Cluster B traits and impulsive-aggressive behavior represent intermediate phenotypes of suicide.

MASS ACCRETION AND ITS EFFECTS ON THE SELF-SIMILARITY OF GAS PROFILES IN THE OUTSKIRTS OF GALAXY CLUSTERS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lau, Erwin T.; Nagai, Daisuke; Avestruz, Camille

2015-06-10

Galaxy clusters exhibit remarkable self-similar behavior which allows us to establish simple scaling relationships between observable quantities and cluster masses, making galaxy clusters useful cosmological probes. Recent X-ray observations suggested that self-similarity may be broken in the outskirts of galaxy clusters. In this work, we analyze a mass-limited sample of massive galaxy clusters from the Omega500 cosmological hydrodynamic simulation to investigate the self-similarity of the diffuse X-ray emitting intracluster medium (ICM) in the outskirts of galaxy clusters. We find that the self-similarity of the outer ICM profiles is better preserved if they are normalized with respect to the mean densitymore » of the universe, while the inner profiles are more self-similar when normalized using the critical density. However, the outer ICM profiles as well as the location of accretion shock around clusters are sensitive to their mass accretion rate, which causes the apparent breaking of self-similarity in cluster outskirts. We also find that the collisional gas does not follow the distribution of collisionless dark matter (DM) perfectly in the infall regions of galaxy clusters, leading to 10% departures in the gas-to-DM density ratio from the cosmic mean value. Our results have a number implications for interpreting observations of galaxy clusters in X-ray and through the Sunyaev–Zel’dovich effect, and their applications to cosmology.« less

Soot superaggregates from flaming wildfires and their direct radiative forcing.

PubMed

Chakrabarty, Rajan K; Beres, Nicholas D; Moosmüller, Hans; China, Swarup; Mazzoleni, Claudio; Dubey, Manvendra K; Liu, Li; Mishchenko, Michael I

2014-07-01

Wildfires contribute significantly to global soot emissions, yet their aerosol formation mechanisms and resulting particle properties are poorly understood and parameterized in climate models. The conventional view holds that soot is formed via the cluster-dilute aggregation mechanism in wildfires and emitted as aggregates with fractal dimension Df ≈ 1.8 mobility diameter Dm ≤ 1 μm, and aerodynamic diameter Da ≤ 300 nm. Here we report the ubiquitous presence of soot superaggregates (SAs) in the outflow from a major wildfire in India. SAs are porous, low-density aggregates of cluster-dilute aggregates with characteristic Df ≈ 2.6, Dm > 1 μm, and Da ≤ 300 nm that form via the cluster-dense aggregation mechanism. We present additional observations of soot SAs in wildfire smoke-laden air masses over Northern California, New Mexico, and Mexico City. At 550 nm wavelength, [corrected] we estimate that SAs contribute, per unit optical depth, up to 35% less atmospheric warming than freshly-emitted (D(f) ≈ 1.8) [corrected] aggregates, and ≈90% more warming than the volume-equivalent spherical soot particles simulated in climate models.

Soot superaggregates from flaming wildfires and their direct radiative forcing

PubMed Central

Chakrabarty, Rajan K.; Beres, Nicholas D.; Moosmüller, Hans; China, Swarup; Mazzoleni, Claudio; Dubey, Manvendra K.; Liu, Li; Mishchenko, Michael I.

2014-01-01

Wildfires contribute significantly to global soot emissions, yet their aerosol formation mechanisms and resulting particle properties are poorly understood and parameterized in climate models. The conventional view holds that soot is formed via the cluster-dilute aggregation mechanism in wildfires and emitted as aggregates with fractal dimension Df ≈ 1.8 mobility diameter Dm ≤ 1 μm, and aerodynamic diameter Da ≤ 300 nm. Here we report the ubiquitous presence of soot superaggregates (SAs) in the outflow from a major wildfire in India. SAs are porous, low-density aggregates of cluster-dilute aggregates with characteristic Df ≈ 2.6, Dm > 1 μm, and Da ≤ 300 nm that form via the cluster-dense aggregation mechanism. We present additional observations of soot SAs in wildfire smoke-laden air masses over Northern California, New Mexico, and Mexico City. We estimate that SAs contribute, per unit optical depth, up to 35% less atmospheric warming than freshly-emitted (Df ≈ 1.8) aggregates, and ≈90% more warming than the volume-equivalent spherical soot particles simulated in climate models. PMID:24981204

Application of asymmetric flow-field flow fractionation to the characterization of colloidal dispersions undergoing aggregation.

PubMed

Lattuada, Marco; Olivo, Carlos; Gauer, Cornelius; Storti, Giuseppe; Morbidelli, Massimo

2010-05-18

The characterization of complex colloidal dispersions is a relevant and challenging problem in colloidal science. In this work, we show how asymmetric flow-field flow fractionation (AF4) coupled to static light scattering can be used for this purpose. As an example of complex colloidal dispersions, we have chosen two systems undergoing aggregation. The first one is a conventional polystyrene latex undergoing reaction-limited aggregation, which leads to the formation of fractal clusters with well-known structure. The second one is a dispersion of elastomeric colloidal particles made of a polymer with a low glass transition temperature, which undergoes coalescence upon aggregation. Samples are withdrawn during aggregation at fixed times, fractionated with AF4 using a two-angle static light scattering unit as a detector. We have shown that from the analysis of the ratio between the intensities of the scattered light at the two angles the cluster size distribution can be recovered, without any need for calibration based on standard elution times, provided that the geometry and scattering properties of particles and clusters are known. The nonfractionated samples have been characterized also by conventional static and dynamic light scattering to determine their average radius of gyration and hydrodynamic radius. The size distribution of coalescing particles has been investigated also through image analysis of cryo-scanning electron microscopy (SEM) pictures. The average radius of gyration and the average hydrodynamic radius of the nonfractionated samples have been calculated and successfully compared to the values obtained from the size distributions measured by AF4. In addition, the data obtained are also in good agreement with calculations made with population balance equations.

Sample size calculations for the design of cluster randomized trials: A summary of methodology.

PubMed

Gao, Fei; Earnest, Arul; Matchar, David B; Campbell, Michael J; Machin, David

2015-05-01

Cluster randomized trial designs are growing in popularity in, for example, cardiovascular medicine research and other clinical areas and parallel statistical developments concerned with the design and analysis of these trials have been stimulated. Nevertheless, reviews suggest that design issues associated with cluster randomized trials are often poorly appreciated and there remain inadequacies in, for example, describing how the trial size is determined and the associated results are presented. In this paper, our aim is to provide pragmatic guidance for researchers on the methods of calculating sample sizes. We focus attention on designs with the primary purpose of comparing two interventions with respect to continuous, binary, ordered categorical, incidence rate and time-to-event outcome variables. Issues of aggregate and non-aggregate cluster trials, adjustment for variation in cluster size and the effect size are detailed. The problem of establishing the anticipated magnitude of between- and within-cluster variation to enable planning values of the intra-cluster correlation coefficient and the coefficient of variation are also described. Illustrative examples of calculations of trial sizes for each endpoint type are included. Copyright © 2015 Elsevier Inc. All rights reserved.

Dual emissions from MnS clusters confined in the sodalite nanocage of a chalcogenide-based semiconductor zeolite.

PubMed

Hu, Dandan; Zhang, Yingying; Lin, Jian; Hou, Yike; Li, Dongsheng; Wu, Tao

2017-03-21

A new host-guest hybrid system with MnS clusters confined in a chalcogenide-based semiconductor zeolite was for the first time constructed and its photoluminescence (PL) properties were also investigated. The existence of MnS clusters in the nanopores of the semiconductor zeolite was revealed by UV-Vis absorption spectroscopy, steady-state fluorescence analysis, Raman as well as Fourier transform infrared (FTIR) spectroscopy. The aggregation state of the entrapped MnS clusters at different measurement temperatures was probed by electron paramagnetic resonance (EPR) spectroscopy. Of significant importance is the fact that the entrapped MnS clusters displayed dual emissions at 518 nm (2.39 eV) and 746 nm (1.66 eV), respectively, and the long-wavelength emission has never been observed in other MnS-confined host-guest systems. These two emission peaks displayed tunable PL intensity affected by the loading level and measurement temperature. This can be explained by the different morphologies of MnS clusters with different aggregation states at the corresponding loading level or measurement temperature. The current study opens a new avenue to construct inorganic chalcogenide cluster involved host-guest systems with a semiconductor zeolite as the host matrix.

Discrete bivariate population balance modelling of heteroaggregation processes.

PubMed

Rollié, Sascha; Briesen, Heiko; Sundmacher, Kai

2009-08-15

Heteroaggregation in binary particle mixtures was simulated with a discrete population balance model in terms of two internal coordinates describing the particle properties. The considered particle species are of different size and zeta-potential. Property space is reduced with a semi-heuristic approach to enable an efficient solution. Aggregation rates are based on deterministic models for Brownian motion and stability, under consideration of DLVO interaction potentials. A charge-balance kernel is presented, relating the electrostatic surface potential to the property space by a simple charge balance. Parameter sensitivity with respect to the fractal dimension, aggregate size, hydrodynamic correction, ionic strength and absolute particle concentration was assessed. Results were compared to simulations with the literature kernel based on geometric coverage effects for clusters with heterogeneous surface properties. In both cases electrostatic phenomena, which dominate the aggregation process, show identical trends: impeded cluster-cluster aggregation at low particle mixing ratio (1:1), restabilisation at high mixing ratios (100:1) and formation of complex clusters for intermediate ratios (10:1). The particle mixing ratio controls the surface coverage extent of the larger particle species. Simulation results are compared to experimental flow cytometric data and show very satisfactory agreement.

Origins of ultra-diffuse galaxies in the Coma cluster - I. Constraints from velocity phase-space

NASA Astrophysics Data System (ADS)

Alabi, Adebusola; Ferré-Mateu, Anna; Romanowsky, Aaron J.; Brodie, Jean; Forbes, Duncan A.; Wasserman, Asher; Bellstedt, Sabine; Martín-Navarro, Ignacio; Pandya, Viraj; Stone, Maria B.; Okabe, Nobuhiro

2018-06-01

We use Keck/DEIMOS spectroscopy to confirm the cluster membership of 16 ultra-diffuse galaxies (UDGs) in the Coma cluster, bringing the total number of spectroscopically confirmed UDGs from the Yagi et al. (Y16) catalog to 25. We also identify a new cluster background UDG, confirming that most (˜95 per cent) of the UDGs in the Y16 catalog belong to the Coma cluster. In this pilot study of Coma UDGs in velocity phase-space, we find evidence of a diverse origin for Coma cluster UDGs, similar to normal dwarf galaxies. Some UDGs in our sample are consistent with being late infalls into the cluster environment while some may have been in the cluster for ≥8 Gyr. The late infallen UDGs have higher absolute relative line-of-sight velocities, bluer optical colors, and within the projected cluster core, are smaller in size, compared to the early infalls. The early infall UDGs, which may also have formed in-situ, have been in the cluster environment for as long as the most luminous galaxies in the Coma cluster and they may be failed galaxies which experienced star formation quenching at earlier epochs.

High energy neutrinos and gamma-ray emission from supernovae in compact star clusters

NASA Astrophysics Data System (ADS)

Bykov, A. M.; Ellison, D. C.; Gladilin, P. E.; Osipov, S. M.

2017-01-01

Compact clusters of young massive stars are observed in the Milky Way and in starburst galaxies. The compact clusters with multiple powerful winds of young massive stars and supernova shocks are favorable sites for high-energy particle acceleration. We argue that expanding young supernova (SN) shells in compact stellar clusters can be very efficient PeV CR accelerators. At a stage when a supernova shock is colliding with collective fast winds from massive stars in a compact cluster the Fermi mechanism allows particle acceleration to energies well above the standard limits of diffusive shock acceleration in an isolated SNR. The energy spectrum of protons in such an accelerator is a hard power-law with a broad spectral upturn above TeV before a break at multi-PeV energies, providing a large energy flux in the high-energy end of the spectrum. The acceleration stage in the colliding shock flow lasts for a few hundred years after the supernova explosion producing high-energy CRs that escape the accelerator and diffuse through the ambient matter producing γ-rays and neutrinos in inelastic nuclear collisions. In starburst galaxies a sizeable fraction of core collapse supernovae is expected to occur in compact star clusters and therefore their high energy gamma-ray and neutrino spectra in the PeV energy regime may differ strongly from that of our Galaxy. To test the model with individual sources we briefly discuss the recent H.E.S.S. detections of gamma-rays from two potential candidate sources, Westerlund 1 and HESS J1806-204 in the Milky Way. We argue that this model of compact star clusters, with typical parameters, could produce a neutrino flux sufficient to explain a fraction of the recently detected IceCube South Pole Observatory neutrinos.

Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions

NASA Astrophysics Data System (ADS)

Nedialkova, Lilia V.; Amat, Miguel A.; Kevrekidis, Ioannis G.; Hummer, Gerhard

2014-09-01

Using the helix-coil transitions of alanine pentapeptide as an illustrative example, we demonstrate the use of diffusion maps in the analysis of molecular dynamics simulation trajectories. Diffusion maps and other nonlinear data-mining techniques provide powerful tools to visualize the distribution of structures in conformation space. The resulting low-dimensional representations help in partitioning conformation space, and in constructing Markov state models that capture the conformational dynamics. In an initial step, we use diffusion maps to reduce the dimensionality of the conformational dynamics of Ala5. The resulting pretreated data are then used in a clustering step. The identified clusters show excellent overlap with clusters obtained previously by using the backbone dihedral angles as input, with small—but nontrivial—differences reflecting torsional degrees of freedom ignored in the earlier approach. We then construct a Markov state model describing the conformational dynamics in terms of a discrete-time random walk between the clusters. We show that by combining fuzzy C-means clustering with a transition-based assignment of states, we can construct robust Markov state models. This state-assignment procedure suppresses short-time memory effects that result from the non-Markovianity of the dynamics projected onto the space of clusters. In a comparison with previous work, we demonstrate how manifold learning techniques may complement and enhance informed intuition commonly used to construct reduced descriptions of the dynamics in molecular conformation space.

Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nedialkova, Lilia V.; Amat, Miguel A.; Kevrekidis, Ioannis G., E-mail: yannis@princeton.edu, E-mail: gerhard.hummer@biophys.mpg.de

Using the helix-coil transitions of alanine pentapeptide as an illustrative example, we demonstrate the use of diffusion maps in the analysis of molecular dynamics simulation trajectories. Diffusion maps and other nonlinear data-mining techniques provide powerful tools to visualize the distribution of structures in conformation space. The resulting low-dimensional representations help in partitioning conformation space, and in constructing Markov state models that capture the conformational dynamics. In an initial step, we use diffusion maps to reduce the dimensionality of the conformational dynamics of Ala5. The resulting pretreated data are then used in a clustering step. The identified clusters show excellent overlapmore » with clusters obtained previously by using the backbone dihedral angles as input, with small—but nontrivial—differences reflecting torsional degrees of freedom ignored in the earlier approach. We then construct a Markov state model describing the conformational dynamics in terms of a discrete-time random walk between the clusters. We show that by combining fuzzy C-means clustering with a transition-based assignment of states, we can construct robust Markov state models. This state-assignment procedure suppresses short-time memory effects that result from the non-Markovianity of the dynamics projected onto the space of clusters. In a comparison with previous work, we demonstrate how manifold learning techniques may complement and enhance informed intuition commonly used to construct reduced descriptions of the dynamics in molecular conformation space.« less

Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions

PubMed Central

Nedialkova, Lilia V.; Amat, Miguel A.; Kevrekidis, Ioannis G.; Hummer, Gerhard

2014-01-01

Using the helix-coil transitions of alanine pentapeptide as an illustrative example, we demonstrate the use of diffusion maps in the analysis of molecular dynamics simulation trajectories. Diffusion maps and other nonlinear data-mining techniques provide powerful tools to visualize the distribution of structures in conformation space. The resulting low-dimensional representations help in partitioning conformation space, and in constructing Markov state models that capture the conformational dynamics. In an initial step, we use diffusion maps to reduce the dimensionality of the conformational dynamics of Ala5. The resulting pretreated data are then used in a clustering step. The identified clusters show excellent overlap with clusters obtained previously by using the backbone dihedral angles as input, with small—but nontrivial—differences reflecting torsional degrees of freedom ignored in the earlier approach. We then construct a Markov state model describing the conformational dynamics in terms of a discrete-time random walk between the clusters. We show that by combining fuzzy C-means clustering with a transition-based assignment of states, we can construct robust Markov state models. This state-assignment procedure suppresses short-time memory effects that result from the non-Markovianity of the dynamics projected onto the space of clusters. In a comparison with previous work, we demonstrate how manifold learning techniques may complement and enhance informed intuition commonly used to construct reduced descriptions of the dynamics in molecular conformation space. PMID:25240340

New mechanisms of cluster diffusion on metal fcc(100) surfaces

NASA Astrophysics Data System (ADS)

Trushin, Oleg; Salo, Petri; Alatalo, Matti; Ala-Nissila, Tapio

2001-03-01

We have studied atomic mechanisms of the diffusion of small clusters on the fcc(100) metal surfaces using semi-empirical and ab-initio molecular static calculations. Primary goal of these studies was to investigate possible many-body mechanisms of cluster motion which can contribute to low temperature crystal growth. We used embedded atom and Glue potentials in semi-empirical simulations of Cu and Al. Combination of the Nudged Elastic Band and Eigenvector Following methods allowed us to find all the possible transition paths for cluster movements on flat terrace. In case of Cu(001) we have found several new mechanisms for diffusion of clusters, including mechanisms called row-shearing and dimer-rotating in which a whole row inside an island moves according to a concerted jump and a dimer rotates at the periphery of an island, respectively. In some cases these mechanisms yield a lower energy barrier than the standard mechanisms.

Analysis of ligand-protein exchange by Clustering of Ligand Diffusion Coefficient Pairs (CoLD-CoP)

NASA Astrophysics Data System (ADS)

Snyder, David A.; Chantova, Mihaela; Chaudhry, Saadia

2015-06-01

NMR spectroscopy is a powerful tool in describing protein structures and protein activity for pharmaceutical and biochemical development. This study describes a method to determine weak binding ligands in biological systems by using hierarchic diffusion coefficient clustering of multidimensional data obtained with a 400 MHz Bruker NMR. Comparison of DOSY spectrums of ligands of the chemical library in the presence and absence of target proteins show translational diffusion rates for small molecules upon interaction with macromolecules. For weak binders such as compounds found in fragment libraries, changes in diffusion rates upon macromolecular binding are on the order of the precision of DOSY diffusion measurements, and identifying such subtle shifts in diffusion requires careful statistical analysis. The "CoLD-CoP" (Clustering of Ligand Diffusion Coefficient Pairs) method presented here uses SAHN clustering to identify protein-binders in a chemical library or even a not fully characterized metabolite mixture. We will show how DOSY NMR and the "CoLD-CoP" method complement each other in identifying the most suitable candidates for lysozyme and wheat germ acid phosphatase.

An aggregation-volume-bias Monte Carlo investigation on the condensation of a Lennard-Jones vapor below the triple point and crystal nucleation in cluster systems: an in-depth evaluation of the classical nucleation theory.

PubMed

Chen, Bin; Kim, Hyunmi; Keasler, Samuel J; Nellas, Ricky B

2008-04-03

The aggregation-volume-bias Monte Carlo based simulation technique, which has led to our recent success in vapor-liquid nucleation research, was extended to the study of crystal nucleation processes. In contrast to conventional bulk-phase techniques, this method deals with crystal nucleation events in cluster systems. This approach was applied to the crystal nucleation of Lennard-Jonesium under a wide range of undercooling conditions from 35% to 13% below the triple point. It was found that crystal nucleation in these model clusters proceeds initially via a vapor-liquid like aggregation followed by the formation of crystals inside the aggregates. The separation of these two stages of nucleation is distinct except at deeper undercooling conditions where the crystal nucleation barrier was found to diminish. The simulation results obtained for these two nucleation steps are separately compared to the classical nucleation theory (CNT). For the vapor-liquid nucleation step, the CNT was shown to provide a reasonable description of the critical cluster size but overestimate the barrier heights, consistent with previous simulation studies. On the contrary, for the crystal nucleation step, nearly perfect agreement with the barrier heights was found between the simulations and the CNT. For the critical cluster size, the comparison is more difficult as the simulation data were found to be sensitive to the definition of the solid cluster, but a stringent criterion and lower undercooling conditions generally lead to results closer with the CNT. Additional simulations at undercooling conditions of 40% or above indicate a nearly barrierless transition from the liquid to crystalline-like structure for sufficiently large clusters, which leads to further departure of the barrier height predicted by the CNT from the simulation data for the aggregation step. This is consistent with the latest experimental results on argon that show an unusually large underestimation of the nucleation rate by the CNT toward deep undercooling conditions.

From the tunneling dimer to the onset of microsolvation: Infrared spectroscopy of allyl radical water aggregates in helium nanodroplets

NASA Astrophysics Data System (ADS)

Leicht, Daniel; Kaufmann, Matin; Pal, Nitish; Schwaab, Gerhard; Havenith, Martina

2017-03-01

The infrared spectrum of allyl:water clusters embedded in helium nanodroplets was recorded. Allyl radicals were produced by flash vacuum pyrolysis and trapped in helium droplets. Deuterated water was added to the doped droplets, and the infrared spectrum of the radical water aggregates was recorded in the frequency range 2570-2820 cm-1. Several absorption bands are observed and assigned to 1:1 and 1:2 allyl:D2O clusters, based on pressure dependent measurements and accompanying quantum chemical calculations. The analysis of the 1:1 cluster spectrum revealed a tunneling splitting as well as a combination band. For the 1:2 cluster, we observe a water dimer-like motif that is bound by one π-hydrogen bond to the allyl radical.

Real-time dynamics of neutrophil clustering in response to phototoxicity-induced cell death and tissue damage in mouse ear dermis.

PubMed

Park, Sang A; Choe, Young Ho; Park, Eunji; Hyun, Young-Min

2018-05-22

Neutrophils are highly motile innate immune cells; they actively migrate in response to inflammatory signals. Using two-photon intravital microscopy, we discovered that neutrophils form stable clusters upon phototoxicity at a certain threshold. Without significant damage to the collagen structure of mouse dermis, neutrophils aggregated together with nearby neutrophils. Surprisingly, this in situ neutrophil clustering resulted in rigorous changes of migratory direction. The density of residing neutrophils was also a critical factor affecting clustering. Additionally, we found that the triggering point of neutrophil aggregation was correlated with the structure of the extracellular matrix in the ear dermis, where autofluorescence was strongly observed. This swarming behavior of neutrophils may reflect an unknown communication mechanism of neutrophils during migration under sterile injury.

Cluster Free Energies from Simple Simulations of Small Numbers of Aggregants: Nucleation of Liquid MTBE from Vapor and Aqueous Phases.

PubMed

Patel, Lara A; Kindt, James T

2017-03-14

We introduce a global fitting analysis method to obtain free energies of association of noncovalent molecular clusters using equilibrated cluster size distributions from unbiased constant-temperature molecular dynamics (MD) simulations. Because the systems simulated are small enough that the law of mass action does not describe the aggregation statistics, the method relies on iteratively determining a set of cluster free energies that, using appropriately weighted sums over all possible partitions of N monomers into clusters, produces the best-fit size distribution. The quality of these fits can be used as an objective measure of self-consistency to optimize the cutoff distance that determines how clusters are defined. To showcase the method, we have simulated a united-atom model of methyl tert-butyl ether (MTBE) in the vapor phase and in explicit water solution over a range of system sizes (up to 95 MTBE in the vapor phase and 60 MTBE in the aqueous phase) and concentrations at 273 K. The resulting size-dependent cluster free energy functions follow a form derived from classical nucleation theory (CNT) quite well over the full range of cluster sizes, although deviations are more pronounced for small cluster sizes. The CNT fit to cluster free energies yielded surface tensions that were in both cases lower than those for the simulated planar interfaces. We use a simple model to derive a condition for minimizing non-ideal effects on cluster size distributions and show that the cutoff distance that yields the best global fit is consistent with this condition.

An Efficient Data Compression Model Based on Spatial Clustering and Principal Component Analysis in Wireless Sensor Networks.

PubMed

Yin, Yihang; Liu, Fengzheng; Zhou, Xiang; Li, Quanzhong

2015-08-07

Wireless sensor networks (WSNs) have been widely used to monitor the environment, and sensors in WSNs are usually power constrained. Because inner-node communication consumes most of the power, efficient data compression schemes are needed to reduce the data transmission to prolong the lifetime of WSNs. In this paper, we propose an efficient data compression model to aggregate data, which is based on spatial clustering and principal component analysis (PCA). First, sensors with a strong temporal-spatial correlation are grouped into one cluster for further processing with a novel similarity measure metric. Next, sensor data in one cluster are aggregated in the cluster head sensor node, and an efficient adaptive strategy is proposed for the selection of the cluster head to conserve energy. Finally, the proposed model applies principal component analysis with an error bound guarantee to compress the data and retain the definite variance at the same time. Computer simulations show that the proposed model can greatly reduce communication and obtain a lower mean square error than other PCA-based algorithms.

A geo-computational algorithm for exploring the structure of diffusion progression in time and space.

PubMed

Chin, Wei-Chien-Benny; Wen, Tzai-Hung; Sabel, Clive E; Wang, I-Hsiang

2017-10-03

A diffusion process can be considered as the movement of linked events through space and time. Therefore, space-time locations of events are key to identify any diffusion process. However, previous clustering analysis methods have focused only on space-time proximity characteristics, neglecting the temporal lag of the movement of events. We argue that the temporal lag between events is a key to understand the process of diffusion movement. Using the temporal lag could help to clarify the types of close relationships. This study aims to develop a data exploration algorithm, namely the TrAcking Progression In Time And Space (TaPiTaS) algorithm, for understanding diffusion processes. Based on the spatial distance and temporal interval between cases, TaPiTaS detects sub-clusters, a group of events that have high probability of having common sources, identifies progression links, the relationships between sub-clusters, and tracks progression chains, the connected components of sub-clusters. Dengue Fever cases data was used as an illustrative case study. The location and temporal range of sub-clusters are presented, along with the progression links. TaPiTaS algorithm contributes a more detailed and in-depth understanding of the development of progression chains, namely the geographic diffusion process.

Extensions to the instantaneous normal mode analysis of cluster dynamics: Diffusion constants and the role of rotations in clusters

NASA Astrophysics Data System (ADS)

Adams, John E.; Stratt, Richard M.

1990-08-01

For the instantaneous normal mode analysis method to be generally useful in studying the dynamics of clusters of arbitrary size, it ought to yield values of atomic self-diffusion constants which agree with those derived directly from molecular dynamics calculations. The present study proposes that such agreement indeed can be obtained if a sufficiently sophisticated formalism for computing the diffusion constant is adopted, such as the one suggested by Madan, Keyes, and Seeley [J. Chem. Phys. 92, 7565 (1990)]. In order to implement this particular formalism, however, we have found it necessary to pay particular attention to the removal from the computed spectra of spurious rotational contributions. The utility of the formalism is demonstrated via a study of small argon clusters, for which numerous results generated using other approaches are available. We find the same temperature dependence of the Ar13 self-diffusion constant that Beck and Marchioro [J. Chem. Phys. 93, 1347 (1990)] do from their direct calculation of the velocity autocorrelation function: The diffusion constant rises quickly from zero to a liquid-like value as the cluster goes through (the finite-size equivalent of) the melting transition.

Light Scattering by Fractal Dust Aggregates. I. Angular Dependence of Scattering

NASA Astrophysics Data System (ADS)

Tazaki, Ryo; Tanaka, Hidekazu; Okuzumi, Satoshi; Kataoka, Akimasa; Nomura, Hideko

2016-06-01

In protoplanetary disks, micron-sized dust grains coagulate to form highly porous dust aggregates. Because the optical properties of these aggregates are not completely understood, it is important to investigate how porous dust aggregates scatter light. In this study, the light scattering properties of porous dust aggregates were calculated using a rigorous method, the T-matrix method, and the results were then compared with those obtained using the Rayleigh-Gans-Debye (RGD) theory and Mie theory with the effective medium approximation (EMT). The RGD theory is applicable to moderately large aggregates made of nearly transparent monomers. This study considered two types of porous dust aggregates—ballistic cluster-cluster agglomerates (BCCAs) and ballistic particle-cluster agglomerates. First, the angular dependence of the scattered intensity was shown to reflect the hierarchical structure of dust aggregates; the large-scale structure of the aggregates is responsible for the intensity at small scattering angles, and their small-scale structure determines the intensity at large scattering angles. Second, it was determined that the EMT underestimates the backward scattering intensity by multiple orders of magnitude, especially in BCCAs, because the EMT averages the structure within the size of the aggregates. It was concluded that the RGD theory is a very useful method for calculating the optical properties of BCCAs.

Flow-driven Assembly of Microcapsule Towers

NASA Astrophysics Data System (ADS)

Shum, Henry; Balazs, Anna

2016-11-01

Large populations of the slime mold, Dictyostelium discoideum, are able to aggregate over a surface and collectively form a long, vertical stalk. Inspired by this biological behavior, we develop a synthetic mechanism for assembling tower-like structures using microcapsules as the building blocks. We accomplish this in simulations by generating a fluid flow field that draws microcapsules together along a surface and lifts them up at a central point. We considered a fluid flow generated by the local release of a chemical species from a patch on the surface. The concentration gradient of the diffusing chemical species causes radial diffusioosmotic flow along the solid surface toward the patch. Adhesive interactions keep the microcapsules attached to the surface as they are drawn together above the patch. To build a tower-like structure, some of the microcapsules must detach from the surface but remain attached to the rest of the cluster. The upward directed fluid flow above the patch then draws out the cluster into a tower shape. The final morphology of the aggregate structure depends on the flow field, the adhesive capsule-capsule and capsule-surface interaction strengths, and the sedimentation force on the capsules. Tuning these factors changes the structures that are produced.

An Experimental Study on the Structure of Cosmic Dust Aggregates and Their Alignment by Motion Relative to Gas.

PubMed

Wurm; Blum

2000-01-20

We experimentally studied the shape of dust grains grown in a cluster-cluster type of aggregation (CCA) and derived characteristic axial ratios to describe the nonsphericity. CCAs might be described by an axial ratio rhoCCA=rg,max&solm0;rg,min approximately 2.0 in the limit of large aggregates, where rg,min and rg,max describe the minimum and maximum radius of gyration, while small aggregates show a somewhat larger value in their mean axial ratio up to rhoCCA approximately 3.0 but rapidly decrease to the limit rhoCCA approximately 2.0. The axial ratios for large aggregates are in agreement with the general findings of different authors for axial ratios of interstellar dust grains that are generally described by rods or spheroids. Beyond this kind of agreement, our approach does not necessarily require a special shape for individual dust grains but rather offers a physical process to generate nonsphericity. Although the simple shapes might be sufficient for first-order applications and are easier to handle analytically, our results offer a firm ground of special axial ratios for rods or spheroids on a more physical basis apart from any ad hoc assumptions. We also find an alignment of the aggregates during sedimentation in a gas along the drift axis leading to an axial ratio of rhoCCA,align=1.21+/-0.02 with respect to the drift axis and an axis perpendicular to this drift. This result is directly applicable to dust grains in protoplanetary disks and planetary atmospheres.

Occurrence of Radio Minihalos in a Mass-limited Sample of Galaxy Clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Giacintucci, Simona; Clarke, Tracy E.; Markevitch, Maxim

2017-06-01

We investigate the occurrence of radio minihalos—diffuse radio sources of unknown origin observed in the cores of some galaxy clusters—in a statistical sample of 58 clusters drawn from the Planck Sunyaev–Zel’dovich cluster catalog using a mass cut ( M {sub 500} > 6 × 10{sup 14} M {sub ⊙}). We supplement our statistical sample with a similarly sized nonstatistical sample mostly consisting of clusters in the ACCEPT X-ray catalog with suitable X-ray and radio data, which includes lower-mass clusters. Where necessary (for nine clusters), we reanalyzed the Very Large Array archival radio data to determine whether a minihalo is present.more » Our total sample includes all 28 currently known and recently discovered radio minihalos, including six candidates. We classify clusters as cool-core or non-cool-core according to the value of the specific entropy floor in the cluster center, rederived or newly derived from the Chandra X-ray density and temperature profiles where necessary (for 27 clusters). Contrary to the common wisdom that minihalos are rare, we find that almost all cool cores—at least 12 out of 15 (80%)—in our complete sample of massive clusters exhibit minihalos. The supplementary sample shows that the occurrence of minihalos may be lower in lower-mass cool-core clusters. No minihalos are found in non-cool cores or “warm cores.” These findings will help test theories of the origin of minihalos and provide information on the physical processes and energetics of the cluster cores.« less

GeV gamma-ray flux upper limits from clusters of galaxies

DOE PAGES

Ackermann, M.; Ajello, M.; Allafort, A.; ...

2010-06-16

The detection of diffuse radio emission associated with clusters of galaxies indicates populations of relativistic leptons infusing the intracluster medium (ICM). Those electrons and positrons are either injected into and accelerated directly in the ICM, or produced as secondary pairs by cosmic-ray ions scattering on ambient protons. Radiation mechanisms involving the energetic leptons together with the decay of neutral pions produced by hadronic interactions have the potential to produce abundant GeV photons. Here in this paper, we report on the search for GeV emission from clusters of galaxies using data collected by the Large Area Telescope on the Fermi Gamma-raymore » Space Telescope from 2008 August to 2010 February. Thirty-three galaxy clusters have been selected according to their proximity and high mass, X-ray flux and temperature, and indications of non-thermal activity for this study. We report upper limits on the photon flux in the range 0.2-100 GeV toward a sample of observed clusters (typical values (1-5) ×10 –9 photon cm –2 s –1) considering both point-like and spatially resolved models for the high-energy emission and discuss how these results constrain the characteristics of energetic leptons and hadrons, and magnetic fields in the ICM. The volume-averaged relativistic-hadron-to-thermal energy density ratio is found to be <5%-10% in several clusters.« less

Diffusion of oxygen interstitials in UO2+x using kinetic Monte Carlo simulations: Role of O/M ratio and sensitivity analysis

NASA Astrophysics Data System (ADS)

Behera, Rakesh K.; Watanabe, Taku; Andersson, David A.; Uberuaga, Blas P.; Deo, Chaitanya S.

2016-04-01

Oxygen interstitials in UO2+x significantly affect the thermophysical properties and microstructural evolution of the oxide nuclear fuel. In hyperstoichiometric Urania (UO2+x), these oxygen interstitials form different types of defect clusters, which have different migration behavior. In this study we have used kinetic Monte Carlo (kMC) to evaluate diffusivities of oxygen interstitials accounting for mono- and di-interstitial clusters. Our results indicate that the predicted diffusivities increase significantly at higher non-stoichiometry (x > 0.01) for di-interstitial clusters compared to a mono-interstitial only model. The diffusivities calculated at higher temperatures compare better with experimental values than at lower temperatures (< 973 K). We have discussed the resulting activation energies achieved for diffusion with all the mono- and di-interstitial models. We have carefully performed sensitivity analysis to estimate the effect of input di-interstitial binding energies on the predicted diffusivities and activation energies. While this article only discusses mono- and di-interstitials in evaluating oxygen diffusion response in UO2+x, future improvements to the model will primarily focus on including energetic definitions of larger stable interstitial clusters reported in the literature. The addition of larger clusters to the kMC model is expected to improve the comparison of oxygen transport in UO2+x with experiment.

Report on simulation of fission gas and fission product diffusion in UO 2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andersson, Anders David; Perriot, Romain Thibault; Pastore, Giovanni

2016-07-22

In UO 2 nuclear fuel, the retention and release of fission gas atoms such as xenon (Xe) are important for nuclear fuel performance by, for example, reducing the fuel thermal conductivity, causing fuel swelling that leads to mechanical interaction with the clad, increasing the plenum pressure and reducing the fuel–clad gap thermal conductivity. We use multi-­scale simulations to determine fission gas diffusion mechanisms as well as the corresponding rates in UO 2 under both intrinsic and irradiation conditions. In addition to Xe and Kr, the fission products Zr, Ru, Ce, Y, La, Sr and Ba have been investigated. Density functionalmore » theory (DFT) calculations are used to study formation, binding and migration energies of small clusters of Xe atoms and vacancies. Empirical potential calculations enable us to determine the corresponding entropies and attempt frequencies for migration as well as investigate the properties of large clusters or small fission gas bubbles. A continuum reaction-­diffusion model is developed for Xe and point defects based on the mechanisms and rates obtained from atomistic simulations. Effective fission gas diffusivities are then obtained by solving this set of equations for different chemical and irradiation conditions using the MARMOT phase field code. The predictions are compared to available experimental data. The importance of the large Xe U3O cluster (a Xe atom in a uranium + oxygen vacancy trap site with two bound uranium vacancies) is emphasized, which is a consequence of its high mobility and high binding energy. We find that the Xe U3O cluster gives Xe diffusion coefficients that are higher for intrinsic conditions than under irradiation over a wide range of temperatures. Under irradiation the fast-­moving Xe U3O cluster recombines quickly with irradiation-induced interstitial U ions, while this mechanism is less important for intrinsic conditions. The net result is higher concentration of the Xe U3O cluster for intrinsic conditions than under irradiation. We speculate that differences in the irradiation conditions and their impact on the Xe U3O cluster can explain the wide range of diffusivities reported in experimental studies. However, all vacancy-­mediated mechanisms underestimate the Xe diffusivity compared to the empirical radiation-­enhanced rate used in most fission gas release models. We investigate the possibility that diffusion of small fission gas bubbles or extended Xe-­vacancy clusters may give rise to the observed radiation-­enhanced diffusion coefficient. These studies highlight the importance of U divacancies and an octahedron coordination of uranium vacancies encompassing a Xe fission gas atom. The latter cluster can migrate via a multistep mechanism with a rather low effective barrier, which together with irradiation-induced clusters of uranium vacancies, gives rise to the irradiation-enhanced diffusion coefficient observed in experiments.« less

Clustering on Magnesium Surfaces – Formation and Diffusion Energies

DOE PAGES

Chu, Haijian; Huang, Hanchen; Wang, Jian

2017-07-12

The formation and diffusion energies of atomic clusters on Mg surfaces determine the surface roughness and formation of faulted structure, which in turn affect the mechanical deformation of Mg. This paper reports first principles density function theory (DFT) based quantum mechanics calculation results of atomic clustering on the low energy surfaces {0001} and {more » $$\\bar{1}$$011} . In parallel, molecular statics calculations serve to test the validity of two interatomic potentials and to extend the scope of the DFT studies. On a {0001} surface, a compact cluster consisting of few than three atoms energetically prefers a face-centered-cubic stacking, to serve as a nucleus of stacking fault. On a {$$\\bar{1}$$011} , clusters of any size always prefer hexagonal-close-packed stacking. Adatom diffusion on surface {$$\\bar{1}$$011} is high anisotropic while isotropic on surface (0001). Three-dimensional Ehrlich–Schwoebel barriers converge as the step height is three atomic layers or thicker. FInally, adatom diffusion along steps is via hopping mechanism, and that down steps is via exchange mechanism.« less

Clustering on Magnesium Surfaces – Formation and Diffusion Energies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chu, Haijian; Huang, Hanchen; Wang, Jian

The formation and diffusion energies of atomic clusters on Mg surfaces determine the surface roughness and formation of faulted structure, which in turn affect the mechanical deformation of Mg. This paper reports first principles density function theory (DFT) based quantum mechanics calculation results of atomic clustering on the low energy surfaces {0001} and {more » $$\\bar{1}$$011} . In parallel, molecular statics calculations serve to test the validity of two interatomic potentials and to extend the scope of the DFT studies. On a {0001} surface, a compact cluster consisting of few than three atoms energetically prefers a face-centered-cubic stacking, to serve as a nucleus of stacking fault. On a {$$\\bar{1}$$011} , clusters of any size always prefer hexagonal-close-packed stacking. Adatom diffusion on surface {$$\\bar{1}$$011} is high anisotropic while isotropic on surface (0001). Three-dimensional Ehrlich–Schwoebel barriers converge as the step height is three atomic layers or thicker. FInally, adatom diffusion along steps is via hopping mechanism, and that down steps is via exchange mechanism.« less

The effect of molecular shape on oligomerization of hydrophobic drugs: Molecular simulations of ciprofloxacin and nutlin

NASA Astrophysics Data System (ADS)

Li, Jianguo; Beuerman, Roger; Verma, Chandra

2018-03-01

Molecular aggregation plays a significant role in modulating the solubility, permeability, and bioactivity of drugs. The propensity to aggregate depends on hydrophobicity and on molecular shape. Molecular dynamics simulations coupled with enhanced sampling methods are used to explore the early stages of oligomerization of two drug molecules which have a strong aggregation propensity, but with contrasting molecule shapes: the antibiotic ciprofloxacin and the anticancer drug Nutlin-3A. The planar shape of ciprofloxacin induces the formation of stable oligomers at all cluster sizes. The aggregation of ciprofloxacin is driven by two-body interactions, and transferring one ciprofloxacin molecule to an existing cluster involves the desolvation of two faces and the concomitant hydrophobic interactions between the two faces; thus, the corresponding free energy of oligomerization weakly depends on the oligomer size. By contrast, Nutlin-3A has a star-shape and hence can only form stable oligomers when the cluster size is greater than 8. Free energy simulations further confirmed that the free energy of oligomer formation for Nutlin-3A becomes more favorable as the oligomer becomes larger. The aggregation of star-shaped Nutlin-3A results from many-body interactions and hence the free energy of cluster formation is strongly dependent on the size. The findings of this study provide atomistic insights into how molecular shape modulates the aggregation behavior of molecules and may be factored into the design of drugs or nano-particles.

Dielectric aggregation kinetics of cells in a uniform AC electric field.

PubMed

Tada, Shigeru; Natsuya, Tomoyuki; Tsukamoto, Akira

2014-01-01

Cell manipulation and separation technologies have potential biological and medical applications, including advanced clinical protocols such as tissue engineering. An aggregation model was developed for a human carcinoma (HeLa) cell suspension exposed to a uniform AC electric field, in order to explore the field-induced structure formation and kinetics of cell aggregates. The momentum equations of cells under the action of the dipole-dipole interaction were solved theoretically and the total time required to form linear string-like cluster was derived. The results were compared with those of a numerical simulation. Experiments using HeLa cells were also performed for comparison. The total time required to form linear string-like clusters was derived from a simple theoretical model of the cell cluster kinetics. The growth rates of the average string length of cell aggregates showed good agreement with those of the numerical simulation. In the experiment, cells were found to form massive clusters on the bottom of a chamber. The results imply that the string-like cluster grows rapidly by longitudinal attraction when the electric field is first applied and that this process slows at later times and is replaced by lateral coagulation of short strings. The findings presented here are expected to enable design of methods for the organization of three-dimensional (3D) cellular structures without the use of micro-fabricated substrates, such as 3D biopolymer scaffolds, to manipulate cells into spatial arrangement.

The Burrell Schmidt Deep Virgo Survey: Tidal Debris, Galaxy Halos, and Diffuse Intracluster Light in the Virgo Cluster

NASA Astrophysics Data System (ADS)

Mihos, J. Christopher; Harding, Paul; Feldmeier, John J.; Rudick, Craig; Janowiecki, Steven; Morrison, Heather; Slater, Colin; Watkins, Aaron

2017-01-01

We present the results of a deep imaging survey of the Virgo cluster of galaxies, concentrated around the cores of Virgo subclusters A and B. The goal of this survey was to detect and study very low surface brightness features present in Virgo, including discrete tidal features, the faint halos of luminous galaxies, and the diffuse intracluster light (ICL). Our observations span roughly 16 degrees2 in two filters, reaching a 3σ limiting depth of {μ }B = 29.5 and {μ }V = 28.5 mag arcsec-2. At these depths, our limiting systematic uncertainties are astrophysical: variations in faint background sources as well as scattered light from galactic dust. We show that this dust-scattered light is well traced by deep far-infrared imaging, making it possible to separate it from true diffuse light in Virgo. We use our imaging to trace and measure the color of the diffuse tidal streams and ICL in the Virgo core near M87, in fields adjacent to the core including the M86/M84 region, and to the south of the core around M49 and subcluster B, along with the more distant W{}\\prime cloud around NGC 4365. Overall, the bulk of the projected ICL is found in the Virgo core and within the W{}\\prime cloud; we find little evidence for an extensive ICL component in the field around M49. The bulk of the ICL we detect is fairly red in color (B - V = 0.7-0.9), indicative of old, evolved stellar populations. Based on the luminosity of the observed ICL features in the cluster, we estimate a total Virgo ICL fraction of 7%-15%. This value is somewhat smaller than that expected for massive, evolved clusters, suggesting that Virgo is still in the process of growing its extended ICL component. We also trace the shape of M87's extremely boxy outer halo out to ˜150 kpc, and show that the current tidal stripping rate from low luminosity galaxies is insufficient to have built M87's outer halo over a Hubble time. We identify a number of previously unknown low surface brightness structures around galaxies projected close to M86 and M84. The extensive diffuse light seen in the infalling W{}\\prime cloud around NGC 4365 is likely to be subsumed in the general Virgo ICL component once the group enters the cluster, illustrating the importance of group infall in generating ICL. Finally, we also identify another large and extremely low surface brightness ultradiffuse galaxy, likely in the process of being shredded by the cluster tidal field. With the survey complete, the full imaging data set is now available for public release.

Oxygen diffusion in alpha-Al2O3. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Cawley, J. D.; Halloran, J. W.; Cooper, A. R.

1984-01-01

Oxygen self diffusion coefficients were determined in single crystal alpha-Al2O3 using the gas exchange technique. The samples were semi-infinite slabs cut from five different boules with varying background impurities. The diffusion direction was parallel to the c-axis. The tracer profiles were determined by two techniques, single spectrum proton activation and secondary ion mass spectrometry. The SIMS proved to be a more useful tool. The determined diffusion coefficients, which were insensitive to impurity levels and oxygen partial pressure, could be described by D = .00151 exp (-572kJ/RT) sq m/s. The insensitivities are discussed in terms of point defect clustering. Two independent models are consistent with the findings, the first considers the clusters as immobile point defect traps which buffer changes in the defect chemistry. The second considers clusters to be mobile and oxygen diffusion to be intrinsic behavior, the mechanism for oxygen transport involving neutral clusters of Schottky quintuplets.

Observations of a nearby filament of galaxy clusters with the Sardinia Radio Telescope

NASA Astrophysics Data System (ADS)

Vacca, Valentina; Murgia, M.; Loi, F. Govoni F.; Vazza, F.; Finoguenov, A.; Carretti, E.; Feretti, L.; Giovannini, G.; Concu, R.; Melis, A.; Gheller, C.; Paladino, R.; Poppi, S.; Valente, G.; Bernardi, G.; Boschin, W.; Brienza, M.; Clarke, T. E.; Colafrancesco, S.; Enßlin, T.; Ferrari, C.; de Gasperin, F.; Gastaldello, F.; Girardi, M.; Gregorini, L.; Johnston-Hollitt, M.; Junklewitz, H.; Orrù, E.; Parma, P.; Perley, R.; Taylor, G. B.

2018-05-01

We report the detection of diffuse radio emission which might be connected to a large-scale filament of the cosmic web covering a 8° × 8° area in the sky, likely associated with a z≈0.1 over-density traced by nine massive galaxy clusters. In this work, we present radio observations of this region taken with the Sardinia Radio Telescope. Two of the clusters in the field host a powerful radio halo sustained by violent ongoing mergers and provide direct proof of intra-cluster magnetic fields. In order to investigate the presence of large-scale diffuse radio synchrotron emission in and beyond the galaxy clusters in this complex system, we combined the data taken at 1.4 GHz with the Sardinia Radio Telescope with higher resolution data taken with the NRAO VLA Sky Survey. We found 28 candidate new sources with a size larger and X-ray emission fainter than known diffuse large-scale synchrotron cluster sources for a given radio power. This new population is potentially the tip of the iceberg of a class of diffuse large-scale synchrotron sources associated with the filaments of the cosmic web. In addition, we found in the field a candidate new giant radio galaxy.

Automated segmentation of white matter fiber bundles using diffusion tensor imaging data and a new density based clustering algorithm.

PubMed

Kamali, Tahereh; Stashuk, Daniel

2016-10-01

Robust and accurate segmentation of brain white matter (WM) fiber bundles assists in diagnosing and assessing progression or remission of neuropsychiatric diseases such as schizophrenia, autism and depression. Supervised segmentation methods are infeasible in most applications since generating gold standards is too costly. Hence, there is a growing interest in designing unsupervised methods. However, most conventional unsupervised methods require the number of clusters be known in advance which is not possible in most applications. The purpose of this study is to design an unsupervised segmentation algorithm for brain white matter fiber bundles which can automatically segment fiber bundles using intrinsic diffusion tensor imaging data information without considering any prior information or assumption about data distributions. Here, a new density based clustering algorithm called neighborhood distance entropy consistency (NDEC), is proposed which discovers natural clusters within data by simultaneously utilizing both local and global density information. The performance of NDEC is compared with other state of the art clustering algorithms including chameleon, spectral clustering, DBSCAN and k-means using Johns Hopkins University publicly available diffusion tensor imaging data. The performance of NDEC and other employed clustering algorithms were evaluated using dice ratio as an external evaluation criteria and density based clustering validation (DBCV) index as an internal evaluation metric. Across all employed clustering algorithms, NDEC obtained the highest average dice ratio (0.94) and DBCV value (0.71). NDEC can find clusters with arbitrary shapes and densities and consequently can be used for WM fiber bundle segmentation where there is no distinct boundary between various bundles. NDEC may also be used as an effective tool in other pattern recognition and medical diagnostic systems in which discovering natural clusters within data is a necessity. Copyright © 2016 Elsevier B.V. All rights reserved.

Spatio-temporal cluster detection of chickenpox in Valencia, Spain in the period 2008-2012.

PubMed

Iftimi, Adina; Martínez-Ruiz, Francisco; Míguez Santiyán, Ana; Montes, Francisco

2015-05-18

Chickenpox is a highly contagious airborne disease caused by Varicella zoster, which affects nearly all non-immune children worldwide with an annual incidence estimated at 80-90 million cases. To analyze the spatiotemporal pattern of the chickenpox incidence in the city of Valencia, Spain two complementary statistical approaches were used. First, we evaluated the existence of clusters and spatio-temporal interaction; secondly, we used this information to find the locations of the spatio-temporal clusters via the space-time permutation model. The first method used detects any aggregation in our data but does not provide the spatial and temporal information. The second method gives the locations, areas and time-frame for the spatio-temporal clusters. An overall decreasing time trend, a pronounced 12-monthly periodicity and two complementary periods were observed. Several areas with high incidence, surrounding the center of the city were identified. The existence of aggregation in time and space was observed, and a number of spatio-temporal clusters were located.

New Scenario of Dynamical Heterogeneity in Supercooled Liquid and Glassy States of 2D Monatomic System.

PubMed

Van Hoang, Vo; Teboul, Victor; Odagaki, Takashi

2015-12-24

Via analysis of spatiotemporal arrangements of atoms based on their dynamics in supercooled liquid and glassy states of a 2D monatomic system with a double-well Lennard-Jones-Gauss (LJG) interaction potential, we find a new scenario of dynamical heterogeneity. Atoms with the same or very close mobility have a tendency to aggregate into clusters. The number of atoms with high mobility (and size of their clusters) increases with decreasing temperature passing over a maximum before decreasing down to zero. Position of the peak moves toward a lower temperature if mobility of atoms in clusters is lower together with an enhancement of height of the peak. In contrast, the number of atoms with very low mobility or solidlike atoms (and size of their clusters) has a tendency to increase with decreasing temperature and then it suddenly increases in the vicinity of the glass transition temperature leading to the formation of a glassy state. A sudden increase in the number of strongly correlated solidlike atoms in the vicinity of a glass transition temperature (Tg) may be an origin of a drastical increase in viscosity of the glass-forming systems approaching the glass transition. In fact, we find that the diffusion coefficient decays exponentially with a fraction of solidlike atoms exhibiting a sudden decrease in the vicinity of the glass transition region.

Subtyping of Children with Developmental Dyslexia via Bootstrap Aggregated Clustering and the Gap Statistic: Comparison with the Double-Deficit Hypothesis

ERIC Educational Resources Information Center

King, Wayne M.; Giess, Sally A.; Lombardino, Linda J.

2007-01-01

Background: The marked degree of heterogeneity in persons with developmental dyslexia has motivated the investigation of possible subtypes. Attempts have proceeded both from theoretical models of reading and the application of unsupervised learning (clustering) methods. Previous cluster analyses of data obtained from persons with reading…

Effects of midstory reduction and thinning in red-cockaded woodpecker cavity tree clusters

Treesearch

Richard N. Conner; D. Craig Rudolph

1991-01-01

The red-cockaded woodpecker's (Picoides borealis) preference for open pine forest is well known (U.S. Fish and Wildl. Serv. 1985). Encroachment of hardwood midstory within redcockaded woodpecker clusters (colonies, aggregations of cavity trees used by groups of woodpeckers, see Walters et al. 1988) is believed to cause cluster abandonment (Hopkins and Lynn 1971,...

Correlation among extinction efficiency and other parameters in an aggregate dust model

NASA Astrophysics Data System (ADS)

Dhar, Tanuj Kumar; Sekhar Das, Himadri

2017-10-01

We study the extinction properties of highly porous Ballistic Cluster-Cluster Aggregate dust aggregates in a wide range of complex refractive indices (1.4≤ n≤ 2.0, 0.001≤ k≤ 1.0) and wavelengths (0.11 {{μ }}{{m}}≤ {{λ }}≤ 3.4 {{μ }} m). An attempt has been made for the first time to investigate the correlation among extinction efficiency ({Q}{ext}), composition of dust aggregates (n,k), wavelength of radiation (λ) and size parameter of the monomers (x). If k is fixed at any value between 0.001 and 1.0, {Q}{ext} increases with increase of n from 1.4 to 2.0. {Q}{ext} and n are correlated via linear regression when the cluster size is small, whereas the correlation is quadratic at moderate and higher sizes of the cluster. This feature is observed at all wavelengths (ultraviolet to optical to infrared). We also find that the variation of {Q}{ext} with n is very small when λ is high. When n is fixed at any value between 1.4 and 2.0, it is observed that {Q}{ext} and k are correlated via a polynomial regression equation (of degree 1, 2, 3 or 4), where the degree of the equation depends on the cluster size, n and λ. The correlation is linear for small size and quadratic/cubic/quartic for moderate and higher sizes. We have also found that {Q}{ext} and x are correlated via a polynomial regression (of degree 3, 4 or 5) for all values of n. The degree of regression is found to be n and k-dependent. The set of relations obtained from our work can be used to model interstellar extinction for dust aggregates in a wide range of wavelengths and complex refractive indices.

Giant Spherical Cluster with I-C140 Fullerene Topology**

PubMed Central

Heinl, Sebastian; Peresypkina, Eugenia; Sutter, Jörg; Scheer, Manfred

2015-01-01

We report on an effective cluster expansion of CuBr-linked aggregates by the increase of the steric bulk of the CpR ligand in the pentatopic molecules [CpRFe(η5-P5)]. Using [CpBIGFe(η5-P5)] (CpBIG=C5(4-nBuC6H4)5), the novel multishell aggregate [{CpBIGFe(η5:2:1:1:1:1:1-P5)}12(CuBr)92] is obtained. It shows topological analogy to the theoretically predicted I-C140 fullerene molecule. The spherical cluster was comprehensively characterized by various methods in solution and in the solid state. PMID:26411255

Air void clustering.

DOT National Transportation Integrated Search

2015-06-01

Air void clustering around coarse aggregate in concrete has been identified as a potential source of : low strengths in concrete mixes by several Departments of Transportation around the country. Research was : carried out to (1) develop a quantitati...

Adsorption and diffusion of fructose in zeolite HZSM-5: selection of models and methods for computational studies.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cheng, L.; Curtiss, L. A.; Assary, R. S.

The adsorption and protonation of fructose in HZSM-5 have been studied for the assessment of models for accurate reaction energy calculations and the evaluation of molecular diffusivity. The adsorption and protonation were calculated using 2T, 5T, and 46T clusters as well as a periodic model. The results indicate that the reaction thermodynamics cannot be predicted correctly using small cluster models, such as 2T or 5T, because these small cluster models fail to represent the electrostatic effect of a zeolite cage, which provides additional stabilization to the ion pair formed upon the protonation of fructose. Structural parameters optimized using the 46Tmore » cluster model agree well with those of the full periodic model; however, the calculated reaction energies are in significant error due to the poor account of dispersion effects by density functional theory. The dispersion effects contribute -30.5 kcal/mol to the binding energy of fructose in the zeolite pore based on periodic model calculations that include dispersion interactions. The protonation of the fructose ternary carbon hydroxyl group was calculated to be exothermic by 5.5 kcal/mol with a reaction barrier of 2.9 kcal/mol using the periodic model with dispersion effects. Our results suggest that the internal diffusion of fructose in HZSM-5 is very likely to be energetically limited and only occurs at high temperature due to the large size of the molecule.« less

Search for low-frequency diffuse radio emission around a shock in the massive galaxy cluster MACS J0744.9+3927

NASA Astrophysics Data System (ADS)

Wilber, A.; Brüggen, M.; Bonafede, A.; Rafferty, D.; Savini, F.; Shimwell, T.; van Weeren, R. J.; Botteon, A.; Cassano, R.; Brunetti, G.; De Gasperin, F.; Wittor, D.; Hoeft, M.; Birzan, L.

2018-05-01

Merging galaxy clusters produce low-Mach-number shocks in the intracluster medium. These shocks can accelerate electrons to relativistic energies that are detectable at radio frequencies. MACS J0744.9+3927 is a massive [M500 = (11.8 ± 2.8) × 1014 M⊙], high-redshift (z = 0.6976) cluster where a Bullet-type merger is presumed to have taken place. Sunyaev-Zel'dovich maps from MUSTANG indicate that a shock, with Mach number M = 1.0-2.9 and an extension of ˜200 kpc, sits near the centre of the cluster. The shock is also detected as a brightness and temperature discontinuity in X-ray observations. To search for diffuse radio emission associated with the merger, we have imaged the cluster with the LOw Frequency ARray (LOFAR) at 120-165 MHz. Our LOFAR radio images reveal previously undetected AGN emission, but do not show clear cluster-scale diffuse emission in the form of a radio relic nor a radio halo. The region of the shock is on the western edge of AGN lobe emission from the brightest cluster galaxy. Correlating the flux of known shock-induced radio relics versus their size, we find that the radio emission overlapping the shocked region in MACS J0744.9+3927 is likely of AGN origin. We argue against the presence of a relic caused by diffusive shock acceleration and suggest that the shock is too weak to accelerate electrons from the intracluster medium.

Magic Numbers in Small Iron Clusters: A First-Principles Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Eunja; Mohrland, Andrew B.; Weck, Philippe F.

2014-10-03

We perform ab initio spin-polarized density functional calculations of Fen aggregates with n ≤ 17 atoms to reveal the origin of the observed magic numbers, which indicate particularly high stability of clusters with 7, 13 and 15 atoms. Our results clarify the controversy regarding the ground state geometry of clusters such as Fe5and indicate that magnetism plays an important role in determining the stability and magic numbers in small iron clusters.

Nucleation and growth in alkaline zinc electrodeposition An Experimental and Theoretical study

NASA Astrophysics Data System (ADS)

Desai, Divyaraj

The current work seeks to investigate the nucleation and growth of zinc electrodeposition in alkaline electrolyte, which is of commercial interest to alkaline zinc batteries for energy storage. The morphology of zinc growth places a severe limitation on the typical cycle life of such batteries. The formation of mossy zinc leads to a progressive deterioration of battery performance while zinc dendrites are responsible for sudden catastrophic battery failure. The problems are identified as the nucleation-controlled formation of mossy zinc and the transport-limited formation of dendritic zinc. Consequently, this thesis work seeks to investigate and accurately simulate the conditions under which such morphologies are formed. The nucleation and early-stage growth of Zn electrodeposits is studied on carbon-coated TEM grids. At low overpotentials, the morphology develops by aggregation at two distinct length scales: ~5 nm diameter monocrystalline nanoclusters form ~50nm diameter polycrystalline aggregates, and second, the aggregates form a branched network. Epitaxial (0002) growth above a critical overpotential leads to the formation of hexagonal single-crystals. A kinetic model is provided using the rate equations of vapor solidification to simulate the evolution of the different morphologies. On solving these equations, we show that aggregation is attributed to cluster impingement and cluster diffusion while single-crystal formation is attributed to direct attachment. The formation of dendritic zinc is investigated using in-operando transmission X-ray microscopy which is a unique technique for imaging metal electrodeposits. The nucleation density of zinc nuclei is lowered using polyaniline films to cover the active nucleation sites. The effect of overpotential is investigated and the morphology shows beautiful in-operando formation of symmetric zinc crystals. A linear perturbation model was developed to predict the growth and formation of these crystals to first-order accuracy. Existing phase-field models of solidification and electrodeposition are used to simulate the growth and formation of individual zinc crystals. The driving force for solidification models (i.e. supersaturation) is reinterpreted in terms of overpotential under the assumption of a conductive electrolyte. The final morphologies are astonishingly similar to those observed in dynamical experiments. Further, the phase-field models obey the predictions of the linear perturbation analysis, which gives good credibility to the phase-field approach to simulate electrodeposition processes.

Micro-heterogeneity versus clustering in binary mixtures of ethanol with water or alkanes.

PubMed

Požar, Martina; Lovrinčević, Bernarda; Zoranić, Larisa; Primorać, Tomislav; Sokolić, Franjo; Perera, Aurélien

2016-08-24

Ethanol is a hydrogen bonding liquid. When mixed in small concentrations with water or alkanes, it forms aggregate structures reminiscent of, respectively, the direct and inverse micellar aggregates found in emulsions, albeit at much smaller sizes. At higher concentrations, micro-heterogeneous mixing with segregated domains is found. We examine how different statistical methods, namely correlation function analysis, structure factor analysis and cluster distribution analysis, can describe efficiently these morphological changes in these mixtures. In particular, we explain how the neat alcohol pre-peak of the structure factor evolves into the domain pre-peak under mixing conditions, and how this evolution differs whether the co-solvent is water or alkane. This study clearly establishes the heuristic superiority of the correlation function/structure factor analysis to study the micro-heterogeneity, since cluster distribution analysis is insensitive to domain segregation. Correlation functions detect the domains, with a clear structure factor pre-peak signature, while the cluster techniques detect the cluster hierarchy within domains. The main conclusion is that, in micro-segregated mixtures, the domain structure is a more fundamental statistical entity than the underlying cluster structures. These findings could help better understand comparatively the radiation scattering experiments, which are sensitive to domains, versus the spectroscopy-NMR experiments, which are sensitive to clusters.

Molecular dynamics study of the role of symmetric tilt grain boundaries on the helium distribution in nickel

NASA Astrophysics Data System (ADS)

Torres, E.; Pencer, J.

2018-04-01

Helium impurities, from either direct implantation or transmutation reactions, have been associated with embrittlement in nickel-based alloys. Helium has very low solubility in nickel, and has been found to aggregate at lattice defects such as vacancies, dislocations, and grain boundaries. The retention and precipitation of helium in nickel-based alloys have deleterious effects on the material mechanical properties. However, the underlying mechanisms that lead to helium effects in the host metal are not fully understood. In the present work, we investigate the role of symmetric tilt grain boundary (STGB) structures on the distribution of helium in nickel using molecular dynamics simulations. We investigate the family of STGBs specific to the 〈 110 〉 tilt axis. The present results indicate that accumulation of helium at the grain boundary may be modulated by details of grain boundary geometry. A plausible correlation between the grain boundary energy and misorientation with the accumulation and mobility of helium is proposed. Small clusters with up to 6 helium atoms show significant interstitial mobility in the nickel bulk, but also become sites for nucleation and grow of more stable helium clusters. High-energy GBs are found mainly populated with small helium clusters. The high mobility of small clusters along the GBs indicates the role of these GBs as fast two-dimensional channels for diffusion. In contrast, the accumulation of helium in large helium clusters at low-energy STGB creates a favorable environment for the formation of large helium bubbles, indicating a potential role for low-energy STGB in promoting helium-induced GB embrittlement.

Graduates of Higher Education in the Food and Agricultural Sciences: An Analysis of Supply/Demand Relationships. Volume I--Agriculture, Natural Resources, and Veterinary Medicine.

ERIC Educational Resources Information Center

Coulter, Kyle Jane, Ed.; Stanton, Marge, Ed.

Information on the current and projected supply of and demand for graduates of higher education in the food and agricultural sciences is presented, based on federal data bases. The supply data are aggregated by 11 educational clusters, and employment demand data are aggregated by eight occupational clusters. Analysis reveals imbalances in the…

Analysis of ligand-protein exchange by Clustering of Ligand Diffusion Coefficient Pairs (CoLD-CoP).

PubMed

Snyder, David A; Chantova, Mihaela; Chaudhry, Saadia

2015-06-01

NMR spectroscopy is a powerful tool in describing protein structures and protein activity for pharmaceutical and biochemical development. This study describes a method to determine weak binding ligands in biological systems by using hierarchic diffusion coefficient clustering of multidimensional data obtained with a 400 MHz Bruker NMR. Comparison of DOSY spectrums of ligands of the chemical library in the presence and absence of target proteins show translational diffusion rates for small molecules upon interaction with macromolecules. For weak binders such as compounds found in fragment libraries, changes in diffusion rates upon macromolecular binding are on the order of the precision of DOSY diffusion measurements, and identifying such subtle shifts in diffusion requires careful statistical analysis. The "CoLD-CoP" (Clustering of Ligand Diffusion Coefficient Pairs) method presented here uses SAHN clustering to identify protein-binders in a chemical library or even a not fully characterized metabolite mixture. We will show how DOSY NMR and the "CoLD-CoP" method complement each other in identifying the most suitable candidates for lysozyme and wheat germ acid phosphatase. Copyright © 2015 Elsevier Inc. All rights reserved.

Food-resources and the influence of spatial pattern on feeding in the phoronid Phoronopsis viridis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ronan, T.E. Jr.

1978-06-01

In the intertidal zone of Bodega Harbor, California, the phoronid, Phoronopsis viridis, aggregates in clusters often composed of thousands of tightly aggregated individuals (up to 150,000/m/sup 2/). Within a dense cluster, there is a spacing problem for expansion of the lophophores. When nearest-neighbor distances are small, a stratification of feeding appendages is a workable solution to the spacing problem, allowing simultaneous expansion of clustered feeding appendages. Suspension-feeding specimens of Phoronopsis expand their lophophores and collect food items from the turbid near-bottom layers of water. Comparison of ingested items with material collected where the phoronids feed indicates a preference for smallmore » (<100 ..mu..m) organic encrusted mineral grains, floc aggregates, and fecal material, all resuspended from the depositional interface. Also taken to a lesser extent are plankton bloom species, such as diatoms and dinoflagellates. The fact that Phoronopsis forms dense assemblages in the intertidal zone has consequences when the community structure of sandflat areas is considered. Although it is probable that no single factor can explain aggregation in Phoronopsis, two possible factors, constituting strong selection pressures for cluster formation, are relative immunity from disturbance by large burrowing infauna and protection from predation by crawling predators.« less

Cluster dynamics and cluster size distributions in systems of self-propelled particles

NASA Astrophysics Data System (ADS)

Peruani, F.; Schimansky-Geier, L.; Bär, M.

2010-12-01

Systems of self-propelled particles (SPP) interacting by a velocity alignment mechanism in the presence of noise exhibit rich clustering dynamics. Often, clusters are responsible for the distribution of (local) information in these systems. Here, we investigate the properties of individual clusters in SPP systems, in particular the asymmetric spreading behavior of clusters with respect to their direction of motion. In addition, we formulate a Smoluchowski-type kinetic model to describe the evolution of the cluster size distribution (CSD). This model predicts the emergence of steady-state CSDs in SPP systems. We test our theoretical predictions in simulations of SPP with nematic interactions and find that our simple kinetic model reproduces qualitatively the transition to aggregation observed in simulations.

Positive feedback can lead to dynamic nanometer-scale clustering on cell membranes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wehrens, Martijn; Rein ten Wolde, Pieter; Mugler, Andrew, E-mail: amugler@purdue.edu

2014-11-28

Clustering of molecules on biological membranes is a widely observed phenomenon. A key example is the clustering of the oncoprotein Ras, which is known to be important for signal transduction in mammalian cells. Yet, the mechanism by which Ras clusters form and are maintained remains unclear. Recently, it has been discovered that activated Ras promotes further Ras activation. Here we show using particle-based simulation that this positive feedback is sufficient to produce persistent clusters of active Ras molecules at the nanometer scale via a dynamic nucleation mechanism. Furthermore, we find that our cluster statistics are consistent with experimental observations ofmore » the Ras system. Interestingly, we show that our model does not support a Turing regime of macroscopic reaction-diffusion patterning, and therefore that the clustering we observe is a purely stochastic effect, arising from the coupling of positive feedback with the discrete nature of individual molecules. These results underscore the importance of stochastic and dynamic properties of reaction diffusion systems for biological behavior.« less

The split in the ancient cold front in the Perseus cluster

NASA Astrophysics Data System (ADS)

Walker, Stephen A.; ZuHone, John; Fabian, Andy; Sanders, Jeremy

2018-04-01

Sloshing cold fronts in clusters, produced as the dense cluster core moves around in the cluster potential in response to in-falling subgroups, provide a powerful probe of the physics of the intracluster medium and the magnetic fields permeating it1,2. These sharp discontinuities in density and temperature rise gradually outwards with age in a characteristic spiral pattern, embedding into the intracluster medium a record of the minor merging activity of clusters: the further from the cluster centre a cold front is, the older it is. Recently, it was discovered that these cold fronts can survive out to extremely large radii in the Perseus cluster3. Here, we report on high-spatial-resolution Chandra observations of the large-scale cold front in Perseus. We find that rather than broadening through diffusion, the cold front remains extremely sharp (consistent with abrupt jumps in density) and instead is split into two sharp edges. These results show that magnetic draping can suppress diffusion for vast periods of time—around 5 Gyr—even as the cold front expands out to nearly half the cluster virial radius.

First evidence of diffuse ultra-steep-spectrum radio emission surrounding the cool core of a cluster

NASA Astrophysics Data System (ADS)

Savini, F.; Bonafede, A.; Brüggen, M.; van Weeren, R.; Brunetti, G.; Intema, H.; Botteon, A.; Shimwell, T.; Wilber, A.; Rafferty, D.; Giacintucci, S.; Cassano, R.; Cuciti, V.; de Gasperin, F.; Röttgering, H.; Hoeft, M.; White, G.

2018-05-01

Diffuse synchrotron radio emission from cosmic-ray electrons is observed at the center of a number of galaxy clusters. These sources can be classified either as giant radio halos, which occur in merging clusters, or as mini halos, which are found only in cool-core clusters. In this paper, we present the first discovery of a cool-core cluster with an associated mini halo that also shows ultra-steep-spectrum emission extending well beyond the core that resembles radio halo emission. The large-scale component is discovered thanks to LOFAR observations at 144 MHz. We also analyse GMRT observations at 610 MHz to characterise the spectrum of the radio emission. An X-ray analysis reveals that the cluster is slightly disturbed, and we suggest that the steep-spectrum radio emission outside the core could be produced by a minor merger that powers electron re-acceleration without disrupting the cool core. This discovery suggests that, under particular circumstances, both a mini and giant halo could co-exist in a single cluster, opening new perspectives for particle acceleration mechanisms in galaxy clusters.

Air void clustering : [technical summary].

DOT National Transportation Integrated Search

2015-06-01

Air void clustering around coarse aggregate in concrete has been : identified as a potential source of low strengths in concrete mixes by : several Departments of Transportation around the country. Research : was carried out to (1) develop a quantita...

An approach to online network monitoring using clustered patterns

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Jinoh; Sim, Alex; Suh, Sang C.

Network traffic monitoring is a core element in network operations and management for various purposes such as anomaly detection, change detection, and fault/failure detection. In this study, we introduce a new approach to online monitoring using a pattern-based representation of the network traffic. Unlike the past online techniques limited to a single variable to summarize (e.g., sketch), the focus of this study is on capturing the network state from the multivariate attributes under consideration. To this end, we employ clustering with its benefit of the aggregation of multidimensional variables. The clustered result represents the state of the network with regardmore » to the monitored variables, which can also be compared with the previously observed patterns visually and quantitatively. Finally, we demonstrate the proposed method with two popular use cases, one for estimating state changes and the other for identifying anomalous states, to confirm its feasibility.« less

An approach to online network monitoring using clustered patterns

DOE PAGES

Kim, Jinoh; Sim, Alex; Suh, Sang C.; ...

2017-03-13

Network traffic monitoring is a core element in network operations and management for various purposes such as anomaly detection, change detection, and fault/failure detection. In this study, we introduce a new approach to online monitoring using a pattern-based representation of the network traffic. Unlike the past online techniques limited to a single variable to summarize (e.g., sketch), the focus of this study is on capturing the network state from the multivariate attributes under consideration. To this end, we employ clustering with its benefit of the aggregation of multidimensional variables. The clustered result represents the state of the network with regardmore » to the monitored variables, which can also be compared with the previously observed patterns visually and quantitatively. Finally, we demonstrate the proposed method with two popular use cases, one for estimating state changes and the other for identifying anomalous states, to confirm its feasibility.« less

An efficient laser vaporization source for chemically modified metal clusters characterized by thermodynamics and kinetics

NASA Astrophysics Data System (ADS)

Masubuchi, Tsugunosuke; Eckhard, Jan F.; Lange, Kathrin; Visser, Bradley; Tschurl, Martin; Heiz, Ulrich

2018-02-01

A laser vaporization cluster source that has a room for cluster aggregation and a reactor volume, each equipped with a pulsed valve, is presented for the efficient gas-phase production of chemically modified metal clusters. The performance of the cluster source is evaluated through the production of Ta and Ta oxide cluster cations, TaxOy+ (y ≥ 0). It is demonstrated that the cluster source produces TaxOy+ over a wide mass range, the metal-to-oxygen ratio of which can easily be controlled by changing the pulse duration that influences the amount of reactant O2 introduced into the cluster source. Reaction kinetic modeling shows that the generation of the oxides takes place under thermalized conditions at less than 300 K, whereas metal cluster cores are presumably created with excess heat. These characteristics are also advantageous to yield "reaction intermediates" of interest via reactions between clusters and reactive molecules in the cluster source, which may subsequently be mass selected for their reactivity measurements.

Information Theory and Voting Based Consensus Clustering for Combining Multiple Clusterings of Chemical Structures.

PubMed

Saeed, Faisal; Salim, Naomie; Abdo, Ammar

2013-07-01

Many consensus clustering methods have been applied in different areas such as pattern recognition, machine learning, information theory and bioinformatics. However, few methods have been used for chemical compounds clustering. In this paper, an information theory and voting based algorithm (Adaptive Cumulative Voting-based Aggregation Algorithm A-CVAA) was examined for combining multiple clusterings of chemical structures. The effectiveness of clusterings was evaluated based on the ability of the clustering method to separate active from inactive molecules in each cluster, and the results were compared with Ward's method. The chemical dataset MDL Drug Data Report (MDDR) and the Maximum Unbiased Validation (MUV) dataset were used. Experiments suggest that the adaptive cumulative voting-based consensus method can improve the effectiveness of combining multiple clusterings of chemical structures. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Spatial arrangement of legionella colonies in intact biofilms from a model cooling water system.

PubMed

Taylor, Michael; Ross, Kirstin; Bentham, Richard

2013-01-01

There is disagreement among microbiologists about whether Legionella requires a protozoan host in order to replicate. This research sought to determine where in biofilm Legionellae are found and whether all biofilm associated Legionella would be located within protozoan hosts. While it is accepted that Legionella colonizes biofilm, its life cycle and nutritional fastidiousness suggest that Legionella employs multiple survival strategies to persist within microbial systems. Fluorescent in situ hybridization (FISH) and confocal laser scanning microscopy (CLSM) demonstrated an undulating biofilm surface architecture and a roughly homogenous distribution of heterotrophic bacteria with clusters of protozoa. Legionella displayed 3 distinct spatial arrangements either contained within or directly associated with protozoa, or dispersed in loosely associated clusters or in tightly packed aggregations of cells forming dense colonial clusters. The formation of discreet clusters of tightly packed Legionella suggests that colony formation is influenced by specific environmental conditions allowing for limited extracellular replication. This work represents the first time that an environmentally representative, multispecies biofilm containing Legionella has been fluorescently tagged and Legionella colony morphology noted within a complex microbial system.

Lagrangian analysis by clustering. An example in the Nordic Seas.

NASA Astrophysics Data System (ADS)

Koszalka, Inga; Lacasce, Joseph H.

2010-05-01

We propose a new method for obtaining average velocities and eddy diffusivities from Lagrangian data. Rather than grouping the drifter-derived velocities in uniform geographical bins, as is commonly done, we group a specified number of nearest-neighbor velocities. This is done via a clustering algorithm operating on the instantaneous positions of the drifters. Thus it is the data distribution itself which determines the positions of the averages and the areal extent of the clusters. A major advantage is that because the number of members is essentially the same for all clusters, the statistical accuracy is more uniform than with geographical bins. We illustrate the technique using synthetic data from a stochastic model, employing a realistic mean flow. The latter is an accurate representation of the surface currents in the Nordic Seas and is strongly inhomogeneous in space. We use the clustering algorithm to extract the mean velocities and diffusivities (both of which are known from the stochastic model). We also compare the results to those obtained with fixed geographical bins. Clustering is more successful at capturing spatial variability of the mean flow and also improves convergence in the eddy diffusivity estimates. We discuss both the future prospects and shortcomings of the new method.

Differential dynamic microscopy of weakly scattering and polydisperse protein-rich clusters

NASA Astrophysics Data System (ADS)

Safari, Mohammad S.; Vorontsova, Maria A.; Poling-Skutvik, Ryan; Vekilov, Peter G.; Conrad, Jacinta C.

2015-10-01

Nanoparticle dynamics impact a wide range of biological transport processes and applications in nanomedicine and natural resource engineering. Differential dynamic microscopy (DDM) was recently developed to quantify the dynamics of submicron particles in solutions from fluctuations of intensity in optical micrographs. Differential dynamic microscopy is well established for monodisperse particle populations, but has not been applied to solutions containing weakly scattering polydisperse biological nanoparticles. Here we use bright-field DDM (BDDM) to measure the dynamics of protein-rich liquid clusters, whose size ranges from tens to hundreds of nanometers and whose total volume fraction is less than 10-5. With solutions of two proteins, hemoglobin A and lysozyme, we evaluate the cluster diffusion coefficients from the dependence of the diffusive relaxation time on the scattering wave vector. We establish that for weakly scattering populations, an optimal thickness of the sample chamber exists at which the BDDM signal is maximized at the smallest sample volume. The average cluster diffusion coefficient measured using BDDM is consistently lower than that obtained from dynamic light scattering at a scattering angle of 90∘. This apparent discrepancy is due to Mie scattering from the polydisperse cluster population, in which larger clusters preferentially scatter more light in the forward direction.

Cross-scale analysis of cluster correspondence using different operational neighborhoods

NASA Astrophysics Data System (ADS)

Lu, Yongmei; Thill, Jean-Claude

2008-09-01

Cluster correspondence analysis examines the spatial autocorrelation of multi-location events at the local scale. This paper argues that patterns of cluster correspondence are highly sensitive to the definition of operational neighborhoods that form the spatial units of analysis. A subset of multi-location events is examined for cluster correspondence if they are associated with the same operational neighborhood. This paper discusses the construction of operational neighborhoods for cluster correspondence analysis based on the spatial properties of the underlying zoning system and the scales at which the zones are aggregated into neighborhoods. Impacts of this construction on the degree of cluster correspondence are also analyzed. Empirical analyses of cluster correspondence between paired vehicle theft and recovery locations are conducted on different zoning methods and across a series of geographic scales and the dynamics of cluster correspondence patterns are discussed.

The Outer Limits of Galaxy Clusters: Observations to the Virial Radius with Suzaku, XMM,and Chandra

NASA Technical Reports Server (NTRS)

Miller, Eric D.; Bautz, Marshall; George, Jithin; Mushotzky, Richard; Davis, David; Henry, J. Patrick

2012-01-01

The outskirts of galaxy clusters, near the virial radius, remain relatively unexplored territory and yet are vital to our understanding of cluster growth, structure, and mass. In this presentation, we show the first results from a program to constrain the sate of the outer intra-cluster medium (ICM) in a large sample of galaxy clusters, exploiting the strengths of three complementary X-ray observatories: Suzaku (low, stable background), XMM-Newton (high sensitivity),and Chandra (good spatial resolution). By carefully combining observations from the cluster core to beyond r200, we are able to identify and reduce systematic uncertainties that would impede our spatial and spectral analysis using a single telescope. Our sample comprises nine clusters at z is approximately 0.1-0.2 fully covered in azimuth to beyond r200, and our analysis indicates that the ICM is not in hydrostatic equilibrium in the cluster outskirts, where we see clear azimuthal variations in temperature and surface brightness. In one of the clusters, we are able to measure the diffuse X-ray emission well beyond r200, and we find that the entropy profile and the gas fraction are consistent with expectations from theory and numerical simulations. These results stand in contrast to recent studies which point to gas clumping in the outskirts; the extent to which differences of cluster environment or instrumental effects factor in this difference remains unclear. From a broader perspective, this project will produce a sizeable fiducial data set for detailed comparison with high-resolution numerical simulations.

Physico-Pathologic Mechanisms Involved in Neurodegeneration: Misfolded Protein-Plasma Membrane Interactions.

PubMed

Shrivastava, Amulya Nidhi; Aperia, Anita; Melki, Ronald; Triller, Antoine

2017-07-05

Several neurodegenerative disorders, such as Alzheimer's and Parkinson's disease, are characterized by prominent loss of synapses and neurons associated with the presence of abnormally structured or misfolded protein assemblies. Cell-to-cell transfer of misfolded proteins has been proposed for the intra-cerebral propagation of these diseases. When released, misfolded proteins diffuse in the 3D extracellular space before binding to the plasma membrane of neighboring cells, where they diffuse on a 2D plane. This reduction in diffusion dimension and the cell surface molecular crowding promote deleterious interactions with native membrane proteins, favoring clustering and further aggregation of misfolded protein assemblies. These processes open up new avenues for therapeutics development targeting the initial interactions of deleterious proteins with the plasma membrane or the subsequent pathological signaling. Copyright © 2017 Elsevier Inc. All rights reserved.

Differential regulation by ATP versus ADP further links CaMKII aggregation to ischemic conditions

PubMed Central

Vest, Rebekah S.; O’Leary, Heather; Bayer, K. Ulrich

2009-01-01

CaMKII, a major mediator of synaptic plasticity, forms extra-synaptic clusters under ischemic conditions. This study further supports self-aggregation of CaMKII holoenzymes as the underlying mechanism. Aggregation in vitro was promoted by mimicking ischemic conditions: low pH (6.8 or less), Ca2+ (and calmodulin), and low ATP and/or high ADP concentration. Mutational analysis showed that high ATP prevented aggregation by a mechanism involving T286 auto-phosphorylation, and indicated requirement for nucleotide binding but not auto-phosphorylation also for extra-synaptic clustering within neurons. These results clarify a previously apparent paradox in the nucleotide and phosphorylation requirement of aggregation, and support a mechanism that involves inter-holoenzyme T286-region/T-site interaction. PMID:19840793

Giant Spherical Cluster with I-C140 Fullerene Topology.

PubMed

Heinl, Sebastian; Peresypkina, Eugenia; Sutter, Jörg; Scheer, Manfred

2015-11-02

We report on an effective cluster expansion of CuBr-linked aggregates by the increase of the steric bulk of the Cp(R) ligand in the pentatopic molecules [Cp(R)Fe(η(5)-P5)]. Using [Cp(BIG)Fe(η(5)-P5)] (Cp(BIG)=C5(4-nBuC6H4)5), the novel multishell aggregate [{Cp(BIG)Fe(η(5:2:1:1:1:1:1)-P5)}12(CuBr)92] is obtained. It shows topological analogy to the theoretically predicted I-C140 fullerene molecule. The spherical cluster was comprehensively characterized by various methods in solution and in the solid state. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Interaction of multiple biomimetic antimicrobial polymers with model bacterial membranes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baul, Upayan, E-mail: upayanb@imsc.res.in; Vemparala, Satyavani, E-mail: vani@imsc.res.in; Kuroda, Kenichi, E-mail: kkuroda@umich.edu

Using atomistic molecular dynamics simulations, interaction of multiple synthetic random copolymers based on methacrylates on prototypical bacterial membranes is investigated. The simulations show that the cationic polymers form a micellar aggregate in water phase and the aggregate, when interacting with the bacterial membrane, induces clustering of oppositely charged anionic lipid molecules to form clusters and enhances ordering of lipid chains. The model bacterial membrane, consequently, develops lateral inhomogeneity in membrane thickness profile compared to polymer-free system. The individual polymers in the aggregate are released into the bacterial membrane in a phased manner and the simulations suggest that the most probablemore » location of the partitioned polymers is near the 1-palmitoyl-2-oleoyl-phosphatidylglycerol (POPG) clusters. The partitioned polymers preferentially adopt facially amphiphilic conformations at lipid-water interface, despite lacking intrinsic secondary structures such as α-helix or β-sheet found in naturally occurring antimicrobial peptides.« less

Polyalanine expansions drive a shift into α-helical clusters without amyloid-fibril formation.

PubMed

Polling, Saskia; Ormsby, Angelique R; Wood, Rebecca J; Lee, Kristie; Shoubridge, Cheryl; Hughes, James N; Thomas, Paul Q; Griffin, Michael D W; Hill, Andrew F; Bowden, Quill; Böcking, Till; Hatters, Danny M

2015-12-01

Polyglutamine (polyGln) expansions in nine human proteins result in neurological diseases and induce the proteins' tendency to form β-rich amyloid fibrils and intracellular deposits. Less well known are at least nine other human diseases caused by polyalanine (polyAla)-expansion mutations in different proteins. The mechanisms of how polyAla aggregates under physiological conditions remain unclear and controversial. We show here that aggregation of polyAla is mechanistically dissimilar to that of polyGln and hence does not exhibit amyloid kinetics. PolyAla assembled spontaneously into α-helical clusters with diverse oligomeric states. Such clustering was pervasive in cells irrespective of visible aggregate formation, and it disrupted the normal physiological oligomeric state of two human proteins natively containing polyAla: ARX and SOX3. This self-assembly pattern indicates that polyAla expansions chronically disrupt protein behavior by imposing a deranged oligomeric status.

Communication: Diverse nanoscale cluster dynamics: Diffusion of 2D epitaxial clusters

NASA Astrophysics Data System (ADS)

Lai, King C.; Evans, James W.; Liu, Da-Jiang

2017-11-01

The dynamics of nanoscale clusters can be distinct from macroscale behavior described by continuum formalisms. For diffusion of 2D clusters of N atoms in homoepitaxial systems mediated by edge atom hopping, macroscale theory predicts simple monotonic size scaling of the diffusion coefficient, DN ˜ N-β, with β = 3/2. However, modeling for nanoclusters on metal(100) surfaces reveals that slow nucleation-mediated diffusion displaying weak size scaling β < 1 occurs for "perfect" sizes Np = L2 and L(L+1) for integer L = 3,4,… (with unique square or near-square ground state shapes), and also for Np+3, Np+4,…. In contrast, fast facile nucleation-free diffusion displaying strong size scaling β ≈ 2.5 occurs for sizes Np+1 and Np+2. DN versus N oscillates strongly between the slowest branch (for Np+3) and the fastest branch (for Np+1). All branches merge for N = O(102), but macroscale behavior is only achieved for much larger N = O(103). This analysis reveals the unprecedented diversity of behavior on the nanoscale.

Determination of Arctic sea ice variability modes on interannual timescales via nonhierarchical clustering

NASA Astrophysics Data System (ADS)

Fučkar, Neven-Stjepan; Guemas, Virginie; Massonnet, François; Doblas-Reyes, Francisco

2015-04-01

Over the modern observational era, the northern hemisphere sea ice concentration, age and thickness have experienced a sharp long-term decline superimposed with strong internal variability. Hence, there is a crucial need to identify robust patterns of Arctic sea ice variability on interannual timescales and disentangle them from the long-term trend in noisy datasets. The principal component analysis (PCA) is a versatile and broadly used method for the study of climate variability. However, the PCA has several limiting aspects because it assumes that all modes of variability have symmetry between positive and negative phases, and suppresses nonlinearities by using a linear covariance matrix. Clustering methods offer an alternative set of dimension reduction tools that are more robust and capable of taking into account possible nonlinear characteristics of a climate field. Cluster analysis aggregates data into groups or clusters based on their distance, to simultaneously minimize the distance between data points in a given cluster and maximize the distance between the centers of the clusters. We extract modes of Arctic interannual sea-ice variability with nonhierarchical K-means cluster analysis and investigate the mechanisms leading to these modes. Our focus is on the sea ice thickness (SIT) as the base variable for clustering because SIT holds most of the climate memory for variability and predictability on interannual timescales. We primarily use global reconstructions of sea ice fields with a state-of-the-art ocean-sea-ice model, but we also verify the robustness of determined clusters in other Arctic sea ice datasets. Applied cluster analysis over the 1958-2013 period shows that the optimal number of detrended SIT clusters is K=3. Determined SIT cluster patterns and their time series of occurrence are rather similar between different seasons and months. Two opposite thermodynamic modes are characterized with prevailing negative or positive SIT anomalies over the Arctic basin. The intermediate mode, with negative anomalies centered on the East Siberian shelf and positive anomalies along the North American side of the basin, has predominately dynamic characteristics. The associated sea ice concentration (SIC) clusters vary more between different seasons and months, but the SIC patterns are physically framed by the SIT cluster patterns.

Radiative properties of flame-generated soot

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koeylue, U.O.; Faeth, G.M.

1993-05-01

Approximate methods for estimating the optical properties of flame-generated soot aggregates were evaluated using existing computer simulations and measurements in the visible and near-infrared portions of the spectrum. The following approximate methods were evaluated for both individual aggregates and polydisperse aggregate populations: the Rayleigh scattering approximation, Mie scattering for an equivalent sphere, and Rayleigh-Debye-Gans (R-D-G) scattering for both given and fractal aggregates. Results of computer simulations involved both prescribed aggregate geometry and numerically generated aggregates by cluster-cluster aggregation; multiple scattering was considered exactly using the mean-field approximation, and ignored using the R-D-G approximation. Measurements involved the angular scattering properties ofmore » soot in the postflame regions of both premixed and nonpremixed flames. The results show that available computer simulations and measurements of soot aggregate optical properties are not adequate to provide a definitive evaluation of the approximate prediction methods. 40 refs., 7 figs., 1 tab.« less

Green-noise halftoning with dot diffusion

NASA Astrophysics Data System (ADS)

Lippens, Stefaan; Philips, Wilfried

2007-02-01

Dot diffusion is a halftoning technique that is based on the traditional error diffusion concept, but offers a high degree of parallel processing by its block based approach. Traditional dot diffusion however suffers from periodicity artifacts. To limit the visibility of these artifacts, we propose grid diffusion, which applies different class matrices for different blocks. Furthermore, in this paper we will discuss two approaches in the dot diffusion framework to generate green-noise halftone patterns. The first approach is based on output dependent feedback (hysteresis), analogous to the standard green-noise error diffusion techniques. We observe that the resulting halftones are rather coarse and highly dependent on the used dot diffusion class matrices. In the second approach we don't limit the diffusion to the nearest neighbors. This leads to less coarse halftones, compared to the first approach. The drawback is that it can only cope with rather limited cluster sizes. We can reduce these drawbacks by combining the two approaches.

Chemistry and Physics of Solid Surfaces 5

DTIC Science & Technology

1984-04-01

associated with dimers and trimers, Type 2 particles form large clusters of 2000-5000 A size in aqueous solution. Luminescence studies carried out with...and rates of energy transfer, real time measurements using ultrashort laser pulses hold great promise. With the possible exception of the stimulated...the dynamic prop- erties of such clusters . The clusters are not stationary entities as origi- nally envisioned. Instead even fairly large aggregates

Universal patterns of equilibrium cluster growth in aqueous sugars observed by dynamic light scattering.

PubMed

Sidebottom, D L; Tran, Tri D

2010-11-01

Dynamic light scattering performed on aqueous solutions of three sugars (glucose, maltose and sucrose) reveal a common pattern of sugar cluster formation with a narrow cluster size distribution. In each case, equilibrium clusters form whose size increases with increasing sugar content in an identical power law manner in advance of a common, critical-like, percolation threshold near 83 wt % sugar. The critical exponent of the power law divergence of the cluster size varies with temperature, increasing with decreasing temperature, due to changes in the strength of the intermolecular hydrogen bond and appears to vanish for temperatures in excess of 90 °C. Detailed analysis of the cluster growth process suggests a two-stage process: an initial cluster phase formed at low volume fractions, ϕ, consisting of noninteracting, monodisperse sugar clusters whose size increases ϕ(1/3) followed by an aggregation stage, active at concentrations above about ϕ=40%, where cluster-cluster contact first occurs.

Clusters of circulating tumor cells traverse capillary-sized vessels

PubMed Central

Au, Sam H.; Storey, Brian D.; Moore, John C.; Tang, Qin; Chen, Yeng-Long; Javaid, Sarah; Sarioglu, A. Fatih; Sullivan, Ryan; Madden, Marissa W.; O’Keefe, Ryan; Haber, Daniel A.; Maheswaran, Shyamala; Langenau, David M.; Stott, Shannon L.; Toner, Mehmet

2016-01-01

Multicellular aggregates of circulating tumor cells (CTC clusters) are potent initiators of distant organ metastasis. However, it is currently assumed that CTC clusters are too large to pass through narrow vessels to reach these organs. Here, we present evidence that challenges this assumption through the use of microfluidic devices designed to mimic human capillary constrictions and CTC clusters obtained from patient and cancer cell origins. Over 90% of clusters containing up to 20 cells successfully traversed 5- to 10-μm constrictions even in whole blood. Clusters rapidly and reversibly reorganized into single-file chain-like geometries that substantially reduced their hydrodynamic resistances. Xenotransplantation of human CTC clusters into zebrafish showed similar reorganization and transit through capillary-sized vessels in vivo. Preliminary experiments demonstrated that clusters could be disrupted during transit using drugs that affected cellular interaction energies. These findings suggest that CTC clusters may contribute a greater role to tumor dissemination than previously believed and may point to strategies for combating CTC cluster-initiated metastasis. PMID:27091969

The Spatial Scale of Convective Aggregation in Cloud Resolving Simulations of Radiative Convective Equilibrium

NASA Astrophysics Data System (ADS)

Patrizio, Casey

A three-dimensional cloud-resolving model (CRM) was used to investigate the preferred separation distance between humid, rainy regions formed by convective aggregation in radiative-convective equilibrium without rotation. We performed the simulations with doubly-periodic square domains of widths 768 km, 1536 km and 3072 km over a time period of about 200 days. The simulations in the larger domains were initialized using multiple copies of the results in the small domain at day 90, plus a small perturbation. With all three domain sizes, the simulations evolved to a single statistically steady convective cluster surrounded by a broader region of dry, subsiding air by about day 150. In the largest domain case, however, we found that an additional convective cluster formed when we the simulation was run for an extended period of time. Specifically, a smaller convective cluster formed at around day 185 at a maximum radial distance from the larger cluster and then re-merged with the larger cluster after about 10 days. We explored how the aggregated state was different in each domain case, before the smaller cluster formed in the large domain. In particular, we investigated changes in the radial structure of the aggregated state by calculating profiles for the water, dynamics and radiation as a function of distance from the center of the convective region. Changes in the vertical structure were also investigated by compositing on the convective region and dry, subsiding region at each height. We found that, with increasing domain size, the convective region boundary layer became more buoyant, the convective cores reached deeper into the troposphere, the mesoscale convective updraft became weaker, and the mesoscale convective region spread out. Additionally, as the domain size was increased, conditions in the remote environment became favorable for convection. We describe a physical mechanism for the weakening of the mesoscale convective updraft and associated broadening of the convective region with increasing domain size, which involves mid-level stable layer enhancement as a result of the deeper convection. Finally, a simple analytical model of the aggregated state was used to explore the dependency of the convective fractional area on the domain size. The simple model solutions that had net radiative cooling and surface evaporation in the convective region were consistent with the simulation results. In particular, the solutions captured the broadening of the convective region, the weakening of the convective region updraft, as well as the positive and declining gross moist stability (GMS) that occurred with increasing domain size in the simulations. Furthermore, the simple model transitioned from positive to negative GMS at a domain length of about 7000 km because the convective region boundary layer became progressively more humid with increasing domain size. This suggests that the spatial scale of the aggregated RCE state in the simulations would be limited to a length scale of about 7000 km, as convectively-active areas are commonly observed to have positive GMS. This work additionally suggests that the processes that influence the water vapor content in the convective region boundary layer, such as convectively-driven turbulent water vapor fluxes, are important for determining the spatial scale of the aggregated RCE state.

Evolution of Radiation Induced Defects in SiC: A Multiscale Simulation Approach

NASA Astrophysics Data System (ADS)

Jiang, Hao

Because of various excellent properties, SiC has been proposed for many applications in nuclear reactors including cladding layers in fuel rod, fission products container in TRISO fuel, and first wall/blanket in magnetic controlled fusion reactors. Upon exposure to high energy radiation environments, point defects and defect clusters are generated in materials in amounts significantly exceeding their equilibrium concentrations. The accumulation of defects can lead to undesired consequences such as crystalline-to-amorphous transformation1, swelling, and embrittlement, and these phenomena can adversely affect the lifetime of SiC based components in nuclear reactors. It is of great importance to understand the accumulation process of these defects in order to estimate change in properties of this material and to design components with superior ability to withstand radiation damages. Defect clusters are widely in SiC irradiated at the operation temperatures of various reactors. These clusters are believed to cause more than half of the overall swelling of irradiated SiC and can potentially lead to lowered thermal conductivity and mechanical strength. It is critical to understand the formation and growth of these clusters. Diffusion of these clusters is one importance piece to determine the growth rate of clusters; however it is unclear so far due to the challenges in simulating rare events. Using a combination of kinetic Activation Relaxation Technique with empirical potential and ab initio based climbing image nudged elastic band method, I performed an extensive search of the migration paths of the most stable carbon tri-interstitial cluster in SiC. This research reveals paths with the lowest energy barriers to migration, rotation, and dissociation of the most stable cluster. Based on these energy barriers, I concluded defect clusters are thermally immobile at temperatures lower than 1500 K and can dissociate into smaller clusters and single interstitials at temperatures beyond that. Even though clusters cannot diffuse by thermal vibrations, we found they can migrate at room temperature under the influence of electron radiation. This is the first direct observation of radiation-induced diffusion of defect clusters in bulk materials. We show that the underlying mechanism of this athermal diffusion is elastic collision between incoming electrons and cluster atoms. Our findings suggest that defect clusters may be mobile under certain irradiation conditions, changing current understanding of cluster annealing process in irradiated SiC. With the knowledge of cluster diffusion in SiC demonstrated in this thesis, we now become able to predict cluster evolution in SiC with good agreement with experimental measurements. This ability can enable us to estimate changes in many properties of irradiated SiC relevant for its applications in reactors. Internal interfaces such as grain boundaries can behave as sinks to radiation induced defects. The ability of GBs to absorb, transport, and annihilate radiation-induced defects (sink strength) is important to understand radiation response of polycrystalline materials and to better design interfaces for improved resistance to radiation damage. Nowadays, it is established GBs' sink strength is not a static property but rather evolves with many factors, including radiation environments, grain size, and GB microstructure. In this thesis, I investigated the response of small-angle tilt and twist GBs to point defects fluxes in SiC. First of all, I found the pipe diffusion of interstitials in tilt GBs is slower than bulk diffusion. This is because the increased interatomic distance at dislocation cores raises the migration barrier of interstitial dumbbells. Furthermore, I show that both the annihilation of interstitials at jogs and jog nucleation from clusters are diffusion-controlled and can occur under off-stoichiometric interstitial fluxes. Finally, a dislocation line model is developed to predict the role of tilt GBs in annihilating radiation damage. The model predicts the role of tilt GBs in annihilating defects depends on the rate of defects segregation to and diffusion along tilt GBs. Tilt GBs mainly serve as diffusion channel for defects to reach other sinks when defect diffusivity is high at boundaries. When defect diffusivity is low, most of the defects segregated to tilt GBs are annihilated by dislocation climb. Up-to-date, the response of twist GBs under irradiation has been rarely reported in literature and is still unclear. It is important to develop atom scale insight on this question in order to predict twist GBs' sink strength for a better understanding of radiation response of polycrystalline materials. By using a combination of molecular dynamics and grand canonical Monte Carlo, here I demonstrate the defect kinetics in {001} and {111} twist GBs and the microstructural evolution of these GBs under defect fluxes in SiC. I found due to the deep potential well for interstitials at dislocation intersections within the interface, the mobility of defects on dislocation grid is retard and this leads to defect accumulation at GBs for many cases. Furthermore, I conclude both types of twist GBs have to form mixed dislocations with edge component in order to absorb accumulated interstitials at the interface. The formation of mixed dislocation is either by interstitial loop nucleation or by dislocation reactions at the interface. The continuous formation and climb of these mixed dislocations make twist GBs unsaturatable sinks to radiation induced defects.

Properties of small Ar sub N-1 K/+/ ionic clusters

NASA Technical Reports Server (NTRS)

Etters, R. D.; Danilowicz, R.; Dugan, J.

1977-01-01

A self-consistent formalism is developed that, based upon a many-body potential, dynamically determines the thermodynamic properties of ionic clusters without an a priori designation of the equilibrium structures. Aggregates consisting of a single closed shell K(+) ion and N-1 isoelectronic argon atoms were studied. The clusters form crystallites at low temperatures, and melting transitions and spontaneous dissociations are indicated. The results confirm experimental evidence that shows that ionic clusters become less stable with increasing N. The crystallite structures formed by four different clusters are isosceles triangle, skewed form, octahedron with ion in the middle, and icosahedron with the ion in the middle.

Trapping of Li(+) Ions by [ThFn](4-n) Clusters Leading to Oscillating Maxwell-Stefan Diffusivity in the Molten Salt LiF-ThF4.

PubMed

Chakraborty, Brahmananda; Kidwai, Sharif; Ramaniah, Lavanya M

2016-08-18

A molten salt mixture of lithium fluoride and thorium fluoride (LiF-ThF4) serves as a fuel as well as a coolant in the most sophisticated molten salt reactor (MSR). Here, we report for the first time dynamic correlations, Onsager coefficients, Maxwell-Stefan (MS) diffusivities, and the concentration dependence of density and enthalpy of the molten salt mixture LiF-ThF4 at 1200 K in the composition range of 2-45% ThF4 and also at eutectic composition in the temperature range of 1123-1600 K using Green-Kubo formalism and equilibrium molecular dynamics simulations. We have observed an interesting oscillating pattern for the MS diffusivity for the cation-cation pair, in which ĐLi-Th oscillates between positive and negative values with the amplitude of the oscillation reducing as the system becomes rich in ThF4. Through the velocity autocorrelation function, vibrational density of states, radial distribution function analysis, and structural snapshots, we establish an interplay between the local structure and multicomponent dynamics and predict that formation of negatively charged [ThFn](4-n) clusters at a higher ThF4 mole % makes positively charged Li(+) ions oscillate between different clusters, with their range of motion reducing as the number of [ThFn](4-n) clusters increases, and finally Li(+) ions almost get trapped at a higher ThF4% when the electrostatic force on Li(+) exerted by various surrounding clusters gets balanced. Although reports on variations of density and enthalpy with temperature exist in the literature, for the first time we report variations of the density and enthalpy of LiF-ThF4 with the concentration of ThF4 (mole %) and fit them with the square root function of ThF4 concentration, which will be very useful for experimentalists to obtain data over a range of concentrations from fitting the formula for design purposes. The formation of [ThFn](4-n) clusters and the reduction in the diffusivity of the ions at a higher ThF4% may limit the percentage of ThF4 that can be used in the MSR to optimize the neutron economy.

Nanoparticles in Mesostructured Polymers: Stabilizations and Morphology Selection

NASA Astrophysics Data System (ADS)

Kim, Jaeup; O'Shaughnessy, Ben

2002-03-01

A major challenge in the rapidly developing field of nano-materials is finding ways to create delicate spatial arrangements of nano-sized particles. Nanostructured polymer phases and ultrathin polymer films offer potential templates to spontaneously generate this spatial organization. Here we present theory of such systems. Our conclusions are as follows. (1) Nanoparticles tending to aggregate into clusters under van der Waals attractions may be stabilized in a stretched polymer environment as offered by tethered thin film brushes or lamellar diblock phases. By extending the hydrodynamic analogy of Williams and Pincus to the real case of the end-annealed Semenov brush, we show cluster formation is strongly influenced: disc-shaped clusters are suppressed in favor of extended cylindrical forms. (2) The final morphology of extended nanoparticle aggregates depends on the polymer environment. If the nanoparticle/air/polymer surface tensions and the degree of chain stretching satisfy certain conditions, the polymer media selects the length scale of nanoparticle clusters. This offers the possibility of tuning nanoparticle aggregate morphology by suitable choice of polymeric media. Our predictions are consistent with experiments at Columbia by Levicky, Durning, Cerise and Liu demonstrating nanoparticle stabilization and morphology selection in ultrathin end-tethered polymer films.

Water clustering in glassy polymers.

PubMed

Davis, Eric M; Elabd, Yossef A

2013-09-12

In this study, water solubility and water clustering in several glassy polymers, including poly(methyl methacrylate) (PMMA), poly(styrene) (PS), and poly(vinylpyrrolidone) (PVP), were measured using both quartz spring microbalance (QSM) and Fourier transform infrared-attenuated total reflectance (FTIR-ATR) spectroscopy. Specifically, QSM was used to determine water solubility, while FTIR-ATR spectroscopy provided a direct, molecular-level measurement of water clustering. The Flory-Huggins theory was employed to obtain a measure of water-polymer interaction and water solubility, through both prediction and regression, where the theory failed to predict water solubility in both PMMA and PVP. Furthermore, a comparison of water clustering between direct FTIR-ATR spectroscopy measurements and predictions from the Zimm-Lundberg clustering analysis produced contradictory results. The failure of the Flory-Huggins theory and Zimm-Lundberg clustering analysis to describe water solubility and water clustering, respectively, in these glassy polymers is in part due to the equilibrium constraints under which these models are derived in contrast to the nonequilibrium state of glassy polymers. Additionally, FTIR-ATR spectroscopy results were compared to temperature-dependent diffusivity data, where a correlation between the activation energy for diffusion and the measured water clustering was observed.

AES based secure low energy adaptive clustering hierarchy for WSNs

NASA Astrophysics Data System (ADS)

Kishore, K. R.; Sarma, N. V. S. N.

2013-01-01

Wireless sensor networks (WSNs) provide a low cost solution in diversified application areas. The wireless sensor nodes are inexpensive tiny devices with limited storage, computational capability and power. They are being deployed in large scale in both military and civilian applications. Security of the data is one of the key concerns where large numbers of nodes are deployed. Here, an energy-efficient secure routing protocol, secure-LEACH (Low Energy Adaptive Clustering Hierarchy) for WSNs based on the Advanced Encryption Standard (AES) is being proposed. This crypto system is a session based one and a new session key is assigned for each new session. The network (WSN) is divided into number of groups or clusters and a cluster head (CH) is selected among the member nodes of each cluster. The measured data from the nodes is aggregated by the respective CH's and then each CH relays this data to another CH towards the gateway node in the WSN which in turn sends the same to the Base station (BS). In order to maintain confidentiality of data while being transmitted, it is necessary to encrypt the data before sending at every hop, from a node to the CH and from the CH to another CH or to the gateway node.

Hidden electronic rule in the “cluster-plus-glue-atom” model

PubMed Central

Du, Jinglian; Dong, Chuang; Melnik, Roderick; Kawazoe, Yoshiyuki; Wen, Bin

2016-01-01

Electrons and their interactions are intrinsic factors to affect the structure and properties of materials. Based on the “cluster-cluster-plus-glue-atom” model, an electron counting rule for complex metallic alloys (CMAs) has been revealed in this work (i. e. the CPGAMEC rule). Our results on the cluster structure and electron concentration of CMAs with apparent cluster features, indicate that the valence electrons’ number per unit cluster formula for these CMAs are specific constants of eight-multiples and twelve-multiples. It is thus termed as specific electrons cluster formula. This CPGAMEC rule has been demonstrated as a useful guidance to direct the design of CMAs with desired properties, while its practical applications and underlying mechanism have been illustrated on the basis of CMAs’ cluster structural features. Our investigation provides an aggregate picture with intriguing electronic rule and atomic structural features of CMAs. PMID:27642002

CONSTRAINTS ON COSMIC RAYS, MAGNETIC FIELDS, AND DARK MATTER FROM GAMMA-RAY OBSERVATIONS OF THE COMA CLUSTER OF GALAXIES WITH VERITAS AND FERMI

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arlen, T.; Aune, T.; Bouvier, A.

2012-10-01

Observations of radio halos and relics in galaxy clusters indicate efficient electron acceleration. Protons should likewise be accelerated and, on account of weak energy losses, can accumulate, suggesting that clusters may also be sources of very high energy (VHE; E > 100 GeV) gamma-ray emission. We report here on VHE gamma-ray observations of the Coma galaxy cluster with the VERITAS array of imaging Cerenkov telescopes, with complementing Fermi Large Area Telescope observations at GeV energies. No significant gamma-ray emission from the Coma Cluster was detected. Integral flux upper limits at the 99% confidence level were measured to be on themore » order of (2-5) Multiplication-Sign 10{sup -8} photons m {sup -2} s {sup -1} (VERITAS, >220 GeV) and {approx}2 Multiplication-Sign 10{sup -6} photons m {sup -2} s {sup -1} (Fermi, 1-3 GeV), respectively. We use the gamma-ray upper limits to constrain cosmic rays (CRs) and magnetic fields in Coma. Using an analytical approach, the CR-to-thermal pressure ratio is constrained to be <16% from VERITAS data and <1.7% from Fermi data (averaged within the virial radius). These upper limits are starting to constrain the CR physics in self-consistent cosmological cluster simulations and cap the maximum CR acceleration efficiency at structure formation shocks to be <50%. Alternatively, this may argue for non-negligible CR transport processes such as CR streaming and diffusion into the outer cluster regions. Assuming that the radio-emitting electrons of the Coma halo result from hadronic CR interactions, the observations imply a lower limit on the central magnetic field in Coma of {approx}(2-5.5) {mu}G, depending on the radial magnetic field profile and on the gamma-ray spectral index. Since these values are below those inferred by Faraday rotation measurements in Coma (for most of the parameter space), this renders the hadronic model a very plausible explanation of the Coma radio halo. Finally, since galaxy clusters are dark matter (DM) dominated, the VERITAS upper limits have been used to place constraints on the thermally averaged product of the total self-annihilation cross section and the relative velocity of the DM particles, ({sigma}v).« less

Constraints on Cosmic Rays, Magnetic Fields, and Dark Matter from Gamma-ray Observations of the Coma Cluster of Galaxies with VERITAS and FERMI

NASA Technical Reports Server (NTRS)

Arlen, T.; Aune, T.; Beilicke, M.; Benbow, W.; Bouvier, A.; Buckley, J. H.; Bugaev, V.; Byrum, K.; Cannon, A.; Cesarini, A.;

D2O clusters isolated in rare-gas solids: Dependence of infrared spectrum on concentration, deposition rate, heating temperature, and matrix material

NASA Astrophysics Data System (ADS)

Shimazaki, Yoichi; Arakawa, Ichiro; Yamakawa, Koichiro

2018-04-01

The infrared absorption spectra of D2O monomers and clusters isolated in rare-gas matrices were systematically reinvestigated under the control of the following factors: the D2O concentration, deposition rate, heating temperature, and rare-gas species. We clearly show that the cluster-size distribution is dependent on not only the D2O concentration but also the deposition rate of a sample; as the rate got higher, smaller clusters were preferentially formed. Under the heating procedures at different temperatures, the cluster-size growth was successfully observed. Since the monomer diffusion was not enough to balance the changes in the column densities of the clusters, the dimer diffusion was likely to contribute the cluster growth. The frequencies of the bonded-OD stretches of (D2O)k with k = 2-6 were almost linearly correlated with the square root of the critical temperature of the matrix material. Additional absorption peaks of (D2O)2 and (D2O)3 in a Xe matrix were assigned to the species trapped in tight accommodation sites.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sehgal, Ray M.; Maroudas, Dimitrios, E-mail: maroudas@ecs.umass.edu, E-mail: ford@ecs.umass.edu; Ford, David M., E-mail: maroudas@ecs.umass.edu, E-mail: ford@ecs.umass.edu

We have developed a coarse-grained description of the phase behavior of the isolated 38-atom Lennard-Jones cluster (LJ{sub 38}). The model captures both the solid-solid polymorphic transitions at low temperatures and the complex cluster breakup and melting transitions at higher temperatures. For this coarse model development, we employ the manifold learning technique of diffusion mapping. The outcome of the diffusion mapping analysis over a broad temperature range indicates that two order parameters are sufficient to describe the cluster's phase behavior; we have chosen two such appropriate order parameters that are metrics of condensation and overall crystallinity. In this well-justified coarse-variable space,more » we calculate the cluster's free energy landscape (FEL) as a function of temperature, employing Monte Carlo umbrella sampling. These FELs are used to quantify the phase behavior and onsets of phase transitions of the LJ{sub 38} cluster.« less

Soot Superaggregates from Flaming Wildfires and Their Direct Radiative Forcing

NASA Technical Reports Server (NTRS)

Chakrabarty, Rajan K.; Beres, Nicholas D.; Moosmuller,Hans; China, Swarup; Mazzoleni, Claudio; Dubey, Manvendra K.; Liu, Li; Mishchenko, Michael I.

2014-01-01

Wildfires contribute significantly to global soot emissions, yet their aerosol formation mechanisms and resulting particle properties are poorly understood and parameterized in climate models. The conventional view holds that soot is formed via the cluster-dilute aggregation mechanism in wildfires and emitted as aggregates with fractal dimension D(sub f) approximately equals 1.8 mobility diameter D(sub m) (is) less than or equal to 1 micron, and aerodynamic diameter D(sub a) (is) less than or equal to 300 nm. Here we report the ubiquitous presence of soot superaggregates (SAs) in the outflow from a major wildfire in India. SAs are porous, low-density aggregates of cluster-dilute aggregates with characteristic D(sub f) approximately equals 2.6,D(sub m) (is) greater than 1 micron, and D(sub a) is less than or equal to 300 nm that form via the cluster-dense aggregation mechanism.We present additional observations of soot SAs in wildfire smoke-laden air masses over Northern California, New Mexico, and Mexico City. We estimate that SAs contribute, per unit optical depth, up to 35% less atmospheric warming than freshly-emitted (D(sub f) approximately equals 1.8) aggregates, and approximately equals 90% more warming than the volume-equivalent spherical soot particles simulated in climate models.

Preparation of graphene on Cu foils by ion implantation with negative carbon clusters

NASA Astrophysics Data System (ADS)

Li, Hui; Shang, Yan-Xia; Zhang, Zao-Di; Wang, Ze-Song; Zhang, Rui; Fu, De-Jun

2015-01-01

We report on few-layer graphene synthesized on Cu foils by ion implantation using negative carbon cluster ions, followed by annealing at 950 °C in vacuum. Raman spectroscopy reveals IG/I2D values varying from 1.55 to 2.38 depending on energy and dose of the cluster ions, indicating formation of multilayer graphene. The measurements show that the samples with more graphene layers have fewer defects. This is interpreted by graphene growth seeded by the first layers formed via outward diffusion of C from the Cu foil, though nonlinear damage and smoothing effects also play a role. Cluster ion implantation overcomes the solubility limit of carbon in Cu, providing a technique for multilayer graphene synthesis. Project supported by the National Natural Science Foundation of China (Grant Nos. 11105100, 11205116, and 11375135) and the State Key Laboratory of Advanced Welding and Joining, Harbin Institute of Technology, China (Grant No. AWJ-M13-03).

Li3Ge3Se6: the first ternary lithium germanium selenide with interesting ∞[Ge6Se12]n chains constructed by ethane-like [Ge2Se6]6- clusters.

PubMed

Li, Guangmao; Zhen, Ni; Chu, Yu; Zhou, Zhongxiang

2017-12-21

Li 3 Ge 3 Se 6 , the first compound of the ternary Li/Ge/Se system, has been synthesized. Note that interesting 1D ∞ [Ge 6 Se 12 ] n chains constructed by ethane-like [Ge 2 Se 6 ] 6- clusters were discovered in its structure. Investigations on the structures of all the [Ge 2 Se 6 ] 6- cluster-containing compounds have shown that only in Li 3 Ge 3 Se 6 are there 1D chains composed of [Ge 2 Se 6 ] 6- clusters, which result from the space limitation within the tunnels surrounded by LiSe 6 octahedra. Raman spectrum was obtained to demonstrate the existence of Ge-Ge bonds. UV-visible-NIR diffuse reflection spectrum showed an optical bandgap of 2.08 eV. Theoretical calculations based on first principles have also been performed for its band structure and density of states to analyze its structure-property relationship.

Rewiring the network. What helps an innovation to diffuse?

NASA Astrophysics Data System (ADS)

Sznajd-Weron, Katarzyna; Szwabiński, Janusz; Weron, Rafał; Weron, Tomasz

2014-03-01

A fundamental question related to innovation diffusion is how the structure of the social network influences the process. Empirical evidence regarding real-world networks of influence is very limited. On the other hand, agent-based modeling literature reports different, and at times seemingly contradictory, results. In this paper we study innovation diffusion processes for a range of Watts-Strogatz networks in an attempt to shed more light on this problem. Using the so-called Sznajd model as the backbone of opinion dynamics, we find that the published results are in fact consistent and allow us to predict the role of network topology in various situations. In particular, the diffusion of innovation is easier on more regular graphs, i.e. with a higher clustering coefficient. Moreover, in the case of uncertainty—which is particularly high for innovations connected to public health programs or ecological campaigns—a more clustered network will help the diffusion. On the other hand, when social influence is less important (i.e. in the case of perfect information), a shorter path will help the innovation to spread in the society and—as a result—the diffusion will be easiest on a random graph.

Microscopic mechanism of nanocrystal formation from solution by cluster aggregation and coalescence

PubMed Central

Hassan, Sergio A.

2011-01-01

Solute-cluster aggregation and particle fusion have recently been suggested as alternative routes to the classical mechanism of nucleation from solution. The role of both processes in the crystallization of an aqueous electrolyte under controlled salt addition is here elucidated by molecular dynamics simulation. The time scale of the simulation allows direct observation of the entire crystallization pathway, from early events in the prenucleation stage to the formation of a nanocrystal in equilibrium with concentrated solution. The precursor originates in a small amorphous aggregate stabilized by hydration forces. The core of the nucleus becomes crystalline over time and grows by coalescence of the amorphous phase deposited at the surface. Imperfections of ion packing during coalescence promote growth of two conjoint crystallites. A parameter of order and calculated cohesive energies reflect the increasing crystalline order and stress relief at the grain boundary. Cluster aggregation plays a major role both in the formation of the nucleus and in the early stages of postnucleation growth. The mechanism identified shares common features with nucleation of solids from the melt and of liquid droplets from the vapor. PMID:21428633

On the radiative properties of soot aggregates - Part 2: Effects of coating

NASA Astrophysics Data System (ADS)

Liu, Fengshan; Yon, Jérôme; Bescond, Alexandre

2016-03-01

The effects of weakly absorbing material coating on soot have attracted considerable research attention in recent years due to the significant influence of such coating on soot radiative properties and the large differences predicted by different numerical models. Soot aggregates were first numerically generated using the diffusion limited cluster aggregation algorithm to produce fractal aggregates formed by log-normally distributed polydisperse spherical primary particles in point-touch. These aggregates were then processed by adding a certain amount of primary particle overlapping and necking to simulate the soot morphology observed from transmission electron microscopy images. After this process, a layer of WAM coating of different thicknesses was added to these more realistic soot aggregates. The radiative properties of these coated soot aggregates over the spectral range of 266-1064 nm were calculated by the discrete dipole approximation (DDA) using the spectrally dependent refractive index of soot for four aggregates containing Np=1, 20, 51 and 96 primary particles. The considered coating thicknesses range from 0% (no coating) up to 100% coating in terms of the primary particle diameter. Coating enhances both the particle absorption and scattering cross sections, with much stronger enhancement to the scattering one, as well as the asymmetry factor and the single scattering albedo. The absorption enhancement is stronger in the UV than in the visible and the near infrared. The simple corrections to the Rayleigh-Debye-Gans fractal aggregates theory for uncoated soot aggregates are found not working for coated soot aggregates. The core-shell model significantly overestimates the absorption enhancement by coating in the visible and the near infrared compared to the DDA results of the coated soot particle. Treating an externally coated soot aggregate as an aggregate formed by individually coated primary particles significantly underestimates the absorption enhancement by coating in the visible and the near infrared.

Effective heating of magnetic nanoparticle aggregates for in vivo nano-theranostic hyperthermia.

PubMed

Wang, Chencai; Hsu, Chao-Hsiung; Li, Zhao; Hwang, Lian-Pin; Lin, Ying-Chih; Chou, Pi-Tai; Lin, Yung-Ya

2017-01-01

Magnetic resonance (MR) nano-theranostic hyperthermia uses magnetic nanoparticles to target and accumulate at the lesions and generate heat to kill lesion cells directly through hyperthermia or indirectly through thermal activation and control releasing of drugs. Preclinical and translational applications of MR nano-theranostic hyperthermia are currently limited by a few major theoretical difficulties and experimental challenges in in vivo conditions. For example, conventional models for estimating the heat generated and the optimal magnetic nanoparticle sizes for hyperthermia do not accurately reproduce reported in vivo experimental results. In this work, a revised cluster-based model was proposed to predict the specific loss power (SLP) by explicitly considering magnetic nanoparticle aggregation in in vivo conditions. By comparing with the reported experimental results of magnetite Fe 3 O 4 and cobalt ferrite CoFe 2 O 4 magnetic nanoparticles, it is shown that the revised cluster-based model provides a more accurate prediction of the experimental values than the conventional models that assume magnetic nanoparticles act as single units. It also provides a clear physical picture: the aggregation of magnetic nanoparticles increases the cluster magnetic anisotropy while reducing both the cluster domain magnetization and the average magnetic moment, which, in turn, shift the predicted SLP toward a smaller magnetic nanoparticle diameter with lower peak values. As a result, the heating efficiency and the SLP values are decreased. The improvement in the prediction accuracy in in vivo conditions is particularly pronounced when the magnetic nanoparticle diameter is in the range of ~10-20 nm. This happens to be an important size range for MR cancer nano-theranostics, as it exhibits the highest efficacy against both primary and metastatic tumors in vivo. Our studies show that a relatively 20%-25% smaller magnetic nanoparticle diameter should be chosen to reach the maximal heating efficiency in comparison with the optimal size predicted by previous models.

Effective heating of magnetic nanoparticle aggregates for in vivo nano-theranostic hyperthermia

PubMed Central

Wang, Chencai; Hsu, Chao-Hsiung; Li, Zhao; Hwang, Lian-Pin; Lin, Ying-Chih; Chou, Pi-Tai; Lin, Yung-Ya

2017-01-01

Magnetic resonance (MR) nano-theranostic hyperthermia uses magnetic nanoparticles to target and accumulate at the lesions and generate heat to kill lesion cells directly through hyperthermia or indirectly through thermal activation and control releasing of drugs. Preclinical and translational applications of MR nano-theranostic hyperthermia are currently limited by a few major theoretical difficulties and experimental challenges in in vivo conditions. For example, conventional models for estimating the heat generated and the optimal magnetic nanoparticle sizes for hyperthermia do not accurately reproduce reported in vivo experimental results. In this work, a revised cluster-based model was proposed to predict the specific loss power (SLP) by explicitly considering magnetic nanoparticle aggregation in in vivo conditions. By comparing with the reported experimental results of magnetite Fe3O4 and cobalt ferrite CoFe2O4 magnetic nanoparticles, it is shown that the revised cluster-based model provides a more accurate prediction of the experimental values than the conventional models that assume magnetic nanoparticles act as single units. It also provides a clear physical picture: the aggregation of magnetic nanoparticles increases the cluster magnetic anisotropy while reducing both the cluster domain magnetization and the average magnetic moment, which, in turn, shift the predicted SLP toward a smaller magnetic nanoparticle diameter with lower peak values. As a result, the heating efficiency and the SLP values are decreased. The improvement in the prediction accuracy in in vivo conditions is particularly pronounced when the magnetic nanoparticle diameter is in the range of ~10–20 nm. This happens to be an important size range for MR cancer nano-theranostics, as it exhibits the highest efficacy against both primary and metastatic tumors in vivo. Our studies show that a relatively 20%–25% smaller magnetic nanoparticle diameter should be chosen to reach the maximal heating efficiency in comparison with the optimal size predicted by previous models. PMID:28894366

Ultra-diffuse cluster galaxies as key to the MOND cluster conundrum

NASA Astrophysics Data System (ADS)

Milgrom, Mordehai

2015-12-01

Modified Newtonian Dynamics (MOND) reduces greatly the mass discrepancy in clusters of galaxies,but does leave a global discrepancy of about a factor of 2 (epitomized by the structure of the Bullet Cluster). It has been proposed, within the minimalist and purist MOND, that clusters harbour some indigenous, yet undetected, cluster baryonic (dark) matter (CBDM), whose total amount is comparable with that of the observed hot gas. Koda et al. have recently identified more than a thousand ultra-diffuse, galaxy-like objects (UDGs) in the Coma cluster. These, they argue, require, within Newtonian dynamics, that they are much more massive than their observed stellar component. Here, I propound that some of the CBDM is internal to UDGs, which endows them with robustness. The rest of the CBDM objects formed in now-disrupted kin of the UDGs, and is dispersed in the intracluster medium. The discovery of cluster UDGs is not in itself a resolution of the MOND cluster conundrum, but it lends greater plausibility to CBDM as its resolution. Alternatively, if the UDGs are only now falling into Coma, their large size and very low surface brightness could result from the inflation due to the MOND, variable external-field effect (EFE). I also consider briefly solutions to the conundrum that invoke more elaborate extensions of purist MOND, e.g. that in clusters, the MOND constant takes up larger than canonical values of the MOND constant. Whatever solves the cluster conundrum within MOND might also naturally account for UDGs.

An Energy Centric Cluster-Based Routing Protocol for Wireless Sensor Networks.

PubMed

Hosen, A S M Sanwar; Cho, Gi Hwan

2018-05-11

Clustering is an effective way to prolong the lifetime of a wireless sensor network (WSN). The common approach is to elect cluster heads to take routing and controlling duty, and to periodically rotate each cluster head's role to distribute energy consumption among nodes. However, a significant amount of energy dissipates due to control messages overhead, which results in a shorter network lifetime. This paper proposes an energy-centric cluster-based routing mechanism in WSNs. To begin with, cluster heads are elected based on the higher ranks of the nodes. The rank is defined by residual energy and average distance from the member nodes. With the role of data aggregation and data forwarding, a cluster head acts as a caretaker for cluster-head election in the next round, where the ranks' information are piggybacked along with the local data sending during intra-cluster communication. This reduces the number of control messages for the cluster-head election as well as the cluster formation in detail. Simulation results show that our proposed protocol saves the energy consumption among nodes and achieves a significant improvement in the network lifetime.

An Energy Centric Cluster-Based Routing Protocol for Wireless Sensor Networks

PubMed Central

Hosen, A. S. M. Sanwar; Cho, Gi Hwan

2018-01-01

Clustering is an effective way to prolong the lifetime of a wireless sensor network (WSN). The common approach is to elect cluster heads to take routing and controlling duty, and to periodically rotate each cluster head’s role to distribute energy consumption among nodes. However, a significant amount of energy dissipates due to control messages overhead, which results in a shorter network lifetime. This paper proposes an energy-centric cluster-based routing mechanism in WSNs. To begin with, cluster heads are elected based on the higher ranks of the nodes. The rank is defined by residual energy and average distance from the member nodes. With the role of data aggregation and data forwarding, a cluster head acts as a caretaker for cluster-head election in the next round, where the ranks’ information are piggybacked along with the local data sending during intra-cluster communication. This reduces the number of control messages for the cluster-head election as well as the cluster formation in detail. Simulation results show that our proposed protocol saves the energy consumption among nodes and achieves a significant improvement in the network lifetime. PMID:29751663

Computer Simulation of Fracture in Aerogels

NASA Technical Reports Server (NTRS)

Good, Brian S.

2006-01-01

Aerogels are of interest to the aerospace community primarily for their thermal properties, notably their low thermal conductivities. While the gels are typically fragile, recent advances in the application of conformal polymer layers to these gels has made them potentially useful as lightweight structural materials as well. In this work, we investigate the strength and fracture behavior of silica aerogels using a molecular statics-based computer simulation technique. The gels' structure is simulated via a Diffusion Limited Cluster Aggregation (DLCA) algorithm, which produces fractal structures representing experimentally observed aggregates of so-called secondary particles, themselves composed of amorphous silica primary particles an order of magnitude smaller. We have performed multi-length-scale simulations of fracture in silica aerogels, in which the interaction b e e n two secondary particles is assumed to be described by a Morse pair potential parameterized such that the potential range is much smaller than the secondary particle size. These Morse parameters are obtained by atomistic simulation of models of the experimentally-observed amorphous silica "bridges," with the fracture behavior of these bridges modeled via molecular statics using a Morse/Coulomb potential for silica. We consider the energetics of the fracture, and compare qualitative features of low-and high-density gel fracture.

NuSTAR observations of the bullet cluster: constraints on inverse Compton emission

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wik, Daniel R.; Hornstrup, A.; Molendi, S.

2014-08-13

Here, the search for diffuse non-thermal inverse Compton (IC) emission from galaxy clusters at hard X-ray energies has been undertaken with many instruments, with most detections being either of low significance or controversial. Because all prior telescopes sensitive at E > 10 keV do not focus light and have degree-scale fields of view, their backgrounds are both high and difficult to characterize. The associated uncertainties result in lower sensitivity to IC emission and a greater chance of false detection. In this work, we present 266 ks NuSTAR observations of the Bullet cluster, which is detected in the energy range 3-30more » keV. NuSTAR's unprecedented hard X-ray focusing capability largely eliminates confusion between diffuse IC and point sources; however, at the highest energies, the background still dominates and must be well understood. To this end, we have developed a complete background model constructed of physically inspired components constrained by extragalactic survey field observations, the specific parameters of which are derived locally from data in non-source regions of target observations. Applying the background model to the Bullet cluster data, we find that the spectrum is well—but not perfectly—described as an isothermal plasma with kT = 14.2 ± 0.2 keV. To slightly improve the fit, a second temperature component is added, which appears to account for lower temperature emission from the cool core, pushing the primary component to kT ~ 15.3 keV. We see no convincing need to invoke an IC component to describe the spectrum of the Bullet cluster, and instead argue that it is dominated at all energies by emission from purely thermal gas. The conservatively derived 90% upper limit on the IC flux of 1.1 × 10 –12 erg s –1 cm –2 (50-100 keV), implying a lower limit on B ≳ 0.2 μG, is barely consistent with detected fluxes previously reported. In addition to discussing the possible origin of this discrepancy, we remark on the potential implications of this analysis for the prospects for detecting IC in galaxy clusters in the future.« less

Endocytic pathway rapidly delivers internalized molecules to lysosomes: an analysis of vesicle trafficking, clustering and mass transfer.

PubMed

Pangarkar, Chinmay; Dinh, Anh-Tuan; Mitragotri, Samir

2012-08-20

Lysosomes play a critical role in intracellular drug delivery. For enzyme-based therapies, they represent a potential target site whereas for nucleic acid or many protein drugs, they represent the potential degradation site. Either way, understanding the mechanisms and processes involved in routing of materials to lysosomes after cellular entry is of high interest to the field of drug delivery. Most therapeutic cargoes other than small hydrophobic molecules enter the cells through endocytosis. Endocytosed cargoes are routed to lysosomes via microtubule-based transport and are ultimately shared by various lysosomes via tethering and clustering of endocytic vesicles followed by exchange of their contents. Using a combined experimental and numerical approach, here we studied the rates of mass transfer into and among the endocytic vesicles in a model cell line, 3T3 fibroblasts. In order to understand the relationship of mass transfer with microtubular transport and vesicle clustering, we varied both properties through various pharmacological agents. At the same time, microtubular transport and vesicle clustering were modeled through diffusion-advection equations and the Smoluchowski equations, respectively. Our analysis revealed that the rate of mass transfer is optimally related to microtubular transport and clustering properties of vesicles. Further, the rate of mass transfer is highest in the innate state of the cell. Any perturbation to either microtubular transport or vesicle aggregation led to reduced mass transfer to lysosome. These results suggest that in the absence of an external intervention the endocytic pathway appears to maximize molecular delivery to lysosomes. Strategies are discussed to reduce mass transfer to lysosomes so as to extend the residence time of molecules in endosomes or late endosomes, thus potentially increasing the likelihood of their escape before disposition in the lysosomes. Copyright © 2012 Elsevier B.V. All rights reserved.

Electric-field-induced association of colloidal particles

NASA Astrophysics Data System (ADS)

Fraden, Seth; Hurd, Alan J.; Meyer, Robert B.

1989-11-01

Dilute suspensions of micron diameter dielectric spheres confined to two dimensions are induced to aggregate linearly by application of an electric field. The growth of the average cluster size agrees well with the Smoluchowski equation, but the evolution of the measured cluster size distribution exhibits significant departures from theory at large times due to the formation of long linear clusters which effectively partition space into isolated one-dimensional strips.

Ion Pairing and Diffusion in Magnesium Electrolytes Based on Magnesium Borohydride.

PubMed

Samuel, Devon; Steinhauser, Carl; Smith, Jeffrey G; Kaufman, Aaron; Radin, Maxwell D; Naruse, Junichi; Hiramatsu, Hidehiko; Siegel, Donald J

2017-12-20

One obstacle to realizing a practical, rechargeable magnesium-ion battery is the development of efficient Mg electrolytes. Electrolytes based on simple Mg(BH 4 ) 2 salts suffer from poor salt solubility and/or low conductivity, presumably due to strong ion pairing. Understanding the molecular-scale processes occurring in these electrolytes would aid in overcoming these performance limitations. Toward this goal, the present study examines the solvation, agglomeration, and transport properties of a family of Mg electrolytes based on the Mg(BH 4 ) 2 salt using classical molecular dynamics. These properties were examined across five different solvents (tetrahydrofuran and the glymes G1-G4) and at four salt concentrations ranging from the dilute limit up to 0.4 M. Significant and irreversible salt agglomeration was observed in all solvents at all nondilute Mg(BH 4 ) 2 concentrations. The degree of clustering observed in these divalent Mg systems is much larger than that reported for electrolytes containing monovalent cations, such as Li. The salt agglomeration rate and diffusivity of Mg 2+ were both observed to correlate with solvent self-diffusivity: electrolytes using longer- (shorter-) chain solvents had the lowest (highest) Mg 2+ diffusivity and agglomeration rates. Incorporation of Mg 2+ into Mg 2+ -BH 4 - clusters significantly reduces the diffusivity of Mg 2+ by restricting displacements to localized motion within largely immobile agglomerates. Consequently, diffusion is increasingly impeded with increasing Mg(BH 4 ) 2 concentration. These data are consistent with the solubility limitations observed experimentally for Mg(BH 4 ) 2 -based electrolytes and highlight the need for strategies that minimize salt agglomeration in electrolytes containing divalent cations.

Effects of Alfvénic Drift on Diffusive Shock Acceleration at Weak Cluster Shocks

NASA Astrophysics Data System (ADS)

Kang, Hyesung; Ryu, Dongsu

2018-03-01

Non-detection of γ-ray emission from galaxy clusters has challenged diffusive shock acceleration (DSA) of cosmic-ray (CR) protons at weak collisionless shocks that are expected to form in the intracluster medium. As an effort to address this problem, we here explore possible roles of Alfvén waves self-excited via resonant streaming instability during the CR acceleration at parallel shocks. The mean drift of Alfvén waves may either increase or decrease the scattering center compression ratio, depending on the postshock cross-helicity, leading to either flatter or steeper CR spectra. We first examine such effects at planar shocks, based on the transport of Alfvén waves in the small amplitude limit. For the shock parameters relevant to cluster shocks, Alfvénic drift flattens the CR spectrum slightly, resulting in a small increase of the CR acceleration efficiency, η. We then consider two additional, physically motivated cases: (1) postshock waves are isotropized via MHD and plasma processes across the shock transition, and (2) postshock waves contain only forward waves propagating along with the flow due to a possible gradient of CR pressure behind the shock. In these cases, Alfvénic drift could reduce η by as much as a factor of five for weak cluster shocks. For the canonical parameters adopted here, we suggest η ∼ 10‑4–10‑2 for shocks with sonic Mach number M s ≈ 2–3. The possible reduction of η may help ease the tension between non-detection of γ-rays from galaxy clusters and DSA predictions.

Kinetics of binary nucleation of vapors in size and composition space.

PubMed

Fisenko, Sergey P; Wilemski, Gerald

2004-11-01

We reformulate the kinetic description of binary nucleation in the gas phase using two natural independent variables: the total number of molecules g and the molar composition x of the cluster. The resulting kinetic equation can be viewed as a two-dimensional Fokker-Planck equation describing the simultaneous Brownian motion of the clusters in size and composition space. Explicit expressions for the Brownian diffusion coefficients in cluster size and composition space are obtained. For characterization of binary nucleation in gases three criteria are established. These criteria establish the relative importance of the rate processes in cluster size and composition space for different gas phase conditions and types of liquid mixtures. The equilibrium distribution function of the clusters is determined in terms of the variables g and x. We obtain an approximate analytical solution for the steady-state binary nucleation rate that has the correct limit in the transition to unary nucleation. To further illustrate our description, the nonequilibrium steady-state cluster concentrations are found by numerically solving the reformulated kinetic equation. For the reformulated transient problem, the relaxation or induction time for binary nucleation was calculated using Galerkin's method. This relaxation time is affected by processes in both size and composition space, but the contributions from each process can be separated only approximately.

Risk Profiles for Injurious Falls in People Over 60: A Population-Based Cohort Study

PubMed Central

Ek, Stina; Rizzuto, Debora; Fratiglioni, Laura; Johnell, Kristina; Xu, Weili

2018-01-01

Abstract Background Although falls in older adults are related to multiple risk factors, these factors have commonly been studied individually. We aimed to identify risk profiles for injurious falls in older adults by detecting clusters of established risk factors and quantifying their impact on fall risk. Methods Participants were 2,566 people, aged 60 years and older, from the population-based Swedish National Study on Aging and Care in Kungsholmen. Injurious falls was defined as hospitalization for or receipt of outpatient care because a fall. Cluster analysis was used to identify aggregation of possible risk factors including chronic diseases, fall-risk increasing drugs (FRIDs), physical and cognitive impairments, and lifestyle-related factors. Associations between the clusters and injurious falls over 3, 5, and 10 years were estimated using flexible parametric survival models. Results Five clusters were identified including: a “healthy”, a “well-functioning with multimorbidity”, a “well-functioning, with multimorbidity and high FRID consumption”, a “physically and cognitively impaired”, and a “disabled” cluster. The risk of injurious falls for all groups was significantly higher than for the first cluster of healthy individuals in the reference category. Hazard ratios (95% confidence intervals) ranged from 1.71 (1.02–2.66) for the second cluster to 12.67 (7.38–21.75) for the last cluster over 3 years of follow-up. The highest risk was observed in the last two clusters with high burden of physical and cognitive impairments. Conclusion Risk factors for injurious fall tend to aggregate, representing different levels of risk for falls. Our findings can be useful to tailor and prioritize clinical and public health interventions. PMID:28605455

A stochastic reaction-diffusion model for protein aggregation on DNA

NASA Astrophysics Data System (ADS)

Voulgarakis, Nikolaos K.

Vital functions of DNA, such as transcription and packaging, depend on the proper clustering of proteins on the double strand. The present study investigates how the interplay between DNA allostery and electrostatic interactions affects protein clustering. The statistical analysis of a simple but transparent computational model reveals two major consequences of this interplay. First, depending on the protein and salt concentration, protein filaments exhibit a bimodal DNA stiffening and softening behavior. Second, within a certain domain of the control parameters, electrostatic interactions can cause energetic frustration that forces proteins to assemble in rigid spiral configurations. Such spiral filaments might trigger both positive and negative supercoiling, which can ultimately promote gene compaction and regulate the promoter. It has been experimentally shown that bacterial histone-like proteins assemble in similar spiral patterns and/or exhibit the same bimodal behavior. The proposed model can, thus, provide computational insights into the physical mechanisms used by proteins to control the mechanical properties of the DNA.

What favors convective aggregation and why?

NASA Astrophysics Data System (ADS)

Muller, Caroline; Bony, Sandrine

2015-07-01

The organization of convection is ubiquitous, but its physical understanding remains limited. One particular type of organization is the spatial self-aggregation of convection, taking the form of cloud clusters, or tropical cyclones in the presence of rotation. We show that several physical processes can give rise to self-aggregation and highlight the key features responsible for it, using idealized simulations. Longwave radiative feedbacks yield a "radiative aggregation." In that case, sufficient spatial variability of radiative cooling rates yields a low-level circulation, which induces the upgradient energy transport and radiative-convective instability. Not only do vertically integrated radiative budgets matter but the vertical profile of cooling is also crucial. Convective aggregation is facilitated when downdrafts below clouds are weak ("moisture-memory aggregation"), and this is sufficient to trigger aggregation in the absence of longwave radiative feedbacks. These results shed some light on the sensitivity of self-aggregation to various parameters, including resolution or domain size.

Communication: Diverse nanoscale cluster dynamics: Diffusion of 2D epitaxial clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lai, King C.; Evans, James W.; Liu, Da -Jiang

The dynamics of nanoscale clusters can be distinct from macroscale behavior described by continuum formalisms. For diffusion of 2D clusters of N atoms in homoepitaxial systems mediated by edge atom hopping, macroscale theory predicts simple monotonic size scaling of the diffusion coefficient, D N ~ N –β, with β = 3/2. However, modeling for nanoclusters on metal(100) surfaces reveals that slow nucleation-mediated diffusion displaying weak size scaling β < 1 occurs for “perfect” sizes N p = L 2 and L(L+1) for integer L = 3,4,… (with unique square or near-square ground state shapes), and also for N p+3, Nmore » p+4,…. In contrast, fast facile nucleation-free diffusion displaying strong size scaling β ≈ 2.5 occurs for sizes N p+1 and N p+2. D N versus N oscillates strongly between the slowest branch (for N p+3) and the fastest branch (for N p+1). All branches merge for N = O(10 2), but macroscale behavior is only achieved for much larger N = O(10 3). Here, this analysis reveals the unprecedented diversity of behavior on the nanoscale.« less

Self-Learning Off-Lattice Kinetic Monte Carlo method as applied to growth on metal surfaces

NASA Astrophysics Data System (ADS)

Trushin, Oleg; Kara, Abdelkader; Rahman, Talat

2007-03-01

We propose a new development in the Self-Learning Kinetic Monte Carlo (SLKMC) method with the goal of improving the accuracy with which atomic mechanisms controlling diffusive processes on metal surfaces may be identified. This is important for diffusion of small clusters (2 - 20 atoms) in which atoms may occupy Off-Lattice positions. Such a procedure is also necessary for consideration of heteroepitaxial growth. The new technique combines an earlier version of SLKMC [1] with the inclusion of off-lattice occupancy. This allows us to include arbitrary positions of adatoms in the modeling and makes the simulations more realistic and reliable. We have tested this new approach for the case of the diffusion of small 2D Cu clusters diffusion on Cu(111) and found good performance and satisfactory agreement with results obtained from previous version of SLKMC. The new method also helped reveal a novel atomic mechanism contributing to cluster migration. We have also applied this method to study the diffusion of Cu clusters on Ag(111), and find that Cu atoms generally prefer to occupy off-lattice sites. [1] O. Trushin, A. Kara, A. Karim, T.S. Rahman Phys. Rev B 2005

Communication: Diverse nanoscale cluster dynamics: Diffusion of 2D epitaxial clusters

DOE PAGES

Lai, King C.; Evans, James W.; Liu, Da -Jiang

2017-11-27

The dynamics of nanoscale clusters can be distinct from macroscale behavior described by continuum formalisms. For diffusion of 2D clusters of N atoms in homoepitaxial systems mediated by edge atom hopping, macroscale theory predicts simple monotonic size scaling of the diffusion coefficient, D N ~ N –β, with β = 3/2. However, modeling for nanoclusters on metal(100) surfaces reveals that slow nucleation-mediated diffusion displaying weak size scaling β < 1 occurs for “perfect” sizes N p = L 2 and L(L+1) for integer L = 3,4,… (with unique square or near-square ground state shapes), and also for N p+3, Nmore » p+4,…. In contrast, fast facile nucleation-free diffusion displaying strong size scaling β ≈ 2.5 occurs for sizes N p+1 and N p+2. D N versus N oscillates strongly between the slowest branch (for N p+3) and the fastest branch (for N p+1). All branches merge for N = O(10 2), but macroscale behavior is only achieved for much larger N = O(10 3). Here, this analysis reveals the unprecedented diversity of behavior on the nanoscale.« less

Clusters of Galaxies and the Cosmic Web with Square Kilometre Array

NASA Astrophysics Data System (ADS)

Kale, Ruta; Dwarakanath, K. S.; Vir Lal, Dharam; Bagchi, Joydeep; Paul, Surajit; Malu, Siddharth; Datta, Abhirup; Parekh, Viral; Sharma, Prateek; Pandey-Pommier, Mamta

2016-12-01

The intra-cluster and inter-galactic media that pervade the large scale structure of the Universe are known to be magnetized at sub-micro Gauss to micro Gauss levels and to contain cosmic rays. The acceleration of cosmic rays and their evolution along with that of magnetic fields in these media is still not well understood. Diffuse radio sources of synchrotron origin associated with the Intra-Cluster Medium (ICM) such as radio halos, relics and mini-halos are direct probes of the underlying mechanisms of cosmic ray acceleration. Observations with radio telescopes such as the Giant Metrewave Radio Telescope, the Very Large Array and the Westerbork Synthesis Radio Telescope have led to the discoveries of about 80 such sources and allowed detailed studies in the frequency range 0.15-1.4 GHz of a few. These studies have revealed scaling relations between the thermal and non-thermal properties of clusters and favour the role of shocks in the formation of radio relics and of turbulent re-acceleration in the formation of radio halos and mini-halos. The radio halos are known to occur in merging clusters and mini-halos are detected in about half of the cool-core clusters. Due to the limitations of current radio telescopes, low mass galaxy clusters and galaxy groups remain unexplored as they are expected to contain much weaker radio sources. Distinguishing between the primary and the secondary models of cosmic ray acceleration mechanisms requires spectral measurements over a wide range of radio frequencies and with high sensitivity. Simulations have also predicted weak diffuse radio sources associated with filaments connecting galaxy clusters. The Square Kilometre Array (SKA) is a next generation radio telescope that will operate in the frequency range of 0.05-20 GHz with unprecedented sensitivities and resolutions. The expected detection limits of SKA will reveal a few hundred to thousand new radio halos, relics and mini-halos providing the first large and comprehensive samples for their study. The wide frequency coverage along with sensitivity to extended structures will be able to constrain the cosmic ray acceleration mechanisms. The higher frequency (>5 GHz) observations will be able to use the Sunyaev-Zel'dovich effect to probe the ICM pressure in addition to tracers such as lobes of head-tail radio sources. The SKA also opens prospects to detect the `off-state' or the lowest level of radio emission from the ICM predicted by the hadronic models and the turbulent re-acceleration models.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goudfrooij, Paul, E-mail: goudfroo@stsci.edu

We study mass functions of globular clusters derived from Hubble Space Telescope/Advanced Camera for Surveys images of the early-type merger remnant galaxy NGC 1316, which hosts a significant population of metal-rich globular clusters of intermediate age ({approx}3 Gyr). For the old, metal-poor ({sup b}lue{sup )} clusters, the peak mass of the mass function M{sub p} increases with internal half-mass density {rho}{sub h} as M{sub p}{proportional_to}{rho}{sub h}{sup 0.44}, whereas it stays approximately constant with galactocentric distance R{sub gal}. The mass functions of these clusters are consistent with a simple scenario in which they formed with a Schechter initial mass function andmore » evolved subsequently by internal two-body relaxation. For the intermediate-age population of metal-rich ({sup r}ed{sup )} clusters, the faint end of the previously reported power-law luminosity function of the clusters with R{sub gal} > 9 kpc is due to many of those clusters having radii larger than the theoretical maximum value imposed by the tidal field of NGC 1316 at their R{sub gal}. This renders disruption by two-body relaxation ineffective. Only a few such diffuse clusters are found in the inner regions of NGC 1316. Completeness tests indicate that this is a physical effect. Using comparisons with star clusters in other galaxies and cluster disruption calculations using published models, we hypothesize that most red clusters in the low-{rho}{sub h} tail of the initial distribution have already been destroyed in the inner regions of NGC 1316 by tidal shocking, and that several remaining low-{rho}{sub h} clusters will evolve dynamically to become similar to 'faint fuzzies' that exist in several lenticular galaxies. Finally, we discuss the nature of diffuse red clusters in early-type galaxies.« less

A SUZAKU SEARCH FOR NONTHERMAL EMISSION AT HARD X-RAY ENERGIES IN THE COMA CLUSTER

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wik, Daniel R.; Sarazin, Craig L.; Finoguenov, Alexis

2009-05-10

The brightest cluster radio halo known resides in the Coma cluster of galaxies. The relativistic electrons producing this diffuse synchrotron emission should also produce inverse Compton emission that becomes competitive with thermal emission from the intracluster medium (ICM) at hard X-ray energies. Thus far, claimed detections of this emission in Coma are controversial. We present a Suzaku HXD-PIN observation of the Coma cluster in order to nail down its nonthermal hard X-ray content. The contribution of thermal emission to the HXD-PIN spectrum is constrained by simultaneously fitting thermal and nonthermal models to it and a spatially equivalent spectrum derived frommore » an XMM-Newton mosaic of the Coma field. We fail to find statistically significant evidence for nonthermal emission in the spectra which are better described by only a single- or multitemperature model for the ICM. Including systematic uncertainties, we derive a 90% upper limit on the flux of nonthermal emission of 6.0 x 10{sup -12} erg s{sup -1} cm{sup -2} (20-80 keV, for {gamma} = 2.0), which implies a lower limit on the cluster-averaged magnetic field of B>0.15 {mu}G. Our flux upper limit is 2.5 times lower than the detected nonthermal flux from RXTE and BeppoSAX. However, if the nonthermal hard X-ray emission in Coma is more spatially extended than the observed radio halo, the Suzaku HXD-PIN may miss some fraction of the emission. A detailed investigation indicates that {approx}50%-67% of the emission might go undetected, which could make our limit consistent with that of Rephaeli and Gruber and Fusco-Femiano et al. The thermal interpretation of the hard Coma spectrum is consistent with recent analyses of INTEGRAL and Swift data.« less

Theory and modeling of particles with DNA-mediated interactions

NASA Astrophysics Data System (ADS)

Licata, Nicholas A.

2008-05-01

In recent years significant attention has been attracted to proposals which utilize DNA for nanotechnological applications. Potential applications of these ideas range from the programmable self-assembly of colloidal crystals, to biosensors and nanoparticle based drug delivery platforms. In Chapter I we introduce the system, which generically consists of colloidal particles functionalized with specially designed DNA markers. The sequence of bases on the DNA markers determines the particle type. Due to the hybridization between complementary single-stranded DNA, specific, type-dependent interactions can be introduced between particles by choosing the appropriate DNA marker sequences. In Chapter II we develop a statistical mechanical description of the aggregation and melting behavior of particles with DNA-mediated interactions. In Chapter III a model is proposed to describe the dynamical departure and diffusion of particles which form reversible key-lock connections. In Chapter IV we propose a method to self-assemble nanoparticle clusters using DNA scaffolds. A natural extension is discussed in Chapter V, the programmable self-assembly of nanoparticle clusters where the desired cluster geometry is encoded using DNA-mediated interactions. In Chapter VI we consider a nanoparticle based drug delivery platform for targeted, cell specific chemotherapy. In Chapter VII we present prospects for future research: the connection between DNA-mediated colloidal crystallization and jamming, and the inverse problem in self-assembly.

Receptor clustering drives polarized assembly of ankyrin.

PubMed

Jefford, G; Dubreuil, R R

2000-09-08

Expression of the L1 family cell adhesion molecule neuroglian in Drosophila S2 cells leads to cell aggregation and polarized ankyrin accumulation at sites of cell-cell contact. Thus neuroglian adhesion generates a spatial cue for polarized assembly of ankyrin and the spectrin cytoskeleton. Here we characterized a chimera of the extracellular and transmembrane domains of rat CD2 fused to the cytoplasmic domain of neuroglian. The chimera was used to test the hypothesis that clustering of neuroglian at sites of adhesion generates the signal that activates ankyrin binding. Abundant expression of the chimera at the plasma membrane was not a sufficient cue to drive ankyrin assembly, since ankyrin remained diffusely distributed throughout the cytoplasm of CD2-neuroglian-expressing cells. However, ankyrin became highly enriched at sites of antibody-induced capping of CD2-neuroglian. Spectrin codistributed with ankyrin at capped sites. A green fluorescent protein-tagged ankyrin was used to monitor ankyrin distribution in living cells. Enhanced green fluorescent protein-ankyrin behaved identically to antibody-stained endogenous ankyrin, proving that the polarized accumulation of ankyrin was not an artifact of fixing and staining cells. We propose a model in which clustering of neuroglian induces a conformational change in the cytoplasmic domain that drives polarized assembly of the spectrin cytoskeleton.

A new mass mortality of juvenile Protoceratops and size-segregated aggregation behaviour in juvenile non-avian dinosaurs.

PubMed

Hone, David W E; Farke, Andrew A; Watabe, Mahito; Shigeru, Suzuki; Tsogtbaatar, Khishigjav

2014-01-01

Monodominant bonebeds are a relatively common occurrence for non-avian dinosaurs, and have been used to infer associative, and potentially genuinely social, behavior. Previously known assemblages are characterized as either mixed size-classes (juvenile and adult-sized specimens together) or single size-classes of individuals (only juveniles or only adult-sized individuals within the assemblage). In the latter case, it is generally unknown if these kinds of size-segregated aggregations characterize only a particular size stage or represent aggregations that happened at all size stages. Ceratopsians ("horned dinosaurs") are known from both types of assemblages. Here we describe a new specimen of the ceratopsian dinosaur Protoceratops andrewsi, Granger and Gregory 1923 from Mongolia representing an aggregation of four mid-sized juvenile animals. In conjunction with existing specimens of groups of P. andrewsi that includes size-clustered aggregations of young juveniles and adult-sized specimens, this new material provides evidence for some degree of size-clustered aggregation behaviour in Protoceratops throughout ontogeny. This continuity of size-segregated (and presumably age-clustered) aggregation is previously undocumented in non-avian dinosaurs. The juvenile group fills a key gap in the available information on aggregations in younger ceratopsians. Although we support the general hypothesis that many non-avian dinosaurs were gregarious and even social animals, we caution that evidence for sociality has been overstated and advocate a more conservative interpretation of some data of 'sociality' in dinosaurs.

A New Mass Mortality of Juvenile Protoceratops and Size-Segregated Aggregation Behaviour in Juvenile Non-Avian Dinosaurs

PubMed Central

Hone, David W. E.; Farke, Andrew A.; Watabe, Mahito; Shigeru, Suzuki; Tsogtbaatar, Khishigjav

2014-01-01

Background Monodominant bonebeds are a relatively common occurrence for non-avian dinosaurs, and have been used to infer associative, and potentially genuinely social, behavior. Previously known assemblages are characterized as either mixed size-classes (juvenile and adult-sized specimens together) or single size-classes of individuals (only juveniles or only adult-sized individuals within the assemblage). In the latter case, it is generally unknown if these kinds of size-segregated aggregations characterize only a particular size stage or represent aggregations that happened at all size stages. Ceratopsians (“horned dinosaurs”) are known from both types of assemblages. Methods/Principal Findings Here we describe a new specimen of the ceratopsian dinosaur Protoceratops andrewsi, Granger and Gregory 1923 from Mongolia representing an aggregation of four mid-sized juvenile animals. In conjunction with existing specimens of groups of P. andrewsi that includes size-clustered aggregations of young juveniles and adult-sized specimens, this new material provides evidence for some degree of size-clustered aggregation behaviour in Protoceratops throughout ontogeny. This continuity of size-segregated (and presumably age-clustered) aggregation is previously undocumented in non-avian dinosaurs. Conclusions The juvenile group fills a key gap in the available information on aggregations in younger ceratopsians. Although we support the general hypothesis that many non-avian dinosaurs were gregarious and even social animals, we caution that evidence for sociality has been overstated and advocate a more conservative interpretation of some data of ‘sociality’ in dinosaurs. PMID:25426957

Clustering and optimal arrangement of enzymes in reaction-diffusion systems.

PubMed

Buchner, Alexander; Tostevin, Filipe; Gerland, Ulrich

2013-05-17

Enzymes within biochemical pathways are often colocalized, yet the consequences of specific spatial enzyme arrangements remain poorly understood. We study the impact of enzyme arrangement on reaction efficiency within a reaction-diffusion model. The optimal arrangement transitions from a cluster to a distributed profile as a single parameter, which controls the probability of reaction versus diffusive loss of pathway intermediates, is varied. We introduce the concept of enzyme exposure to explain how this transition arises from the stochastic nature of molecular reactions and diffusion.

Use of ion-mobility mass spectrometry (IMS-MS) to map polyoxometalate Keplerate clusters and their supramolecular assemblies.

PubMed

Robbins, Philip J; Surman, Andrew J; Thiel, Johannes; Long, De-Liang; Cronin, Leroy

2013-03-07

We present the high-resolution (HRES-MS) and ion-mobility (IMS-MS) mass spectrometry studies of icosahedral nanoscale polyoxometalate-based {L(30)}{(Mo)Mo(5)} Keplerate clusters, and demonstrate the use of IMS-MS to resolve and map intact nanoclusters, and its potential for the discovery of new structures, in this case the first gas phase observation of 'proto-clustering' of higher order Keplerate supramolecular aggregates.

Using exploratory data analysis to identify and predict patterns of human Lyme disease case clustering within a multistate region, 2010-2014.

PubMed

Hendricks, Brian; Mark-Carew, Miguella

2017-02-01

Lyme disease is the most commonly reported vectorborne disease in the United States. The objective of our study was to identify patterns of Lyme disease reporting after multistate inclusion to mitigate potential border effects. County-level human Lyme disease surveillance data were obtained from Kentucky, Maryland, Ohio, Pennsylvania, Virginia, and West Virginia state health departments. Rate smoothing and Local Moran's I was performed to identify clusters of reporting activity and identify spatial outliers. A logistic generalized estimating equation was performed to identify significant associations in disease clustering over time. Resulting analyses identified statistically significant (P=0.05) clusters of high reporting activity and trends over time. High reporting activity aggregated near border counties in high incidence states, while low reporting aggregated near shared county borders in non-high incidence states. Findings highlight the need for exploratory surveillance approaches to describe the extent to which state level reporting affects accurate estimation of Lyme disease progression. Copyright © 2017 Elsevier Ltd. All rights reserved.

Clusters of cultures: diversity in meaning of family value and gender role items across Europe.

PubMed

van Vlimmeren, Eva; Moors, Guy B D; Gelissen, John P T M

2017-01-01

Survey data are often used to map cultural diversity by aggregating scores of attitude and value items across countries. However, this procedure only makes sense if the same concept is measured in all countries. In this study we argue that when (co)variances among sets of items are similar across countries, these countries share a common way of assigning meaning to the items. Clusters of cultures can then be observed by doing a cluster analysis on the (co)variance matrices of sets of related items. This study focuses on family values and gender role attitudes. We find four clusters of cultures that assign a distinct meaning to these items, especially in the case of gender roles. Some of these differences reflect response style behavior in the form of acquiescence. Adjusting for this style effect impacts on country comparisons hence demonstrating the usefulness of investigating the patterns of meaning given to sets of items prior to aggregating scores into cultural characteristics.

Charging of nanoparticles in stationary plasma in a gas aggregation cluster source

NASA Astrophysics Data System (ADS)

Blažek, J.; Kousal, J.; Biederman, H.; Kylián, O.; Hanuš, J.; Slavínská, D.

2015-10-01

Clusters that grow into nanoparticles near the magnetron target of the gas aggregation cluster source (GAS) may acquire electric charge by collecting electrons and ions or through other mechanisms like secondary- or photo-electron emissions. The region of the GAS close to magnetron may be considered as stationary plasma. The steady state charge distribution on nanoparticles can be determined by means of three possible models—fluid model, kinetic model and model employing Monte Carlo simulations—of cluster charging. In the paper the mathematical and numerical aspects of these models are analyzed in detail and close links between them are clarified. Among others it is shown that Monte Carlo simulation may be considered as a particular numerical technique of solving kinetic equations. Similarly the equations of the fluid model result, after some approximation, from averaged kinetic equations. A new algorithm solving an in principle unlimited set of kinetic equations is suggested. Its efficiency is verified on physical models based on experimental input data.

Cluster geometry and survival probability in systems driven by reaction diffusion dynamics

NASA Astrophysics Data System (ADS)

Windus, Alastair; Jensen, Henrik J.

2008-11-01

We consider a reaction-diffusion model incorporating the reactions A→phi, A→2A and 2A→3A. Depending on the relative rates for sexual and asexual reproduction of the quantity A, the model exhibits either a continuous or first-order absorbing phase transition to an extinct state. A tricritical point separates the two phase lines. While we comment on this critical behaviour, the main focus of the paper is on the geometry of the population clusters that form. We observe the different cluster structures that arise at criticality for the three different types of critical behaviour and show that there exists a linear relationship for the survival probability against initial cluster size at the tricritical point only.

Fluctuating micro-heterogeneity in water-tert-butyl alcohol mixtures and lambda-type divergence of the mean cluster size with phase transition-like multiple anomalies

NASA Astrophysics Data System (ADS)

Banerjee, Saikat; Furtado, Jonathan; Bagchi, Biman

2014-05-01

Water-tert-butyl alcohol (TBA) binary mixture exhibits a large number of thermodynamic and dynamic anomalies. These anomalies are observed at surprisingly low TBA mole fraction, with xTBA ≈ 0.03-0.07. We demonstrate here that the origin of the anomalies lies in the local structural changes that occur due to self-aggregation of TBA molecules. We observe a percolation transition of the TBA molecules at xTBA ≈ 0.05. We note that "islands" of TBA clusters form even below this mole fraction, while a large spanning cluster emerges above that mole fraction. At this percolation threshold, we observe a lambda-type divergence in the fluctuation of the size of the largest TBA cluster, reminiscent of a critical point. Alongside, the structure of water is also perturbed, albeit weakly, by the aggregation of TBA molecules. There is a monotonic decrease in the tetrahedral order parameter of water, while the dipole moment correlation shows a weak nonlinearity. Interestingly, water molecules themselves exhibit a reverse percolation transition at higher TBA concentration, xTBA ≈ 0.45, where large spanning water clusters now break-up into small clusters. This is accompanied by significant divergence of the fluctuations in the size of largest water cluster. This second transition gives rise to another set of anomalies around. Both the percolation transitions can be regarded as manifestations of Janus effect at small molecular level.

Fluctuating micro-heterogeneity in water-tert-butyl alcohol mixtures and lambda-type divergence of the mean cluster size with phase transition-like multiple anomalies.

PubMed

Banerjee, Saikat; Furtado, Jonathan; Bagchi, Biman

2014-05-21

Water-tert-butyl alcohol (TBA) binary mixture exhibits a large number of thermodynamic and dynamic anomalies. These anomalies are observed at surprisingly low TBA mole fraction, with x(TBA) ≈ 0.03-0.07. We demonstrate here that the origin of the anomalies lies in the local structural changes that occur due to self-aggregation of TBA molecules. We observe a percolation transition of the TBA molecules at x(TBA) ≈ 0.05. We note that "islands" of TBA clusters form even below this mole fraction, while a large spanning cluster emerges above that mole fraction. At this percolation threshold, we observe a lambda-type divergence in the fluctuation of the size of the largest TBA cluster, reminiscent of a critical point. Alongside, the structure of water is also perturbed, albeit weakly, by the aggregation of TBA molecules. There is a monotonic decrease in the tetrahedral order parameter of water, while the dipole moment correlation shows a weak nonlinearity. Interestingly, water molecules themselves exhibit a reverse percolation transition at higher TBA concentration, x(TBA) ≈ 0.45, where large spanning water clusters now break-up into small clusters. This is accompanied by significant divergence of the fluctuations in the size of largest water cluster. This second transition gives rise to another set of anomalies around. Both the percolation transitions can be regarded as manifestations of Janus effect at small molecular level.

High Resolution Diffusion Tensor Imaging of Cortical-Subcortical White Matter Tracts in TBI

DTIC Science & Technology

2010-10-01

by the individual (e.g., car full of lettuce ) or words that share phonemic qualities (e.g., chair/cat; sofa/soup). The observed bidirectional...subjective clustering score minus the expected subjective clustering score. An example is if the word pair car/ lettuce (subjective observed score of 1) is...adjusted subjective clustering formula of observed subjective clustering (car/ lettuce , subjective observed score of 1) minus expected subjective

Predicting vacancy-mediated diffusion of interstitial solutes in α -Fe

NASA Astrophysics Data System (ADS)

Barouh, Caroline; Schuler, Thomas; Fu, Chu-Chun; Jourdan, Thomas

2015-09-01

Based on a systematic first-principles study, the lowest-energy migration mechanisms and barriers for small vacancy-solute clusters (VnXm ) are determined in α -Fe for carbon, nitrogen, and oxygen, which are the most frequent interstitial solutes in several transition metals. We show that the dominant clusters present at thermal equilibrium (V X and V X2 ) have very reduced mobility compared to isolated solutes, while clusters composed of a solute bound to a small vacancy cluster may be significantly more mobile. In particular, V3X is found to be the fastest cluster for all three solutes. This result relies on the large diffusivity of the most compact trivacancy in a bcc lattice. Therefore, it may also be expected for interstitial solutes in other bcc metals. In the case of iron, we find that V3X may be as fast as or even more mobile than an interstitial solute. At variance with common assumptions, the trapping of interstitial solutes by vacancies does not necessarily decrease the mobility of the solute. Additionally, cluster dynamics simulations are performed considering a simple iron system with supersaturation of vacancies, in order to investigate the impacts of small mobile vacancy-solute clusters on properties such as the transport of solute and the cluster size distributions.

Colloidal heteroaggregation: a strategy to prepare composite materials

NASA Astrophysics Data System (ADS)

López-López, J. M.; Schmitt, A.; Moncho-Jordá, A.; Hidalgo-Álvarez, R.

2009-01-01

In this work, we make use of single-cluster light-scattering (SCLS) experiments and Brownian dynamics (BD) simulations in order to investigate the formation of binary clusters of oppositely-charged colloidal particles by heteroaggregation processes. Two parameters determinate the stability, size and structure of the clusters: the relative concentration of both species x and the range of the particle-particle interactions κa. SCLS experiments reveal that stable binary clusters arise in asymmetric systems when particle-particle interactions are long-ranged. These stable aggregates group in bell-shaped distributions that correspond to compact clusters with different orders, i.e., with a given number of minority particles. It is found that x controls the distribution of the clusters among the different orders and κa determine the average size of the clusters belonging to each order. Finally, BD simulations allow us to interpret all these results within the the frame of the classic Hogg-Healy-Fuersternau theory.

Coevolutionary dynamics with clustering behaviors on cyclic competition

NASA Astrophysics Data System (ADS)

Dong, Linrong; Yang, Guangcan

2012-05-01

We propose a dynamic model for describing clustering behaviors on a cyclic game, in which the same species form a cluster to compete. The rates of consuming the prey depend not only on the individual competing ability v, but also on the two interacting cluster’s sizes. The fragmentation and coagulation rates of the clusters are related to the cohesive strength among the individuals. A new parameter u is introduced to indicate the uniting degree. We find that the probability distribution of the clustering sizes is almost a power law in a large regime specified by the two parameters, which reflects the scale-free behavior in complex systems. In addition, the exponential magnitudes are mostly in the range of real social systems. Our simulation shows that clustering promotes biodiversity. At steady state, the amounts about the three species evolve tempestuously with asymmetric period; the aggregations about big size’s clusters to compete are obvious and on-off intermittence.

Clustering impact regime with shocks in freely evolving granular gas

NASA Astrophysics Data System (ADS)

Isobe, Masaharu

2017-06-01

A freely cooling granular gas without any external force evolves from the initial homogeneous state to the inhomogeneous clustering state, at which the energy decay deviates from the Haff's law. The asymptotic behavior of energy in the inelastic hard sphere model have been predicted by several theories, which are based on the mode coupling theory or extension of inelastic hard rods gas. In this study, we revisited the clustering regime of freely evolving granular gas via large-scale molecular dynamics simulation with up to 16.7 million inelastic hard disks. We found novel regime regarding on collisions between "clusters" spontaneously appearing after clustering regime, which can only be identified more than a few million particles system. The volumetric dilatation pattern of semicircular shape originated from density shock propagation are well characterized on the appearing of "cluster impact" during the aggregation process of clusters.

Cluster self-organization of nanotubes in a nematic phase: The percolation behavior and appearance of optical singularities

NASA Astrophysics Data System (ADS)

Ponevchinsky, V. V.; Goncharuk, A. I.; Vasil'Ev, V. I.; Lebovka, N. I.; Soskin, M. S.

2010-03-01

The structural features, as well as the optical and electrophysical properties of a 5CB nematic liquid crystal with additions of multilayer carbon nanotubes, have been investigated in the concentration range C = 0.0025-0.1 wt %. The self-aggregation of nanotubes into clusters with a fractal structure occurs in the liquid crystal. At 0.025 wt %, the clusters are merged, initiating the percolation transition of the composite to a state with a high electric conductivity. The strong interaction of 5CB molecules with the surface of nanotube clusters is responsible for the formation of micron surface liquid crystal layers with an irregular field of elastic stresses and a complex structure of birefringence. They are easily observed in a polarization microscope and visualize directly invisible submicron nanotube aggregates. Their transverse size increases when an electric field is applied to the liquid crystal cell. Two mechanisms of the generation of optical singularities in the passing laser beam have been revealed. Optical vortices appear in the speckle fields of laser radiation scattered at the indented boundaries of the nanotube clusters, whereas the birefringence of the beam in surface liquid-crystal layers is accompanied by the appearance of polarization C points.

{Nb288O768(OH)48(CO3)12}: A Macromolecular Polyoxometalate with Niobium Atoms Close to 300.

PubMed

Wu, Yan-Lan; Li, Xin-Xiong; Qi, Yan-Jie; Yu, Hao; Jin, Lu; Zheng, Shou-Tian

2018-05-29

A protein-sized (ca. 4.2 ᵡ 4.2 ᵡ 3.6 nm3) non-biologically derived molecule {Nb288O768(OH)48(CO3)12} (Nb288) containing up to 288 niobium atoms has been obtained, which is by far the largest and the highest nuclearity polyoxoniobate (PONb). Particularly, in terms of metal nuclearity number, Nb288 is the second largest cluster so far reported in classic polyoxometalate chemistry (V, Mo, W, Nb, and Ta). Nb288 can be described as a giant windmill-like cluster aggregate of six brand-new, nanoscale high-nuclearity PONb units {Nb47O128(OH)6(CO3)2} (Nb47) joined together by six additional Nb ions. Interestingly, the in situ generated 47-nuclearity Nb47 units can be isolated and bridged by copper complexes to form an inorganic-organic hybrid three-dimensional PONb framework, which exhibits effective catalytic activity for hydrolyzing nerve agent simulant of dimethyl methylphosphonate. The unique Nb47 cluster also provides a new type of topology to very limited family of Nb-O clusters. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mitochondrial nucleoid clusters protect newly synthesized mtDNA during Doxorubicin- and Ethidium Bromide-induced mitochondrial stress

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alán, Lukáš, E-mail: lukas.alan@fgu.cas.cz; Špaček

Mitochondrial DNA (mtDNA) is compacted in ribonucleoprotein complexes called nucleoids, which can divide or move within the mitochondrial network. Mitochondrial nucleoids are able to aggregate into clusters upon reaction with intercalators such as the mtDNA depletion agent Ethidium Bromide (EB) or anticancer drug Doxorobicin (DXR). However, the exact mechanism of nucleoid clusters formation remains unknown. Resolving these processes may help to elucidate the mechanisms of DXR-induced cardiotoxicity. Therefore, we addressed the role of two key nucleoid proteins; mitochondrial transcription factor A (TFAM) and mitochondrial single-stranded binding protein (mtSSB); in the formation of mitochondrial nucleoid clusters during the action of intercalators.more » We found that both intercalators cause numerous aberrations due to perturbing their native status. By blocking mtDNA replication, both agents also prevented mtDNA association with TFAM, consequently causing nucleoid aggregation into large nucleoid clusters enriched with TFAM, co-existing with the normal nucleoid population. In the later stages of intercalation (> 48 h), TFAM levels were reduced to 25%. In contrast, mtSSB was released from mtDNA and freely distributed within the mitochondrial network. Nucleoid clusters mostly contained nucleoids with newly replicated mtDNA, however the nucleoid population which was not in replication mode remained outside the clusters. Moreover, the nucleoid clusters were enriched with p53, an anti-oncogenic gatekeeper. We suggest that mitochondrial nucleoid clustering is a mechanism for protecting nucleoids with newly replicated DNA against intercalators mediating genotoxic stress. These results provide new insight into the common mitochondrial response to mtDNA stress and can be implied also on DXR-induced mitochondrial cytotoxicity. - Highlights: • The mechanism for mitochondrial nucleoid clustering is proposed. • DNA intercalators (Doxorubicin or Ethidium Bromide) prevent TFAM binding to mtDNA. • Replicating nucleoids are less prone to DNA intercalator and preserve more TFAM. • Nucleoid clusters mostly contain nucleoids with newly replicated mtDNA. • Recently replicated nucleoids are protected in clusters by increased TFAM and p53.« less

Aqueous formation and manipulation of the iron-oxo Keggin ion

NASA Astrophysics Data System (ADS)

Sadeghi, Omid; Zakharov, Lev N.; Nyman, May

2015-03-01

There is emerging evidence that growth of synthetic and natural phases occurs by the aggregation of prenucleation clusters, rather than classical atom-by-atom growth. Ferrihydrite, an iron oxyhydroxide mineral, is the common form of Fe3+ in soils and is also in the ferritin protein. We isolated a 10 angstrom discrete iron-oxo cluster (known as the Keggin ion, Fe13) that has the same structural features as ferrihydrite. The stabilization and manipulation of this highly reactive polyanion in water is controlled exclusively by its counterions. Upon dissolution of Fe13 in water with precipitation of its protecting Bi3+-counterions, it rapidly aggregates to ~22 angstrom spherical ferrihydrite nanoparticles. Fe13 may therefore also be a prenucleation cluster for ferrihydrite formation in natural systems, including by microbial and cellular processes.

The Heterogeneous P-Median Problem for Categorization Based Clustering

ERIC Educational Resources Information Center

Blanchard, Simon J.; Aloise, Daniel; DeSarbo, Wayne S.

2012-01-01

The p-median offers an alternative to centroid-based clustering algorithms for identifying unobserved categories. However, existing p-median formulations typically require data aggregation into a single proximity matrix, resulting in masked respondent heterogeneity. A proposed three-way formulation of the p-median problem explicitly considers…

Hierarchical Star Formation in Turbulent Media: Evidence from Young Star Clusters

NASA Astrophysics Data System (ADS)

Grasha, K.; Elmegreen, B. G.; Calzetti, D.; Adamo, A.; Aloisi, A.; Bright, S. N.; Cook, D. O.; Dale, D. A.; Fumagalli, M.; Gallagher, J. S., III; Gouliermis, D. A.; Grebel, E. K.; Kahre, L.; Kim, H.; Krumholz, M. R.; Lee, J. C.; Messa, M.; Ryon, J. E.; Ubeda, L.

2017-06-01

We present an analysis of the positions and ages of young star clusters in eight local galaxies to investigate the connection between the age difference and separation of cluster pairs. We find that star clusters do not form uniformly but instead are distributed so that the age difference increases with the cluster pair separation to the 0.25-0.6 power, and that the maximum size over which star formation is physically correlated ranges from ˜200 pc to ˜1 kpc. The observed trends between age difference and separation suggest that cluster formation is hierarchical both in space and time: clusters that are close to each other are more similar in age than clusters born further apart. The temporal correlations between stellar aggregates have slopes that are consistent with predictions of turbulence acting as the primary driver of star formation. The velocity associated with the maximum size is proportional to the galaxy’s shear, suggesting that the galactic environment influences the maximum size of the star-forming structures.

Uniform deposition of size-selected clusters using Lissajous scanning

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beniya, Atsushi; Watanabe, Yoshihide, E-mail: e0827@mosk.tytlabs.co.jp; Hirata, Hirohito

2016-05-15

Size-selected clusters can be deposited on the surface using size-selected cluster ion beams. However, because of the cross-sectional intensity distribution of the ion beam, it is difficult to define the coverage of the deposited clusters. The aggregation probability of the cluster depends on coverage, whereas cluster size on the surface depends on the position, despite the size-selected clusters are deposited. It is crucial, therefore, to deposit clusters uniformly on the surface. In this study, size-selected clusters were deposited uniformly on surfaces by scanning the cluster ions in the form of Lissajous pattern. Two sets of deflector electrodes set in orthogonalmore » directions were placed in front of the sample surface. Triangular waves were applied to the electrodes with an irrational frequency ratio to ensure that the ion trajectory filled the sample surface. The advantages of this method are simplicity and low cost of setup compared with raster scanning method. The authors further investigated CO adsorption on size-selected Pt{sub n} (n = 7, 15, 20) clusters uniformly deposited on the Al{sub 2}O{sub 3}/NiAl(110) surface and demonstrated the importance of uniform deposition.« less

Adsorption and dynamics of Si atoms at the monolayer Pb/Si(111) surface

NASA Astrophysics Data System (ADS)

Kumar, Rakesh; Fang, Chuang-Kai; Lee, Chih-Hao; Hwang, Ing-Shouh

2017-06-01

In this work, we studied the adsorption behavior of deposited Si atoms along with their diffusion and other dynamic processes on a Pb monolayer-covered Si(111) surface from 125 to 230 K using a variable-temperature scanning tunneling microscope. The Pb-covered Si(111) surface forms a low-symmetry rowlike (√{7 }×√{3 } ) structure in this temperature range and the Si atoms bind favorably to two specific on-top sites (T1 A and T1 B) on the trimer row after deposition at the sample temperature of ˜125 K . The Si atoms were immobile at low temperatures and started to switch between the two neighboring T1 A and T1 B sites within the same trimer when the temperature was raised to ˜150 K . When the temperature was raised above ˜160 K , the adsorbed Si atoms could hop to other trimers along the same trimer row. Below ˜170 K , short hops to adjacent trimers dominated, but long hops dominated at temperatures above ˜170 K . The activation energy and prefactor for the Si atoms diffusion were derived through analysis of continuous-time imaging at temperatures from 160 to 174 K. In addition, irreversible aggregation of single Si atoms into Si clusters started to occur at the phase boundaries or defective sites at temperatures above ˜170 K . At temperature above ˜180 K , nearly all Si atoms aggregated into clusters, which may have important implications for the atomic mechanism of epitaxial growth of Si on the Pb-covered Si(111) surface. In addition, our study provides strong evidence for breaking in the mirror symmetry in the (√{7 }×√{3 } )-Pb structure, which has implications for the atomic model of this controversial structure.

The Swift BAT Perspective on Non-Thermal Emission in HIFLUGCS Galaxy Clusters

NASA Technical Reports Server (NTRS)

Wik, Daniel R.

2011-01-01

The search for diffuse non-thermal, inverse Compton (IC) emission from galaxy clusters at hard X-ray energies has been underway for many years, with most detections being either of low significance or controversial. Until recently, comprehensive surveys of hard X-ray emission from clusters were not possible; instead, individually proposed-for. long observations would be collated from the archive. With the advent of the Swift BAT all sky survey, any c1u,;ter's emission above 14 keV can be probed with nearly uniform sensitivity. which is comparable to that of RXTE, Beppo-SAX, and Suzaku with the 58-month version of the survey. In this work. we search for non-thermal excess emission above the exponentially decreasing, high energy thermal emission in the flux-limited HIFLUGCS sample. The BAT emission from many of the detected clusters is marginally extended; we are able to extract the total flux for these clusters using fiducial models for their spatial extent. To account for thermal emission at BAT energies, XMM-Newton EPIC spectra are extracted from coincident spatial regions so that both the thermal and non-thermal spectral components can be determined simultaneou,;ly in joint fits. We find marginally significant IC components in 6 clusters, though after closer inspection and consideration of systematic errors we are unable to claim a clear detection in any of them. The spectra of all clusters are also summed to enhance a cumulative non-thermal signal not quite detectable in individual clusters. After constructing a model based on single temperature

LOFAR discovery of a double radio halo system in Abell 1758 and radio/X-ray study of the cluster pair

NASA Astrophysics Data System (ADS)

Botteon, A.; Shimwell, T. W.; Bonafede, A.; Dallacasa, D.; Brunetti, G.; Mandal, S.; van Weeren, R. J.; Brüggen, M.; Cassano, R.; de Gasperin, F.; Hoang, D. N.; Hoeft, M.; Röttgering, H. J. A.; Savini, F.; White, G. J.; Wilber, A.; Venturi, T.

2018-05-01

Radio halos and radio relics are diffuse synchrotron sources that extend over Mpc-scales and are found in a number of merger galaxy clusters. They are believed to form as a consequence of the energy that is dissipated by turbulence and shocks in the intra-cluster medium (ICM). However, the precise physical processes that generate these steep synchrotron spectrum sources are still poorly constrained. We present a new LOFAR observation of the double galaxy cluster Abell 1758. This system is composed of A1758N, a massive cluster hosting a known giant radio halo, and A1758S, which is a less massive cluster whose diffuse radio emission is confirmed here for the first time. Our observations have revealed a radio halo and a candidate radio relic in A1758S, and a suggestion of emission along the bridge connecting the two systems which deserves confirmation. We combined the LOFAR data with archival VLA and GMRT observations to constrain the spectral properties of the diffuse emission. We also analyzed a deep archival Chandra observation and used this to provide evidence that A1758N and A1758S are in a pre-merger phase. The ICM temperature across the bridge that connects the two systems shows a jump which might indicate the presence of a transversal shock generated in the initial stage of the merger.

Globular Clusters Shine in a Galaxy Lacking Dark Matter

NASA Astrophysics Data System (ADS)

Kohler, Susanna

2018-04-01

You may have seen recent news about NGC 1052DF2, a galaxy that was discovered to have little or no dark matter. Now, a new study explores what NGC 1052DF2 does have: an enigmatic population of unusually large and luminous globular clusters.Keck/LRIS spectra (left and right) and HST images (center) of the 11 clusters associated with NGC 1052DF2. The color images each span 1 1. [van Dokkum et al. 2018]An Unusual DwarfThe ultra-diffuse galaxy NGC 1052DF2, originally identified with the Dragonfly Telescope Array, has puzzled astronomers since the discovery that its dynamical mass determined by the motions of globular-cluster-like objects spotted within it is essentially the same as its stellar mass. This equivalence implies that the galaxy is strangely lacking dark matter; the upper limit set on its dark matter halo is 400 times smaller than what we would expect for such a dwarf galaxy.Led by Pieter van Dokkum (Yale University), the team that made this discovery has now followed up with detailed Hubble Space Telescope imaging and Keck spectroscopy. Their goal? To explore the objects that allowed them to make the dynamical-mass measurement: the oddly bright globular clusters of NGC 1052DF2.Sizes (circularized half-light radii) vs. absolute magnitudes for globular clusters in NGC1052DF2 (black) and the Milky Way (red). [Adapted from van Dokkum et al. 2018]Whats Up with the Globular Clusters?Van Dokkum and collaborators spectroscopically confirmed 11 compact objects associated with the faint galaxy. These objects are globular-cluster-like in their appearance, but the peak of their luminosity distribution is offset by a factor of four from globular clusters of other galaxies; these globular clusters are significantly brighter than is typical.Using the Hubble imaging, the authors determined that NGC 1052DF2s globular clusters are more than twice the size of the Milky Ways globular clusters in the same luminosity range. As is typical for globular clusters, they are an old ( 9.3 billion years) population and metal-poor.Rethinking Formation TheoriesThe long-standing picture of galaxies has closely connected old, metal-poor globular clusters to the galaxies dark-matter halos. Past studies have found that the ratio between the total globular-cluster mass and the overall mass of a galaxy (i.e., all dark + baryonic matter) holds remarkably constant across galaxies its typically 3 x 10-5. This has led researchers to believe that properties of the dark-matter halo may determine globular-cluster formation.The luminosity function of the compact objects in NGC 1052DF2. The red and blue curves show the luminosity functions of globular clusters in the Milky Way and in the typical ultra-diffuse galaxies of the Coma cluster, respectively. NGC 1052DF2s globular clusters peak at a significantly higher luminosity. [Adapted from van Dokkum et al. 2018]NGC 1052DF2, with a globular-cluster mass thats 3% of the mass of the galaxy ( 1000 times the expected ratio!), defies this picture. This unusual galaxy therefore demonstrates that the usual relation between globular-cluster mass and total galaxy mass probably isnt due to a fundamental connection between the dark-matter halo and globular-cluster formation. Instead, van Dokkum and collaborators suggest, globular-cluster formation may ultimately be a baryon-driven process.As with all unexpected discoveries in astronomy, we must now determine whether NGC 1052DF2 is simply a fluke, or whether it represents a new class of object we can expect to find more of. Either way, this unusual galaxy is forcing us to rethink what we know about galaxies and the star clusters they host.CitationPieter van Dokkum et al 2018 ApJL 856 L30. doi:10.3847/2041-8213/aab60b

Enhanced magnetostriction derived from magnetic single domain structures in cluster-assembled SmCo films

NASA Astrophysics Data System (ADS)

Bai, Yulong; Yang, Bo; Guo, Fei; Lu, Qingshan; Zhao, Shifeng

2017-11-01

Cluster-assembled SmCo alloy films were prepared by low energy cluster beam deposition. The structure, magnetic domain, magnetization, and magnetostriction of the films were characterized. It is shown that the as-prepared films are assembled in compact and uniformly distributed spherical cluster nanoparticles, most of which, after vacuum in situ annealing at 700 K, aggregated to form cluster islands. These cluster islands result in transformations from superparamagnetic states to magnetic single domain (MSD) states in the films. Such MSD structures contribute to the enhanced magnetostrictive behaviors with a saturation magnetostrictive coefficient of 160 × 10-6 in comparison to 105 × 10-6 for the as-prepared films. This work demonstrates candidate materials that could be applied in nano-electro-mechanical systems, low power information storage, and weak magnetic detecting devices.

Infrared Extinction Performance of Randomly Oriented Microbial-Clustered Agglomerate Materials.

PubMed

Li, Le; Hu, Yihua; Gu, Youlin; Zhao, Xinying; Xu, Shilong; Yu, Lei; Zheng, Zhi Ming; Wang, Peng

2017-11-01

In this study, the spatial structure of randomly distributed clusters of fungi An0429 spores was simulated using a cluster aggregation (CCA) model, and the single scattering parameters of fungi An0429 spores were calculated using the discrete dipole approximation (DDA) method. The transmittance of 10.6 µm infrared (IR) light in the aggregated fungi An0429 spores swarm is simulated by using the Monte Carlo method. Several parameters that affect the transmittance of 10.6 µm IR light, such as the number and radius of original fungi An0429 spores, porosity of aggregated fungi An0429 spores, and density of aggregated fungi An0429 spores of the formation aerosol area were discussed. Finally, the transmittances of microbial materials with different qualities were measured in the dynamic test platform. The simulation results showed that the parameters analyzed were closely connected with the extinction performance of fungi An0429 spores. By controlling the value of the influencing factors, the transmittance could be lower than a certain threshold to meet the requirement of attenuation in application. In addition, the experimental results showed that the Monte Carlo method could well reflect the attenuation law of IR light in fungi An0429 spore agglomerates swarms.

Innovations in the Teaching of Behavioral Sciences in the Preclinical Curriculum

ERIC Educational Resources Information Center

Mack, Kevin

2005-01-01

Objective: In problem-based learning curricula, cases are usually clustered into identified themes or organ systems. While this method of aggregating cases presents clear advantages in terms of resource alignment and student focus, an alternative "hidden cluster" approach provides rich opportunities for content integration. Method: The author…

Growth of polymer-metal nanocomposites by pulsed laser deposition

NASA Astrophysics Data System (ADS)

Röder, Johanna; Faupel, Jörg; Krebs, Hans-Ulrich

2008-12-01

Complex polymer-metal nanocomposites have a wide range of applications, e.g. as flexible displays and packaging materials. Pulsed laser deposition was applied to form nanostructured materials consisting of metal clusters (Ag, Au, Pd and Cu) embedded in a polymer (polycarbonate, PC) matrix. The size and amount of the metal clusters are controlled by the number of laser pulses hitting the respective targets. For Cu and Pd, smaller clusters and higher cluster densities are obtained as in the cases of Ag and Au due to a stronger reactivity with the polymers and thus a lower diffusivity. Implantation effects, differences in metal diffusivity and reactivity on the polymer surfaces, and the coalescence properties are discussed with respect to the observed microstructures on PC and compared to the metal growth on poly (methyl methacrylate), PMMA.

Diffusion of two-dimensional epitaxial clusters on metal (100) surfaces: Facile versus nucleation-mediated behavior and their merging for larger sizes

NASA Astrophysics Data System (ADS)

Lai, King C.; Liu, Da-Jiang; Evans, James W.

2017-12-01

For diffusion of two-dimensional homoepitaxial clusters of N atoms on metal (100) surfaces mediated by edge atom hopping, macroscale continuum theory suggests that the diffusion coefficient scales like DN˜ N-β with β =3 /2 . However, we find quite different and diverse behavior in multiple size regimes. These include: (i) facile diffusion for small sizes N <9 ; (ii) slow nucleation-mediated diffusion with small β <1 for "perfect" sizes N = Np= L2 or L (L +1 ) , for L =3 ,4 , ... having unique ground-state shapes, for moderate sizes 9 ≤N ≤O (102) ; the same also applies for N =Np+3 , Np+ 4 , ... (iii) facile diffusion but with large β >2 for N =Np+1 and Np+2 also for moderate sizes 9 ≤N ≤O (102) ; (iv) merging of the above distinct branches and subsequent anomalous scaling with 1 ≲β <3 /2 , reflecting the quasifacetted structure of clusters, for larger N =O (102) to N =O (103) ; (v) classic scaling with β =3 /2 for very large N =O (103) and above. The specified size ranges apply for typical model parameters. We focus on the moderate size regime where we show that diffusivity cycles quasiperiodically from the slowest branch for Np+3 (not Np) to the fastest branch for Np+1 . Behavior is quantified by kinetic Monte Carlo simulation of an appropriate stochastic lattice-gas model. However, precise analysis must account for a strong enhancement of diffusivity for short time increments due to back correlation in the cluster motion. Further understanding of this enhancement, of anomalous size scaling behavior, and of the merging of various branches, is facilitated by combinatorial analysis of the number of the ground-state and low-lying excited state cluster configurations, and also of kink populations.

Diffusion of two-dimensional epitaxial clusters on metal (100) surfaces: Facile versus nucleation-mediated behavior and their merging for larger sizes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lai, King C.; Liu, Da -Jiang; Evans, James W.

For diffusion of two-dimensional homoepitaxial clusters of N atoms on metal(100) surfaces mediated by edge atom hopping, macroscale continuum theory suggests that the diffusion coefficient scales like DN ~ N -β with β = 3/2. However, we find quite different and diverse behavior in multiple size regimes. These include: (i) facile diffusion for small sizes N < 9; (ii) slow nucleation-mediated diffusion with small β < 1 for “perfect” sizes N = N p = L 2 or L(L+1), for L = 3, 4,… having unique ground state shapes, for moderate sizes 9 ≤ N ≤ O(10 2); the samemore » also applies for N = N p +3, N p + 4,… (iii) facile diffusion but with large β > 2 for N = Np + 1 and N p + 2 also for moderate sizes 9 ≤ N ≤ O(10 2); (iv) merging of the above distinct branches and subsequent anomalous scaling with 1 ≲ β < 3/2, reflecting the quasi-facetted structure of clusters, for larger N = O(10 2) to N = O(10 3); and (v) classic scaling with β = 3/2 for very large N = O(103) and above. The specified size ranges apply for typical model parameters. We focus on the moderate size regime where show that diffusivity cycles quasi-periodically from the slowest branch for N p + 3 (not Np) to the fastest branch for Np + 1. Behavior is quantified by Kinetic Monte Carlo simulation of an appropriate stochastic lattice-gas model. However, precise analysis must account for a strong enhancement of diffusivity for short time increments due to back-correlation in the cluster motion. Further understanding of this enhancement, of anomalous size scaling behavior, and of the merging of various branches, is facilitated by combinatorial analysis of the number of the ground state and low-lying excited state cluster configurations, and also of kink populations.« less

Diffusion of two-dimensional epitaxial clusters on metal (100) surfaces: Facile versus nucleation-mediated behavior and their merging for larger sizes

DOE PAGES

Lai, King C.; Liu, Da -Jiang; Evans, James W.

2017-12-05

For diffusion of two-dimensional homoepitaxial clusters of N atoms on metal(100) surfaces mediated by edge atom hopping, macroscale continuum theory suggests that the diffusion coefficient scales like DN ~ N -β with β = 3/2. However, we find quite different and diverse behavior in multiple size regimes. These include: (i) facile diffusion for small sizes N < 9; (ii) slow nucleation-mediated diffusion with small β < 1 for “perfect” sizes N = N p = L 2 or L(L+1), for L = 3, 4,… having unique ground state shapes, for moderate sizes 9 ≤ N ≤ O(10 2); the samemore » also applies for N = N p +3, N p + 4,… (iii) facile diffusion but with large β > 2 for N = Np + 1 and N p + 2 also for moderate sizes 9 ≤ N ≤ O(10 2); (iv) merging of the above distinct branches and subsequent anomalous scaling with 1 ≲ β < 3/2, reflecting the quasi-facetted structure of clusters, for larger N = O(10 2) to N = O(10 3); and (v) classic scaling with β = 3/2 for very large N = O(103) and above. The specified size ranges apply for typical model parameters. We focus on the moderate size regime where show that diffusivity cycles quasi-periodically from the slowest branch for N p + 3 (not Np) to the fastest branch for Np + 1. Behavior is quantified by Kinetic Monte Carlo simulation of an appropriate stochastic lattice-gas model. However, precise analysis must account for a strong enhancement of diffusivity for short time increments due to back-correlation in the cluster motion. Further understanding of this enhancement, of anomalous size scaling behavior, and of the merging of various branches, is facilitated by combinatorial analysis of the number of the ground state and low-lying excited state cluster configurations, and also of kink populations.« less

Radio observations of the double-relic galaxy cluster Abell 1240

NASA Astrophysics Data System (ADS)

Hoang, D. N.; Shimwell, T. W.; van Weeren, R. J.; Intema, H. T.; Röttgering, H. J. A.; Andrade-Santos, F.; Akamatsu, H.; Bonafede, A.; Brunetti, G.; Dawson, W. A.; Golovich, N.; Best, P. N.; Botteon, A.; Brüggen, M.; Cassano, R.; de Gasperin, F.; Hoeft, M.; Stroe, A.; White, G. J.

2018-05-01

We present LOFAR 120 - 168 MHz images of the merging galaxy cluster Abell 1240 that hosts double radio relics. In combination with the GMRT 595 - 629 MHz and VLA 2 - 4 GHz data, we characterised the spectral and polarimetric properties of the radio emission. The spectral indices for the relics steepen from their outer edges towards the cluster centre and the electric field vectors are approximately perpendicular to the major axes of the relics. The results are consistent with the picture that these relics trace large-scale shocks propagating outwards during the merger. Assuming diffusive shock acceleration (DSA), we obtain shock Mach numbers of M=2.4 and 2.3 for the northern and southern shocks, respectively. For M≲ 3 shocks, a pre-existing population of mildly relativistic electrons is required to explain the brightness of the relics due to the high (>10 per cent) particle acceleration efficiency required. However, for M≳ 4 shocks the required efficiency is ≳ 1% and ≳ 0.5%, respectively, which is low enough for shock acceleration directly from the thermal pool. We used the fractional polarization to constrain the viewing angle to ≥53 ± 3° and ≥39 ± 5° for the northern and southern shocks, respectively. We found no evidence for diffuse emission in the cluster central region. If the halo spans the entire region between the relics (˜1.8 Mpc) our upper limit on the power is P1.4GHz = (1.4 ± 0.6) × 1023 W Hz-1 which is approximately equal to the anticipated flux from a cluster of this mass. However, if the halo is smaller than this, our constraints on the power imply that the halo is underluminous.

Zinc and cadmium complexes of a plant metallothionein under radical stress: desulfurisation reactions associated with the formation of trans-lipids in model membranes.

PubMed

Torreggiani, Armida; Domènech, Jordi; Orihuela, Ruben; Ferreri, Carla; Atrian, Sílvia; Capdevila, Mercè; Chatgilialoglu, Chryssostomos

2009-06-08

Metallothioneins (MTs) are sulfur-rich proteins capable of binding metal ions to give metal clusters. The metal-MT aggregates used in this work were Zn- and Cd-QsMT, where QsMT is an MT from the plant Quercus suber. Reactions of reductive reactive species (H(*) atoms and e(aq)(-)), produced by gamma irradiation of water, with Zn- and Cd-QsMT were carried out in both aqueous solutions and vesicle suspensions, and were characterized by different approaches. By using a biomimetic model based on unsaturated lipid vesicle suspensions, the occurrence of tandem protein/lipid damage was shown. The reactions of reductive reactive species with methionine residues and/or sulfur-containing ligands afford diffusible sulfur-centred radicals, which migrate from the aqueous phase to the lipid bilayer and transform the cis double bond of the oleate moiety into the trans isomer. Tailored experiments allowed the reaction mechanism to be elucidated in some detail. The formation of sulfur-centred radicals is accompanied by the modification of the metal-QsMT complexes, which were monitored by various spectroscopic and spectrometric techniques (Raman, CD, and ESI-MS). Attack of the H(*) atom and e(aq)(-) on the metal-QsMT aggregates can induce significant structural changes such as partial deconstruction and/or rearrangement of the metal clusters and breaking of the protein backbone. Substantial differences were observed in the behaviour of the Zn- and Cd-QsMT aggregates towards the reactive species, depending on the different folding of the polypeptide in these two cases.

Crystallization process of a three-dimensional complex plasma

NASA Astrophysics Data System (ADS)

Steinmüller, Benjamin; Dietz, Christopher; Kretschmer, Michael; Thoma, Markus H.

2018-05-01

Characteristic timescales and length scales for phase transitions of real materials are in ranges where a direct visualization is unfeasible. Therefore, model systems can be useful. Here, the crystallization process of a three-dimensional complex plasma under gravity conditions is considered where the system ranges up to a large extent into the bulk plasma. Time-resolved measurements exhibit the process down to a single-particle level. Primary clusters, consisting of particles in the solid state, grow vertically and, secondarily, horizontally. The box-counting method shows a fractal dimension of df≈2.72 for the clusters. This value gives a hint that the formation process is a combination of local epitaxial and diffusion-limited growth. The particle density and the interparticle distance to the nearest neighbor remain constant within the clusters during crystallization. All results are in good agreement with former observations of a single-particle layer.

Inference With Difference-in-Differences With a Small Number of Groups: A Review, Simulation Study, and Empirical Application Using SHARE Data.

PubMed

Rokicki, Slawa; Cohen, Jessica; Fink, Günther; Salomon, Joshua A; Landrum, Mary Beth

2018-01-01

Difference-in-differences (DID) estimation has become increasingly popular as an approach to evaluate the effect of a group-level policy on individual-level outcomes. Several statistical methodologies have been proposed to correct for the within-group correlation of model errors resulting from the clustering of data. Little is known about how well these corrections perform with the often small number of groups observed in health research using longitudinal data. First, we review the most commonly used modeling solutions in DID estimation for panel data, including generalized estimating equations (GEE), permutation tests, clustered standard errors (CSE), wild cluster bootstrapping, and aggregation. Second, we compare the empirical coverage rates and power of these methods using a Monte Carlo simulation study in scenarios in which we vary the degree of error correlation, the group size balance, and the proportion of treated groups. Third, we provide an empirical example using the Survey of Health, Ageing, and Retirement in Europe. When the number of groups is small, CSE are systematically biased downwards in scenarios when data are unbalanced or when there is a low proportion of treated groups. This can result in over-rejection of the null even when data are composed of up to 50 groups. Aggregation, permutation tests, bias-adjusted GEE, and wild cluster bootstrap produce coverage rates close to the nominal rate for almost all scenarios, though GEE may suffer from low power. In DID estimation with a small number of groups, analysis using aggregation, permutation tests, wild cluster bootstrap, or bias-adjusted GEE is recommended.

The Stellar Populations of Two Ultra-diffuse Galaxies from Optical and Near-infrared Photometry

NASA Astrophysics Data System (ADS)

Pandya, Viraj; Romanowsky, Aaron J.; Laine, Seppo; Brodie, Jean P.; Johnson, Benjamin D.; Glaccum, William; Villaume, Alexa; Cuillandre, Jean-Charles; Gwyn, Stephen; Krick, Jessica; Lasker, Ronald; Martín-Navarro, Ignacio; Martinez-Delgado, David; van Dokkum, Pieter

2018-05-01

We present observational constraints on the stellar populations of two ultra-diffuse galaxies (UDGs) using optical through near-infrared (NIR) spectral energy distribution (SED) fitting. Our analysis is enabled by new Spitzer-IRAC 3.6 and 4.5 μm imaging, archival optical imaging, and the prospector fully Bayesian SED fitting framework. Our sample contains one field UDG (DGSAT I), one Virgo cluster UDG (VCC 1287), and one Virgo cluster dwarf elliptical for comparison (VCC 1122). We find that the optical–NIR colors of the three galaxies are significantly different from each other. We infer that VCC 1287 has an old (≳7.7 Gyr) and surprisingly metal-poor ([Z/Z ⊙] ≲ ‑1.0) stellar population, even after marginalizing over uncertainties on diffuse interstellar dust. In contrast, the field UDG DGSAT I shows evidence of being younger than the Virgo UDG, with an extended star formation history and an age posterior extending down to ∼3 Gyr. The stellar metallicity of DGSAT I is sub-solar but higher than that of the Virgo UDG, with [Z/{Z}ȯ ]=-{0.63}-0.62+0.35; in the case of exactly zero diffuse interstellar dust, DGSAT I may even have solar metallicity. With VCC 1287 and several Coma UDGs, a general picture is emerging where cluster UDGs may be “failed” galaxies, but the field UDG DGSAT I seems more consistent with a stellar feedback-induced expansion scenario. In the future, our approach can be applied to a large and diverse sample of UDGs down to faint surface brightness limits, with the goal of constraining their stellar ages, stellar metallicities, and circumstellar and diffuse interstellar dust content.

Theoretical insight into Cobalt subnano-clusters adsorption on α-Al{sub 2}O{sub 3} (0001)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, Fen-e; Ren, Jun, E-mail: jun.ren@nuc.edu.cn; Wang, Qiang

The investigation on the structural stability, nucleation, growth and interaction of cobalt cluster Con(n=2–7) on the α-Al{sub 2}O{sub 3}(0001) surface by using density functional theory methods has been reported. Energetically, the most favorable adsorption sites were identified and the strongest adsorption energy cluster is the tetrahedral Co{sub 4} cluster. On the other hand, the nucleation of Con(n=2–7) clusters on the surface is exothermic and thermodynamically favorable. Moreover, even-odd alternation was found with respect to clusters nucleation as a function of the number of cobalt atoms (for n=1–7). Meanwhile, the Co{sub n} clusters can be adsorbed on the surface stably owingmore » to the charge transfer from Co atoms to Al and O atoms of the Al{sub 2}O{sub 3} substrate. In addition, we establish the crucial importance of monomer, dimer and trimer diffusion on the surface. The diffusion of the monomer cobalt from Al{sup (3)} to O{sup (5)} or O{sup (5)} to Al{sup (4)} site is quite easy on the Al{sub 2}O{sub 3}(0001) surface, whereas the diffusion of the Co{sub 2} dimer is thermodynamically unfavorable by compared with that of the Co adatom and Co{sub 3} trimer. - Graphical abstract: Diffusion process of Co adatom on the α-Al{sub 2}O{sub 3} (0001) surface, Al{sup (3)} site→O{sup (5)} site→Al{sup (4)} site. Potential energy surface for diffusion of a single Co atom from Al{sup (3)} to O{sup (5)} site, and from O{sup (5)} to Al{sup (4)} site on the surface. The activation energy of the two migration processes from Al{sup (3)} to O{sup (5)} and O{sup (5)} to Al{sup (4)} are 0.06 and 0.09 eV, respectively. This implies the monomer is quite mobile on the surface under typical growth conditions.« less

A novel magnetic resonance imaging segmentation technique for determining diffuse intrinsic pontine glioma tumor volume.

PubMed

Singh, Ranjodh; Zhou, Zhiping; Tisnado, Jamie; Haque, Sofia; Peck, Kyung K; Young, Robert J; Tsiouris, Apostolos John; Thakur, Sunitha B; Souweidane, Mark M

2016-11-01

OBJECTIVE Accurately determining diffuse intrinsic pontine glioma (DIPG) tumor volume is clinically important. The aims of the current study were to 1) measure DIPG volumes using methods that require different degrees of subjective judgment; and 2) evaluate interobserver agreement of measurements made using these methods. METHODS Eight patients from a Phase I clinical trial testing convection-enhanced delivery (CED) of a therapeutic antibody were included in the study. Pre-CED, post-radiation therapy axial T2-weighted images were analyzed using 2 methods requiring high degrees of subjective judgment (picture archiving and communication system [PACS] polygon and Volume Viewer auto-contour methods) and 1 method requiring a low degree of subjective judgment (k-means clustering segmentation) to determine tumor volumes. Lin's concordance correlation coefficients (CCCs) were calculated to assess interobserver agreement. RESULTS The CCCs of measurements made by 2 observers with the PACS polygon and the Volume Viewer auto-contour methods were 0.9465 (lower 1-sided 95% confidence limit 0.8472) and 0.7514 (lower 1-sided 95% confidence limit 0.3143), respectively. Both were considered poor agreement. The CCC of measurements made using k-means clustering segmentation was 0.9938 (lower 1-sided 95% confidence limit 0.9772), which was considered substantial strength of agreement. CONCLUSIONS The poor interobserver agreement of PACS polygon and Volume Viewer auto-contour methods highlighted the difficulty in consistently measuring DIPG tumor volumes using methods requiring high degrees of subjective judgment. k-means clustering segmentation, which requires a low degree of subjective judgment, showed better interobserver agreement and produced tumor volumes with delineated borders.

Privacy protection versus cluster detection in spatial epidemiology.

PubMed

Olson, Karen L; Grannis, Shaun J; Mandl, Kenneth D

2006-11-01

Patient data that includes precise locations can reveal patients' identities, whereas data aggregated into administrative regions may preserve privacy and confidentiality. We investigated the effect of varying degrees of address precision (exact latitude and longitude vs the center points of zip code or census tracts) on detection of spatial clusters of cases. We simulated disease outbreaks by adding supplementary spatially clustered emergency department visits to authentic hospital emergency department syndromic surveillance data. We identified clusters with a spatial scan statistic and evaluated detection rate and accuracy. More clusters were identified, and clusters were more accurately detected, when exact locations were used. That is, these clusters contained at least half of the simulated points and involved few additional emergency department visits. These results were especially apparent when the synthetic clustered points crossed administrative boundaries and fell into multiple zip code or census tracts. The spatial cluster detection algorithm performed better when addresses were analyzed as exact locations than when they were analyzed as center points of zip code or census tracts, particularly when the clustered points crossed administrative boundaries. Use of precise addresses offers improved performance, but this practice must be weighed against privacy concerns in the establishment of public health data exchange policies.

Intracluster light in clusters of galaxies at redshifts 0.4 < z < 0.8

NASA Astrophysics Data System (ADS)

Guennou, L.; Adami, C.; Da Rocha, C.; Durret, F.; Ulmer, M. P.; Allam, S.; Basa, S.; Benoist, C.; Biviano, A.; Clowe, D.; Gavazzi, R.; Halliday, C.; Ilbert, O.; Johnston, D.; Just, D.; Kron, R.; Kubo, J. M.; Le Brun, V.; Marshall, P.; Mazure, A.; Murphy, K. J.; Pereira, D. N. E.; Rabaça, C. R.; Rostagni, F.; Rudnick, G.; Russeil, D.; Schrabback, T.; Slezak, E.; Tucker, D.; Zaritsky, D.

2012-01-01

Context. The study of intracluster light (ICL) can help us to understand the mechanisms taking place in galaxy clusters, and to place constraints on the cluster formation history and physical properties. However, owing to the intrinsic faintness of ICL emission, most searches and detailed studies of ICL have been limited to redshifts z < 0.4. Aims: To help us extend our knowledge of ICL properties to higher redshifts and study the evolution of ICL with redshift, we search for ICL in a subsample of ten clusters detected by the ESO Distant Cluster Survey (EDisCS), at redshifts 0.4 < z < 0.8, that are also part of our DAFT/FADA Survey. Methods: We analyze the ICL by applying the OV WAV package, a wavelet-based technique, to deep HST ACS images in the F814W filter and to V-band VLT/FORS2 images of three clusters. Detection levels are assessed as a function of the diffuse light source surface brightness using simulations. Results: In the F814W filter images, we detect diffuse light sources in all the clusters, with typical sizes of a few tens of kpc (assuming that they are at the cluster redshifts). The ICL detected by stacking the ten F814W images shows an 8σ detection in the source center extending over a ~50 × 50 kpc2 area, with a total absolute magnitude of -21.6 in the F814W filter, equivalent to about two L∗ galaxies per cluster. We find a weak correlation between the total F814W absolute magnitude of the ICL and the cluster velocity dispersion and mass. There is no apparent correlation between the cluster mass-to-light ratio (M/L) and the amount of ICL, and no evidence of any preferential orientation in the ICL source distribution. We find no strong variation in the amount of ICL between z = 0 and z = 0.8. In addition, we find wavelet-detected compact objects (WDCOs) in the three clusters for which data in two bands are available; these objects are probably very faint compact galaxies that in some cases are members of the respective clusters and comparable to the faint dwarf galaxies of the Local Group. Conclusions: We show that the ICL is prevalent in clusters at least up to redshift z = 0.8. In the future, we propose to detect the ICL at even higher redshifts, to determine wether there is a particular stage of cluster evolution where it was stripped from galaxies and spread into the intracluster medium. Based on observations made at ESO Telescopes at the Paranal Observatory under programme ID 082.A-0374. Also based on the use of the NASA/IPAC Extragalactic Database (NED) which is operated by the Jet Propulsion Laboratory, California Institute of Technology, under contract with the National Aeronautics and Space Administration. Based on observations made with the NASA/ESA Hubble Space Telescope, obtained from the data archives at the Space Telescope European Coordinating Facility and the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555.

A first constraint on the average mass of ultra-diffuse galaxies from weak gravitational lensing

NASA Astrophysics Data System (ADS)

Sifón, Cristóbal; van der Burg, Remco F. J.; Hoekstra, Henk; Muzzin, Adam; Herbonnet, Ricardo

2018-01-01

The recent discovery of thousands of ultra-diffuse galaxies (UDGs) in nearby galaxy clusters has opened a new window into the process of galaxy formation and evolution. Several scenarios have been proposed to explain the formation history of UDGs, and their ability to survive in the harsh cluster environments. A key requirement to distinguish between these scenarios is a measurement of their halo masses which, due to their low surface brightnesses, has proven difficult if one relies on stellar tracers of the potential. We exploit weak gravitational lensing, a technique that does not depend on these baryonic tracers, to measure the average subhalo mass of 784 UDGs selected in 18 clusters at z ≤ 0.09. Our sample of UDGs has a median stellar mass 〈m⋆〉 = 2 × 108 M⊙ and a median effective radius 〈reff〉 = 2.8 kpc. We constrain the average mass of subhaloes within 30 kpc to log mUDG(r < 30 kpc)/M⊙ ≤ 10.99 at 95 per cent credibility, implying an effective virial mass log m200/M⊙ ≤ 11.80, and a lower limit on the stellar mass fraction within 10 kpc of 1.0 per cent. Such mass is consistent with a simple extrapolation of the subhalo-to-stellar mass relation of typical satellite galaxies in massive clusters. However, our analysis is not sensitive to scatter about this mean mass; the possibility remains that extreme UDGs reside in haloes as massive as the Milky Way.

A class of compact dwarf galaxies from disruptive processes in galaxy clusters.

PubMed

Drinkwater, M J; Gregg, M D; Hilker, M; Bekki, K; Couch, W J; Ferguson, H C; Jones, J B; Phillipps, S

2003-05-29

Dwarf galaxies have attracted increased attention in recent years, because of their susceptibility to galaxy transformation processes within rich galaxy clusters. Direct evidence for these processes, however, has been difficult to obtain, with a small number of diffuse light trails and intra-cluster stars being the only signs of galaxy disruption. Furthermore, our current knowledge of dwarf galaxy populations may be very incomplete, because traditional galaxy surveys are insensitive to extremely diffuse or compact galaxies. Aware of these concerns, we recently undertook an all-object survey of the Fornax galaxy cluster. This revealed a new population of compact members, overlooked in previous conventional surveys. Here we demonstrate that these 'ultra-compact' dwarf galaxies are structurally and dynamically distinct from both globular star clusters and known types of dwarf galaxy, and thus represent a new class of dwarf galaxy. Our data are consistent with the interpretation that these are the remnant nuclei of disrupted dwarf galaxies, making them an easily observed tracer of galaxy disruption.

The Stormy Life of Galaxy Clusters

NASA Astrophysics Data System (ADS)

Rudnick, Lawrence

2018-01-01

Galaxy clusters, the largest gravitationally bound structures, hold the full history of their baryonic evolution, serve as important cosmological tools and allow us to probe unique physical regimes in their diffuse plasmas. With characteristic dynamical timescales of 107-109 years, these diffuse thermal and relativistic media continue to evolve, as dark matter drives major mergers and more gentle continuing accretion. The history of this assembly is encoded in the plasmas, and a wide range of observational and theoretical investigations are aimed at decoding their signatures. X-ray temperature and density variations, low Mach number shocks, and "cold front" discontinuities all illuminate clusters' continued evolution. Radio structures and spectra are passive indicators of merger shocks, while radio galaxy distortions reveal the complex motions in the intracluster medium. Deep in cluster cores, AGNs associated with brightest cluster galaxies provide ongoing energy, and perhaps even stabilize the intracluster medium. In this talk, we will recount this evolving picture of the stormy ICM, and suggest areas of likely advance in the coming years.

Transport and mixing in strongly coupled dusty plasma medium

NASA Astrophysics Data System (ADS)

Dharodi, Vikram; Das, Amita; Patel, Bhavesh

2016-10-01

The generalized hydrodynamic (GHD) fluid model has been employed to study the transport and mixing properties of Dusty plasma medium in strong coupling limit. The response of lighter electron and ion species to the dust motion is taken to be instantaneous i.e. inertia-less. Thus the electron and ion density are presumed to follow the Boltzman relation. In the incompressible limit (i-GHD) the model supports Transverse Shear wave in contrast to the Hydrodynamic fluids. It has been shown that the presence of these waves leads to a better mixing of fluid in this case. Several cases of flow configuration have been considered for the study. The transport and mixing attributes have been quantified by studying the dynamical evolution of tracer particles in the system. The diffusion and clustering of these test particles are directly linked to the mixing characteristic of a medium. The displacement of these particles provides for a quantitative estimate of the diffusion coefficient of the medium. It is shown that these test particles often organize themselves in spatially inhomogeneous pattern leading to the phenomena of clustering.

A model of jam formation in congested traffic

NASA Astrophysics Data System (ADS)

Bunzarova, N. Zh; Pesheva, N. C.; Priezzhev, V. B.; Brankov, J. G.

2017-12-01

We study a model of irreversible jam formation in congested vehicular traffic on an open segment of a single-lane road. The vehicles obey a stochastic discrete-time dynamics which is a limiting case of the generalized Totally Asymmetric Simple Exclusion Process. Its characteristic features are: (a) the existing clusters of jammed cars cannot break into parts; (b) when the leading vehicle of a cluster hops to the right, the whole cluster follows it deterministically, and (c) any two clusters of vehicles, occupying consecutive positions on the chain, may become nearest-neighbors and merge irreversibly into a single cluster. The above dynamics was used in a one-dimensional model of irreversible aggregation by Bunzarova and Pesheva [Phys. Rev. E 95, 052105 (2017)]. The model has three stationary non-equilibrium phases, depending on the probabilities of injection (α), ejection (β), and hopping (p) of particles: a many-particle one, MP, a completely jammed phase CF, and a mixed MP+CF phase. An exact expression for the stationary probability P(1) of a completely jammed configuration in the mixed MP+CF phase is obtained. The gap distribution between neighboring clusters of jammed cars at large lengths L of the road is studied. Three regimes of evolution of the width of a single gap are found: (i) growing gaps with length of the order O(L) when β > p; (ii) shrinking gaps with length of the order O(1) when β < p; and (iii) critical gaps at β = p, of the order O(L 1/2). These results are supported by extensive Monte Carlo calculations.

Effect of sharp maximum in ion diffusivity for liquid xenon

NASA Astrophysics Data System (ADS)

Lankin, A. V.; Orekhov, M. A.

2016-11-01

Ion diffusion in a liquid usually could be treated as a movement of an ion cluster in a viscous media. For small ions this leads to a special feature: diffusion coefficient is either independent of the ion size or increases with it. We find a different behavior for small ions in liquid xenon. Calculation of the dependence of an ion diffusion coefficient in liquid xenon on the ion size is carried out. Classical molecular dynamics method is applied. Calculated dependence of the ion diffusion coefficient on its radius has sharp maximums at the ion radiuses 1.75 and 2 Å. Every maximum is placed between two regions with different stable ion cluster configurations. This leads to the instability of these configurations in a small region between them. Consequently ion with radius near 1.75 or 2 Å could jump from one configuration to another. This increases the speed of the diffusion. A simple qualitative model for this effect is suggested. The decomposition of the ion movement into continuous and jump diffusion shows that continuous part of the diffusion is the same as for the ion cluster in the stable region.

On the multi-scale description of micro-structured fluids composed of aggregating rods

NASA Astrophysics Data System (ADS)

Perez, Marta; Scheuer, Adrien; Abisset-Chavanne, Emmanuelle; Ammar, Amine; Chinesta, Francisco; Keunings, Roland

2018-05-01

When addressing the flow of concentrated suspensions composed of rods, dense clusters are observed. Thus, the adequate modelling and simulation of such a flow requires addressing the kinematics of these dense clusters and their impact on the flow in which they are immersed. In a former work, we addressed a first modelling framework of these clusters, assumed so dense that they were considered rigid and their kinematics (flow-induced rotation) were totally defined by a symmetric tensor c with unit trace representing the cluster conformation. Then, the rigid nature of the clusters was relaxed, assuming them deformable, and a model giving the evolution of both the cluster shape and its microstructural orientation descriptor (the so-called shape and orientation tensors) was proposed. This paper compares the predictions coming from those models with finer-scale discrete simulations inspired from molecular dynamics modelling.

Thermodynamic properties of small aggregates of rare-gas atoms

NASA Technical Reports Server (NTRS)

Etters, R. D.; Kaelberer, J.

1975-01-01

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

Morphology of clusters of attractive dry and wet self-propelled spherical particle suspensions.

PubMed

Alarcón, Francisco; Valeriani, Chantal; Pagonabarraga, Ignacio

2017-01-25

In order to assess the effect of hydrodynamics in the assembly of active attractive spheres, we simulate a semi-dilute suspension of attractive self-propelled spherical particles in a quasi-two dimensional geometry comparing the case with and without hydrodynamics interactions. To start with, independent of the presence of hydrodynamics, we observe that depending on the ratio between attraction and propulsion, particles either coarsen or aggregate forming finite-size clusters. Focusing on the clustering regime, we characterize two different cluster parameters, i.e. their morphology and orientational order, and compare the case when active particles behave either as pushers or pullers (always in the regime where inter-particle attractions compete with self-propulsion). Studying cluster phases for squirmers with respect to those obtained for active Brownian disks (indicated as ABPs), we have shown that hydrodynamics alone can sustain a cluster phase of active swimmers (pullers), while ABPs form cluster phases due to the competition between attraction and self-propulsion. The structural properties of the cluster phases of squirmers and ABPs are similar, although squirmers show sensitivity to active stresses. Active Brownian disks resemble weakly pusher squirmer suspensions in terms of cluster size distribution, structure of the radius of gyration on the cluster size and degree of cluster polarity.

Clustervision: Visual Supervision of Unsupervised Clustering.

PubMed

Kwon, Bum Chul; Eysenbach, Ben; Verma, Janu; Ng, Kenney; De Filippi, Christopher; Stewart, Walter F; Perer, Adam

2018-01-01

Clustering, the process of grouping together similar items into distinct partitions, is a common type of unsupervised machine learning that can be useful for summarizing and aggregating complex multi-dimensional data. However, data can be clustered in many ways, and there exist a large body of algorithms designed to reveal different patterns. While having access to a wide variety of algorithms is helpful, in practice, it is quite difficult for data scientists to choose and parameterize algorithms to get the clustering results relevant for their dataset and analytical tasks. To alleviate this problem, we built Clustervision, a visual analytics tool that helps ensure data scientists find the right clustering among the large amount of techniques and parameters available. Our system clusters data using a variety of clustering techniques and parameters and then ranks clustering results utilizing five quality metrics. In addition, users can guide the system to produce more relevant results by providing task-relevant constraints on the data. Our visual user interface allows users to find high quality clustering results, explore the clusters using several coordinated visualization techniques, and select the cluster result that best suits their task. We demonstrate this novel approach using a case study with a team of researchers in the medical domain and showcase that our system empowers users to choose an effective representation of their complex data.

Multifractal Approach to Time Clustering of Earthquakes. Application to Mt. Vesuvio Seismicity

NASA Astrophysics Data System (ADS)

Codano, C.; Alonzo, M. L.; Vilardo, G.

The clustering structure of the Vesuvian earthquakes occurring is investigated by means of statistical tools: the inter-event time distribution, the running mean and the multifractal analysis. The first cannot clearly distinguish between a Poissonian process and a clustered one due to the difficulties of clearly distinguishing between an exponential distribution and a power law one. The running mean test reveals the clustering of the earthquakes, but looses information about the structure of the distribution at global scales. The multifractal approach can enlighten the clustering at small scales, while the global behaviour remains Poissonian. Subsequently the clustering of the events is interpreted in terms of diffusive processes of the stress in the earth crust.

A Scalable Monitoring for the CMS Filter Farm Based on Elasticsearch

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andre, J.M.; et al.

2015-12-23

A flexible monitoring system has been designed for the CMS File-based Filter Farm making use of modern data mining and analytics components. All the metadata and monitoring information concerning data flow and execution of the HLT are generated locally in the form of small documents using the JSON encoding. These documents are indexed into a hierarchy of elasticsearch (es) clusters along with process and system log information. Elasticsearch is a search server based on Apache Lucene. It provides a distributed, multitenant-capable search and aggregation engine. Since es is schema-free, any new information can be added seamlessly and the unstructured informationmore » can be queried in non-predetermined ways. The leaf es clusters consist of the very same nodes that form the Filter Farm thus providing natural horizontal scaling. A separate central” es cluster is used to collect and index aggregated information. The fine-grained information, all the way to individual processes, remains available in the leaf clusters. The central es cluster provides quasi-real-time high-level monitoring information to any kind of client. Historical data can be retrieved to analyse past problems or correlate them with external information. We discuss the design and performance of this system in the context of the CMS DAQ commissioning for LHC Run 2.« less

Electron attenuation in free, neutral ethane clusters.

PubMed

Winkler, M; Myrseth, V; Harnes, J; Børve, K J

2014-10-28

The electron effective attenuation length (EAL) in free, neutral ethane clusters has been determined at 40 eV kinetic energy by combining carbon 1s x-ray photoelectron spectroscopy and theoretical lineshape modeling. More specifically, theory is employed to form model spectra on a grid in cluster size (N) and EAL (λ), allowing N and λ to be determined by optimizing the goodness-of-fit χ(2)(N, λ) between model and observed spectra. Experimentally, the clusters were produced in an adiabatic-expansion setup using helium as the driving gas, spanning a range of 100-600 molecules in mean cluster size. The effective attenuation length was determined to be 8.4 ± 1.9 Å, in good agreement with an independent estimate of 10 Å formed on the basis of molecular electron-scattering data and Monte Carlo simulations. The aggregation state of the clusters as well as the cluster temperature and its importance to the derived EAL value are discussed in some depth.

From bismuth oxide/hydroxide precursor clusters towards stable oxides: Proton transfer reactions and structural reorganization govern the stability of [Bi18O13(OH)10]-nitrate clusters

NASA Astrophysics Data System (ADS)

Walther, M.; Zahn, D.

2018-01-01

Structural relaxation and stability of a Bi18-cluster as obtained from association of [Bi6O4(OH)4](NO3)6 precursor clusters in DMSO solution is investigated from a combination of quantum chemical calculations and μs-scale molecular dynamics simulations using empirical interaction potentials. The Bi18-cluster undergoes a OH⋯OH proton transfer reaction, followed by considerable structural relaxation. While the aggregation of the Bi18-cluster is induced by the dissociation of a single nitrate ion leading to [Bi6O4(OH)4](NO3)5+ as an activated precursor species that can bind two more Bi6-clusters, we find the [Bi18O13(OH)10](NO3)18-x+x species (explored for x = 1-6) rather inert against either nitrate dissociation, collision with Bi6-precursors or combinations thereof.

Mapping Health Data: Improved Privacy Protection With Donut Method Geomasking

PubMed Central

Hampton, Kristen H.; Fitch, Molly K.; Allshouse, William B.; Doherty, Irene A.; Gesink, Dionne C.; Leone, Peter A.; Serre, Marc L.; Miller, William C.

2010-01-01

A major challenge in mapping health data is protecting patient privacy while maintaining the spatial resolution necessary for spatial surveillance and outbreak identification. A new adaptive geomasking technique, referred to as the donut method, extends current methods of random displacement by ensuring a user-defined minimum level of geoprivacy. In donut method geomasking, each geocoded address is relocated in a random direction by at least a minimum distance, but less than a maximum distance. The authors compared the donut method with current methods of random perturbation and aggregation regarding measures of privacy protection and cluster detection performance by masking multiple disease field simulations under a range of parameters. Both the donut method and random perturbation performed better than aggregation in cluster detection measures. The performance of the donut method in geoprivacy measures was at least 42.7% higher and in cluster detection measures was less than 4.8% lower than that of random perturbation. Results show that the donut method provides a consistently higher level of privacy protection with a minimal decrease in cluster detection performance, especially in areas where the risk to individual geoprivacy is greatest. PMID:20817785

Mapping health data: improved privacy protection with donut method geomasking.

PubMed

Hampton, Kristen H; Fitch, Molly K; Allshouse, William B; Doherty, Irene A; Gesink, Dionne C; Leone, Peter A; Serre, Marc L; Miller, William C

2010-11-01

A major challenge in mapping health data is protecting patient privacy while maintaining the spatial resolution necessary for spatial surveillance and outbreak identification. A new adaptive geomasking technique, referred to as the donut method, extends current methods of random displacement by ensuring a user-defined minimum level of geoprivacy. In donut method geomasking, each geocoded address is relocated in a random direction by at least a minimum distance, but less than a maximum distance. The authors compared the donut method with current methods of random perturbation and aggregation regarding measures of privacy protection and cluster detection performance by masking multiple disease field simulations under a range of parameters. Both the donut method and random perturbation performed better than aggregation in cluster detection measures. The performance of the donut method in geoprivacy measures was at least 42.7% higher and in cluster detection measures was less than 4.8% lower than that of random perturbation. Results show that the donut method provides a consistently higher level of privacy protection with a minimal decrease in cluster detection performance, especially in areas where the risk to individual geoprivacy is greatest.

Label-free sensitive luminescence biosensor for immunoglobulin G based on Ag6Au6 ethisterone cluster-estrogen receptor α aggregation and graphene.

PubMed

Chen, Nannan; Guo, Wenjing; Lin, Zhixiang; Wei, Qiaohua; Chen, Guonan

2018-08-01

A specific and label-free "on-off-on" luminescence biosensor based on a novel heterometallic cluster [Ag 6 Au 6 (ethisterone) 12 ]-estrogen receptor α (Ag 6 Au 6 Eth-ERα) aggregation utilizing graphene oxide (GO) as a quencher to lead a small background signal was firstly constructed to detect immunoglobulin G (IgG) with a simple process and high selectivity. The efficient photoluminescent (PL) Ag 6 Au 6 Eth-ERα aggregation is strongly quenched by GO. In the presence of IgG, the PL of this system will be restored, and perceivable by human eyes under UV lamp excitation (365 nm). The quenching mechanism of GO on Ag 6 Au 6 Eth-ERα and enhancement mechanism of IgG on Ag 6 Au 6 Eth-ERα-GO were investigated in detail. Under the optimum conditions, the biosensor for high sensitive IgG detection expressed a wider linear range of 0.0078-10 ng/mL and a lower detection limit of 0.65 pg/mL with good stability and repeatability, which provided a new approach for label-free IgG detection. Copyright © 2018 Elsevier B.V. All rights reserved.

Mpc-scale diffuse radio emission in two massive cool-core clusters of galaxies

NASA Astrophysics Data System (ADS)

Sommer, Martin W.; Basu, Kaustuv; Intema, Huib; Pacaud, Florian; Bonafede, Annalisa; Babul, Arif; Bertoldi, Frank

2017-04-01

Radio haloes are diffuse synchrotron sources on scales of ˜1 Mpc that are found in merging clusters of galaxies, and are believed to be powered by electrons re-accelerated by merger-driven turbulence. We present measurements of extended radio emission on similarly large scales in two clusters of galaxies hosting cool cores: Abell 2390 and Abell 2261. The analysis is based on interferometric imaging with the Karl G. Jansky Very Large Array, Very Large Array and Giant Metrewave Radio Telescope. We present detailed radio images of the targets, subtract the compact emission components and measure the spectral indices for the diffuse components. The radio emission in A2390 extends beyond a known sloshing-like brightness discontinuity, and has a very steep in-band spectral slope at 1.5 GHz that is similar to some known ultrasteep spectrum radio haloes. The diffuse signal in A2261 is more extended than in A2390 but has lower luminosity. X-ray morphological indicators, derived from XMM-Newton X-ray data, place these clusters in the category of relaxed or regular systems, although some asymmetric features that can indicate past minor mergers are seen in the X-ray brightness images. If these two Mpc-scale radio sources are categorized as giant radio haloes, they question the common assumption of radio haloes occurring exclusively in clusters undergoing violent merging activity, in addition to commonly used criteria for distinguishing between radio haloes and minihaloes.

An Aggregate of Four Anthrax Cases during the Dry Summer of 2011 in Epirus, Greece.

PubMed

Gaitanis, Georgios; Lolis, Christos J; Tsartsarakis, Antonios; Kalogeropoulos, Chris; Leveidiotou-Stefanou, Stamatina; Bartzokas, Aristidis; Bassukas, Ioannis D

2016-01-01

Human anthrax is currently a sporadic disease in Europe, without significant regional clustering. To report an unexpected aggregate of anthrax cases and correlate local climatic factors with yearly anthrax admissions. Clinical description of a geographical-temporal anthrax aggregate, correlation of disease admissions with local weather data in the period 2001-2014 and literature reports of anthrax clusters from Europe in the last 20 years. We identified 5 cases, all cutaneous: an unexpected aggregate of 4 cases in mid-summer 2011 (including a probable human-to-human transmission) and a sporadic case in August 2005, all in relatively dry periods (p < 0.05). Remarkably, 3/6 reports of human anthrax aggregates from Europe were observed in Balkan Peninsula countries in the year 2011. In the light of the predicted climatic change, unexpected anthrax aggregates during dry periods in southern Europe underscore the risk of future anthrax re-emergence on this continent. © 2015 S. Karger AG, Basel.

Dynamic characterization of external and internal mass transport in heterotrophic biofilms from microsensors measurements.

PubMed

Guimerà, Xavier; Dorado, Antonio David; Bonsfills, Anna; Gabriel, Gemma; Gabriel, David; Gamisans, Xavier

2016-10-01

Knowledge of mass transport mechanisms in biofilm-based technologies such as biofilters is essential to improve bioreactors performance by preventing mass transport limitation. External and internal mass transport in biofilms was characterized in heterotrophic biofilms grown on a flat plate bioreactor. Mass transport resistance through the liquid-biofilm interphase and diffusion within biofilms were quantified by in situ measurements using microsensors with a high spatial resolution (<50 μm). Experimental conditions were selected using a mathematical procedure based on the Fisher Information Matrix to increase the reliability of experimental data and minimize confidence intervals of estimated mass transport coefficients. The sensitivity of external and internal mass transport resistances to flow conditions within the range of typical fluid velocities over biofilms (Reynolds numbers between 0.5 and 7) was assessed. Estimated external mass transfer coefficients at different liquid phase flow velocities showed discrepancies with studies considering laminar conditions in the diffusive boundary layer near the liquid-biofilm interphase. The correlation of effective diffusivity with flow velocities showed that the heterogeneous structure of biofilms defines the transport mechanisms inside biofilms. Internal mass transport was driven by diffusion through cell clusters and aggregates at Re below 2.8. Conversely, mass transport was driven by advection within pores, voids and water channels at Re above 5.6. Between both flow velocities, mass transport occurred by a combination of advection and diffusion. Effective diffusivities estimated at different biofilm densities showed a linear increase of mass transport resistance due to a porosity decrease up to biofilm densities of 50 g VSS·L(-1). Mass transport was strongly limited at higher biofilm densities. Internal mass transport results were used to propose an empirical correlation to assess the effective diffusivity within biofilms considering the influence of hydrodynamics and biofilm density. Copyright © 2016 Elsevier Ltd. All rights reserved.

Widespread Micropollutant Monitoring in the Hudson River Estuary Reveals Spatiotemporal Micropollutant Clusters and Their Sources.

PubMed

Carpenter, Corey M G; Helbling, Damian E

2018-06-05

The objective of this study was to identify sources of micropollutants in the Hudson River Estuary (HRE). We collected 127 grab samples at 17 sites along the HRE over 2 years and screened for up to 200 micropollutants. We quantified 168 of the micropollutants in at least one of the samples. Atrazine, gabapentin, metolachlor, and sucralose were measured in every sample. We used data-driven unsupervised methods to cluster the micropollutants on the basis of their spatiotemporal occurrence and normalized-concentration patterns. Three major clusters of micropollutants were identified: ubiquitous and mixed-use (core micropollutants), sourced from sewage treatment plant outfalls (STP micropollutants), and derived from diffuse upstream sources (diffuse micropollutants). Each of these clusters was further refined into subclusters that were linked to specific sources on the basis of relationships identified through geospatial analysis of watershed features. Evaluation of cumulative loadings of each subcluster revealed that the Mohawk River and Rondout Creek are major contributors of most core micropollutants and STP micropollutants and the upper HRE is a major contributor of diffuse micropollutants. These data provide the first comprehensive evaluation of micropollutants in the HRE and define distinct spatiotemporal micropollutant clusters that are linked to sources and conserved across surface water systems around the world.

Self-assembled nanoparticle aggregates: Organizing disorder for high performance surface-enhanced spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fasolato, C.; Center for Life Nanoscience@Sapienza, Istituto Italiano di Tecnologia, Rome; Domenici, F., E-mail: fabiodomenici@gmail.com

2015-06-23

The coherent oscillations of the surface electron gas, known as surface plasmons, in metal nanostructures can give rise to the localization of intense electromagnetic fields at the metal-dielectric interface. These strong fields are exploited in surface enhanced spectroscopies, such as Surface Enhanced Raman Scattering (SERS), for the detection and characterization of molecules at very low concentration. Still, the implementation of SERS-based biosensors requires a high level of reproducibility, combined with cheap and simple fabrication methods. For this purpose, SERS substrates based on self-assembled aggregates of commercial metallic nanoparticles (Nps) can meet all the above requests. Following this line, we reportmore » on a combined micro-Raman and Atomic Force Microscopy (AFM) analysis of the SERS efficiency of micrometric silver Np aggregates (enhancement factors up to 10{sup 9}) obtained by self-assembly. Despite the intrinsic disordered nature of these Np clusters, we were able to sort out some general rules relating the specific aggregate morphology to its plasmonic response. We found strong evidences of cooperative effects among the NPs within the cluster and namely a clear dependence of the SERS-efficiency on both the cluster area (basically linear) and the number of stacked NPs layers. A cooperative action among the superimposed layers has been proved also by electromagnetic simulations performed on simplified nanostructures consisting of stacking planes of ordered Nps. Being clear the potentialities of these disordered self-assembled clusters, in terms of both easy fabrication and signal enhancement, we developed a specific nanofabrication protocol, based on electron beam lithography and molecular functionalization, that allowed for a fine control of the Np assemblies into designed shapes fixing their area and height. In particular, we fabricated 2D ordered arrays of disordered clusters choosing gold Nps owing to their high stability. AFM measurements confirmed the regularity in spacing and size (i.e. area and layer number) of the aggregates. Preliminary SERS measurements confirm the high signal enhancement and demonstrate a quite good reproducibility over large number of aggregates within 100×100 μm{sup 2} 2D super-structure. The availability of such a multisensor could allow a careful statistical analysis of the SERS response, thus leading to a reliable quantitative estimate of the presence of relevant molecular species even at ultra-low concentration.« less

Patterns of victimization between and within peer clusters in a high school social network.

PubMed

Swartz, Kristin; Reyns, Bradford W; Wilcox, Pamela; Dunham, Jessica R

2012-01-01

This study presents a descriptive analysis of patterns of violent victimization between and within the various cohesive clusters of peers comprising a sample of more than 500 9th-12th grade students from one high school. Social network analysis techniques provide a visualization of the overall friendship network structure and allow for the examination of variation in victimization across the various peer clusters within the larger network. Social relationships among clusters with varying levels of victimization are also illustrated so as to provide a sense of possible spatial clustering or diffusion of victimization across proximal peer clusters. Additionally, to provide a sense of the sorts of peer clusters that support (or do not support) victimization, characteristics of clusters at both the high and low ends of the victimization scale are discussed. Finally, several of the peer clusters at both the high and low ends of the victimization continuum are "unpacked", allowing examination of within-network individual-level differences in victimization for these select clusters.

Hierarchical Star Formation in Turbulent Media: Evidence from Young Star Clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grasha, K.; Calzetti, D.; Elmegreen, B. G.

We present an analysis of the positions and ages of young star clusters in eight local galaxies to investigate the connection between the age difference and separation of cluster pairs. We find that star clusters do not form uniformly but instead are distributed so that the age difference increases with the cluster pair separation to the 0.25–0.6 power, and that the maximum size over which star formation is physically correlated ranges from ∼200 pc to ∼1 kpc. The observed trends between age difference and separation suggest that cluster formation is hierarchical both in space and time: clusters that are closemore » to each other are more similar in age than clusters born further apart. The temporal correlations between stellar aggregates have slopes that are consistent with predictions of turbulence acting as the primary driver of star formation. The velocity associated with the maximum size is proportional to the galaxy’s shear, suggesting that the galactic environment influences the maximum size of the star-forming structures.« less

Precision of systematic and random sampling in clustered populations: habitat patches and aggregating organisms.

PubMed

McGarvey, Richard; Burch, Paul; Matthews, Janet M

2016-01-01

Natural populations of plants and animals spatially cluster because (1) suitable habitat is patchy, and (2) within suitable habitat, individuals aggregate further into clusters of higher density. We compare the precision of random and systematic field sampling survey designs under these two processes of species clustering. Second, we evaluate the performance of 13 estimators for the variance of the sample mean from a systematic survey. Replicated simulated surveys, as counts from 100 transects, allocated either randomly or systematically within the study region, were used to estimate population density in six spatial point populations including habitat patches and Matérn circular clustered aggregations of organisms, together and in combination. The standard one-start aligned systematic survey design, a uniform 10 x 10 grid of transects, was much more precise. Variances of the 10 000 replicated systematic survey mean densities were one-third to one-fifth of those from randomly allocated transects, implying transect sample sizes giving equivalent precision by random survey would need to be three to five times larger. Organisms being restricted to patches of habitat was alone sufficient to yield this precision advantage for the systematic design. But this improved precision for systematic sampling in clustered populations is underestimated by standard variance estimators used to compute confidence intervals. True variance for the survey sample mean was computed from the variance of 10 000 simulated survey mean estimates. Testing 10 published and three newly proposed variance estimators, the two variance estimators (v) that corrected for inter-transect correlation (ν₈ and ν(W)) were the most accurate and also the most precise in clustered populations. These greatly outperformed the two "post-stratification" variance estimators (ν₂ and ν₃) that are now more commonly applied in systematic surveys. Similar variance estimator performance rankings were found with a second differently generated set of spatial point populations, ν₈ and ν(W) again being the best performers in the longer-range autocorrelated populations. However, no systematic variance estimators tested were free from bias. On balance, systematic designs bring more narrow confidence intervals in clustered populations, while random designs permit unbiased estimates of (often wider) confidence interval. The search continues for better estimators of sampling variance for the systematic survey mean.

Live-cell imaging reveals the dynamics and function of single-telomere TERRA molecules in cancer cells.

PubMed

Avogaro, Laura; Querido, Emmanuelle; Dalachi, Myriam; Jantsch, Michael F; Chartrand, Pascal; Cusanelli, Emilio

2018-04-16

Telomeres cap the ends of eukaryotic chromosomes, protecting them from degradation and erroneous recombination events which may lead to genome instability. Telomeres are transcribed giving rise to telomeric repeat-containing RNAs, called TERRA. The TERRA long noncoding RNAs have been proposed to play important roles in telomere biology, including heterochromatin formation and telomere length homeostasis. While TERRA RNAs are predominantly nuclear and localize at telomeres, little is known about the dynamics and function of TERRA molecules expressed from individual telomeres. Herein, we developed an assay to image endogenous TERRA molecules expressed from a single telomere in living human cancer cells. We show that single-telomere TERRA can be detected as TERRA RNA single particles which freely diffuse within the nucleus. Furthermore, TERRA molecules aggregate forming TERRA clusters. Three-dimensional size distribution and single particle tracking analyses revealed distinct sizes and dynamics for TERRA RNA single particles and clusters. Simultaneous time lapse confocal imaging of TERRA particles and telomeres showed that TERRA clusters transiently co-localize with telomeres. Finally, we used chemically modified antisense oligonucleotides to deplete TERRA molecules expressed from a single telomere. Single-telomere TERRA depletion resulted in increased DNA damage at telomeres and elsewhere in the genome. These results suggest that single-telomere TERRA transcripts participate in the maintenance of genomic integrity in human cancer cells.

Utility of K-Means clustering algorithm in differentiating apparent diffusion coefficient values between benign and malignant neck pathologies

PubMed Central

Srinivasan, A.; Galbán, C.J.; Johnson, T.D.; Chenevert, T.L.; Ross, B.D.; Mukherji, S.K.

2014-01-01

Purpose The objective of our study was to analyze the differences between apparent diffusion coefficient (ADC) partitions (created using the K-Means algorithm) between benign and malignant neck lesions and evaluate its benefit in distinguishing these entities. Material and methods MRI studies of 10 benign and 10 malignant proven neck pathologies were post-processed on a PC using in-house software developed in MATLAB (The MathWorks, Inc., Natick, MA). Lesions were manually contoured by two neuroradiologists with the ADC values within each lesion clustered into two (low ADC-ADCL, high ADC-ADCH) and three partitions (ADCL, intermediate ADC-ADCI, ADCH) using the K-Means clustering algorithm. An unpaired two-tailed Student’s t-test was performed for all metrics to determine statistical differences in the means between the benign and malignant pathologies. Results Statistically significant difference between the mean ADCL clusters in benign and malignant pathologies was seen in the 3 cluster models of both readers (p=0.03, 0.022 respectively) and the 2 cluster model of reader 2 (p=0.04) with the other metrics (ADCH, ADCI, whole lesion mean ADC) not revealing any significant differences. Receiver operating characteristics curves demonstrated the quantitative difference in mean ADCH and ADCL in both the 2 and 3 cluster models to be predictive of malignancy (2 clusters: p=0.008, area under curve=0.850, 3 clusters: p=0.01, area under curve=0.825). Conclusion The K-Means clustering algorithm that generates partitions of large datasets may provide a better characterization of neck pathologies and may be of additional benefit in distinguishing benign and malignant neck pathologies compared to whole lesion mean ADC alone. PMID:20007723

Return period estimates for European windstorm clusters: a multi-model perspective

NASA Astrophysics Data System (ADS)

Renggli, Dominik; Zimmerli, Peter

2017-04-01

Clusters of storms over Europe can lead to very large aggregated losses. Realistic return period estimates for such cluster are therefore of vital interest to the (re)insurance industry. Such return period estimates are usually derived from historical storm activity statistics of the last 30 to 40 years. However, climate models provide an alternative source, potentially representing thousands of simulated storm seasons. In this study, we made use of decadal hindcast data from eight different climate models in the CMIP5 archive. We used an objective tracking algorithm to identify individual windstorms in the climate model data. The algorithm also computes a (population density weighted) Storm Severity Index (SSI) for each of the identified storms (both on a continental and more regional basis). We derived return period estimates for the cluster seasons 1990, 1999, 2013/2014 and 1884 in the following way: For each climate model, we extracted two different exceedance frequency curves. The first describes the exceedance frequency (or the return period as the inverse of it) of a given SSI level due to an individual storm occurrence. The second describes the exceedance frequency of the seasonally aggregated SSI level (i.e. the sum of the SSI values of all storms in a given season). Starting from appropriate return period assumptions for each individual storm of a historical cluster (e.g. Anatol, Lothar and Martin in 1999) and using the first curve, we extracted the SSI levels at the corresponding return periods. Summing these SSI values results in the seasonally aggregated SSI value. Combining this with the second (aggregated) exceedance frequency curve results in return period estimate of the historical cluster season. Since we do this for each model separately, we obtain eight different return period estimates for each historical cluster. In this way, we obtained the following return period estimates: 50 to 80 years for the 1990 season, 20 to 45 years for the 1999 season, 3 to 4 years for the 2013/2014 season, and 14 to 16 years for the 1884 season. More detailed results show substantial variation between five different regions (UK, France, Germany, Benelux and Scandinavia), as expected from the path and footprints of the different events. For example, the 1990 season is estimated to be well beyond a 100-year season for Germany and Benelux. 1999 clearly was an extreme season for France, whereas the1884 was very disruptive for the UK. Such return period estimates can be used as an independent benchmark for other approaches quantifying clustering of European windstorms. The study might also serve as an example to derive similar risk measures also for other climate-related perils from a robust, publicly available data source.

COOL CORE CLUSTERS FROM COSMOLOGICAL SIMULATIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rasia, E.; Borgani, S.; Murante, G.

2015-11-01

We present results obtained from a set of cosmological hydrodynamic simulations of galaxy clusters, aimed at comparing predictions with observational data on the diversity between cool-core (CC) and non-cool-core (NCC) clusters. Our simulations include the effects of stellar and active galactic nucleus (AGN) feedback and are based on an improved version of the smoothed particle hydrodynamics code GADGET-3, which ameliorates gas mixing and better captures gas-dynamical instabilities by including a suitable artificial thermal diffusion. In this Letter, we focus our analysis on the entropy profiles, the primary diagnostic we used to classify the degree of cool-coreness of clusters, and themore » iron profiles. In keeping with observations, our simulated clusters display a variety of behaviors in entropy profiles: they range from steadily decreasing profiles at small radii, characteristic of CC systems, to nearly flat core isentropic profiles, characteristic of NCC systems. Using observational criteria to distinguish between the two classes of objects, we find that they occur in similar proportions in both simulations and observations. Furthermore, we also find that simulated CC clusters have profiles of iron abundance that are steeper than those of NCC clusters, which is also in agreement with observational results. We show that the capability of our simulations to generate a realistic CC structure in the cluster population is due to AGN feedback and artificial thermal diffusion: their combined action allows us to naturally distribute the energy extracted from super-massive black holes and to compensate for the radiative losses of low-entropy gas with short cooling time residing in the cluster core.« less

Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes

PubMed Central

Shimo, Hanae; Arjunan, Satya Nanda Vel; Machiyama, Hiroaki; Nishino, Taiko; Suematsu, Makoto; Fujita, Hideaki; Tomita, Masaru; Takahashi, Koichi

2015-01-01

Oxidative stress mediated clustering of membrane protein band 3 plays an essential role in the clearance of damaged and aged red blood cells (RBCs) from the circulation. While a number of previous experimental studies have observed changes in band 3 distribution after oxidative treatment, the details of how these clusters are formed and how their properties change under different conditions have remained poorly understood. To address these issues, a framework that enables the simultaneous monitoring of the temporal and spatial changes following oxidation is needed. In this study, we established a novel simulation strategy that incorporates deterministic and stochastic reactions with particle reaction-diffusion processes, to model band 3 cluster formation at single molecule resolution. By integrating a kinetic model of RBC antioxidant metabolism with a model of band 3 diffusion, we developed a model that reproduces the time-dependent changes of glutathione and clustered band 3 levels, as well as band 3 distribution during oxidative treatment, observed in prior studies. We predicted that cluster formation is largely dependent on fast reverse reaction rates, strong affinity between clustering molecules, and irreversible hemichrome binding. We further predicted that under repeated oxidative perturbations, clusters tended to progressively grow and shift towards an irreversible state. Application of our model to simulate oxidation in RBCs with cytoskeletal deficiency also suggested that oxidation leads to more enhanced clustering compared to healthy RBCs. Taken together, our model enables the prediction of band 3 spatio-temporal profiles under various situations, thus providing valuable insights to potentially aid understanding mechanisms for removing senescent and premature RBCs. PMID:26046580

Cool Core Clusters from Cosmological Simulations

NASA Astrophysics Data System (ADS)

Rasia, E.; Borgani, S.; Murante, G.; Planelles, S.; Beck, A. M.; Biffi, V.; Ragone-Figueroa, C.; Granato, G. L.; Steinborn, L. K.; Dolag, K.

2015-11-01

We present results obtained from a set of cosmological hydrodynamic simulations of galaxy clusters, aimed at comparing predictions with observational data on the diversity between cool-core (CC) and non-cool-core (NCC) clusters. Our simulations include the effects of stellar and active galactic nucleus (AGN) feedback and are based on an improved version of the smoothed particle hydrodynamics code GADGET-3, which ameliorates gas mixing and better captures gas-dynamical instabilities by including a suitable artificial thermal diffusion. In this Letter, we focus our analysis on the entropy profiles, the primary diagnostic we used to classify the degree of cool-coreness of clusters, and the iron profiles. In keeping with observations, our simulated clusters display a variety of behaviors in entropy profiles: they range from steadily decreasing profiles at small radii, characteristic of CC systems, to nearly flat core isentropic profiles, characteristic of NCC systems. Using observational criteria to distinguish between the two classes of objects, we find that they occur in similar proportions in both simulations and observations. Furthermore, we also find that simulated CC clusters have profiles of iron abundance that are steeper than those of NCC clusters, which is also in agreement with observational results. We show that the capability of our simulations to generate a realistic CC structure in the cluster population is due to AGN feedback and artificial thermal diffusion: their combined action allows us to naturally distribute the energy extracted from super-massive black holes and to compensate for the radiative losses of low-entropy gas with short cooling time residing in the cluster core.

Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes.

PubMed

Shimo, Hanae; Arjunan, Satya Nanda Vel; Machiyama, Hiroaki; Nishino, Taiko; Suematsu, Makoto; Fujita, Hideaki; Tomita, Masaru; Takahashi, Koichi

2015-06-01

Oxidative stress mediated clustering of membrane protein band 3 plays an essential role in the clearance of damaged and aged red blood cells (RBCs) from the circulation. While a number of previous experimental studies have observed changes in band 3 distribution after oxidative treatment, the details of how these clusters are formed and how their properties change under different conditions have remained poorly understood. To address these issues, a framework that enables the simultaneous monitoring of the temporal and spatial changes following oxidation is needed. In this study, we established a novel simulation strategy that incorporates deterministic and stochastic reactions with particle reaction-diffusion processes, to model band 3 cluster formation at single molecule resolution. By integrating a kinetic model of RBC antioxidant metabolism with a model of band 3 diffusion, we developed a model that reproduces the time-dependent changes of glutathione and clustered band 3 levels, as well as band 3 distribution during oxidative treatment, observed in prior studies. We predicted that cluster formation is largely dependent on fast reverse reaction rates, strong affinity between clustering molecules, and irreversible hemichrome binding. We further predicted that under repeated oxidative perturbations, clusters tended to progressively grow and shift towards an irreversible state. Application of our model to simulate oxidation in RBCs with cytoskeletal deficiency also suggested that oxidation leads to more enhanced clustering compared to healthy RBCs. Taken together, our model enables the prediction of band 3 spatio-temporal profiles under various situations, thus providing valuable insights to potentially aid understanding mechanisms for removing senescent and premature RBCs.

First Principles Studies for Lithium Intercalation and Diffusion Behaviors in MoS2 treated with the Compressive Sensing Cluster Expansion

NASA Astrophysics Data System (ADS)

Liu, Chi-Ping; Zhou, Fei; Ozolins, Vidvuds

2014-03-01

Molybdenum disulfide (MoS2) is a good candidate electrode material for high capacity energy storage applications, such as lithium ion batteries and supercapacitors. In this work, we investigate lithium intercalation and diffusion kinetics in MoS2 by using first-principles density-functional theory (DFT) calculations. Two different lithium intercalation sites (1-H and 2-T) in MoS2 are found to be stable for lithium intercalation at different van der Waals' (vdW) gap distances. It is found that both thermodynamic and kinetic properties are highly related to the interlayer vdW gap distance, and that the optimal gap distance leads to effective solid-state diffusion in MoS2. Additionally, through the use of compressive sensing, we build accurate cluster expansion models to study the thermodynamic properties of MoS2 at high lithium content by truncating the higher order effective clusters with significant contributions. The results show that compressive sensing cluster expansion is a rigorous and powerful tool for model construction for advanced electrochemical applications in the future.

Diffusion Geometry Unravels the Emergence of Functional Clusters in Collective Phenomena.

PubMed

De Domenico, Manlio

2017-04-21

Collective phenomena emerge from the interaction of natural or artificial units with a complex organization. The interplay between structural patterns and dynamics might induce functional clusters that, in general, are different from topological ones. In biological systems, like the human brain, the overall functionality is often favored by the interplay between connectivity and synchronization dynamics, with functional clusters that do not coincide with anatomical modules in most cases. In social, sociotechnical, and engineering systems, the quest for consensus favors the emergence of clusters. Despite the unquestionable evidence for mesoscale organization of many complex systems and the heterogeneity of their interconnectivity, a way to predict and identify the emergence of functional modules in collective phenomena continues to elude us. Here, we propose an approach based on random walk dynamics to define the diffusion distance between any pair of units in a networked system. Such a metric allows us to exploit the underlying diffusion geometry to provide a unifying framework for the intimate relationship between metastable synchronization, consensus, and random search dynamics in complex networks, pinpointing the functional mesoscale organization of synthetic and biological systems.

Diffusion Geometry Unravels the Emergence of Functional Clusters in Collective Phenomena

NASA Astrophysics Data System (ADS)

De Domenico, Manlio

2017-04-01

Collective phenomena emerge from the interaction of natural or artificial units with a complex organization. The interplay between structural patterns and dynamics might induce functional clusters that, in general, are different from topological ones. In biological systems, like the human brain, the overall functionality is often favored by the interplay between connectivity and synchronization dynamics, with functional clusters that do not coincide with anatomical modules in most cases. In social, sociotechnical, and engineering systems, the quest for consensus favors the emergence of clusters. Despite the unquestionable evidence for mesoscale organization of many complex systems and the heterogeneity of their interconnectivity, a way to predict and identify the emergence of functional modules in collective phenomena continues to elude us. Here, we propose an approach based on random walk dynamics to define the diffusion distance between any pair of units in a networked system. Such a metric allows us to exploit the underlying diffusion geometry to provide a unifying framework for the intimate relationship between metastable synchronization, consensus, and random search dynamics in complex networks, pinpointing the functional mesoscale organization of synthetic and biological systems.

Infrared Coronet Cluster

NASA Image and Video Library

2007-09-13

This image from NASA Spitzer Space Telescope shows young stars plus diffuse emission from dust. The Corona Australis region containing, at its heart, the Coronet cluster is one of the nearest and most active regions of ongoing star formation.

Optimization of b-value distribution for biexponential diffusion-weighted MR imaging of normal prostate.

PubMed

Jambor, Ivan; Merisaari, Harri; Aronen, Hannu J; Järvinen, Jukka; Saunavaara, Jani; Kauko, Tommi; Borra, Ronald; Pesola, Marko

2014-05-01

To determine the optimal b-value distribution for biexponential diffusion-weighted imaging (DWI) of normal prostate using both a computer modeling approach and in vivo measurements. Optimal b-value distributions for the fit of three parameters (fast diffusion Df, slow diffusion Ds, and fraction of fast diffusion f) were determined using Monte-Carlo simulations. The optimal b-value distribution was calculated using four individual optimization methods. Eight healthy volunteers underwent four repeated 3 Tesla prostate DWI scans using both 16 equally distributed b-values and an optimized b-value distribution obtained from the simulations. The b-value distributions were compared in terms of measurement reliability and repeatability using Shrout-Fleiss analysis. Using low noise levels, the optimal b-value distribution formed three separate clusters at low (0-400 s/mm2), mid-range (650-1200 s/mm2), and high b-values (1700-2000 s/mm2). Higher noise levels resulted into less pronounced clustering of b-values. The clustered optimized b-value distribution demonstrated better measurement reliability and repeatability in Shrout-Fleiss analysis compared with 16 equally distributed b-values. The optimal b-value distribution was found to be a clustered distribution with b-values concentrated in the low, mid, and high ranges and was shown to improve the estimation quality of biexponential DWI parameters of in vivo experiments. Copyright © 2013 Wiley Periodicals, Inc.

Self-organization of local magnetoplasma structures in the upper layers of the solar convection zone

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chumak, O. V., E-mail: chuo@yandex.ru

Self-organization and evolution of magnetoplasma structures in the upper layers of the solar convection zone are discussed as a process of diffuse aggregation of magnetic flux tubes. Equations describing the tube motion under the action of magnetic interaction forces, hydrodynamic forces, and random forces are written explicitly. The process of aggregation of magnetic flux tubes into magnetic flux clusters of different shapes and dimensions is simulated numerically. The obtained structures are compared with the observed morphological types of sunspot groups. The quantitative comparison with the observational data was performed by comparing the fractal dimensions of the photospheric magnetic structures observedmore » in solar active regions with those of structures obtained in the numerical experiment. The model has the following free parameters: the numbers of magnetic flux tubes with opposite polarities on the considered area element (Nn and Ns), the average radius of the cross section of the magnetic flux tube (a), its effective length (l), the twist factor of the tube field (k), and the absolute value of the average velocity of chaotic tube displacements (d). Variations in these parameters in physically reasonable limits leads to the formation of structures (tube clusters of different morphological types) having different fractal dimensions. Using the NOAA 10488 active region, which appeared and developed into a complicated configuration near the central meridian, as an example, it is shown that good quantitative agreement between the fractal dimensions is achieved at the following parameters of the model: Nn = Ns = 250 ± 50; a = 150 ± 50 km; l ∼ 5000 km, and d = 80 ± 10 m/s. These results do not contradict the observational data and theoretical estimates obtained in the framework of the Parker “spaghetti” model and provide new information on the physical processes resulting in the origin and evolution of local magnetic plasma structures in the near-photospheric layers of the solar convection zone.« less

Non Thermal Emission from Clusters of Galaxies: the Importance of a Joint LOFAR/Simbol-X View

NASA Astrophysics Data System (ADS)

Ferrari, C.

2009-05-01

Deep radio observations of galaxy clusters have revealed the existence of diffuse radio sources (``halos'' and ``relics'') related to the presence of relativistic electrons and weak magnetic fields in the intracluster volume. I will outline our current knowledge about the presence and properties of this non-thermal cluster component. Despite the recent progress made in observational and theoretical studies of the non-thermal emission in galaxy clusters, a number of open questions about its origin and its effects on the thermo-dynamical evolution of galaxy clusters need to be answered. I will show the importance of combining galaxy cluster observations by new-generation instruments such as LOFAR and Simbol-X. A deeper knowledge of the non-thermal cluster component, together with statistical studies of radio halos and relics, will allow to test the current cluster formation scenario and to better constrain the physics of large scale structure evolution.

Noise reduction in the intracellular pom1p gradient by a dynamic clustering mechanism.

PubMed

Saunders, Timothy E; Pan, Kally Z; Angel, Andrew; Guan, Yinghua; Shah, Jagesh V; Howard, Martin; Chang, Fred

2012-03-13

Chemical gradients can generate pattern formation in biological systems. In the fission yeast Schizosaccharomyces pombe, a cortical gradient of pom1p (a DYRK-type protein kinase) functions to position sites of cytokinesis and cell polarity and to control cell length. Here, using quantitative imaging, fluorescence correlation spectroscopy, and mathematical modeling, we study how its gradient distribution is formed. Pom1p gradients exhibit large cell-to-cell variability, as well as dynamic fluctuations in each individual gradient. Our data lead to a two-state model for gradient formation in which pom1p molecules associate with the plasma membrane at cell tips and then diffuse on the membrane while aggregating into and fragmenting from clusters, before disassociating from the membrane. In contrast to a classical one-component gradient, this two-state gradient buffers against cell-to-cell variations in protein concentration. This buffering mechanism, together with time averaging to reduce intrinsic noise, allows the pom1p gradient to specify positional information in a robust manner. Copyright © 2012 Elsevier Inc. All rights reserved.

Thermodynamics and Kinetics of Prenucleation Clusters, Classical and Non-Classical Nucleation.

PubMed

Zahn, Dirk

2015-07-20

Recent observations of prenucleation species and multi-stage crystal nucleation processes challenge the long-established view on the thermodynamics of crystal formation. Here, we review and generalize extensions to classical nucleation theory. Going beyond the conventional implementation as has been used for more than a century now, nucleation inhibitors, precursor clusters and non-classical nucleation processes are rationalized as well by analogous concepts based on competing interface and bulk energy terms. This is illustrated by recent examples of species formed prior to/instead of crystal nucleation and multi-step nucleation processes. Much of the discussed insights were obtained from molecular simulation using advanced sampling techniques, briefly summarized herein for both nucleation-controlled and diffusion-controlled aggregate formation. © 2015 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA. This is an open access article under the terms of the Creative Commons Attribution Non-Commercial NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

Adsorption and Diffusion of Fructose in Zeolite HZSM-5: Selection of Models and Methods for Computational Studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cheng, Lei; Curtiss, Larry A.; Assary, Rajeev S.

The adsorption and protonation of fructose inHZSM-5 have been studied for the assessment of models for accurate reaction energy calculations and the evaluation of molecular diffusivity. The adsorption and protonation were calculated using 2T, 5T, and 46T clusters as well as a periodic model. The results indicate that the reaction thermodynamics cannot be predicted correctly using small cluster models, such as 2T or 5T, because these small cluster models fail to represent the electrostatic effect of a zeolite cage, which provides additional stabilization to the ion pair formed upon the protonation of fructose. Structural parameters optimized using the 46T clustermore » model agree well with those of the full periodic model; however, the calculated reaction energies are in significant error due to the poor account of dispersion effects by density functional theory. The dispersion effects contribute -30.5 kcal/mol to the binding energy of fructose in the zeolite pore based on periodic model calculations that include dispersion interactions. The protonation of the fructose ternary carbon hydroxyl group was calculated to be exothermic by 5.5 kcal/mol with a reaction barrier of 2.9 kcal/mol using the periodic model with dispersion effects. Our results suggest that the internal diffusion of fructose in HZSM-5 is very likely to be energetically limited and only occurs at high temperature due to the large size of the molecule.« less

Hierarchical cluster-tendency analysis of the group structure in the foreign exchange market

NASA Astrophysics Data System (ADS)

Wu, Xin-Ye; Zheng, Zhi-Gang

2013-08-01

A hierarchical cluster-tendency (HCT) method in analyzing the group structure of networks of the global foreign exchange (FX) market is proposed by combining the advantages of both the minimal spanning tree (MST) and the hierarchical tree (HT). Fifty currencies of the top 50 World GDP in 2010 according to World Bank's database are chosen as the underlying system. By using the HCT method, all nodes in the FX market network can be "colored" and distinguished. We reveal that the FX networks can be divided into two groups, i.e., the Asia-Pacific group and the Pan-European group. The results given by the hierarchical cluster-tendency method agree well with the formerly observed geographical aggregation behavior in the FX market. Moreover, an oil-resource aggregation phenomenon is discovered by using our method. We find that gold could be a better numeraire for the weekly-frequency FX data.

Privacy Protection Versus Cluster Detection in Spatial Epidemiology

PubMed Central

Olson, Karen L.; Grannis, Shaun J.; Mandl, Kenneth D.

2006-01-01

Objectives. Patient data that includes precise locations can reveal patients’ identities, whereas data aggregated into administrative regions may preserve privacy and confidentiality. We investigated the effect of varying degrees of address precision (exact latitude and longitude vs the center points of zip code or census tracts) on detection of spatial clusters of cases. Methods. We simulated disease outbreaks by adding supplementary spatially clustered emergency department visits to authentic hospital emergency department syndromic surveillance data. We identified clusters with a spatial scan statistic and evaluated detection rate and accuracy. Results. More clusters were identified, and clusters were more accurately detected, when exact locations were used. That is, these clusters contained at least half of the simulated points and involved few additional emergency department visits. These results were especially apparent when the synthetic clustered points crossed administrative boundaries and fell into multiple zip code or census tracts. Conclusions. The spatial cluster detection algorithm performed better when addresses were analyzed as exact locations than when they were analyzed as center points of zip code or census tracts, particularly when the clustered points crossed administrative boundaries. Use of precise addresses offers improved performance, but this practice must be weighed against privacy concerns in the establishment of public health data exchange policies. PMID:17018828

SOTXTSTREAM: Density-based self-organizing clustering of text streams.

PubMed

Bryant, Avory C; Cios, Krzysztof J

2017-01-01

A streaming data clustering algorithm is presented building upon the density-based self-organizing stream clustering algorithm SOSTREAM. Many density-based clustering algorithms are limited by their inability to identify clusters with heterogeneous density. SOSTREAM addresses this limitation through the use of local (nearest neighbor-based) density determinations. Additionally, many stream clustering algorithms use a two-phase clustering approach. In the first phase, a micro-clustering solution is maintained online, while in the second phase, the micro-clustering solution is clustered offline to produce a macro solution. By performing self-organization techniques on micro-clusters in the online phase, SOSTREAM is able to maintain a macro clustering solution in a single phase. Leveraging concepts from SOSTREAM, a new density-based self-organizing text stream clustering algorithm, SOTXTSTREAM, is presented that addresses several shortcomings of SOSTREAM. Gains in clustering performance of this new algorithm are demonstrated on several real-world text stream datasets.

Baryons at the edge of the X-ray-brightest galaxy cluster.

PubMed

Simionescu, Aurora; Allen, Steven W; Mantz, Adam; Werner, Norbert; Takei, Yoh; Morris, R Glenn; Fabian, Andrew C; Sanders, Jeremy S; Nulsen, Paul E J; George, Matthew R; Taylor, Gregory B

2011-03-25

Studies of the diffuse x-ray-emitting gas in galaxy clusters have provided powerful constraints on cosmological parameters and insights into plasma astrophysics. However, measurements of the faint cluster outskirts have become possible only recently. Using data from the Suzaku x-ray telescope, we determined an accurate, spatially resolved census of the gas, metals, and dark matter out to the edge of the Perseus Cluster. Contrary to previous results, our measurements of the cluster baryon fraction are consistent with the expected universal value at half of the virial radius. The apparent baryon fraction exceeds the cosmic mean at larger radii, suggesting a clumpy distribution of the gas, which is important for understanding the ongoing growth of clusters from the surrounding cosmic web.

Star-like supramolecular polymers fabricated by a Keplerate cluster with cationic terminated polymers and their self-assembly into vesicles.

PubMed

Zhang, Qian; He, Lipeng; Wang, Hui; Zhang, Cheng; Liu, Weisheng; Bu, Weifeng

2012-07-18

The electrostatic combination of a Keplerate cluster, [Mo(132)O(372)(CH(3)COO)(30)(H(2)O)(72)](42-) with cationic terminated poly(styrene) yields polyoxometalate-based supramolecular star polymers, which can further self-assemble into vesicular aggregates in CHCl(3)-MeOH mixed solvent.

The HectoMAP Cluster Survey. II. X-Ray Clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sohn, Jubee; Chon, Gayoung; Bohringer, Hans

Here, we apply a friends-of-friends algorithm to the HectoMAP redshift survey and cross-identify associated X-ray emission in the ROSAT All-Sky Survey data (RASS). The resulting flux-limited catalog of X-ray cluster surveys is complete to a limiting flux of ~3 × 10 –13 erg s –1 cm –2 and includes 15 clusters (7 newly discovered) with redshifts z ≤ 0.4. HectoMAP is a dense survey (~1200 galaxies deg –2) that provides ~50 members (median) in each X-ray cluster. We provide redshifts for the 1036 cluster members. Subaru/Hyper Suprime-Cam imaging covers three of the X-ray systems and confirms that they are impressivemore » clusters. The HectoMAP X-ray clusters have an L X–σ cl scaling relation similar to that of known massive X-ray clusters. The HectoMAP X-ray cluster sample predicts ~12,000 ± 3000 detectable X-ray clusters in RASS to the limiting flux, comparable with previous estimates.« less

The HectoMAP Cluster Survey. II. X-Ray Clusters

DOE PAGES

Sohn, Jubee; Chon, Gayoung; Bohringer, Hans; ...

2018-03-10

Here, we apply a friends-of-friends algorithm to the HectoMAP redshift survey and cross-identify associated X-ray emission in the ROSAT All-Sky Survey data (RASS). The resulting flux-limited catalog of X-ray cluster surveys is complete to a limiting flux of ~3 × 10 –13 erg s –1 cm –2 and includes 15 clusters (7 newly discovered) with redshifts z ≤ 0.4. HectoMAP is a dense survey (~1200 galaxies deg –2) that provides ~50 members (median) in each X-ray cluster. We provide redshifts for the 1036 cluster members. Subaru/Hyper Suprime-Cam imaging covers three of the X-ray systems and confirms that they are impressivemore » clusters. The HectoMAP X-ray clusters have an L X–σ cl scaling relation similar to that of known massive X-ray clusters. The HectoMAP X-ray cluster sample predicts ~12,000 ± 3000 detectable X-ray clusters in RASS to the limiting flux, comparable with previous estimates.« less

Directed clustering coefficient as a measure of systemic risk in complex banking networks

NASA Astrophysics Data System (ADS)

Tabak, Benjamin M.; Takami, Marcelo; Rocha, Jadson M. C.; Cajueiro, Daniel O.; Souza, Sergio R. S.

2014-01-01

Recent literature has focused on the study of systemic risk in complex networks. It is clear now, after the crisis of 2008, that the aggregate behavior of the interaction among agents is not straightforward and it is very difficult to predict. Contributing to this debate, this paper shows that the directed clustering coefficient may be used as a measure of systemic risk in complex networks. Furthermore, using data from the Brazilian interbank network, we show that the directed clustering coefficient is negatively correlated with domestic interest rates.

Quantum dynamics of small H2 and D2 clusters in the large cage of structure II clathrate hydrate: Energetics, occupancy, and vibrationally averaged cluster structures

NASA Astrophysics Data System (ADS)

Sebastianelli, Francesco; Xu, Minzhong; Bačić, Zlatko

2008-12-01

We report diffusion Monte Carlo (DMC) calculations of the quantum translation-rotation (T-R) dynamics of one to five para-H2 (p-H2) and ortho-D2 (o-D2) molecules inside the large hexakaidecahedral (51264) cage of the structure II clathrate hydrate, which was taken to be rigid. These calculations provide a quantitative description of the size evolution of the ground-state properties, energetics, and the vibrationally averaged geometries, of small (p-H2)n and (o-D2)n clusters, n=1-5, in nanoconfinement. The zero-point energy (ZPE) of the T-R motions rises steeply with the cluster size, reaching 74% of the potential well depth for the caged (p-H2)4. At low temperatures, the rapid increase of the cluster ZPE as a function of n is the main factor that limits the occupancy of the large cage to at most four H2 or D2 molecules, in agreement with experiments. Our DMC results concerning the vibrationally averaged spatial distribution of four D2 molecules, their mean distance from the cage center, the D2-D2 separation, and the specific orientation and localization of the tetrahedral (D2)4 cluster relative to the framework of the large cage, agree very well with the low-temperature neutron diffraction experiments involving the large cage with the quadruple D2 occupancy.

Quantum dynamics of small H2 and D2 clusters in the large cage of structure II clathrate hydrate: energetics, occupancy, and vibrationally averaged cluster structures.

PubMed

Sebastianelli, Francesco; Xu, Minzhong; Bacić, Zlatko

2008-12-28

We report diffusion Monte Carlo (DMC) calculations of the quantum translation-rotation (T-R) dynamics of one to five para-H(2) (p-H(2)) and ortho-D(2) (o-D(2)) molecules inside the large hexakaidecahedral (5(12)6(4)) cage of the structure II clathrate hydrate, which was taken to be rigid. These calculations provide a quantitative description of the size evolution of the ground-state properties, energetics, and the vibrationally averaged geometries, of small (p-H(2))(n) and (o-D(2))(n) clusters, n=1-5, in nanoconfinement. The zero-point energy (ZPE) of the T-R motions rises steeply with the cluster size, reaching 74% of the potential well depth for the caged (p-H(2))(4). At low temperatures, the rapid increase of the cluster ZPE as a function of n is the main factor that limits the occupancy of the large cage to at most four H(2) or D(2) molecules, in agreement with experiments. Our DMC results concerning the vibrationally averaged spatial distribution of four D(2) molecules, their mean distance from the cage center, the D(2)-D(2) separation, and the specific orientation and localization of the tetrahedral (D(2))(4) cluster relative to the framework of the large cage, agree very well with the low-temperature neutron diffraction experiments involving the large cage with the quadruple D(2) occupancy.

Stochastic fire-diffuse-fire model with realistic cluster dynamics.

PubMed

Calabrese, Ana; Fraiman, Daniel; Zysman, Daniel; Ponce Dawson, Silvina

2010-09-01

Living organisms use waves that propagate through excitable media to transport information. Ca2+ waves are a paradigmatic example of this type of processes. A large hierarchy of Ca2+ signals that range from localized release events to global waves has been observed in Xenopus laevis oocytes. In these cells, Ca2+ release occurs trough inositol 1,4,5-trisphosphate receptors (IP3Rs) which are organized in clusters of channels located on the membrane of the endoplasmic reticulum. In this article we construct a stochastic model for a cluster of IP3R 's that replicates the experimental observations reported in [D. Fraiman, Biophys. J. 90, 3897 (2006)]. We then couple this phenomenological cluster model with a reaction-diffusion equation, so as to have a discrete stochastic model for calcium dynamics. The model we propose describes the transition regimes between isolated release and steadily propagating waves as the IP3 concentration is increased.

DNA-Mediated Self-Organization of Polymeric Nanocompartments Leads to Interconnected Artificial Organelles.

PubMed

Liu, Juan; Postupalenko, Viktoriia; Lörcher, Samuel; Wu, Dalin; Chami, Mohamed; Meier, Wolfgang; Palivan, Cornelia G

2016-11-09

Self-organization of nanocomponents was mainly focused on solid nanoparticles, quantum dots, or liposomes to generate complex architectures with specific properties, but intrinsically limited or not developed enough, to mimic sophisticated structures with biological functions in cells. Here, we present a biomimetic strategy to self-organize synthetic nanocompartments (polymersomes) into clusters with controlled properties and topology by exploiting DNA hybridization to interconnect polymersomes. Molecular and external factors affecting the self-organization served to design clusters mimicking the connection of natural organelles: fine-tune of the distance between tethered polymersomes, different topologies, no fusion of clustered polymersomes, and no aggregation. Unexpected, extended DNA bridges that result from migration of the DNA strands inside the thick polymer membrane (about 12 nm) represent a key stability and control factor, not yet exploited for other synthetic nano-object networks. The replacement of the empty polymersomes with artificial organelles, already reported for single polymersome architecture, will provide an excellent platform for the development of artificial systems mimicking natural organelles or cells and represents a fundamental step in the engineering of molecular factories.

Clustering Effects on Dynamics in Ionomer Solutions: A Neutron Spin Echo Insight

NASA Astrophysics Data System (ADS)

Perahia, Dvora; Wijesinghe, Sidath; Senanayake, Manjula; Wickramasinghe, Anuradhi; Mohottalalage, Supun S.; Ohl, Michael

Ionizable blocks in ionomers associate into aggregates serving as physical cross-links and concurrently form transport pathways. The dynamics of ionomers underline their functionality. Incorporating small numbers of ionic groups into polymers significantly constraint their dynamics. Recent computational studies demonstrated a direct correlation between ionic cluster morphology and polymer dynamics. Here using neutron spin echo, we probe the segmental dynamics of polystyrene sulfonate (PSS) as the degree of sulfonation of the PSS and the solution dielectrics are varied. Specifically, 20Wt% PSS of 11,000 g/mol with polydispersity of 1.02 with 3% and 9% sulfonation were studies in toluene (dielectric constant ɛ = 2.8), a good solvent for polystyrene, and with 5Wt% of ethanol (ɛ = 24.3l) added. The dynamic structure factor S(q,t) was analyzed with a single exponential except for a limited q range where two time constants associated with constraint and mobile segments were detected. S(q,t) exhibits several distinctive time and length scales for the dynamics with a crossover appearing at the length scale of the ionic clusters. NSF DMR 1611136.

Porphyrins as Templates for Site-Selective Atomic Layer Deposition: Vapor Metalation and in Situ Monitoring of Island Growth

DOE Office of Scientific and Technical Information (OSTI.GOV)

Avila, Jason R.; Emery, Jonathan D.; Pellin, Michael J.

Examinations of enzymatic catalysts suggest one key to efficient catalytic activity is discrete size metallo clusters. Mimicking enzymatic cluster systems is synthetically challenging because conventional solution methods are prone to aggregation or require capping of the cluster, thereby limiting its catalytic activity. We introduce site-selective atomic layer deposition (ALD) on porphyrins as an alternative approach to grow isolated metal oxide islands that are spatially separated. Surface-bound tetra-acid free base porphyrins (H2TCPP) may be metalated with Mn using conventional ALD precursor exposure to induce homogeneous hydroxide synthetic handles which acts as a nucleation point for subsequent ALD MnO island growth. Analyticalmore » fitting of in situ QCM mass uptake reveals island growth to be hemispherical with a convergence radius of 1.74 nm. This growth mode is confirmed with synchrotron grazing-incidence small-angle X-ray scattering (GISAXS) measurements. Finally, we extend this approach to other ALD chemistries to demonstrate the generality of this route to discrete metallo island materials.« less

Dynamic behaviour of nanometre-sized defect clusters emitted from an atomic displacement cascade in Au at 50 K

NASA Astrophysics Data System (ADS)

Ono, K.; Miyamoto, M.; Arakawa, K.; Birtcher, R. C.

2017-09-01

We demonstrate the emission of nanometre-sized defect clusters from an isolated displacement cascade formed by irradiation of high-energy self-ions and their subsequent 1-D motion in Au at 50 K, using in situ electron microscopy. The small defect clusters emitted from a displacement cascade exhibited correlated back-and-forth 1-D motion along the [-1 1 0] direction and coalescence which results in their growth and reduction of their mobility. From the analysis of the random 1-D motion, the diffusivity of the small cluster was evaluated. Correlated 1-D motion and coalescence of clusters were understood via elastic interaction between small clusters. These results provide direct experimental evidence of the migration of small defect clusters and defect cascade evolution at low temperature.

Hybrid Percolation Transition in Cluster Merging Processes: Continuously Varying Exponents

NASA Astrophysics Data System (ADS)

Cho, Y. S.; Lee, J. S.; Herrmann, H. J.; Kahng, B.

2016-01-01

Consider growing a network, in which every new connection is made between two disconnected nodes. At least one node is chosen randomly from a subset consisting of g fraction of the entire population in the smallest clusters. Here we show that this simple strategy for improving connection exhibits a more unusual phase transition, namely a hybrid percolation transition exhibiting the properties of both first-order and second-order phase transitions. The cluster size distribution of finite clusters at a transition point exhibits power-law behavior with a continuously varying exponent τ in the range 2 <τ (g )≤2.5 . This pattern reveals a necessary condition for a hybrid transition in cluster aggregation processes, which is comparable to the power-law behavior of the avalanche size distribution arising in models with link-deleting processes in interdependent networks.

Clustering behavior of hermit crabs (Decapoda, Anomura) in an intertidal rocky shore at São Sebastião, southeastern Brazil.

PubMed

Turra, A; Leite, F P

2000-02-01

The clustering behavior and cluster composition of hermit crabs as well as the patterns of shell utilization of clustered and scattered individuals were studied. This study was conducted in the intertidal region of Grande Beach, São Sebastião, southeastern Brazil. Samples were taken both in randomized transects and 1 m2 quadrats during low tide periods. Crabs were counted, measured (shield length), and sexed. Shells were identified and had their adequacy and condition (physical damage and incrustation) recorded. Clusters occurred mainly in air exposed areas and were dominated or composed only by Clibanarius antillensis. Other species like Paguristes tortugae, Pagurus criniticornis, and Calcinus tibicen were also present in these clusters, but in small numbers. Only one monospecific aggregation composed by individuals of P. criniticornis was recorded in tide pools. Almost all crabs were inactive, despite some that were submerged in tide pools. Most of the individuals of C. antillensis were clustered (70.88%). Scattered individuals were larger than clustered ones and occupied mainly shells of Tegula viridula, which seemed to be the most adequate shell to the crabs. Clustered individuals used less incrusted shells than isolated ones. In general, clustering in Grande Beach presented the same patterns of size and sex distribution, and shell utilization than others already studied, with the exception of the smaller cluster size registered in this area.

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.

Ballistic aggregation in systems of inelastic particles: Cluster growth, structure, and aging

NASA Astrophysics Data System (ADS)

Paul, Subhajit; Das, Subir K.

2017-07-01

We study far-from-equilibrium dynamics in models of freely cooling granular gas and ballistically aggregating compact clusters. For both the cases, from event-driven molecular dynamics simulations, we have presented detailed results on structure and dynamics in space dimensions d =1 and 2. Via appropriate analyses it has been confirmed that the ballistic aggregation mechanism applies in d =1 granular gases as well. Aging phenomena for this mechanism, in both the dimensions, have been studied via the two-time density autocorrelation function. This quantity is demonstrated to exhibit scaling property similar to that in the standard phase transition kinetics. The corresponding functional forms have been quantified and the outcomes have been discussed in connection with the structural properties. Our results on aging establish a more complete equivalence between the granular gas and the ballistic aggregation models in d =1 .

A novel magnetic resonance imaging segmentation technique for determining diffuse intrinsic pontine glioma tumor volume

PubMed Central

Singh, Ranjodh; Zhou, Zhiping; Tisnado, Jamie; Haque, Sofia; Peck, Kyung K.; Young, Robert J.; Tsiouris, Apostolos John; Thakur, Sunitha B.; Souweidane, Mark M.

2017-01-01

OBJECTIVE Accurately determining diffuse intrinsic pontine glioma (DIPG) tumor volume is clinically important. The aims of the current study were to 1) measure DIPG volumes using methods that require different degrees of subjective judgment; and 2) evaluate interobserver agreement of measurements made using these methods. METHODS Eight patients from a Phase I clinical trial testing convection-enhanced delivery (CED) of a therapeutic antibody were included in the study. Pre-CED, post–radiation therapy axial T2-weighted images were analyzed using 2 methods requiring high degrees of subjective judgment (picture archiving and communication system [PACS] polygon and Volume Viewer auto-contour methods) and 1 method requiring a low degree of subjective judgment (k-means clustering segmentation) to determine tumor volumes. Lin’s concordance correlation coefficients (CCCs) were calculated to assess interobserver agreement. RESULTS The CCCs of measurements made by 2 observers with the PACS polygon and the Volume Viewer auto-contour methods were 0.9465 (lower 1-sided 95% confidence limit 0.8472) and 0.7514 (lower 1-sided 95% confidence limit 0.3143), respectively. Both were considered poor agreement. The CCC of measurements made using k-means clustering segmentation was 0.9938 (lower 1-sided 95% confidence limit 0.9772), which was considered substantial strength of agreement. CONCLUSIONS The poor interobserver agreement of PACS polygon and Volume Viewer auto-contour methods high-lighted the difficulty in consistently measuring DIPG tumor volumes using methods requiring high degrees of subjective judgment. k-means clustering segmentation, which requires a low degree of subjective judgment, showed better interob-server agreement and produced tumor volumes with delineated borders. PMID:27391980

Modeling of the Modulation by Buffers of Ca2+ Release through Clusters of IP3 Receptors

PubMed Central

Zeller, S.; Rüdiger, S.; Engel, H.; Sneyd, J.; Warnecke, G.; Parker, I.; Falcke, M.

2009-01-01

Abstract Intracellular Ca2+ release is a versatile second messenger system. It is modeled here by reaction-diffusion equations for the free Ca2+ and Ca2+ buffers, with spatially discrete clusters of stochastic IP3 receptor channels (IP3Rs) controlling the release of Ca2+ from the endoplasmic reticulum. IP3Rs are activated by a small rise of the cytosolic Ca2+ concentration and inhibited by large concentrations. Buffering of cytosolic Ca2+ shapes global Ca2+ transients. Here we use a model to investigate the effect of buffers with slow and fast reaction rates on single release spikes. We find that, depending on their diffusion coefficient, fast buffers can either decouple clusters or delay inhibition. Slow buffers have little effect on Ca2+ release, but affect the time course of the signals from the fluorescent Ca2+ indicator mainly by competing for Ca2+. At low [IP3], fast buffers suppress fluorescence signals, slow buffers increase the contrast between bulk signals and signals at open clusters, and large concentrations of buffers, either fast or slow, decouple clusters. PMID:19686646

Structural and magnetic evolution of bimetallic MnAu clusters driven by asymmetric atomic migration.

PubMed

Wei, Xiaohui; Zhou, Rulong; Lefebvre, Williams; He, Kai; Le Roy, Damien; Skomski, Ralph; Li, Xingzhong; Shield, Jeffrey E; Kramer, Matthew J; Chen, Shuang; Zeng, Xiao Cheng; Sellmyer, David J

2014-03-12

The nanoscale structural, compositional, and magnetic properties are examined for annealed MnAu nanoclusters. The MnAu clusters order into the L1(0) structure, and monotonic size-dependences develop for the composition and lattice parameters, which are well reproduced by our density functional theory calculations. Simultaneously, Mn diffusion forms 5 Å nanoshells on larger clusters inducing significant magnetization in an otherwise antiferromagnetic system. The differing atomic mobilities yield new cluster nanostructures that can be employed generally to create novel physical properties.

Comparing cluster-level dynamic treatment regimens using sequential, multiple assignment, randomized trials: Regression estimation and sample size considerations.

PubMed

NeCamp, Timothy; Kilbourne, Amy; Almirall, Daniel

2017-08-01

Cluster-level dynamic treatment regimens can be used to guide sequential treatment decision-making at the cluster level in order to improve outcomes at the individual or patient-level. In a cluster-level dynamic treatment regimen, the treatment is potentially adapted and re-adapted over time based on changes in the cluster that could be impacted by prior intervention, including aggregate measures of the individuals or patients that compose it. Cluster-randomized sequential multiple assignment randomized trials can be used to answer multiple open questions preventing scientists from developing high-quality cluster-level dynamic treatment regimens. In a cluster-randomized sequential multiple assignment randomized trial, sequential randomizations occur at the cluster level and outcomes are observed at the individual level. This manuscript makes two contributions to the design and analysis of cluster-randomized sequential multiple assignment randomized trials. First, a weighted least squares regression approach is proposed for comparing the mean of a patient-level outcome between the cluster-level dynamic treatment regimens embedded in a sequential multiple assignment randomized trial. The regression approach facilitates the use of baseline covariates which is often critical in the analysis of cluster-level trials. Second, sample size calculators are derived for two common cluster-randomized sequential multiple assignment randomized trial designs for use when the primary aim is a between-dynamic treatment regimen comparison of the mean of a continuous patient-level outcome. The methods are motivated by the Adaptive Implementation of Effective Programs Trial which is, to our knowledge, the first-ever cluster-randomized sequential multiple assignment randomized trial in psychiatry.

Spatial and temporal clustering of dengue virus transmission in Thai villages.

PubMed

Mammen, Mammen P; Pimgate, Chusak; Koenraadt, Constantianus J M; Rothman, Alan L; Aldstadt, Jared; Nisalak, Ananda; Jarman, Richard G; Jones, James W; Srikiatkhachorn, Anon; Ypil-Butac, Charity Ann; Getis, Arthur; Thammapalo, Suwich; Morrison, Amy C; Libraty, Daniel H; Green, Sharone; Scott, Thomas W

2008-11-04

Transmission of dengue viruses (DENV), the leading cause of arboviral disease worldwide, is known to vary through time and space, likely owing to a combination of factors related to the human host, virus, mosquito vector, and environment. An improved understanding of variation in transmission patterns is fundamental to conducting surveillance and implementing disease prevention strategies. To test the hypothesis that DENV transmission is spatially and temporally focal, we compared geographic and temporal characteristics within Thai villages where DENV are and are not being actively transmitted. Cluster investigations were conducted within 100 m of homes where febrile index children with (positive clusters) and without (negative clusters) acute dengue lived during two seasons of peak DENV transmission. Data on human infection and mosquito infection/density were examined to precisely (1) define the spatial and temporal dimensions of DENV transmission, (2) correlate these factors with variation in DENV transmission, and (3) determine the burden of inapparent and symptomatic infections. Among 556 village children enrolled as neighbors of 12 dengue-positive and 22 dengue-negative index cases, all 27 DENV infections (4.9% of enrollees) occurred in positive clusters (p < 0.01; attributable risk [AR] = 10.4 per 100; 95% confidence interval 1-19.8 per 100]. In positive clusters, 12.4% of enrollees became infected in a 15-d period and DENV infections were aggregated centrally near homes of index cases. As only 1 of 217 pairs of serologic specimens tested in positive clusters revealed a recent DENV infection that occurred prior to cluster initiation, we attribute the observed DENV transmission subsequent to cluster investigation to recent DENV transmission activity. Of the 1,022 female adult Ae. aegypti collected, all eight (0.8%) dengue-infected mosquitoes came from houses in positive clusters; none from control clusters or schools. Distinguishing features between positive and negative clusters were greater availability of piped water in negative clusters (p < 0.01) and greater number of Ae. aegypti pupae per person in positive clusters (p = 0.04). During primarily DENV-4 transmission seasons, the ratio of inapparent to symptomatic infections was nearly 1:1 among child enrollees. Study limitations included inability to sample all children and mosquitoes within each cluster and our reliance on serologic rather than virologic evidence of interval infections in enrollees given restrictions on the frequency of blood collections in children. Our data reveal the remarkably focal nature of DENV transmission within a hyperendemic rural area of Thailand. These data suggest that active school-based dengue case detection prompting local spraying could contain recent virus introductions and reduce the longitudinal risk of virus spread within rural areas. Our results should prompt future cluster studies to explore how host immune and behavioral aspects may impact DENV transmission and prevention strategies. Cluster methodology could serve as a useful research tool for investigation of other temporally and spatially clustered infectious diseases.

Spatial and Temporal Clustering of Dengue Virus Transmission in Thai Villages

PubMed Central

Mammen, Mammen P; Pimgate, Chusak; Koenraadt, Constantianus J. M; Rothman, Alan L; Aldstadt, Jared; Nisalak, Ananda; Jarman, Richard G; Jones, James W; Srikiatkhachorn, Anon; Ypil-Butac, Charity Ann; Getis, Arthur; Thammapalo, Suwich; Morrison, Amy C; Libraty, Daniel H; Green, Sharone; Scott, Thomas W

2008-01-01

Background Transmission of dengue viruses (DENV), the leading cause of arboviral disease worldwide, is known to vary through time and space, likely owing to a combination of factors related to the human host, virus, mosquito vector, and environment. An improved understanding of variation in transmission patterns is fundamental to conducting surveillance and implementing disease prevention strategies. To test the hypothesis that DENV transmission is spatially and temporally focal, we compared geographic and temporal characteristics within Thai villages where DENV are and are not being actively transmitted. Methods and Findings Cluster investigations were conducted within 100 m of homes where febrile index children with (positive clusters) and without (negative clusters) acute dengue lived during two seasons of peak DENV transmission. Data on human infection and mosquito infection/density were examined to precisely (1) define the spatial and temporal dimensions of DENV transmission, (2) correlate these factors with variation in DENV transmission, and (3) determine the burden of inapparent and symptomatic infections. Among 556 village children enrolled as neighbors of 12 dengue-positive and 22 dengue-negative index cases, all 27 DENV infections (4.9% of enrollees) occurred in positive clusters (p < 0.01; attributable risk [AR] = 10.4 per 100; 95% confidence interval 1–19.8 per 100]. In positive clusters, 12.4% of enrollees became infected in a 15-d period and DENV infections were aggregated centrally near homes of index cases. As only 1 of 217 pairs of serologic specimens tested in positive clusters revealed a recent DENV infection that occurred prior to cluster initiation, we attribute the observed DENV transmission subsequent to cluster investigation to recent DENV transmission activity. Of the 1,022 female adult Ae. aegypti collected, all eight (0.8%) dengue-infected mosquitoes came from houses in positive clusters; none from control clusters or schools. Distinguishing features between positive and negative clusters were greater availability of piped water in negative clusters (p < 0.01) and greater number of Ae. aegypti pupae per person in positive clusters (p = 0.04). During primarily DENV-4 transmission seasons, the ratio of inapparent to symptomatic infections was nearly 1:1 among child enrollees. Study limitations included inability to sample all children and mosquitoes within each cluster and our reliance on serologic rather than virologic evidence of interval infections in enrollees given restrictions on the frequency of blood collections in children. Conclusions Our data reveal the remarkably focal nature of DENV transmission within a hyperendemic rural area of Thailand. These data suggest that active school-based dengue case detection prompting local spraying could contain recent virus introductions and reduce the longitudinal risk of virus spread within rural areas. Our results should prompt future cluster studies to explore how host immune and behavioral aspects may impact DENV transmission and prevention strategies. Cluster methodology could serve as a useful research tool for investigation of other temporally and spatially clustered infectious diseases. PMID:18986209

Whole brain white matter connectivity analysis using machine learning: An application to autism.

PubMed

Zhang, Fan; Savadjiev, Peter; Cai, Weidong; Song, Yang; Rathi, Yogesh; Tunç, Birkan; Parker, Drew; Kapur, Tina; Schultz, Robert T; Makris, Nikos; Verma, Ragini; O'Donnell, Lauren J

2018-05-15

In this paper, we propose an automated white matter connectivity analysis method for machine learning classification and characterization of white matter abnormality via identification of discriminative fiber tracts. The proposed method uses diffusion MRI tractography and a data-driven approach to find fiber clusters corresponding to subdivisions of the white matter anatomy. Features extracted from each fiber cluster describe its diffusion properties and are used for machine learning. The method is demonstrated by application to a pediatric neuroimaging dataset from 149 individuals, including 70 children with autism spectrum disorder (ASD) and 79 typically developing controls (TDC). A classification accuracy of 78.33% is achieved in this cross-validation study. We investigate the discriminative diffusion features based on a two-tensor fiber tracking model. We observe that the mean fractional anisotropy from the second tensor (associated with crossing fibers) is most affected in ASD. We also find that local along-tract (central cores and endpoint regions) differences between ASD and TDC are helpful in differentiating the two groups. These altered diffusion properties in ASD are associated with multiple robustly discriminative fiber clusters, which belong to several major white matter tracts including the corpus callosum, arcuate fasciculus, uncinate fasciculus and aslant tract; and the white matter structures related to the cerebellum, brain stem, and ventral diencephalon. These discriminative fiber clusters, a small part of the whole brain tractography, represent the white matter connections that could be most affected in ASD. Our results indicate the potential of a machine learning pipeline based on white matter fiber clustering. Copyright © 2017 Elsevier Inc. All rights reserved.

Diffuse Optical Light in Galaxy Clusters. II. Correlations with Cluster Properties

NASA Astrophysics Data System (ADS)

Krick, J. E.; Bernstein, R. A.

2007-08-01

We have measured the flux, profile, color, and substructure in the diffuse intracluster light (ICL) in a sample of 10 galaxy clusters with a range of mass, morphology, redshift, and density. Deep, wide-field observations for this project were made in two bands at the 1 m Swope and 2.5 m du Pont telescopes at Las Campanas Observatory. Careful attention in reduction and analysis was paid to the illumination correction, background subtraction, point-spread function determination, and galaxy subtraction. ICL flux is detected in both bands in all 10 clusters ranging from 7.6×1010 to 7.0×1011 h-170 Lsolar in r and 1.4×1010 to 1.2×1011 h-170 Lsolar in the B band. These fluxes account for 6%-22% of the total cluster light within one-quarter of the virial radius in r and 4%-21% in the B band. Average ICL B-r colors range from 1.5 to 2.8 mag when k- and evolution corrected to the present epoch. In several clusters we also detect ICL in group environments near the cluster center and up to 1 h-170 Mpc distant from the cluster center. Our sample, having been selected from the Abell sample, is incomplete in that it does not include high-redshift clusters with low density, low flux, or low mass, and it does not include low-redshift clusters with high flux, high mass, or high density. This bias makes it difficult to interpret correlations between ICL flux and cluster properties. Despite this selection bias, we do find that the presence of a cD galaxy corresponds to both centrally concentrated galaxy profiles and centrally concentrated ICL profiles. This is consistent with ICL either forming from galaxy interactions at the center or forming at earlier times in groups and later combining in the center.

The Magellanic Bridge Cluster NGC 796: Deep Optical AO Imaging Reveals the Stellar Content and Initial Mass Function of a Massive Open Cluster

NASA Astrophysics Data System (ADS)

Kalari, Venu M.; Carraro, Giovanni; Evans, Christopher J.; Rubio, Monica

2018-04-01

NGC 796 is a massive young cluster located 59 kpc from us in the diffuse intergalactic medium of the 1/5–1/10 Z⊙ Magellanic Bridge, allowing us to probe variations in star formation and stellar evolution processes as a function of metallicity in a resolved fashion, and providing a link between resolved studies of nearby solar-metallicity and unresolved distant metal-poor clusters located in high-redshift galaxies. In this paper, we present adaptive optics griHα imaging of NGC 796 (at 0.″5, which is ∼0.14 pc at the cluster distance) along with optical spectroscopy of two bright members to quantify the cluster properties. Our aim is to explore whether star formation and stellar evolution vary as a function of metallicity by comparing the properties of NGC 796 to higher-metallicity clusters. We find an age of {20}-5+12 Myr from isochronal fitting of the cluster main sequence in the color–magnitude diagram. Based on the cluster luminosity function, we derive a top-heavy stellar initial mass function (IMF) with a slope α = 1.99 ± 0.2, hinting at a metallicity and/or environmental dependence of the IMF, which may lead to a top-heavy IMF in the early universe. Study of the Hα emission-line stars reveals that classical Be stars constitute a higher fraction of the total B-type stars when compared with similar clusters at greater metallicity, providing some support to the chemically homogeneous theory of stellar evolution. Overall, NGC 796 has a total estimated mass of 990 ± 200 M⊙, and a core radius of 1.4 ± 0.3 pc, which classifies it as a massive young open cluster, unique in the diffuse interstellar medium of the Magellanic Bridge.

Galaxy Clusters: A Novel Look at Diffuse Baryons Withstanding Dark Matter Gravity

NASA Astrophysics Data System (ADS)

Cavaliere, A.; Lapi, A.; Fusco-Femiano, R.

2009-06-01

In galaxy clusters, the equilibria of the intracluster plasma (ICP) and of the gravitationally dominant dark matter (DM) are governed by the hydrostatic equation and by the Jeans equation, respectively; in either case gravity is withstood by the corresponding, entropy-modulated pressure. Jeans, with the DM "entropy" set to K vprop r α and α ≈ 1.25-1.3 applying from groups to rich clusters, yields our radial α-profiles these, compared to the empirical Navarro-Frenk-White distribution, are flatter at the center and steeper in the outskirts as required by recent gravitational lensing data. In the ICP, on the other hand, the entropy run k(r) is mainly shaped by shocks, as steadily set by supersonic accretion of gas at the cluster boundary, and intermittently driven from the center by merging events or by active galactic nuclei (AGNs); the resulting equilibrium is described by the exact yet simple formalism constituting our ICP Supermodel. With two parameters, this accurately represents the runs of density n(r) and temperature T(r) as required by up-to-date X-ray data on surface brightness and spectroscopy for both cool core (CC) and non-cool core (NCC) clusters; the former are marked by a middle temperature peak, whose location is predicted from rich clusters to groups. The Supermodel inversely links the inner runs of n(r) and T(r), and highlights their central scaling with entropy nc vprop k -1 c and Tc vprop k 0.35 c , to yield radiative cooling times tc ≈ 0.3(kc /15 keV cm2)1.2 Gyr. We discuss the stability of the central values so focused: against radiative erosion of kc in the cool dense conditions of CC clusters, that triggers recurrent AGN activities resetting it back; or against energy inputs from AGNs and mergers whose effects are saturated by the hot central conditions of NCC clusters. From the Supermodel, we also derive as limiting cases the classic polytropic β-models, and the "mirror" model with T(r) vprop σ2(r) suitable for NCC and CC clusters, respectively; these limiting cases highlight how the ICP temperature T(r) strives to mirror the DM velocity dispersion σ2(r) away from energy and entropy injections. Finally, we discuss how the Supermodel connects information derived from X-ray and gravitational lensing observations.

Stepwise Nucleation of Aniline: Emergence of Spectroscopic Fingerprints of the Liquid Phase.

PubMed

Leon, Iker; Usabiaga, Imanol; Arnaiz, Pedro Felipe; Lesarri, Alberto; Fernández, Jose Andres

2018-06-11

We deal here with the controlled nucleation of aniline from the isolated molecule until formation of a moderately large aggregate: aniline nonamer. The structure of the cluster at each step of the nucleation was unravelled combining mass-resolved IR spectroscopy and computational chemistry, demonstrating that aggregation is primarily guided by formation of extensive N-H···N hydrogen bond networks that give the aggregates a sort of branched backbone, in clear competition with multiple N-H/C-H···pi and pi···pi interactions. The result is the co-existence of close nucleation paths connecting relational aggregates. The delicate balance of molecular forces makes the aniline clusters a challenge for molecular orbital calculations and an ideal system to refine the present nucleation models. Noticeably, spectroscopic signatures characteristic of the condensed phase are apparent in the nanometer-size aggregates formed in this work. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Diffusion and Mixing in Globular Clusters

NASA Astrophysics Data System (ADS)

Meiron, Yohai; Kocsis, Bence

2018-03-01

Collisional relaxation describes the stochastic process with which a self-gravitating system near equilibrium evolves in phase-space due to the fluctuating gravitational field of the system. The characteristic timescale of this process is called the relaxation time. In this paper, we highlight the difference between two measures of the relaxation time in globular clusters: (1) the diffusion time with which the isolating integrals of motion (i.e., energy E and angular momentum magnitude L) of individual stars change stochastically and (2) the asymptotic timescale required for a family of orbits to mix in the cluster. More specifically, the former corresponds to the instantaneous rate of change of a star’s E or L, while the latter corresponds to the timescale for the stars to statistically forget their initial conditions. We show that the diffusion timescales of E and L vary systematically around the commonly used half-mass relaxation time in different regions of the cluster by a factor of ∼10 and ∼100, respectively, for more than 20% of the stars. We define the mixedness of an orbital family at any given time as the correlation coefficient between its E or L probability distribution functions and those of the whole cluster. Using Monte Carlo simulations, we find that mixedness converges asymptotically exponentially with a decay timescale that is ∼10 times the half-mass relaxation time.

Nature of water and hydrogen reactions on transition metal surfaces studied by scanning tunneling microscopy

NASA Astrophysics Data System (ADS)

Tatarkhanov, Mouslim Magomedovich

Scanning Tunneling Microscopy (STM) has already been established as a tool for the investigation of simple reaction mechanisms. In this work I present results of two parallel studies using STM: first, hydrogen on Ru(0001) surface and second, water on Ru(0001) and Pd(111). In both studies initial stages of adsorption up to saturation monolayer coverage were investigated by variable temperature scanning tunneling microscopy (VT STM). The first step of the hydrogen adsorption study was the identification and characterization of the various coverage structures on clean Ru(0001). Hydrogen was found to adsorb dissociatively forming ( 3x3 )R30°, 3 domains of (2x1), (2x2)-3H and (1x1) for increasing coverages of theta=0.3 ML, 0.5 ML, 0.75 ML and 0.1 ML respectively. Some of these structures were observed to coexist at intermediate coverage values. In addition effects of impurities such as oxygen and carbon on hydrogen adsorption has been discussed. Next, near saturation coverage the interesting mechanism of how H 2 dissociates and binds to the surface of Ru(0001) has been observed. We found that the H2 dissociation takes place only on Ru sites where the metal atom is not bound to any H atom. Such active sites are formed when at least 3 H-vacancies aggregate by thermal diffusion. Sites formed by single H-vacancies (i.e. unoccupied Ru sites) or pairs of adjoining vacancies were found to be unreactive toward H2. H-vacancies were observed as single entities diffusing on the surface at 50 K and able to form transient triangular shaped aggregations where H2 molecules dissociated. It was found that the diffusion and aggregation of the H-vacancies is essential in creation of active sites where dissociative adsorption of hydrogen occurs. The first step of water studies was the initial stages of growth of water on the hexagonal surfaces of Pd(111) and Ru(0001) in the temperature range between 40 K and 130 K. In addition, DFT calculations and STM image simulations were used to validate the models. Below 130 K water dissociation does not occur at any appreciable rate and only molecular films are formed. At these temperatures the kinetics of water growth leads to structures where the molecules bind to the metal substrate through the O-lone pair while making 3 H-bonds with neighboring molecules and form clusters of hexagonal units with a honeycomb structure. This bonding geometry imposes limitations to the size of the clusters, with unsaturated H-bonds confined to the cluster periphery. It is found that growth proceeds by attachement of water molecules to the edge of the clusters by H-bonds. These molecules bind only weakly to the metal substrate and can hop around the edges. Comparison of DFT and STM image calculations with experiments shows that on Pd the edge-attached molecules form two different structures, a metastable one where the molecule is elevated by 2.7 A with respect to the cluster molecules, and another where they are elevated by only 0.4 A. On Ru only the less elevated (0.4 A higher) edge-attached molecules are observed. In next final step, water structures on Ru(0001) were studied at temperatures above 140K. STM findings were backed by x-ray absorption spectroscopy. Additional DFT calculations and STM simulations provided validation of proposed models. It was found that while undissociated water layers are metastable below 140 K, heating above this temperature produces drastic transformations whereby a fraction of the water molecules partially dissociate and form mixed H 2O-OH structures. XPS and XAS revealed the presence of hydroxyl groups with their O-H bond essentiallymostly parallel to the surface. STM images show that the mixed H2O-OH structures consist of long narrow stripes aligned with the three crystallographic directions perpendicular to the close-packed atomic rows of the Ru(0001) substrate. The internal structure of the stripes is a honeycomb network of H-bonded water and hydroxyl species. We found that the metastable low temperature molecular phase can also be converted to a mixed H2O-OH phase through excitation by the tunneling electrons when their energy is 0.5 eV or higher above the Fermi level. Structural models based on the STM images were used for Density Functional Theory optimizations of the stripes geometry. The optimized geometry was then utilized to calculate STM images for comparison with the experiment.

Clustering and Phase Transitions on a Neutral Landscape

NASA Astrophysics Data System (ADS)

Scott, Adam; King, Dawn; Maric, Nevena; Bahar, Sonya

2012-02-01

The problem of speciation and species aggregation on a neutral landscape, subject to random mutational fluctuations rather than selective drive, has been a focus of research since the seminal work of Kimura on genetic drift. These ideas have received increased attention due to the more recent development of a neutral ecological theory by Hubbell. De Aguiar et al. recently demonstrated, in a computational model, that speciation can occur under neutral conditions; this study bears some comparison with more mathematical studies of clustering on neutral landscapes in the context of branching and annihilating random walks. Here, we show that clustering can occur on a neutral landscape where the dimensions specify the simulated organisms' phenotypes. Unlike the De Aguiar et al. model, we simulate sympatric speciation: the organisms cluster phenotypically, but are not spatially separated. Moreover, we find that clustering occurs not only in the case of assortative mating, but also in the case of asexual fission. Clustering is not observed in a control case where organisms can mate randomly. We find that the population size and the number of clusters undergo phase-transition-like behavior as the maximum mutation size is varied.

Microstructural abnormalities of the brain white matter in attention-deficit/hyperactivity disorder

PubMed Central

Chen, Lizhou; Huang, Xiaoqi; Lei, Du; He, Ning; Hu, Xinyu; Chen, Ying; Li, Yuanyuan; Zhou, Jinbo; Guo, Lanting; Kemp, Graham J.; Gong, Qiyong

2015-01-01

Background Attention-deficit/hyperactivity disorder (ADHD) is an early-onset neurodevelopmental disorder with multiple behavioural problems and executive dysfunctions for which neuroimaging studies have reported a variety of abnormalities, with inconsistencies partly owing to confounding by medication and concurrent psychiatric disease. We aimed to investigate the microstructural abnormalities of white matter in unmedicated children and adolescents with pure ADHD and to explore the association between these abnormalities and behavioural symptoms and executive functions. Methods We assessed children and adolescents with ADHD and healthy controls using psychiatric interviews. Behavioural problems were rated using the revised Conners’ Parent Rating Scale, and executive functions were measured using the Stroop Colour-Word Test and the Wisconsin Card Sorting test. We acquired diffusion tensor imaging data using a 3 T MRI system, and we compared diffusion parameters, including fractional anisotropy (FA) and mean, axial and radial diffusivities, between the 2 groups. Results Thirty-three children and adolescents with ADHD and 35 healthy controls were included in our study. In patients compared with controls, FA was increased in the left posterior cingulum bundle as a result of both increased axial diffusivity and decreased radial diffusivity. In addition, the averaged FA of the cluster in this region correlated with behavioural measures as well as executive function in patients with ADHD. Limitations This study was limited by its cross-sectional design and small sample size. The cluster size of the significant result was small. Conclusion Our findings suggest that white matter abnormalities within the limbic network could be part of the neural underpinning of behavioural problems and executive dysfunction in patients with ADHD. PMID:25853285

Observation of small cluster formation in concentrated monoclonal antibody solutions and its implications to solution viscosity.

PubMed

Yearley, Eric J; Godfrin, Paul D; Perevozchikova, Tatiana; Zhang, Hailiang; Falus, Peter; Porcar, Lionel; Nagao, Michihiro; Curtis, Joseph E; Gawande, Pradad; Taing, Rosalynn; Zarraga, Isidro E; Wagner, Norman J; Liu, Yun

2014-04-15

Monoclonal antibodies (mAbs) are a major class of biopharmaceuticals. It is hypothesized that some concentrated mAb solutions exhibit formation of a solution phase consisting of reversibly self-associated aggregates (or reversible clusters), which is speculated to be responsible for their distinct solution properties. Here, we report direct observation of reversible clusters in concentrated solutions of mAbs using neutron spin echo. Specifically, a stable mAb solution is studied across a transition from dispersed monomers in dilute solution to clustered states at more concentrated conditions, where clusters of a preferred size are observed. Once mAb clusters have formed, their size, in contrast to that observed in typical globular protein solutions, is observed to remain nearly constant over a wide range of concentrations. Our results not only conclusively establish a clear relationship between the undesirable high viscosity of some mAb solutions and the formation of reversible clusters with extended open structures, but also directly observe self-assembled mAb protein clusters of preferred small finite size similar to that in micelle formation that dominate the properties of concentrated mAb solutions. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Surface enhanced Raman spectroscopy (SERS) from a molecule adsorbed on a nanoscale silver particle cluster in a holographic plate

NASA Astrophysics Data System (ADS)

Jusinski, Leonard E.; Bahuguna, Ramen; Das, Amrita; Arya, Karamjeet

2006-02-01

Surface enhanced Raman spectroscopy has become a viable technique for the detection of single molecules. This highly sensitive technique is due to the very large (up to 14 orders in magnitude) enhancement in the Raman cross section when the molecule is adsorbed on a metal nanoparticle cluster. We report here SERS (Surface Enhanced Raman Spectroscopy) experiments performed by adsorbing analyte molecules on nanoscale silver particle clusters within the gelatin layer of commercially available holographic plates which have been developed and fixed. The Ag particles range in size between 5 - 30 nanometers (nm). Sample preparation was performed by immersing the prepared holographic plate in an analyte solution for a few minutes. We report here the production of SERS signals from Rhodamine 6G (R6G) molecules of nanomolar concentration. These measurements demonstrate a fast, low cost, reproducible technique of producing SERS substrates in a matter of minutes compared to the conventional procedure of preparing Ag clusters from colloidal solutions. SERS active colloidal solutions require up to a full day to prepare. In addition, the preparations of colloidal aggregates are not consistent in shape, contain additional interfering chemicals, and do not generate consistent SERS enhancement. Colloidal solutions require the addition of KCl or NaCl to increase the ionic strength to allow aggregation and cluster formation. We find no need to add KCl or NaCl to create SERS active clusters in the holographic gelatin matrix. These holographic plates, prepared using simple, conventional procedures, can be stored in an inert environment and preserve SERS activity after several weeks subsequent to preparation.

Comparison of Clustering Techniques for Residential Energy Behavior using Smart Meter Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jin, Ling; Lee, Doris; Sim, Alex

Current practice in whole time series clustering of residential meter data focuses on aggregated or subsampled load data at the customer level, which ignores day-to-day differences within customers. This information is critical to determine each customer’s suitability to various demand side management strategies that support intelligent power grids and smart energy management. Clustering daily load shapes provides fine-grained information on customer attributes and sources of variation for subsequent models and customer segmentation. In this paper, we apply 11 clustering methods to daily residential meter data. We evaluate their parameter settings and suitability based on 6 generic performance metrics and post-checkingmore » of resulting clusters. Finally, we recommend suitable techniques and parameters based on the goal of discovering diverse daily load patterns among residential customers. To the authors’ knowledge, this paper is the first robust comparative review of clustering techniques applied to daily residential load shape time series in the power systems’ literature.« less

Two-stage color palettization for error diffusion

NASA Astrophysics Data System (ADS)

Mitra, Niloy J.; Gupta, Maya R.

2002-06-01

Image-adaptive color palettization chooses a decreased number of colors to represent an image. Palettization is one way to decrease storage and memory requirements for low-end displays. Palettization is generally approached as a clustering problem, where one attempts to find the k palette colors that minimize the average distortion for all the colors in an image. This would be the optimal approach if the image was to be displayed with each pixel quantized to the closest palette color. However, to improve the image quality the palettization may be followed by error diffusion. In this work, we propose a two-stage palettization where the first stage finds some m << k clusters, and the second stage chooses palette points that cover the spread of each of the M clusters. After error diffusion, this method leads to better image quality at less computational cost and with faster display speed than full k-means palettization.

Aggregation of luteinizing hormone receptors in granulosa cells: a possible mechanism of desensitization to the hormone.

PubMed Central

Amsterdam, A; Berkowitz, A; Nimrod, A; Kohen, F

1980-01-01

The temporal relationship between redistribution of receptors to lutropin (luteinizing hormone)/human chorionic gonadotropin in cultured rat ovarian granulosa cells and the cellular response to hormonal challenge were studied. Visualization of receptor-bound human chorionic gonadotropin by indirect immunofluorescence, with hormone-specific antibodies after fixation with 2% formaldehyde, revealed the existence of small clusters around the entire cell circumference 5--20 min after exposure to the hormone at 37 degrees C. Such small receptor aggregates were also evident if hormone incubation was at 4 degrees C or if cells were fixed with 2% formaldehyde before incubation. Larger clusters were evident after prolonged incubation with the hormone (2--4 hr) at 37 degrees C. The later change coincided with diminished cyclic AMP accumulation in respose to challenge with fresh hormone. When the fixation step was omitted and antibodies to human chorionic gonadotropin were applied after hormonal binding, acceleration of both receptor clustering and the desensitization process was observed. This maneuver also induced capping of the hormone receptors. In contrast, monovalent Fab' fragments of the antibodies were without effect. Internalization of the bound hormone in lysosomes, and subsequent degradation, was evident 8 hr after hormonal application and was not accelerated by the antibodies. It is suggested that clustering of the luteinizing hormone receptors may play a role in cellular responsiveness to the hormone. Massive aggregation of the receptors may desensitize the cell by interferring with coupling to adenylate cyclase. Images PMID:6251459

ATCA 16 cm observation of CIZA J1358.9-4750: Implication of merger stage and constraint on non-thermal properties

NASA Astrophysics Data System (ADS)

Akahori, Takuya; Kato, Yuichi; Nakazawa, Kazuhiro; Ozawa, Takeaki; Gu, Liyi; Takizawa, Motokazu; Fujita, Yutaka; Nakanishi, Hiroyuki; Okabe, Nobuhiro; Makishima, Kazuo

2018-06-01

We report the Australia Telescope Compact Array 16 cm observation of CIZA J1358.9-4750. Recent X-ray studies imply that this galaxy cluster is composed of merging, binary clusters. Using the EW367 configuration, we found no significant diffuse radio emission in and around the cluster. An upper limit of the total radio power at 1.4 GHz is ˜1.1 × 1022 W Hz-1 in 30 square arcminutes, which is a typical size for radio relics. It is known that an empirical relation holds between the total radio power and X-ray luminosity of the host cluster. The upper limit is about one order of magnitude lower than the power expected from the relation. Very young (˜70 Myr) shocks with low Mach numbers (˜1.3), which are often seen at an early stage of merger simulations, are suggested by the previous X-ray observation. The shocks may generate cosmic-ray electrons with a steep energy spectrum, which is consistent with non-detection of bright (>1023 W Hz-1) relic in this 16 cm band observation. Based on the assumption of energy equipartition, the upper limit gives a magnetic field strength of below 0.68f(Dlos/1 Mpc)-1(γmin/200)-1 μG, where f is the cosmic-ray total energy density over the cosmic-ray electron energy density, Dlos is the depth of the shock wave along the sightline, and γmin is the lower cutoff Lorentz factor of the cosmic-ray electron energy spectrum.

Dark field differential dynamic microscopy enables accurate characterization of the roto-translational dynamics of bacteria and colloidal clusters

NASA Astrophysics Data System (ADS)

Cerbino, Roberto; Piotti, Davide; Buscaglia, Marco; Giavazzi, Fabio

2018-01-01

Micro- and nanoscale objects with anisotropic shape are key components of a variety of biological systems and inert complex materials, and represent fundamental building blocks of novel self-assembly strategies. The time scale of their thermal motion is set by their translational and rotational diffusion coefficients, whose measurement may become difficult for relatively large particles with small optical contrast. Here we show that dark field differential dynamic microscopy is the ideal tool for probing the roto-translational Brownian motion of anisotropic shaped particles. We demonstrate our approach by successful application to aqueous dispersions of non-motile bacteria and of colloidal aggregates of spherical particles.

Reexamining cluster radioactivity in trans-lead nuclei with consideration of specific density distributions in daughter nuclei and clusters

NASA Astrophysics Data System (ADS)

Qian, Yibin; Ren, Zhongzhou; Ni, Dongdong

2016-08-01

We further investigate the cluster emission from heavy nuclei beyond the lead region in the framework of the preformed cluster model. The refined cluster-core potential is constructed by the double-folding integral of the density distributions of the daughter nucleus and the emitted cluster, where the radius or the diffuseness parameter in the Fermi density distribution formula is determined according to the available experimental data on the charge radii and the neutron skin thickness. The Schrödinger equation of the cluster-daughter relative motion is then solved within the outgoing Coulomb wave-function boundary conditions to obtain the decay width. It is found that the present decay width of cluster emitters is clearly enhanced as compared to that in the previous case, which involved the fixed parametrization for the density distributions of daughter nuclei and clusters. Among the whole procedure, the nuclear deformation of clusters is also introduced into the calculations, and the degree of its influence on the final decay half-life is checked to some extent. Moreover, the effect from the bubble density distribution of clusters on the final decay width is carefully discussed by using the central depressed distribution.

Computational Modeling of Radiation Phenomenon in SiC for Nuclear Applications

NASA Astrophysics Data System (ADS)

Ko, Hyunseok

Silicon carbide (SiC) material has been investigated for promising nuclear materials owing to its superior thermo-mechanical properties, and low neutron cross-section. While the interest in SiC has been increasing, the lack of fundamental understanding in many radiation phenomena is an important issue. More specifically, these phenomena in SiC include the fission gas transport, radiation induced defects and its evolution, radiation effects on the mechanical stability, matrix brittleness of SiC composites, and low thermal conductivities of SiC composites. To better design SiC and SiC composite materials for various nuclear applications, understanding each phenomenon and its significance under specific reactor conditions is important. In this thesis, we used various modeling approaches to understand the fundamental radiation phenomena in SiC for nuclear applications in three aspects: (a) fission product diffusion through SiC, (b) optimization of thermodynamic stable self-interstitial atom clusters, (c) interface effect in SiC composite and their change upon radiation. In (a) fission product transport work, we proposed that Ag/Cs diffusion in high energy grain boundaries may be the upper boundary in unirradiated SiC at relevant temperature, and radiation enhanced diffusion is responsible for fast diffusion measured in post-irradiated fuel particles. For (b) the self-interstitial cluster work, thermodynamically stable clusters are identified as a function of cluster size, shape, and compositions using a genetic algorithm. We found that there are compositional and configurational transitions for stable clusters as the cluster size increases. For (c) the interface effect in SiC composite, we investigated recently proposed interface, which is CNT reinforced SiC composite. The analytical model suggests that CNT/SiC composites have attractive mechanical and thermal properties, and these fortify the argument that SiC composites are good candidate materials for the cladding. We used grand canonical monte carlo to optimize the interface, as a part of the stepping stone for further study using the interface.

Annihilating vacancies via dynamic reflection and emission of interstitials in nano-crystal tungsten

NASA Astrophysics Data System (ADS)

Li, Xiangyan; Duan, Guohua; Xu, Yichun; Zhang, Yange; Liu, Wei; Liu, C. S.; Liang, Yunfeng; Chen, Jun-Ling; Luo, G.-N.

2017-11-01

Radiation damage not only seriously degrades the mechanical properties of tungsten (W) but also enhances hydrogen retention in the material. Introducing a large amount of defect sinks, e.g. grain boundaries (GBs) is an effective method for improving radiation-resistance of W. However, the mechanism by which the vacancies are dynamically annihilated at long timescale in nano-crystal W is still not clear. The dynamic picture for eliminating vacancies with single interstitials and small interstitial-clusters has been investigated by combining molecular dynamics, molecular statics and object Kinetic Monte Carlo methods. On one hand, the annihilation of bulk vacancies was enhanced due to the reflection of an interstitial-cluster of parallel ≤ft< 1 1 1 \\right> crowdions by the GB. The interstitial-cluster was observed to be reflected back into the grain interior when approaching a locally dense GB region. Near this region, the energy landscape for the interstitial was featured by a shoulder, different to the decreasing energy landscape of the interstitial near a locally loose region as indicative of the sink role of the GB. The bulk vacancy on the reflection path was annihilated. On the other hand, the dynamic interstitial emission efficiently anneals bulk vacancies. The single interstitial trapped at the GB firstly moved along the GB quickly and clustered to be the di-interstitial therein, reducing its mobility to a value comparable to that that for bulk vacancy diffusion. Then, the bulk vacancy was recombined via the coupled motion of the di-interstitial along the GB, the diffusion of the vacancy towards the GB and the accompanying interstitial emission. These results suggest that GBs play an efficient role in improving radiation-tolerance of nano-crystal W via reflecting highly-mobile interstitials and interstitial-clusters into the bulk and annihilating bulk vacancies, and via complex coupling of in-boundary interstitial diffusion, clustering of the interstitial and vacancy diffusion in the bulk.

Unveiling the Synchrotron Cosmic Web: Pilot Study

NASA Astrophysics Data System (ADS)

Brown, Shea; Rudnick, Lawrence; Pfrommer, Christoph; Jones, Thomas

2011-10-01

The overall goal of this project is to challenge our current theoretical understanding of the relativistic particle populations in the inter-galactic medium (IGM) through deep 1.4 GHz observations of 13 massive, high-redshift clusters of galaxies. Designed to compliment/extend the GMRT radio halo survey (Venturi et al. 2007), these observations will attempt to detect the peaks of the purported synchrotron cosmic-web, and place serious limits on models of CR acceleration and magnetic field amplification during large-scale structure formation. The primary goals of this survey are: 1) Confirm the bi-modal nature of the radio halo population, which favors turbulent re-acceleration of cosmic-ray electrons (CRe) during cluster mergers as the source of the diffuse radio emission; 2) Directly test hadronic secondary models which predict the presence of cosmic-ray protons (CRp) in the cores of massive X-ray clusters; 3) Search in polarization for shock structures, a potential source of CR acceleration in the IGM.

Thermal aggregation of human immunoglobulin G in arginine solutions: Contrasting effects of stabilizers and destabilizers.

PubMed

Yoshizawa, Shunsuke; Arakawa, Tsutomu; Shiraki, Kentaro

2017-11-01

Arginine is widely used as aggregation suppressor of proteins in biotechnology and pharmaceutics. However, why the effect of arginine depends on the types of proteins and stresses, including monoclonal antibodies, is still unclear. Here we investigated the precise processes of the thermal aggregation of human immunoglobulin G (IgG) in the presence of additives. As expected, arginine was the best additive to suppress the formation of insoluble aggregates during heat treatment, though it was unable to preserve the monomer content. A systematic analysis of the additives showed that sugars and kosmotropic ion inhibit the formation of soluble oligomers. These behaviors indicate that the thermal aggregation of IgG occurs by (i) the formation of soluble oligomers, which is triggered by the unfolding process that can be stabilized by typical osmolytes, and (ii) the formation of insoluble aggregates through weak cluster-cluster interactions, which can be suppressed by arginine. Understanding the detailed mechanism of arginine will provide useful information for the rational formulation design of antibodies. Copyright © 2017 Elsevier B.V. All rights reserved.

Pore-scale supercritical CO 2 dissolution and mass transfer under drainage conditions

DOE PAGES

Chang, Chun; Zhou, Quanlin; Oostrom, Mart; ...

2016-12-05

Recently, both core- and pore-scale imbibition experiments have shown non-equilibrium dissolution of supercritical CO 2 (scCO 2) and a prolonged depletion of residual scCO 2. In this paper, pore-scale scCO 2 dissolution and mass transfer under drainage conditions were investigated using a two-dimensional heterogeneous micromodel and a novel fluorescent water dye with a sensitive pH range between 3.7 and 6.5. Drainage experiments were conducted at 9 MPa and 40 °C by injecting scCO 2 into the sandstone-analogue pore network initially saturated by water without dissolved CO 2 (dsCO 2). During the experiments, time-lapse images of dye intensity, reflecting water pH,more » were obtained. These images show non-uniform pH in individual pores and pore clusters, with average pH levels gradually decreasing with time. Further analysis on selected pores and pore clusters shows that (1) rate-limited mass transfer prevails with slowly decreasing pH over time when the scCO 2-water interface area is low with respect to the volume of water-filled pores and pore clusters, (2) fast scCO 2 dissolution and phase equilibrium occurs when scCO 2 bubbles invade into water-filled pores, significantly enhancing the area-to-volume ratio, and (3) a transition from rate-limited to diffusion-limited mass transfer occurs in a single pore when a medium area-to-volume ratio is prevalent. The analysis also shows that two fundamental processes – scCO 2 dissolution at phase interfaces and diffusion of dsCO 2 at the pore scale (10–100 µm) observed after scCO 2 bubble invasion into water-filled pores without pore throat constraints – are relatively fast. The overall slow dissolution of scCO 2 in the millimeter-scale micromodel can be attributed to the small area-to-volume ratios that represent pore-throat configurations and characteristics of phase interfaces. Finally, this finding is applicable for the behavior of dissolution at pore, core, and field scales when water-filled pores and pore clusters of varying size are surrounded by scCO 2 at narrow pore throats.« less

Pore-scale supercritical CO 2 dissolution and mass transfer under drainage conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chang, Chun; Zhou, Quanlin; Oostrom, Mart

Recently, both core- and pore-scale imbibition experiments have shown non-equilibrium dissolution of supercritical CO 2 (scCO 2) and a prolonged depletion of residual scCO 2. In this paper, pore-scale scCO 2 dissolution and mass transfer under drainage conditions were investigated using a two-dimensional heterogeneous micromodel and a novel fluorescent water dye with a sensitive pH range between 3.7 and 6.5. Drainage experiments were conducted at 9 MPa and 40 °C by injecting scCO 2 into the sandstone-analogue pore network initially saturated by water without dissolved CO 2 (dsCO 2). During the experiments, time-lapse images of dye intensity, reflecting water pH,more » were obtained. These images show non-uniform pH in individual pores and pore clusters, with average pH levels gradually decreasing with time. Further analysis on selected pores and pore clusters shows that (1) rate-limited mass transfer prevails with slowly decreasing pH over time when the scCO 2-water interface area is low with respect to the volume of water-filled pores and pore clusters, (2) fast scCO 2 dissolution and phase equilibrium occurs when scCO 2 bubbles invade into water-filled pores, significantly enhancing the area-to-volume ratio, and (3) a transition from rate-limited to diffusion-limited mass transfer occurs in a single pore when a medium area-to-volume ratio is prevalent. The analysis also shows that two fundamental processes – scCO 2 dissolution at phase interfaces and diffusion of dsCO 2 at the pore scale (10–100 µm) observed after scCO 2 bubble invasion into water-filled pores without pore throat constraints – are relatively fast. The overall slow dissolution of scCO 2 in the millimeter-scale micromodel can be attributed to the small area-to-volume ratios that represent pore-throat configurations and characteristics of phase interfaces. Finally, this finding is applicable for the behavior of dissolution at pore, core, and field scales when water-filled pores and pore clusters of varying size are surrounded by scCO 2 at narrow pore throats.« less

Pore-scale supercritical CO 2 dissolution and mass transfer under drainage conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chang, Chun; Zhou, Quanlin; Oostrom, Mart

Abstract: Recently, both core- and pore-scale imbibition experiments have shown non-equilibrium dissolution of supercritical CO 2 (scCO 2) and a prolonged depletion of residual scCO 2. In this study, pore-scale scCO 2 dissolution and mass transfer under drainage conditions were investigated using a two-dimensional heterogeneous micromodel and a novel fluorescent water dye with a sensitive pH range between 3.7 and 6.5. Drainage experiments were conducted at 9 MPa and 40 °C by injecting scCO 2 into the sandstone-analogue pore network initially saturated by water without dissolved CO 2 (dsCO 2). During the experiments, time-lapse images of dye intensity, reflecting watermore » pH, were obtained. These images show non-uniform pH in individual pores and pore clusters, with average pH levels gradually decreasing with time. Further analysis on selected pores and pore clusters shows that (1) rate-limited mass transfer prevails with slowly decreasing pH over time when the scCO 2-water interface area is low with respect to the volume of water-filled pores and pore clusters, (2) fast scCO 2 dissolution and phase equilibrium occurs when scCO 2 bubbles invade into water-filled pores, significantly enhancing the area-to-volume ratio, and (3) a transition from rate-limited to diffusion-limited mass transfer occurs in a single pore when a medium area-to-volume ratio is prevalent. The analysis also shows that two fundamental processes – scCO 2 dissolution at phase interfaces and diffusion of dsCO 2 at the pore scale (10-100 µm) observed after scCO 2 bubble invasion into water-filled pores without pore throat constraints – are relatively fast. The overall slow dissolution of scCO 2 in the millimeter-scale micromodel can be attributed to the small area-to-volume ratios that represent pore-throat configurations and characteristics of phase interfaces. This finding is applicable for the behavior of dissolution at pore, core, and field scales when water-filled pores and pore clusters of varying size are surrounded by scCO 2 at narrow pore throats.« less

On the coherent rotation of diffuse matter in numerical simulations of clusters of galaxies

NASA Astrophysics Data System (ADS)

Baldi, Anna Silvia; De Petris, Marco; Sembolini, Federico; Yepes, Gustavo; Lamagna, Luca; Rasia, Elena

2017-03-01

We present a study on the coherent rotation of the intracluster medium and dark matter components of simulated galaxy clusters extracted from a volume-limited sample of the MUSIC project. The set is re-simulated with three different recipes for the gas physics: (I) non-radiative, (II) radiative without active galactic nuclei (AGN) feedback and (III) radiative with AGN feedback. Our analysis is based on the 146 most massive clusters identified as relaxed, 57 per cent of the total sample. We classify these objects as rotating and non-rotating according to the gas spin parameter, a quantity that can be related to cluster observations. We find that 4 per cent of the relaxed sample is rotating according to our criterion. By looking at the radial profiles of their specific angular momentum vector, we find that the solid body model is not a suitable description of rotational motions. The radial profiles of the velocity of the dark matter show a prevalence of the random velocity dispersion. Instead, the intracluster medium profiles are characterized by a comparable contribution from the tangential velocity and the dispersion. In general, the dark matter component dominates the dynamics of the clusters, as suggested by the correlation between its angular momentum and the gas one, and by the lack of relevant differences among the three sets of simulations.

Genotyping and spatial analysis of pulmonary tuberculosis and diabetes cases in the state of Veracruz, Mexico.

PubMed

Blanco-Guillot, Francles; Castañeda-Cediel, M Lucía; Cruz-Hervert, Pablo; Ferreyra-Reyes, Leticia; Delgado-Sánchez, Guadalupe; Ferreira-Guerrero, Elizabeth; Montero-Campos, Rogelio; Bobadilla-Del-Valle, Miriam; Martínez-Gamboa, Rosa Areli; Torres-González, Pedro; Téllez-Vazquez, Norma; Canizales-Quintero, Sergio; Yanes-Lane, Mercedes; Mongua-Rodríguez, Norma; Ponce-de-León, Alfredo; Sifuentes-Osornio, José; García-García, Lourdes

2018-01-01

Genotyping and georeferencing in tuberculosis (TB) have been used to characterize the distribution of the disease and occurrence of transmission within specific groups and communities. The objective of this study was to test the hypothesis that diabetes mellitus (DM) and pulmonary TB may occur in spatial and molecular aggregations. Retrospective cohort study of patients with pulmonary TB. The study area included 12 municipalities in the Sanitary Jurisdiction of Orizaba, Veracruz, México. Patients with acid-fast bacilli in sputum smears and/or Mycobacterium tuberculosis in sputum cultures were recruited from 1995 to 2010. Clinical (standardized questionnaire, physical examination, chest X-ray, blood glucose test and HIV test), microbiological, epidemiological, and molecular evaluations were carried out. Patients were considered "genotype-clustered" if two or more isolates from different patients were identified within 12 months of each other and had six or more IS6110 bands in an identical pattern, or < 6 bands with identical IS6110 RFLP patterns and spoligotype with the same spacer oligonucleotides. Residential and health care centers addresses were georeferenced. We used a Jeep hand GPS. The coordinates were transferred from the GPS files to ArcGIS using ArcMap 9.3. We evaluated global spatial aggregation of patients in IS6110-RFLP/ spoligotype clusters using global Moran´s I. Since global distribution was not random, we evaluated "hotspots" using Getis-Ord Gi* statistic. Using bivariate and multivariate analysis we analyzed sociodemographic, behavioral, clinic and bacteriological conditions associated with "hotspots". We used STATA® v13.1 for all statistical analysis. From 1995 to 2010, 1,370 patients >20 years were diagnosed with pulmonary TB; 33% had DM. The proportion of isolates that were genotyped was 80.7% (n = 1105), of which 31% (n = 342) were grouped in 91 genotype clusters with 2 to 23 patients each; 65.9% of total clusters were small (2 members) involving 35.08% of patients. Twenty three (22.7) percent of cases were classified as recent transmission. Moran`s I indicated that distribution of patients in IS6110-RFLP/spoligotype clusters was not random (Moran`s I = 0.035468, Z value = 7.0, p = 0.00). Local spatial analysis showed statistically significant spatial aggregation of patients in IS6110-RFLP/spoligotype clusters identifying "hotspots" and "coldspots". GI* statistic showed that the hotspot for spatial clustering was located in Camerino Z. Mendoza municipality; 14.6% (50/342) of patients in genotype clusters were located in a hotspot; of these, 60% (30/50) lived with DM. Using logistic regression the statistically significant variables associated with hotspots were: DM [adjusted Odds Ratio (aOR) 7.04, 95% Confidence interval (CI) 3.03-16.38] and attending the health center in Camerino Z. Mendoza (aOR18.04, 95% CI 7.35-44.28). The combination of molecular and epidemiological information with geospatial data allowed us to identify the concurrence of molecular clustering and spatial aggregation of patients with DM and TB. This information may be highly useful for TB control programs.

Simulation study of poled low-water ionomers with different architectures

NASA Astrophysics Data System (ADS)

Allahyarov, Elshad; Taylor, Philip L.; Löwen, Hartmut

2011-11-01

The role of the ionomer architecture in the formation of ordered structures in poled membranes is investigated by molecular dynamics computer simulations. It is shown that the length of the sidechain Ls controls both the areal density of cylindrical aggregates Nc and the diameter of these cylinders in the poled membrane. The backbone segment length Lb tunes the average diameter Ds of cylindrical clusters and the average number of sulfonates Ns in each cluster. A simple empirical formula is noted for the dependence of the number density of induced rod-like aggregates on the sidechain length Ls within the parameter range considered in this study.

Directional virtual backbone based data aggregation scheme for Wireless Visual Sensor Networks.

PubMed

Zhang, Jing; Liu, Shi-Jian; Tsai, Pei-Wei; Zou, Fu-Min; Ji, Xiao-Rong

2018-01-01

Data gathering is a fundamental task in Wireless Visual Sensor Networks (WVSNs). Features of directional antennas and the visual data make WVSNs more complex than the conventional Wireless Sensor Network (WSN). The virtual backbone is a technique, which is capable of constructing clusters. The version associating with the aggregation operation is also referred to as the virtual backbone tree. In most of the existing literature, the main focus is on the efficiency brought by the construction of clusters that the existing methods neglect local-balance problems in general. To fill up this gap, Directional Virtual Backbone based Data Aggregation Scheme (DVBDAS) for the WVSNs is proposed in this paper. In addition, a measurement called the energy consumption density is proposed for evaluating the adequacy of results in the cluster-based construction problems. Moreover, the directional virtual backbone construction scheme is proposed by considering the local-balanced factor. Furthermore, the associated network coding mechanism is utilized to construct DVBDAS. Finally, both the theoretical analysis of the proposed DVBDAS and the simulations are given for evaluating the performance. The experimental results prove that the proposed DVBDAS achieves higher performance in terms of both the energy preservation and the network lifetime extension than the existing methods.

Clustering of health-related behaviors among early and mid-adolescents in Tuscany: results from a representative cross-sectional study

PubMed Central

Lazzeri, Giacomo; Panatto, Donatella; Domnich, Alexander; Arata, Lucia; Pammolli, Andrea; Simi, Rita; Giacchi, Mariano Vincenzo; Amicizia, Daniela; Gasparini, Roberto

2018-01-01

Abstract Background A huge amount of literature suggests that adolescents’ health-related behaviors tend to occur in clusters, and the understanding of such behavioral clustering may have direct implications for the effective tailoring of health-promotion interventions. Despite the usefulness of analyzing clustering, Italian data on this topic are scant. This study aimed to evaluate the clustering patterns of health-related behaviors. Methods The present study is based on data from the Health Behaviors in School-aged Children (HBSC) study conducted in Tuscany in 2010, which involved 3291 11-, 13- and 15-year olds. To aggregate students’ data on 22 health-related behaviors, factor analysis and subsequent cluster analysis were performed. Results Factor analysis revealed eight factors, which were dubbed in accordance with their main traits: ‘Alcohol drinking’, ‘Smoking’, ‘Physical activity’, ‘Screen time’, ‘Signs & symptoms’, ‘Healthy eating’, ‘Violence’ and ‘Sweet tooth’. These factors explained 67% of variance and underwent cluster analysis. A six-cluster κ-means solution was established with a 93.8% level of classification validity. The between-cluster differences in both mean age and gender distribution were highly statistically significant. Conclusions Health-compromising behaviors are common among Tuscan teens and occur in distinct clusters. These results may be used by schools, health-promotion authorities and other stakeholders to design and implement tailored preventive interventions in Tuscany. PMID:27908972

Clustering of health-related behaviors among early and mid-adolescents in Tuscany: results from a representative cross-sectional study.

PubMed

Lazzeri, Giacomo; Panatto, Donatella; Domnich, Alexander; Arata, Lucia; Pammolli, Andrea; Simi, Rita; Giacchi, Mariano Vincenzo; Amicizia, Daniela; Gasparini, Roberto

2018-03-01

A huge amount of literature suggests that adolescents' health-related behaviors tend to occur in clusters, and the understanding of such behavioral clustering may have direct implications for the effective tailoring of health-promotion interventions. Despite the usefulness of analyzing clustering, Italian data on this topic are scant. This study aimed to evaluate the clustering patterns of health-related behaviors. The present study is based on data from the Health Behaviors in School-aged Children (HBSC) study conducted in Tuscany in 2010, which involved 3291 11-, 13- and 15-year olds. To aggregate students' data on 22 health-related behaviors, factor analysis and subsequent cluster analysis were performed. Factor analysis revealed eight factors, which were dubbed in accordance with their main traits: 'Alcohol drinking', 'Smoking', 'Physical activity', 'Screen time', 'Signs & symptoms', 'Healthy eating', 'Violence' and 'Sweet tooth'. These factors explained 67% of variance and underwent cluster analysis. A six-cluster κ-means solution was established with a 93.8% level of classification validity. The between-cluster differences in both mean age and gender distribution were highly statistically significant. Health-compromising behaviors are common among Tuscan teens and occur in distinct clusters. These results may be used by schools, health-promotion authorities and other stakeholders to design and implement tailored preventive interventions in Tuscany.

The Gaia-ESO Survey: evidence of atomic diffusion in M67?

NASA Astrophysics Data System (ADS)

Bertelli Motta, C.; Pasquali, A.; Richer, J.; Michaud, G.; Salaris, M.; Bragaglia, A.; Magrini, L.; Randich, S.; Grebel, E. K.; Adibekyan, V.; Blanco-Cuaresma, S.; Drazdauskas, A.; Fu, X.; Martell, S.; Tautvaišienė, G.; Gilmore, G.; Alfaro, E. J.; Bensby, T.; Flaccomio, E.; Koposov, S. E.; Korn, A. J.; Lanzafame, A. C.; Smiljanic, R.; Bayo, A.; Carraro, G.; Casey, A. R.; Costado, M. T.; Damiani, F.; Franciosini, E.; Heiter, U.; Hourihane, A.; Jofré, P.; Lardo, C.; Lewis, J.; Monaco, L.; Morbidelli, L.; Sacco, G. G.; Sousa, S. G.; Worley, C. C.; Zaggia, S.

2018-07-01

Investigating the chemical homogeneity of stars born from the same molecular cloud at virtually the same time is very important for our understanding of the chemical enrichment of the interstellar medium and with it the chemical evolution of the Galaxy. One major cause of inhomogeneities in the abundances of open clusters is stellar evolution of the cluster members. In this work, we investigate variations in the surface chemical composition of member stars of the old open cluster M67 as a possible consequence of atomic diffusion effects taking place during the main-sequence phase. The abundances used are obtained from high-resolution UVES/FLAMES spectra within the framework of the Gaia-ESO Survey. We find that the surface abundances of stars on the main sequence decrease with increasing mass reaching a minimum at the turn-off. After deepening of the convective envelope in subgiant branch stars, the initial surface abundances are restored. We found the measured abundances to be consistent with the predictions of stellar evolutionary models for a cluster with the age and metallicity of M67. Our findings indicate that atomic diffusion poses a non-negligible constraint on the achievable precision of chemical tagging methods.

Application of diffusion maps to identify human factors of self-reported anomalies in aviation.

PubMed

Andrzejczak, Chris; Karwowski, Waldemar; Mikusinski, Piotr

2012-01-01

A study investigating what factors are present leading to pilots submitting voluntary anomaly reports regarding their flight performance was conducted. Diffusion Maps (DM) were selected as the method of choice for performing dimensionality reduction on text records for this study. Diffusion Maps have seen successful use in other domains such as image classification and pattern recognition. High-dimensionality data in the form of narrative text reports from the NASA Aviation Safety Reporting System (ASRS) were clustered and categorized by way of dimensionality reduction. Supervised analyses were performed to create a baseline document clustering system. Dimensionality reduction techniques identified concepts or keywords within records, and allowed the creation of a framework for an unsupervised document classification system. Results from the unsupervised clustering algorithm performed similarly to the supervised methods outlined in the study. The dimensionality reduction was performed on 100 of the most commonly occurring words within 126,000 text records describing commercial aviation incidents. This study demonstrates that unsupervised machine clustering and organization of incident reports is possible based on unbiased inputs. Findings from this study reinforced traditional views on what factors contribute to civil aviation anomalies, however, new associations between previously unrelated factors and conditions were also found.

The Gaia-ESO Survey: Evidence of atomic diffusion in M67?

NASA Astrophysics Data System (ADS)

Motta, C. Bertelli; Pasquali, A.; Richer, J.; Michaud, G.; Salaris, M.; Bragaglia, A.; Magrini, L.; Randich, S.; Grebel, E. K.; Adibekyan, V.; Blanco-Cuaresma, S.; Drazdauskas, A.; Fu, X.; Martell, S.; TautvaišienÄ--, G.; Gilmore, G.; Alfaro, E. J.; Bensby, T.; Flaccomio, E.; Koposov, S. E.; Korn, A. J.; Lanzafame, A. C.; Smiljanic, R.; Bayo, A.; Carraro, G.; Casey, A. R.; Costado, M. T.; Damiani, F.; Franciosini, E.; Heiter, U.; Hourihane, A.; Jofré, P.; Lardo, C.; Lewis, J.; Monaco, L.; Morbidelli, L.; Sacco, G. G.; Sousa, S. G.; Worley, C. C.; Zaggia, S.

2018-04-01

Investigating the chemical homogeneity of stars born from the same molecular cloud at virtually the same time is very important for our understanding of the chemical enrichment of the interstellar medium and with it the chemical evolution of the Galaxy. One major cause of inhomogeneities in the abundances of open clusters is stellar evolution of the cluster members. In this work, we investigate variations in the surface chemical composition of member stars of the old open cluster M67 as a possible consequence of atomic diffusion effects taking place during the main-sequence phase. The abundances used are obtained from high-resolution UVES/FLAMES spectra within the framework of the Gaia-ESO Survey. We find that the surface abundances of stars on the main sequence decrease with increasing mass reaching a minimum at the turn-off. After deepening of the convective envelope in sub-giant branch stars, the initial surface abundances are restored. We found the measured abundances to be consistent with the predictions of stellar evolutionary models for a cluster with the age and metallicity of M67. Our findings indicate that atomic diffusion poses a non-negligible constraint on the achievable precision of chemical tagging methods.

fluff: exploratory analysis and visualization of high-throughput sequencing data

PubMed Central

Georgiou, Georgios

2016-01-01

Summary. In this article we describe fluff, a software package that allows for simple exploration, clustering and visualization of high-throughput sequencing data mapped to a reference genome. The package contains three command-line tools to generate publication-quality figures in an uncomplicated manner using sensible defaults. Genome-wide data can be aggregated, clustered and visualized in a heatmap, according to different clustering methods. This includes a predefined setting to identify dynamic clusters between different conditions or developmental stages. Alternatively, clustered data can be visualized in a bandplot. Finally, fluff includes a tool to generate genomic profiles. As command-line tools, the fluff programs can easily be integrated into standard analysis pipelines. The installation is straightforward and documentation is available at http://fluff.readthedocs.org. Availability. fluff is implemented in Python and runs on Linux. The source code is freely available for download at https://github.com/simonvh/fluff. PMID:27547532

Dynamics of magnetic-field-induced clustering in ionic ferrofluids from Raman scattering

NASA Astrophysics Data System (ADS)

Heinrich, D.; Goñi, A. R.; Thomsen, C.

2007-03-01

Using Raman spectroscopy, the authors have investigated the aggregation/disgregation of magnetic nanoparticles in dense ionic ferrofluids (IFF) into clusters due to the action of an inhomogeneous external magnetic field. Evidence for changes in particle density and/or effective cluster size were obtained from the variation of the Raman intensity in a time window from 10sto10min for magnetic fields up to 350mT and at a temperature of 28°C. Clustering sets in already at very low fields (>15mT) and the IFF samples exhibit a clear hysteresis in the Raman spectra after releasing the magnetic field, which lasts for many hours at room temperature. The authors determined the characteristic times of the two competing processes, that of field-induced cluster formation and, at room temperature, that of thermal-activated dissociation, to range from 100to150s.

Bimetallic Ag-Pt Sub-nanometer Supported Clusters as Highly Efficient and Robust Oxidation Catalysts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Negreiros, Fabio R.; Halder, Avik; Yin, Chunrong

A combined experimental and theoretical investigation of Ag-Pt sub-nanometer clusters as heterogeneous catalysts in the CO -> CO2 reaction (COox) is presented. Ag9Pt2 and Ag9Pt3 clusters are size-selected in the gas phase, deposited on an ultrathin amorphous alumina support, and tested as catalysts experimentally under realistic conditions and by first-principles simulations at realistic coverage. Insitu GISAXS/TPRx demonstrates that the clusters do not sinter or deactivate even after prolonged exposure to reactants at high temperature, and present comparable, extremely high COox catalytic efficiency. Such high activity and stability are ascribed to a synergic role of Ag and Pt in ultranano-aggregates, inmore » which Pt anchors the clusters to the support and binds and activates two CO molecules, while Ag binds and activates O-2, and Ag/Pt surface proximity disfavors poisoning by CO or oxidized species.« less

Users matter : multi-agent systems model of high performance computing cluster users.

DOE Office of Scientific and Technical Information (OSTI.GOV)

North, M. J.; Hood, C. S.; Decision and Information Sciences

2005-01-01

High performance computing clusters have been a critical resource for computational science for over a decade and have more recently become integral to large-scale industrial analysis. Despite their well-specified components, the aggregate behavior of clusters is poorly understood. The difficulties arise from complicated interactions between cluster components during operation. These interactions have been studied by many researchers, some of whom have identified the need for holistic multi-scale modeling that simultaneously includes network level, operating system level, process level, and user level behaviors. Each of these levels presents its own modeling challenges, but the user level is the most complex duemore » to the adaptability of human beings. In this vein, there are several major user modeling goals, namely descriptive modeling, predictive modeling and automated weakness discovery. This study shows how multi-agent techniques were used to simulate a large-scale computing cluster at each of these levels.« less

H{sub 2} MOLECULAR CLUSTERS WITH EMBEDDED MOLECULES AND ATOMS AS THE SOURCE OF THE DIFFUSE INTERSTELLAR BANDS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bernstein, L. S.; Clark, F. O.; Lynch, D. K., E-mail: larry@spectral.com, E-mail: dave@thulescientific.com

2013-05-01

We suggest that the diffuse interstellar bands (DIBs) arise from absorption lines of electronic transitions in molecular clusters primarily composed of a single molecule, atom, or ion ({sup s}eed{sup )}, embedded in a single-layer shell of H{sub 2} molecules. Less abundant variants of the cluster, including two seed molecules and/or a two-layer shell of H{sub 2} molecules, may also occur. The lines are broadened, blended, and wavelength-shifted by interactions between the seed and surrounding H{sub 2} shell. We refer to these clusters as contaminated H{sub 2} clusters (CHCs). We show that CHC spectroscopy matches the diversity of observed DIB spectralmore » profiles and provides good fits to several DIB profiles based on a rotational temperature of 10 K. CHCs arise from {approx}centimeter-sized, dirty H{sub 2} ice balls, called contaminated H{sub 2} ice macro-particles (CHIMPs), formed in cold, dense, giant molecular clouds (GMCs), and later released into the interstellar medium (ISM) upon GMC disruption. Attractive interactions, arising from Van der Waals and ion-induced dipole potentials, between the seeds and H{sub 2} molecules enable CHIMPs to attain centimeter-sized dimensions. When an ultraviolet (UV) photon is absorbed in the outer layer of a CHIMP, it heats the icy matrix and expels CHCs into the ISM. While CHCs are quickly destroyed by absorbing UV photons, they are replenished by the slowly eroding CHIMPs. Since CHCs require UV photons for their release, they are most abundant at, but not limited to, the edges of UV-opaque molecular clouds, consistent with the observed, preferred location of DIBs. An inherent property of CHCs, which can be characterized as nanometer size, spinning, dipolar dust grains, is that they emit in the radio-frequency region. We also show that the CHCs offer a natural explanation for the anomalous microwave emission feature in the {approx}10-100 GHz spectral region.« less

Teenage suicide cluster formation and contagion: implications for primary care

PubMed Central

Johansson, Lars; Lindqvist, Per; Eriksson, Anders

2006-01-01

Background We have previously studied unintentional as well as intentional injury deaths among teenagers living in the four northernmost counties, forming approximately 55% of Sweden with 908,000 inhabitants in 1991. During this work, we found what we suspected to be a suicide cluster among teenagers and we also suspected contagion since there were links between these cases. In this present study, we investigate the occurrence of suicide clustering among teenagers, analyze cluster definitions, and suggest preventive measures. Methods A retrospective study of teenager suicides autopsied at the Department of Forensic Medicine in Umeå, Sweden, during 1981 through 2000. Police reports, autopsy protocols, and medical records were studied in all cases, and the police officers that conducted the investigation at the scene were interviewed in all cluster cases. Parents of the suicide victims of the first cluster were also interviewed. Two aggregations of teenager suicides were detected and evaluated as possible suicide clusters using the US Centers for Disease Control definition of a suicide cluster. Results Two clusters including six teenagers were confirmed, and contagion was established within each cluster. Conclusion The general practitioner is identified as a key person in the aftermath of a teenage suicide since the general practitioner often meet the family, friends of the deceased, and other acquaintances early in the process after a suicide. This makes the general practitioner suitable to initiate contacts with others involved in the well-being of the young, in order to prevent suicide cluster formation and para-suicidal activities. PMID:16707009

Radiation damage in cubic ZrO 2 and yttria-stabilized zirconia from molecular dynamics simulations

DOE PAGES

Aidhy, Dilpuneet S.; Zhang, Yanwen; Weber, William J.

2014-11-20

Here, we perform molecular dynamics simulation on cubic ZrO 2 and yttria-stabilized zirconia (YSZ) to elucidate defect cluster formation resulting from radiation damage, and evaluate the impact of Y-dopants. Interstitial clusters composed of split-interstitial building blocks, i.e., Zr-Zr or Y-Zr are formed. Moreover, oxygen vacancies control cation defect migration; in their presence, Zr interstitials aggregate to form split-interstitials whereas in their absence Zr interstitials remain immobile, as isolated single-interstitials. Y-doping prevents interstitial cluster formation due to sequestration of oxygen vacancies.

Coresets vs clustering: comparison of methods for redundancy reduction in very large white matter fiber sets

NASA Astrophysics Data System (ADS)

Alexandroni, Guy; Zimmerman Moreno, Gali; Sochen, Nir; Greenspan, Hayit

2016-03-01

Recent advances in Diffusion Weighted Magnetic Resonance Imaging (DW-MRI) of white matter in conjunction with improved tractography produce impressive reconstructions of White Matter (WM) pathways. These pathways (fiber sets) often contain hundreds of thousands of fibers, or more. In order to make fiber based analysis more practical, the fiber set needs to be preprocessed to eliminate redundancies and to keep only essential representative fibers. In this paper we demonstrate and compare two distinctive frameworks for selecting this reduced set of fibers. The first framework entails pre-clustering the fibers using k-means, followed by Hierarchical Clustering and replacing each cluster with one representative. For the second clustering stage seven distance metrics were evaluated. The second framework is based on an efficient geometric approximation paradigm named coresets. Coresets present a new approach to optimization and have huge success especially in tasks requiring large computation time and/or memory. We propose a modified version of the coresets algorithm, Density Coreset. It is used for extracting the main fibers from dense datasets, leaving a small set that represents the main structures and connectivity of the brain. A novel approach, based on a 3D indicator structure, is used for comparing the frameworks. This comparison was applied to High Angular Resolution Diffusion Imaging (HARDI) scans of 4 healthy individuals. We show that among the clustering based methods, that cosine distance gives the best performance. In comparing the clustering schemes with coresets, Density Coreset method achieves the best performance.

Cross-correlating the γ-ray Sky with Catalogs of Galaxy Clusters

NASA Astrophysics Data System (ADS)

Branchini, Enzo; Camera, Stefano; Cuoco, Alessandro; Fornengo, Nicolao; Regis, Marco; Viel, Matteo; Xia, Jun-Qing

2017-01-01

We report the detection of a cross-correlation signal between Fermi Large Area Telescope diffuse γ-ray maps and catalogs of clusters. In our analysis, we considered three different catalogs: WHL12, redMaPPer, and PlanckSZ. They all show a positive correlation with different amplitudes, related to the average mass of the objects in each catalog, which also sets the catalog bias. The signal detection is confirmed by the results of a stacking analysis. The cross-correlation signal extends to rather large angular scales, around 1°, that correspond, at the typical redshift of the clusters in these catalogs, to a few to tens of megaparsecs, I.e., the typical scale-length of the large-scale structures in the universe. Most likely this signal is contributed by the cumulative emission from active galactic nuclei (AGNs) associated with the filamentary structures that converge toward the high peaks of the matter density field in which galaxy clusters reside. In addition, our analysis reveals the presence of a second component, more compact in size and compatible with a point-like emission from within individual clusters. At present, we cannot distinguish between the two most likely interpretations for such a signal, I.e., whether it is produced by AGNs inside clusters or if it is a diffuse γ-ray emission from the intracluster medium. We argue that this latter, intriguing, hypothesis might be tested by applying this technique to a low-redshift large-mass cluster sample.

Diffuse Optical Light in Galaxy Clusters. I. Abell 3888

NASA Astrophysics Data System (ADS)

Krick, J. E.; Bernstein, R. A.; Pimbblet, K. A.

2006-01-01

We are undertaking a program to measure the characteristics of the intracluster light (ICL; total flux, profile, color, and substructure) in a sample of 10 galaxy clusters with a range of cluster mass, morphology, and redshift. We present here the methods and results for the first cluster in that sample, A3888. We have identified an ICL component in A3888 in V and r that contains 13%+/-5% of the total cluster light and extends to 700 h-170 kpc (~0.3r200) from the center of the cluster. The ICL color in our smallest radial bin is V-r=0.3+/-0.1, similar to the central cluster elliptical galaxies. The ICL is redder than the galaxies at 400 h-170 kpc1) with a high-metallicity (1.0 Zsolar

Wave failure at strong coupling in intracellular C a2 + signaling system with clustered channels

NASA Astrophysics Data System (ADS)

Li, Xiang; Wu, Yuning; Gao, Xuejuan; Cai, Meichun; Shuai, Jianwei

2018-01-01

As an important intracellular signal, C a2 + ions control diverse cellular functions. In this paper, we discuss the C a2 + signaling with a two-dimensional model in which the inositol 1,4,5-trisphosphate (I P3 ) receptor channels are distributed in clusters on the endoplasmic reticulum membrane. The wave failure at large C a2 + diffusion coupling is discussed in detail in the model. We show that with varying model parameters the wave failure is a robust behavior with either deterministic or stochastic channel dynamics. We suggest that the wave failure should be a general behavior in inhomogeneous diffusing systems with clustered excitable regions and may occur in biological C a2 + signaling systems.

Dynamics and cluster formation in charged and uncharged Ficoll70 solutions

NASA Astrophysics Data System (ADS)

Palit, Swomitra; Yethiraj, Anand

2017-08-01

We apply pulsed-field-gradient NMR (PFG NMR) technique to measure the translational diffusion for both uncharged and charged polysaccharide (Ficoll70) in water. Analysis of the data indicates that the NMR signal attenuation above a certain packing fraction can be adequately fitted with a bi-exponential function. The self-diffusion measurements also show that the Ficoll70, an often-used compact, spherical polysucrose molecule, is itself nonideal, exhibiting signs of both softness and attractive interactions in the form of a stable suspension consisting of monomers and clusters. Further, we can quantify the fraction of monomers and clusters. This work strengthens the picture of the existence of a bound water layer within and around a porous Ficoll70 particle.

Study on the thermal resistance in secondary particles chain of silica aerogel by molecular dynamics simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, M.; Department of Physics, University of Chinese Academy of Sciences, Beijing 100049; Qiu, L., E-mail: qiulin111@sina.com, E-mail: jzzhengxinghua@163.com

2014-09-07

In this article, molecular dynamics simulation was performed to study the heat transport in secondary particles chain of silica aerogel. The two adjacent particles as the basic heat transport unit were modelled to characterize the heat transfer through the calculation of thermal resistance and vibrational density of states (VDOS). The total thermal resistance of two contact particles was predicted by non-equilibrium molecular dynamics simulations (NEMD). The defects were formed by deleting atoms in the system randomly first and performing heating and quenching process afterwards to achieve the DLCA (diffusive limited cluster-cluster aggregation) process. This kind of treatment showed a verymore » reasonable prediction of thermal conductivity for the silica aerogels compared with the experimental values. The heat transport was great suppressed as the contact length increased or defect concentration increased. The constrain effect of heat transport was much significant when contact length fraction was in the small range (<0.5) or the defect concentration is in the high range (>0.5). Also, as the contact length increased, the role of joint thermal resistance played in the constraint of heat transport was increasing. However, the defect concentration did not affect the share of joint thermal resistance as the contact length did. VDOS of the system was calculated by numerical method to characterize the heat transport from atomic vibration view. The smaller contact length and greater defect concentration primarily affected the longitudinal acoustic modes, which ultimately influenced the heat transport between the adjacent particles.« less

Non-invasive quantification of tumour heterogeneity in water diffusivity to differentiate malignant from benign tissues of urinary bladder: a phase I study.

PubMed

Nguyen, Huyen T; Shah, Zarine K; Mortazavi, Amir; Pohar, Kamal S; Wei, Lai; Jia, Guang; Zynger, Debra L; Knopp, Michael V

2017-05-01

To quantify the heterogeneity of the tumour apparent diffusion coefficient (ADC) using voxel-based analysis to differentiate malignancy from benign wall thickening of the urinary bladder. Nineteen patients with histopathological findings of their cystectomy specimen were included. A data set of voxel-based ADC values was acquired for each patient's lesion. Histogram analysis was performed on each data set to calculate uniformity (U) and entropy (E). The k-means clustering of the voxel-wised ADC data set was implemented to measure mean intra-cluster distance (MICD) and largest inter-cluster distance (LICD). Subsequently, U, E, MICD, and LICD for malignant tumours were compared with those for benign lesions using a two-sample t-test. Eleven patients had pathological confirmation of malignancy and eight with benign wall thickening. Histogram analysis showed that malignant tumours had a significantly higher degree of ADC heterogeneity with lower U (P = 0.016) and higher E (P = 0.005) than benign lesions. In agreement with these findings, k-means clustering of voxel-wise ADC indicated that bladder malignancy presented with significantly higher MICD (P < 0.001) and higher LICD (P = 0.002) than benign wall thickening. The quantitative assessment of tumour diffusion heterogeneity using voxel-based ADC analysis has the potential to become a non-invasive tool to distinguish malignant from benign tissues of urinary bladder cancer. • Heterogeneity is an intrinsic characteristic of tumoral tissue. • Non-invasive quantification of tumour heterogeneity can provide adjunctive information to improve cancer diagnosis accuracy. • Histogram analysis and k-means clustering can quantify tumour diffusion heterogeneity. • The quantification helps differentiate malignant from benign urinary bladder tissue.

On the Analysis of Case-Control Studies in Cluster-correlated Data Settings.

PubMed

Haneuse, Sebastien; Rivera-Rodriguez, Claudia

2018-01-01

In resource-limited settings, long-term evaluation of national antiretroviral treatment (ART) programs often relies on aggregated data, the analysis of which may be subject to ecological bias. As researchers and policy makers consider evaluating individual-level outcomes such as treatment adherence or mortality, the well-known case-control design is appealing in that it provides efficiency gains over random sampling. In the context that motivates this article, valid estimation and inference requires acknowledging any clustering, although, to our knowledge, no statistical methods have been published for the analysis of case-control data for which the underlying population exhibits clustering. Furthermore, in the specific context of an ongoing collaboration in Malawi, rather than performing case-control sampling across all clinics, case-control sampling within clinics has been suggested as a more practical strategy. To our knowledge, although similar outcome-dependent sampling schemes have been described in the literature, a case-control design specific to correlated data settings is new. In this article, we describe this design, discuss balanced versus unbalanced sampling techniques, and provide a general approach to analyzing case-control studies in cluster-correlated settings based on inverse probability-weighted generalized estimating equations. Inference is based on a robust sandwich estimator with correlation parameters estimated to ensure appropriate accounting of the outcome-dependent sampling scheme. We conduct comprehensive simulations, based in part on real data on a sample of N = 78,155 program registrants in Malawi between 2005 and 2007, to evaluate small-sample operating characteristics and potential trade-offs associated with standard case-control sampling or when case-control sampling is performed within clusters.

Coronal Mass Ejection Data Clustering and Visualization of Decision Trees

NASA Astrophysics Data System (ADS)

Ma, Ruizhe; Angryk, Rafal A.; Riley, Pete; Filali Boubrahimi, Soukaina

2018-05-01

Coronal mass ejections (CMEs) can be categorized as either “magnetic clouds” (MCs) or non-MCs. Features such as a large magnetic field, low plasma-beta, and low proton temperature suggest that a CME event is also an MC event; however, so far there is neither a definitive method nor an automatic process to distinguish the two. Human labeling is time-consuming, and results can fluctuate owing to the imprecise definition of such events. In this study, we approach the problem of MC and non-MC distinction from a time series data analysis perspective and show how clustering can shed some light on this problem. Although many algorithms exist for traditional data clustering in the Euclidean space, they are not well suited for time series data. Problems such as inadequate distance measure, inaccurate cluster center description, and lack of intuitive cluster representations need to be addressed for effective time series clustering. Our data analysis in this work is twofold: clustering and visualization. For clustering we compared the results from the popular hierarchical agglomerative clustering technique to a distance density clustering heuristic we developed previously for time series data clustering. In both cases, dynamic time warping will be used for similarity measure. For classification as well as visualization, we use decision trees to aggregate single-dimensional clustering results to form a multidimensional time series decision tree, with averaged time series to present each decision. In this study, we achieved modest accuracy and, more importantly, an intuitive interpretation of how different parameters contribute to an MC event.

Paramagnetic Attraction of Impurity-Helium Solids

NASA Technical Reports Server (NTRS)

Bernard, E. P.; Boltnev, R. E.; Khmelenko, V. V.; Lee, D. M.

2003-01-01

Impurity-helium solids are formed when a mixture of impurity and helium gases enters a volume of superfluid helium. Typical choices of impurity gas are hydrogen deuteride, deuterium, nitrogen, neon and argon, or a mixture of these. These solids consist of individual impurity atoms and molecules as well as clusters of impurity atoms and molecules covered with layers of solidified helium. The clusters have an imperfect crystalline structure and diameters ranging up to 90 angstroms, depending somewhat on the choice of impurity. Immediately following formation the clusters aggregate into loosely connected porous solids that are submerged in and completely permeated by the liquid helium. Im-He solids are extremely effective at stabilizing high concentrations of free radicals, which can be introduced by applying a high power RF dis- charge to the impurity gas mixture just before it strikes the super fluid helium. Average concentrations of 10(exp 19) nitrogen atoms/cc and 5 x 10(exp 18) deuterium atoms/cc can be achieved this way. It shows a typical sample formed from a mixture of atomic and molecular hydrogen and deuterium. It shows typical sample formed from atomic and molecular nitrogen. Much of the stability of Im-He solids is attributed to their very large surface area to volume ratio and their permeation by super fluid helium. Heat resulting from a chance meeting and recombination of free radicals is quickly dissipated by the super fluid helium instead of thermally promoting the diffusion of other nearby free radicals.

LIGHT SCATTERING BY FRACTAL DUST AGGREGATES. I. ANGULAR DEPENDENCE OF SCATTERING

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tazaki, Ryo; Tanaka, Hidekazu; Okuzumi, Satoshi

2016-06-01

In protoplanetary disks, micron-sized dust grains coagulate to form highly porous dust aggregates. Because the optical properties of these aggregates are not completely understood, it is important to investigate how porous dust aggregates scatter light. In this study, the light scattering properties of porous dust aggregates were calculated using a rigorous method, the T -matrix method, and the results were then compared with those obtained using the Rayleigh–Gans–Debye (RGD) theory and Mie theory with the effective medium approximation (EMT). The RGD theory is applicable to moderately large aggregates made of nearly transparent monomers. This study considered two types of porousmore » dust aggregates—ballistic cluster–cluster agglomerates (BCCAs) and ballistic particle–cluster agglomerates. First, the angular dependence of the scattered intensity was shown to reflect the hierarchical structure of dust aggregates; the large-scale structure of the aggregates is responsible for the intensity at small scattering angles, and their small-scale structure determines the intensity at large scattering angles. Second, it was determined that the EMT underestimates the backward scattering intensity by multiple orders of magnitude, especially in BCCAs, because the EMT averages the structure within the size of the aggregates. It was concluded that the RGD theory is a very useful method for calculating the optical properties of BCCAs.« less

The case for electron re-acceleration at galaxy cluster shocks

NASA Astrophysics Data System (ADS)

van Weeren, Reinout J.; Andrade-Santos, Felipe; Dawson, William A.; Golovich, Nathan; Lal, Dharam V.; Kang, Hyesung; Ryu, Dongsu; Brìggen, Marcus; Ogrean, Georgiana A.; Forman, William R.; Jones, Christine; Placco, Vinicius M.; Santucci, Rafael M.; Wittman, David; Jee, M. James; Kraft, Ralph P.; Sobral, David; Stroe, Andra; Fogarty, Kevin

2017-01-01

On the largest scales, the Universe consists of voids and filaments making up the cosmic web. Galaxy clusters are located at the knots in this web, at the intersection of filaments. Clusters grow through accretion from these large-scale filaments and by mergers with other clusters and groups. In a growing number of galaxy clusters, elongated Mpc-sized radio sources have been found1,2 . Also known as radio relics, these regions of diffuse radio emission are thought to trace relativistic electrons in the intracluster plasma accelerated by low-Mach-number shocks generated by cluster-cluster merger events 3 . A long-standing problem is how low-Mach-number shocks can accelerate electrons so efficiently to explain the observed radio relics. Here, we report the discovery of a direct connection between a radio relic and a radio galaxy in the merging galaxy cluster Abell 3411-3412 by combining radio, X-ray and optical observations. This discovery indicates that fossil relativistic electrons from active galactic nuclei are re-accelerated at cluster shocks. It also implies that radio galaxies play an important role in governing the non-thermal component of the intracluster medium in merging clusters.