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

EPA Science Inventory

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

Efficient Agent-Based Models for Non-Genomic Evolution

NASA Technical Reports Server (NTRS)

Gupta, Nachi; Agogino, Adrian; Tumer, Kagan

2006-01-01

Modeling dynamical systems composed of aggregations of primitive proteins is critical to the field of astrobiological science involving early evolutionary structures and the origins of life. Unfortunately traditional non-multi-agent methods either require oversimplified models or are slow to converge to adequate solutions. This paper shows how to address these deficiencies by modeling the protein aggregations through a utility based multi-agent system. In this method each agent controls the properties of a set of proteins assigned to that agent. Some of these properties determine the dynamics of the system, such as the ability for some proteins to join or split other proteins, while additional properties determine the aggregation s fitness as a viable primitive cell. We show that over a wide range of starting conditions, there are mechanisins that allow protein aggregations to achieve high values of overall fitness. In addition through the use of agent-specific utilities that remain aligned with the overall global utility, we are able to reach these conclusions with 50 times fewer learning steps.

A cell-based assay for aggregation inhibitors as therapeutics of polyglutamine-repeat disease and validation in Drosophila

NASA Astrophysics Data System (ADS)

Apostol, Barbara L.; Kazantsev, Alexsey; Raffioni, Simona; Illes, Katalin; Pallos, Judit; Bodai, Laszlo; Slepko, Natalia; Bear, James E.; Gertler, Frank B.; Hersch, Steven; Housman, David E.; Marsh, J. Lawrence; Michels Thompson, Leslie

2003-05-01

The formation of polyglutamine-containing aggregates and inclusions are hallmarks of pathogenesis in Huntington's disease that can be recapitulated in model systems. Although the contribution of inclusions to pathogenesis is unclear, cell-based assays can be used to screen for chemical compounds that affect aggregation and may provide therapeutic benefit. We have developed inducible PC12 cell-culture models to screen for loss of visible aggregates. To test the validity of this approach, compounds that inhibit aggregation in the PC12 cell-based screen were tested in a Drosophila model of polyglutamine-repeat disease. The disruption of aggregation in PC12 cells strongly correlates with suppression of neuronal degeneration in Drosophila. Thus, the engineered PC12 cells coupled with the Drosophila model provide a rapid and effective method to screen and validate compounds.

Three-dimensional Myoblast Aggregates--Effects of Modeled Microgravity

NASA Technical Reports Server (NTRS)

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

2006-01-01

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

Simulating Fiber Ordering and Aggregation In Shear Flow Using Dissipative Particle Dynamics

NASA Astrophysics Data System (ADS)

Stimatze, Justin T.

We have developed a mesoscale simulation of fiber aggregation in shear flow using LAMMPS and its implementation of dissipative particle dynamics. Understanding fiber aggregation in shear flow and flow-induced microstructural fiber networks is critical to our interest in high-performance composite materials. Dissipative particle dynamics enables the consideration of hydrodynamic interactions between fibers through the coarse-grained simulation of the matrix fluid. Correctly simulating hydrodynamic interactions and accounting for fluid forces on the microstructure is required to correctly model the shear-induced aggregation process. We are able to determine stresses, viscosity, and fiber forces while simulating the evolution of a model fiber system undergoing shear flow. Fiber-fiber contact interactions are approximated by combinations of common pairwise forces, allowing the exploration of interaction-influenced fiber behaviors such as aggregation and bundling. We are then able to quantify aggregate structure and effective volume fraction for a range of relevant system and fiber-fiber interaction parameters. Our simulations have demonstrated several aggregate types dependent on system parameters such as shear rate, short-range attractive forces, and a resistance to relative rotation while in contact. A resistance to relative rotation at fiber-fiber contact points has been found to strongly contribute to an increased angle between neighboring aggregated fibers and therefore an increase in average aggregate volume fraction. This increase in aggregate volume fraction is strongly correlated with a significant enhancement of system viscosity, leading us to hypothesize that controlling the resistance to relative rotation during manufacturing processes is important when optimizing for desired composite material characteristics.

Monosized aggregates -- A new model

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

Gopal, M.

1997-08-01

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

Island size distribution with hindered aggregation

NASA Astrophysics Data System (ADS)

González, Diego Luis; Camargo, Manuel; Sánchez, Julián A.

2018-05-01

We study the effect of hindered aggregation on the island formation processes for a one-dimensional model of epitaxial growth with arbitrary nucleus size i . In the proposed model, the attachment of monomers to islands is hindered by an aggregation barrier, ɛa, which decreases the hopping rate of monomers to the islands. As ɛa increases, the system exhibits a crossover between two different regimes; namely, from diffusion-limited aggregation to attachment-limited aggregation. The island size distribution, P (s ) , is calculated for different values of ɛa by a self-consistent approach involving the nucleation and aggregation capture kernels. The results given by the analytical model are compared with those from kinetic Monte Carlo simulations, finding a close agreement between both sets of data for all considered values of i and ɛa. As the aggregation barrier increases, the spatial effect of fluctuations on the density of monomers can be neglected and P (s ) smoothly approximates to the limit distribution P (s ) =δs ,i +1 . In the crossover regime the system features a complex and rich behavior, which can be explained in terms of the characteristic timescales of different microscopic processes.

A phase field approach for multicellular aggregate fusion in biofabrication.

PubMed

Yang, Xiaofeng; Sun, Yi; Wang, Qi

2013-07-01

We present a modeling and computational approach to study fusion of multicellular aggregates during tissue and organ fabrication, which forms the foundation for the scaffold-less biofabrication of tissues and organs known as bioprinting. It is known as the phase field method, where multicellular aggregates are modeled as mixtures of multiphase complex fluids whose phase mixing or separation is governed by interphase force interactions, mimicking the cell-cell interaction in the multicellular aggregates, and intermediate range interaction mediated by the surrounding hydrogel. The material transport in the mixture is dictated by hydrodynamics as well as forces due to the interphase interactions. In a multicellular aggregate system with fixed number of cells and fixed amount of the hydrogel medium, the effect of cell differentiation, proliferation, and death are neglected in the current model, which can be readily included in the model, and the interaction between different components is dictated by the interaction energy between cell and cell as well as between cell and medium particles, respectively. The modeling approach is applicable to transient simulations of fusion of cellular aggregate systems at the time and length scale appropriate to biofabrication. Numerical experiments are presented to demonstrate fusion and cell sorting during tissue and organ maturation processes in biofabrication.

The aggregate timberland assessment system—ATLAS: a comprehensive timber projection model.

Treesearch

J.R. Mills; J.C. Kincaid

1992-01-01

The aggregate timberland assessment system is a time-based deterministic timber projection model. It was developed by the USDA Forest Service to address broad policy questions related to future timber supplies for the 1989 Renewable Resources Planning Act timber assessment. An open framework design allows for customizing inputs to account for regional and subregional...

Influence of polysaccharides on wine protein aggregation.

PubMed

Jaeckels, Nadine; Meier, Miriam; Dietrich, Helmut; Will, Frank; Decker, Heinz; Fronk, Petra

2016-06-01

Polysaccharides are the major high-molecular weight components of wines. In contrast, proteins occur only in small amounts in wine, but contribute to haze formation. The detailed mechanism of aggregation of these proteins, especially in combination with other wine components, remains unclear. This study demonstrates the different aggregation behavior between a buffer and a model wine system by dynamic light scattering. Arabinogalactan-protein, for example, shows an increased aggregation in the model wine system, while in the buffer system a reducing effect is observed. Thus, we could show the importance to examine the behavior of wine additives under conditions close to reality, instead of simpler buffer systems. Additional experiments on melting points of wine proteins reveal that only some isoforms of thaumatin-like proteins and chitinases are involved in haze formation. We can confirm interactions between polysaccharides and proteins, but none of these polysaccharides is able to prevent haze in wine. Copyright © 2016. Published by Elsevier Ltd.

INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY: Aggregation Behaviors of a Two-Species System with Lose-Lose Interactions

NASA Astrophysics Data System (ADS)

Song, Mei-Xia; Lin, Zhen-Quan; Li, Xiao-Dong; Ke, Jian-Hong

2010-06-01

We propose an aggregation evolution model of two-species (A- and B-species) aggregates to study the prevalent aggregation phenomena in social and economic systems. In this model, A- and B-species aggregates perform self-exchange-driven growths with the exchange rate kernels K (k,l) = Kkl and L(k,l) = Lkl, respectively, and the two species aggregates perform self-birth processes with the rate kernels J1(k) = J1k and J2(k) = J2k, and meanwhile the interaction between the aggregates of different species A and B causes a lose-lose scheme with the rate kernel H(k,l) = Hkl. Based on the mean-field theory, we investigated the evolution behaviors of the two species aggregates to study the competitions among above three aggregate evolution schemes on the distinct initial monomer concentrations A0 and B0 of the two species. The results show that the evolution behaviors of A- and B-species are crucially dominated by the competition between the two self-birth processes, and the initial monomer concentrations A0 and B0 play important roles, while the lose-lose scheme play important roles in some special cases.

INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY: Competition Between Self-birth and Catalyzed Death in Aggregation Growth with Catalysis Injection

NASA Astrophysics Data System (ADS)

Chen, Dan; Lin, Zhen-Quan; Sun, Yun-Fei; Ke, Jian-Hong

2009-12-01

We propose two irreversible aggregation growth models of aggregates of two distinct species (A and B) to study the interactions between virus aggregates and medicine efficacy aggregates in the virus-medicine cooperative evolution system. The A-species aggregates evolve driven by self monomer birth and B-species aggregate-catalyzed monomer death in model I and by self birth, catalyzed death, and self monomer exchange reactions in model II, while the catalyst B-species aggregates are assumed to be injected into the system sustainedly or at a periodic time-dependent rate. The kinetic behaviors of the A-species aggregates are investigated by the rate equation approach based on the mean-field theory with the self birth rate kernel IA(k) = Ik, catalyzed death rate kernel JAB(k) = Jk and self exchange rate kernel KA (k, l) = Kkl. The kinetic behaviors of the A-species aggregates are mainly dominated by the competition between the two effects of the self birth (with the effective rate I) and the catalyzed death (with the effective rate JB0), while the effects of the self exchanges of the A-species aggregates which appear in an effective rate KA0 play important roles in the cases of I > JB0 and I = JB0. The evolution behaviors of the total mass MA1(t) and the total aggregate number MA0 (t) are obtained, and the aggregate size distribution αk (t) of species A is found to approach a generalized scaling form in the case of I >= JB0 and a special modified scaling form in the case of I < JB0. The periodical evolution of the B-monomers concentration plays an exponential form of the periodic modulation.

Ultrafast exciton migration in an HJ-aggregate: Potential surfaces and quantum dynamics

NASA Astrophysics Data System (ADS)

Binder, Robert; Polkehn, Matthias; Ma, Tianji; Burghardt, Irene

2017-01-01

Quantum dynamical and electronic structure calculations are combined to investigate the mechanism of exciton migration in an oligothiophene HJ aggregate, i.e., a combination of oligomer chains (J-type aggregates) and stacked aggregates of such chains (H-type aggregates). To this end, a Frenkel exciton model is parametrized by a recently introduced procedure [Binder et al., J. Chem. Phys. 141, 014101 (2014)] which uses oligomer excited-state calculations to perform an exact, point-wise mapping of coupled potential energy surfaces to an effective Frenkel model. Based upon this parametrization, the Multi-Layer Multi-Configuration Time-Dependent Hartree (ML-MCTDH) method is employed to investigate ultrafast dynamics of exciton transfer in a small, asymmetric HJ aggregate model composed of 30 sites and 30 active modes. For a partially delocalized initial condition, it is shown that a torsional defect confines the trapped initial exciton, and planarization induces an ultrafast resonant transition between an HJ-aggregated segment and a covalently bound "dangling chain" end. This model is a minimal realization of experimentally investigated mixed systems exhibiting ultrafast exciton transfer between aggregated, highly planarized chains and neighboring disordered segments.

Aggregation Trade Offs in Family Based Recommendations

NASA Astrophysics Data System (ADS)

Berkovsky, Shlomo; Freyne, Jill; Coombe, Mac

Personalized information access tools are frequently based on collaborative filtering recommendation algorithms. Collaborative filtering recommender systems typically suffer from a data sparsity problem, where systems do not have sufficient user data to generate accurate and reliable predictions. Prior research suggested using group-based user data in the collaborative filtering recommendation process to generate group-based predictions and partially resolve the sparsity problem. Although group recommendations are less accurate than personalized recommendations, they are more accurate than general non-personalized recommendations, which are the natural fall back when personalized recommendations cannot be generated. In this work we present initial results of a study that exploits the browsing logs of real families of users gathered in an eHealth portal. The browsing logs allowed us to experimentally compare the accuracy of two group-based recommendation strategies: aggregated group models and aggregated predictions. Our results showed that aggregating individual models into group models resulted in more accurate predictions than aggregating individual predictions into group predictions.

Persistent homology analysis of ion aggregations and hydrogen-bonding networks.

PubMed

Xia, Kelin

2018-05-16

Despite the great advancement of experimental tools and theoretical models, a quantitative characterization of the microscopic structures of ion aggregates and their associated water hydrogen-bonding networks still remains a challenging problem. In this paper, a newly-invented mathematical method called persistent homology is introduced, for the first time, to quantitatively analyze the intrinsic topological properties of ion aggregation systems and hydrogen-bonding networks. The two most distinguishable properties of persistent homology analysis of assembly systems are as follows. First, it does not require a predefined bond length to construct the ion or hydrogen-bonding network. Persistent homology results are determined by the morphological structure of the data only. Second, it can directly measure the size of circles or holes in ion aggregates and hydrogen-bonding networks. To validate our model, we consider two well-studied systems, i.e., NaCl and KSCN solutions, generated from molecular dynamics simulations. They are believed to represent two morphological types of aggregation, i.e., local clusters and extended ion networks. It has been found that the two aggregation types have distinguishable topological features and can be characterized by our topological model very well. Further, we construct two types of networks, i.e., O-networks and H2O-networks, for analyzing the topological properties of hydrogen-bonding networks. It is found that for both models, KSCN systems demonstrate much more dramatic variations in their local circle structures with a concentration increase. A consistent increase of large-sized local circle structures is observed and the sizes of these circles become more and more diverse. In contrast, NaCl systems show no obvious increase of large-sized circles. Instead a consistent decline of the average size of the circle structures is observed and the sizes of these circles become more and more uniform with a concentration increase. As far as we know, these unique intrinsic topological features in ion aggregation systems have never been pointed out before. More importantly, our models can be directly used to quantitatively analyze the intrinsic topological invariants, including circles, loops, holes, and cavities, of any network-like structures, such as nanomaterials, colloidal systems, biomolecular assemblies, among others. These topological invariants cannot be described by traditional graph and network models.

H-aggregate analysis of P3HT thin films-Capability and limitation of photoluminescence and UV/Vis spectroscopy.

PubMed

Ehrenreich, Philipp; Birkhold, Susanne T; Zimmermann, Eugen; Hu, Hao; Kim, Kwang-Dae; Weickert, Jonas; Pfadler, Thomas; Schmidt-Mende, Lukas

2016-09-01

Polymer morphology and aggregation play an essential role for efficient charge carrier transport and charge separation in polymer-based electronic devices. It is a common method to apply the H-aggregate model to UV/Vis or photoluminescence spectra in order to analyze polymer aggregation. In this work we present strategies to obtain reliable and conclusive information on polymer aggregation and morphology based on the application of an H-aggregate analysis on UV/Vis and photoluminescence spectra. We demonstrate, with P3HT as model system, that thickness dependent reflection behavior can lead to misinterpretation of UV/Vis spectra within the H-aggregate model. Values for the exciton bandwidth can deviate by a factor of two for polymer thicknesses below 150 nm. In contrast, photoluminescence spectra are found to be a reliable basis for characterization of polymer aggregation due to their weaker dependence on the wavelength dependent refractive index of the polymer. We demonstrate this by studying the influence of surface characteristics on polymer aggregation for spin-coated thin-films that are commonly used in organic and hybrid solar cells.

Relaxation times and modes of disturbed aggregate distribution in micellar solutions with fusion and fission of micelles

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

Zakharov, Anatoly I.; Adzhemyan, Loran Ts.; Shchekin, Alexander K., E-mail: akshch@list.ru

2015-09-28

We have performed direct numerical calculations of the kinetics of relaxation in the system of surfactant spherical micelles under joint action of the molecular mechanism with capture and emission of individual surfactant molecules by molecular aggregates and the mechanism of fusion and fission of the aggregates. As a basis, we have taken the difference equations of aggregation and fragmentation in the form of the generalized kinetic Smoluchowski equations for aggregate concentrations. The calculations have been made with using the droplet model of molecular surfactant aggregates and two modified Smoluchowski models for the coefficients of aggregate-monomer and aggregate-aggregate fusions which takemore » into account the effects of the aggregate size and presence of hydrophobic spots on the aggregate surface. A full set of relaxation times and corresponding relaxation modes for nonequilibrium aggregate distribution in the aggregation number has been found. The dependencies of these relaxation times and modes on the total concentration of surfactant in the solution and the special parameter controlling the probability of fusion in collisions of micelles with other micelles have been studied.« less

How the morphology of dusts influences packing density in small solar system bodies

NASA Astrophysics Data System (ADS)

Zangmeister, C.; Radney, J. G.; Zachariah, M. R.

2014-12-01

Large planetary seedlings, comets, and nanoscale soot particles are made from rigid, aggregated subunits that are compacted under low compression into larger structures spanning over 10 orders of magnitude in dimensional space. Here, we demonstrate that the packing density (Φf) of compacted rigid aggregates is independent of spatial scale for systems under weak compaction, a regime that includes small solar system bodies. The Φf of rigid aggregated structures across 6 orders of magnitude were measured using nanoscale spherical soot aerosol composed of aggregates with ≈ 17 nm monomeric subunits and aggregates made from uniform monomeric 6 mm spherical subunits at the macroscale. We find Φf = 0.36 ± 0.02 at both the nano- and macroscale. These values are remarkably similar to qf observed for comet nuclei and measured values of other rigid aggregated systems across a wide variety of spatial and formative conditions. We present a packing model that incorporates the aggregate morphology and show that Φf is independent of both monomer and aggregate size. These observations suggest thatqf of rigid aggregates is independent of spatial dimension across varied formative conditions ranging from interstellar space to pharmaceutical manufacturing.

Common Cause Failure Modeling: Aerospace Versus Nuclear

NASA Technical Reports Server (NTRS)

Stott, James E.; Britton, Paul; Ring, Robert W.; Hark, Frank; Hatfield, G. Spencer

2010-01-01

Aggregate nuclear plant failure data is used to produce generic common-cause factors that are specifically for use in the common-cause failure models of NUREG/CR-5485. Furthermore, the models presented in NUREG/CR-5485 are specifically designed to incorporate two significantly distinct assumptions about the methods of surveillance testing from whence this aggregate failure data came. What are the implications of using these NUREG generic factors to model the common-cause failures of aerospace systems? Herein, the implications of using the NUREG generic factors in the modeling of aerospace systems are investigated in detail and strong recommendations for modeling the common-cause failures of aerospace systems are given.

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.

Dynamic properties of polydisperse colloidal particles in the presence of thermal gradient studied by a modified Brownian dynamic model

NASA Astrophysics Data System (ADS)

Song, Dongxing; Jin, Hui; Jing, Dengwei; Wang, Xin

2018-03-01

Aggregation and migration of colloidal particles under the thermal gradient widely exists in nature and many industrial processes. In this study, dynamic properties of polydisperse colloidal particles in the presence of thermal gradient were studied by a modified Brownian dynamic model. Other than the traditional forces on colloidal particles, including Brownian force, hydrodynamic force, and electrostatic force from other particles, the electrostatic force from the asymmetric ionic diffusion layer under a thermal gradient has been considered and introduced into the Brownian dynamic model. The aggregation ratio of particles (R A), the balance time (t B) indicating the time threshold when {{R}A} becomes constant, the porosity ({{P}BA} ), fractal dimension (D f) and distributions of concentration (DISC) and aggregation (DISA) for the aggregated particles were discussed based on this model. The aggregated structures formed by polydisperse particles are less dense and the particles therein are loosely bonded. Also it showed a quite large compressibility as the increases of concentration and interparticle potential can significantly increase the fractal dimension. The thermal gradient can induce two competitive factors leading to a two-stage migration of particles. When t<{{t}B} , the unsynchronized aggregation is dominant and the particles slightly migrate along the thermal gradient. When t>{{t}B} , the thermophoresis becomes dominant thus the migrations of particles are against the thermal gradient. The effect of thermophoresis on the aggregate structures was found to be similar to the effect of increasing particle concentration. This study demonstrates how the thermal gradient affects the aggregation of monodisperse and polydisperse particles and can be a guide for the biomimetics and precise control of colloid system under the thermal gradient. Moreover, our model can be easily extended to other more complex colloidal systems considering shear, temperature fluctuation, surfactant, etc.

Boundary-layer diabatic processes, the virtual effect, and convective self-aggregation

NASA Astrophysics Data System (ADS)

Yang, D.

2017-12-01

The atmosphere can self-organize into long-lasting large-scale overturning circulations over an ocean surface with uniform temperature. This phenomenon is referred to as convective self-aggregation and has been argued to be important for tropical weather and climate systems. Here we use a 1D shallow water model and a 2D cloud-resolving model (CRM) to show that boundary-layer diabatic processes are essential for convective self-aggregation. We will show that boundary-layer radiative cooling, convective heating, and surface buoyancy flux help convection self-aggregate because they generate available potential energy (APE), which sustains the overturning circulation. We will also show that evaporative cooling in the boundary layer (cold pool) inhibits convective self-aggregation by reducing APE. Both the shallow water model and CRM results suggest that the enhanced virtual effect of water vapor can lead to convective self-aggregation, and this effect is mainly in the boundary layer. This study proposes new dynamical feedbacks for convective self-aggregation and complements current studies that focus on thermodynamic feedbacks.

Fragmentation approach to the point-island model with hindered aggregation: Accessing the barrier energy

NASA Astrophysics Data System (ADS)

González, Diego Luis; Pimpinelli, Alberto; Einstein, T. L.

2017-07-01

We study the effect of hindered aggregation on the island formation process in a one- (1D) and two-dimensional (2D) point-island model for epitaxial growth with arbitrary critical nucleus size i . In our model, the attachment of monomers to preexisting islands is hindered by an additional attachment barrier, characterized by length la. For la=0 the islands behave as perfect sinks while for la→∞ they behave as reflecting boundaries. For intermediate values of la, the system exhibits a crossover between two different kinds of processes, diffusion-limited aggregation and attachment-limited aggregation. We calculate the growth exponents of the density of islands and monomers for the low coverage and aggregation regimes. The capture-zone (CZ) distributions are also calculated for different values of i and la. In order to obtain a good spatial description of the nucleation process, we propose a fragmentation model, which is based on an approximate description of nucleation inside of the gaps for 1D and the CZs for 2D. In both cases, the nucleation is described by using two different physically rooted probabilities, which are related with the microscopic parameters of the model (i and la). We test our analytical model with extensive numerical simulations and previously established results. The proposed model describes excellently the statistical behavior of the system for arbitrary values of la and i =1 , 2, and 3.

RCCS bioreactor-based modelled microgravity induces significant changes on in vitro 3D neuroglial cell cultures.

PubMed

Morabito, Caterina; Steimberg, Nathalie; Mazzoleni, Giovanna; Guarnieri, Simone; Fanò-Illic, Giorgio; Mariggiò, Maria A

2015-01-01

We propose a human-derived neuro-/glial cell three-dimensional in vitro model to investigate the effects of microgravity on cell-cell interactions. A rotary cell-culture system (RCCS) bioreactor was used to generate a modelled microgravity environment, and morphofunctional features of glial-like GL15 and neuronal-like SH-SY5Y cells in three-dimensional individual cultures (monotypic aggregates) and cocultures (heterotypic aggregates) were analysed. Cell survival was maintained within all cell aggregates over 2 weeks of culture. Moreover, compared to cells as traditional static monolayers, cell aggregates cultured under modelled microgravity showed increased expression of specific differentiation markers (e.g., GL15 cells: GFAP, S100B; SH-SY5Y cells: GAP43) and modulation of functional cell-cell interactions (e.g., N-CAM and Cx43 expression and localisation). In conclusion, this culture model opens a wide range of specific investigations at the molecular, biochemical, and morphological levels, and it represents an important tool for in vitro studies into dynamic interactions and responses of nervous system cell components to microgravity environmental conditions.

RCCS Bioreactor-Based Modelled Microgravity Induces Significant Changes on In Vitro 3D Neuroglial Cell Cultures

PubMed Central

Mazzoleni, Giovanna; Fanò-Illic, Giorgio; Mariggiò, Maria A.

2015-01-01

We propose a human-derived neuro-/glial cell three-dimensional in vitro model to investigate the effects of microgravity on cell-cell interactions. A rotary cell-culture system (RCCS) bioreactor was used to generate a modelled microgravity environment, and morphofunctional features of glial-like GL15 and neuronal-like SH-SY5Y cells in three-dimensional individual cultures (monotypic aggregates) and cocultures (heterotypic aggregates) were analysed. Cell survival was maintained within all cell aggregates over 2 weeks of culture. Moreover, compared to cells as traditional static monolayers, cell aggregates cultured under modelled microgravity showed increased expression of specific differentiation markers (e.g., GL15 cells: GFAP, S100B; SH-SY5Y cells: GAP43) and modulation of functional cell-cell interactions (e.g., N-CAM and Cx43 expression and localisation). In conclusion, this culture model opens a wide range of specific investigations at the molecular, biochemical, and morphological levels, and it represents an important tool for in vitro studies into dynamic interactions and responses of nervous system cell components to microgravity environmental conditions. PMID:25654124

Natural Aggregation Approach based Home Energy Manage System with User Satisfaction Modelling

NASA Astrophysics Data System (ADS)

Luo, F. J.; Ranzi, G.; Dong, Z. Y.; Murata, J.

2017-07-01

With the prevalence of advanced sensing and two-way communication technologies, Home Energy Management System (HEMS) has attracted lots of attentions in recent years. This paper proposes a HEMS that optimally schedules the controllable Residential Energy Resources (RERs) in a Time-of-Use (TOU) pricing and high solar power penetrated environment. The HEMS aims to minimize the overall operational cost of the home, and the user’s satisfactions and requirements on the operation of different household appliances are modelled and considered in the HEMS. Further, a new biological self-aggregation intelligence based optimization technique previously proposed by the authors, i.e., Natural Aggregation Algorithm (NAA), is applied to solve the proposed HEMS optimization model. Simulations are conducted to validate the proposed method.

Improving wave forecasting by integrating ensemble modelling and machine learning

NASA Astrophysics Data System (ADS)

O'Donncha, F.; Zhang, Y.; James, S. C.

2017-12-01

Modern smart-grid networks use technologies to instantly relay information on supply and demand to support effective decision making. Integration of renewable-energy resources with these systems demands accurate forecasting of energy production (and demand) capacities. For wave-energy converters, this requires wave-condition forecasting to enable estimates of energy production. Current operational wave forecasting systems exhibit substantial errors with wave-height RMSEs of 40 to 60 cm being typical, which limits the reliability of energy-generation predictions thereby impeding integration with the distribution grid. In this study, we integrate physics-based models with statistical learning aggregation techniques that combine forecasts from multiple, independent models into a single "best-estimate" prediction of the true state. The Simulating Waves Nearshore physics-based model is used to compute wind- and currents-augmented waves in the Monterey Bay area. Ensembles are developed based on multiple simulations perturbing input data (wave characteristics supplied at the model boundaries and winds) to the model. A learning-aggregation technique uses past observations and past model forecasts to calculate a weight for each model. The aggregated forecasts are compared to observation data to quantify the performance of the model ensemble and aggregation techniques. The appropriately weighted ensemble model outperforms an individual ensemble member with regard to forecasting wave conditions.

Principles for problem aggregation and assignment in medium scale multiprocessors

NASA Technical Reports Server (NTRS)

Nicol, David M.; Saltz, Joel H.

1987-01-01

One of the most important issues in parallel processing is the mapping of workload to processors. This paper considers a large class of problems having a high degree of potential fine grained parallelism, and execution requirements that are either not predictable, or are too costly to predict. The main issues in mapping such a problem onto medium scale multiprocessors are those of aggregation and assignment. We study a method of parameterized aggregation that makes few assumptions about the workload. The mapping of aggregate units of work onto processors is uniform, and exploits locality of workload intensity to balance the unknown workload. In general, a finer aggregate granularity leads to a better balance at the price of increased communication/synchronization costs; the aggregation parameters can be adjusted to find a reasonable granularity. The effectiveness of this scheme is demonstrated on three model problems: an adaptive one-dimensional fluid dynamics problem with message passing, a sparse triangular linear system solver on both a shared memory and a message-passing machine, and a two-dimensional time-driven battlefield simulation employing message passing. Using the model problems, the tradeoffs are studied between balanced workload and the communication/synchronization costs. Finally, an analytical model is used to explain why the method balances workload and minimizes the variance in system behavior.

Application of the expanded Creme RIFM consumer exposure model to fragrance ingredients in cosmetic, personal care and air care products.

PubMed

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

2017-06-01

As part of a joint project between the Research Institute for Fragrance Materials (RIFM) and Creme Global, a Monte Carlo model (here named the Creme RIFM model) has been developed to estimate consumer exposure to ingredients in personal care products. Details of the model produced in Phase 1 of the project have already been published. Further data on habits and practises have been collected which enable the model to estimate consumer exposure from dermal, oral and inhalation routes for 25 product types. . In addition, more accurate concentration data have been obtained which allow levels of fragrance ingredients in these product types to be modelled. Described is the use of this expanded model to estimate aggregate systemic exposure for eight fragrance ingredients. Results are shown for simulated systemic exposure (expressed as μg/kg bw/day) for each fragrance ingredient in each product type, along with simulated aggregate exposure. Highest fragrance exposure generally occurred from use of body lotions, body sprays and hydroalcoholic products. For the fragrances investigated, aggregate exposure calculated using this model was 11.5-25 fold lower than that calculated using deterministic methodology. The Creme RIFM model offers a very comprehensive and powerful tool for estimating aggregate exposure to fragrance ingredients. Copyright © 2017. Published by Elsevier Inc.

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

NASA Astrophysics Data System (ADS)

Seibt, Joachim; Sláma, Vladislav; Mančal, Tomáš

2016-12-01

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

Kinetic Monte Carlo and cellular particle dynamics simulations of multicellular systems

NASA Astrophysics Data System (ADS)

Flenner, Elijah; Janosi, Lorant; Barz, Bogdan; Neagu, Adrian; Forgacs, Gabor; Kosztin, Ioan

2012-03-01

Computer modeling of multicellular systems has been a valuable tool for interpreting and guiding in vitro experiments relevant to embryonic morphogenesis, tumor growth, angiogenesis and, lately, structure formation following the printing of cell aggregates as bioink particles. Here we formulate two computer simulation methods: (1) a kinetic Monte Carlo (KMC) and (2) a cellular particle dynamics (CPD) method, which are capable of describing and predicting the shape evolution in time of three-dimensional multicellular systems during their biomechanical relaxation. Our work is motivated by the need of developing quantitative methods for optimizing postprinting structure formation in bioprinting-assisted tissue engineering. The KMC and CPD model parameters are determined and calibrated by using an original computational-theoretical-experimental framework applied to the fusion of two spherical cell aggregates. The two methods are used to predict the (1) formation of a toroidal structure through fusion of spherical aggregates and (2) cell sorting within an aggregate formed by two types of cells with different adhesivities.

Effects of crowders on the equilibrium and kinetic properties of protein aggregation

NASA Astrophysics Data System (ADS)

Bridstrup, John; Yuan, Jian-Min

2016-08-01

The equilibrium and kinetic properties of protein aggregation systems in the presence of crowders are investigated using simple, illuminating models based on mass-action laws. Our model yields analytic results for equilibrium properties of protein aggregates, which fit experimental data of actin and ApoC-II with crowders reasonably well. When the effects of crowders on rate constants are considered, our kinetic model is in good agreement with experimental results for actin with dextran as the crowder. Furthermore, the model shows that as crowder volume fraction increases, the length distribution of fibrils becomes narrower and shifts to shorter values due to volume exclusion.

Fragmentation approach to the point-island model with hindered aggregation: Accessing the barrier energy.

PubMed

González, Diego Luis; Pimpinelli, Alberto; Einstein, T L

2017-07-01

We study the effect of hindered aggregation on the island formation process in a one- (1D) and two-dimensional (2D) point-island model for epitaxial growth with arbitrary critical nucleus size i. In our model, the attachment of monomers to preexisting islands is hindered by an additional attachment barrier, characterized by length l_{a}. For l_{a}=0 the islands behave as perfect sinks while for l_{a}→∞ they behave as reflecting boundaries. For intermediate values of l_{a}, the system exhibits a crossover between two different kinds of processes, diffusion-limited aggregation and attachment-limited aggregation. We calculate the growth exponents of the density of islands and monomers for the low coverage and aggregation regimes. The capture-zone (CZ) distributions are also calculated for different values of i and l_{a}. In order to obtain a good spatial description of the nucleation process, we propose a fragmentation model, which is based on an approximate description of nucleation inside of the gaps for 1D and the CZs for 2D. In both cases, the nucleation is described by using two different physically rooted probabilities, which are related with the microscopic parameters of the model (i and l_{a}). We test our analytical model with extensive numerical simulations and previously established results. The proposed model describes excellently the statistical behavior of the system for arbitrary values of l_{a} and i=1, 2, and 3.

Models of cooperative dynamics from biomolecules to magnets

NASA Astrophysics Data System (ADS)

Mobley, David Lowell

This work details application of computer models to several biological systems (prion diseases and Alzheimer's disease) and a magnetic system. These share some common themes, which are discussed. Here, simple lattice-based models are applied to aggregation of misfolded protein in prion diseases like Mad Cow disease. These can explain key features of the diseases. The modeling is based on aggregation being essential in establishing the time-course of infectivity. Growth of initial aggregates is assumed to dominate the experimentally observed lag phase. Subsequent fission, regrowth, and fission set apart the exponential doubling phase in disease progression. We explore several possible modes of growth for 2-D aggregates and suggest the model providing the best explanation for the experimental data. We develop testable predictions from this model. Like prion disease, Alzheimer's disease (AD) is an amyloid disease characterized by large aggregates in the brain. However, evidence increasingly points away from these as the toxic agent and towards oligomers of the Abeta peptide. We explore one possible toxicity mechanism---insertion of Abeta into cell membranes and formation of harmful ion channels. We find that mutations in this peptide which cause familial Alzheimer's disease (FAD) also affect the insertion of this peptide into membranes in a fairly consistent way, suggesting that this toxicity mechanism may be relevant biologically. We find a particular inserted configuration which may be especially harmful and develop testable predictions to verify whether or not this is the case. Nucleation is an essential feature of our models for prion disease, in that it protects normal, healthy individuals from getting prion disease. Nucleation is important in many other areas, and we modify our lattice-based nucleation model to apply to a hysteretic magnetic system where nucleation has been suggested to be important. From a simple model, we find qualitative agreement with experiment, and make testable experimental predictions concerning time-dependence and temperature-dependence of the major hysteresis loop and reversal curves which have been experimentally verified. We argue why this model may be suitable for systems like these and explain implications for Ising-like models. We suggest implications for future modeling work. Finally, we present suggestions for future work in all three areas.

Derivation of optimal joint operating rules for multi-purpose multi-reservoir water-supply system

NASA Astrophysics Data System (ADS)

Tan, Qiao-feng; Wang, Xu; Wang, Hao; Wang, Chao; Lei, Xiao-hui; Xiong, Yi-song; Zhang, Wei

2017-08-01

The derivation of joint operating policy is a challenging task for a multi-purpose multi-reservoir system. This study proposed an aggregation-decomposition model to guide the joint operation of multi-purpose multi-reservoir system, including: (1) an aggregated model based on the improved hedging rule to ensure the long-term water-supply operating benefit; (2) a decomposed model to allocate the limited release to individual reservoirs for the purpose of maximizing the total profit of the facing period; and (3) a double-layer simulation-based optimization model to obtain the optimal time-varying hedging rules using the non-dominated sorting genetic algorithm II, whose objectives were to minimize maximum water deficit and maximize water supply reliability. The water-supply system of Li River in Guangxi Province, China, was selected for the case study. The results show that the operating policy proposed in this study is better than conventional operating rules and aggregated standard operating policy for both water supply and hydropower generation due to the use of hedging mechanism and effective coordination among multiple objectives.

Probability density function characterization for aggregated large-scale wind power based on Weibull mixtures

DOE PAGES

Gomez-Lazaro, Emilio; Bueso, Maria C.; Kessler, Mathieu; ...

2016-02-02

Here, the Weibull probability distribution has been widely applied to characterize wind speeds for wind energy resources. Wind power generation modeling is different, however, due in particular to power curve limitations, wind turbine control methods, and transmission system operation requirements. These differences are even greater for aggregated wind power generation in power systems with high wind penetration. Consequently, models based on one-Weibull component can provide poor characterizations for aggregated wind power generation. With this aim, the present paper focuses on discussing Weibull mixtures to characterize the probability density function (PDF) for aggregated wind power generation. PDFs of wind power datamore » are firstly classified attending to hourly and seasonal patterns. The selection of the number of components in the mixture is analyzed through two well-known different criteria: the Akaike information criterion (AIC) and the Bayesian information criterion (BIC). Finally, the optimal number of Weibull components for maximum likelihood is explored for the defined patterns, including the estimated weight, scale, and shape parameters. Results show that multi-Weibull models are more suitable to characterize aggregated wind power data due to the impact of distributed generation, variety of wind speed values and wind power curtailment.« less

Validation of TxDOT flexible pavement skid prediction model : workshop : student guide.

DOT National Transportation Integrated Search

2017-05-01

Course Materials: : Background summary of Research Project 0-5627. : Short presentation of research tasks and findings from Research Project 0-6746. : Aggregate characterization with Aggregate Imaging Measurement System (AIMS) and Micro-D...

ACToR A Aggregated Computational Toxicology Resource

EPA Science Inventory

We are developing the ACToR system (Aggregated Computational Toxicology Resource) to serve as a repository for a variety of types of chemical, biological and toxicological data that can be used for predictive modeling of chemical toxicology.

ACToR A Aggregated Computational Toxicology Resource (S)

EPA Science Inventory

We are developing the ACToR system (Aggregated Computational Toxicology Resource) to serve as a repository for a variety of types of chemical, biological and toxicological data that can be used for predictive modeling of chemical toxicology.

Activity-driven changes in the mechanical properties of fire ant aggregations

NASA Astrophysics Data System (ADS)

Tennenbaum, Michael; Fernandez-Nieves, Alberto

2017-11-01

Fire ant aggregations are active materials composed of individual constituents that are able to transform internal energy into work. We find using rheology and direct visualization that the aggregation undergoes activity cycles that affect the mechanical properties of the system. When the activity is high, the aggregation approximately equally stores and dissipates energy, it is more homogeneous, and exerts a high outward force. When the activity is low, the aggregation is predominantly elastic, it is more heterogeneous, and it exerts a small outward force. We rationalize our results using a simple kinetic model where the number of active ants within the aggregation is the essential quantity.

Contrasting self-aggregation over land and ocean surfaces

NASA Astrophysics Data System (ADS)

Inda Diaz, H. A.; O'Brien, T. A.

2017-12-01

The spontaneous organization of convection into clusters, or self-aggregation, demonstrably changes the nature and statistics of precipitation. While there has been much recent progress in this area, the processes that control self-aggregation are still poorly understood. Most of the work to date has focused on self-aggregation over ocean-like surfaces, but it is particularly pressing to understand what controls convective aggregation over land, since the associated change in precipitation statistics—between non-aggregated and aggregated convection—could have huge impacts on society and infrastructure. Radiative-convective equilibrium (RCE), has been extensively used as an idealized framework to study the tropical atmosphere. Self-aggregation manifests in numerous numerical models of RCE, nevertheless, there is still a lack of understanding in how it relates to convective organization in the observed world. Numerous studies have examined self-aggregation using idealized Cloud Resolving Models (CRMs) and General Circulation Models over the ocean, however very little work has been done on RCE and self-aggregation over land. Idealized models of RCE over ocean have shown that aggregation is sensitive to sea surface temperature (SST), more intense precipitation occurs in aggregated systems, and a variety of feedbacks—such as surface flux, cloud radiative, and upgradient moisture transport— contribute to the maintenance of aggregation, however it is not clear if these results apply over land. Progress in this area could help relate understanding of self-aggregation in idealized simulations to observations. In order to explore the behavior of self-aggregation over land, we use a CRM to simulate idealized RCE over land. In particular, we examine the aggregation of convection and how it compares with aggregation over ocean. Based on previous studies, where a variety of different CRMs exhibit a SST threshold below which self-aggregation does not occur, we hypothesize that idealized land simulations will exhibit similar threshold behavior when there is an adequate surface moisture supply. We systematically explore this by varying parameters that exert strong control on the surface enthalpy and moisture budget, such as type of land, surface albedo, and greenhouse gas concentration.

Single-wall nanohorn structure and distribution of incorporated materials

NASA Astrophysics Data System (ADS)

Maigne, Alan; Gloter, Alexandre; Ajima, Kumiko; Colliex, Christian; Iijima, Sumio

2005-03-01

Single-wall carbon nanohorns (SWNHs) are unique spherical-aggregates of single-wall carbon quasi-nanotubes. So far, the observable area has been limited to the aggregate surfaces. We studied core-region structure with TEM using thickness measurement method, EELS, and EDS, and found that carbon density was uniform over the whole aggregate. This result allows to modelize the core-region and to clarify previous models of SWNHs. We used same tools to investigate the incorporation of materials such as fullerenes or platinium compounds. We found that particles can even be incorporated in the core-region and that their distribution in the aggregate depends on their concentration. The information available with these models should be useful in the study of SWNH applications to, for example, drug delivery system.

Uncoupling of Protein Aggregation and Neurodegeneration in a Mouse Amyotrophic Lateral Sclerosis Model.

PubMed

Lee, Joo-Yong; Kawaguchi, Yoshiharu; Li, Ming; Kapur, Meghan; Choi, Su Jin; Kim, Hak-June; Park, Song-Yi; Zhu, Haining; Yao, Tso-Pang

2015-01-01

Aberrant accumulation of protein aggregates is a pathological hallmark of many neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). Although a buildup of protein aggregates frequently leads to cell death, whether it is the key pathogenic factor in driving neurodegenerative disease remains controversial. HDAC6, a cytosolic ubiquitin-binding deacetylase, has emerged as an important regulator of ubiquitin-dependent quality control autophagy, a lysosome-dependent degradative system responsible for the disposal of misfolded protein aggregates and damaged organelles. Here, we show that in cell models HDAC6 plays a protective role against multiple disease-associated and aggregation-prone cytosolic proteins by facilitating their degradation. We further show that HDAC6 is required for efficient localization of lysosomes to protein aggregates, indicating that lysosome targeting to autophagic substrates is regulated. Supporting a critical role of HDAC6 in protein aggregate disposal in vivo, genetic ablation of HDAC6 in a transgenic SOD1G93A mouse, a model of ALS, leads to dramatic accumulation of ubiquitinated SOD1G93A protein aggregates. Surprisingly, despite a robust buildup of SOD1G93A aggregates, deletion of HDAC6 only moderately modified the motor phenotypes. These findings indicate that SOD1G93A aggregation is not the only determining factor to drive neurodegeneration in ALS, and that HDAC6 likely modulates neurodegeneration through additional mechanisms beyond protein aggregate clearance. © 2015 S. Karger AG, Basel.

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

Enciso, Marta, E-mail: m.enciso@latrobe.edu.au; Schütte, Christof, E-mail: schuette@zib.de; Zuse Institute Berlin, Berlin

We employ a recently developed coarse-grained model for peptides and proteins where the effect of pH is automatically included. We explore the effect of pH in the aggregation process of the amyloidogenic peptide KTVIIE and two related sequences, using three different pH environments. Simulations using large systems (24 peptides chains per box) allow us to describe the formation of realistic peptide aggregates. We evaluate the thermodynamic and kinetic implications of changes in sequence and pH upon peptide aggregation, and we discuss how a minimalistic coarse-grained model can account for these details.

Collective effects of torsion in FtsZ filaments

NASA Astrophysics Data System (ADS)

González de Prado Salas, Pablo; Tarazona, Pedro

2016-04-01

Recent evidence points to the presence of torsion in FtsZ bonds. In addition, experiments with FtsZ mutants on surfaces resulted in new aggregates that cannot be explained by older models for FtsZ dynamics. We use an interaction model for FtsZ derived from molecular dynamics simulations and expand a fine-grained lattice model used to describe FtsZ aggregates on a surface. This new model includes different anchoring angles for the monomers and allows bond twist, two ingredients that oppose each other resulting in a more dynamic and interesting system. We study the role and importance of these conflicting elements and how the aggregates are characterized by the different interaction parameters.

Effects of protopine on blood platelet aggregation. II. Effect on metabolic system of adenosine 3',5'-cyclic monophosphate in platelets.

PubMed

Shiomoto, H; Matsuda, H; Kubo, M

1990-08-01

The mode of action of protopine on rabbit platelet aggregation was investigated in the metabolic system of adenosine 3',5'-cyclic monophosphate (cyclic AMP) in vitro experimental models. The inhibitory activity of protopine on adenosine 5'-diphosphate induced platelet aggregation was increased in the presence of prostaglandin I2 or papaverine in platelets. Protopine elevated content of the basal cyclic AMP accumulation in platelets and enhanced activity of crude adenylate cyclase prepared from platelets, but was ineffective on cyclic AMP phosphodiesterase. It is concluded that protopine has an inhibitory activity on platelet aggregation, activates adenylate cyclase and increases cyclic AMP content in platelets, in addition to other inhibitory actions in the metabolic system of cyclic AMP.

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

DTIC Science & Technology

2013-09-30

statistical models for signal-processing algorithm development. These in turn will help to develop a capability to statistically forecast the impact of...aggregations of fish based on higher-order statistical measures describable in terms of physical and system parameters. Environmentally , these models...processing. In this experiment, we had good ground truth on (1) and (2), and had control over (3) and (4) except for environmentally -imposed restrictions

Aggregation of montmorillonite and organic matter in aqueous media containing artificial seawater.

PubMed

Furukawa, Yoko; Watkins, Janet L; Kim, Jinwook; Curry, Kenneth J; Bennett, Richard H

2009-01-23

The dispersion-aggregation behaviors of suspended colloids in rivers and estuaries are affected by the compositions of suspended materials (i.e., clay minerals vs. organic macromolecules) and salinity. Laboratory experiments were conducted to investigate the dispersion and aggregation mechanisms of suspended particles under simulated river and estuarine conditions. The average hydrodynamic diameters of suspended particles (representing degree of aggregation) and zeta potential (representing the electrokinetic properties of suspended colloids and aggregates) were determined for systems containing suspended montmorillonite, humic acid, and/or chitin at the circumneutral pH over a range of salinity (0 - 7.2 psu). The montmorillonite-only system increased the degree of aggregation with salinity increase, as would be expected for suspended colloids whose dispersion-aggregation behavior is largely controlled by the surface electrostatic properties and van der Waals forces. When montmorillonite is combined with humic acid or chitin, the aggregation of montmorillonite was effectively inhibited. The surface interaction energy model calculations reveal that the steric repulsion, rather than the increase in electronegativity, is the primary cause for the inhibition of aggregation by the addition of humic acid or chitin. These results help explain the range of dispersion-aggregation behaviors observed in natural river and estuarine systems. It is postulated that the composition of suspended particles, specifically the availability of steric polymers such as those contained in humic acid, determine whether the river suspension is rapidly aggregated and settled or remains dispersed in suspension when it encounters increasingly saline environments of estuaries and oceans.

Atomistic Structure of Mineral Nano-aggregates from Simulated Compaction and Dewatering.

PubMed

Ho, Tuan Anh; Greathouse, Jeffery A; Wang, Yifeng; Criscenti, Louise J

2017-11-10

The porosity of clay aggregates is an important property governing chemical reactions and fluid flow in low-permeability geologic formations and clay-based engineered barrier systems. Pore spaces in clays include interlayer and interparticle pores. Under compaction and dewatering, the size and geometry of such pore spaces may vary significantly (sub-nanometer to microns) depending on ambient physical and chemical conditions. Here we report a molecular dynamics simulation method to construct a complex and realistic clay-like nanoparticle aggregate with interparticle pores and grain boundaries. The model structure is then used to investigate the effect of dewatering and water content on micro-porosity of the aggregates. The results suggest that slow dewatering would create more compact aggregates compared to fast dewatering. Furthermore, the amount of water present in the aggregates strongly affects the particle-particle interactions and hence the aggregate structure. Detailed analyses of particle-particle and water-particle interactions provide a molecular-scale view of porosity and texture development of the aggregates. The simulation method developed here may also aid in modeling the synthesis of nanostructured materials through self-assembly of nanoparticles.

Atomistic Structure of Mineral Nano-aggregates from Simulated Compaction and Dewatering

DOE PAGES

Ho, Tuan Anh; Greathouse, Jeffery A.; Wang, Yifeng; ...

2017-11-10

The porosity of clay aggregates is an important property governing chemical reactions and fluid flow in low-permeability geologic formations and clay-based engineered barrier systems. Pore spaces in clays include interlayer and interparticle pores. Under compaction and dewatering, the size and geometry of such pore spaces may vary significantly (sub-nanometer to microns) depending on ambient physical and chemical conditions. Here we report a molecular dynamics simulation method to construct a complex and realistic clay-like nanoparticle aggregate with interparticle pores and grain boundaries. The model structure is then used to investigate the effect of dewatering and water content on micro-porosity of themore » aggregates. The results suggest that slow dewatering would create more compact aggregates compared to fast dewatering. Furthermore, the amount of water present in the aggregates strongly affects the particle-particle interactions and hence the aggregate structure. Detailed analyses of particle-particle and water-particle interactions provide a molecular-scale view of porosity and texture development of the aggregates. The simulation method developed here may also aid in modeling the synthesis of nanostructured materials through self-assembly of nanoparticles.« less

The problem with simple lumped parameter models: Evidence from tritium mean transit times

NASA Astrophysics Data System (ADS)

Stewart, Michael; Morgenstern, Uwe; Gusyev, Maksym; Maloszewski, Piotr

2017-04-01

Simple lumped parameter models (LPMs) based on assuming homogeneity and stationarity in catchments and groundwater bodies are widely used to model and predict hydrological system outputs. However, most systems are not homogeneous or stationary, and errors resulting from disregard of the real heterogeneity and non-stationarity of such systems are not well understood and rarely quantified. As an example, mean transit times (MTTs) of streamflow are usually estimated from tracer data using simple LPMs. The MTT or transit time distribution of water in a stream reveals basic catchment properties such as water flow paths, storage and mixing. Importantly however, Kirchner (2016a) has shown that there can be large (several hundred percent) aggregation errors in MTTs inferred from seasonal cycles in conservative tracers such as chloride or stable isotopes when they are interpreted using simple LPMs (i.e. a range of gamma models or GMs). Here we show that MTTs estimated using tritium concentrations are similarly affected by aggregation errors due to heterogeneity and non-stationarity when interpreted using simple LPMs (e.g. GMs). The tritium aggregation error series from the strong nonlinearity between tritium concentrations and MTT, whereas for seasonal tracer cycles it is due to the nonlinearity between tracer cycle amplitudes and MTT. In effect, water from young subsystems in the catchment outweigh water from old subsystems. The main difference between the aggregation errors with the different tracers is that with tritium it applies at much greater ages than it does with seasonal tracer cycles. We stress that the aggregation errors arise when simple LPMs are applied (with simple LPMs the hydrological system is assumed to be a homogeneous whole with parameters representing averages for the system). With well-chosen compound LPMs (which are combinations of simple LPMs) on the other hand, aggregation errors are very much smaller because young and old water flows are treated separately. "Well-chosen" means that the compound LPM is based on hydrologically- and geologically-validated information, and the choice can be assisted by matching simulations to time series of tritium measurements. References: Kirchner, J.W. (2016a): Aggregation in environmental systems - Part 1: Seasonal tracer cycles quantify young water fractions, but not mean transit times, in spatially heterogeneous catchments. Hydrol. Earth Syst. Sci. 20, 279-297. Stewart, M.K., Morgenstern, U., Gusyev, M.A., Maloszewski, P. 2016: Aggregation effects on tritium-based mean transit times and young water fractions in spatially heterogeneous catchments and groundwater systems, and implications for past and future applications of tritium. Submitted to Hydrol. Earth Syst. Sci., 10 October 2016, doi:10.5194/hess-2016-532.

Theoretical deposition of carcinogenic particle aggregates in the upper respiratory tract.

PubMed

Sturm, Robert

2013-10-01

Numerous particles suspended in the atmosphere are composed of smaller particular components that form aggregates with highly irregular shape. Such aggregates, among which dusts and soot are the most prominent examples, may be taken up into the respiratory tract and, in the worst case, initiate a malignant transformation of lung cells. Particle aggregates were theoretically modelled by using small spheres with equal diameters (1 nm) and arranging them randomly. This procedure resulted in the generation of various aggregate shapes (chain-like, loose, compact), for which essential parameters such as dynamic shape factors, χ, and aerodynamic diameters, dae , were computed. Deposition of aggregates consisting of 10, 50, 100, and 1,000 nano-spheres was simulated for the uppermost parts of the human respiratory system (extrathoracic region and airway generation 0 to 4), thereby distinguishing between sitting and light-work breathing as well as between nasal and oral inhalation. Based upon the modelling results, aggregate deposition in the human respiratory system can be described as a function of (I) aerodynamic diameter; (II) inhaled particle position within the airway system; and (III) breathing conditions. Therefore, highest deposition values were obtained for nano-scale aggregates (<10 nm), whereas larger aggregates exhibited slightly to significantly reduced deposition probabilities. Extrathoracic regions and uppermost bronchi (generations 0 to 1) were marked by most effective particle capture. Any increase of inhaled air volumes and reduction of breathing times resulted in an enhancement of deposition probabilities of larger particles. Based on the results derived from this study it may be concluded that small particle aggregates are accumulated in the uppermost compartments of the human respiratory tract, where they may unfold their unwholesome potential. In the case of carcinogenic particles being stored in epithelial cells for a longer time span, malignant transformations starting with the formation of cancerous cells and ending with the growth of a tumour have to be assumed.

Evaluation of Aggregated Ag85B Antigen for Its Biophysical Properties, Immunogenicity, and Vaccination Potential in a Murine Model of Tuberculosis Infection

PubMed Central

Ahmad, Faraz; Zubair, Swaleha; Gupta, Pushpa; Gupta, Umesh Datta; Patel, Rakesh; Owais, Mohammad

2017-01-01

Protein aggregates have been reported to act as a reservoir that can release biologically active, native form of precursor protein. Keeping this fact into consideration, it is tempting to exploit protein aggregate-based antigen delivery system as a functional vaccine to expand desirable immunological response in the host. Herein, we explored the capacity of aggregated Ag85B of Mycobacterium tuberculosis (Mtb) to act as a prophylactic vaccine system that releases the precursor antigen in slow and sustained manner. Being particulate system with exposed hydrophobic residues, aggregated Ag85B is likely to be avidly taken up by both phagocytosis as well as fusion with plasma membrane of antigen presenting cells, leading to its direct delivery to their cytosol. Its unique ability to access cytosol of target cells is further evident from the fact that immunization with aggregated Ag85B led to the induction of Th1-dominant immune response along with upregulated expression of qualitatively superior polyfunctional T cells in the mice. Antibodies generated following immunization with aggregated antigen recognized both native and monomeric Ag85B released from protein aggregate. The implicated immunization strategy offers protection at par to that of established BCG vaccine with desirable central and effector memory responses against subsequent Mtb aerosol challenge. The study highlights the potential of aggregated Ag85B as promising antigen delivery system and paves the way to design better prophylactic regimes against various intracellular pathogens including Mtb. PMID:29230211

Novel polyglutamine model uncouples proteotoxicity from aging.

PubMed

Christie, Nakeirah T M; Lee, Amy L; Fay, Hannah G; Gray, Amelia A; Kikis, Elise A

2014-01-01

Polyglutamine expansions in certain proteins are the genetic determinants for nine distinct progressive neurodegenerative disorders and resultant age-related dementia. In these cases, neurodegeneration is due to the aggregation propensity and resultant toxic properties of the polyglutamine-containing proteins. We are interested in elucidating the underlying mechanisms of toxicity of the protein ataxin-3, in which a polyglutamine expansion is the genetic determinant for Machado-Joseph Disease (MJD), also referred to as spinocerebellar ataxia 3 (SCA3). To this end, we have developed a novel model for ataxin-3 protein aggregation, by expressing a disease-related polyglutamine-containing fragment of ataxin-3 in the genetically tractable body wall muscle cells of the model system C. elegans. Here, we demonstrate that this ataxin-3 fragment aggregates in a polyQ length-dependent manner in C. elegans muscle cells and that this aggregation is associated with cellular dysfunction. However, surprisingly, this aggregation and resultant toxicity was not influenced by aging. This is in contrast to polyglutamine peptides alone whose aggregation/toxicity is highly dependent on age. Thus, the data presented here not only describe a new polyglutamine model, but also suggest that protein context likely influences the cellular interactions of the polyglutamine-containing protein and thereby modulates its toxic properties.

Multi-regime transport model for leaching behavior of heterogeneous porous materials.

PubMed

Sanchez, F; Massry, I W; Eighmy, T; Kosson, D S

2003-01-01

Utilization of secondary materials in civil engineering applications (e.g. as substitutes for natural aggregates or binder constituents) requires assessment of the physical and environment properties of the product. Environmental assessment often necessitates evaluation of the potential for constituent release through leaching. Currently most leaching models used to estimate long-term field performance assume that the species of concern is uniformly dispersed in a homogeneous porous material. However, waste materials are often comprised of distinct components such as coarse or fine aggregates in a cement concrete or waste encapsulated in a stabilized matrix. The specific objectives of the research presented here were to (1) develop a one-dimensional, multi-regime transport model (i.e. MRT model) to describe the release of species from heterogeneous porous materials and, (2) evaluate simple limit cases using the model for species when release is not dependent on pH. Two different idealized model systems were considered: (1) a porous material contaminated with the species of interest and containing inert aggregates and, (2) a porous material containing the contaminant of interest only in the aggregates. The effect of three factors on constituent release were examined: (1) volume fraction of material occupied by the aggregates compared to a homogeneous porous material, (2) aggregate size and, (3) differences in mass transfer rates between the binder and the aggregates. Simulation results confirmed that assuming homogeneous materials to evaluate the release of contaminants from porous waste materials may result in erroneous long-term field performance assessment.

Disease-Associated Mutant Ubiquitin Causes Proteasomal Impairment and Enhances the Toxicity of Protein Aggregates

PubMed Central

Tank, Elizabeth M. H.; True, Heather L.

2009-01-01

Protein homeostasis is critical for cellular survival and its dysregulation has been implicated in Alzheimer's disease (AD) and other neurodegenerative disorders. Despite the growing appreciation of the pathogenic mechanisms involved in familial forms of AD, much less is known about the sporadic cases. Aggregates found in both familial and sporadic AD often include proteins other than those typically associated with the disease. One such protein is a mutant form of ubiquitin, UBB+1, a frameshift product generated by molecular misreading of a wild-type ubiquitin gene. UBB+1 has been associated with multiple disorders. UBB+1 cannot function as a ubiquitin molecule, and it is itself a substrate for degradation by the ubiquitin/proteasome system (UPS). Accumulation of UBB+1 impairs the proteasome system and enhances toxic protein aggregation, ultimately resulting in cell death. Here, we describe a novel model system to investigate how UBB+1 impairs UPS function and whether it plays a causal role in protein aggregation. We expressed a protein analogous to UBB+1 in yeast (Ubext) and demonstrated that it caused UPS impairment. Blocking ubiquitination of Ubext or weakening its interactions with other ubiquitin-processing proteins reduced the UPS impairment. Expression of Ubext altered the conjugation of wild-type ubiquitin to a UPS substrate. The expression of Ubext markedly enhanced cellular susceptibility to toxic protein aggregates but, surprisingly, did not induce or alter nontoxic protein aggregates in yeast. Taken together, these results suggest that Ubext interacts with more than one protein to elicit impairment of the UPS and affect protein aggregate toxicity. Furthermore, we suggest a model whereby chronic UPS impairment could inflict deleterious consequences on proper protein aggregate sequestration. PMID:19214209

Maximal aggregation of polynomial dynamical systems

PubMed Central

Cardelli, Luca; Tschaikowski, Max

2017-01-01

Ordinary differential equations (ODEs) with polynomial derivatives are a fundamental tool for understanding the dynamics of systems across many branches of science, but our ability to gain mechanistic insight and effectively conduct numerical evaluations is critically hindered when dealing with large models. Here we propose an aggregation technique that rests on two notions of equivalence relating ODE variables whenever they have the same solution (backward criterion) or if a self-consistent system can be written for describing the evolution of sums of variables in the same equivalence class (forward criterion). A key feature of our proposal is to encode a polynomial ODE system into a finitary structure akin to a formal chemical reaction network. This enables the development of a discrete algorithm to efficiently compute the largest equivalence, building on approaches rooted in computer science to minimize basic models of computation through iterative partition refinements. The physical interpretability of the aggregation is shown on polynomial ODE systems for biochemical reaction networks, gene regulatory networks, and evolutionary game theory. PMID:28878023

Aggregation of peptides in the tube model with correlated sidechain orientations

NASA Astrophysics Data System (ADS)

Hung, Nguyen Ba; Hoang, Trinh Xuan

2015-06-01

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

Bead-Level Characterization of Early-Stage Amyloid β42 Aggregates: Nuclei and Ionic Concentration Effects.

PubMed

Hu, Dingkun; Zhao, Wei; Zhu, Yong; Ai, Hongqi; Kang, Baotao

2017-11-16

A growing body of evidence shows that soluble β-amyloid (Aβ) aggregates, oligomers, and even protofibrils, may be more neurotoxic than fibrils. Here, we employ a coarse grain model to investigate the aggregation of 75mer Aβ 42 oligomers and the salt effect, the cornerstone of fibril evolution. We find that the oligomer morphologies generated by seventy-five monomers or mixed by both fifty monomers and five preset pentameric nuclei are different (spherical vs. bar-/disk-shaped) and are characterize by a full of coil content (former) and >70 % β-turn content (latter), indicating a novel role of the nuclei played in the early aggregation stage. The aggregation for the former oligomer adopts a master-nucleus mechanism, whereas for the latter combination of monomers and pentamers a multi-nuclei one is found. The random salt ions will distribute around the aggregates to form several ion shells as the aggregation develops. A unique two-fold gap between the shells is observed in the system containing 100 mm NaCl, endowing the physiological salt concentration with special implications. Meanwhile, an accurate ion-solute cutoff distance (0.66 nm) is predicted, and recommended to apply to many other aggregated biomolecular systems. The present distribution scenario of ions can be generalized to other aggregated systems, although it is strictly dependent on the identity of a specific aggregate, such as its charge and composition. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

NASA Astrophysics Data System (ADS)

Karakas, Ahmet; Turner, Keith

2004-07-01

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

Comparison of particle swarm optimization and differential evolution for aggregators' profit maximization in the demand response system

NASA Astrophysics Data System (ADS)

Wisittipanit, Nuttachat; Wisittipanich, Warisa

2018-07-01

Demand response (DR) refers to changes in the electricity use patterns of end-users in response to incentive payment designed to prompt lower electricity use during peak periods. Typically, there are three players in the DR system: an electric utility operator, a set of aggregators and a set of end-users. The DR model used in this study aims to minimize the operator's operational cost and offer rewards to aggregators, while profit-maximizing aggregators compete to sell DR services to the operator and provide compensation to end-users for altering their consumption profiles. This article presents the first application of two metaheuristics in the DR system: particle swarm optimization (PSO) and differential evolution (DE). The objective is to optimize the incentive payments during various periods to satisfy all stakeholders. The results show that DE significantly outperforms PSO, since it can attain better compensation rates, lower operational costs and higher aggregator profits.

Thermodynamics of Protein Aggregation

NASA Astrophysics Data System (ADS)

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

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

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

NASA Technical Reports Server (NTRS)

Sun, Dengfeng; Sridhar, Banavar; Grabbe, Shon

2010-01-01

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

A microfabricated platform to form three-dimensional toroidal multicellular aggregate.

PubMed

Masuda, Taisuke; Takei, Natsuki; Nakano, Takuma; Anada, Takahisa; Suzuki, Osamu; Arai, Fumihito

2012-12-01

Techniques that allow cells to self-assemble into three-dimensional (3D) spheroid microtissues provide powerful in vitro models that are becoming increasingly popular in fields such as stem cell research, tissue engineering, and cancer biology. Appropriate simulation of the 3D environment in which tissues normally develop and function is crucial for the engineering of in vitro models that can be used for the formation of complex tissues. We have developed a unique multicellular aggregate formation platform that utilizes a maskless gray-scale photolithography. The cellular aggregate formed using this platform has a toroidal-like geometry and includes a micro lumen that facilitates the supply of oxygen and growth factors and the expulsion of waste products. As a result, this platform was capable of rapidly producing hundreds of multicellular aggregates at a time, and of regulating the diameter of aggregates with complex design. These toroidal multicellular aggregates can grow as long-term culture. In addition, the micro lumen can be used as a continuous channel and for the insertion of a vascular system or a nerve system into the assembled tissue. These platform characteristics highlight its potential to be used in a wide variety of applications, e.g. as a bioactuator, as a micro-machine component or in drug screening and tissue engineering.

Aggregation of montmorillonite and organic matter in aqueous media containing artificial seawater

PubMed Central

2009-01-01

Background The dispersion-aggregation behaviors of suspended colloids in rivers and estuaries are affected by the compositions of suspended materials (i.e., clay minerals vs. organic macromolecules) and salinity. Laboratory experiments were conducted to investigate the dispersion and aggregation mechanisms of suspended particles under simulated river and estuarine conditions. The average hydrodynamic diameters of suspended particles (representing degree of aggregation) and zeta potential (representing the electrokinetic properties of suspended colloids and aggregates) were determined for systems containing suspended montmorillonite, humic acid, and/or chitin at the circumneutral pH over a range of salinity (0 – 7.2 psu). Results The montmorillonite-only system increased the degree of aggregation with salinity increase, as would be expected for suspended colloids whose dispersion-aggregation behavior is largely controlled by the surface electrostatic properties and van der Waals forces. When montmorillonite is combined with humic acid or chitin, the aggregation of montmorillonite was effectively inhibited. The surface interaction energy model calculations reveal that the steric repulsion, rather than the increase in electronegativity, is the primary cause for the inhibition of aggregation by the addition of humic acid or chitin. Conclusion These results help explain the range of dispersion-aggregation behaviors observed in natural river and estuarine systems. It is postulated that the composition of suspended particles, specifically the availability of steric polymers such as those contained in humic acid, determine whether the river suspension is rapidly aggregated and settled or remains dispersed in suspension when it encounters increasingly saline environments of estuaries and oceans. PMID:19166595

Microfluidic model experiments on the injectability of monoclonal antibody solutions

NASA Astrophysics Data System (ADS)

Duchene, Charles; Filipe, Vasco; Nakach, Mostafa; Huille, Sylvain; Lindner, Anke

2017-11-01

Autoinjection devices that allow patients to self-administer medicine are becoming used more frequently; however, this advance comes with an increased need for precision in the injection process. The rare occurrence of protein aggregates in solutions of monoclonal antibodies constitutes a threat to the reliability of such devices. Here we study the flow of protein solutions containing aggregates in microfluidic model systems, mimicking injection devices, to gain fundamental understanding of the catastrophic clogging of constrictions of given size. We form aggregates by mechanically shaking or heating antibody solutions and then inject these solutions into microfluidic channels with varying types of constrictions. Geometrical clogging occurs when aggregates reach the size of the constriction and can in some cases be undone by increasing the applied pressure. We perform systematic experiments varying the relative aggregate size and the flow rate or applied pressure. The mechanical deformation of aggregates during their passage through constrictions is investigated to gain a better understanding of the clogging and unclogging mechanisms.

Distributed Trust Management for Validating SLA Choreographies

NASA Astrophysics Data System (ADS)

Haq, Irfan Ul; Alnemr, Rehab; Paschke, Adrian; Schikuta, Erich; Boley, Harold; Meinel, Christoph

For business workflow automation in a service-enriched environment such as a grid or a cloud, services scattered across heterogeneous Virtual Organizations (VOs) can be aggregated in a producer-consumer manner, building hierarchical structures of added value. In order to preserve the supply chain, the Service Level Agreements (SLAs) corresponding to the underlying choreography of services should also be incrementally aggregated. This cross-VO hierarchical SLA aggregation requires validation, for which a distributed trust system becomes a prerequisite. Elaborating our previous work on rule-based SLA validation, we propose a hybrid distributed trust model. This new model is based on Public Key Infrastructure (PKI) and reputation-based trust systems. It helps preventing SLA violations by identifying violation-prone services at service selection stage and actively contributes in breach management at the time of penalty enforcement.

Markov chain aggregation and its applications to combinatorial reaction networks.

PubMed

Ganguly, Arnab; Petrov, Tatjana; Koeppl, Heinz

2014-09-01

We consider a continuous-time Markov chain (CTMC) whose state space is partitioned into aggregates, and each aggregate is assigned a probability measure. A sufficient condition for defining a CTMC over the aggregates is presented as a variant of weak lumpability, which also characterizes that the measure over the original process can be recovered from that of the aggregated one. We show how the applicability of de-aggregation depends on the initial distribution. The application section is devoted to illustrate how the developed theory aids in reducing CTMC models of biochemical systems particularly in connection to protein-protein interactions. We assume that the model is written by a biologist in form of site-graph-rewrite rules. Site-graph-rewrite rules compactly express that, often, only a local context of a protein (instead of a full molecular species) needs to be in a certain configuration in order to trigger a reaction event. This observation leads to suitable aggregate Markov chains with smaller state spaces, thereby providing sufficient reduction in computational complexity. This is further exemplified in two case studies: simple unbounded polymerization and early EGFR/insulin crosstalk.

Not just fractal surfaces, but surface fractal aggregates: Derivation of the expression for the structure factor and its applications

NASA Astrophysics Data System (ADS)

Besselink, R.; Stawski, T. M.; Van Driessche, A. E. S.; Benning, L. G.

2016-12-01

Densely packed surface fractal aggregates form in systems with high local volume fractions of particles with very short diffusion lengths, which effectively means that particles have little space to move. However, there are no prior mathematical models, which would describe scattering from such surface fractal aggregates and which would allow the subdivision between inter- and intraparticle interferences of such aggregates. Here, we show that by including a form factor function of the primary particles building the aggregate, a finite size of the surface fractal interfacial sub-surfaces can be derived from a structure factor term. This formalism allows us to define both a finite specific surface area for fractal aggregates and the fraction of particle interfacial sub-surfaces at the perimeter of an aggregate. The derived surface fractal model is validated by comparing it with an ab initio approach that involves the generation of a "brick-in-a-wall" von Koch type contour fractals. Moreover, we show that this approach explains observed scattering intensities from in situ experiments that followed gypsum (CaSO4 ṡ 2H2O) precipitation from highly supersaturated solutions. Our model of densely packed "brick-in-a-wall" surface fractal aggregates may well be the key precursor step in the formation of several types of mosaic- and meso-crystals.

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.

Modeling the reversible kinetics of neutrophil aggregation under hydrodynamic shear.

PubMed Central

Neelamegham, S; Taylor, A D; Hellums, J D; Dembo, M; Smith, C W; Simon, S I

1997-01-01

Neutrophil emigration into inflamed tissue is mediated by beta 2-integrin and L-selectin adhesion receptors. Homotypic neutrophil aggregation is also dependent on these molecules, and it provides a model system in which to study adhesion dynamics. In the current study we formulated a mathematical model for cellular aggregation in a linear shear field based on Smoluchowski's two-body collision theory. Neutrophil suspensions activated with chemotactic stimulus and sheared in a cone-plate viscometer rapidly aggregate. Over a range of shear rates (400-800 s-1), approximately 90% of the single cells were recruited into aggregates ranging from doublets to groupings larger than sextuplets. The adhesion efficiency fit to these kinetics reached maximum levels of > 70%. Formed aggregates remained intact and resistant to shear up to 120 s, at which time they spontaneously dissociated back to singlets. The rate of cell disaggregation was linearly proportional to the applied shear rate, and it was approximately 60% lower for doublets as compared to larger aggregates. By accounting for the time-dependent changes in adhesion efficiency, disaggregation rate, and the effects of aggregate geometry, we succeeded in predicting the reversible kinetics of aggregation over a wide range of shear rates and cell concentrations. The combination of viscometry with flow cytometry and mathematical analysis as presented here represents a novel approach to differentiating between the effects of hydrodynamics and the intrinsic biological processes that control cell adhesion. Images FIGURE 3 FIGURE 5 PMID:9083659

A mechanistic model for the evolution of multicellularity

NASA Astrophysics Data System (ADS)

Amado, André; Batista, Carlos; Campos, Paulo R. A.

2018-02-01

Through a mechanistic approach we investigate the formation of aggregates of variable sizes, accounting mechanisms of aggregation, dissociation, death and reproduction. In our model, cells can produce two metabolites, but the simultaneous production of both metabolites is costly in terms of fitness. Thus, the formation of larger groups can favor the aggregates to evolve to a configuration where division of labor arises. It is assumed that the states of the cells in a group are those that maximize organismal fitness. In the model it is considered that the groups can grow linearly, forming a chain, or compactly keeping a roughly spherical shape. Starting from a population consisting of single-celled organisms, we observe the formation of groups with variable sizes and usually much larger than two-cell aggregates. Natural selection can favor the formation of large groups, which allows the system to achieve new and larger fitness maxima.

Dynamics of proteins aggregation. I. Universal scaling in unbounded media

NASA Astrophysics Data System (ADS)

Zheng, Size; Javidpour, Leili; Shing, Katherine S.; Sahimi, Muhammad

2016-10-01

It is well understood that in some cases proteins do not fold correctly and, depending on their environment, even properly-folded proteins change their conformation spontaneously, taking on a misfolded state that leads to protein aggregation and formation of large aggregates. An important factor that contributes to the aggregation is the interactions between the misfolded proteins. Depending on the aggregation environment, the aggregates may take on various shapes forming larger structures, such as protein plaques that are often toxic. Their deposition in tissues is a major contributing factor to many neuro-degenerative diseases, such as Alzheimer's, Parkinson's, amyotrophic lateral sclerosis, and prion. This paper represents the first part in a series devoted to molecular simulation of protein aggregation. We use the PRIME, a meso-scale model of proteins, together with extensive discontinuous molecular dynamics simulation to study the aggregation process in an unbounded fluid system, as the first step toward MD simulation of the same phenomenon in crowded cellular environments. Various properties of the aggregates have been computed, including dynamic evolution of aggregate-size distribution, mean aggregate size, number of peptides that contribute to the formation of β sheets, number of various types of hydrogen bonds formed in the system, radius of gyration of the aggregates, and the aggregates' diffusivity. We show that many of such quantities follow dynamic scaling, similar to those for aggregation of colloidal clusters. In particular, at long times the mean aggregate size S(t) grows with time as, S(t) ˜ tz, where z is the dynamic exponent. To our knowledge, this is the first time that the qualitative similarity between aggregation of proteins and colloidal aggregates has been pointed out.

Temperature dependence of aggregated structure of β-carotene by absorption spectral experiment and simulation

NASA Astrophysics Data System (ADS)

Lu, Liping; Wu, Jie; Wei, Liangshu; Wu, Fang

2016-12-01

β-carotene can self-assemble to form J- or H-type aggregate in hydrophilic environments, which is crucial for the proper functioning of biological system. Although several ways controlling the formation of the two types of aggregate in hydrated ethanol have been investigated in recent years, our study provided another way to control whether J- or H- β-carotene was formed and presented a method to investigate the aggregated structure. For this purpose, the aggregates of β-carotene formed at different temperatures were studied by UV-Vis spectra and a computational method based on Frenkel exciton was applied to simulate the absorption spectra to obtain the aggregated structure of the β-carotene. The analysis showed that β-carotene formed weakly coupled H-aggregate at 15 °C in 1:1 ethanol-water solvent, and with the increase of temperature it tended to form J-type of aggregate. The absorption spectral simulation based on one-dimensional Frenkel exciton model revealed that good fit with the experiment was obtained with distance between neighbor molecules r = 0.82 nm, disorder of the system D = 1500 cm- 1 for H-type and r = 1.04 nm, D = 1800 cm- 1 for J-type.

A microcomputer program for energy assessment and aggregation using the triangular probability distribution

USGS Publications Warehouse

Crovelli, R.A.; Balay, R.H.

1991-01-01

A general risk-analysis method was developed for petroleum-resource assessment and other applications. The triangular probability distribution is used as a model with an analytic aggregation methodology based on probability theory rather than Monte-Carlo simulation. Among the advantages of the analytic method are its computational speed and flexibility, and the saving of time and cost on a microcomputer. The input into the model consists of a set of components (e.g. geologic provinces) and, for each component, three potential resource estimates: minimum, most likely (mode), and maximum. Assuming a triangular probability distribution, the mean, standard deviation, and seven fractiles (F100, F95, F75, F50, F25, F5, and F0) are computed for each component, where for example, the probability of more than F95 is equal to 0.95. The components are aggregated by combining the means, standard deviations, and respective fractiles under three possible siutations (1) perfect positive correlation, (2) complete independence, and (3) any degree of dependence between these two polar situations. A package of computer programs named the TRIAGG system was written in the Turbo Pascal 4.0 language for performing the analytic probabilistic methodology. The system consists of a program for processing triangular probability distribution assessments and aggregations, and a separate aggregation routine for aggregating aggregations. The user's documentation and program diskette of the TRIAGG system are available from USGS Open File Services. TRIAGG requires an IBM-PC/XT/AT compatible microcomputer with 256kbyte of main memory, MS-DOS 3.1 or later, either two diskette drives or a fixed disk, and a 132 column printer. A graphics adapter and color display are optional. ?? 1991.

Determination of the critical micelle concentration in simulations of surfactant systems

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

Santos, Andrew P.; Panagiotopoulos, Athanassios Z., E-mail: azp@princeton.edu

Alternative methods for determining the critical micelle concentration (cmc) are investigated using canonical and grand canonical Monte Carlo simulations of a lattice surfactant model. A common measure of the cmc is the “free” (unassociated) surfactant concentration in the presence of micellar aggregates. Many prior simulations of micellizing systems have observed a decrease in the free surfactant concentration with overall surfactant loading for both ionic and nonionic surfactants, contrary to theoretical expectations from mass-action models of aggregation. In the present study, we investigate a simple lattice nonionic surfactant model in implicit solvent, for which highly reproducible simulations are possible in bothmore » the canonical (NVT) and grand canonical (μVT) ensembles. We confirm the previously observed decrease of free surfactant concentration at higher overall loadings and propose an algorithm for the precise calculation of the excluded volume and effective concentration of unassociated surfactant molecules in the accessible volume of the solution. We find that the cmc can be obtained by correcting the free surfactant concentration for volume exclusion effects resulting from the presence of micellar aggregates. We also develop an improved method for determination of the cmc based on the maximum in curvature for the osmotic pressure curve determined from μVT simulations. Excellent agreement in cmc and other micellar properties between NVT and μVT simulations of different system sizes is observed. The methodological developments in this work are broadly applicable to simulations of aggregating systems using any type of surfactant model (atomistic/coarse grained) or solvent description (explicit/implicit)« less

Balancing aggregation and smoothing errors in inverse models

DOE PAGES

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

2015-06-30

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

Balancing aggregation and smoothing errors in inverse models

NASA Astrophysics Data System (ADS)

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

2015-01-01

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

Balancing aggregation and smoothing errors in inverse models

NASA Astrophysics Data System (ADS)

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

2015-06-01

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

Shear-induced reaction-limited aggregation kinetics of Brownian particles at arbitrary concentrations

NASA Astrophysics Data System (ADS)

Zaccone, Alessio; Gentili, Daniele; Wu, Hua; Morbidelli, Massimo

2010-04-01

The aggregation of interacting Brownian particles in sheared concentrated suspensions is an important issue in colloid and soft matter science per se. Also, it serves as a model to understand biochemical reactions occurring in vivo where both crowding and shear play an important role. We present an effective medium approach within the Smoluchowski equation with shear which allows one to calculate the encounter kinetics through a potential barrier under shear at arbitrary colloid concentrations. Experiments on a model colloidal system in simple shear flow support the validity of the model in the concentration range considered. By generalizing Kramers' rate theory to the presence of shear and collective hydrodynamics, our model explains the significant increase in the shear-induced reaction-limited aggregation kinetics upon increasing the colloid concentration.

A local PDE model of aggregation formation in bacterial colonies

NASA Astrophysics Data System (ADS)

Chavy-Waddy, Paul-Christopher; Kolokolnikov, Theodore

2016-10-01

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

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.

A facile in vitro model to study rapid mineralization in bone tissues.

PubMed

Deegan, Anthony J; Aydin, Halil M; Hu, Bin; Konduru, Sandeep; Kuiper, Jan Herman; Yang, Ying

2014-09-16

Mineralization in bone tissue involves stepwise cell-cell and cell-ECM interaction. Regulation of osteoblast culture microenvironments can tailor osteoblast proliferation and mineralization rate, and the quality and/or quantity of the final calcified tissue. An in vitro model to investigate the influencing factors is highly required. We developed a facile in vitro model in which an osteoblast cell line and aggregate culture (through the modification of culture well surfaces) were used to mimic intramembranous bone mineralization. The effect of culture environments including culture duration (up to 72 hours for rapid mineralization study) and aggregates size (monolayer culture as control) on mineralization rate and mineral quantity/quality were examined by osteogenic gene expression (PCR) and mineral markers (histological staining, SEM-EDX and micro-CT). Two size aggregates (on average, large aggregates were 745 μm and small 79 μm) were obtained by the facile technique with high yield. Cells in aggregate culture generated visible and quantifiable mineralized matrix within 24 hours, whereas cells in monolayer failed to do so by 72 hours. The gene expression of important ECM molecules for bone formation including collagen type I, alkaline phosphatase, osteopontin and osteocalcin, varied temporally, differed between monolayer and aggregate cultures, and depended on aggregate size. Monolayer specimens stayed in a proliferation phase for the first 24 hours, and remained in matrix synthesis up to 72 hours; whereas the small aggregates were in the maturation phase for the first 24 and 48 hour cultures and then jumped to a mineralization phase at 72 hours. Large aggregates were in a mineralization phase at all these three time points and produced 36% larger bone nodules with a higher calcium content than those in the small aggregates after just 72 hours in culture. This study confirms that aggregate culture is sufficient to induce rapid mineralization and that aggregate size determines the mineralization rate. Mineral content depended on aggregate size and culture duration. Thus, our culture system may provide a good model to study regulation factors at different development phases of the osteoblastic lineage.

Flow Partitioning in Fully Saturated Soil Aggregates

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

Yang, Xiaofan; Richmond, Marshall C.; Scheibe, Timothy D.

2014-03-30

Microbes play an important role in facilitating organic matter decomposition in soils, which is a major component of the global carbon cycle. Microbial dynamics are intimately coupled to environmental transport processes, which control access to labile organic matter and other nutrients that are needed for the growth and maintenance of microorganisms. Transport of soluble nutrients in the soil system is arguably most strongly impacted by preferential flow pathways in the soil. Since the physical structure of soils can be characterized as being formed from constituent micro aggregates which contain internal porosity, one pressing question is the partitioning of the flowmore » among the “inter-aggregate” and “intra-aggregate” pores and how this may impact overall solute transport within heterogeneous soil structures. The answer to this question is particularly important in evaluating assumptions to be used in developing upscaled simulations based on highly-resolved mechanistic models. We constructed a number of diverse multi-aggregate structures with different packing ratios by stacking micro-aggregates containing internal pores and varying the size and shape of inter-aggregate pore spacing between them. We then performed pore-scale flow simulations using computational fluid dynamics methods to determine the flow patterns in these aggregate-of-aggregates structures and computed the partitioning of the flow through intra- and inter-aggregate pores as a function of the spacing between the aggregates. The results of these numerical experiments demonstrate that soluble nutrients are largely transported via flows through inter-aggregate pores. Although this result is consistent with intuition, we have also been able to quantify the relative flow capacity of the two domains under various conditions. For example, in our simulations, the flow capacity through the aggregates (intra-aggregate flow) was less than 2% of the total flow when the spacing between the aggregates was larger than 18 micron. Inter-aggregate pores continued to be the dominant flow pathways even at much smaller spacing; intra-aggregate flow was less than 10% of the total flow when the inter- and intra-aggregate pore sizes were comparable. Such studies are making it possible to identify which model upscaling assumptions are realistic and what computational methods are required for detailed numerical investigation of microbial carbon cycling dynamics in soil systems.« less

Sustainability in Supply Chain Management: Aggregate Planning from Sustainability Perspective.

PubMed

Türkay, Metin; Saraçoğlu, Öztürk; Arslan, Mehmet Can

2016-01-01

Supply chain management that considers the flow of raw materials, products and information has become a focal issue in modern manufacturing and service systems. Supply chain management requires effective use of assets and information that has far reaching implications beyond satisfaction of customer demand, flow of goods, services or capital. Aggregate planning, a fundamental decision model in supply chain management, refers to the determination of production, inventory, capacity and labor usage levels in the medium term. Traditionally standard mathematical programming formulation is used to devise the aggregate plan so as to minimize the total cost of operations. However, this formulation is purely an economic model that does not include sustainability considerations. In this study, we revise the standard aggregate planning formulation to account for additional environmental and social criteria to incorporate triple bottom line consideration of sustainability. We show how these additional criteria can be appended to traditional cost accounting in order to address sustainability in aggregate planning. We analyze the revised models and interpret the results on a case study from real life that would be insightful for decision makers.

Sustainability in Supply Chain Management: Aggregate Planning from Sustainability Perspective

PubMed Central

Türkay, Metin; Saraçoğlu, Öztürk; Arslan, Mehmet Can

2016-01-01

Supply chain management that considers the flow of raw materials, products and information has become a focal issue in modern manufacturing and service systems. Supply chain management requires effective use of assets and information that has far reaching implications beyond satisfaction of customer demand, flow of goods, services or capital. Aggregate planning, a fundamental decision model in supply chain management, refers to the determination of production, inventory, capacity and labor usage levels in the medium term. Traditionally standard mathematical programming formulation is used to devise the aggregate plan so as to minimize the total cost of operations. However, this formulation is purely an economic model that does not include sustainability considerations. In this study, we revise the standard aggregate planning formulation to account for additional environmental and social criteria to incorporate triple bottom line consideration of sustainability. We show how these additional criteria can be appended to traditional cost accounting in order to address sustainability in aggregate planning. We analyze the revised models and interpret the results on a case study from real life that would be insightful for decision makers. PMID:26807848

Direct Visualization of Aggregate Morphology and Dynamics in a Model Soil Organic–Mineral System

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

Hufschmid, Ryan; Newcomb, Christina J.; Grate, Jay W.

Interactions between mineral surfaces and organic matter are ubiquitous in soils and the environment. Through both physical and chemical mechanisms, organic-mineral assemblages prevent decomposition of soil organic matter by limiting accessibility or reducing efficacy of enzymes and microbes. To understand the mechanisms underlying organic-mineral interactions, researchers have begun to interrogate these systems at smaller length scales. Current techniques that maintain a hydrated state and allow researchers to characterize nanometer length scales are limited. Here we chose a model organic-mineral system and performed complementary imaging techniques that enable direct nanoscale observations in environmentally relevant conditions: cryogenic TEM and in-situ liquid cellmore » TEM. We observed a three-fold increase in aggregate size of goethite nanoparticles upon addition of a model organic phosphate ligand and quantification of nanoparticle orientation reveals a preference for side-to-side interactions independent of the addition of an organic ligand. Additionally, in-situ liquid cell TEM experiments provides a dynamic view of the interactions allowing us to report velocities of mineral assemblages during aggregation and disaggregation, which could potentially provide binding energetics and kinetic parameters about organic-mineral and mineral-mineral systems.« less

Economic dynamics with financial fragility and mean-field interaction: A model

NASA Astrophysics Data System (ADS)

Di Guilmi, C.; Gallegati, M.; Landini, S.

2008-06-01

Following Aoki’s statistical mechanics methodology [Masanao Aoki, New Approaches to Macroeconomic Modeling, Cambridge University Press, 1996; Masanao Aoki, Modeling Aggregate Behaviour and Fluctuations in Economics, Cambridge University Press, 2002; Masanao Aoki, and Hiroshi Yoshikawa, Reconstructing Macroeconomics, Cambridge University Press, 2006], we provide some insights into the well-known works of [Bruce Greenwald, Joseph Stiglitz, Macroeconomic models with equity and credit rationing, in: R. Hubbard (Ed.), Information, Capital Markets and Investment, Chicago University Press, Chicago, 1990; Bruce Greenwald, Joseph Stiglitz, Financial markets imperfections and business cycles, Quarterly journal of Economics (1993)]. Specifically, we reach analytically a closed form solution of their models overcoming the aggregation problem. The key idea is to represent the economy as an evolving complex system, composed by heterogeneous interacting agents, that can be partitioned into a space of macroscopic states. This meso level of aggregation permits to adopt mean-field interaction modeling and master equation techniques.

Lattice animals in diffusion limited binary colloidal system

NASA Astrophysics Data System (ADS)

Shireen, Zakiya; Babu, Sujin B.

2017-08-01

In a soft matter system, controlling the structure of the amorphous materials has been a key challenge. In this work, we have modeled irreversible diffusion limited cluster aggregation of binary colloids, which serves as a model for chemical gels. Irreversible aggregation of binary colloidal particles leads to the formation of a percolating cluster of one species or both species which are also called bigels. Before the formation of the percolating cluster, the system forms a self-similar structure defined by a fractal dimension. For a one component system when the volume fraction is very small, the clusters are far apart from each other and the system has a fractal dimension of 1.8. Contrary to this, we will show that for the binary system, we observe the presence of lattice animals which has a fractal dimension of 2 irrespective of the volume fraction. When the clusters start inter-penetrating, we observe a fractal dimension of 2.5, which is the same as in the case of the one component system. We were also able to predict the formation of bigels using a simple inequality relation. We have also shown that the growth of clusters follows the kinetic equations introduced by Smoluchowski for diffusion limited cluster aggregation. We will also show that the chemical distance of a cluster in the flocculation regime will follow the same scaling law as predicted for the lattice animals. Further, we will also show that irreversible binary aggregation comes under the universality class of the percolation theory.

Effects of recombinant protein misfolding and aggregation on bacterial membranes.

PubMed

Ami, D; Natalello, A; Schultz, T; Gatti-Lafranconi, P; Lotti, M; Doglia, S M; de Marco, A

2009-02-01

The expression of recombinant proteins is known to induce a metabolic rearrangement in the host cell. We used aggregation-sensitive model systems to study the effects elicited in Escherichia coli cells by the aggregation of recombinant glutathione-S-transferase and its fusion with the green fluorescent protein that, according to the expression conditions, accumulate intracellularly as soluble protein, or soluble and insoluble aggregates. We show that the folding state of the recombinant protein and the complexity of the intracellular aggregates critically affect the cell response. Specifically, protein misfolding and aggregation induce changes in specific host proteins involved in lipid metabolism and oxidative stress, a reduction in the membrane permeability, as well as a rearrangement of its lipid composition. The temporal evolution of the host cell response and that of the aggregation process pointed out that the misfolded protein and soluble aggregates are responsible for the membrane modifications and the changes in the host protein levels. Interestingly, native recombinant protein and large insoluble aggregates do not seem to activate stress markers and membrane rearrangements.

An energy landscape approach to protein aggregation

NASA Astrophysics Data System (ADS)

Buell, Alexander; Knowles, Tuomas

2012-02-01

Protein aggregation into ordered fibrillar structures is the hallmark of a class of diseases, the most prominent examples of which are Alzheimer's and Parkinson's disease. Recent results (e.g. Baldwin et al. J. Am. Chem. Soc. 2011) suggest that the aggregated state of a protein is in many cases thermodynamically more stable than the soluble state. Therefore the solubility of proteins in a cellular context appears to be to a large extent under kinetic control. Here, we first present a conceptual framework for the description of protein aggregation ( see AK Buell et al., Phys. Rev. Lett. 2010) that is an extension to the generally accepted energy landscape model for protein folding. Then we apply this model to analyse and interpret a large set of experimental data on the kinetics of protein aggregation, acquired mainly with a novel biosensing approach (see TPJK Knowles et al, Proc. Nat. Acad. Sc. 2007). We show how for example the effect of sequence modifications on the kinetics and thermodynamics of human lysozyme aggregation can be understood and quantified (see AK Buell et al., J. Am. Chem. Soc. 2011). These results have important implications for therapeutic strategies against protein aggregation disorders, in this case lysozyme systemic amyloidosis.

Self-organized, near-critical behavior during aggregation in Dictyostelium discoideum

NASA Astrophysics Data System (ADS)

de Palo, Giovanna; Yi, Darvin; Gregor, Thomas; Endres, Robert

During starvation, the social amoeba Dictyostelium discoideum aggregates artfully via pattern formation into a multicellular slug and finally spores. The aggregation process is mediated by the secretion and sensing of cyclic adenosine monophosphate, leading to the synchronized movement of cells. The whole process is a remarkable example of collective behavior, spontaneously emerging from single-cell chemotaxis. Despite this phenomenon being broadly studied, a precise characterization of the transition from single cells to multicellularity has been elusive. Here, using fluorescence imaging data of thousands of cells, we investigate the role of cell shape in aggregation, demonstrating remarkable transitions in cell behavior. To better understand their functional role, we analyze cell-cell correlations and provide evidence for self-organization at the onset of aggregation (as opposed to leader cells), with features of criticality in this finite system. To capture the mechanism of self-organization, we extend a detailed single-cell model of D.discoideum chemotaxis by adding cell-cell communication. We then use these results to extract a minimal set of rules leading to aggregation in the population model. If universal, similar rules may explain other types of collective cell behavior.

Inverting pump-probe spectroscopy for state tomography of excitonic systems.

PubMed

Hoyer, Stephan; Whaley, K Birgitta

2013-04-28

We propose a two-step protocol for inverting ultrafast spectroscopy experiments on a molecular aggregate to extract the time-evolution of the excited state density matrix. The first step is a deconvolution of the experimental signal to determine a pump-dependent response function. The second step inverts this response function to obtain the quantum state of the system, given a model for how the system evolves following the probe interaction. We demonstrate this inversion analytically and numerically for a dimer model system, and evaluate the feasibility of scaling it to larger molecular aggregates such as photosynthetic protein-pigment complexes. Our scheme provides a direct alternative to the approach of determining all Hamiltonian parameters and then simulating excited state dynamics.

Numerical modeling of sorption kinetics of organic compounds to soil and sediment particles

NASA Astrophysics Data System (ADS)

Wu, Shian-chee; Gschwend, Phillip M.

1988-08-01

A numerical model is developed to simulate hydrophobic organic compound sorption kinetics, based on a retarded intraaggregate diffusion conceptualization of this solid-water exchange process. This model was used to ascertain the sensitivity of the sorption process for various sorbates to nonsteady solution concentrations and to polydisperse soil or sediment aggregate particle size distributions. Common approaches to modeling sorption kinetics amount to simplifications of our model and appear justified only when (1) the concentration fluctuations occur on a time scale which matches the sorption timescale of interest and (2) the particle size distribution is relatively narrow. Finally, a means is provided to estimate the extent of approach of a sorbing system to equilibrium as a function of aggregate size, chemical diffusivity and hydrophobicity, and system solids concentration.

Performance of the Multi-Radar Multi-Sensor System over the Lower Colorado River, Texas

NASA Astrophysics Data System (ADS)

Bayabil, H. K.; Sharif, H. O.; Fares, A.; Awal, R.; Risch, E.

2017-12-01

Recently observed increases in intensities and frequencies of climate extremes (e.g., floods, dam failure, and overtopping of river banks) necessitate the development of effective disaster prevention and mitigation strategies. Hydrologic models can be useful tools in predicting such events at different spatial and temporal scales. However, accuracy and prediction capability of such models are often constrained by the availability of high-quality representative hydro-meteorological data (e.g., precipitation) that are required to calibrate and validate such models. Improved technologies and products such as the Multi-Radar Multi-Sensor (MRMS) system that allows gathering and transmission of vast meteorological data have been developed to provide such data needs. While the MRMS data are available with high spatial and temporal resolutions (1 km and 15 min, respectively), its accuracy in estimating precipitation is yet to be fully investigated. Therefore, the main objective of this study is to evaluate the performance of the MRMS system in effectively capturing precipitation over the Lower Colorado River, Texas using observations from a dense rain gauge network. In addition, effects of spatial and temporal aggregation scales on the performance of the MRMS system were evaluated. Point scale comparisons were made at 215 gauging locations using rain gauges and MRMS data from May 2015. Moreover, the effects of temporal and spatial data aggregation scales (30, 45, 60, 75, 90, 105, and 120 min) and (4 to 50 km), respectively on the performance of the MRMS system were tested. Overall, the MRMS system (at 15 min temporal resolution) captured precipitation reasonably well, with an average R2 value of 0.65 and RMSE of 0.5 mm. In addition, spatial and temporal data aggregations resulted in increases in R2 values. However, reduction in RMSE was achieved only with an increase in spatial aggregations.

Scaling water and energy fluxes in climate systems - Three land-atmospheric modeling experiments

NASA Technical Reports Server (NTRS)

Wood, Eric F.; Lakshmi, Venkataraman

1993-01-01

Three numerical experiments that investigate the scaling of land-surface processes - either of the inputs or parameters - are reported, and the aggregated processes are compared to the spatially variable case. The first is the aggregation of the hydrologic response in a catchment due to rainfall during a storm event and due to evaporative demands during interstorm periods. The second is the spatial and temporal aggregation of latent heat fluxes, as calculated from SiB. The third is the aggregation of remotely sensed land vegetation and latent and sensible heat fluxes using TM data from the FIFE experiment of 1987 in Kansas. In all three experiments it was found that the surface fluxes and land characteristics can be scaled, and that macroscale models based on effective parameters are sufficient to account for the small-scale heterogeneities investigated.

A distributed snow-evolution modeling system (SnowModel)

Treesearch

Glen E. Liston; Kelly Elder

2006-01-01

SnowModel is a spatially distributed snow-evolution modeling system designed for application in landscapes, climates, and conditions where snow occurs. It is an aggregation of four submodels: MicroMet defines meteorological forcing conditions, EnBal calculates surface energy exchanges, SnowPack simulates snow depth and water-equivalent evolution, and SnowTran-3D...

Modeling and self-assembly behavior of PEG-PLA-PEG triblock copolymers in aqueous solution

NASA Astrophysics Data System (ADS)

Wu, Xiaohan; Li, Suming; Coumes, Fanny; Darcos, Vincent; Lai Kee Him, Joséphine; Bron, Patrick

2013-09-01

A series of poly(ethylene glycol)-polylactide-poly(ethylene glycol) (PEG-PLA-PEG) triblock copolymers with symmetric or asymmetric chain structures were synthesized by combination of ring-opening polymerization and copper-catalyzed click chemistry. The resulting copolymers were used to prepare self-assembled aggregates by dialysis. Various architectures such as nanotubes, polymersomes and spherical micelles were observed from transmission electron microscopy (TEM), cryo-TEM and atomic force microscopy (AFM) measurements. The formation of diverse aggregates is explained by modeling from the angle of both geometry and thermodynamics. From the angle of geometry, a ``blob'' model based on the Daoud-Cotton model for star polymers is proposed to describe the aggregate structures and structural changes with copolymer composition and molar mass. In fact, the copolymer chains extend in aqueous medium to form single layer polymersomes to minimize the system's free energy if one of the two PEG blocks is short enough. The curvature of polymersomes is dependent on the chain structure of copolymers, especially on the length of PLA blocks. A constant branch number of aggregates (f) is thus required to preserve the morphology of polymersomes. Meanwhile, the aggregation number (Nagg) determined from the thermodynamics of self-assembly is roughly proportional to the total length of polymer chains. Comparing f to Nagg, the aggregates take the form of polymersomes if Nagg ~ f, and change to nanotubes if Nagg > f to conform to the limits from both curvature and aggregation number. The length of nanotubes is mainly determined by the difference between Nagg and f. However, the hollow structure becomes unstable when both PEG segments are too long, and the aggregates eventually collapse to yield spherical micelles. Therefore, this work gives new insights into the self-assembly behavior of PEG-PLA-PEG triblock copolymers in aqueous solution which present great interest for biomedical and pharmaceutical applications.A series of poly(ethylene glycol)-polylactide-poly(ethylene glycol) (PEG-PLA-PEG) triblock copolymers with symmetric or asymmetric chain structures were synthesized by combination of ring-opening polymerization and copper-catalyzed click chemistry. The resulting copolymers were used to prepare self-assembled aggregates by dialysis. Various architectures such as nanotubes, polymersomes and spherical micelles were observed from transmission electron microscopy (TEM), cryo-TEM and atomic force microscopy (AFM) measurements. The formation of diverse aggregates is explained by modeling from the angle of both geometry and thermodynamics. From the angle of geometry, a ``blob'' model based on the Daoud-Cotton model for star polymers is proposed to describe the aggregate structures and structural changes with copolymer composition and molar mass. In fact, the copolymer chains extend in aqueous medium to form single layer polymersomes to minimize the system's free energy if one of the two PEG blocks is short enough. The curvature of polymersomes is dependent on the chain structure of copolymers, especially on the length of PLA blocks. A constant branch number of aggregates (f) is thus required to preserve the morphology of polymersomes. Meanwhile, the aggregation number (Nagg) determined from the thermodynamics of self-assembly is roughly proportional to the total length of polymer chains. Comparing f to Nagg, the aggregates take the form of polymersomes if Nagg ~ f, and change to nanotubes if Nagg > f to conform to the limits from both curvature and aggregation number. The length of nanotubes is mainly determined by the difference between Nagg and f. However, the hollow structure becomes unstable when both PEG segments are too long, and the aggregates eventually collapse to yield spherical micelles. Therefore, this work gives new insights into the self-assembly behavior of PEG-PLA-PEG triblock copolymers in aqueous solution which present great interest for biomedical and pharmaceutical applications. Electronic supplementary information (ESI) available: 1H-NMR, DOSY, FTIR, and GPC measurements, methods and results of the copolymers in PEG-PLA-PEG synthesis. See DOI: 10.1039/c3nr02899b

The effect of pH and concentration upon aggregation transitions in aqueous solutions of poloxamine T701.

PubMed

Armstrong, J K; Chowdhry, B Z; Snowden, M J; Dong, J; Leharne, S A

2001-10-23

Thermally induced aggregation transitions have been investigated for aqueous solutions of the poloxamine block copolymer T701-(OE(4)OP(13))(2)NCH(2)CH(2)N(OP(13)OE(4))(2)-using differential scanning calorimetry. The calorimetric signals obtained were fitted to a mass action model description of aggregation using a previously reported analytical procedure (Patterson et al., Langmuir 13 (1997) 2219). The presence of a central ethylene diamine moiety in the molecular structure renders the T701 molecule basic; this was confirmed and measured by acid/base titration. Basicity is shown to have an important impact upon aggregation. At low pH (2.5), the poloxamine exists in its protonated form and the bulk solution proton concentration is sufficient to suppress de-protonation, aggregation-as a consequence-is shifted to a higher temperature range. Any increase in pH reduces the temperature range over which aggregation occurs. The derived experimental calorimetric parameters, obtained from model fitting procedures, can be used to compute the fraction of poloxamine existing in an aggregated form, at any particular temperature. The data sets obtained were interpolated to show that at human body temperature (310.6 K) the fraction of poloxamine found in its aggregated form is zero at a pH of 2.5. However at a pH of 6.8, the percentage aggregation increases to about 85%. These aggregation characteristics of T701 have important implications for the design of drug delivery systems, which incorporate poloxamines.

A colloidal singularity reveals the crucial role of colloidal stability for nanomaterials in-vitro toxicity testing: nZVI-microalgae colloidal system as a case study.

PubMed

Gonzalo, Soledad; Llaneza, Veronica; Pulido-Reyes, Gerardo; Fernández-Piñas, Francisca; Bonzongo, Jean Claude; Leganes, Francisco; Rosal, Roberto; García-Calvo, Eloy; Rodea-Palomares, Ismael

2014-01-01

Aggregation raises attention in Nanotoxicology due to its methodological implications. Aggregation is a physical symptom of a more general physicochemical condition of colloidal particles, namely, colloidal stability. Colloidal stability is a global indicator of the tendency of a system to reduce its net surface energy, which may be achieved by homo-aggregation or hetero-aggregation, including location at bio-interfaces. However, the role of colloidal stability as a driver of ENM bioactivity has received little consideration thus far. In the present work, which focuses on the toxicity of nanoscaled Fe° nanoparticles (nZVI) towards a model microalga, we demonstrate that colloidal stability is a fundamental driver of ENM bioactivity, comprehensively accounting for otherwise inexplicable differential biological effects. The present work throws light on basic aspects of Nanotoxicology, and reveals a key factor which may reconcile contradictory results on the influence of aggregation in bioactivity of ENMs.

A Colloidal Singularity Reveals the Crucial Role of Colloidal Stability for Nanomaterials In-Vitro Toxicity Testing: nZVI-Microalgae Colloidal System as a Case Study

PubMed Central

Fernández-Piñas, Francisca; Bonzongo, Jean Claude; Leganes, Francisco; Rosal, Roberto; García-Calvo, Eloy; Rodea-Palomares, Ismael

2014-01-01

Aggregation raises attention in Nanotoxicology due to its methodological implications. Aggregation is a physical symptom of a more general physicochemical condition of colloidal particles, namely, colloidal stability. Colloidal stability is a global indicator of the tendency of a system to reduce its net surface energy, which may be achieved by homo-aggregation or hetero-aggregation, including location at bio-interfaces. However, the role of colloidal stability as a driver of ENM bioactivity has received little consideration thus far. In the present work, which focuses on the toxicity of nanoscaled Fe° nanoparticles (nZVI) towards a model microalga, we demonstrate that colloidal stability is a fundamental driver of ENM bioactivity, comprehensively accounting for otherwise inexplicable differential biological effects. The present work throws light on basic aspects of Nanotoxicology, and reveals a key factor which may reconcile contradictory results on the influence of aggregation in bioactivity of ENMs. PMID:25340509

Programmed coherent coupling in a synthetic DNA-based excitonic circuit

NASA Astrophysics Data System (ADS)

Boulais, Étienne; Sawaya, Nicolas P. D.; Veneziano, Rémi; Andreoni, Alessio; Banal, James L.; Kondo, Toru; Mandal, Sarthak; Lin, Su; Schlau-Cohen, Gabriela S.; Woodbury, Neal W.; Yan, Hao; Aspuru-Guzik, Alán; Bathe, Mark

2018-02-01

Natural light-harvesting systems spatially organize densely packed chromophore aggregates using rigid protein scaffolds to achieve highly efficient, directed energy transfer. Here, we report a synthetic strategy using rigid DNA scaffolds to similarly program the spatial organization of densely packed, discrete clusters of cyanine dye aggregates with tunable absorption spectra and strongly coupled exciton dynamics present in natural light-harvesting systems. We first characterize the range of dye-aggregate sizes that can be templated spatially by A-tracts of B-form DNA while retaining coherent energy transfer. We then use structure-based modelling and quantum dynamics to guide the rational design of higher-order synthetic circuits consisting of multiple discrete dye aggregates within a DX-tile. These programmed circuits exhibit excitonic transport properties with prominent circular dichroism, superradiance, and fast delocalized exciton transfer, consistent with our quantum dynamics predictions. This bottom-up strategy offers a versatile approach to the rational design of strongly coupled excitonic circuits using spatially organized dye aggregates for use in coherent nanoscale energy transport, artificial light-harvesting, and nanophotonics.

Aggregation of the rhizospheric bacterium Azospirillum brasilense in response to oxygen

NASA Astrophysics Data System (ADS)

Abdoun, Hamid; McMillan, Mary; Pereg, Lily

2016-04-01

Azospirillum brasilense spp. have ecological, scientific and agricultural importance. As model plant growth promoting rhizobacteria they interact with a large variety of plants, including important food and cash crops. Azospirillum strains are known for their production of plant growth hormones that enhance root systems and for their ability to fix nitrogen. Azospirillum cells transform in response to environmental cues. The production of exopolysaccharides and cell aggregation during cellular transformation are important steps in the attachment of Azospirillum to roots. We investigate signals that induce cellular transformation and aggregation in the Azospirillum and report on the importance of oxygen to the process of aggregation in this rhizospheric bacterium.

Curcumin inhibits aggregation of alpha-synuclein.

PubMed

Pandey, Neeraj; Strider, Jeffrey; Nolan, William C; Yan, Sherry X; Galvin, James E

2008-04-01

Aggregation of amyloid-beta protein (Abeta) is a key pathogenic event in Alzheimer's disease (AD). Curcumin, a constituent of the Indian spice Turmeric is structurally similar to Congo Red and has been demonstrated to bind Abeta amyloid and prevent further oligomerization of Abeta monomers onto growing amyloid beta-sheets. Reasoning that oligomerization kinetics and mechanism of amyloid formation are similar in Parkinson's disease (PD) and AD, we investigated the effect of curcumin on alpha-synuclein (AS) protein aggregation. In vitro model of AS aggregation was developed by treatment of purified AS protein (wild-type) with 1 mM Fe3+ (Fenton reaction). It was observed that the addition of curcumin inhibited aggregation in a dose-dependent manner and increased AS solubility. The aggregation-inhibiting effect of curcumin was next investigated in cell culture utilizing catecholaminergic SH-SY5Y cell line. A model system was developed in which the red fluorescent protein (DsRed2) was fused with A53T mutant of AS and its aggregation examined under different concentrations of curcumin. To estimate aggregation in an unbiased manner, a protocol was developed in which the images were captured automatically through a high-throughput cell-based screening microscope. The obtained images were processed automatically for aggregates within a defined dimension of 1-6 microm. Greater than 32% decrease in mutant alpha-synuclein aggregation was observed within 48 h subsequent to curcumin addition. Our data suggest that curcumin inhibits AS oligomerization into higher molecular weight aggregates and therefore should be further explored as a potential therapeutic compound for PD and related disorders.

Dynamics of proteins aggregation. II. Dynamic scaling in confined media

NASA Astrophysics Data System (ADS)

Zheng, Size; Shing, Katherine S.; Sahimi, Muhammad

2018-03-01

In this paper, the second in a series devoted to molecular modeling of protein aggregation, a mesoscale model of proteins together with extensive discontinuous molecular dynamics simulation is used to study the phenomenon in a confined medium. The medium, as a model of a crowded cellular environment, is represented by a spherical cavity, as well as cylindrical tubes with two aspect ratios. The aggregation process leads to the formation of β sheets and eventually fibrils, whose deposition on biological tissues is believed to be a major factor contributing to many neuro-degenerative diseases, such as Alzheimer's, Parkinson's, and amyotrophic lateral sclerosis diseases. Several important properties of the aggregation process, including dynamic evolution of the total number of the aggregates, the mean aggregate size, and the number of peptides that contribute to the formation of the β sheets, have been computed. We show, similar to the unconfined media studied in Paper I [S. Zheng et al., J. Chem. Phys. 145, 134306 (2016)], that the computed properties follow dynamic scaling, characterized by power laws. The existence of such dynamic scaling in unconfined media was recently confirmed by experiments. The exponents that characterize the power-law dependence on time of the properties of the aggregation process in spherical cavities are shown to agree with those in unbounded fluids at the same protein density, while the exponents for aggregation in the cylindrical tubes exhibit sensitivity to the geometry of the system. The effects of the number of amino acids in the protein, as well as the size of the confined media, have also been studied. Similarities and differences between aggregation in confined and unconfined media are described, including the possibility of no fibril formation, if confinement is severe.

Validation of a multi-criteria evaluation model for animal welfare.

PubMed

Martín, P; Czycholl, I; Buxadé, C; Krieter, J

2017-04-01

The aim of this paper was to validate an alternative multi-criteria evaluation system to assess animal welfare on farms based on the Welfare Quality® (WQ) project, using an example of welfare assessment of growing pigs. This alternative methodology aimed to be more transparent for stakeholders and more flexible than the methodology proposed by WQ. The WQ assessment protocol for growing pigs was implemented to collect data in different farms in Schleswig-Holstein, Germany. In total, 44 observations were carried out. The aggregation system proposed in the WQ protocol follows a three-step aggregation process. Measures are aggregated into criteria, criteria into principles and principles into an overall assessment. This study focussed on the first two steps of the aggregation. Multi-attribute utility theory (MAUT) was used to produce a value of welfare for each criterion and principle. The utility functions and the aggregation function were constructed in two separated steps. The MACBETH (Measuring Attractiveness by a Categorical-Based Evaluation Technique) method was used for utility function determination and the Choquet integral (CI) was used as an aggregation operator. The WQ decision-makers' preferences were fitted in order to construct the utility functions and to determine the CI parameters. The validation of the MAUT model was divided into two steps, first, the results of the model were compared with the results of the WQ project at criteria and principle level, and second, a sensitivity analysis of our model was carried out to demonstrate the relative importance of welfare measures in the different steps of the multi-criteria aggregation process. Using the MAUT, similar results were obtained to those obtained when applying the WQ protocol aggregation methods, both at criteria and principle level. Thus, this model could be implemented to produce an overall assessment of animal welfare in the context of the WQ protocol for growing pigs. Furthermore, this methodology could also be used as a framework in order to produce an overall assessment of welfare for other livestock species. Two main findings are obtained from the sensitivity analysis, first, a limited number of measures had a strong influence on improving or worsening the level of welfare at criteria level and second, the MAUT model was not very sensitive to an improvement in or a worsening of single welfare measures at principle level. The use of weighted sums and the conversion of disease measures into ordinal scores should be reconsidered.

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

NASA Astrophysics Data System (ADS)

Barberis, Lucas; Peruani, Fernando

2016-12-01

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

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

PubMed

Barberis, Lucas; Peruani, Fernando

2016-12-09

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

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

USGS Publications Warehouse

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

1992-01-01

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

Using partial site aggregation to reduce bias in random utility travel cost models

NASA Astrophysics Data System (ADS)

Lupi, Frank; Feather, Peter M.

1998-12-01

We propose a "partial aggregation" strategy for defining the recreation sites that enter choice sets in random utility models. Under the proposal, the most popular sites and sites that will be the subject of policy analysis enter choice sets as individual sites while remaining sites are aggregated into groups of similar sites. The scheme balances the desire to include all potential substitute sites in the choice sets with practical data and modeling constraints. Unlike fully aggregate models, our analysis and empirical applications suggest that the partial aggregation approach reasonably approximates the results of a disaggregate model. The partial aggregation approach offers all of the data and computational advantages of models with aggregate sites but does not suffer from the same degree of bias as fully aggregate models.

Aggregate driver model to enable predictable behaviour

NASA Astrophysics Data System (ADS)

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

2015-09-01

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

Effects of Charge-Transfer Excitons on the Photophysics of Organic Semiconductors

NASA Astrophysics Data System (ADS)

Hestand, Nicholas J.

The field of organic electronics has received considerable attention over the past several years due to the promise of novel electronic materials that are cheap, flexible and light weight. While some devices based on organic materials have already emerged on the market (e.g. organic light emitting diodes), a deeper understanding of the excited states within the condensed phase is necessary both to improve current commercial products and to develop new materials for applications that are currently in the commercial pipeline (e.g. organic photovoltaics, wearable displays, and field effect transistors). To this end, a model for pi-conjugated molecular aggregates and crystals is developed and analyzed. The model considers two types of electronic excitations, namely Frenkel and charge-transfer excitons, both of which play a prominent role in determining the nature of the excited states within tightly-packed organic systems. The former consist of an electron-hole pair bound to the same molecule while in the later the electron and hole are located on different molecules. The model also considers the important nuclear reorganization that occurs when the system switches between electronic states. This is achieved using a Holstein-style Hamiltonian that includes linear vibronic coupling of the electronic states to the nuclear motion associated with the high frequency vinyl-stretching and ring-breathing modes. Analysis of the model reveals spectroscopic signatures of charge-transfer mediated J- and H-aggregation in systems where the photophysical properties are determined primarily by charge-transfer interactions. Importantly, such signatures are found to be sensitive to the relative phase of the intermolecular electron and hole transfer integrals, and the relative energy of the Frenkel and charge-transfer states. When the charge-transfer integrals are in phase and the energy of the charge-transfer state is higher than the Frenkel state, the system exhibits J-aggregate characteristics including a positive band curvature, a red shifted main absorption peak, and an increase in the ratio of the first two vibronic peaks relative to the monomer. On the other hand, when the charge-transfer integrals are out of phase and the energy of the charge-transfer state is higher than the Frenkel state, the system exhibits H-aggregate characteristics including a negative band curvature, a blue shifted main absorption peak, and a decrease in the ratio of the first two vibronic peaks relative to the monomer. Notably, these signatures are consistent with those exhibited by Coulombically coupled J- and H-aggregates. Additional signatures of charge-transfer J- and H-aggregation are also discovered, the most notable of which is the appearance of a second absorption band when the charge-transfer integrals are in phase and the charge-transfer and Frenkel excitons are near resonance. In such instances, the peak-to-peak spacing is found to be proportional to the sum of the electron and hole transfer integrals. Further analysis of the charge-transfer interactions within the context of an effective Frenkel exciton coupling reveals that the charge-transfer interactions interfere directly with the intermolecular Coulombic coupling. The interference can be either constructive or destructive resulting in either enhanced or suppressed J- or H- aggregate behavior relative to what is expected based on Coulombic coupling alone. Such interferences result in four new aggregate types, namely HH-, HJ-, JH-, and JJ-aggregates, where the first letter indicates the nature of the Coulombic coupling and the second indicates the nature of the charge-transfer coupling. Vibronic signatures of such aggregates are developed and provide a means by which to rapidly screen materials for certain electronic characteristics. Notably, a large total (Coulombic plus charge-transfer) exciton coupling is associated with an absorption spectrum in which the ratio of the first two vibronic peaks deviates significantly from that of the unaggregated monomer. Hence, strongly coupled, high exciton mobility aggregates can be readily distinguished from low mobility aggregates by the ratio of their first two vibronic peaks. (Abstract shortened by ProQuest.).

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

PubMed

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

2011-07-01

Inclusion bodies are insoluble protein aggregates usually found in recombinant bacteria when they are forced to produce heterologous protein species. These particles are formed by polypeptides that cross-interact through sterospecific contacts and that are steadily deposited in either the cell's cytoplasm or the periplasm. An important fraction of eukaryotic proteins form inclusion bodies in bacteria, which has posed major problems in the development of the biotechnology industry. Over the last decade, the fine dissection of the quality control system in bacteria and the recognition of the amyloid-like architecture of inclusion bodies have provided dramatic insights on the dynamic biology of these aggregates. We discuss here the relevant aspects, in the interface between cell physiology and structural biology, which make inclusion bodies unique models for the study of protein aggregation, amyloid formation and prion biology in a physiologically relevant background. © 2011 The Authors Journal compilation © 2011 FEBS.

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 .

Nonequilibrium simulations of model ionomers in an oscillating electric field

DOE PAGES

Ting, Christina L.; Sorensen-Unruh, Karen E.; Stevens, Mark J.; ...

2016-07-25

Here, we perform molecular dynamics simulations of a coarse-grained model of ionomer melts in an applied oscillating electric field. The frequency-dependent conductivity and susceptibility are calculated directly from the current density and polarization density, respectively. At high frequencies, we find a peak in the real part of the conductivity due to plasma oscillations of the ions. At lower frequencies, the dynamic response of the ionomers depends on the ionic aggregate morphology in the system, which consists of either percolated or isolated aggregates. We show that the dynamic response of the model ionomers to the applied oscillating field can be understoodmore » by comparison with relevant time scales in the systems, obtained from independent calculations.« less

Nonequilibrium simulations of model ionomers in an oscillating electric field

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

Ting, Christina L.; Sorensen-Unruh, Karen E.; Stevens, Mark J.

Here, we perform molecular dynamics simulations of a coarse-grained model of ionomer melts in an applied oscillating electric field. The frequency-dependent conductivity and susceptibility are calculated directly from the current density and polarization density, respectively. At high frequencies, we find a peak in the real part of the conductivity due to plasma oscillations of the ions. At lower frequencies, the dynamic response of the ionomers depends on the ionic aggregate morphology in the system, which consists of either percolated or isolated aggregates. We show that the dynamic response of the model ionomers to the applied oscillating field can be understoodmore » by comparison with relevant time scales in the systems, obtained from independent calculations.« less

Modeling and numerical simulations of growth and morphologies of three dimensional aggregated silver films

NASA Astrophysics Data System (ADS)

Davis, L. J.; Boggess, M.; Kodpuak, E.; Deutsch, M.

2012-11-01

We report on a model for the deposition of three dimensional, aggregated nanocrystalline silver films, and an efficient numerical simulation method developed for visualizing such structures. We compare our results to a model system comprising chemically deposited silver films with morphologies ranging from dilute, uniform distributions of nanoparticles to highly porous aggregated networks. Disordered silver films grown in solution on silica substrates are characterized using digital image analysis of high resolution scanning electron micrographs. While the latter technique provides little volume information, plane-projected (two dimensional) island structure and surface coverage may be reliably determined. Three parameters governing film growth are evaluated using these data and used as inputs for the deposition model, greatly reducing computing requirements while still providing direct access to the complete (bulk) structure of the films throughout the growth process. We also show how valuable three dimensional characteristics of the deposited materials can be extracted using the simulated structures.

Toward a Common Structure in Demographic Educational Modeling and Simulation: A Complex Systems Approach

ERIC Educational Resources Information Center

Guevara, Porfirio

2014-01-01

This article identifies elements and connections that seem to be relevant to explain persistent aggregate behavioral patterns in educational systems when using complex dynamical systems modeling and simulation approaches. Several studies have shown what factors are at play in educational fields, but confusion still remains about the underlying…

The Effects of Temperature and Precipitation on the Yield of Zea Mays L. I the Southeastern United States

NASA Astrophysics Data System (ADS)

Stooksbury, David Emory

Three families of straightforward maize (Zea mays L.) yield/climate models using monthly temperature and precipitation terms are produced. One family of models uses USDA's Crop Reporting Districts (CRD) as its scale of aggregation. The other two families of models use three different district aggregates based on climate or yield patterns. The climate and yield districts are determined by using a two-stage cluster analysis. The CRD-based family of models perform as well as the climate and yield based models. All models explain between 80% and 90% of the variance in maize yield. The most important climate term affecting maize yield in the South is the daily maximum temperature at pollination time. The higher the maximum temperature, the lower the yield. Above normal minimum temperature during pollination increases yield in the Middle South. Weather that favors early planting and rapid vegetative growth increases yield. Ideal maize yield weather includes a dry period during planting followed by a warm period during vegetative growth. Moisture variables are important only during the planting and harvest periods when above normal precipitation delays field work and thereby reduces yield. The model results indicate that the dire predictions about the fate of Southern agriculture in a trace gas warmed world may not be true. This is due to the overwhelming influence of the daily maximum temperature on yield. An optimum aggregate for climate impact studies was not found. I postulate that this is due to the dynamic nature of the American maize production system. For most climate impact studies on a dynamic agricultural system, there does not need to be a concern about the model aggregation.

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

PubMed

Golz, Emily K; Vander Griend, Douglas A

2013-01-15

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

Approximation methods for stochastic petri nets

NASA Technical Reports Server (NTRS)

Jungnitz, Hauke Joerg

1992-01-01

Stochastic Marked Graphs are a concurrent decision free formalism provided with a powerful synchronization mechanism generalizing conventional Fork Join Queueing Networks. In some particular cases the analysis of the throughput can be done analytically. Otherwise the analysis suffers from the classical state explosion problem. Embedded in the divide and conquer paradigm, approximation techniques are introduced for the analysis of stochastic marked graphs and Macroplace/Macrotransition-nets (MPMT-nets), a new subclass introduced herein. MPMT-nets are a subclass of Petri nets that allow limited choice, concurrency and sharing of resources. The modeling power of MPMT is much larger than that of marked graphs, e.g., MPMT-nets can model manufacturing flow lines with unreliable machines and dataflow graphs where choice and synchronization occur. The basic idea leads to the notion of a cut to split the original net system into two subnets. The cuts lead to two aggregated net systems where one of the subnets is reduced to a single transition. A further reduction leads to a basic skeleton. The generalization of the idea leads to multiple cuts, where single cuts can be applied recursively leading to a hierarchical decomposition. Based on the decomposition, a response time approximation technique for the performance analysis is introduced. Also, delay equivalence, which has previously been introduced in the context of marked graphs by Woodside et al., Marie's method and flow equivalent aggregation are applied to the aggregated net systems. The experimental results show that response time approximation converges quickly and shows reasonable accuracy in most cases. The convergence of Marie's method and flow equivalent aggregation are applied to the aggregated net systems. The experimental results show that response time approximation converges quickly and shows reasonable accuracy in most cases. The convergence of Marie's is slower, but the accuracy is generally better. Delay equivalence often fails to converge, while flow equivalent aggregation can lead to potentially bad results if a strong dependence of the mean completion time on the interarrival process exists.

Nanoscale studies link amyloid maturity with polyglutamine diseases onset

NASA Astrophysics Data System (ADS)

Ruggeri, F. S.; Vieweg, S.; Cendrowska, U.; Longo, G.; Chiki, A.; Lashuel, H. A.; Dietler, G.

2016-08-01

The presence of expanded poly-glutamine (polyQ) repeats in proteins is directly linked to the pathogenesis of several neurodegenerative diseases, including Huntington’s disease. However, the molecular and structural basis underlying the increased toxicity of aggregates formed by proteins containing expanded polyQ repeats remain poorly understood, in part due to the size and morphological heterogeneity of the aggregates they form in vitro. To address this knowledge gap and technical limitations, we investigated the structural, mechanical and morphological properties of fibrillar aggregates at the single molecule and nanometer scale using the first exon of the Huntingtin protein as a model system (Exon1). Our findings demonstrate a direct correlation of the morphological and mechanical properties of Exon1 aggregates with their structural organization at the single aggregate and nanometric scale and provide novel insights into the molecular and structural basis of Huntingtin Exon1 aggregation and toxicity.

Dose response of surfactants to attenuate gas embolism related platelet aggregation

NASA Astrophysics Data System (ADS)

Eckmann, David M.; Eckmann, Yonaton Y.; Tomczyk, Nancy

2014-03-01

Intravascular gas embolism promotes blood clot formation, cellular activation, and adhesion events, particularly with platelets. Populating the interface with surfactants is a chemical-based intervention to reduce injury from gas embolism. We studied platelet activation and platelet aggregation, prominent adverse responses to blood contact with bubbles. We examined dose-response relationships for two chemically distinct surfactants to attenuate the rise in platelet function stimulated by exposure to microbubbles. Significant reduction in platelet aggregation and platelet activation occurred with increasing concentration of the surfactants, indicating presence of a saturable system. A population balance model for platelet aggregation in the presence of embolism bubbles and surfactants was developed. Monte Carlo simulations for platelet aggregation were performed. Results agree qualitatively with experimental findings. Surfactant dose-dependent reductions in platelet activation and aggregation indicate inhibition of the gas/liquid interface's ability to stimulate cellular activation mechanically.

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

Initial condition of stochastic self-assembly

NASA Astrophysics Data System (ADS)

Davis, Jason K.; Sindi, Suzanne S.

2016-02-01

The formation of a stable protein aggregate is regarded as the rate limiting step in the establishment of prion diseases. In these systems, once aggregates reach a critical size the growth process accelerates and thus the waiting time until the appearance of the first critically sized aggregate is a key determinant of disease onset. In addition to prion diseases, aggregation and nucleation is a central step of many physical, chemical, and biological process. Previous studies have examined the first-arrival time at a critical nucleus size during homogeneous self-assembly under the assumption that at time t =0 the system was in the all-monomer state. However, in order to compare to in vivo biological experiments where protein constituents inherited by a newly born cell likely contain intermediate aggregates, other possibilities must be considered. We consider one such possibility by conditioning the unique ergodic size distribution on subcritical aggregate sizes; this least-informed distribution is then used as an initial condition. We make the claim that this initial condition carries fewer assumptions than an all-monomer one and verify that it can yield significantly different averaged waiting times relative to the all-monomer condition under various models of assembly.

Radiative-convective equilibrium model intercomparison project

NASA Astrophysics Data System (ADS)

Wing, Allison A.; Reed, Kevin A.; Satoh, Masaki; Stevens, Bjorn; Bony, Sandrine; Ohno, Tomoki

2018-03-01

RCEMIP, an intercomparison of multiple types of models configured in radiative-convective equilibrium (RCE), is proposed. RCE is an idealization of the climate system in which there is a balance between radiative cooling of the atmosphere and heating by convection. The scientific objectives of RCEMIP are three-fold. First, clouds and climate sensitivity will be investigated in the RCE setting. This includes determining how cloud fraction changes with warming and the role of self-aggregation of convection in climate sensitivity. Second, RCEMIP will quantify the dependence of the degree of convective aggregation and tropical circulation regimes on temperature. Finally, by providing a common baseline, RCEMIP will allow the robustness of the RCE state across the spectrum of models to be assessed, which is essential for interpreting the results found regarding clouds, climate sensitivity, and aggregation, and more generally, determining which features of tropical climate a RCE framework is useful for. A novel aspect and major advantage of RCEMIP is the accessibility of the RCE framework to a variety of models, including cloud-resolving models, general circulation models, global cloud-resolving models, single-column models, and large-eddy simulation models.

Dynamics and mechanisms of asbestos-fiber aggregate growth in water

NASA Astrophysics Data System (ADS)

Wu, L.; Ortiz, C. P.; Jerolmack, D. J.

2015-12-01

Most colloidal particles including asbestos fibers form aggregates in water, when solution chemistry provides favorable conditions. To date, the growth of colloidal aggregates has been observed in many model systems under optical and scanning electron microscopy; however, all of these studies have used near-spherical particles. The highly elongated nature of asbestos fibers may cause anomalous aggregate growth and morphology, but this has never been examined. Although the exposure pathway of concern for asbestos is through the air, asbestos particles typically reside in soil that is at least partially saturated, and aggregates formed in the aqueous phase may influence the mobility of particles in the environment. Here we study solution-phase aggregation kinetics of asbestos fibers using a liquid-cell by in situ microscopy, over micron to centimeter length scales and from a tenth of a second to hours. We employ an elliptical particle tracking technique to determine particle trajectories and to quantify diffusivity. Experiments reveal that diffusing fibers join by cross linking, but that such linking is sometimes reversible. The resulting aggregates are very sparse and non-compact, with a fractal dimension that is lower than any previously reported value. Their morphology, growth rate and particle size distribution exhibit non-classical behavior that deviates significantly from observations of aggregates composed of near-spherical particles. We also perform experiments using synthetic colloidal particles, and compare these to asbestos in order to separate the controls of particle shape vs. material properties. This direct method for quantitatively observing aggregate growth is a first step toward predicting asbestos fiber aggregate size distributions in the environment. Moreover, many emerging environmental contaminants - such as carbon nanotubes - are elongated colloids, and our work suggests that theories for aggregate growth may need to be modified in order to model these particles.

Report of a Workshop on Membrane Biophysics Held June 25 - July 15, 1984.

DTIC Science & Technology

1984-07-15

J.A. (1984) Identification of aggregated Markovian models: application to the nicotinic acetylcholine receptor. Prof. of the Neyman-Kiefer Memorial...for future biological applications of the system. We have also discovered that the kinetic and equilibrium 0 properties of the binding depend...consists of aggregation of phycobiliproteins, -- namely phycoerythrin, phycocyanin , and allophycocyanin, which collectively form the phycobilisomes. Each

Molecular Chaperone Dysfunction in Neurodegenerative Diseases and Effects of Curcumin

PubMed Central

Frautschy, Sally

2014-01-01

The intra- and extracellular accumulation of misfolded and aggregated amyloid proteins is a common feature in several neurodegenerative diseases, which is thought to play a major role in disease severity and progression. The principal machineries maintaining proteostasis are the ubiquitin proteasomal and lysosomal autophagy systems, where heat shock proteins play a crucial role. Many protein aggregates are degraded by the lysosomes, depending on aggregate size, peptide sequence, and degree of misfolding, while others are selectively tagged for removal by heat shock proteins and degraded by either the proteasome or phagosomes. These systems are compromised in different neurodegenerative diseases. Therefore, developing novel targets and classes of therapeutic drugs, which can reduce aggregates and maintain proteostasis in the brains of neurodegenerative models, is vital. Natural products that can modulate heat shock proteins/proteosomal pathway are considered promising for treating neurodegenerative diseases. Here we discuss the current knowledge on the role of HSPs in protein misfolding diseases and knowledge gained from animal models of Alzheimer's disease, tauopathies, and Huntington's diseases. Further, we discuss the emerging treatment regimens for these diseases using natural products, like curcumin, which can augment expression or function of heat shock proteins in the cell. PMID:25386560

SU-E-T-186: Cloud-Based Quality Assurance Application for Linear Accelerator Commissioning

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

Rogers, J

2015-06-15

Purpose: To identify anomalies and safety issues during data collection and modeling for treatment planning systems Methods: A cloud-based quality assurance system (AQUIRE - Automated QUalIty REassurance) has been developed to allow the uploading and analysis of beam data aquired during the treatment planning system commissioning process. In addition to comparing and aggregating measured data, tools have also been developed to extract dose from the treatment planning system for end-to-end testing. A gamma index is perfomed on the data to give a dose difference and distance-to-agreement for validation that a beam model is generating plans consistent with the beam datamore » collection. Results: Over 20 linear accelerators have been commissioning using this platform, and a variety of errors and potential saftey issues have been caught through the validation process. For example, the gamma index of 2% dose, 2mm DTA is quite sufficient to see curves not corrected for effective point of measurement. Also, data imported into the database is analyzed against an aggregate of similar linear accelerators to show data points that are outliers. The resulting curves in the database exhibit a very small standard deviation and imply that a preconfigured beam model based on aggregated linear accelerators will be sufficient in most cases. Conclusion: With the use of this new platform for beam data commissioning, errors in beam data collection and treatment planning system modeling are greatly reduced. With the reduction in errors during acquisition, the resulting beam models are quite similar, suggesting that a common beam model may be possible in the future. Development is ongoing to create routine quality assurance tools to compare back to the beam data acquired during commissioning. I am a medical physicist for Alzyen Medical Physics, and perform commissioning services.« less

Disease spread across multiple scales in a spatial hierarchy: effect of host spatial structure and of inoculum quantity and distribution.

PubMed

Gosme, Marie; Lucas, Philippe

2009-07-01

Spatial patterns of both the host and the disease influence disease spread and crop losses. Therefore, the manipulation of these patterns might help improve control strategies. Considering disease spread across multiple scales in a spatial hierarchy allows one to capture important features of epidemics developing in space without using explicitly spatialized variables. Thus, if the system under study is composed of roots, plants, and planting hills, the effect of host spatial pattern can be studied by varying the number of plants per planting hill. A simulation model based on hierarchy theory was used to simulate the effects of large versus small planting hills, low versus high level of initial infections, and aggregated versus uniform distribution of initial infections. The results showed that aggregating the initially infected plants always resulted in slower epidemics than spreading out the initial infections uniformly. Simulation results also showed that, in most cases, disease epidemics were slower in the case of large host aggregates (100 plants/hill) than with smaller aggregates (25 plants/hill), except when the initially infected plants were both numerous and spread out uniformly. The optimal strategy for disease control depends on several factors, including initial conditions. More importantly, the model offers a framework to account for the interplay between the spatial characteristics of the system, rates of infection, and aggregation of the disease.

The emergence of coordination in public good games

NASA Astrophysics Data System (ADS)

Hichri, W.; Kirman, A.

2007-01-01

In physical models it is well understood that the aggregate behaviour of a system is not in one to one correspondence with the behaviour of the average individual element of that system. Yet, in many economic models the behaviour of aggregates is thought of as corresponding to that of an individual. A typical example is that of public goods experiments. A systematic feature of such experiments is that, with repetition, people contribute less to public goods. A typical explanation is that people “learn to play Nash” or something approaching it. To justify such an explanation, an individual learning model is tested on average or aggregate data. In this paper we will examine this idea by analysing average and individual behaviour in a series of public goods experiments. We analyse data from a series of games of contributions to public goods and as is usual, we test a learning model on the average data. We then look at individual data, examine the changes that this produces and see if some general model such as the EWA (Expected Weighted Attraction) with varying parameters can account for individual behaviour. We find that once we disaggregate data such models have poor explanatory power. Groups do not learn as supposed, their behaviour differs markedly from one group to another, and the behaviour of the individuals who make up the groups also varies within groups. The decline in aggregate contributions cannot be explained by resorting to a uniform model of individual behaviour. However, the Nash equilibrium of such a game is a total payment for all the individuals and there is some convergence of the group in this respect. Yet the individual contributions do not converge. How the individuals “self-organsise” to coordinate, even in this limited way remains to be explained.

Spectroscopic investigation of inner filter effect by magnolol solutions

NASA Astrophysics Data System (ADS)

Li, Hongmei; YuzhuHu

2007-12-01

Spectroscopy is useful tool for aggregation studies on fluorephores. One of the major problems with this technique is that the inner filter effect becomes unavoidable since the samples are used at high concentration. In this work, our investigation on magnolol spectroscopic properties shows that the inner filter effect (IFE) of fluorescence plays a critical role in the spectra of magnolol. The strong dependence of the fluorescence parameters on the concentration accounts for the apparent experimental evidence of magnolol aggregation at high concentrations. There are some questions despite the aggregation model based on fluorescent aggregates seems to describe the behavior of the system. The mathematical correction on the emission intensities shows the linear fluorescence-concentration relationship. Furthermore, we propose a mathematic model of excitation spectrum based on the primary IFE (absorption of light of excitation wavelength), which provide a correct explanation of the unusual spectral shift and spectral narrowing in the excitation spectra of magnolol at high concentrations. The shapes of spectra are completely independent on magnolol aggregation and are due only to experimental artifacts, i.e. IFE.

A test of the cross-scale resilience model: Functional richness in Mediterranean-climate ecosystems

USGS Publications Warehouse

Wardwell, D.A.; Allen, Craig R.; Peterson, G.D.; Tyre, A.J.

2008-01-01

Ecological resilience has been proposed to be generated, in part, in the discontinuous structure of complex systems. Environmental discontinuities are reflected in discontinuous, aggregated animal body mass distributions. Diversity of functional groups within body mass aggregations (scales) and redundancy of functional groups across body mass aggregations (scales) has been proposed to increase resilience. We evaluate that proposition by analyzing mammalian and avian communities of Mediterranean-climate ecosystems. We first determined that body mass distributions for each animal community were discontinuous. We then calculated the variance in richness of function across aggregations in each community, and compared observed values with distributions created by 1000 simulations using a null of random distribution of function, with the same n, number of discontinuities and number of functional groups as the observed data. Variance in the richness of functional groups across scales was significantly lower in real communities than in simulations in eight of nine sites. The distribution of function across body mass aggregations in the animal communities we analyzed was non-random, and supports the contentions of the cross-scale resilience model. ?? 2007 Elsevier B.V. All rights reserved.

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

PubMed

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

2016-06-01

Numerous mutations and covalent modifications of the highly abundant, long-lived crystallins of the eye lens cause their aggregation leading to progressive opacification of the lens, cataract. The nature and biochemical mechanisms of the aggregation process are poorly understood, as neither amyloid nor native-state polymers are commonly found in opaque lenses. The βγ-crystallin fold contains four highly conserved buried tryptophans, which can be oxidized to more hydrophilic products, such as kynurenine, upon UV-B irradiation. We mimicked this class of oxidative damage using Trp→Glu point mutants of human γD-crystallin. Such substitutions may represent a model of UV-induced photodamage-introduction of a charged group into the hydrophobic core generating "denaturation from within." The effects of Trp→Glu substitutions were highly position dependent. While each was destabilizing, only the two located in the bottom of the double Greek key fold-W42E and W130E-yielded robust aggregation of partially unfolded intermediates at 37°C and pH 7. The αB-crystallin chaperone suppressed aggregation of W130E, but not W42E, indicating distinct aggregation pathways from damage in the N-terminal vs C-terminal domain. The W130E aggregates had loosely fibrillar morphology, yet were nonamyloid, noncovalent, showed little surface hydrophobicity, and formed at least 20°C below the melting temperature of the native β-sheets. These features are most consistent with domain-swapped polymerization. Aggregation of partially destabilized crystallins under physiological conditions, as occurs in this class of point mutants, could provide a simple in vitro model system for drug discovery and optimization. © 2016 The Protein Society.

A Technical Description of the Officer Procurement Model (TOPOPS). Final Report.

ERIC Educational Resources Information Center

Akman, Allan; And Others

The Total Objective Plan for the Officer Procurement System (TOPOPS) is an aggregate-level, computer-based model of the Air Force Officer procurement system developed to operate on the UNIVAC 1108 system. It is designed to simulate officer accession and training and achieve optimal solutions in terms of either cost minimization or accession…

Sequence dependent aggregation of peptides and fibril formation

NASA Astrophysics Data System (ADS)

Hung, Nguyen Ba; Le, Duy-Manh; Hoang, Trinh X.

2017-09-01

Deciphering the links between amino acid sequence and amyloid fibril formation is key for understanding protein misfolding diseases. Here we use Monte Carlo simulations to study the aggregation of short peptides in a coarse-grained model with hydrophobic-polar (HP) amino acid sequences and correlated side chain orientations for hydrophobic contacts. A significant heterogeneity is observed in the aggregate structures and in the thermodynamics of aggregation for systems of different HP sequences and different numbers of peptides. Fibril-like ordered aggregates are found for several sequences that contain the common HPH pattern, while other sequences may form helix bundles or disordered aggregates. A wide variation of the aggregation transition temperatures among sequences, even among those of the same hydrophobic fraction, indicates that not all sequences undergo aggregation at a presumable physiological temperature. The transition is found to be the most cooperative for sequences forming fibril-like structures. For a fibril-prone sequence, it is shown that fibril formation follows the nucleation and growth mechanism. Interestingly, a binary mixture of peptides of an aggregation-prone and a non-aggregation-prone sequence shows the association and conversion of the latter to the fibrillar structure. Our study highlights the role of a sequence in selecting fibril-like aggregates and also the impact of a structural template on fibril formation by peptides of unrelated sequences.

[Survival strategy of photosynthetic organisms. 1. Variability of the extent of light-harvesting pigment aggregation as a structural factor optimizing the function of oligomeric photosynthetic antenna. Model calculations].

PubMed

Fetisova, Z G

2004-01-01

In accordance with our concept of rigorous optimization of photosynthetic machinery by a functional criterion, this series of papers continues purposeful search in natural photosynthetic units (PSU) for the basic principles of their organization that we predicted theoretically for optimal model light-harvesting systems. This approach allowed us to determine the basic principles for the organization of a PSU of any fixed size. This series of papers deals with the problem of structural optimization of light-harvesting antenna of variable size controlled in vivo by the light intensity during the growth of organisms, which accentuates the problem of antenna structure optimization because optimization requirements become more stringent as the PSU increases in size. In this work, using mathematical modeling for the functioning of natural PSUs, we have shown that the aggregation of pigments of model light-harvesting antenna, being one of universal optimizing factors, furthermore allows controlling the antenna efficiency if the extent of pigment aggregation is a variable parameter. In this case, the efficiency of antenna increases with the size of the elementary antenna aggregate, thus ensuring the high efficiency of the PSU irrespective of its size; i.e., variation in the extent of pigment aggregation controlled by the size of light-harvesting antenna is biologically expedient.

Influence of Network Model Detail on Estimated Health Effects of Drinking Water Contamination Events

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

Davis, Michael J.; Janke, Robert

Network model detail can influence the accuracy of results from analyses of water distribution systems. Previous work has shown the limitations of skeletonized network models when considering water quality and hydraulic effects. Loss of model detail is potentially less important for aggregated effects such as the systemwide health effects associated with a contamination event, but has received limited attention. The influence of model detail on such effects is examined here by comparing results obtained for contamination events using three large network models and several skeletonized versions of the models. Loss of model detail decreases the accuracy of estimated aggregated adversemore » effects related to contamination events. It has the potential to have a large negative influence on the results of consequence assessments and the design of contamination warning systems. However, the adverse influence on analysis results can be minimized by restricting attention to high percentile effects (i.e., 95th percentile or higher).« less

In-silico analysis on biofabricating vascular networks using kinetic Monte Carlo simulations.

PubMed

Sun, Yi; Yang, Xiaofeng; Wang, Qi

2014-03-01

We present a computational modeling approach to study the fusion of multicellular aggregate systems in a novel scaffold-less biofabrication process, known as 'bioprinting'. In this novel technology, live multicellular aggregates are used as fundamental building blocks to make tissues or organs (collectively known as the bio-constructs,) via the layer-by-layer deposition technique or other methods; the printed bio-constructs embedded in maturogens, consisting of nutrient-rich bio-compatible hydrogels, are then placed in bioreactors to undergo the cellular aggregate fusion process to form the desired functional bio-structures. Our approach reported here is an agent-based modeling method, which uses the kinetic Monte Carlo (KMC) algorithm to evolve the cellular system on a lattice. In this method, the cells and the hydrogel media, in which cells are embedded, are coarse-grained to material's points on a three-dimensional (3D) lattice, where the cell-cell and cell-medium interactions are quantified by adhesion and cohesion energies. In a multicellular aggregate system with a fixed number of cells and fixed amount of hydrogel media, where the effect of cell differentiation, proliferation and death are tactically neglected, the interaction energy is primarily dictated by the interfacial energy between cell and cell as well as between cell and medium particles on the lattice, respectively, based on the differential adhesion hypothesis. By using the transition state theory to track the time evolution of the multicellular system while minimizing the interfacial energy, KMC is shown to be an efficient time-dependent simulation tool to study the evolution of the multicellular aggregate system. In this study, numerical experiments are presented to simulate fusion and cell sorting during the biofabrication process of vascular networks, in which the bio-constructs are fabricated via engineering designs. The results predict the feasibility of fabricating the vascular structures via the bioprinting technology and demonstrate the morphological development process during cellular aggregate fusion in various engineering designed structures. The study also reveals that cell sorting will perhaps not significantly impact the final fabricated products, should the maturation process be well-controlled in bioprinting.

Network Aggregation in Transportation Planning : Volume I : Summary and Survey

DOT National Transportation Integrated Search

1978-04-01

Volume 1 summarizes research on network aggregation in transportation models. It includes a survey of network aggregation practices, definition of an extraction aggregation model, computational results on a heuristic implementation of the model, and ...

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

NASA Astrophysics Data System (ADS)

Bratko, D.; Blanch, H. W.

2001-01-01

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

Evaluation of a non-Arrhenius model for therapeutic monoclonal antibody aggregation.

PubMed

Kayser, Veysel; Chennamsetty, Naresh; Voynov, Vladimir; Helk, Bernhard; Forrer, Kurt; Trout, Bernhardt L

2011-07-01

Understanding antibody aggregation is of great significance for the pharmaceutical industry. We studied the aggregation of five different therapeutic monoclonal antibodies (mAbs) with size-exclusion chromatography-high-performance liquid chromatography (SEC-HPLC), fluorescence spectroscopy, electron microscopy, and light scattering methods at various temperatures with the aim of gaining insight into the aggregation process and developing models of it. In particular, we find that the kinetics can be described by a second-order model and are non-Arrhenius. Thus, we develop a non-Arrhenius model to connect accelerated aggregation experiments at high temperature to long-term storage experiments at low temperature. We evaluate our model by predicting mAb aggregation and comparing it with long-term behavior. Our results suggest that the number of monomers and mAb conformations within aggregates vary with the size and age of the aggregates, and that only certain sizes of aggregates are populated in the solution. We also propose a kinetic model based on conformational changes of proteins and monomer peak loss kinetics from SEC-HPLC. This model could be employed for a detail analysis of mAb aggregation kinetics. Copyright © 2011 Wiley-Liss, Inc. and the American Pharmacists Association

Computational design and biophysical characterization of aggregation-resistant point mutations for γD crystallin illustrate a balance of conformational stability and intrinsic aggregation propensity.

PubMed

Sahin, Erinc; Jordan, Jacob L; Spatara, Michelle L; Naranjo, Andrea; Costanzo, Joseph A; Weiss, William F; Robinson, Anne Skaja; Fernandez, Erik J; Roberts, Christopher J

2011-02-08

γD crystallin is a natively monomeric eye-lens protein that is associated with hereditary juvenile cataract formation. It is an attractive model system as a multidomain Greek-key protein that aggregates through partially folded intermediates. Point mutations M69Q and S130P were used to test (1) whether the protein-design algorithm RosettaDesign would successfully predict mutants that are resistant to aggregation when combined with informatic sequence-based predictors of peptide aggregation propensity and (2) how the mutations affected relative unfolding free energies (ΔΔG(un)) and intrinsic aggregation propensity (IAP). M69Q was predicted to have ΔΔG(un) ≫ 0, without significantly affecting IAP. S130P was predicted to have ΔΔG(un) ∼ 0 but with reduced IAP. The stability, conformation, and aggregation kinetics in acidic solution were experimentally characterized and compared for the variants and wild-type (WT) protein using circular dichroism and intrinsic fluorescence spectroscopy, calorimetric and chemical unfolding, thioflavin-T binding, chromatography, static laser light scattering, and kinetic modeling. Monomer secondary and tertiary structures of both variants were indistinguishable from WT, while ΔΔG(un) > 0 for M69Q and ΔΔG(un) < 0 for S130P. Surprisingly, despite being the least conformationally stable, S130P was the most resistant to aggregation, indicating a significant decrease of its IAP compared to WT and M69Q.

Modelling the tumour microenvironment in long-term microencapsulated 3D co-cultures recapitulates phenotypic features of disease progression.

PubMed

Estrada, Marta F; Rebelo, Sofia P; Davies, Emma J; Pinto, Marta T; Pereira, Hugo; Santo, Vítor E; Smalley, Matthew J; Barry, Simon T; Gualda, Emilio J; Alves, Paula M; Anderson, Elizabeth; Brito, Catarina

2016-02-01

3D cell tumour models are generated mainly in non-scalable culture systems, using bioactive scaffolds. Many of these models fail to reflect the complex tumour microenvironment and do not allow long-term monitoring of tumour progression. To overcome these limitations, we have combined alginate microencapsulation with agitation-based culture systems, to recapitulate and monitor key aspects of the tumour microenvironment and disease progression. Aggregates of MCF-7 breast cancer cells were microencapsulated in alginate, either alone or in combination with human fibroblasts, then cultured for 15 days. In co-cultures, the fibroblasts arranged themselves around the tumour aggregates creating distinct epithelial and stromal compartments. The presence of fibroblasts resulted in secretion of pro-inflammatory cytokines and deposition of collagen in the stromal compartment. Tumour cells established cell-cell contacts and polarised around small lumina in the interior of the aggregates. Over the culture period, there was a reduction in oestrogen receptor and membranous E-cadherin alongside loss of cell polarity, increased collective cell migration and enhanced angiogenic potential in co-cultures. These phenotypic alterations, typical of advanced stages of cancer, were not observed in the mono-cultures of MCF-7 cells. The proposed model system constitutes a new tool to study tumour-stroma crosstalk, disease progression and drug resistance mechanisms. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

A computational framework for modeling targets as complex adaptive systems

NASA Astrophysics Data System (ADS)

Santos, Eugene; Santos, Eunice E.; Korah, John; Murugappan, Vairavan; Subramanian, Suresh

2017-05-01

Modeling large military targets is a challenge as they can be complex systems encompassing myriad combinations of human, technological, and social elements that interact, leading to complex behaviors. Moreover, such targets have multiple components and structures, extending across multiple spatial and temporal scales, and are in a state of change, either in response to events in the environment or changes within the system. Complex adaptive system (CAS) theory can help in capturing the dynamism, interactions, and more importantly various emergent behaviors, displayed by the targets. However, a key stumbling block is incorporating information from various intelligence, surveillance and reconnaissance (ISR) sources, while dealing with the inherent uncertainty, incompleteness and time criticality of real world information. To overcome these challenges, we present a probabilistic reasoning network based framework called complex adaptive Bayesian Knowledge Base (caBKB). caBKB is a rigorous, overarching and axiomatic framework that models two key processes, namely information aggregation and information composition. While information aggregation deals with the union, merger and concatenation of information and takes into account issues such as source reliability and information inconsistencies, information composition focuses on combining information components where such components may have well defined operations. Since caBKBs can explicitly model the relationships between information pieces at various scales, it provides unique capabilities such as the ability to de-aggregate and de-compose information for detailed analysis. Using a scenario from the Network Centric Operations (NCO) domain, we will describe how our framework can be used for modeling targets with a focus on methodologies for quantifying NCO performance metrics.

RBC aggregation based system for long-term photoplethysmography (PPG): new prospects for PPG applications

NASA Astrophysics Data System (ADS)

Shvartsman, Leonid D.; Tverskoy, Boris

2015-03-01

We present system for long-term continuous PPG monitoring, and physical model for PPG analysis. The system is based on ideology of light scattering modulated by the process of RBC aggregation. OXIRATE's system works in reflection geometry. The sensor is tiny, completely mobile phone compatible, it can be placed nearly everywhere on the body surface. These technical features allow all-night comfortable PPG monitoring that was performed and analyzed. We can define various sleep stages on the basis of different reproducible time-behavior of PPG signal. Our system of PPG monitoring was used also for reflection pulse oximetry and for extreme PPG studies, such as diving.

Informed herbivore movement and interplant communication determine the effects of induced resistance in an individual-based model.

PubMed

Rubin, Ilan N; Ellner, Stephen P; Kessler, André; Morrell, Kimberly A

2015-09-01

1. Plant induced resistance to herbivory affects the spatial distribution of herbivores, as well as their performance. In recent years, theories regarding the benefit to plants of induced resistance have shifted from ideas of optimal resource allocation towards a more eclectic set of theories that consider spatial and temporal plant variability and the spatial distribution of herbivores among plants. However, consensus is lacking on whether induced resistance causes increased herbivore aggregation or increased evenness, as both trends have been experimentally documented. 2. We created a spatial individual-based model that can describe many plant-herbivore systems with induced resistance, in order to analyse how different aspects of induced resistance might affect herbivore distribution, and the total damage to a plant population, during a growing season. 3. We analyse the specific effects on herbivore aggregation of informed herbivore movement (preferential movement to less-damaged plants) and of information transfer between plants about herbivore attacks, in order to identify mechanisms driving both aggregation and evenness. We also investigate how the resulting herbivore distributions affect the total damage to plants and aggregation of damage. 4. Even, random and aggregated herbivore distributions can all occur in our model with induced resistance. Highest levels of aggregation occurred in the models with informed herbivore movement, and the most even distributions occurred when the average number of herbivores per plant was low. With constitutive resistance, only random distributions occur. Damage to plants was spatially correlated, unless plants recover very quickly from damage; herbivore spatial autocorrelation was always weak. 5. Our model and results provide a simple explanation for the apparent conflict between experimental results, indicating that both increased aggregation and increased evenness of herbivores can result from induced resistance. We demonstrate that information transfer from plants to herbivores, and from plants to neighbouring plants, can both be major factors in determining non-random herbivore distributions. © 2015 The Authors. Journal of Animal Ecology © 2015 British Ecological Society.

Reliability model generator

NASA Technical Reports Server (NTRS)

Cohen, Gerald C. (Inventor); McMann, Catherine M. (Inventor)

1991-01-01

An improved method and system for automatically generating reliability models for use with a reliability evaluation tool is described. The reliability model generator of the present invention includes means for storing a plurality of low level reliability models which represent the reliability characteristics for low level system components. In addition, the present invention includes means for defining the interconnection of the low level reliability models via a system architecture description. In accordance with the principles of the present invention, a reliability model for the entire system is automatically generated by aggregating the low level reliability models based on the system architecture description.

Emulating a System Dynamics Model with Agent-Based Models: A Methodological Case Study in Simulation of Diabetes Progression

DOE PAGES

Schryver, Jack; Nutaro, James; Shankar, Mallikarjun

2015-10-30

An agent-based simulation model hierarchy emulating disease states and behaviors critical to progression of diabetes type 2 was designed and implemented in the DEVS framework. The models are translations of basic elements of an established system dynamics model of diabetes. In this model hierarchy, which mimics diabetes progression over an aggregated U.S. population, was dis-aggregated and reconstructed bottom-up at the individual (agent) level. Four levels of model complexity were defined in order to systematically evaluate which parameters are needed to mimic outputs of the system dynamics model. Moreover, the four estimated models attempted to replicate stock counts representing disease statesmore » in the system dynamics model, while estimating impacts of an elderliness factor, obesity factor and health-related behavioral parameters. Health-related behavior was modeled as a simple realization of the Theory of Planned Behavior, a joint function of individual attitude and diffusion of social norms that spread over each agent s social network. Although the most complex agent-based simulation model contained 31 adjustable parameters, all models were considerably less complex than the system dynamics model which required numerous time series inputs to make its predictions. In all three elaborations of the baseline model provided significantly improved fits to the output of the system dynamics model. The performances of the baseline agent-based model and its extensions illustrate a promising approach to translate complex system dynamics models into agent-based model alternatives that are both conceptually simpler and capable of capturing main effects of complex local agent-agent interactions.« less

Emulating a System Dynamics Model with Agent-Based Models: A Methodological Case Study in Simulation of Diabetes Progression

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

Schryver, Jack; Nutaro, James; Shankar, Mallikarjun

An agent-based simulation model hierarchy emulating disease states and behaviors critical to progression of diabetes type 2 was designed and implemented in the DEVS framework. The models are translations of basic elements of an established system dynamics model of diabetes. In this model hierarchy, which mimics diabetes progression over an aggregated U.S. population, was dis-aggregated and reconstructed bottom-up at the individual (agent) level. Four levels of model complexity were defined in order to systematically evaluate which parameters are needed to mimic outputs of the system dynamics model. Moreover, the four estimated models attempted to replicate stock counts representing disease statesmore » in the system dynamics model, while estimating impacts of an elderliness factor, obesity factor and health-related behavioral parameters. Health-related behavior was modeled as a simple realization of the Theory of Planned Behavior, a joint function of individual attitude and diffusion of social norms that spread over each agent s social network. Although the most complex agent-based simulation model contained 31 adjustable parameters, all models were considerably less complex than the system dynamics model which required numerous time series inputs to make its predictions. In all three elaborations of the baseline model provided significantly improved fits to the output of the system dynamics model. The performances of the baseline agent-based model and its extensions illustrate a promising approach to translate complex system dynamics models into agent-based model alternatives that are both conceptually simpler and capable of capturing main effects of complex local agent-agent interactions.« less

21 CFR 864.5700 - Automated platelet aggregation system.

Code of Federal Regulations, 2011 CFR

2011-04-01

... addition of an aggregating reagent to a platelet-rich plasma. (b) Classification. Class II (performance... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Automated platelet aggregation system. 864.5700... § 864.5700 Automated platelet aggregation system. (a) Identification. An automated platelet aggregation...

21 CFR 864.5700 - Automated platelet aggregation system.

Code of Federal Regulations, 2014 CFR

2014-04-01

... addition of an aggregating reagent to a platelet-rich plasma. (b) Classification. Class II (performance... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Automated platelet aggregation system. 864.5700... § 864.5700 Automated platelet aggregation system. (a) Identification. An automated platelet aggregation...

21 CFR 864.5700 - Automated platelet aggregation system.

Code of Federal Regulations, 2013 CFR

2013-04-01

... addition of an aggregating reagent to a platelet-rich plasma. (b) Classification. Class II (performance... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Automated platelet aggregation system. 864.5700... § 864.5700 Automated platelet aggregation system. (a) Identification. An automated platelet aggregation...

21 CFR 864.5700 - Automated platelet aggregation system.

Code of Federal Regulations, 2010 CFR

2010-04-01

... addition of an aggregating reagent to a platelet-rich plasma. (b) Classification. Class II (performance... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Automated platelet aggregation system. 864.5700... § 864.5700 Automated platelet aggregation system. (a) Identification. An automated platelet aggregation...

21 CFR 864.5700 - Automated platelet aggregation system.

Code of Federal Regulations, 2012 CFR

2012-04-01

... addition of an aggregating reagent to a platelet-rich plasma. (b) Classification. Class II (performance... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Automated platelet aggregation system. 864.5700... § 864.5700 Automated platelet aggregation system. (a) Identification. An automated platelet aggregation...

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

PubMed

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

2016-03-01

Drug discovery for neurodegenerative diseases is particularly challenging because of the discrepancies in drug effects between in vitro and in vivo studies. These discrepancies occur in part because current cell culture systems used for drug screening have many limitations. First, few cell culture systems accurately model human aging or neurodegenerative diseases. Second, drug efficacy may differ between dividing and stationary cells, the latter resembling nondividing neurons in the CNS. Brain aggregates (BrnAggs) derived from embryonic day 15 gestation mouse embryos may represent neuropathogenic processes in prion disease and reflect in vivo drug efficacy. Here, we report a new method for the production of BrnAggs suitable for drug screening and suggest that BrnAggs can model additional neurological diseases such as tauopathies. We also report a functional assay with BrnAggs by measuring electrophysiological activities. Our data suggest that BrnAggs could serve as an effective in vitro cell culture system for drug discovery for neurodegenerative diseases. © 2016 American Association of Neuropathologists, Inc. All rights reserved.

Model Calibration in Watershed Hydrology

NASA Technical Reports Server (NTRS)

Yilmaz, Koray K.; Vrugt, Jasper A.; Gupta, Hoshin V.; Sorooshian, Soroosh

2009-01-01

Hydrologic models use relatively simple mathematical equations to conceptualize and aggregate the complex, spatially distributed, and highly interrelated water, energy, and vegetation processes in a watershed. A consequence of process aggregation is that the model parameters often do not represent directly measurable entities and must, therefore, be estimated using measurements of the system inputs and outputs. During this process, known as model calibration, the parameters are adjusted so that the behavior of the model approximates, as closely and consistently as possible, the observed response of the hydrologic system over some historical period of time. This Chapter reviews the current state-of-the-art of model calibration in watershed hydrology with special emphasis on our own contributions in the last few decades. We discuss the historical background that has led to current perspectives, and review different approaches for manual and automatic single- and multi-objective parameter estimation. In particular, we highlight the recent developments in the calibration of distributed hydrologic models using parameter dimensionality reduction sampling, parameter regularization and parallel computing.

Reconstructing Exposures from Biomarkers using Exposure-Pharmacokinetic Modeling - A Case Study with Carbaryl

EPA Science Inventory

Sources of uncertainty involved in exposure reconstruction for a short half-life chemical, carbaryl, were characterized using the Cumulative and Aggregate Risk Evaluation System (CARES), an exposure model, and a human physiologically based pharmacokinetic (PBPK) model. CARES was...

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.

Metabolic states following accumulation of intracellular aggregates: implications for neurodegenerative diseases.

PubMed

Vazquez, Alexei

2013-01-01

The formation of intracellular aggregates is a common etiology of several neurodegenerative diseases. Mitochondrial defects and oxidative stress has been pointed as the major mechanistic links between the accumulation of intracellular aggregates and cell death. In this work we propose a "metabolic cell death by overcrowding" as an alternative hypothesis. Using a model of neuron metabolism, we predict that as the concentration of protein aggregates increases the neurons transit through three different metabolic phases. The first phase (0-6 mM) corresponds with the normal neuron state, where the neuronal activity is sustained by the oxidative phosphorylation of lactate. The second phase (6-8.6 mM) is characterized by a mixed utilization of lactate and glucose as energy substrates and a switch from ammonia uptake to ammonia release by neurons. In the third phase (8.6-9.3 mM) neurons are predicted to support their energy demands from glycolysis and an alternative pathway for energy generation, involving reactions from serine synthesis, one carbon metabolism and the glycine cleavage system. The model also predicts a decrease in the maximum neuronal capacity for energy generation with increasing the concentration of protein aggregates. Ultimately this maximum capacity becomes zero when the protein aggregates reach a concentration of about 9.3 mM, predicting the cessation of neuronal activity.

Modeling the Capillary Pressure for the Migration of the Liquid Phase in Granular Solid-Liquid-Vapor Systems: Application to the Control of the Composition Profile in W-Cu FGM Materials

NASA Astrophysics Data System (ADS)

Missiaen, Jean-Michel; Raharijaona, Jean-Joël; Delannay, Francis

2016-11-01

A model is developed to compute the capillary pressure for the migration of the liquid phase out or into a uniform solid-liquid-vapor system. The capillary pressure is defined as the reduction of the overall interface energy per volume increment of the transferred fluid phase. The model takes into account the particle size of the solid particle aggregate, the packing configuration (coordination number, porosity), the volume fractions of the different phases, and the values of the interface energies in the system. The model is used for analyzing the stability of the composition profile during processing of W-Cu functionally graded materials combining a composition gradient with a particle size gradient. The migration pressure is computed with the model in two stages: (1) just after the melting of copper, i.e., when sintering and shape accommodation of the W particle aggregate can still be neglected and (2) at high temperature, when the system is close to full density with equilibrium particle shape. The model predicts well the different stages of liquid-phase migration observed experimentally.

Estimation of polydispersity in aggregating red blood cells by quantitative ultrasound backscatter analysis.

PubMed

de Monchy, Romain; Rouyer, Julien; Destrempes, François; Chayer, Boris; Cloutier, Guy; Franceschini, Emilie

2018-04-01

Quantitative ultrasound techniques based on the backscatter coefficient (BSC) have been commonly used to characterize red blood cell (RBC) aggregation. Specifically, a scattering model is fitted to measured BSC and estimated parameters can provide a meaningful description of the RBC aggregates' structure (i.e., aggregate size and compactness). In most cases, scattering models assumed monodisperse RBC aggregates. This study proposes the Effective Medium Theory combined with the polydisperse Structure Factor Model (EMTSFM) to incorporate the polydispersity of aggregate size. From the measured BSC, this model allows estimating three structural parameters: the mean radius of the aggregate size distribution, the width of the distribution, and the compactness of the aggregates. Two successive experiments were conducted: a first experiment on blood sheared in a Couette flow device coupled with an ultrasonic probe, and a second experiment, on the same blood sample, sheared in a plane-plane rheometer coupled to a light microscope. Results demonstrated that the polydisperse EMTSFM provided the best fit to the BSC data when compared to the classical monodisperse models for the higher levels of aggregation at hematocrits between 10% and 40%. Fitting the polydisperse model yielded aggregate size distributions that were consistent with direct light microscope observations at low hematocrits.

Interactions Between the Cross-Shore Structure of Small Pelagic Fish Population, Offshore Industrial Fisheries and Near Shore Artisanal Fisheries: A Mathematical Approach.

PubMed

Mchich, Rachid; Brochier, Timothée; Auger, Pierre; Brehmer, Patrice

2016-12-01

This work presents a mathematical model describing the interactions between the cross-shore structure of small pelagic fish population an their exploitation by coastal and offshore fisheries. The complete model is a system of seven ODE's governing three stocks of small pelagic fish population moving and growing between three zones. Two types of fishing fleets are inter-acting with the fish population, industrial boats, constrained to offshore area, and artisanal boats, operating from the shore. Two time scales were considered and we use aggregation methods that allow us to reduce the dimension of the model and to obtain an aggregated model, which is a four dimension one. The analysis of the aggregated model is performed. We discuss the possible equilibriums and their meaning in terms of fishery management. An interesting equilibrium state can be obtained for which we can expect coexistence and a stable equilibrium state between fish stocks and fishing efforts. Some identification parameters are also given in the discussion part of the model.

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

NASA Astrophysics Data System (ADS)

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

2015-03-01

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

A Framework for Distributed Problem Solving

NASA Astrophysics Data System (ADS)

Leone, Joseph; Shin, Don G.

1989-03-01

This work explores a distributed problem solving (DPS) approach, namely the AM/AG model, to cooperative memory recall. The AM/AG model is a hierarchic social system metaphor for DPS based on the Mintzberg's model of organizations. At the core of the model are information flow mechanisms, named amplification and aggregation. Amplification is a process of expounding a given task, called an agenda, into a set of subtasks with magnified degree of specificity and distributing them to multiple processing units downward in the hierarchy. Aggregation is a process of combining the results reported from multiple processing units into a unified view, called a resolution, and promoting the conclusion upward in the hierarchy. The combination of amplification and aggregation can account for a memory recall process which primarily relies on the ability of making associations between vast amounts of related concepts, sorting out the combined results, and promoting the most plausible ones. The amplification process is discussed in detail. An implementation of the amplification process is presented. The process is illustrated by an example.

Evolution of mixed surfactant aggregates in solutions and at solid/solution interfaces

NASA Astrophysics Data System (ADS)

Zhang, Rui

Surfactant systems have been widely used in such as enhanced oil recovery, waste treatment and metallurgy, etc., in order to solve the problem of global energy crisis, to remove the pollutants and to generate novel energy resources. Almost all surfactant systems are invariably mixtures due to beneficial and economic considerations. The sizes and shapes of aggregates in solutions and at solid/solution interfaces become important, since the nanostructures of mixed aggregates determine solution and adsorption properties. A major hurdle in science is the lack of information on the type of complexes and aggregates formed by mixtures and the lack of techniques for deriving such information. Using techniques such as analytical ultracentrifuge, small angle neutron scattering, surface tension, fluorescence, cryo-TEM, light scattering and ultrafiltration, the nanostructures of aggregates of sugar based n-dodecyl-beta-D-maltoside (DM) and nonionic pentaethyleneglycol monododecyl ether or nonyl phenol ethoxylated decyl ether (NP-10) and their mixtures have been investigated to prove the hypothesis that the aggregation behavior is linked to packing of the surfactant governed by the molecular interactions as well as the molecular structures. The results from both sedimentation velocity and sedimentation equilibrium experiments suggest coexistence of two types of micelles in nonyl phenol ethoxylated decyl ether solutions and its mixtures with n-dodecyl-beta-D-maltoside while only one micellar species is present in n-dodecyl-beta-D-maltoside solutions, in good agreement with those from small angle neutron scattering, cryo-TEM, light scattering and ultrafiltration. Type I micelles were primary micelles at cmc while type II micelles were elongated micelles. On the other hand, the nanostructures of mixed surface aggregates have been quantitatively predicted for the first time using a modified packing index. As a continuation of the Somasundaran-Fuersteneau adsorption model, a modified one-step model has been developed to fully understand the adsorption behavior of surfactant mixtures and obtained thermodynamic information on aggregation number and standard free energy for surface aggregation. The findings are expected to provide fundamental basis for the design optimal surfactant schemes for desired purposes.

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.

Behavioural modelling of irrigation decision making under water scarcity

NASA Astrophysics Data System (ADS)

Foster, T.; Brozovic, N.; Butler, A. P.

2013-12-01

Providing effective policy solutions to aquifer depletion caused by abstraction for irrigation is a key challenge for socio-hydrology. However, most crop production functions used in hydrological models do not capture the intraseasonal nature of irrigation planning, or the importance of well yield in land and water use decisions. Here we develop a method for determining stochastic intraseasonal water use that is based on observed farmer behaviour but is also theoretically consistent with dynamically optimal decision making. We use the model to (i) analyse the joint land and water use decision by farmers; (ii) to assess changes in behaviour and production risk in response to water scarcity; and (iii) to understand the limits of applicability of current methods in policy design. We develop a biophysical model of water-limited crop yield building on the AquaCrop model. The model is calibrated and applied to case studies of irrigated corn production in Nebraska and Texas. We run the model iteratively, using long-term climate records, to define two formulations of the crop-water production function: (i) the aggregate relationship between total seasonal irrigation and yield (typical of current approaches); and (ii) the stochastic response of yield and total seasonal irrigation to the choice of an intraseasonal soil moisture target and irrigated area. Irrigated area (the extensive margin decision) and per-area irrigation intensity (the intensive margin decision) are then calculated for different seasonal water restrictions (corresponding to regulatory policies) and well yield constraints on intraseasonal abstraction rates (corresponding to aquifer system limits). Profit- and utility-maximising decisions are determined assuming risk neutrality and varying degrees of risk aversion, respectively. Our results demonstrate that the formulation of the production function has a significant impact on the response to water scarcity. For low well yields, which are the major concern for farmers in areas of aquifer depletion or recurrent drought, the stochastic model demonstrates that partial-area irrigation is optimal irrespective of the size of water supply restrictions. This effect is not produced by the aggregate model, which cannot account for the variability of the production function with changes in irrigated area that control intraseasonal irrigation application rates. In addition, the aggregate model overstates the willingness of a risk-averse farmer to adjust on the intensive margin in response to water supply restrictions. This is due to the inability of aggregate models to specify correctly the production risk associated with intensive margin adjustments. Consequently, aggregate models give unrealistic estimates of water demand and underestimate the negative impacts on profitability of declining groundwater resources. Reliance on aggregate models will limit the ability of socio-hydrology to guide policy responses to groundwater scarcity. Our stochastic methodology provides a more realistic tool to study the management of groundwater in coupled human-water systems.

Kinetics of a Migration-Driven Aggregation-Fragmentation Process

NASA Astrophysics Data System (ADS)

Zhuang, You-Yi; Lin, Zhen-Quan; Ke, Jian-Hong

2003-08-01

We propose a reversible model of the migration-driven aggregation-fragmentation process with the symmetric migration rate kernels K(k;j)=K^'(k;j)=λ kj^v and the constant aggregation rates I1, I2 and fragmentation rates J1, J2. Based on the mean-field theory, we investigate the evolution behavior of the aggregate size distributions in several cases with different values of index υ. We find that the fragmentation reaction plays a more important role in the kinetic behaviors of the system than the aggregation and migration. When J1=0 and J2 =0, the aggregate size distributions ak(t) and bk(t) obey the conventional scaling law, while when J1>0 and J2>0, they obey the modified scaling law with an exponential scaling function. The total mass of either species remains conserved. The project supported by National Natural Science Foundation of China under Grant Nos. 10275048 and 10175008, and Natural Science Foundation of Zhejiang Province of China under Grant No. 102067

Estimating linear temporal trends from aggregated environmental monitoring data

USGS Publications Warehouse

Erickson, Richard A.; Gray, Brian R.; Eager, Eric A.

2017-01-01

Trend estimates are often used as part of environmental monitoring programs. These trends inform managers (e.g., are desired species increasing or undesired species decreasing?). Data collected from environmental monitoring programs is often aggregated (i.e., averaged), which confounds sampling and process variation. State-space models allow sampling variation and process variations to be separated. We used simulated time-series to compare linear trend estimations from three state-space models, a simple linear regression model, and an auto-regressive model. We also compared the performance of these five models to estimate trends from a long term monitoring program. We specifically estimated trends for two species of fish and four species of aquatic vegetation from the Upper Mississippi River system. We found that the simple linear regression had the best performance of all the given models because it was best able to recover parameters and had consistent numerical convergence. Conversely, the simple linear regression did the worst job estimating populations in a given year. The state-space models did not estimate trends well, but estimated population sizes best when the models converged. We found that a simple linear regression performed better than more complex autoregression and state-space models when used to analyze aggregated environmental monitoring data.

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.

Comprehensive modeling of critical health care activities, costs, and data needs within the context of addiction rehabilitiation

NASA Astrophysics Data System (ADS)

Hoffman, Kenneth J.; Keithley, Hudson

1994-12-01

There are few systems which aggregate standardized pertinent clinical observations of discrete patient problems and resolutions. The systematic information supplied by clinicians is generally provided to justify reimbursement from insurers. Insurers, by their nature, and expert in modeling health care costs by diagnosis, procedures, and population risk groups. Medically, they rely on clinician generated diagnostic and coded procedure information. Clinicians will document a patient's status at a discrete point in time through narrative. Clinical notes do not support aggregate and systematic analysis of outcome. A methodology exists and has been used by the US Army Drug and Alcohol Program to model the clinical activities, associated costs, and data requirements of an outpatient clinic. This has broad applicability for a comprehensive health care system to which patient costs and data requirements can be established.

The impact of anisotropy and interaction range on the self-assembly of Janus ellipsoids

NASA Astrophysics Data System (ADS)

Ruth, D. P.; Gunton, J. D.; Rickman, J. M.; Li, Wei

2014-12-01

We assess the roles of anisotropy and interaction range on the self-assembly of Janus colloidal particles. In particular, Monte Carlo simulation is employed to investigate the propensity for the formation of aggregates in a spheroidal model of a colloid having a relatively short-ranged interaction that is consistent with experimentally realizable systems. By monitoring the equilibrium distribution of aggregates as a function of temperature and density, we identify a "micelle" transition temperature and discuss its dependence on particle shape. We find that, unlike systems with longer ranged interactions, this system does not form micelles below a transition temperature at low density. Rather, larger clusters comprising 20-40 particles characterize the transition. We then examine the dependence of the second virial coefficient on particle shape and well width to determine how these important system parameters affect aggregation. Finally, we discuss possible strategies suggested by this work to promote self-assembly for the encapsulation of particles.

Experimental volcanic ash aggregation: Internal structuring of accretionary lapilli and the role of liquid bonding

NASA Astrophysics Data System (ADS)

Mueller, Sebastian B.; Kueppers, Ulrich; Ayris, Paul M.; Jacob, Michael; Dingwell, Donald B.

2016-01-01

Explosive volcanic eruptions can release vast quantities of pyroclastic material into Earth's atmosphere, including volcanic ash, particles with diameters less than two millimeters. Ash particles can cluster together to form aggregates, in some cases reaching up to several centimeters in size. Aggregation alters ash transport and settling behavior compared to un-aggregated particles, influencing ash distribution and deposit stratigraphy. Accretionary lapilli, the most commonly preserved type of aggregates within the geologic record, can exhibit complex internal stratigraphy. The processes involved in the formation and preservation of these aggregates remain poorly constrained quantitatively. In this study, we simulate the variable gas-particle flow conditions which may be encountered within eruption plumes and pyroclastic density currents via laboratory experiments using the ProCell Lab System® of Glatt Ingenieurtechnik GmbH. In this apparatus, solid particles are set into motion in a fluidized bed over a range of well-controlled boundary conditions (particle concentration, air flow rate, gas temperature, humidity, liquid composition). Experiments were conducted with soda-lime glass beads and natural volcanic ash particles under a range of experimental conditions. Both glass beads and volcanic ash exhibited the capacity for aggregation, but stable aggregates could only be produced when materials were coated with high but volcanically-relevant concentrations of NaCl. The growth and structure of aggregates was dependent on the initial granulometry, while the rate of aggregate formation increased exponentially with increasing relative humidity (12-45% RH), before overwetting promoted mud droplet formation. Notably, by use of a broad granulometry, we generated spherical, internally structured aggregates similar to some accretionary pellets found in volcanic deposits. Adaptation of a powder-technology model offers an explanation for the origin of natural accretionary pellets, suggesting them to be the result of a particular granulometry and fast-acting selective aggregation processes. For such aggregates to survive deposition and be preserved in the deposits of eruption plumes and pyroclastic density currents likely requires a significant pre-existing salt load on ash surfaces, and rapid aggregate drying prior to deposition or interaction with a more energetic environment. Our results carry clear benefits for future efforts to parameterize models of ash transport and deposition in the field.

Learning about individuals' health from aggregate data.

PubMed

Colbaugh, Rich; Glass, Kristin

2017-07-01

There is growing awareness that user-generated social media content contains valuable health-related information and is more convenient to collect than typical health data. For example, Twitter has been employed to predict aggregate-level outcomes, such as regional rates of diabetes and child poverty, and to identify individual cases of depression and food poisoning. Models which make aggregate-level inferences can be induced from aggregate data, and consequently are straightforward to build. In contrast, learning models that produce individual-level (IL) predictions, which are more informative, usually requires a large number of difficult-to-acquire labeled IL examples. This paper presents a new machine learning method which achieves the best of both worlds, enabling IL models to be learned from aggregate labels. The algorithm makes predictions by combining unsupervised feature extraction, aggregate-based modeling, and optimal integration of aggregate-level and IL information. Two case studies illustrate how to learn health-relevant IL prediction models using only aggregate labels, and show that these models perform as well as state-of-the-art models trained on hundreds or thousands of labeled individuals.

Sequestration of synaptic proteins by alpha-synuclein aggregates leading to neurotoxicity is inhibited by small peptide

PubMed Central

Choi, Mal-Gi; Kim, Mi Jin; Kim, Do-Geun; Yu, Ri; Jang, You-Na

2018-01-01

α-Synuclein (α-syn) is a major component of Lewy bodies found in synucleinopathies including Parkinson’s disease (PD) and Dementia with Lewy Bodies (DLB). Under the pathological conditions, α-syn tends to generate a diverse form of aggregates showing toxicity to neuronal cells and able to transmit across cells. However, mechanisms by which α-syn aggregates affect cytotoxicity in neurons have not been fully elucidated. Here we report that α-syn aggregates preferentially sequester specific synaptic proteins such as vesicle-associated membrane protein 2 (VAMP2) and synaptosomal-associated protein 25 (SNAP25) through direct binding which is resistant to SDS. The sequestration effect of α-syn aggregates was shown in a cell-free system, cultured primary neurons, and PD mouse model. Furthermore, we identified a specific blocking peptide derived from VAMP2 which partially inhibited the sequestration by α-syn aggregates and contributed to reduced neurotoxicity. These results provide a mechanism of neurotoxicity mediated by α-syn aggregates and suggest that the blocking peptide interfering with the pathological role of α-syn aggregates could be useful for designing a potential therapeutic drug for the treatment of PD. PMID:29608598

Cellular Particle Dynamics simulation of biomechanical relaxation processes of multi-cellular systems

NASA Astrophysics Data System (ADS)

McCune, Matthew; Kosztin, Ioan

2013-03-01

Cellular Particle Dynamics (CPD) is a theoretical-computational-experimental framework for describing and predicting the time evolution of biomechanical relaxation processes of multi-cellular systems, such as fusion, sorting and compression. In CPD, cells are modeled as an ensemble of cellular particles (CPs) that interact via short range contact interactions, characterized by an attractive (adhesive interaction) and a repulsive (excluded volume interaction) component. The time evolution of the spatial conformation of the multicellular system is determined by following the trajectories of all CPs through numerical integration of their equations of motion. Here we present CPD simulation results for the fusion of both spherical and cylindrical multi-cellular aggregates. First, we calibrate the relevant CPD model parameters for a given cell type by comparing the CPD simulation results for the fusion of two spherical aggregates to the corresponding experimental results. Next, CPD simulations are used to predict the time evolution of the fusion of cylindrical aggregates. The latter is relevant for the formation of tubular multi-cellular structures (i.e., primitive blood vessels) created by the novel bioprinting technology. Work supported by NSF [PHY-0957914]. Computer time provided by the University of Missouri Bioinformatics Consortium.

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.

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

Hansen, Timothy M.; Palmintier, Bryan; Suryanarayanan, Siddharth

As more Smart Grid technologies (e.g., distributed photovoltaic, spatially distributed electric vehicle charging) are integrated into distribution grids, static distribution simulations are no longer sufficient for performing modeling and analysis. GridLAB-D is an agent-based distribution system simulation environment that allows fine-grained end-user models, including geospatial and network topology detail. A problem exists in that, without outside intervention, once the GridLAB-D simulation begins execution, it will run to completion without allowing the real-time interaction of Smart Grid controls, such as home energy management systems and aggregator control. We address this lack of runtime interaction by designing a flexible communication interface, Bus.pymore » (pronounced bus-dot-pie), that uses Python to pass messages between one or more GridLAB-D instances and a Smart Grid simulator. This work describes the design and implementation of Bus.py, discusses its usefulness in terms of some Smart Grid scenarios, and provides an example of an aggregator-based residential demand response system interacting with GridLAB-D through Bus.py. The small scale example demonstrates the validity of the interface and shows that an aggregator using said interface is able to control residential loads in GridLAB-D during runtime to cause a reduction in the peak load on the distribution system in (a) peak reduction and (b) time-of-use pricing cases.« less

Small file aggregation in a parallel computing system

DOEpatents

Faibish, Sorin; Bent, John M.; Tzelnic, Percy; Grider, Gary; Zhang, Jingwang

2014-09-02

Techniques are provided for small file aggregation in a parallel computing system. An exemplary method for storing a plurality of files generated by a plurality of processes in a parallel computing system comprises aggregating the plurality of files into a single aggregated file; and generating metadata for the single aggregated file. The metadata comprises an offset and a length of each of the plurality of files in the single aggregated file. The metadata can be used to unpack one or more of the files from the single aggregated file.

GEOMETRIC CROSS SECTIONS OF DUST AGGREGATES AND A COMPRESSION MODEL FOR AGGREGATE COLLISIONS

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

Suyama, Toru; Wada, Koji; Tanaka, Hidekazu

2012-07-10

Geometric cross sections of dust aggregates determine their coupling with disk gas, which governs their motions in protoplanetary disks. Collisional outcomes also depend on geometric cross sections of initial aggregates. In a previous paper, we performed three-dimensional N-body simulations of sequential collisions of aggregates composed of a number of sub-micron-sized icy particles and examined radii of gyration (and bulk densities) of the obtained aggregates. We showed that collisional compression of aggregates is not efficient and that aggregates remain fluffy. In the present study, we examine geometric cross sections of the aggregates. Their cross sections decrease due to compression as wellmore » as to their gyration radii. It is found that a relation between the cross section and the gyration radius proposed by Okuzumi et al. is valid for the compressed aggregates. We also refine the compression model proposed in our previous paper. The refined model enables us to calculate the evolution of both gyration radii and cross sections of growing aggregates and reproduces well our numerical results of sequential aggregate collisions. The refined model can describe non-equal-mass collisions as well as equal-mass cases. Although we do not take into account oblique collisions in the present study, oblique collisions would further hinder compression of aggregates.« less

NON-SPATIAL CALIBRATIONS OF A GENERAL UNIT MODEL FOR ECOSYSTEM SIMULATIONS. (R825792)

EPA Science Inventory

General Unit Models simulate system interactions aggregated within one spatial unit of resolution. For unit models to be applicable to spatial computer simulations, they must be formulated generally enough to simulate all habitat elements within the landscape. We present the d...

NON-SPATIAL CALIBRATIONS OF A GENERAL UNIT MODEL FOR ECOSYSTEM SIMULATIONS. (R827169)

EPA Science Inventory

General Unit Models simulate system interactions aggregated within one spatial unit of resolution. For unit models to be applicable to spatial computer simulations, they must be formulated generally enough to simulate all habitat elements within the landscape. We present the d...

River Mixing in the Amazon as a Driver of Concentration-Discharge Relationships

NASA Astrophysics Data System (ADS)

Bouchez, Julien; Moquet, Jean-Sébastien; Espinoza, Jhan Carlo; Martinez, Jean-Michel; Guyot, Jean-Loup; Lagane, Christelle; Filizola, Naziano; Noriega, Luis; Hidalgo Sanchez, Liz; Pombosa, Rodrigo

2017-11-01

Large hydrological systems aggregate compositionally different waters derived from a variety of pathways. In the case of continental-scale rivers, such aggregation occurs noticeably at confluences between tributaries. Here we explore how such aggregation can affect solute concentration-discharge (C-Q) relationships and thus obscure the message carried by these relationships in terms of weathering properties of the Critical Zone. We build up a simple model for tributary mixing to predict the behavior of C-Q relationships during aggregation. We test a set of predictions made in the context of the largest world's river, the Amazon. In particular, we predict that the C-Q relationships of the rivers draining heterogeneous catchments should be the most "dilutional" and should display the widest hysteresis loops. To check these predictions, we compute 10 day-periodicity time series of Q and major solute (Si, Ca2+, Mg2+, K+, Na+, Cl-, SO42-) C and fluxes (F) for 13 gauging stations located throughout the Amazon basin. In agreement with the model predictions, C-Q relationships of most solutes shift from a fairly "chemostatic" behavior (nearly constant C) at the Andean mountain front and in pure lowland areas, to more "dilutional" patterns (negative C-Q relationship) toward the system mouth. More prominent C-Q hysteresis loops are also observed at the most downstream stations. Altogether, this study suggests that mixing of water and solutes between different flowpaths exerts a strong control on C-Q relationships of large-scale hydrological systems.

Development of Coarse Grained Models for Long Chain Alkanes

NASA Astrophysics Data System (ADS)

Gyawali, Gaurav; Sternfield, Samuel; Hwang, In Chul; Rick, Steven; Kumar, Revati; Rick Group Team; Kumar Group Team

Modeling aggregation in aqueous solution is a challenge for molecular simulations as it involves long time scales, a range of length scales, and the correct balance of hydrophobic and hydrophilic interactions. We have developed a coarse-grained model fast enough for the rapid testing of molecular structures for their aggregation properties. This model, using the Stillinger-Weber potential, achieves efficiency through a reduction in the number of interaction sites and the use of short-ranged interactions. The model can be two to three orders of magnitude more efficient than conventional all atom simulations, yet through a careful parameterization process and the use of many-body interactions can be remarkably accurate. We have developed models for long chain alkanes in water that reproduce the thermodynamics and structure of water-alkane and liquid alkane systems.

Modeling Multivalent Ligand-Receptor Interactions with Steric Constraints on Configurations of Cell-Surface Receptor Aggregates

PubMed Central

Monine, Michael I.; Posner, Richard G.; Savage, Paul B.; Faeder, James R.; Hlavacek, William S.

2010-01-01

Abstract We use flow cytometry to characterize equilibrium binding of a fluorophore-labeled trivalent model antigen to bivalent IgE-FcεRI complexes on RBL cells. We find that flow cytometric measurements are consistent with an equilibrium model for ligand-receptor binding in which binding sites are assumed to be equivalent and ligand-induced receptor aggregates are assumed to be acyclic. However, this model predicts extensive receptor aggregation at antigen concentrations that yield strong cellular secretory responses, which is inconsistent with the expectation that large receptor aggregates should inhibit such responses. To investigate possible explanations for this discrepancy, we evaluate four rule-based models for interaction of a trivalent ligand with a bivalent cell-surface receptor that relax simplifying assumptions of the equilibrium model. These models are simulated using a rule-based kinetic Monte Carlo approach to investigate the kinetics of ligand-induced receptor aggregation and to study how the kinetics and equilibria of ligand-receptor interaction are affected by steric constraints on receptor aggregate configurations and by the formation of cyclic receptor aggregates. The results suggest that formation of linear chains of cyclic receptor dimers may be important for generating secretory signals. Steric effects that limit receptor aggregation and transient formation of small receptor aggregates may also be important. PMID:20085718

STXM/C 1s-NEXAFS study of Eu(III) and Uranyl humic acid aggregates at different pH

NASA Astrophysics Data System (ADS)

Plaschke, M.; Rothe, J.; Denecke, M. A.; Geckeis, H.

2010-04-01

Humic acids (HA) are chemically heterogeneous and structurally ill-defined biopolymers which are able to bind traces of actinides or lanthanides. Due to their dimensions in the colloidal size range they may affect transport of these elements in aquatic systems. Eu(III)- and UO22+-HA aggregates have been investigated by Scanning Transmission X-ray Microscopy (STXM) and C 1s-NEXAFS under systematic variation of pH. In the Eu(III)- and UO22+-HA systems aggregate morphologies at near neutral pH were similar to those observed in previous studies: optically dense zones (high absorption at the carbon K-edge) are embedded in a matrix of less dense material. C 1s-NEXAFS signatures observed in the different zones, i.e., the intensity of the characteristic complexation feature previously experimentally described and recently theoretically characterized, strongly depends on sample pH. In the alkaline regime (pH 9) with added carbonate, co-precipitation of Eu(III)-carbonate (or ternary carbonate/(oxo)hydroxide complexes) with the Eu(III)-HA majority fraction is observed but Eu(III) binding to HA over carbonate in the dense zones seems to be favoured. The UO22+-HA system exhibits in alkaline solution more compact morphologies combined with a strong metal ion complexation effect in the NEXAFS. Eu(III) and UO22+ polyacrylic acid (PAA) aggregates used as HA model systems show similar spectral trends; these aggregates exhibit highly branched morphologies without segregation into zones with different NEXAFS signatures. The chemical environment such as pH or the type of metal cation strongly influences both HA aggregate morphologies and NEXAFS spectral signatures. These can, in turn, be used as indicators of the strength of lanthanide or actinide ion bound HA interaction.

Using Human iPSC-Derived Neurons to Model TAU Aggregation

PubMed Central

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

2015-01-01

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

Piecewise Polynomial Aggregation as Preprocessing for Data Numerical Modeling

NASA Astrophysics Data System (ADS)

Dobronets, B. S.; Popova, O. A.

2018-05-01

Data aggregation issues for numerical modeling are reviewed in the present study. The authors discuss data aggregation procedures as preprocessing for subsequent numerical modeling. To calculate the data aggregation, the authors propose using numerical probabilistic analysis (NPA). An important feature of this study is how the authors represent the aggregated data. The study shows that the offered approach to data aggregation can be interpreted as the frequency distribution of a variable. To study its properties, the density function is used. For this purpose, the authors propose using the piecewise polynomial models. A suitable example of such approach is the spline. The authors show that their approach to data aggregation allows reducing the level of data uncertainty and significantly increasing the efficiency of numerical calculations. To demonstrate the degree of the correspondence of the proposed methods to reality, the authors developed a theoretical framework and considered numerical examples devoted to time series aggregation.

The effect of desmopressin on platelet aggregation defect in systemic amyloidosis: a preliminary report.

PubMed

Demiroğlu, H; Barişta, I; Gürsoy, M; Oymak, O; Dündar, S

1996-05-01

Systemic amyloidosis may often be complicated with haemorrhagic tendency. The causes of this manifestation are factor deficiencies, hyperfibrinolysis and vasculopathy. In order to investigate the role of platelets, if any, we performed platelet aggregation tests with different aggregants in 10 patients with systemic amyloidosis due to familial Mediterranean fever and 10 healthy controls. Platelet aggregation was defective with different aggregants (ADP, epinephrine, collagen) in patients compared with controls. Platelet aggregation tests repeated after desmopressin (DDAVP) administration were normalized. These findings may suggest a role of a platelet aggregation defect in haemorrhagic diathesis complicating systemic amyloidosis. DDAVP may benefit patients with this disease in case of bleeding and before surgical interventions.

APPLYING THE PATUXENT LANDSCAPE UNIT MODEL TO HUMAN DOMINATED ECOSYSTEMS: THE CASE OF AGRICULTURE. (R827169)

EPA Science Inventory

Non-spatial dynamics are core to landscape simulations. Unit models simulate system interactions aggregated within one space unit of resolution used within a spatial model. For unit models to be applicable to spatial simulations they have to be formulated in a general enough w...

Cell-to-cell Transmission of Polyglutamine Aggregates in C. elegans

PubMed Central

Kim, Dong-Kyu; Cho, Kyu-Won; Ahn, Woo Jung; Perez-Acuña, Dayana; Jeong, Hyunsu; Lee, He-Jin

2017-01-01

Huntington disease (HD) is an inherited neurodegenerative disorder characterized by motor and cognitive dysfunction caused by expansion of polyglutamine (polyQ) repeat in exon 1 of huntingtin (HTT). In patients, the number of glutamine residues in polyQ tracts are over 35, and it is correlated with age of onset, severity, and disease progression. Expansion of polyQ increases the propensity for HTT protein aggregation, process known to be implicated in neurodegeneration. These pathological aggregates can be transmitted from neuron to another neuron, and this process may explain the pathological spreading of polyQ aggregates. Here, we developed an in vivo model for studying transmission of polyQ aggregates in a highly quantitative manner in real time. HTT exon 1 with expanded polyQ was fused with either N-terminal or C-terminal fragments of Venus fluorescence protein and expressed in pharyngeal muscles and associated neurons, respectively, of C. elegans. Transmission of polyQ proteins was detected using bimolecular fluorescence complementation (BiFC). Mutant polyQ (Q97) was transmitted much more efficiently than wild type polyQ (Q25) and forms numerous inclusion bodies as well. The transmission of Q97 was gradually increased with aging of animal. The animals with polyQ transmission exhibited degenerative phenotypes, such as nerve degeneration, impaired pharyngeal pumping behavior, and reduced life span. The C. elegans model presented here would be a useful in vivo model system for the study of polyQ aggregate propagation and might be applied to the screening of genetic and chemical modifiers of the propagation. PMID:29302199

Probing the interplay between amyloidogenic proteins and membranes using lipid monolayers and bilayers.

PubMed

Relini, Annalisa; Marano, Nadia; Gliozzi, Alessandra

2014-05-01

Many degenerative diseases such as Alzheimer's and Parkinson's involve proteins that have a tendency to misfold and aggregate eventually forming amyloid fibers. This review describes the use of monolayers, bilayers, supported membranes, and vesicles as model systems that have helped elucidate the mechanisms and consequences of the interactions between amyloidogenic proteins and membranes. These are twofold: membranes favor the formation of amyloid structures and these induce damage in those membranes. We describe studies that show how interfaces, especially charged ones, favor amyloidogenic protein aggregation by several means. First, surfaces increase the effective protein concentration reducing a three-dimensional system to a two-dimensional one. Second, charged surfaces allow electrostatic interactions with the protein. Anionic lipids as well as rafts, rich in cholesterol and gangliosides, prove to play an especially important role. Finally, these amphipathic systems also offer a hydrophobic environment favoring conformational changes, oligomerization, and eventual formation of mature fibers. In addition, we examine several models for membrane permeabilization: protein pores, leakage induced by extraction of lipids, chaotic pores, and membrane tension, presenting illustrative examples of experimental evidence in support of these models. The picture that emerges from recent work is one where more than one mechanism is in play. Which mechanism prevails depends on the protein, its aggregation state, and the lipid environment in which the interactions occur. © 2013.

Models and Methods of Aggregating Linguistic Information in Multi-criteria Hierarchical Quality Assessment Systems

NASA Astrophysics Data System (ADS)

Azarnova, T. V.; Titova, I. A.; Barkalov, S. A.

2018-03-01

The article presents an algorithm for obtaining an integral assessment of the quality of an organization from the perspective of customers, based on the method of aggregating linguistic information on a multilevel hierarchical system of quality assessment. The algorithm is of a constructive nature, it provides not only the possibility of obtaining an integral evaluation, but also the development of a quality improvement strategy based on the method of linguistic decomposition, which forms the minimum set of areas of work with clients whose quality change will allow obtaining the required level of integrated quality assessment.

Amyloid and membrane complexity: The toxic interplay revealed by AFM.

PubMed

Canale, Claudio; Oropesa-Nuñez, Reinier; Diaspro, Alberto; Dante, Silvia

2018-01-01

Lipid membranes play a fundamental role in the pathological development of protein misfolding diseases. Several pieces of evidence suggest that the lipid membrane could act as a catalytic surface for protein aggregation. Furthermore, a leading theory indicates the interaction between the cell membrane and misfolded oligomer species as the responsible for cytotoxicity, hence, for neurodegeneration in disorders such as Alzheimer's and Parkinson's disease. The definition of the mechanisms that drive the interaction between pathological protein aggregates and plasma membrane is fundamental for the development of effective therapies for a large class of diseases. Atomic force microscopy (AFM) has been employed to study how amyloid aggregates affect the cell physiological properties. Considerable efforts were spent to characterize the interaction with model systems, i.e., planar supported lipid bilayers, but some works also addressed the problem directly on living cells. Here, an overview of the main works involving the use of the AFM on both model system and living cells will be provided. Different kind of approaches will be presented, as well as the main results derived from the AFM analysis. Copyright © 2017 Elsevier Ltd. All rights reserved.

Development of a multi-criteria evaluation system to assess growing pig welfare.

PubMed

Martín, P; Traulsen, I; Buxadé, C; Krieter, J

2017-03-01

The aim of this paper was to present an alternative multi-criteria evaluation model to assess animal welfare on farms based on the Welfare Quality® (WQ) project, using an example of welfare assessment of growing pigs. The WQ assessment protocol follows a three-step aggregation process. Measures are aggregated into criteria, criteria into principles and principles into an overall assessment. This study focussed on the first step of the aggregation. Multi-attribute utility theory (MAUT) was used to produce a value of welfare for each criterion. The utility functions and the aggregation function were constructed in two separated steps. The Measuring Attractiveness by a Categorical Based Evaluation Technique (MACBETH) method was used for utility function determination and the Choquet Integral (CI) was used as an aggregation operator. The WQ decision-makers' preferences were fitted in order to construct the utility functions and to determine the CI parameters. The methods were tested with generated data sets for farms of growing pigs. Using the MAUT, similar results were obtained to the ones obtained applying the WQ protocol aggregation methods. It can be concluded that due to the use of an interactive approach such as MACBETH, this alternative methodology is more transparent and more flexible than the methodology proposed by WQ, which allows the possibility to modify the model according, for instance, to new scientific knowledge.

Model for amorphous aggregation processes

NASA Astrophysics Data System (ADS)

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

2009-11-01

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

Aggregation work at polydisperse micellization: ideal solution and "dressed micelle" models comparing to molecular dynamics simulations.

PubMed

Burov, S V; Shchekin, A K

2010-12-28

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

AggModel: A soil organic matter model with measurable pools for use in incubation studies

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

Segoli, Moran; De Gryze, S.; Dou, Fugen

2013-01-01

Current soil organic matter (SOM) models are empirical in nature by employing few conceptual SOM pools that have a specific turnover time, but that are not measurable and have no direct relationship with soil structural properties. Most soil particles are held together in aggregates and the number, size and stability of these aggregates significantly affect the size and amount of organic matter contained in these aggregates, and its susceptibility to decomposition. While it has been shown that soil aggregates and their dynamics can be measured directly in the laboratory and in the field, the impact of soil aggregate dynamics onmore » SOM decomposition has not been explicitly incorporated in ecosystem models. Here, we present AggModel, a conceptual and simulation model that integrates soil aggregate and SOM dynamics. In AggModel, we consider unaggregated and microaggregated soil that can exist within or external to macroaggregated soil. Each of the four aggregate size classes contains particulate organic matter and mineral-associated organic matter fractions. We used published data from laboratory incubations to calibrate and validate the biological and environmental effects on the rate of formation and breakdown of macroaggregates and microaggregates, and the organic matter dynamics within these different aggregate fractions. After calibration, AggModel explained more than 70% of the variation in aggregate masses and over 90% of the variation in aggregate-associated carbon. The model estimated the turnover time of macroaggregates as 32 days and 166 days for microaggregates. Sensitivity analysis of AggModel parameterization supported the notion that macroaggregate turnover rate has a strong control over microaggregate masses and, hence, carbon sequestration. In addition to AggModel being a proof-of-concept, the advantage of a model that is based on measurable SOM fractions is that its internal structure and dynamics can be directly calibrated and validated by using experimental data. In conclusion, AggModel successfully incorporates the explicit representation for the turnover of soil aggregates and their influence on SOM dynamics and can form the basis for new SOM modules within existing ecosystem models.« less

Sensitivity of geographic information system outputs to errors in remotely sensed data

NASA Technical Reports Server (NTRS)

Ramapriyan, H. K.; Boyd, R. K.; Gunther, F. J.; Lu, Y. C.

1981-01-01

The sensitivity of the outputs of a geographic information system (GIS) to errors in inputs derived from remotely sensed data (RSD) is investigated using a suitability model with per-cell decisions and a gridded geographic data base whose cells are larger than the RSD pixels. The process of preparing RSD as input to a GIS is analyzed, and the errors associated with classification and registration are examined. In the case of the model considered, it is found that the errors caused during classification and registration are partially compensated by the aggregation of pixels. The compensation is quantified by means of an analytical model, a Monte Carlo simulation, and experiments with Landsat data. The results show that error reductions of the order of 50% occur because of aggregation when 25 pixels of RSD are used per cell in the geographic data base.

Exciton interference revealed by energy dependent exciton transfer rate for ring-structured molecular systems.

PubMed

Yan, Yun-An

2016-01-14

The quantum interference is an intrinsic phenomenon in quantum physics for photon and massive quantum particles. In principle, the quantum interference may also occur with quasi-particles, such as the exciton. In this study, we show how the exciton quantum interference can be significant in aggregates through theoretical simulations with hierarchical equations of motion. The systems under investigation are generalized donor-bridge-acceptor model aggregates with the donor consisting of six homogeneous sites assuming the nearest neighbor coupling. For the models with single-path bridge, the exciton transfer time only shows a weak excitation energy dependence. But models with double-path bridge have a new short transfer time scale and the excitation energy dependence of the exciton transfer time assumes clear peak structure which is detectable with today's nonlinear spectroscopy. This abnormality is attributed to the exciton quantum interference and the condition for a clear observation in experiment is also explored.

Aggregation effects on tritium-based mean transit times and young water fractions in spatially heterogeneous catchments and groundwater systems

NASA Astrophysics Data System (ADS)

Stewart, Michael K.; Morgenstern, Uwe; Gusyev, Maksym A.; Małoszewski, Piotr

2017-09-01

Kirchner (2016a) demonstrated that aggregation errors due to spatial heterogeneity, represented by two homogeneous subcatchments, could cause severe underestimation of the mean transit times (MTTs) of water travelling through catchments when simple lumped parameter models were applied to interpret seasonal tracer cycle data. Here we examine the effects of such errors on the MTTs and young water fractions estimated using tritium concentrations in two-part hydrological systems. We find that MTTs derived from tritium concentrations in streamflow are just as susceptible to aggregation bias as those from seasonal tracer cycles. Likewise, groundwater wells or springs fed by two or more water sources with different MTTs will also have aggregation bias. However, the transit times over which the biases are manifested are different because the two methods are applicable over different time ranges, up to 5 years for seasonal tracer cycles and up to 200 years for tritium concentrations. Our virtual experiments with two water components show that the aggregation errors are larger when the MTT differences between the components are larger and the amounts of the components are each close to 50 % of the mixture. We also find that young water fractions derived from tritium (based on a young water threshold of 18 years) are almost immune to aggregation errors as were those derived from seasonal tracer cycles with a threshold of about 2 months.

Simulations of Sea Level Rise Effects on Complex Coastal Systems

NASA Astrophysics Data System (ADS)

Niedoroda, A. W.; Ye, M.; Saha, B.; Donoghue, J. F.; Reed, C. W.

2009-12-01

It is now established that complex coastal systems with elements such as beaches, inlets, bays, and rivers adjust their morphologies according to time-varying balances in between the processes that control the exchange of sediment. Accelerated sea level rise introduces a major perturbation into the sediment-sharing systems. A modeling framework based on a new SL-PR model which is an advanced version of the aggregate-scale CST Model and the event-scale CMS-2D and CMS-Wave combination have been used to simulate the recent evolution of a portion of the Florida panhandle coast. This combination of models provides a method to evaluate coefficients in the aggregate-scale model that were previously treated as fitted parameters. That is, by carrying out simulations of a complex coastal system with runs of the event-scale model representing more than a year it is now possible to directly relate the coefficients in the large-scale SL-PR model to measureable physical parameters in the current and wave fields. This cross-scale modeling procedure has been used to simulate the shoreline evolution at the Santa Rosa Island, a long barrier which houses significant military infrastructure at the north Gulf Coast. The model has been used to simulate 137 years of measured shoreline change and to extend these to predictions of future rates of shoreline migration.

Aggregative Learning Method and Its Application for Communication Quality Evaluation

NASA Astrophysics Data System (ADS)

Akhmetov, Dauren F.; Kotaki, Minoru

2007-12-01

In this paper, so-called Aggregative Learning Method (ALM) is proposed to improve and simplify the learning and classification abilities of different data processing systems. It provides a universal basis for design and analysis of mathematical models of wide class. A procedure was elaborated for time series model reconstruction and analysis for linear and nonlinear cases. Data approximation accuracy (during learning phase) and data classification quality (during recall phase) are estimated from introduced statistic parameters. The validity and efficiency of the proposed approach have been demonstrated through its application for monitoring of wireless communication quality, namely, for Fixed Wireless Access (FWA) system. Low memory and computation resources were shown to be needed for the procedure realization, especially for data classification (recall) stage. Characterized with high computational efficiency and simple decision making procedure, the derived approaches can be useful for simple and reliable real-time surveillance and control system design.

κ-Casein terminates casein micelle build-up by its "soft" secondary structure.

PubMed

Nagy, Krisztina; Váró, György; Szalontai, Balázs

2012-11-01

In our previous paper (Nagy et al. in J Biol Chem 285:38811-38817, 2010) by using a multilayered model system, we showed that, from α-casein, aggregates (similar to natural casein micelles) can be built up step by step if Ca-phosphate nanocluster incorporation is ensured between the protein adsorption steps. It remained, however, an open question whether the growth of the aggregates can be terminated, similarly to in nature with casein micelles. Here, we show that, in the presence of Ca-phosphate nanoclusters, upon adsorbing onto earlier α-casein surfaces, the secondary structure of α-casein remains practically unaffected, but κ-casein exhibits considerable changes in its secondary structure as manifested by a shift toward having more β-structures. In the absence of Ca-phosphate, only κ-casein can still adsorb onto the underlying casein surface; this κ-casein also expresses considerable shift toward β-structures. In addition, this κ-casein cover terminates casein aggregation; no further adsorption of either α- or κ-casein can be achieved. These results, while obtained on a model system, may show that the Ca-insensitive κ-casein can, indeed, be the outer layer of the casein micelles, not only because of its "hairy" extrusion into the water phase, but because of its "softer" secondary structure, which can "occlude" the interacting motifs serving casein aggregation. We think that the revealed nature of the molecular interactions, and the growth mechanism found here, might be useful to understand the aggregation process of casein micelles also in vivo.

Aggregation of Human S100A8 and S100A9 Amyloidogenic Proteins Perturbs Proteostasis in a Yeast Model

PubMed Central

Eremenko, Ekaterina; Ben-Zvi, Anat; Morozova-Roche, Ludmilla A.; Raveh, Dina

2013-01-01

Amyloid aggregates of the calcium-binding EF-hand proteins, S100A8 and S100A9, have been found in the corpora amylacea of patients with prostate cancer and may play a role in carcinogenesis. Here we present a novel model system using the yeast Saccharomyces cerevisiae to study human S100A8 and S100A9 aggregation and toxicity. We found that S100A8, S100A9 and S100A8/9 cotransfomants form SDS-resistant non-toxic aggregates in yeast cells. Using fluorescently tagged proteins, we showed that S100A8 and S100A9 accumulate in foci. After prolonged induction, S100A8 foci localized to the cell vacuole, whereas the S100A9 foci remained in the cytoplasm when present alone, but entered the vacuole in cotransformants. Biochemical analysis of the proteins indicated that S100A8 and S100A9 alone or coexpressed together form amyloid-like aggregates in yeast. Expression of S100A8 and S100A9 in wild type yeast did not affect cell viability, but these proteins were toxic when expressed on a background of unrelated metastable temperature-sensitive mutant proteins, Cdc53-1p, Cdc34-2p, Srp1-31p and Sec27-1p. This finding suggests that the expression and aggregation of S100A8 and S100A9 may limit the capacity of the cellular proteostasis machinery. To test this hypothesis, we screened a set of chaperone deletion mutants and found that reducing the levels of the heat-shock proteins Hsp104p and Hsp70p was sufficient to induce S100A8 and S100A9 toxicity. This result indicates that the chaperone activity of the Hsp104/Hsp70 bi-chaperone system in wild type cells is sufficient to reduce S100A8 and S100A9 amyloid toxicity and preserve cellular proteostasis. Expression of human S100A8 and S100A9 in yeast thus provides a novel model system for the study of the interaction of amyloid deposits with the proteostasis machinery. PMID:23483999

Three-dimensional forward modeling of DC resistivity using the aggregation-based algebraic multigrid method

NASA Astrophysics Data System (ADS)

Chen, Hui; Deng, Ju-Zhi; Yin, Min; Yin, Chang-Chun; Tang, Wen-Wu

2017-03-01

To speed up three-dimensional (3D) DC resistivity modeling, we present a new multigrid method, the aggregation-based algebraic multigrid method (AGMG). We first discretize the differential equation of the secondary potential field with mixed boundary conditions by using a seven-point finite-difference method to obtain a large sparse system of linear equations. Then, we introduce the theory behind the pairwise aggregation algorithms for AGMG and use the conjugate-gradient method with the V-cycle AGMG preconditioner (AGMG-CG) to solve the linear equations. We use typical geoelectrical models to test the proposed AGMG-CG method and compare the results with analytical solutions and the 3DDCXH algorithm for 3D DC modeling (3DDCXH). In addition, we apply the AGMG-CG method to different grid sizes and geoelectrical models and compare it to different iterative methods, such as ILU-BICGSTAB, ILU-GCR, and SSOR-CG. The AGMG-CG method yields nearly linearly decreasing errors, whereas the number of iterations increases slowly with increasing grid size. The AGMG-CG method is precise and converges fast, and thus can improve the computational efficiency in forward modeling of three-dimensional DC resistivity.

Chemical colloids versus biological colloids: a comparative study for the elucidation of the mechanism of protein fiber formation

NASA Technical Reports Server (NTRS)

Xu, Shaohua; Wu, David; Arnsdorf, Morton; Johnson, Robert; Getz, Godfrey S.; Cabana, Veneracion G.

2005-01-01

Fiber formation from murine serum amyloid A1 (SAA) was compared to the linear aggregation and fiber formation of colloidal gold particles. Here we report the similarities of these processes. Upon incubation with acetic acid, SAA misfolds and adopts a new conformation, which we termed saa. saa apparently is less soluble than SAA in aqueous solution; it aggregates and forms nucleation units and then fibers. The fibers appear as a string of the nucleation units. Additionally, an external electric field promotes saa fiber formation. These properties of saa are reminiscent of colloidal gold formation from gold ions and one-dimensional aggregation of the gold colloids. Colloidal gold particles were also found to be capable of aggregating one-dimensionally under an electric field or in the presence of polylysine. These gold fibers resembled in structure that of saa fibers. In summary, protein aggregation and formation of fibers appear to follow the generalized principles derived in colloidal science for the aggregation of atoms and molecules, including polymers such as polypeptides. The analysis of colloidal gold formation and of one-dimensional aggregation provides a simple model system for the elucidation of some aspects of protein fiber formation.

A critical-like collective state leads to long-range cell communication in Dictyostelium discoideum aggregation

PubMed Central

De Palo, Giovanna; Yi, Darvin; Endres, Robert G.

2017-01-01

The transition from single-cell to multicellular behavior is important in early development but rarely studied. The starvation-induced aggregation of the social amoeba Dictyostelium discoideum into a multicellular slug is known to result from single-cell chemotaxis towards emitted pulses of cyclic adenosine monophosphate (cAMP). However, how exactly do transient, short-range chemical gradients lead to coherent collective movement at a macroscopic scale? Here, we developed a multiscale model verified by quantitative microscopy to describe behaviors ranging widely from chemotaxis and excitability of individual cells to aggregation of thousands of cells. To better understand the mechanism of long-range cell—cell communication and hence aggregation, we analyzed cell—cell correlations, showing evidence of self-organization at the onset of aggregation (as opposed to following a leader cell). Surprisingly, cell collectives, despite their finite size, show features of criticality known from phase transitions in physical systems. By comparing wild-type and mutant cells with impaired aggregation, we found the longest cell—cell communication distance in wild-type cells, suggesting that criticality provides an adaptive advantage and optimally sized aggregates for the dispersal of spores. PMID:28422986

Towards representing human behavior and decision making in Earth system models - an overview of techniques and approaches

NASA Astrophysics Data System (ADS)

Müller-Hansen, Finn; Schlüter, Maja; Mäs, Michael; Donges, Jonathan F.; Kolb, Jakob J.; Thonicke, Kirsten; Heitzig, Jobst

2017-11-01

Today, humans have a critical impact on the Earth system and vice versa, which can generate complex feedback processes between social and ecological dynamics. Integrating human behavior into formal Earth system models (ESMs), however, requires crucial modeling assumptions about actors and their goals, behavioral options, and decision rules, as well as modeling decisions regarding human social interactions and the aggregation of individuals' behavior. Here, we review existing modeling approaches and techniques from various disciplines and schools of thought dealing with human behavior at different levels of decision making. We demonstrate modelers' often vast degrees of freedom but also seek to make modelers aware of the often crucial consequences of seemingly innocent modeling assumptions. After discussing which socioeconomic units are potentially important for ESMs, we compare models of individual decision making that correspond to alternative behavioral theories and that make diverse modeling assumptions about individuals' preferences, beliefs, decision rules, and foresight. We review approaches to model social interaction, covering game theoretic frameworks, models of social influence, and network models. Finally, we discuss approaches to studying how the behavior of individuals, groups, and organizations can aggregate to complex collective phenomena, discussing agent-based, statistical, and representative-agent modeling and economic macro-dynamics. We illustrate the main ingredients of modeling techniques with examples from land-use dynamics as one of the main drivers of environmental change bridging local to global scales.

Stoichiometry of Nck-dependent actin polymerization in living cells

PubMed Central

Ditlev, Jonathon A.; Michalski, Paul J.; Huber, Greg; Rivera, Gonzalo M.; Mohler, William A.

2012-01-01

Regulation of actin dynamics through the Nck/N-WASp (neural Wiskott–Aldrich syndrome protein)/Arp2/3 pathway is essential for organogenesis, cell invasiveness, and pathogen infection. Although many of the proteins involved in this pathway are known, the detailed mechanism by which it functions remains undetermined. To examine the signaling mechanism, we used a two-pronged strategy involving computational modeling and quantitative experimentation. We developed predictions for Nck-dependent actin polymerization using the Virtual Cell software system. In addition, we used antibody-induced aggregation of membrane-targeted Nck SH3 domains to test these predictions and to determine how the number of molecules in Nck aggregates and the density of aggregates affected localized actin polymerization in living cells. Our results indicate that the density of Nck molecules in aggregates is a critical determinant of actin polymerization. Furthermore, results from both computational simulations and experimentation support a model in which the Nck/N-WASp/Arp2/3 stoichiometry is 4:2:1. These results provide new insight into activities involving localized actin polymerization, including tumor cell invasion, microbial pathogenesis, and T cell activation. PMID:22613834

Cybernetic integration of experiments into the CVT system

NASA Technical Reports Server (NTRS)

Helvey, T. C.

1972-01-01

The research to develop a cybernetic model which is a static aggregate of the existing interaction in the CVT is reported. The experiments involving man considered necessary for cybernetic integration are listed. Topics discussed include: the modeling dynamic interactions for two competing systems; aspects of man-man integration in the CVT; and establishment of optimum number of research crew for the CVT.

Culturing and applications of rotating wall vessel bioreactor derived 3D epithelial cell models.

PubMed

Radtke, Andrea L; Herbst-Kralovetz, Melissa M

2012-04-03

Cells and tissues in the body experience environmental conditions that influence their architecture, intercellular communications, and overall functions. For in vitro cell culture models to accurately mimic the tissue of interest, the growth environment of the culture is a critical aspect to consider. Commonly used conventional cell culture systems propagate epithelial cells on flat two-dimensional (2-D) impermeable surfaces. Although much has been learned from conventional cell culture systems, many findings are not reproducible in human clinical trials or tissue explants, potentially as a result of the lack of a physiologically relevant microenvironment. Here, we describe a culture system that overcomes many of the culture condition boundaries of 2-D cell cultures, by using the innovative rotating wall vessel (RWV) bioreactor technology. We and others have shown that organotypic RWV-derived models can recapitulate structure, function, and authentic human responses to external stimuli similarly to human explant tissues (1-6). The RWV bioreactor is a suspension culture system that allows for the growth of epithelial cells under low physiological fluid shear conditions. The bioreactors come in two different formats, a high-aspect rotating vessel (HARV) or a slow-turning lateral vessel (STLV), in which they differ by their aeration source. Epithelial cells are added to the bioreactor of choice in combination with porous, collagen-coated microcarrier beads (Figure 1A). The cells utilize the beads as a growth scaffold during the constant free fall in the bioreactor (Figure 1B). The microenvironment provided by the bioreactor allows the cells to form three-dimensional (3-D) aggregates displaying in vivo-like characteristics often not observed under standard 2-D culture conditions (Figure 1D). These characteristics include tight junctions, mucus production, apical/basal orientation, in vivo protein localization, and additional epithelial cell-type specific properties. The progression from a monolayer of epithelial cells to a fully differentiated 3-D aggregate varies based on cell type(1, 7-13). Periodic sampling from the bioreactor allows for monitoring of epithelial aggregate formation, cellular differentiation markers and viability (Figure 1D). Once cellular differentiation and aggregate formation is established, the cells are harvested from the bioreactor, and similar assays performed on 2-D cells can be applied to the 3-D aggregates with a few considerations (Figure 1E-G). In this work, we describe detailed steps of how to culture 3-D epithelial cell aggregates in the RWV bioreactor system and a variety of potential assays and analyses that can be executed with the 3-D aggregates. These analyses include, but are not limited to, structural/morphological analysis (confocal, scanning and transmission electron microscopy), cytokine/chemokine secretion and cell signaling (cytometric bead array and Western blot analysis), gene expression analysis (real-time PCR), toxicological/drug analysis and host-pathogen interactions. The utilization of these assays set the foundation for more in-depth and expansive studies such as metabolomics, transcriptomics, proteomics and other array-based applications. Our goal is to present a non-conventional means of culturing human epithelial cells to produce organotypic 3-D models that recapitulate the human in vivo tissue, in a facile and robust system to be used by researchers with diverse scientific interests.

A probabilistic mechanical model for prediction of aggregates’ size distribution effect on concrete compressive strength

NASA Astrophysics Data System (ADS)

Miled, Karim; Limam, Oualid; Sab, Karam

2012-06-01

To predict aggregates' size distribution effect on the concrete compressive strength, a probabilistic mechanical model is proposed. Within this model, a Voronoi tessellation of a set of non-overlapping and rigid spherical aggregates is used to describe the concrete microstructure. Moreover, aggregates' diameters are defined as statistical variables and their size distribution function is identified to the experimental sieve curve. Then, an inter-aggregate failure criterion is proposed to describe the compressive-shear crushing of the hardened cement paste when concrete is subjected to uniaxial compression. Using a homogenization approach based on statistical homogenization and on geometrical simplifications, an analytical formula predicting the concrete compressive strength is obtained. This formula highlights the effects of cement paste strength and aggregates' size distribution and volume fraction on the concrete compressive strength. According to the proposed model, increasing the concrete strength for the same cement paste and the same aggregates' volume fraction is obtained by decreasing both aggregates' maximum size and the percentage of coarse aggregates. Finally, the validity of the model has been discussed through a comparison with experimental results (15 concrete compressive strengths ranging between 46 and 106 MPa) taken from literature and showing a good agreement with the model predictions.

Grid Integrated Type 3 Wind Systems - Modeling, and Line Protection Performance Analysis using the RTDS

NASA Astrophysics Data System (ADS)

Jain, Rishabh

In this thesis, the line protection elements and their supervisory elements are analyzed in context of Type 3 (Doubly Fed Induction Generator based) grid integrated wind turbine systems. The underlying converter and controller design algorithms and topologies are discussed. A detailed controller for the Type 3 wind turbine system is designed and integrated to the grid using the RTDS. An alternative to the conventional PLL for tracking of rotor frequency is designed and implemented. A comparative analysis of the performance of an averaged model and the corresponding switching model is presented. After completing the WT model design, the averaged model is used to model an aggregate 10-generator equivalent model tied to a 230kV grid via a 22kV collector. This model is a great asset to understand dynamics, and the unfaulted and faulted behavior of aggregated and single-turbine Type 3 WT systems. The model is then utilized to analyze the response of conventional protection schemes (Line current Differential and Mho Distance elements) and their respective supervisory elements of modern commercial protection relays in real time by hardware-in-the-loop simulation using the RTDS. Differences in the behavior of these elements compared to conventional power systems is noted. Fault are analyzed from the relay's perspective and the reasons for the observed behavior are presented. Challenges associated with sequence components and relay sensitivity are discussed and alternate practices to circumvent these issues are recommended.

[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.

Describing Myxococcus xanthus Aggregation Using Ostwald Ripening Equations for Thin Liquid Films

PubMed Central

Bahar, Fatmagül; Pratt-Szeliga, Philip C.; Angus, Stuart; Guo, Jiaye; Welch, Roy D.

2014-01-01

When starved, a swarm of millions of Myxococcus xanthus cells coordinate their movement from outward swarming to inward coalescence. The cells then execute a synchronous program of multicellular development, arranging themselves into dome shaped aggregates. Over the course of development, about half of the initial aggregates disappear, while others persist and mature into fruiting bodies. This work seeks to develop a quantitative model for aggregation that accurately simulates which will disappear and which will persist. We analyzed time-lapse movies of M. xanthus development, modeled aggregation using the equations that describe Ostwald ripening of droplets in thin liquid films, and predicted the disappearance and persistence of aggregates with an average accuracy of 85%. We then experimentally validated a prediction that is fundamental to this model by tracking individual fluorescent cells as they moved between aggregates and demonstrating that cell movement towards and away from aggregates correlates with aggregate disappearance. Describing development through this model may limit the number and type of molecular genetic signals needed to complete M. xanthus development, and it provides numerous additional testable predictions. PMID:25231319

Kinetic and Stochastic Models of 1D yeast ``prions"

NASA Astrophysics Data System (ADS)

Kunes, Kay

2005-03-01

Mammalian prion proteins (PrP) are of public health interest because of mad cow and chronic wasting diseases. Yeasts have proteins, which can undergo similar reconformation and aggregation processes to PrP; yeast ``prions" are simpler to experimentally study and model. Recent in vitro studies of the SUP35 protein (1), showed long aggregates and pure exponential growth of the misfolded form. To explain this data, we have extended a previous model of aggregation kinetics along with our own stochastic approach (2). Both models assume reconformation only upon aggregation, and include aggregate fissioning and an initial nucleation barrier. We find for sufficiently small nucleation rates or seeding by small dimer concentrations that we can achieve the requisite exponential growth and long aggregates.

Iron Promotes the Toxicity of Amyloid β Peptide by Impeding Its Ordered Aggregation*

PubMed Central

Liu, Beinan; Moloney, Aileen; Meehan, Sarah; Morris, Kyle; Thomas, Sally E.; Serpell, Louise C.; Hider, Robert; Marciniak, Stefan J.; Lomas, David A.; Crowther, Damian C.

2011-01-01

We have previously shown that overexpressing subunits of the iron-binding protein ferritin can rescue the toxicity of the amyloid β (Aβ) peptide in our Drosophila model system. These data point to an important pathogenic role for iron in Alzheimer disease. In this study, we have used an iron-selective chelating compound and RNAi-mediated knockdown of endogenous ferritin to further manipulate iron in the brain. We confirm that chelation of iron protects the fly from the harmful effects of Aβ. To understand the pathogenic mechanisms, we have used biophysical techniques to see how iron affects Aβ aggregation. We find that iron slows the progression of the Aβ peptide from an unstructured conformation to the ordered cross-β fibrils that are characteristic of amyloid. Finally, using mammalian cell culture systems, we have shown that iron specifically enhances Aβ toxicity but only if the metal is present throughout the aggregation process. These data support the hypothesis that iron delays the formation of well ordered aggregates of Aβ and so promotes its toxicity in Alzheimer disease. PMID:21147772

Iron promotes the toxicity of amyloid beta peptide by impeding its ordered aggregation.

PubMed

Liu, Beinan; Moloney, Aileen; Meehan, Sarah; Morris, Kyle; Thomas, Sally E; Serpell, Louise C; Hider, Robert; Marciniak, Stefan J; Lomas, David A; Crowther, Damian C

2011-02-11

We have previously shown that overexpressing subunits of the iron-binding protein ferritin can rescue the toxicity of the amyloid β (Aβ) peptide in our Drosophila model system. These data point to an important pathogenic role for iron in Alzheimer disease. In this study, we have used an iron-selective chelating compound and RNAi-mediated knockdown of endogenous ferritin to further manipulate iron in the brain. We confirm that chelation of iron protects the fly from the harmful effects of Aβ. To understand the pathogenic mechanisms, we have used biophysical techniques to see how iron affects Aβ aggregation. We find that iron slows the progression of the Aβ peptide from an unstructured conformation to the ordered cross-β fibrils that are characteristic of amyloid. Finally, using mammalian cell culture systems, we have shown that iron specifically enhances Aβ toxicity but only if the metal is present throughout the aggregation process. These data support the hypothesis that iron delays the formation of well ordered aggregates of Aβ and so promotes its toxicity in Alzheimer disease.

Design of a microfluidic system for red blood cell aggregation investigation.

PubMed

Mehri, R; Mavriplis, C; Fenech, M

2014-06-01

The purpose of this paper is to design a microfluidic apparatus capable of providing controlled flow conditions suitable for red blood cell (RBC) aggregation analysis. The linear velocity engendered from the controlled flow provides constant shear rates used to qualitatively analyze RBC aggregates. The design of the apparatus is based on numerical and experimental work. The numerical work consists of 3D numerical simulations performed using a research computational fluid dynamics (CFD) solver, Nek5000, while the experiments are conducted using a microparticle image velocimetry system. A Newtonian model is tested numerically and experimentally, then blood is tested experimentally under several conditions (hematocrit, shear rate, and fluid suspension) to be compared to the simulation results. We find that using a velocity ratio of 4 between the two Newtonian fluids, the layer corresponding to blood expands to fill 35% of the channel thickness where the constant shear rate is achieved. For blood experiments, the velocity profile in the blood layer is approximately linear, resulting in the desired controlled conditions for the study of RBC aggregation under several flow scenarios.

Impact of Spatial Soil and Climate Input Data Aggregation on Regional Yield Simulations

PubMed Central

Hoffmann, Holger; Zhao, Gang; Asseng, Senthold; Bindi, Marco; Biernath, Christian; Constantin, Julie; Coucheney, Elsa; Dechow, Rene; Doro, Luca; Eckersten, Henrik; Gaiser, Thomas; Grosz, Balázs; Heinlein, Florian; Kassie, Belay T.; Kersebaum, Kurt-Christian; Klein, Christian; Kuhnert, Matthias; Lewan, Elisabet; Moriondo, Marco; Nendel, Claas; Priesack, Eckart; Raynal, Helene; Roggero, Pier P.; Rötter, Reimund P.; Siebert, Stefan; Specka, Xenia; Tao, Fulu; Teixeira, Edmar; Trombi, Giacomo; Wallach, Daniel; Weihermüller, Lutz; Yeluripati, Jagadeesh; Ewert, Frank

2016-01-01

We show the error in water-limited yields simulated by crop models which is associated with spatially aggregated soil and climate input data. Crop simulations at large scales (regional, national, continental) frequently use input data of low resolution. Therefore, climate and soil data are often generated via averaging and sampling by area majority. This may bias simulated yields at large scales, varying largely across models. Thus, we evaluated the error associated with spatially aggregated soil and climate data for 14 crop models. Yields of winter wheat and silage maize were simulated under water-limited production conditions. We calculated this error from crop yields simulated at spatial resolutions from 1 to 100 km for the state of North Rhine-Westphalia, Germany. Most models showed yields biased by <15% when aggregating only soil data. The relative mean absolute error (rMAE) of most models using aggregated soil data was in the range or larger than the inter-annual or inter-model variability in yields. This error increased further when both climate and soil data were aggregated. Distinct error patterns indicate that the rMAE may be estimated from few soil variables. Illustrating the range of these aggregation effects across models, this study is a first step towards an ex-ante assessment of aggregation errors in large-scale simulations. PMID:27055028

Impact of Spatial Soil and Climate Input Data Aggregation on Regional Yield Simulations.

PubMed

Hoffmann, Holger; Zhao, Gang; Asseng, Senthold; Bindi, Marco; Biernath, Christian; Constantin, Julie; Coucheney, Elsa; Dechow, Rene; Doro, Luca; Eckersten, Henrik; Gaiser, Thomas; Grosz, Balázs; Heinlein, Florian; Kassie, Belay T; Kersebaum, Kurt-Christian; Klein, Christian; Kuhnert, Matthias; Lewan, Elisabet; Moriondo, Marco; Nendel, Claas; Priesack, Eckart; Raynal, Helene; Roggero, Pier P; Rötter, Reimund P; Siebert, Stefan; Specka, Xenia; Tao, Fulu; Teixeira, Edmar; Trombi, Giacomo; Wallach, Daniel; Weihermüller, Lutz; Yeluripati, Jagadeesh; Ewert, Frank

2016-01-01

We show the error in water-limited yields simulated by crop models which is associated with spatially aggregated soil and climate input data. Crop simulations at large scales (regional, national, continental) frequently use input data of low resolution. Therefore, climate and soil data are often generated via averaging and sampling by area majority. This may bias simulated yields at large scales, varying largely across models. Thus, we evaluated the error associated with spatially aggregated soil and climate data for 14 crop models. Yields of winter wheat and silage maize were simulated under water-limited production conditions. We calculated this error from crop yields simulated at spatial resolutions from 1 to 100 km for the state of North Rhine-Westphalia, Germany. Most models showed yields biased by <15% when aggregating only soil data. The relative mean absolute error (rMAE) of most models using aggregated soil data was in the range or larger than the inter-annual or inter-model variability in yields. This error increased further when both climate and soil data were aggregated. Distinct error patterns indicate that the rMAE may be estimated from few soil variables. Illustrating the range of these aggregation effects across models, this study is a first step towards an ex-ante assessment of aggregation errors in large-scale simulations.

Aggregating the response in time series regression models, applied to weather-related cardiovascular mortality

NASA Astrophysics Data System (ADS)

Masselot, Pierre; Chebana, Fateh; Bélanger, Diane; St-Hilaire, André; Abdous, Belkacem; Gosselin, Pierre; Ouarda, Taha B. M. J.

2018-07-01

In environmental epidemiology studies, health response data (e.g. hospitalization or mortality) are often noisy because of hospital organization and other social factors. The noise in the data can hide the true signal related to the exposure. The signal can be unveiled by performing a temporal aggregation on health data and then using it as the response in regression analysis. From aggregated series, a general methodology is introduced to account for the particularities of an aggregated response in a regression setting. This methodology can be used with usually applied regression models in weather-related health studies, such as generalized additive models (GAM) and distributed lag nonlinear models (DLNM). In particular, the residuals are modelled using an autoregressive-moving average (ARMA) model to account for the temporal dependence. The proposed methodology is illustrated by modelling the influence of temperature on cardiovascular mortality in Canada. A comparison with classical DLNMs is provided and several aggregation methods are compared. Results show that there is an increase in the fit quality when the response is aggregated, and that the estimated relationship focuses more on the outcome over several days than the classical DLNM. More precisely, among various investigated aggregation schemes, it was found that an aggregation with an asymmetric Epanechnikov kernel is more suited for studying the temperature-mortality relationship.

Hydrodynamic effects on β-amyloid (16-22) peptide aggregation

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

Chiricotto, Mara; Sterpone, Fabio, E-mail: fabio.sterpone@ibpc.fr; Melchionna, Simone

Computer simulations based on simplified representations are routinely used to explore the early steps of amyloid aggregation. However, when protein models with implicit solvent are employed, these simulations miss the effect of solvent induced correlations on the aggregation kinetics and lifetimes of metastable states. In this work, we apply the multi-scale Lattice Boltzmann Molecular Dynamics technique (LBMD) to investigate the initial aggregation phases of the amyloid Aβ{sub 16−22} peptide. LBMD includes naturally hydrodynamic interactions (HIs) via a kinetic on-lattice representation of the fluid kinetics. The peptides are represented by the flexible OPEP coarse-grained force field. First, we have tuned themore » essential parameters that control the coupling between the molecular and fluid evolutions in order to reproduce the experimental diffusivity of elementary species. The method is then deployed to investigate the effect of HIs on the aggregation of 100 and 1000 Aβ{sub 16−22} peptides. We show that HIs clearly impact the aggregation process and the fluctuations of the oligomer sizes by favouring the fusion and exchange dynamics of oligomers between aggregates. HIs also guide the growth of the leading largest cluster. For the 100 Aβ{sub 16−22} peptide system, the simulation of ∼300 ns allowed us to observe the transition from ellipsoidal assemblies to an elongated and slightly twisted aggregate involving almost the totality of the peptides. For the 1000 Aβ{sub 16−22} peptides, a system of unprecedented size at quasi-atomistic resolution, we were able to explore a branched disordered fibril-like structure that has never been described by other computer simulations, but has been observed experimentally.« less

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

A Conceptual View of the Officer Procurement Model (TOPOPS). Technical Report No. 73-73.

ERIC Educational Resources Information Center

Akman, Allan; Nordhauser, Fred

This report presents the conceptual design of a computer-based linear programing model of the Air Force officer procurement system called TOPOPS. The TOPOPS model is an aggregate model which simulates officer accession and training and is directed at optimizing officer procurement in terms of either minimizing cost or maximizing accession quality…

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

A 3D human neural cell culture system for modeling Alzheimer’s disease

PubMed Central

Kim, Young Hye; Choi, Se Hoon; D’Avanzo, Carla; Hebisch, Matthias; Sliwinski, Christopher; Bylykbashi, Enjana; Washicosky, Kevin J.; Klee, Justin B.; Brüstle, Oliver; Tanzi, Rudolph E.; Kim, Doo Yeon

2015-01-01

Stem cell technologies have facilitated the development of human cellular disease models that can be used to study pathogenesis and test therapeutic candidates. These models hold promise for complex neurological diseases such as Alzheimer’s disease (AD) because existing animal models have been unable to fully recapitulate all aspects of pathology. We recently reported the characterization of a novel three-dimensional (3D) culture system that exhibits key events in AD pathogenesis, including extracellular aggregation of β-amyloid and accumulation of hyperphosphorylated tau. Here we provide instructions for the generation and analysis of 3D human neural cell cultures, including the production of genetically modified human neural progenitor cells (hNPCs) with familial AD mutations, the differentiation of the hNPCs in a 3D matrix, and the analysis of AD pathogenesis. The 3D culture generation takes 1–2 days. The aggregation of β-amyloid is observed after 6-weeks of differentiation followed by robust tau pathology after 10–14 weeks. PMID:26068894

Influence of the valine zipper region on the structure and aggregation of the basic leucine zipper (bZIP) domain of activating transcription factor 5 (ATF5).

PubMed

Ciaccio, Natalie A; Reynolds, T Steele; Middaugh, C Russell; Laurence, Jennifer S

2012-11-05

Protein aggregation is a major problem for biopharmaceuticals. While the control of aggregation is critically important for the future of protein pharmaceuticals, mechanisms of aggregate assembly, particularly the role that structure plays, are still poorly understood. Increasing evidence indicates that partially folded intermediates critically influence the aggregation pathway. We have previously reported the use of the basic leucine zipper (bZIP) domain of activating transcription factor 5 (ATF5) as a partially folded model system to investigate protein aggregation. This domain contains three regions with differing structural propensity: a N-terminal polybasic region, a central helical leucine zipper region, and a C-terminal extended valine zipper region. Additionally, a centrally positioned cysteine residue readily forms an intermolecular disulfide bond that reduces aggregation. Computational analysis of ATF5 predicts that the valine zipper region facilitates self-association. Here we test this hypothesis using a truncated mutant lacking the C-terminal valine zipper region. We compare the structure and aggregation of this mutant to the wild-type (WT) form under both reducing and nonreducing conditions. Our data indicate that removal of this region results in a loss of α-helical structure in the leucine zipper and a change in the mechanism of self-association. The mutant form displays increased association at low temperature but improved resistance to thermally induced aggregation.

Amyloid β-sheet mimics that antagonize protein aggregation and reduce amyloid toxicity

NASA Astrophysics Data System (ADS)

Cheng, Pin-Nan; Liu, Cong; Zhao, Minglei; Eisenberg, David; Nowick, James S.

2012-11-01

The amyloid protein aggregation associated with diseases such as Alzheimer's, Parkinson's and type II diabetes (among many others) features a bewildering variety of β-sheet-rich structures in transition from native proteins to ordered oligomers and fibres. The variation in the amino-acid sequences of the β-structures presents a challenge to developing a model system of β-sheets for the study of various amyloid aggregates. Here, we introduce a family of robust β-sheet macrocycles that can serve as a platform to display a variety of heptapeptide sequences from different amyloid proteins. We have tailored these amyloid β-sheet mimics (ABSMs) to antagonize the aggregation of various amyloid proteins, thereby reducing the toxicity of amyloid aggregates. We describe the structures and inhibitory properties of ABSMs containing amyloidogenic peptides from the amyloid-β peptide associated with Alzheimer's disease, β2-microglobulin associated with dialysis-related amyloidosis, α-synuclein associated with Parkinson's disease, islet amyloid polypeptide associated with type II diabetes, human and yeast prion proteins, and Tau, which forms neurofibrillary tangles.

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.

Perceived and Implicit Ranking of Academic Journals: An Optimization Choice Model

ERIC Educational Resources Information Center

Xie, Frank Tian; Cai, Jane Z.; Pan, Yue

2012-01-01

A new system of ranking academic journals is proposed in this study and optimization choice model used to analyze data collected from 346 faculty members in a business discipline. The ranking model uses the aggregation of perceived, implicit sequencing of academic journals by academicians, therefore eliminating several key shortcomings of previous…

Modeling the impact of soil aggregate size on selenium immobilization

NASA Astrophysics Data System (ADS)

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

2013-03-01

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

Modeling the impact of soil aggregate size on selenium immobilization

NASA Astrophysics Data System (ADS)

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

2012-09-01

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

Heterogeneous database integration in biomedicine.

PubMed

Sujansky, W

2001-08-01

The rapid expansion of biomedical knowledge, reduction in computing costs, and spread of internet access have created an ocean of electronic data. The decentralized nature of our scientific community and healthcare system, however, has resulted in a patchwork of diverse, or heterogeneous, database implementations, making access to and aggregation of data across databases very difficult. The database heterogeneity problem applies equally to clinical data describing individual patients and biological data characterizing our genome. Specifically, databases are highly heterogeneous with respect to the data models they employ, the data schemas they specify, the query languages they support, and the terminologies they recognize. Heterogeneous database systems attempt to unify disparate databases by providing uniform conceptual schemas that resolve representational heterogeneities, and by providing querying capabilities that aggregate and integrate distributed data. Research in this area has applied a variety of database and knowledge-based techniques, including semantic data modeling, ontology definition, query translation, query optimization, and terminology mapping. Existing systems have addressed heterogeneous database integration in the realms of molecular biology, hospital information systems, and application portability.

Clinical Summarization Capabilities of Commercially-available and Internally-developed Electronic Health Records

PubMed Central

Laxmisan, A.; McCoy, A.B.; Wright, A.; Sittig, D.F.

2012-01-01

Objective Clinical summarization, the process by which relevant patient information is electronically summarized and presented at the point of care, is of increasing importance given the increasing volume of clinical data in electronic health record systems (EHRs). There is a paucity of research on electronic clinical summarization, including the capabilities of currently available EHR systems. Methods We compared different aspects of general clinical summary screens used in twelve different EHR systems using a previously described conceptual model: AORTIS (Aggregation, Organization, Reduction, Interpretation and Synthesis). Results We found a wide variation in the EHRs’ summarization capabilities: all systems were capable of simple aggregation and organization of limited clinical content, but only one demonstrated an ability to synthesize information from the data. Conclusion Improvement of the clinical summary screen functionality for currently available EHRs is necessary. Further research should identify strategies and methods for creating easy to use, well-designed clinical summary screens that aggregate, organize and reduce all pertinent patient information as well as provide clinical interpretations and synthesis as required. PMID:22468161

Surface properties of heat-induced soluble soy protein aggregates of different molecular masses.

PubMed

Guo, Fengxian; Xiong, Youling L; Qin, Fang; Jian, Huajun; Huang, Xiaolin; Chen, Jie

2015-02-01

Suspensions (2% and 5%, w/v) of soy protein isolate (SPI) were heated at 80, 90, or 100 °C for different time periods to produce soluble aggregates of different molecular sizes to investigate the relationship between particle size and surface properties (emulsions and foams). Soluble aggregates generated in these model systems were characterized by gel permeation chromatography and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Heat treatment increased surface hydrophobicity, induced SPI aggregation via hydrophobic interaction and disulfide bonds, and formed soluble aggregates of different sizes. Heating of 5% SPI always promoted large-size aggregate (LA; >1000 kDa) formation irrespective of temperature, whereas the aggregate size distribution in 2% SPI was temperature dependent: the LA fraction progressively rose with temperature (80→90→100 °C), corresponding to the attenuation of medium-size aggregates (MA; 670 to 1000 kDa) initially abundant at 80 °C. Heated SPI with abundant LA (>50%) promoted foam stability. LA also exhibited excellent emulsifying activity and stabilized emulsions by promoting the formation of small oil droplets covered with a thick interfacial protein layer. However, despite a similar influence on emulsion stability, MA enhanced foaming capacity but were less capable of stabilizing emulsions than LA. The functionality variation between heated SPI samples is clearly related to the distribution of aggregates that differ in molecular size and surface activity. The findings may encourage further research to develop functional SPI aggregates for various commercial applications. © 2015 Institute of Food Technologists®

More Fluorous Surface Modifier Makes it Less Oleophobic: Fluorinated-Siloxane Copolymer/PDMS Coatings

PubMed Central

Zhang, Wei; Zheng, Ying; Orsini, Lorenzo; Morelli, Andrea; Galli, Giancarlo; Chiellini, Emo; Carpenter, Everett E.; Wynne, Kenneth J.

2010-01-01

A copolyacrylate with semifluorinated and polydimethylsiloxane side chains (D5-3) was used as a surface modifier for a condensation cured PDMS coating. The decyl fluorous group is represented by “D”; “5” is a 5 kDa silicone, and “3” the mole ratio of fluorous to silicone side chain. Wetting behavior was assessed by dynamic contact angle (DCA) analysis using isopropanol, which differentiates silicone and fluorous wetting behavior. Interestingly, a maximum in surface oleophobicity was found at low D5-3 concentration (0.4 wt%). Higher concentrations result in decreased oleophobicity reflected in decreased contact angles. To understand this unexpected observation, dynamic light scattering (DLS) studies were initiated on a model system consisting of hydroxyl-terminated PDMS (18 kDa) containing varying amounts of D5-3. DLS revealed D5-3 aggregation as a function of temperature and concentration. A model is proposed by which D5-3 surface concentration is depleted via phase separation favoring D5-3 aggregation at concentrations >0.4 wt%, that is, the CMC. This model suggests increasing aggregate / micelle concentrations at increased D5-3 concentration. Bulk morphologies studied by scanning electron microscopy (SEM) and atomic force microscopy (AFM) support this model by showing increased aggregate concentrations with increased D5-3 >0.4 wt%. PMID:20000339

Multi-criteria, personalized route planning using quantifier-guided ordered weighted averaging operators

NASA Astrophysics Data System (ADS)

Nadi, S.; Delavar, M. R.

2011-06-01

This paper presents a generic model for using different decision strategies in multi-criteria, personalized route planning. Some researchers have considered user preferences in navigation systems. However, these prior studies typically employed a high tradeoff decision strategy, which used a weighted linear aggregation rule, and neglected other decision strategies. The proposed model integrates a pairwise comparison method and quantifier-guided ordered weighted averaging (OWA) aggregation operators to form a personalized route planning method that incorporates different decision strategies. The model can be used to calculate the impedance of each link regarding user preferences in terms of the route criteria, criteria importance and the selected decision strategy. Regarding the decision strategy, the calculated impedance lies between aggregations that use a logical "and" (which requires all the criteria to be satisfied) and a logical "or" (which requires at least one criterion to be satisfied). The calculated impedance also includes taking the average of the criteria scores. The model results in multiple alternative routes, which apply different decision strategies and provide users with the flexibility to select one of them en-route based on the real world situation. The model also defines the robust personalized route under different decision strategies. The influence of different decision strategies on the results are investigated in an illustrative example. This model is implemented in a web-based geographical information system (GIS) for Isfahan in Iran and verified in a tourist routing scenario. The results demonstrated, in real world situations, the validity of the route planning carried out in the model.

Approximate reduction of linear population models governed by stochastic differential equations: application to multiregional models.

PubMed

Sanz, Luis; Alonso, Juan Antonio

2017-12-01

In this work we develop approximate aggregation techniques in the context of slow-fast linear population models governed by stochastic differential equations and apply the results to the treatment of populations with spatial heterogeneity. Approximate aggregation techniques allow one to transform a complex system involving many coupled variables and in which there are processes with different time scales, by a simpler reduced model with a fewer number of 'global' variables, in such a way that the dynamics of the former can be approximated by that of the latter. In our model we contemplate a linear fast deterministic process together with a linear slow process in which the parameters are affected by additive noise, and give conditions for the solutions corresponding to positive initial conditions to remain positive for all times. By letting the fast process reach equilibrium we build a reduced system with a lesser number of variables, and provide results relating the asymptotic behaviour of the first- and second-order moments of the population vector for the original and the reduced system. The general technique is illustrated by analysing a multiregional stochastic system in which dispersal is deterministic and the rate growth of the populations in each patch is affected by additive noise.

Oil-Price Shocks: Beyond Standard Aggregate Demand/Aggregate Supply Analysis.

ERIC Educational Resources Information Center

Elwood, S. Kirk

2001-01-01

Explores the problems of portraying oil-price shocks using the aggregate demand/aggregate supply model. Presents a simple modification of the model that differentiates between production and absorption of goods, which enables it to better reflect the effects of oil-price shocks on open economies. (RLH)

Aggregation of Carbocyanine Dyes in Choline Chloride-Based Deep Eutectic Solvents in the Presence of an Aqueous Base.

PubMed

Pal, Mahi; Yadav, Anita; Pandey, Siddharth

2017-09-26

Deep eutectic solvents (DESs) have shown potential as novel media to support molecular aggregation. The self-aggregation behavior of two common and popular carbocyanine dyes, 5,5',6,6'-tetrachloro-1,1'-diethyl-3,3'-di(4-sulfobutyl)-benzimidazole carbocyanine (TDBC) and 5,5'-dichloro-3,3'-di(3-sulfopropyl)-9-methyl-benzothiacarbo cyanine (DMTC), is investigated within DES-based systems under ambient conditions. Although TDBC is known to form J-aggregates in basic aqueous solution, DMTC forms H-aggregates under similar conditions. The DESs used, glyceline and reline, are composed of salt choline chloride and two vastly different H-bond donors, glycerol and urea, respectively, in 1:2 mol ratios. Both DESs in the presence of base are found to support J-aggregates of TDBC. These fluorescent J-aggregates are characterized by small Stokes' shifts and subnanosecond fluorescence lifetimes. Under similar conditions, DMTC forms fluorescent H-aggregates along with J-aggregates within the two DES-based systems. The addition of cationic surfactant cetyltrimethylammonium bromide (CTAB) below its critical micelle concentration (cmc) to a TDBC solution of aqueous base-added glyceline shows the prominent presence of J-aggregates, and increasing the CTAB concentration to above cmc results in the disruption of J-aggregates and the formation of unprecedented H-aggregates. DMTC exclusively forms H-aggregates within a CTAB solution of aqueous base-added glyceline irrespective of the surfactant concentration. Anionic surfactant, sodium dodecylsulfate (SDS), present below its cmc within aqueous base-added DESs supports J-aggregation by TDBC; for similar SDS addition, DMTC forms H-aggregates within the glyceline-based system whereas both H- and J-aggregates exist within the reline-based system. A comparison of the carbocyanine dye behavior in various aqueous base-added DES systems to that in aqueous basic media reveals contrasting aggregation tendencies and/or efficiencies. Surfactants as additives are demonstrated to control and modulate carbocyanine dye self-aggregation within DES-based media. The unique nature of DESs as alternate media toward affecting cyanine dye aggregation is highlighted.

Stability of volcanic ash aggregates and break-up processes.

PubMed

Mueller, Sebastian B; Kueppers, Ulrich; Ametsbichler, Jonathan; Cimarelli, Corrado; Merrison, Jonathan P; Poret, Matthieu; Wadsworth, Fabian B; Dingwell, Donald B

2017-08-07

Numerical modeling of ash plume dispersal is an important tool for forecasting and mitigating potential hazards from volcanic ash erupted during explosive volcanism. Recent tephra dispersal models have been expanded to account for dynamic ash aggregation processes. However, there are very few studies on rates of disaggregation during transport. It follows that current models regard ash aggregation as irrevocable and may therefore overestimate aggregation-enhanced sedimentation. In this experimental study, we use industrial granulation techniques to artificially produce aggregates. We subject these to impact tests and evaluate their resistance to break-up processes. We find a dependence of aggregate stability on primary particle size distribution and solid particle binder concentration. We posit that our findings could be combined with eruption source parameters and implemented in future tephra dispersal models.

Broadband classification and statistics of echoes from aggregations of fish measured by long-range, mid-frequency sonar.

PubMed

Jones, Benjamin A; Stanton, Timothy K; Colosi, John A; Gauss, Roger C; Fialkowski, Joseph M; Michael Jech, J

2017-06-01

For horizontal-looking sonar systems operating at mid-frequencies (1-10 kHz), scattering by fish with resonant gas-filled swimbladders can dominate seafloor and surface reverberation at long-ranges (i.e., distances much greater than the water depth). This source of scattering, which can be difficult to distinguish from other sources of scattering in the water column or at the boundaries, can add spatio-temporal variability to an already complex acoustic record. Sparsely distributed, spatially compact fish aggregations were measured in the Gulf of Maine using a long-range broadband sonar with continuous spectral coverage from 1.5 to 5 kHz. Observed echoes, that are at least 15 decibels above background levels in the horizontal-looking sonar data, are classified spectrally by the resonance features as due to swimbladder-bearing fish. Contemporaneous multi-frequency echosounder measurements (18, 38, and 120 kHz) and net samples are used in conjunction with physics-based acoustic models to validate this approach. Furthermore, the fish aggregations are statistically characterized in the long-range data by highly non-Rayleigh distributions of the echo magnitudes. These distributions are accurately predicted by a computationally efficient, physics-based model. The model accounts for beam-pattern and waveguide effects as well as the scattering response of aggregations of fish.

Prediction of EPR Spectra of Lyotropic Liquid Crystals using a Combination of Molecular Dynamics Simulations and the Model-Free Approach.

PubMed

Prior, Christopher; Oganesyan, Vasily S

2017-09-21

We report the first application of fully atomistic molecular dynamics (MD) simulations to the prediction of the motional electron paramagnetic resonance (EPR) spectra of lyotropic liquid crystals in different aggregation states doped with a paramagnetic spin probe. The purpose of this study is twofold. First, given that EPR spectra are highly sensitive to the motions and order of the spin probes doped within lyotropic aggregates, simulation of EPR line shapes from the results of MD modelling provides an ultimate test bed for the force fields currently employed to model such systems. Second, the EPR line shapes are simulated using the motional parameters extracted from MD trajectories using the Model-Free (MF) approach. Thus a combined MD-EPR methodology allowed us to test directly the validity of the application of the MF approach to systems with multi-component molecular motions. All-atom MD simulations using the General AMBER Force Field (GAFF) have been performed on sodium dodecyl sulfate (SDS) and dodecyltrimethylammonium chloride (DTAC) liquid crystals. The resulting MD trajectories were used to predict and interpret the EPR spectra of pre-micellar, micellar, rod and lamellar aggregates. The predicted EPR spectra demonstrate good agreement with most of experimental line shapes thus confirming the validity of both the force fields employed and the MF approach for the studied systems. At the same time simulation results confirm that GAFF tends to overestimate the packing and the order of the carbonyl chains of the surfactant molecules. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Extended Relation Metadata for SCORM-Based Learning Content Management Systems

ERIC Educational Resources Information Center

Lu, Eric Jui-Lin; Horng, Gwoboa; Yu, Chia-Ssu; Chou, Ling-Ying

2010-01-01

To increase the interoperability and reusability of learning objects, Advanced Distributed Learning Initiative developed a model called Content Aggregation Model (CAM) to describe learning objects and express relationships between learning objects. However, the suggested relations defined in the CAM can only describe structure-oriented…

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

NASA Astrophysics Data System (ADS)

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

2015-01-01

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

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

PubMed

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

2015-01-01

Changes in nanoparticle size and shape due to particle-particle interactions (i.e., aggregation or agglomeration) may significantly alter particle mobility and retention in porous media. To date, however, few modeling studies have considered the coupling of transport and particle aggregation processes. The majority of particle transport models employ an Eulerian modeling framework and are, consequently, limited in the types of collisions and aggregate sizes that can be considered. In this work, a more general Lagrangian modeling framework is developed and implemented to explore coupled nanoparticle aggregation and transport processes. The model was verified through comparison of model simulations to published results of an experimental and Eulerian modeling study (Raychoudhury et al., 2012) of carboxymethyl cellulose (CMC)-modified nano-sized zero-valent iron particle (nZVI) transport and retention in water-saturated sand columns. A model sensitivity analysis reveals the influence of influent particle concentration (ca. 70 to 700 mg/L), primary particle size (10-100 nm) and pore water velocity (ca. 1-6 m/day) on particle-particle, and, consequently, particle-collector interactions. Model simulations demonstrate that, when environmental conditions promote particle-particle interactions, neglecting aggregation effects can lead to under- or over-estimation of nanoparticle mobility. Results also suggest that the extent to which higher order particle-particle collisions influence aggregation kinetics will increase with the fraction of primary particles. This work demonstrates the potential importance of time-dependent aggregation processes on nanoparticle mobility and provides a numerical model capable of capturing/describing these interactions in water-saturated porous media. Copyright © 2014 Elsevier B.V. All rights reserved.

Effects of Hydrostatic Loading on a Self-Aggregating, Suspension Culture–Derived Cartilage Tissue Analog

PubMed Central

Kraft, Jeffrey J.; Jeong, Changhoon; Novotny, John E.; Seacrist, Thomas; Chan, Gilbert; Domzalski, Marcin; Turka, Christina M.; Richardson, Dean W.; Dodge, George R.

2011-01-01

Objective: Many approaches are being taken to generate cartilage replacement materials. The goal of this study was to use a self-aggregating suspension culture model of chondrocytes with mechanical preconditioning. Design: Our model differs from others in that it is based on a scaffold-less, self-aggregating culture model that produces a cartilage tissue analog that has been shown to share many similarities with the natural cartilage phenotype. Owing to the known loaded environment under which chondrocytes function in vivo, we hypothesized that applying force to the suspension culture–derived chondrocyte biomass would improve its cartilage-like characteristics and provide a new model for engineering cartilage tissue analogs. Results: In this study, we used a specialized hydrostatic pressure bioreactor system to apply mechanical forces during the growth phase to improve biochemical and biophysical properties of the biomaterial formed. We demonstrated that using this high-density suspension culture, a biomaterial more consistent with the hyaline cartilage phenotype was produced without any foreign material added. Unpassaged chondrocytes responded to a physiologically relevant hydrostatic load by significantly increasing gene expression of critical cartilage molecule collagen and aggrecan along with other cartilage relevant genes, CD44, perlecan, decorin, COMP, and iNOS. Conclusions: This study describes a self-aggregating bioreactor model without foreign material or scaffold in which chondrocytes form a cartilage tissue analog with many features similar to native cartilage. This study represents a promising scaffold-less, methodological advancement in cartilage tissue engineering with potential translational applications to cartilage repair. PMID:26069584

Effects of Hydrostatic Loading on a Self-Aggregating, Suspension Culture-Derived Cartilage Tissue Analog.

PubMed

Kraft, Jeffrey J; Jeong, Changhoon; Novotny, John E; Seacrist, Thomas; Chan, Gilbert; Domzalski, Marcin; Turka, Christina M; Richardson, Dean W; Dodge, George R

2011-07-01

Many approaches are being taken to generate cartilage replacement materials. The goal of this study was to use a self-aggregating suspension culture model of chondrocytes with mechanical preconditioning. Our model differs from others in that it is based on a scaffold-less, self-aggregating culture model that produces a cartilage tissue analog that has been shown to share many similarities with the natural cartilage phenotype. Owing to the known loaded environment under which chondrocytes function in vivo, we hypothesized that applying force to the suspension culture-derived chondrocyte biomass would improve its cartilage-like characteristics and provide a new model for engineering cartilage tissue analogs. In this study, we used a specialized hydrostatic pressure bioreactor system to apply mechanical forces during the growth phase to improve biochemical and biophysical properties of the biomaterial formed. We demonstrated that using this high-density suspension culture, a biomaterial more consistent with the hyaline cartilage phenotype was produced without any foreign material added. Unpassaged chondrocytes responded to a physiologically relevant hydrostatic load by significantly increasing gene expression of critical cartilage molecule collagen and aggrecan along with other cartilage relevant genes, CD44, perlecan, decorin, COMP, and iNOS. This study describes a self-aggregating bioreactor model without foreign material or scaffold in which chondrocytes form a cartilage tissue analog with many features similar to native cartilage. This study represents a promising scaffold-less, methodological advancement in cartilage tissue engineering with potential translational applications to cartilage repair.

Comparison of mHTT Antibodies in Huntington’s Disease Mouse Models Reveal Specific Binding Profiles and Steady-State Ubiquitin Levels with Disease Development

PubMed Central

Bayram-Weston, Zubeyde; Jones, Lesley; Dunnett, Stephen B.; Brooks, Simon P.

2016-01-01

Huntington’s disease (HD) cellular pathology is characterised by the aggregation of mutant huntingtin (mHTT) protein into inclusion bodies. The present paper compared the sensitivity of five widely used mHTT antibodies (S830; MW8; EM48; 1C2; ubiquitin) against mice from five commonly used HD mouse models (R6/1; YAC128; HdhQ92; B6 HdhQ150; B6 x129/Ola HdhQ150) at two ages to determine: the most sensitive antibodies for each model; whether mHTT antibody binding differed depending on aggregation stage (diffuse versus frank inclusion); the role of ubiquitin during aggregation as the ubiquitin proteosome system has been implicated in disease development. The models demonstrated unique profiles of antibody binding even when the models varied only by background strain (HdhQ150). MW8 was highly sensitive for detecting frank inclusions in all lines whereas EM48, ubiquitin and 1C2 demonstrated consistent staining in all models irrespective of age or form of mHTT. MW8 and S830 were the most sensitive antibodies with 1C2 the least. Ubiquitin levels were stable for each model regardless of age. Ubiquitin was particularly sensitive in young YAC128 mice that demonstrate an absence of inclusions until ~12 months of age suggesting high affinity to mHTT in its diffuse form. The data indicate that generalisations across models regarding the quantification of aggregations may not be valid and that mHTT antibody binding is unique to the mouse model and sensitive to changes in inclusion development. PMID:27196694

Evaluating North American Electric Grid Reliability Using the Barabasi-Albert Network Model

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

Chassin, David P.; Posse, Christian

2005-09-15

The reliability of electric transmission systems is examined using a scale-free model of network topology and failure propagation. The topologies of the North American eastern and western electric grids are analyzed to estimate their reliability based on the Barabási-Albert network model. A commonly used power system reliability index is computed using a simple failure propagation model. The results are compared to the values of power system reliability indices previously obtained using other methods and they suggest that scale-free network models are usable to estimate aggregate electric grid reliability.

Evaluating North American Electric Grid Reliability Using the Barabasi-Albert Network Model

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

Chassin, David P.; Posse, Christian

2005-09-15

The reliability of electric transmission systems is examined using a scale-free model of network topology and failure propagation. The topologies of the North American eastern and western electric grids are analyzed to estimate their reliability based on the Barabasi-Albert network model. A commonly used power system reliability index is computed using a simple failure propagation model. The results are compared to the values of power system reliability indices previously obtained using standard power engineering methods, and they suggest that scale-free network models are usable to estimate aggregate electric grid reliability.

Cost-Efficient and Multi-Functional Secure Aggregation in Large Scale Distributed Application

PubMed Central

Zhang, Ping; Li, Wenjun; Sun, Hua

2016-01-01

Secure aggregation is an essential component of modern distributed applications and data mining platforms. Aggregated statistical results are typically adopted in constructing a data cube for data analysis at multiple abstraction levels in data warehouse platforms. Generating different types of statistical results efficiently at the same time (or referred to as enabling multi-functional support) is a fundamental requirement in practice. However, most of the existing schemes support a very limited number of statistics. Securely obtaining typical statistical results simultaneously in the distribution system, without recovering the original data, is still an open problem. In this paper, we present SEDAR, which is a SEcure Data Aggregation scheme under the Range segmentation model. Range segmentation model is proposed to reduce the communication cost by capturing the data characteristics, and different range uses different aggregation strategy. For raw data in the dominant range, SEDAR encodes them into well defined vectors to provide value-preservation and order-preservation, and thus provides the basis for multi-functional aggregation. A homomorphic encryption scheme is used to achieve data privacy. We also present two enhanced versions. The first one is a Random based SEDAR (REDAR), and the second is a Compression based SEDAR (CEDAR). Both of them can significantly reduce communication cost with the trade-off lower security and lower accuracy, respectively. Experimental evaluations, based on six different scenes of real data, show that all of them have an excellent performance on cost and accuracy. PMID:27551747

Cost-Efficient and Multi-Functional Secure Aggregation in Large Scale Distributed Application.

PubMed

Zhang, Ping; Li, Wenjun; Sun, Hua

2016-01-01

Secure aggregation is an essential component of modern distributed applications and data mining platforms. Aggregated statistical results are typically adopted in constructing a data cube for data analysis at multiple abstraction levels in data warehouse platforms. Generating different types of statistical results efficiently at the same time (or referred to as enabling multi-functional support) is a fundamental requirement in practice. However, most of the existing schemes support a very limited number of statistics. Securely obtaining typical statistical results simultaneously in the distribution system, without recovering the original data, is still an open problem. In this paper, we present SEDAR, which is a SEcure Data Aggregation scheme under the Range segmentation model. Range segmentation model is proposed to reduce the communication cost by capturing the data characteristics, and different range uses different aggregation strategy. For raw data in the dominant range, SEDAR encodes them into well defined vectors to provide value-preservation and order-preservation, and thus provides the basis for multi-functional aggregation. A homomorphic encryption scheme is used to achieve data privacy. We also present two enhanced versions. The first one is a Random based SEDAR (REDAR), and the second is a Compression based SEDAR (CEDAR). Both of them can significantly reduce communication cost with the trade-off lower security and lower accuracy, respectively. Experimental evaluations, based on six different scenes of real data, show that all of them have an excellent performance on cost and accuracy.

NMR investigations of self-aggregation characteristics of SDS in a model assembled tri-block copolymer solution.

PubMed

Kumar, B V N Phani; Priyadharsini, S Umayal; Prameela, G K S; Mandal, Asit Baran

2011-08-01

The present work was undertaken with a view to understand the influence of a model non-ionic tri-block copolymer PEO-PPO-PEO (poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide)) with molecular weight 5800 i.e., P123 [(EO)(20)-(PO)(70)-(EO)(20)] on the self-aggregation characteristics of the anionic surfactant sodium dodecylsulfate (SDS) in aqueous solution (D(2)O) using NMR chemical shift, self-diffusion and nuclear spin-relaxation as suitable experimental probes. In addition, polymer diffusion has been monitored as a function of SDS concentration. The concentration-dependent chemical shift, diffusion data and relaxation data indicated the significant interaction of polymeric micelles with SDS monomers and micelles at lower and intermediate concentrations of SDS, whereas the weak interaction of the polymer with SDS micelles at higher concentrations of SDS. It has been observed that SDS starts aggregating on the polymer at a lower concentration i.e., critical aggregation concentration (cac=1.94 mM) compared to polymer-free situation, and the onset of secondary micelle concentration (C(2)=27.16 mM) points out the saturation of the 0.2 wt% polymer or free SDS monomers/micelles at higher concentrations of SDS. It has also been observed that the parameter cac is almost independent in the polymer concentrations of study. The TMS (tetramethylsilane) has been used as a solubilizate to measure the bound diffusion coefficient of SDS-polymer mixed system. The self-diffusion data were analyzed using two-site exchange model and the obtained information on aggregation dynamics was commensurate with that inferred from chemical shift and relaxation data. The information on slow motions of polymer-SDS system was also extracted using spin-spin and spin-lattice relaxation rate measurements. The relaxation data points out the disintegration of polymer network at higher concentrations of SDS. The present NMR investigations have been well corroborated by surface tension and conductivity measurements. Copyright © 2011 Elsevier Inc. All rights reserved.

Modeling slip system strength evolution in Ti-7Al informed by in-situ grain stress measurements

DOE PAGES

Pagan, Darren C.; Shade, Paul A; Barton, Nathan R.; ...

2017-02-17

Far-field high-energy X-ray diffraction microscopy is used to asses the evolution of slip system strengths in hexagonal close-packed (HCP) Ti-7A1 during tensile deformation in-situ. The following HCP slip system families are considered: basal < a >, prismatic < a >, pyramidal < a >, and first-order pyramidal < c + a >. A 1 mm length of the specimen's gauge section, marked with fiducials and comprised of an aggregate of over 500 grains, is tracked during continuous deformation. The response of each slip system family is quantified using 'slip system strength curves' that are calculated from the average stress tensorsmore » of each grain over the applied deformation history. These curves, which plot the average resolved shear stress for each slip system family versus macroscopic strain, represent a mesoscopic characterization of the aggregate response. A short time-scale transient softening is observed in the basal < a >, prismatic < a >, and pyramidal < a > slip systems, while a long time-scale transient hardening is observed in the pyramidal < c + a > slip systems. These results are used to develop a slip system strength model as part of an elasto-viscoplastic constitutive model for the single crystal behavior. A suite of finite element simulations is performed on a virtual polycrystal to demonstrate the relative effects of the different parameters in the slip system strength model. Finally, the model is shown to accurately capture the macroscopic stress-strain response using parameters that are chosen to capture the mesoscopic slip system responses.« less

Ligand-promoted protein folding by biased kinetic partitioning.

PubMed

Hingorani, Karan S; Metcalf, Matthew C; Deming, Derrick T; Garman, Scott C; Powers, Evan T; Gierasch, Lila M

2017-04-01

Protein folding in cells occurs in the presence of high concentrations of endogenous binding partners, and exogenous binding partners have been exploited as pharmacological chaperones. A combined mathematical modeling and experimental approach shows that a ligand improves the folding of a destabilized protein by biasing the kinetic partitioning between folding and alternative fates (aggregation or degradation). Computationally predicted inhibition of test protein aggregation and degradation as a function of ligand concentration are validated by experiments in two disparate cellular systems.

Ligand-Promoted Protein Folding by Biased Kinetic Partitioning

PubMed Central

Hingorani, Karan S.; Metcalf, Matthew C.; Deming, Derrick T.; Garman, Scott C.; Powers, Evan T.; Gierasch, Lila M.

2017-01-01

Protein folding in cells occurs in the presence of high concentrations of endogenous binding partners, and exogenous binding partners have been exploited as pharmacological chaperones. A combined mathematical modeling and experimental approach shows that a ligand improves the folding of a destabilized protein by biasing the kinetic partitioning between folding and alternative fates (aggregation or degradation). Computationally predicted inhibition of test protein aggregation and degradation as a function of ligand concentration are validated by experiments in two disparate cellular systems. PMID:28218913

Inoculation of α-synuclein preformed fibrils into the mouse gastrointestinal tract induces Lewy body-like aggregates in the brainstem via the vagus nerve.

PubMed

Uemura, Norihito; Yagi, Hisashi; Uemura, Maiko T; Hatanaka, Yusuke; Yamakado, Hodaka; Takahashi, Ryosuke

2018-05-11

Intraneuronal α-synuclein (α-Syn) aggregates known as Lewy bodies (LBs) and the loss of dopaminergic neurons in the substantia nigra pars compacta (SNpc) are the pathological hallmarks of Parkinson's disease (PD). Braak's hypothesis based on autopsy studies suggests that Lewy pathology initially occurs in the enteric nervous system (ENS) and then travels retrogradely to the dorsal motor nucleus of the vagus nerve (dmX), proceeding from there in a caudo-rostral direction. Recent evidence that α-Syn aggregates propagate between interconnected neurons supports this hypothesis. However, there is no direct evidence demonstrating this transmission from the ENS to the dmX and then to the SNpc. We inoculated α-Syn preformed fibrils (PFFs) or phosphate-buffered saline (PBS) into the mouse gastric wall and analyzed the progression of the pathology. The mice inoculated with α-Syn PFFs, but not with PBS, developed phosphorylated α-Syn (p-α-Syn)-positive LB-like aggregates in the dmX at 45 days postinoculation. This aggregate formation was completely abolished when vagotomy was performed prior to inoculation of α-Syn PFFs, suggesting that the aggregates in the dmX were retrogradely induced via the vagus nerve. Unexpectedly, the number of neurons containing p-α-Syn-positive aggregates in the dmX decreased over time, and no further caudo-rostral propagation beyond the dmX was observed up to 12 months postinoculation. P-α-Syn-positive aggregates were also present in the myenteric plexus at 12 months postinoculation. However, unlike in patients with PD, there was no cell-type specificity in neurons containing those aggregates in this model. These results indicate that α-Syn PFF inoculation into the mouse gastrointestinal tract can induce α-Syn pathology resembling that of very early PD, but other factors are apparently required if further progression of PD pathology is to be replicated in this animal model.

Aggregation and disaggregation kinetics of human blood platelets: Part II. Shear-induced platelet aggregation.

PubMed Central

Huang, P Y; Hellums, J D

1993-01-01

A population balance equation (PBE) mathematical model for analyzing platelet aggregation kinetics was developed in Part I (Huang, P. Y., and J. D. Hellums. 1993. Biophys. J. 65: 334-343) of a set of three papers. In this paper, Part II, platelet aggregation and related reactions are studied in the uniform, known shear stress field of a rotational viscometer, and interpreted by means of the model. Experimental determinations are made of the platelet-aggregate particle size distributions as they evolve in time under the aggregating influence of shear stress. The PBE model is shown to give good agreement with experimental determinations when either a reversible (aggregation and disaggregation) or an irreversible (no disaggregation) form of the model is used. This finding suggests that for the experimental conditions studied disaggregation processes are of only secondary importance. During shear-induced platelet aggregation, only a small fraction of platelet collisions result in the binding together of the involved platelets. The modified collision efficiency is approximately zero for shear rates below 3000 s-1. It increases with shear rates above 3000 s-1 to about 0.01 for a shear rate of 8000 s-1. Addition of platelet chemical agonists yields order of magnitude increases in collision efficiency. The collision efficiency for shear-induced platelet aggregation is about an order of magnitude less at 37 degrees C than at 24 degrees C. The PBE model gives a much more accurate representation of aggregation kinetics than an earlier model based on a monodispersed particle size distribution. PMID:8369442

Aggregating the response in time series regression models, applied to weather-related cardiovascular mortality.

PubMed

Masselot, Pierre; Chebana, Fateh; Bélanger, Diane; St-Hilaire, André; Abdous, Belkacem; Gosselin, Pierre; Ouarda, Taha B M J

2018-07-01

In environmental epidemiology studies, health response data (e.g. hospitalization or mortality) are often noisy because of hospital organization and other social factors. The noise in the data can hide the true signal related to the exposure. The signal can be unveiled by performing a temporal aggregation on health data and then using it as the response in regression analysis. From aggregated series, a general methodology is introduced to account for the particularities of an aggregated response in a regression setting. This methodology can be used with usually applied regression models in weather-related health studies, such as generalized additive models (GAM) and distributed lag nonlinear models (DLNM). In particular, the residuals are modelled using an autoregressive-moving average (ARMA) model to account for the temporal dependence. The proposed methodology is illustrated by modelling the influence of temperature on cardiovascular mortality in Canada. A comparison with classical DLNMs is provided and several aggregation methods are compared. Results show that there is an increase in the fit quality when the response is aggregated, and that the estimated relationship focuses more on the outcome over several days than the classical DLNM. More precisely, among various investigated aggregation schemes, it was found that an aggregation with an asymmetric Epanechnikov kernel is more suited for studying the temperature-mortality relationship. Copyright © 2018. Published by Elsevier B.V.

An online detection system for aggregate sizes and shapes based on digital image processing

NASA Astrophysics Data System (ADS)

Yang, Jianhong; Chen, Sijia

2017-02-01

Traditional aggregate size measuring methods are time-consuming, taxing, and do not deliver online measurements. A new online detection system for determining aggregate size and shape based on a digital camera with a charge-coupled device, and subsequent digital image processing, have been developed to overcome these problems. The system captures images of aggregates while falling and flat lying. Using these data, the particle size and shape distribution can be obtained in real time. Here, we calibrate this method using standard globules. Our experiments show that the maximum particle size distribution error was only 3 wt%, while the maximum particle shape distribution error was only 2 wt% for data derived from falling aggregates, having good dispersion. In contrast, the data for flat-lying aggregates had a maximum particle size distribution error of 12 wt%, and a maximum particle shape distribution error of 10 wt%; their accuracy was clearly lower than for falling aggregates. However, they performed well for single-graded aggregates, and did not require a dispersion device. Our system is low-cost and easy to install. It can successfully achieve online detection of aggregate size and shape with good reliability, and it has great potential for aggregate quality assurance.

Agents, Bayes, and Climatic Risks - a modular modelling approach

NASA Astrophysics Data System (ADS)

Haas, A.; Jaeger, C.

2005-08-01

When insurance firms, energy companies, governments, NGOs, and other agents strive to manage climatic risks, it is by no way clear what the aggregate outcome should and will be. As a framework for investigating this subject, we present the LAGOM model family. It is based on modules depicting learning social agents. For managing climate risks, our agents use second order probabilities and update them by means of a Bayesian mechanism while differing in priors and risk aversion. The interactions between these modules and the aggregate outcomes of their actions are implemented using further modules. The software system is implemented as a series of parallel processes using the CIAMn approach. It is possible to couple modules irrespective of the language they are written in, the operating system under which they are run, and the physical location of the machine.

Decomposition of the fluoroethylene carbonate additive and the glue effect of lithium fluoride products for the solid electrolyte interphase: an ab initio study.

PubMed

Okuno, Yukihiro; Ushirogata, Keisuke; Sodeyama, Keitaro; Tateyama, Yoshitaka

2016-03-28

Additives in the electrolyte solution of lithium-ion batteries (LIBs) have a large impact on the performance of the solid electrolyte interphase (SEI) that forms on the anode and is a key to the stability and durability of LIBs. We theoretically investigated effects of fluoroethylene carbonate (FEC), a representative additive, that has recently attracted considerable attention for the enhancement of cycling stability of silicon electrodes and the improvement of reversibility of sodium-ion batteries. First, we intensively examined the reductive decompositions by ring-opening, hydrogen fluoride (HF) elimination to form a vinylene carbonate (VC) additive and intermolecular chemical reactions of FEC in the ethylene carbonate (EC) electrolyte, by using density functional theory (DFT) based molecular dynamics and the blue-moon ensemble technique for the free energy profile. The results show that the most plausible product of the FEC reductive decomposition is lithium fluoride (LiF), and that the reactivity of FEC to anion radicals is found to be inert compared to the VC additive. We also investigated the effects of the generated LiF on the SEI by using two model systems; (1) LiF molecules distributed in a model aggregate of organic SEI film components (SFCs) and (2) a LiF aggregate interfaced with the SFC aggregate. DFT calculations of the former system show that F atoms form strong bindings with the Li atoms of multiple organic SFC molecules and play as a joint connecting them. In the latter interface system, the LiF aggregate adsorbs the organic SFCs through the F-Li bindings. These results suggest that LiF moieties play the role of glue in the organic SFC within the SEI film. We also examined the interface structure between a LiF aggregate and a lithiated silicon anode, and found that they are strongly bound. This strong binding is likely to be related to the effectiveness of the FEC additive in the electrolyte for the silicon anode.

Retiring the Short-Run Aggregate Supply Curve

ERIC Educational Resources Information Center

Elwood, S. Kirk

2010-01-01

The author argues that the aggregate demand/aggregate supply (AD/AS) model is significantly improved--although certainly not perfected--by trimming it of the short-run aggregate supply (SRAS) curve. Problems with the SRAS curve are shown first for the AD/AS model that casts the AD curve as identifying the equilibrium level of output associated…

Small angle x ray scattering studies of reverse micelles in supercritical fluids

NASA Astrophysics Data System (ADS)

Pfund, D. M.; Fulton, J. L.

1994-10-01

The nature of aggregates formed in a supercritical fluid determines its solvent power and selectivity. Small angle X ray scattering (SAXS) is a powerful tool for studying the properties of aggregates with sizes in the 10(angstrom) to 200(angstrom) range. It is also useful in studying those interparticle interactions which operate over a similar distance. The authors have used SAXS to examine the aggregates formed in pure fluids, in mixtures and in fluid/surfactant/water systems. The scattered intensity as a function of angle depends on the geometry, polydispersity, X ray contrast, and interaction strength of the particles as well as on the phase behavior of the system. In this paper the authors present the results of modeling the X-ray scattering from AOT/water reverse micelles in supercritical propane and in propane/carbon dioxide mixtures. They examine the effect of dilution with CO2 anti-solvent on the phase behavior of the system and on the strength of intermicellar attractions. A better understanding of these systems must be obtained before the applications of supercritical reverse micelle systems to extractions, reactions, and enhanced oil recovery can be fully developed.

Local growth of dust- and ice-mixed aggregates as cometary building blocks in the solar nebula

NASA Astrophysics Data System (ADS)

Lorek, S.; Lacerda, P.; Blum, J.

2018-03-01

Context. Comet formation by gravitational instability requires aggregates that trigger the streaming instability and cluster in pebble-clouds. These aggregates form as mixtures of dust and ice from (sub-)micrometre-sized dust and ice grains via coagulation in the solar nebula. Aim. We investigate the growth of aggregates from (sub-)micrometre-sized dust and ice monomer grains. We are interested in the properties of these aggregates: whether they might trigger the streaming instability, how they compare to pebbles found on comets, and what the implications are for comet formation in collapsing pebble-clouds. Methods: We used Monte Carlo simulations to study the growth of aggregates through coagulation locally in the comet-forming region at 30 au. We used a collision model that can accommodate sticking, bouncing, fragmentation, and porosity of dust- and ice-mixed aggregates. We compared our results to measurements of pebbles on comet 67P/Churyumov-Gerasimenko. Results: We find that aggregate growth becomes limited by radial drift towards the Sun for 1 μm sized monomers and by bouncing collisions for 0.1 μm sized monomers before the aggregates reach a Stokes number that would trigger the streaming instability (Stmin). We argue that in a bouncing-dominated system, aggregates can reach Stmin through compression in bouncing collisions if compression is faster than radial drift. In the comet-forming region ( 30 au), aggregates with Stmin have volume-filling factors of 10-2 and radii of a few millimetres. These sizes are comparable to the sizes of pebbles found on comet 67P/Churyumov-Gerasimenko. The porosity of the aggregates formed in the solar nebula would imply that comets formed in pebble-clouds with masses equivalent to planetesimals of the order of 100 km in diameter.

A Comparative Study of Spatial Aggregation Methodologies under the BioEarth Framework

NASA Astrophysics Data System (ADS)

Chandrasekharan, B.; Rajagopalan, K.; Malek, K.; Stockle, C. O.; Adam, J. C.; Brady, M.

2014-12-01

The increasing probability of water resource scarcity due to climate change has highlighted the need for adopting an economic focus in modelling water resource uses. Hydro-economic models, developed by integrating economic optimization with biophysical crop models, are driven by the economic value of water, revealing it's most efficient uses and helping policymakers evaluate different water management strategies. One of the challenges in integrating biophysical models with economic models is the difference in the spatial scales in which they operate. Biophysical models that provide crop production functions typically run at smaller scale than economic models, and substantial spatial aggregation is required. However, any aggregation introduces a bias, i.e., a discrepancy between the functional value at the higher spatial scale and the value at the spatial scale of the aggregated units. The objective of this work is to study the sensitivity of net economic benefits in the Yakima River basin (YRB) to different spatial aggregation methods for crop production functions. The spatial aggregation methodologies that we compare involve agro-ecological zones (AEZs) and aggregation levels that reflect water management regimes (e.g. irrigation districts). Aggregation bias can distort the underlying data and result in extreme solutions. In order to avoid this we use an economic optimization model that incorporates the synthetic and historical crop mixes approach (Onal & Chen, 2012). This restricts the solutions between the weighted averages of historical and simulated feasible planting decisions, with the weights associated with crop mixes being treated as endogenous variables. This study is focused on 5 major irrigation districts of the YRB in the Pacific Northwest US. The biophysical modeling framework we use, BioEarth, includes the coupled hydrology and crop growth model, VIC-Cropsyst and an economic optimization model. Preliminary findings indicate that the standard approach of developing AEZs does not perform well when overlaid with irrigation districts. Moreover, net economic benefits were significantly different between the two aggregation methodologies. Therefore, while developing hydro-economic models, significant consideration should be placed on the aggregation methodology.

The applicability of physical optics in the millimetre and sub-millimetre spectral region. Part II: Application to a three-component model of ice cloud and its evaluation against the bulk single-scattering properties of various other aggregate models

NASA Astrophysics Data System (ADS)

Baran, Anthony J.; Ishimoto, Hiroshi; Sourdeval, Odran; Hesse, Evelyn; Harlow, Chawn

2018-02-01

The bulk single-scattering properties of various randomly oriented aggregate ice crystal models are compared and contrasted at a number of frequencies between 89 and 874 GHz. The model ice particles consist of the ten-branched plate aggregate, five-branched plate aggregate, eight-branched hexagonal aggregate, Voronoi ice aggregate, six-branched hollow bullet rosette, hexagonal column of aspect ratio unity, and the ten-branched hexagonal aggregate. The bulk single-scattering properties of the latter two ice particle models have been calculated using the light scattering methods described in Part I, which represent the two most extreme members of an ensemble model of cirrus ice crystals. In Part I, it was shown that the method of physical optics could be combined with the T-matrix at a size parameter of about 18 to compute the bulk integral ice optical properties and the phase function in the microwave to sufficient accuracy to be of practical value. Here, the bulk single-scattering properties predicted by the two ensemble model members and the Voronoi model are shown to generally bound those of all other models at frequencies between 89 and 874 GHz, thus representing a three-component model of ice cloud that can be generally applied to the microwave, rather than using many differing ice particle models. Moreover, the Voronoi model and hollow bullet rosette scatter similarly to each other in the microwave. Furthermore, from the various comparisons, the importance of assumed shapes of the particle size distribution as well as cm-sized ice aggregates is demonstrated.

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

PubMed Central

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

2011-01-01

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

Selectivity and stoichiometry boosting of beta-cyclodextrin in cationic/anionic surfactant systems: when host-guest equilibrium meets biased aggregation equilibrium.

PubMed

Jiang, Lingxiang; Yu, Caifang; Deng, Manli; Jin, Changwen; Wang, Yilin; Yan, Yun; Huang, Jianbin

2010-02-18

Cationic surfactant/anionic surfactant/beta-CD ternary aqueous systems provide a platform for the coexistence of the host-guest (beta-CD/surfactant) equilibrium and the biased aggregation (monomeric/aggregated surfactants) equilibrium. We report here that the interplay between the two equilibria dominates the systems as follows. (1) The biased aggregation equilibrium imposes an apparent selectivity on the host-guest equilibrium, namely, beta-CD has to always selectively bind the major surfactant (molar fraction > 0.5) even if binding constants of beta-CD to the pair of surfactants are quite similar. (2) In return, the host-guest equilibrium amplifies the bias of the aggregation equilibrium, that is, the selective binding partly removes the major surfactant from the aggregates and leaves the aggregate composition approaching the electroneutral mixing stoichiometry. (3) This composition variation enhances electrostatic attractions between oppositely charged surfactant head groups, thus resulting in less-curved aggregates. In particular, the present apparent host-guest selectivity is of remarkably high values, and the selectivity stems from the bias of the aggregation equilibrium rather than the difference in binding constants. Moreover, beta-CD is defined as a "stoichiometry booster" for the whole class of cationic/anionic surfactant systems, which provides an additional degree of freedom to directly adjust aggregate compositions of the systems. The stoichiometry boosting of the compositions can in turn affect or even determine microstructures and macroproperties of the systems.

Self-organizing biochemical cycle in dynamic feedback with soil structure

NASA Astrophysics Data System (ADS)

Vasilyeva, Nadezda; Vladimirov, Artem; Smirnov, Alexander; Matveev, Sergey; Tyrtyshnikov, Evgeniy; Yudina, Anna; Milanovskiy, Evgeniy; Shein, Evgeniy

2016-04-01

In the present study we perform bifurcation analysis of a physically-based mathematical model of self-organized structures in soil (Vasilyeva et al., 2015). The state variables in this model included microbial biomass, two organic matter types, oxygen, carbon dioxide, water content and capillary pore size. According to our previous experimental studies, organic matter affinity to water is an important property affecting soil structure. Therefore, organic matter wettability was taken as principle distinction between organic matter types in this model. It considers general known biological feedbacks with soil physical properties formulated as a system of parabolic type non-linear partial differential equations with elements of discrete modeling for water and pore formation. The model shows complex behavior, involving emergence of temporal and spatial irregular auto-oscillations from initially homogeneous distributions. The energy of external impact on a system was defined by a constant oxygen level on the boundary. Non-linear as opposed to linear oxygen diffusion gives possibility of modeling anaerobic micro-zones formation (organic matter conservation mechanism). For the current study we also introduced population competition of three different types of microorganisms according to their mobility/feeding (diffusive, moving and fungal growth). The strongly non-linear system was solved and parameterized by time-optimized algorithm combining explicit and implicit (matrix form of Thomas algorithm) methods considering the time for execution of the evaluated time-step according to accuracy control. The integral flux of the CO2 state variable was used as a macroscopic parameter to describe system as a whole and validation was carried out on temperature series of moisture dependence for soil heterotrophic respiration data. Thus, soil heterotrophic respiration can be naturally modeled as an integral result of complex dynamics on microscale, arising from biological processes formulated as a sum of state variables products, with no need to introduce any saturation functions, such as Mikhaelis-Menten type kinetics, inside the model. Analyzed dynamic soil model is being further developed to describe soil structure formation and its effect on organic matter decomposition at macro-scale, to predict changes with external perturbations. To link micro- and macro-scales we additionally model soil particles aggregation process. The results from local biochemical soil organic matter cycle serve as inputs to aggregation process, while the output aggregate size distributions define physical properties in the soil profile, these in turn serve as dynamic parameters in local biochemical cycles. The additional formulation is a system of non-linear ordinary differential equations, including Smoluchowski-type equations for aggregation and reaction kinetics equations for coagulation/adsorption/adhesion processes. Vasilyeva N.A., Ingtem J.G., Silaev D.A. Nonlinear dynamical model of microbial growth in soil medium. Computational Mathematics and Modeling, vol. 49, p.31-44, 2015 (in Russian). English version is expected in corresponding vol.27, issue 2, 2016.

Holographic Characterization of Colloidal Fractal Aggregates

NASA Astrophysics Data System (ADS)

Wang, Chen; Cheong, Fook Chiong; Ruffner, David B.; Zhong, Xiao; Ward, Michael D.; Grier, David G.

In-line holographic microscopy images of micrometer-scale fractal aggregates can be interpreted with the Lorenz-Mie theory of light scattering and an effective-sphere model to obtain each aggregate's size and the population-averaged fractal dimension. We demonstrate this technique experimentally using model fractal clusters of polystyrene nanoparticles and fractal protein aggregates composed of bovine serum albumin and bovine pancreas insulin. This technique can characterize several thousand aggregates in ten minutes and naturally distinguishes aggregates from contaminants such as silicone oil droplets. Work supported by the SBIR program of the NSF.

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

NASA Astrophysics Data System (ADS)

Kunes, Kay; Cox, Daniel; Singh, Rajiv

2004-03-01

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

A numerical model for aggregations formation and magnetic driving of spherical particles based on OpenFOAM®.

PubMed

Karvelas, E G; Lampropoulos, N K; Sarris, I E

2017-04-01

This work presents a numerical model for the formation of particle aggregations under the influence of a permanent constant magnetic field and their driving process under a gradient magnetic field, suitably created by a Magnetic Resonance Imaging (MRI) device. The model is developed in the OpenFOAM platform and it is successfully compared to the existing experimental and numerical results in terms of aggregates size and their motion in water solutions. Furthermore, several series of simulations are performed for two common types of particles of different diameter in order to verify their aggregation and flow behaviour, under various constant and gradient magnetic fields in the usual MRI working range. Moreover, the numerical model is used to measure the mean length of aggregations, the total time needed to form and their mean velocity under different permanent and gradient magnetic fields. The present model is found to predict successfully the size, velocity and distribution of aggregates. In addition, our simulations showed that the mean length of aggregations is proportional to the permanent magnetic field magnitude and particle diameter according to the relation : l¯ a =7.5B 0 d i 3/2 . The mean velocity of the aggregations is proportional to the magnetic gradient, according to : u¯ a =6.63G˜B 0 and seems to reach a steady condition after a certain period of time. The mean time needed for particles to aggregate is proportional to permanent magnetic field magnitude, scaled by the relationship : t¯ a ∝7B 0 . A numerical model to predict the motion of magnetic particles for medical application is developed. This model is found suitable to predict the formation of aggregations and their motion under the influence of permanent and gradient magnetic fields, respectively, that are produced by an MRI device. The magnitude of the external constant magnetic field is the most important parameter for the aggregations formation and their driving. Copyright © 2017 Elsevier B.V. All rights reserved.

Forecasting Hourly Water Demands With Seasonal Autoregressive Models for Real-Time Application

NASA Astrophysics Data System (ADS)

Chen, Jinduan; Boccelli, Dominic L.

2018-02-01

Consumer water demands are not typically measured at temporal or spatial scales adequate to support real-time decision making, and recent approaches for estimating unobserved demands using observed hydraulic measurements are generally not capable of forecasting demands and uncertainty information. While time series modeling has shown promise for representing total system demands, these models have generally not been evaluated at spatial scales appropriate for representative real-time modeling. This study investigates the use of a double-seasonal time series model to capture daily and weekly autocorrelations to both total system demands and regional aggregated demands at a scale that would capture demand variability across a distribution system. Emphasis was placed on the ability to forecast demands and quantify uncertainties with results compared to traditional time series pattern-based demand models as well as nonseasonal and single-seasonal time series models. Additional research included the implementation of an adaptive-parameter estimation scheme to update the time series model when unobserved changes occurred in the system. For two case studies, results showed that (1) for the smaller-scale aggregated water demands, the log-transformed time series model resulted in improved forecasts, (2) the double-seasonal model outperformed other models in terms of forecasting errors, and (3) the adaptive adjustment of parameters during forecasting improved the accuracy of the generated prediction intervals. These results illustrate the capabilities of time series modeling to forecast both water demands and uncertainty estimates at spatial scales commensurate for real-time modeling applications and provide a foundation for developing a real-time integrated demand-hydraulic model.

76 FR 28467 - Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-17

... Price Index (PPI), BLS recently developed an experimental aggregation system that includes price changes... indexes. The PPI program recently developed an experimental aggregation system that includes goods price... (business inputs, excluding capital investment). The experimental aggregation system was introduced with the...

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

PubMed Central

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

2012-01-01

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

Reduced-Order Models for Load Management in the Power Grid

NASA Astrophysics Data System (ADS)

Alizadeh, Mahnoosh

In recent years, considerable research efforts have been directed towards designing control schemes that can leverage the inherent flexibility of electricity demand that is not tapped into in today's electricity markets. It is expected that these control schemes will be carried out by for-profit entities referred to as aggregators that operate at the edge of the power grid network. While the aggregator control problem is receiving much attention, more high-level questions of how these aggregators should plan their market participation, interact with the main grid and with each other, remain rather understudied. Answering these questions requires a large-scale model for the aggregate flexibility that can be harnessed from the a population of customers, particularly for residences and small businesses. The contribution of this thesis towards this goal is divided into three parts: In Chapter 3, a reduced-order model for a large population of heterogeneous appliances is provided by clustering load profiles that share similar degrees of freedom together. The use of such reduced-order model for system planning and optimal market decision making requires a foresighted approximation of the number of appliances that will join each cluster. Thus, Chapter 4 provides a systematic framework to generate such forecasts for the case of Electric Vehicles, based on real-world battery charging data. While these two chapters set aside the economic side that is naturally involved with participation in demand response programs and mainly focus on the control problem, Chapter 5 is dedicated to the study of optimal pricing mechanisms in order to recruit heterogeneous customers in a demand response program in which an aggregator can directly manage their appliances' load under their specified preferences. Prices are proportional to the wholesale market savings that can result from each recruitment event.

A PFC2D model of the interactions between the tire and the aggregate filled arrester bed on escape ramp

NASA Astrophysics Data System (ADS)

Qin, Pin-pin; Chen, Chui-ce; Pei, Shi-kang; Li, Xin

2017-06-01

The stopping distance of a runaway vehicle is determined by the entry speed, the design of aggregate-filled arrester bed and the longitudinal grade of escape ramp. Although numerous previous studies have been carried out on the influence of speed and grade on stopping distance, taking into account aggregate properties is rare. Firstly, this paper analyzes the interactions between the tire and the aggregate. The tire and the aggregate are abstracted into a big particle unit and a particle combination unit consisting of lots of aggregates, respectively. Secondly this paper proposes an assumption that this interaction is a kind of particle flow. Later, this paper uses some particle properties to describe the tire-particle unit and aggregate-particle unit respectively, then puts forward several simplified steps of modeling by particle flow code in 2 dimensions (PFC2D). Therefore, a PFC2D micro-simulation model of the interactions between the tire and the aggregate is proposed. The parameters of particle properties are then calibrated by three groups of numerical tests. The calibrated model is verified by eight full-scale arrester bed testing data to demonstrate its feasibility and accuracy. This model provides escape ramp designers a feasible simulation method not only for predicting the stopping distance but also considering the aggregate properties.

Dynamics of mutated GFAP aggregates revealed by real-time imaging of an astrocyte model of Alexander disease.

PubMed

Mignot, Cyril; Delarasse, Cécile; Escaich, Séverine; Della Gaspera, Bruno; Noé, Eric; Colucci-Guyon, Emma; Babinet, Charles; Pekny, Milos; Vicart, Patrick; Boespflug-Tanguy, Odile; Dautigny, André; Rodriguez, Diana; Pham-Dinh, Danielle

2007-08-01

Alexander disease (AxD) is a rare neurodegenerative disorder characterized by large cytoplasmic aggregates in astrocytes and myelin abnormalities and caused by dominant mutations in the gene encoding glial fibrillary acidic protein (GFAP), the main intermediate filament protein in astrocytes. We tested the effects of three mutations (R236H, R76H and L232P) associated with AxD in cells transiently expressing mutated GFAP fused to green fluorescent protein (GFP). Mutated GFAP-GFP expressed in astrocytes formed networks or aggregates similar to those found in the brains of patients with the disease. Time-lapse recordings of living astrocytes showed that aggregates of mutated GFAP-GFP may either disappear, associated with cell survival, or coalesce in a huge juxtanuclear structure associated with cell death. Immunolabeling of fixed cells suggested that this gathering of aggregates forms an aggresome-like structure. Proteasome inhibition and immunoprecipitation assays revealed mutated GFAP-GFP ubiquitination, suggesting a role of the ubiquitin-proteasome system in the disaggregation process. In astrocytes from wild-type-, GFAP-, and vimentin-deficient mice, mutated GFAP-GFP aggregated or formed a network, depending on qualitative and quantitative interactions with normal intermediate filament partners. Particularly, vimentin displayed an anti-aggregation effect on mutated GFAP. Our data indicate a dynamic and reversible aggregation of mutated GFAP, suggesting that therapeutic approaches may be possible.

Compressive strength and hydration processes of concrete with recycled aggregates

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

Koenders, Eduardus A.B., E-mail: e.a.b.koenders@coc.ufrj.br; Microlab, Delft University of Technology; Pepe, Marco, E-mail: mapepe@unisa.it

2014-02-15

This paper deals with the correlation between the time evolution of the degree of hydration and the compressive strength of Recycled Aggregate Concrete (RAC) for different water to cement ratios and initial moisture conditions of the Recycled Concrete Aggregates (RCAs). Particularly, the influence of such moisture conditions is investigated by monitoring the hydration process and determining the compressive strength development of fully dry or fully saturated recycled aggregates in four RAC mixtures. Hydration processes are monitored via temperature measurements in hardening concrete samples and the time evolution of the degree of hydration is determined through a 1D hydration and heatmore » flow model. The effect of the initial moisture condition of RCAs employed in the considered concrete mixtures clearly emerges from this study. In fact, a novel conceptual method is proposed to predict the compressive strength of RAC-systems, from the initial mixture parameters and the hardening conditions. -- Highlights: •The concrete industry is more and more concerned with sustainability issues. •The use of recycled aggregates is a promising solution to enhance sustainability. •Recycled aggregates affect both hydration processes and compressive strength. •A fundamental approach is proposed to unveil the influence of recycled aggregates. •Some experimental comparisons are presented to validate the proposed approach.« less

Building aggregate timber supply models from individual harvest choice

Treesearch

Maksym Polyakov; David N. Wear; Robert Huggett

2009-01-01

Timber supply has traditionally been modelled using aggregate data. In this paper, we build aggregate supply models for four roundwood products for the US state of North Carolina from a stand-level harvest choice model applied to detailed forest inventory. The simulated elasticities of pulpwood supply are much lower than reported by previous studies. Cross price...

An Aggregate IRT Procedure for Exploratory Factor Analysis

ERIC Educational Resources Information Center

Camilli, Gregory; Fox, Jean-Paul

2015-01-01

An aggregation strategy is proposed to potentially address practical limitation related to computing resources for two-level multidimensional item response theory (MIRT) models with large data sets. The aggregate model is derived by integration of the normal ogive model, and an adaptation of the stochastic approximation expectation maximization…

Teaching Aggregate Demand and Supply Models

ERIC Educational Resources Information Center

Wells, Graeme

2010-01-01

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

CMAQ Community Survey Results

EPA Pesticide Factsheets

In 2016, CMAQ users worldwide participated in a survey circulated by the University of North Carolina's Community Modeling and Analysis System (CMAS) center. The aggregated results allow us to better understand the attributes of the CMAQ user community.

Intra-aggregate CO2 enrichment: a modelling approach for aerobic soils

NASA Astrophysics Data System (ADS)

Schlotter, D.; Schack-Kirchner, H.

2013-02-01

CO2 concentration gradients inside soil aggregates, caused by the respiration of soil microorganisms and fungal hyphae, might lead to variations in the soil solution chemistry on a mm-scale, and to an underestimation of the CO2 storage. But, up to now, there seems to be no feasible method for measuring CO2 inside natural aggregates with sufficient spatial resolution. We combined a one-dimensional model for gas diffusion in the inter-aggregate pore space with a cylinder diffusion model, simulating the consumption/production and diffusion of O2 and CO2 inside soil aggregates with air- and water-filled pores. Our model predicts that for aerobic respiration (respiratory quotient = 1) the intra-aggregate increase in the CO2 partial pressure can never be higher than 0.9 kPa for siliceous, and 0.1 kPa for calcaric aggregates, independent of the level of water-saturation. This suggests that only for siliceous aggregates CO2 produced by aerobic respiration might cause a high small-scale spatial variability in the soil solution chemistry. In calcaric aggregates, however, the contribution of carbonate species to the CO2 transport should lead to secondary carbonates on the aggregate surfaces. As regards the total CO2 storage in aerobic soils, both siliceous and calcaric, the effect of intra-aggregate CO2 gradients seems to be negligible. To assess the effect of anaerobic respiration on the intra-aggregate CO2 gradients, the development of a device for measuring CO2 on a mm-scale in soils is indispensable.

Kinetic model for astaxanthin aggregation in water-methanol mixtures

NASA Astrophysics Data System (ADS)

Giovannetti, Rita; Alibabaei, Leila; Pucciarelli, Filippo

2009-07-01

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

Universal timescales in the rheology of spheroid cell aggregates

NASA Astrophysics Data System (ADS)

Yu, Miao; Mahtabfar, Aria; Beleen, Paul; Foty, Ramsey; Zahn, Jeffrey; Shreiber, David; Liu, Liping; Lin, Hao

2017-11-01

The rheological properties of tissue play important roles in key biological processes including embryogenesis, cancer metastasis, and wound healing. Spheroid cell aggregate is a particularly interesting model system for the study of these phenomena. In the long time, they behave like drops with a surface tension. In the short, viscoelasticity also needs to be considered. In this work, we discover two coupled and universal timescales for spheroid aggregates. A total of 12 aggregate types (total aggregate number n =290) derived from L and GBM (glioblastoma multiforme) cells are studied with microtensiometer to obtain their surface tension. They are also allowed to relax upon release of the compression forces. The two timescales are observed during the relaxation process; their values do not depend on compression time nor the degree of deformation, and are consistent among all 12 types. Following prior work (Yu et al., Phys. Rev. Lett., 115:128303; Liu et al., J. Mech. Phys. Solids, 98:309-329) we use a rigorous mathematical theory to interpret the results, which reveals intriguing properties of the aggregates on both tissue and cellular levels. The mechanics of multicellular organization reflects both complexity and regularity due to strong active regulation.

Inhibition of Insulin Amyloid Fibrillation by a Novel Amphipathic Heptapeptide

PubMed Central

Ratha, Bhisma N.; Ghosh, Anirban; Brender, Jeffrey R.; Gayen, Nilanjan; Ilyas, Humaira; Neeraja, Chilukoti; Das, Kali P.; Mandal, Atin K.; Bhunia, Anirban

2016-01-01

The aggregation of insulin into amyloid fibers has been a limiting factor in the development of fast acting insulin analogues, creating a demand for excipients that limit aggregation. Despite the potential demand, inhibitors specifically targeting insulin have been few in number. Here we report a non-toxic and serum stable-designed heptapeptide, KR7 (KPWWPRR-NH2), that differs significantly from the primarily hydrophobic sequences that have been previously used to interfere with insulin amyloid fibrillation. Thioflavin T fluorescence assays, circular dichroism spectroscopy, and one-dimensional proton NMR experiments suggest KR7 primarily targets the fiber elongation step with little effect on the early oligomerization steps in the lag time period. From confocal fluorescence and atomic force microscopy experiments, the net result appears to be the arrest of aggregation in an early, non-fibrillar aggregation stage. This mechanism is noticeably different from previous peptide-based inhibitors, which have primarily shifted the lag time with little effect on later stages of aggregation. As insulin is an important model system for understanding protein aggregation, the new peptide may be an important tool for understanding peptide-based inhibition of amyloid formation. PMID:27679488

Multiscale modelling of dual-porosity porous media; a computational pore-scale study for flow and solute transport

NASA Astrophysics Data System (ADS)

de Vries, Enno T.; Raoof, Amir; van Genuchten, Martinus Th.

2017-07-01

Many environmental and agricultural applications involve the transport of water and dissolved constituents through aggregated soil profiles, or porous media that are structured, fractured or macroporous in other ways. During the past several decades, various process-based macroscopic models have been used to simulate contaminant transport in such media. Many of these models consider advective-dispersive transport through relatively large inter-aggregate pore domains, while exchange with the smaller intra-aggregate pores is assumed to be controlled by diffusion. Exchange of solute between the two domains is often represented using a first-order mass transfer coefficient, which is commonly obtained by fitting to observed data. This study aims to understand and quantify the solute exchange term by applying a dual-porosity pore-scale network model to relatively large domains, and analysing the pore-scale results in terms of the classical dual-porosity (mobile-immobile) transport formulation. We examined the effects of key parameters (notably aggregate porosity and aggregate permeability) on the main dual-porosity model parameters, i.e., the mobile water fraction (ϕm) and the mass transfer coefficient (α). Results were obtained for a wide range of aggregate porosities (between 0.082 and 0.700). The effect of aggregate permeability was explored by varying pore throat sizes within the aggregates. Solute breakthrough curves (BTCs) obtained with the pore-scale network model at several locations along the domain were analysed using analytical solutions of the dual-porosity model to obtain estimates of ϕm and α. An increase in aggregate porosity was found to decrease ϕm and increase α, leading to considerable tailing in the BTCs. Changes in the aggregate pore throat size affected the relative flow velocity between the intra- and inter-aggregate domains. Higher flow velocities within the aggregates caused a change in the transport regime from diffusion dominated to more advection dominated. This change increased the exchange rate of solutes between the mobile and immobile domains, with a related increase in the value of the mass transfer coefficient and less tailing in the BTCs.

Monte Carlo and mean-field studies of phase evolution in concentrated surfactant solutions

NASA Astrophysics Data System (ADS)

Bohbot, Yardena; Ben-Shaul, Avinoam; Granek, Rony; Gelbart, William M.

1995-11-01

A two-dimensional lattice model, originally introduced by Granek et al. [J. Chem. Phys. 101, 4331 (1994)], is used to demonstrate the intricate coupling between the intramicellar interactions that determine the optimal aggregation geometry of surfactant molecules in dilute solution, and the intermicellar interactions that govern the phase behavior at higher concentrations. Three very different scenarios of self-assembly and phase evolution are analyzed in detail, based on Monte Carlo studies and theoretical interpretations involving mean-field, Landau-Ginzburg, Bethe-Peierls, and virial expansion schemes. The basic particles in the model are ``unit micelles'' which, due to spontaneous self-assembly or because of excluded area interactions, can fuse to form larger aggregates. These aggregates are envisaged as flat micelles composed of a bilayerlike body surrounded by a curved semitoroidal rim. The system's Hamiltonian involves one- through four-body potentials between the unit micelles, which account for their tendency to form aggregates of different shapes, e.g., elongated vs disklike micelles. Equivalently, the configurational energy of the system is a sum of micellar self-energies involving the packing free energies of the constituent molecules in the bilayer body and in rim segments of different local curvature. The rim energy is a sum of a line tension term and a 1D curvature energy which depends on the rim spontaneous curvature and bending rigidity. Different combinations of these molecular parameters imply different optimal packing geometries and hence different self-assembly and phase behaviors. The emphasis in this paper is on systems of ``curvature loving'' amphiphiles which, in our model, are characterized by negative line tension. The three systems studied are: (i) A dilute solution of stable disklike micelles which, upon increasing the concentration, undergoes a first-order phase transition to a continuous bilayer with isolated hole defects. An intermediate modulated ``checkerboard'' phase appears under certain conditions at low temperatures. (ii) A system of unit micelles which in dilute solution tend to associate into linear micelles. These micelles are rodlike at low temperatures, becoming increasingly more flexible as the temperature increases. Upon increasing the concentration the micelles grow and undergo (in 2D) a continuous transition into nematic and ``stripe'' phases of long rods. At still higher concentrations the micellar stripes fuse into continuous sheets with line defects. (iii) A system in which, already in dilute solution, the micelles favor the formation of branched aggregates, analogous to the branched cylindrical micelles recently observed in certain surfactant solutions. As the concentration increases the micelles associate into networks (``gels'') composed of a mesh of linear micelles linked by ``T-like'' intermicellar junctions. The network may span the entire system or phase separate and coexist with a dilute micellar phase, depending on the details of the molecular packing parameters.

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

Buitrago, C. Francisco; Bolintineanu, Dan; Seitz, Michelle E.

Designing acid- and ion-containing polymers for optimal proton, ion, or water transport would benefit profoundly from predictive models or theories that relate polymer structures with ionomer morphologies. Recently, atomistic molecular dynamics (MD) simulations were performed to study the morphologies of precise poly(ethylene-co-acrylic acid) copolymer and ionomer melts. Here, we present the first direct comparisons between scattering profiles, I(q), calculated from these atomistic MD simulations and experimental X-ray data for 11 materials. This set of precise polymers has spacers of exactly 9, 15, or 21 carbons between acid groups and has been partially neutralized with Li, Na, Cs, or Zn. Inmore » these polymers, the simulations at 120 °C reveal ionic aggregates with a range of morphologies, from compact, isolated aggregates (type 1) to branched, stringy aggregates (type 2) to branched, stringy aggregates that percolate through the simulation box (type 3). Excellent agreement is found between the simulated and experimental scattering peak positions across all polymer types and aggregate morphologies. The shape of the amorphous halo in the simulated I(q) profile is in excellent agreement with experimental I(q). We found that the modified hard-sphere scattering model fits both the simulation and experimental I(q) data for type 1 aggregate morphologies, and the aggregate sizes and separations are in agreement. Given the stringy structure in types 2 and 3, we develop a scattering model based on cylindrical aggregates. Both the spherical and cylindrical scattering models fit I(q) data from the polymers with type 2 and 3 aggregates equally well, and the extracted aggregate radii and inter- and intra-aggregate spacings are in agreement between simulation and experiment. Furthermore, these dimensions are consistent with real-space analyses of the atomistic MD simulations. By combining simulations and experiments, the ionomer scattering peak can be associated with the average distance between branches of type 2 or 3 aggregates. Furthermore, this direct comparison of X-ray scattering data to the atomistic MD simulations is a substantive step toward providing a comprehensive, predictive model for ionomer morphology, gives substantial support for this atomistic MD model, and provides new credibility to the presence of stringy, branched, and percolated ionic aggregates in precise ionomer melts.« less

On macroeconomic characteristics of pharmaceutical generics and the potential for manufacturing and consumption under fuzzy conditions.

PubMed

Gascón, Fernando; de la Fuente, David; Puente, Javier; Lozano, Jesús

2007-11-01

The aim of this paper is to develop a methodology that is useful for analyzing, from a macroeconomic perspective, the aggregate demand and the aggregate supply features of the market of pharmaceutical generics. In order to determine the potential consumption and the potential production of pharmaceutical generics in different countries, two fuzzy decision support systems are proposed. Two fuzzy decision support systems, both based on the Mamdani model, were applied in this paper. These systems, generated by Matlab Toolbox 'Fuzzy' (v. 2.0), are able to determine the potential of a country for the manufacturing or the consumption of pharmaceutical generics. The systems make use of three macroeconomic input variables. In an empirical application of our proposed methodology, the potential towards consumption and manufacturing in Holland, Sweden, Italy and Spain has been estimated from national indicators. Cross-country comparisons are made and graphical surfaces are analyzed in order to interpret the results. The main contribution of this work is the development of a methodology that is useful for analyzing aggregate demand and aggregate supply characteristics of pharmaceutical generics. The methodology is valid for carrying out a systematic analysis of the potential generics have at a macrolevel in different countries. The main advantages of the use of fuzzy decision support systems in the context of pharmaceutical generics are the flexibility in the construction of the system, the speed in interpreting the results offered by the inference and surface maps and the ease with which a sensitivity analysis of the potential behavior of a given country may be performed.

Generic solar photovoltaic system dynamic simulation model specification

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

Ellis, Abraham; Behnke, Michael Robert; Elliott, Ryan Thomas

This document is intended to serve as a specification for generic solar photovoltaic (PV) system positive-sequence dynamic models to be implemented by software developers and approved by the WECC MVWG for use in bulk system dynamic simulations in accordance with NERC MOD standards. Two specific dynamic models are included in the scope of this document. The first, a Central Station PV System model, is intended to capture the most important dynamic characteristics of large scale (> 10 MW) PV systems with a central Point of Interconnection (POI) at the transmission level. The second, a Distributed PV System model, is intendedmore » to represent an aggregation of smaller, distribution-connected systems that comprise a portion of a composite load that might be modeled at a transmission load bus.« less

On the origin of the phase-space diffusion limit in (dis)ordered protein aggregation

NASA Astrophysics Data System (ADS)

Gadomski, A.; Siódmiak, J.; Santamaría-Holek, I.

2013-08-01

Derivation of a phase-space diffusion limit (D-L) allows to obtain a useful formula for a characteristic width of the macroion-channeling filter, controlling model (dis)ordered protein aggregations in a non-ideal aqueous solution. The channel’s width is estimated at the order of an inner half-width of the Stern-type double layer circumventing the growing object and depends in turn on an interplay of the local thermal and electrostatic conditions. The interfacial channeling effect manifests at the edge of biomolecular hydration-duration dependent (non)Markovianity of the system. The interface vs. solution aggregation late-time dynamics are discussed in such local (non)isothermal context with the aim to suggest their experimental assessment.

Full reinforcement operators in aggregation techniques.

PubMed

Yager, R R; Rybalov, A

1998-01-01

We introduce the concept of upward reinforcement in aggregation as one in which a collection of high scores can reinforce or corroborate each other to give an even higher score than any of the individual arguments. The concept of downward reinforcement is also introduced as one in which low scores reinforce each other. Our concern is with full reinforcement aggregation operators, those exhibiting both upward and downward reinforcement. It is shown that the t-norm and t-conorm operators are not full reinforcement operators. A class of operators called fixed identity MICA operators are shown to exhibit the property of full reinforcement. We present some families of these operators. We use the fuzzy system modeling technique to provide further examples of these operators.

Soil aggregation and aggregating agents as affected by long term contrasting management of an Anthrosol

NASA Astrophysics Data System (ADS)

Zhang, Shulan; Wang, Renjie; Yang, Xueyun; Sun, Benhua; Li, Qinghui

2016-12-01

Soil aggregation was studied in a 21-year experiment conducted on an Anthrosol. The soil management regimes consisted of cropland abandonment, bare fallow without vegetation and cropping system. The cropping system was combined with the following nutrient management treatments: control (CONTROL, no nutrient input); nitrogen, phosphorus and potassium (NPK); straw plus NPK (SNPK); and manure (M) plus NPK (MNPK). Compared with the CONTROL treatment, the abandonment treatment significantly increased the formation of large soil macroaggregates (>2 mm) and consequently improved the stability of aggregates in the surface soil layer due to enhancement of hyphal length and of soil organic matter content. However, in response to long-term bare fallow treatment aggregate stability was low, as were the levels of aggregating agents. Long term fertilization significantly redistributed macroaggregates; this could be mainly ascribed to soil organic matter contributing to the formation of 0.5-2 mm classes of aggregates and a decrease in the formation of the >2 mm class of aggregates, especially in the MNPK treatment. Overall, hyphae represented a major aggregating agent in both of the systems tested, while soil organic compounds played significantly different roles in stabilizing aggregates in Anthrosol when the cropping system and the soil management regimes were compared.

Soil aggregation and aggregating agents as affected by long term contrasting management of an Anthrosol

PubMed Central

Zhang, Shulan; Wang, Renjie; Yang, Xueyun; Sun, Benhua; Li, Qinghui

2016-01-01

Soil aggregation was studied in a 21-year experiment conducted on an Anthrosol. The soil management regimes consisted of cropland abandonment, bare fallow without vegetation and cropping system. The cropping system was combined with the following nutrient management treatments: control (CONTROL, no nutrient input); nitrogen, phosphorus and potassium (NPK); straw plus NPK (SNPK); and manure (M) plus NPK (MNPK). Compared with the CONTROL treatment, the abandonment treatment significantly increased the formation of large soil macroaggregates (>2 mm) and consequently improved the stability of aggregates in the surface soil layer due to enhancement of hyphal length and of soil organic matter content. However, in response to long-term bare fallow treatment aggregate stability was low, as were the levels of aggregating agents. Long term fertilization significantly redistributed macroaggregates; this could be mainly ascribed to soil organic matter contributing to the formation of 0.5–2 mm classes of aggregates and a decrease in the formation of the >2 mm class of aggregates, especially in the MNPK treatment. Overall, hyphae represented a major aggregating agent in both of the systems tested, while soil organic compounds played significantly different roles in stabilizing aggregates in Anthrosol when the cropping system and the soil management regimes were compared. PMID:27958366

Dynamics of micelle formation from temperature-jump Monte Carlo simulations.

PubMed

Heinzelmann, G; Seide, P; Figueiredo, W

2015-11-01

In the present work we perform temperature jumps in a surfactant solution by means of Monte Carlo simulations, investigating the dynamics of micelle formation. We use a lattice model that allows orientational freedom and hydrogen bonding for solvent molecules, which can make a connection between the different time scales of hydrogen bond formation and amphiphilic aggregation. When we perform a large jump between a high-temperature nonmicellized state and a micellized state, there is strong hysteresis between the heating and cooling processes, the latter showing the formation of premicelles that act as nucleation centers for the assembly of larger aggregates and the former is a drive for dissociation of the existing aggregates. Hysteresis is not seen when we perform a small jump between two states that can be both micellized or nonmicellized. Looking for a more detailed analysis of the hydrophobic effect that drives aggregation, we compare the time evolution of the solvent hydrogen bonds in our system close and far from micelles and how that is affected by the formation of large clusters at low temperatures. We find a strong connection between them, with the total number of hydrogen bonds in the system always increasing when micelles are formed. To gain insights into the mechanism of premicellar formation and growth, we measure the lifetime of micellized amphiphiles as a function of the aggregate size and the stage of the aggregation process. Our results indicate that the premicelles are always unstable, quickly exchanging amphiphiles with the solution due to their low probabilty in equilibrium. Furthermore, we find that the stability of individual surfactants in micelles increases with the aggregate size, with the lifetime of amphiphiles in large micelles being as much as 35 times longer than in the case of the unstable premicellar region.

Aggregation in Network Models for Transportation Planning

DOT National Transportation Integrated Search

1978-02-01

This report documents research performed on techniques of aggregation applied to network models used in transportation planning. The central objective of this research has been to identify, extend, and evaluate methods of aggregation so as to improve...

Evaluating Health Information Systems Using Ontologies.

PubMed

Eivazzadeh, Shahryar; Anderberg, Peter; Larsson, Tobias C; Fricker, Samuel A; Berglund, Johan

2016-06-16

There are several frameworks that attempt to address the challenges of evaluation of health information systems by offering models, methods, and guidelines about what to evaluate, how to evaluate, and how to report the evaluation results. Model-based evaluation frameworks usually suggest universally applicable evaluation aspects but do not consider case-specific aspects. On the other hand, evaluation frameworks that are case specific, by eliciting user requirements, limit their output to the evaluation aspects suggested by the users in the early phases of system development. In addition, these case-specific approaches extract different sets of evaluation aspects from each case, making it challenging to collectively compare, unify, or aggregate the evaluation of a set of heterogeneous health information systems. The aim of this paper is to find a method capable of suggesting evaluation aspects for a set of one or more health information systems-whether similar or heterogeneous-by organizing, unifying, and aggregating the quality attributes extracted from those systems and from an external evaluation framework. On the basis of the available literature in semantic networks and ontologies, a method (called Unified eValuation using Ontology; UVON) was developed that can organize, unify, and aggregate the quality attributes of several health information systems into a tree-style ontology structure. The method was extended to integrate its generated ontology with the evaluation aspects suggested by model-based evaluation frameworks. An approach was developed to extract evaluation aspects from the ontology that also considers evaluation case practicalities such as the maximum number of evaluation aspects to be measured or their required degree of specificity. The method was applied and tested in Future Internet Social and Technological Alignment Research (FI-STAR), a project of 7 cloud-based eHealth applications that were developed and deployed across European Union countries. The relevance of the evaluation aspects created by the UVON method for the FI-STAR project was validated by the corresponding stakeholders of each case. These evaluation aspects were extracted from a UVON-generated ontology structure that reflects both the internally declared required quality attributes in the 7 eHealth applications of the FI-STAR project and the evaluation aspects recommended by the Model for ASsessment of Telemedicine applications (MAST) evaluation framework. The extracted evaluation aspects were used to create questionnaires (for the corresponding patients and health professionals) to evaluate each individual case and the whole of the FI-STAR project. The UVON method can provide a relevant set of evaluation aspects for a heterogeneous set of health information systems by organizing, unifying, and aggregating the quality attributes through ontological structures. Those quality attributes can be either suggested by evaluation models or elicited from the stakeholders of those systems in the form of system requirements. The method continues to be systematic, context sensitive, and relevant across a heterogeneous set of health information systems.

Reducing C-terminal truncation mitigates synucleinopathy and neurodegeneration in a transgenic model of multiple system atrophy

PubMed Central

Bassil, Fares; Fernagut, Pierre-Olivier; Bezard, Erwan; Pruvost, Alain; Leste-Lasserre, Thierry; Hoang, Quyen Q.; Ringe, Dagmar; Petsko, Gregory A.; Meissner, Wassilios G.

2016-01-01

Multiple system atrophy (MSA) is a sporadic orphan neurodegenerative disorder. No treatment is currently available to slow down the aggressive neurodegenerative process, and patients die within a few years after disease onset. The cytopathological hallmark of MSA is the accumulation of alpha-synuclein (α-syn) aggregates in affected oligodendrocytes. Several studies point to α-syn oligomerization and aggregation as a mediator of neurotoxicity in synucleinopathies including MSA. C-terminal truncation by the inflammatory protease caspase-1 has recently been implicated in the mechanisms that promote aggregation of α-syn in vitro and in neuronal cell models of α-syn toxicity. We present here an in vivo proof of concept of the ability of the caspase-1 inhibitor prodrug VX-765 to mitigate α-syn pathology and to mediate neuroprotection in proteolipid protein α-syn (PLP-SYN) mice, a transgenic mouse model of MSA. PLP-SYN and age-matched wild-type mice were treated for a period of 11 wk with VX-765 or placebo. VX-765 prevented motor deficits in PLP-SYN mice compared with placebo controls. More importantly, VX-765 was able to limit the progressive toxicity of α-syn aggregation by reducing its load in the striatum of PLP-SYN mice. Not only did VX-765 reduce truncated α-syn, but it also decreased its monomeric and oligomeric forms. Finally, VX-765 showed neuroprotective effects by preserving tyrosine hydroxylase-positive neurons in the substantia nigra of PLP-SYN mice. In conclusion, our results suggest that VX-765, a drug that was well tolerated in a 6 wk-long phase II trial in patients with epilepsy, is a promising candidate to achieve disease modification in synucleinopathies by limiting α-syn accumulation. PMID:27482103

Evaluating antithrombotic activity of HY023016 on rat hypercoagulable model.

PubMed

Chen, Qiu-Fang; Li, Yun-Zhan; Wang, Xin-Hui; Su, You-Rui; Cui, Shuang; Miao, Ming-Xing; Jiang, Zhen-Zhou; Jiang, Mei-Ling; Jiang, Ai-Dou; Chen, Xiang; Xu, Yun-Gen; Gong, Guo-Qing

2016-06-15

The generation of thrombus is not considered as an isolated progression without other pathologic processes, which may also enhance procoagulant state. The purpose of this study was to assess whether HY023016, a novel dabigatran prodrug and an oral direct thrombin inhibitor, or dabigatran etexilate, another thrombin inhibitor can improve the state of whole blood hypercoagulability in vitro/vivo. By using whole blood flow cytometry we explored the effects of HY023016 and dabigatran etexilate on thrombin and ADP-induced human platelet-leukocyte aggregation generated in vitro. With the method of continuous infusion of thrombin intravenous, we successfully established a rat hypercoagulable model and evaluated the effect of HY023016 or dabigatran etexilate in vivo. HY023016 was able to inhibit thrombin- or ADP-induced platelet P-selectin or CD40L expression, leukocyte CD11b expression and formation of platelet-leukocyte aggregates in dose-dependent manner. Dabigatran etexilate was unable to affect ADP-induced platelet P-selectin or CD40L expression, leukocyte CD11b expression and formation of platelet-leukocyte aggregates. Based on rat hypercoagulable model, dabigatran etexilate could reverse thrombin-induced circulatory system hypercoagulable state in a concentration-dependent manner. Dabigatran etexilate also inhibited electrical stimulation induced formation of arterial thrombus in rat under hypercoagulable state, and extracorporal circulation-induced formation of thrombus in dose-dependent manner. Compared with dabigatran etexilate, HY023016 showed nearly equal or even better antithrombotic activity, regardless of reversing the cycle of rat hypercoagulable state or inhibiting platelet-leukocyte aggregation. In surrmary, HY023016 could effectively improve hypercoagulable state of circulatory system. Copyright © 2016. Published by Elsevier B.V.

Exciton interference revealed by energy dependent exciton transfer rate for ring-structured molecular systems

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

Yan, Yun-An, E-mail: yunan@gznc.edu.cn

2016-01-14

The quantum interference is an intrinsic phenomenon in quantum physics for photon and massive quantum particles. In principle, the quantum interference may also occur with quasi-particles, such as the exciton. In this study, we show how the exciton quantum interference can be significant in aggregates through theoretical simulations with hierarchical equations of motion. The systems under investigation are generalized donor-bridge-acceptor model aggregates with the donor consisting of six homogeneous sites assuming the nearest neighbor coupling. For the models with single-path bridge, the exciton transfer time only shows a weak excitation energy dependence. But models with double-path bridge have a newmore » short transfer time scale and the excitation energy dependence of the exciton transfer time assumes clear peak structure which is detectable with today’s nonlinear spectroscopy. This abnormality is attributed to the exciton quantum interference and the condition for a clear observation in experiment is also explored.« less

A Blood-Brain Barrier (BBB) Disrupter Is Also a Potent α-Synuclein (α-syn) Aggregation Inhibitor

PubMed Central

Shaltiel-Karyo, Ronit; Frenkel-Pinter, Moran; Rockenstein, Edward; Patrick, Christina; Levy-Sakin, Michal; Schiller, Abigail; Egoz-Matia, Nirit; Masliah, Eliezer; Segal, Daniel; Gazit, Ehud

2013-01-01

The development of disease-modifying therapy for Parkinson disease has been a main drug development challenge, including the need to deliver the therapeutic agents to the brain. Here, we examined the ability of mannitol to interfere with the aggregation process of α-synuclein in vitro and in vivo in addition to its blood-brain barrier-disrupting properties. Using in vitro studies, we demonstrated the effect of mannitol on α-synuclein aggregation. Although low concentration of mannitol inhibited the formation of fibrils, high concentration significantly decreased the formation of tetramers and high molecular weight oligomers and shifted the secondary structure of α-synuclein from α-helical to a different structure, suggesting alternative potential pathways for aggregation. When administered to a Parkinson Drosophila model, mannitol dramatically corrected its behavioral defects and reduced the amount of α-synuclein aggregates in the brains of treated flies. In the mThy1-human α-synuclein transgenic mouse model, a decrease in α-synuclein accumulation was detected in several brain regions following treatment, suggesting that mannitol promotes α-synuclein clearance in the cell bodies. It appears that mannitol has a general neuroprotective effect in the transgenic treated mice, which includes the dopaminergic system. We therefore suggest mannitol as a basis for a dual mechanism therapeutic agent for the treatment of Parkinson disease. PMID:23637226

A blood-brain barrier (BBB) disrupter is also a potent α-synuclein (α-syn) aggregation inhibitor: a novel dual mechanism of mannitol for the treatment of Parkinson disease (PD).

PubMed

Shaltiel-Karyo, Ronit; Frenkel-Pinter, Moran; Rockenstein, Edward; Patrick, Christina; Levy-Sakin, Michal; Schiller, Abigail; Egoz-Matia, Nirit; Masliah, Eliezer; Segal, Daniel; Gazit, Ehud

2013-06-14

The development of disease-modifying therapy for Parkinson disease has been a main drug development challenge, including the need to deliver the therapeutic agents to the brain. Here, we examined the ability of mannitol to interfere with the aggregation process of α-synuclein in vitro and in vivo in addition to its blood-brain barrier-disrupting properties. Using in vitro studies, we demonstrated the effect of mannitol on α-synuclein aggregation. Although low concentration of mannitol inhibited the formation of fibrils, high concentration significantly decreased the formation of tetramers and high molecular weight oligomers and shifted the secondary structure of α-synuclein from α-helical to a different structure, suggesting alternative potential pathways for aggregation. When administered to a Parkinson Drosophila model, mannitol dramatically corrected its behavioral defects and reduced the amount of α-synuclein aggregates in the brains of treated flies. In the mThy1-human α-synuclein transgenic mouse model, a decrease in α-synuclein accumulation was detected in several brain regions following treatment, suggesting that mannitol promotes α-synuclein clearance in the cell bodies. It appears that mannitol has a general neuroprotective effect in the transgenic treated mice, which includes the dopaminergic system. We therefore suggest mannitol as a basis for a dual mechanism therapeutic agent for the treatment of Parkinson disease.

CAMELOT: A machine learning approach for coarse-grained simulations of aggregation of block-copolymeric protein sequences

PubMed Central

Ruff, Kiersten M.; Harmon, Tyler S.; Pappu, Rohit V.

2015-01-01

We report the development and deployment of a coarse-graining method that is well suited for computer simulations of aggregation and phase separation of protein sequences with block-copolymeric architectures. Our algorithm, named CAMELOT for Coarse-grained simulations Aided by MachinE Learning Optimization and Training, leverages information from converged all atom simulations that is used to determine a suitable resolution and parameterize the coarse-grained model. To parameterize a system-specific coarse-grained model, we use a combination of Boltzmann inversion, non-linear regression, and a Gaussian process Bayesian optimization approach. The accuracy of the coarse-grained model is demonstrated through direct comparisons to results from all atom simulations. We demonstrate the utility of our coarse-graining approach using the block-copolymeric sequence from the exon 1 encoded sequence of the huntingtin protein. This sequence comprises of 17 residues from the N-terminal end of huntingtin (N17) followed by a polyglutamine (polyQ) tract. Simulations based on the CAMELOT approach are used to show that the adsorption and unfolding of the wild type N17 and its sequence variants on the surface of polyQ tracts engender a patchy colloid like architecture that promotes the formation of linear aggregates. These results provide a plausible explanation for experimental observations, which show that N17 accelerates the formation of linear aggregates in block-copolymeric N17-polyQ sequences. The CAMELOT approach is versatile and is generalizable for simulating the aggregation and phase behavior of a range of block-copolymeric protein sequences. PMID:26723608

Carbon availability structures microbial community composition and function in soil aggregate fractions

NASA Astrophysics Data System (ADS)

Hofmockel, K. S.; Bach, E.; Williams, R.; Howe, A.

2014-12-01

Identifying the microbial metabolic pathways that most strongly influence ecosystem carbon (C) cycling requires a deeper understanding of the availability and accessibility of microbial substrates. A first step towards this goal is characterizing the relationships between microbial community function and soil C chemistry in a field context. For this perspective, soil aggregate fractions can be used as model systems that scale between microbe-substrate interactions and ecosystem C cycling and storage. The present study addresses how physicochemical variation among soil aggregate fractions influences the composition and functional potential of C cycling microbial communities. We report variation across soil aggregates using plot scale biological replicates from biofuel agroecosystems (fertilized, reconstructed, tallgrass prairie). Our results suggest that C and nitrogen (N) chemistry significantly differ among aggregate fractions. This leads to variation in microbial community composition, which was better characterized among aggregates than by using the whole soil. In fact by considering soil aggregation, we were able to characterize almost 2000 more taxa than whole soil alone, resulting in 65% greater community richness. Availability of C and N strongly influenced the composition of microbial communities among soil aggregate fractions. The normalized abundance of microbial functional guilds among aggregate fractions correlated with C and N chemistry, as did functional potential, measured by extracellular enzyme activity. Metagenomic results suggest that soil aggregate fractions select for functionally distinct microbial communities, which may significantly influence decomposition and soil C storage. Our study provides support for the premise that integration of soil aggregate chemistry, especially microaggregates that have greater microbial richness and occur at spatial scales relevant to microbial community functioning, may be necessary to understand the role of microbial communities on terrestrial C and N cycling.

Creep stability of the proposed AIDA mission target 65803 Didymos: I. Discrete cohesionless granular physics model

NASA Astrophysics Data System (ADS)

Zhang, Yun; Richardson, Derek C.; Barnouin, Olivier S.; Maurel, Clara; Michel, Patrick; Schwartz, Stephen R.; Ballouz, Ronald-Louis; Benner, Lance A. M.; Naidu, Shantanu P.; Li, Junfeng

2017-09-01

As the target of the proposed Asteroid Impact & Deflection Assessment (AIDA) mission, the near-Earth binary asteroid 65803 Didymos represents a special class of binary asteroids, those whose primaries are at risk of rotational disruption. To gain a better understanding of these binary systems and to support the AIDA mission, this paper investigates the creep stability of the Didymos primary by representing it as a cohesionless self-gravitating granular aggregate subject to rotational acceleration. To achieve this goal, a soft-sphere discrete element model (SSDEM) capable of simulating granular systems in quasi-static states is implemented and a quasi-static spin-up procedure is carried out. We devise three critical spin limits for the simulated aggregates to indicate their critical states triggered by reshaping and surface shedding, internal structural deformation, and shear failure, respectively. The failure condition and mode, and shear strength of an aggregate can all be inferred from the three critical spin limits. The effects of arrangement and size distribution of constituent particles, bulk density, spin-up path, and interparticle friction are numerically explored. The results show that the shear strength of a spinning self-gravitating aggregate depends strongly on both its internal configuration and material parameters, while its failure mode and mechanism are mainly affected by its internal configuration. Additionally, this study provides some constraints on the possible physical properties of the Didymos primary based on observational data and proposes a plausible formation mechanism for this binary system. With a bulk density consistent with observational uncertainty and close to the maximum density allowed for the asteroid, the Didymos primary in certain configurations can remain geo-statically stable without requiring cohesion.

Effect of homogenisation in formation of thermally induced aggregates in a non- and low- fat milk model system with microparticulated whey proteins.

PubMed

Torres, Isabel Celigueta; Nieto, Gema; Nylander, Tommy; Simonsen, Adam Cohen; Tolkach, Alexander; Ipsen, Richard

2017-05-01

The objective of the research presented in this paper was to investigate how different characteristics of whey protein microparticles (MWP) added to milk as fat replacers influence intermolecular interactions occurring with other milk proteins during homogenisation and heating. These interactions are responsible for the formation of heat-induced aggregates that influence the texture and sensory characteristics of the final product. The formation of heat-induced complexes was studied in non- and low-fat milk model systems, where microparticulated whey protein (MWP) was used as fat replacer. Five MWP types with different particle characteristics were utilised and three heat treatments used: 85 °C for 15 min, 90 °C for 5 min and 95 °C for 2 min. Surface characteristics of the protein aggregates were expressed as the number of available thiol groups and the surface net charge. Intermolecular interactions involved in the formation of protein aggregates were studied by polyacrylamide gel electrophoresis and the final complexes visualised by darkfield microscopy. Homogenisation of non-fat milk systems led to partial adsorption of caseins onto microparticles, independently of the type of microparticle. On the contrary, homogenisation of low-fat milk resulted in preferential adsorption of caseins onto fat globules, rather than onto microparticles. Further heating of the milk, led to the formation of heat induced complexes with different sizes and characteristics depending on the type of MWP and the presence or not of fat. The results highlight the importance of controlling homogenisation and heat processing in yoghurt manufacture in order to induce desired changes in the surface reactivity of the microparticles and thereby promote effective protein interactions.

Continuum-level modelling of cellular adhesion and matrix production in aggregates.

PubMed

Geris, Liesbet; Ashbourn, Joanna M A; Clarke, Tim

2011-05-01

Key regulators in tissue-engineering processes such as cell culture and cellular organisation are the cell-cell and cell-matrix interactions. As mathematical models are increasingly applied to investigate biological phenomena in the biomedical field, it is important, for some applications, that these models incorporate an adequate description of cell adhesion. This study describes the development of a continuum model that represents a cell-in-gel culture system used in bone-tissue engineering, namely that of a cell aggregate embedded in a hydrogel. Cell adhesion is modelled through the use of non-local (integral) terms in the partial differential equations. The simulation results demonstrate that the effects of cell-cell and cell-matrix adhesion are particularly important for the survival and growth of the cell population and the production of extracellular matrix by the cells, concurring with experimental observations in the literature.

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

PubMed

Ebrahimi, Ali; Or, Dani

2016-09-01

Microbial communities inhabiting soil aggregates dynamically adjust their activity and composition in response to variations in hydration and other external conditions. These rapid dynamics shape signatures of biogeochemical activity and gas fluxes emitted from soil profiles. Recent mechanistic models of microbial processes in unsaturated aggregate-like pore networks revealed a highly dynamic interplay between oxic and anoxic microsites jointly shaped by hydration conditions and by aerobic and anaerobic microbial community abundance and self-organization. The spatial extent of anoxic niches (hotspots) flicker in time (hot moments) and support substantial anaerobic microbial activity even in aerated soil profiles. We employed an individual-based model for microbial community life in soil aggregate assemblies represented by 3D angular pore networks. Model aggregates of different sizes were subjected to variable water, carbon and oxygen contents that varied with soil depth as boundary conditions. The study integrates microbial activity within aggregates of different sizes and soil depth to obtain estimates of biogeochemical fluxes from the soil profile. The results quantify impacts of dynamic shifts in microbial community composition on CO2 and N2 O production rates in soil profiles in good agreement with experimental data. Aggregate size distribution and the shape of resource profiles in a soil determine how hydration dynamics shape denitrification and carbon utilization rates. Results from the mechanistic model for microbial activity in aggregates of different sizes were used to derive parameters for analytical representation of soil biogeochemical processes across large scales of practical interest for hydrological and climate models. © 2016 John Wiley & Sons Ltd.

A preference aggregation model and application in AHP-group decision making

NASA Astrophysics Data System (ADS)

Yang, Taiyi; Yang, De; Chao, Xiangrui

2018-04-01

Group decision making process integrate individual preferences to obtain the group preference by applying aggregation rules and preference relations. The two most useful approaches, the aggregation of individual judgements and the aggregation of individual priorities, traditionally are employed in the Analytic Hierarchy Process to deal with group decision making problems. In both cases, it is assumed that the group preference is approximate weighted mathematical expectation of individual judgements and individual priorities. We propose new preference aggregation methods using optimization models in order to obtain group preference which is close to all individual priorities. Some illustrative examples are finally examined to demonstrate proposed models for application.

Integrating plug-in electric vehicles into the electric power system

NASA Astrophysics Data System (ADS)

Wu, Di

This dissertation contributes to our understanding of how plug-in hybrid electric vehicles (PHEVs) and plug-in battery-only electric vehicles (EVs)---collectively termed plug-in electric vehicles (PEVs)---could be successfully integrated with the electric power system. The research addresses issues at a diverse range of levels pertaining to light-duty vehicles, which account for the majority of highway vehicle miles traveled, energy consumed by highway travel modes, and carbon dioxide emissions from on-road sources. Specifically, the following topics are investigated: (i) On-board power electronics topologies for bidirectional vehicle-to-grid and grid-to-vehicle power transfer; (ii) The estimation of the electric energy and power consumption by fleets of light-duty PEVs; (iii) An operating framework for the scheduling and dispatch of electric power by PEV aggregators; (iv) The pricing of electricity by PHEV aggregators and how it affects the decision-making process of a cost-conscious PHEV owner; (v) The impacts on distribution systems from PEVs under aggregator control; (vi) The modeling of light-duty PEVs for long-term energy and transportation planning at a national scale.

Volcanic ash aggregation in the lab - can we mimic natural processes?

NASA Astrophysics Data System (ADS)

Mueller, Sebastian B.; Kueppers, Ulrich; Jacob, Michael; Ayris, Paul; Cimarelli, Corrado; Dingwell, Donald B.; Guttzeit, Melanie; Hess, Kai-Uwe; Walter, Ulrich

2015-04-01

Explosive volcanic eruptions release large amounts of particles into the atmosphere. Volcanic ash, by definition pyroclasts smaller than 2 mm, can be distributed around the globe by prevailing winds. Ash poses hazards to aviation industry by melting in jet turbines, to human health by entering respiration systems and to society by damaging infrastructure. Under certain circumstances, ash particles can cluster together and build ash aggregates. Aggregates range in size from few mm to few cm and may exhibit complex internal stratigraphy. During growth, weight, density and aerodynamic properties change, leading to a significantly different settling behavior compared to individual ash particles. Although ash aggregation has been frequently observed in the geologic record, the physical and chemical mechanisms generating the aggregates remain poorly understood. During several field campaigns, we collected numerous ash aggregates and analyzed their textural, chemical and mechanical properties. Based on this knowledge, we have designed experiments using the ProCell Lab System® of Glatt Ingenieurtechnik GmbH, Germany. In this device, a continuous fluidized bed can be applied on solid particles and simulate gas-particle flow conditions as they would be expected in volcanic plumes or pyroclastic density currents. The geological record and direct observations have shown that both processes are capable of producing ash aggregates. As starting material we used Na-glass beads as an analogue and volcanic ash from Laacher See Volcano, Eifel Volcanic Field, Germany. We define parameters such as grainsize, specific surface area and concentration of the starting material, degree of turbulence, temperature and moisture in the process chamber and the composition of the liquid phase to influence form, size, stability and production rate of aggregates. We were able to experimentally produce round, unstructured ash pellets up to 5mm in diameter. A detailed textural description highlights the strongly different properties of single ash grains and ash aggregates. These experiments aim at experimentally constraining the boundary conditions required for the generation of strong ash aggregates. A better mechanistic understanding will serve for more adequate ash mass distribution modeling.

Resolving the multifaceted mechanisms of the ferric chloride thrombosis model using an interdisciplinary microfluidic approach

PubMed Central

Ciciliano, Jordan C.; Sakurai, Yumiko; Myers, David R.; Fay, Meredith E.; Hechler, Beatrice; Meeks, Shannon; Li, Renhao; Dixon, J. Brandon; Lyon, L. Andrew; Gachet, Christian

2015-01-01

The mechanism of action of the widely used in vivo ferric chloride (FeCl3) thrombosis model remains poorly understood; although endothelial cell denudation is historically cited, a recent study refutes this and implicates a role for erythrocytes. Given the complexity of the in vivo environment, an in vitro reductionist approach is required to systematically isolate and analyze the biochemical, mass transfer, and biological phenomena that govern the system. To this end, we designed an “endothelial-ized” microfluidic device to introduce controlled FeCl3 concentrations to the molecular and cellular components of blood and vasculature. FeCl3 induces aggregation of all plasma proteins and blood cells, independent of endothelial cells, by colloidal chemistry principles: initial aggregation is due to binding of negatively charged blood components to positively charged iron, independent of biological receptor/ligand interactions. Full occlusion of the microchannel proceeds by conventional pathways, and can be attenuated by antithrombotic agents and loss-of-function proteins (as in IL4-R/Iba mice). As elevated FeCl3 concentrations overcome protective effects, the overlap between charge-based aggregation and clotting is a function of mass transfer. Our physiologically relevant in vitro system allows us to discern the multifaceted mechanism of FeCl3-induced thrombosis, thereby reconciling literature findings and cautioning researchers in using the FeCl3 model. PMID:25931587

Proteins aggregation and human diseases

NASA Astrophysics Data System (ADS)

Hu, Chin-Kun

2015-04-01

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

Point-to-point migration functions and gravity model renormalization: approaches to aggregation in spatial interaction modeling.

PubMed

Slater, P B

1985-08-01

Two distinct approaches to assessing the effect of geographic scale on spatial interactions are modeled. In the first, the question of whether a distance deterrence function, which explains interactions for one system of zones, can also succeed on a more aggregate scale, is examined. Only the two-parameter function for which it is found that distances between macrozones are weighted averaged of distances between component zones is satisfactory in this regard. Estimation of continuous (point-to-point) functions--in the form of quadrivariate cubic polynomials--for US interstate migration streams, is then undertaken. Upon numerical integration, these higher order surfaces yield predictions of interzonal and intrazonal movements at any scale of interest. Test of spatial stationarity, isotropy, and symmetry of interstate migration are conducted in this framework.

The effects of vibronic coupling on the photophysics of pi-conjugated oligomers and polymers

NASA Astrophysics Data System (ADS)

Yamagata, Hajime

A theoretical model describing photophysics of pi-conjugated aggregates, such as molecular crystals and polymer thin films, is developed. A Holstein-like Hamiltonian expressed with a multi-particle basis set is used to evaluate absorption and photoluminescence (PL) spectra. An analysis with line strength ratio proves to be a powerful diagnostic tool to obtain additional spectral signatures with which to distinguish H- vs. J-aggregation. For the H-aggregates absorption peak ratio, A 0-0/A 0-1, diminishes as the excitonic coupling increases. Also the PL peak ratio, I 0-0/I 0-1, is zero at T=0K with no disorder and the value increases as temperature and disorder increase. By contrast the J-aggregates show the opposite trends. Furthermore we will show the PL peak ratio provides a direct measurement of the exciton coherence length for a linear J-aggregate and could be expressed as I0-0/I 0-1 = Ncoh/gamma2. We will also show that it is inversely proportional to square root of temperature (T-1/2). Applying our theory to the herringbone style oligoacene molecular crystals, we show the lowest singlet exciton states are highly influenced by charge transfer (CT) states and the well known energetic gap in two polarized absorption spectra, so called Davydov Splitting (DS), is a product of the interaction. We have successfully reproduced the DS for all three oligoacenes without any free parameters. Inspired by the CT contribution in oligoacene crystals, we further develop Wannier-Mott exciton model and apply to disorder-free polydiacetylene (PDA) quantum wires, which have been shown to be extremely emissive. We will show the quantum wire is a J-aggregate and we once again derive the peak ratio and the coherence size relation, I0-0/I 0-1 = kappaNcoh/gamma 2, where kappa is a prefactor close to unity. Typical photophysical properties of polymer pi-stacks such as those occurring in P3HT films are well explained by the simple linear H-aggregate model. However several groups have started seeing more J-like behaviors amongst "improved" (less disordered) polymer films such as increased values of A 0-0/A 0-1 and I 0-0/I 0-1 and higher radiative rates. With the new perception of a single polymer chain being a J-aggregate, we apply our new theory to pi-stack of polymer chains. We call this HJ-aggregate model since the interchain interaction induces H-aggregation. In the study we show a competition between intrachain and interchain interactions that leads to unique photophysical features. The new model is capable of explaining a wide range of polymer systems and most importantly the theory uncovers the mechanism of the improved polymer films; reducing disorder urges increasing intrachain reactions within each chain, thus enhancing more J-like spectral features.

A new model to improve aggregate air traffic demand predictions

DOT National Transportation Integrated Search

2007-08-20

Federal Aviation Administration (FAA) air traffic flow management (TFM) : decision-making is based primarily on a comparison of predictions of traffic demand and : available capacity at various National Airspace System (NAS) elements such as airports...

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

NASA Astrophysics Data System (ADS)

Minton, Allen

2014-08-01

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

Predictive modeling of multicellular structure formation by using Cellular Particle Dynamics simulations

NASA Astrophysics Data System (ADS)

McCune, Matthew; Shafiee, Ashkan; Forgacs, Gabor; Kosztin, Ioan

2014-03-01

Cellular Particle Dynamics (CPD) is an effective computational method for describing and predicting the time evolution of biomechanical relaxation processes of multicellular systems. A typical example is the fusion of spheroidal bioink particles during post bioprinting structure formation. In CPD cells are modeled as an ensemble of cellular particles (CPs) that interact via short-range contact interactions, characterized by an attractive (adhesive interaction) and a repulsive (excluded volume interaction) component. The time evolution of the spatial conformation of the multicellular system is determined by following the trajectories of all CPs through integration of their equations of motion. CPD was successfully applied to describe and predict the fusion of 3D tissue construct involving identical spherical aggregates. Here, we demonstrate that CPD can also predict tissue formation involving uneven spherical aggregates whose volumes decrease during the fusion process. Work supported by NSF [PHY-0957914]. Computer time provided by the University of Missouri Bioinformatics Consortium.

Composing problem solvers for simulation experimentation: a case study on steady state estimation.

PubMed

Leye, Stefan; Ewald, Roland; Uhrmacher, Adelinde M

2014-01-01

Simulation experiments involve various sub-tasks, e.g., parameter optimization, simulation execution, or output data analysis. Many algorithms can be applied to such tasks, but their performance depends on the given problem. Steady state estimation in systems biology is a typical example for this: several estimators have been proposed, each with its own (dis-)advantages. Experimenters, therefore, must choose from the available options, even though they may not be aware of the consequences. To support those users, we propose a general scheme to aggregate such algorithms to so-called synthetic problem solvers, which exploit algorithm differences to improve overall performance. Our approach subsumes various aggregation mechanisms, supports automatic configuration from training data (e.g., via ensemble learning or portfolio selection), and extends the plugin system of the open source modeling and simulation framework James II. We show the benefits of our approach by applying it to steady state estimation for cell-biological models.

Effects of protopine on blood platelet aggregation. III. Effect of protopine on the metabolic system of arachidonic acid in platelets.

PubMed

Shiomoto, H; Matsuda, H; Kubo, M

1991-02-01

The mode of action of protopine on blood platelet aggregation was investigated in the metabolic system of arachidonic acid and in liberation of platelet activating factor using in vitro experimental models. Protopine inhibited the releases of arachidonic acid and platelet activating factor from platelet membrane phospholipids. Protopine also inhibited the conversion of prostaglandin G2 to thromboxane A2, as well as carboxyheptyl imidazole, a thromboxane synthetase inhibitor. These results indicated that protopine functions both as a phospholipase inhibitor and a thromboxane synthetase inhibitor. It is expected that protopine can be applied for treatment of thrombosis as an antiplatelet drug.

Turbulence-induced channel crosstalk in an orbital angular momentum-multiplexed free-space optical link

NASA Astrophysics Data System (ADS)

Anguita, Jaime A.; Neifeld, Mark A.; Vasic, Bane V.

2008-05-01

A multichannel free-space optical (FSO) communication system based on orbital angular momentum (OAM)-carrying beams is studied. We numerically analyze the effects of atmospheric turbulence on the system and find that turbulence induces attenuation and crosstalk among channels. Based on a model in which the constituent channels are binary symmetric and crosstalk is a Gaussian noise source, we find optimal sets of OAM states at each turbulence condition studied and determine the aggregate capacity of the multichannel system at those conditions. OAM-multiplexed FSO systems that operate in the weak turbulence regime are found to offer good performance. We verify that the aggregate capacity decreases as the turbulence increases. A per-channel bit-error rate evaluation is presented to show the uneven effects of crosstalk on the constituent channels.

Evaluating Health Information Systems Using Ontologies

PubMed Central

Anderberg, Peter; Larsson, Tobias C; Fricker, Samuel A; Berglund, Johan

2016-01-01

Background There are several frameworks that attempt to address the challenges of evaluation of health information systems by offering models, methods, and guidelines about what to evaluate, how to evaluate, and how to report the evaluation results. Model-based evaluation frameworks usually suggest universally applicable evaluation aspects but do not consider case-specific aspects. On the other hand, evaluation frameworks that are case specific, by eliciting user requirements, limit their output to the evaluation aspects suggested by the users in the early phases of system development. In addition, these case-specific approaches extract different sets of evaluation aspects from each case, making it challenging to collectively compare, unify, or aggregate the evaluation of a set of heterogeneous health information systems. Objectives The aim of this paper is to find a method capable of suggesting evaluation aspects for a set of one or more health information systems—whether similar or heterogeneous—by organizing, unifying, and aggregating the quality attributes extracted from those systems and from an external evaluation framework. Methods On the basis of the available literature in semantic networks and ontologies, a method (called Unified eValuation using Ontology; UVON) was developed that can organize, unify, and aggregate the quality attributes of several health information systems into a tree-style ontology structure. The method was extended to integrate its generated ontology with the evaluation aspects suggested by model-based evaluation frameworks. An approach was developed to extract evaluation aspects from the ontology that also considers evaluation case practicalities such as the maximum number of evaluation aspects to be measured or their required degree of specificity. The method was applied and tested in Future Internet Social and Technological Alignment Research (FI-STAR), a project of 7 cloud-based eHealth applications that were developed and deployed across European Union countries. Results The relevance of the evaluation aspects created by the UVON method for the FI-STAR project was validated by the corresponding stakeholders of each case. These evaluation aspects were extracted from a UVON-generated ontology structure that reflects both the internally declared required quality attributes in the 7 eHealth applications of the FI-STAR project and the evaluation aspects recommended by the Model for ASsessment of Telemedicine applications (MAST) evaluation framework. The extracted evaluation aspects were used to create questionnaires (for the corresponding patients and health professionals) to evaluate each individual case and the whole of the FI-STAR project. Conclusions The UVON method can provide a relevant set of evaluation aspects for a heterogeneous set of health information systems by organizing, unifying, and aggregating the quality attributes through ontological structures. Those quality attributes can be either suggested by evaluation models or elicited from the stakeholders of those systems in the form of system requirements. The method continues to be systematic, context sensitive, and relevant across a heterogeneous set of health information systems. PMID:27311735

Energy challenges in optical access and aggregation networks.

PubMed

Kilper, Daniel C; Rastegarfar, Houman

2016-03-06

Scalability is a critical issue for access and aggregation networks as they must support the growth in both the size of data capacity demands and the multiplicity of access points. The number of connected devices, the Internet of Things, is growing to the tens of billions. Prevailing communication paradigms are reaching physical limitations that make continued growth problematic. Challenges are emerging in electronic and optical systems and energy increasingly plays a central role. With the spectral efficiency of optical systems approaching the Shannon limit, increasing parallelism is required to support higher capacities. For electronic systems, as the density and speed increases, the total system energy, thermal density and energy per bit are moving into regimes that become impractical to support-for example requiring single-chip processor powers above the 100 W limit common today. We examine communication network scaling and energy use from the Internet core down to the computer processor core and consider implications for optical networks. Optical switching in data centres is identified as a potential model from which scalable access and aggregation networks for the future Internet, with the application of integrated photonic devices and intelligent hybrid networking, will emerge. © 2016 The Author(s).

Red mud flocculation process in alumina production

NASA Astrophysics Data System (ADS)

Fedorova, E. R.; Firsov, A. Yu

2018-05-01

The process of thickening and washing red mud is a gooseneck of alumina production. The existing automated systems of the thickening process control involve stabilizing the parameters of the primary technological circuits of the thickener. The actual direction of scientific research is the creation and improvement of models and systems of the thickening process control by model. But the known models do not fully consider the presence of perturbing effects, in particular the particle size distribution in the feed process, distribution of floccules by size after the aggregation process in the feed barrel. The article is devoted to the basic concepts and terms used in writing the population balance algorithm. The population balance model is implemented in the MatLab environment. The result of the simulation is the particle size distribution after the flocculation process. This model allows one to foreseen the distribution range of floccules after the process of aggregation of red mud in the feed barrel. The mud of Jamaican bauxite was acting as an industrial sample of red mud; Cytec Industries of HX-3000 series with a concentration of 0.5% was acting as a flocculant. When simulating, model constants obtained in a tubular tank in the laboratories of CSIRO (Australia) were used.

Constraining biosphere CO2 flux at regional scale with WRF-CO2 4DVar assimilation system

NASA Astrophysics Data System (ADS)

Zheng, T.

2017-12-01

The WRF-CO2 4DVar assimilation system is updated to include (1) operators for tower based observations (2) chemistry initial and boundary condition in the state vector (3) mechanism for aggregation from simulation model grid to state vector space. The update system is first tested with synthetic data to ensure its accuracy. The system is then used to test regional scale CO2 inversion at MCI (Midcontinental intensive) sites where CO2 mole fraction data were collected at multiple high towers during 2007-2008. The model domain is set to center on Iowa and include 8 towers within its boundary, and it is of 12x12km horizontal grid spacing. First, the relative impacts of the initial and boundary condition are assessed by the system's adjoint model. This is done with 24, 48, 72 hour time span. Second, we assessed the impacts of the transport error, including the misrepresentation of the boundary layer and cumulus activities. Third, we evaluated the different aggregation approach from the native model grid to the control variables (including scaling factors for flux, initial and boundary conditions). Four, we assessed the inversion performance using CO2 observation with different time-interval, and from different tower levels. We also examined the appropriate treatment of the background and observation error covariance in relation with these varying observation data sets.

Modelling the breakup of solid aggregates in turbulent flows

NASA Astrophysics Data System (ADS)

B?Bler, Matth?Us U.; Morbidelli, Massimo; Ba?Dyga, Jerzy

The breakup of solid aggregates suspended in a turbulent flow is considered. The aggregates are assumed to be small with respect to the Kolmogorov length scale and the flow is assumed to be homogeneous. Further, it is assumed that breakup is caused by hydrodynamic stresses acting on the aggregates, and breakup is therefore assumed to follow a first-order kinetic where KB(x) is the breakup rate function and x is the aggregate mass. To model KB(x), it is assumed that an aggregate breaks instantaneously when the surrounding flow is violent enough to create a hydrodynamic stress that exceeds a critical value required to break the aggregate. For aggregates smaller than the Kolmogorov length scale the hydrodynamic stress is determined by the viscosity and local energy dissipation rate whose fluctuations are highly intermittent. Hence, the first-order breakup kinetics are governed by the frequency with which the local energy dissipation rate exceeds a critical value (that corresponds to the critical stress). A multifractal model is adopted to describe the statistical properties of the local energy dissipation rate, and a power-law relation is used to relate the critical energy dissipation rate above which breakup occurs to the aggregate mass. The model leads to an expression for KB(x) that is zero below a limiting aggregate mass, and diverges for x . When simulating the breakup process, the former leads to an asymptotic mean aggregate size whose scaling with the mean energy dissipation rate differs by one third from the scaling expected in a non-fluctuating flow.

Geraniol attenuates α-synuclein expression and neuromuscular impairment through increase dopamine content in MPTP intoxicated mice by dose dependent manner.

PubMed

Rekha, Karamkolly R; Selvakumar, Govindasamy P; Santha, Karunanithi; Inmozhi Sivakamasundari, Ramu

2013-11-01

Parkinson's disease (PD) is characterized by progressive loss of dopamine (DA) neurons in the nigrostriatal system and by the presence of Lewy bodies (LB), proteinaceous inclusions mainly composed of filamentous α-synuclein (α-Syn) aggregates. 1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) was adopted to generate PD models in C57BL/6 mice. In the present study, we investigated the effect of geraniol (GE) against α-Syn aggregation on MPTP induced mouse model of PD in dose dependant manner. When pretreatment of GE improved neuromuscular impairment, TH expressions and decreases α-Syn expressions in MPTP intoxicated PD mice by dose dependent manner. In addition, we confirmed that sub-chronic administration of MPTP in mice leads to permanent neuromuscular deficits and depletion of dopamine and its metabolites. Our results suggest that GE is beneficial for the treatment of PD associated with neuromuscular disability and LB aggregation. Crown Copyright © 2013. Published by Elsevier Inc. All rights reserved.

Peptide multifunctionalized gold nanorods decrease toxicity of β-amyloid peptide in a Caenorhabditis elegans model of Alzheimer's disease.

PubMed

Morales-Zavala, Francisco; Arriagada, Hector; Hassan, Natalia; Velasco, Carolina; Riveros, Ana; Álvarez, Alejandra R; Minniti, Alicia N; Rojas-Silva, Ximena; Muñoz, Luis L; Vasquez, Rodrigo; Rodriguez, Katherine; Sanchez-Navarro, Macarena; Giralt, Ernest; Araya, Eyleen; Aldunate, Rebeca; Kogan, Marcelo J

2017-10-01

The properties of nanometric materials make nanotechnology a promising platform for tackling problems of contemporary medicine. In this work, gold nanorods were synthetized and stabilized with polyethylene glycols and modified with two kinds of peptides. The D1 peptide that recognizes toxic aggregates of Aβ, a peptide involved in Alzheimer's disease (AD); and the Angiopep 2 that can be used to deliver nanorods to the mammalian central nervous system. The nanoconjugates were characterized using absorption spectrophotometry, dynamic light scattering, and transmission electron microscopy, among other techniques. We determined that the nanoconjugate does not affect neuronal viability; it penetrates the cells, and decreases aggregation of Aβ peptide in vitro. We also showed that when we apply our nanosystem to a Caenorhabditis elegans AD model, the toxicity of aggregated Aβ peptide is decreased. This work may contribute to the development of therapies for AD based on metallic nanoparticles. Copyright © 2017 Elsevier Inc. All rights reserved.

Interactions of lysozyme in concentrated electrolyte solutions from dynamic light-scattering measurements.

PubMed Central

Kuehner, D E; Heyer, C; Rämsch, C; Fornefeld, U M; Blanch, H W; Prausnitz, J M

1997-01-01

The diffusion of hen egg-white lysozyme has been studied by dynamic light scattering in aqueous solutions of ammonium sulfate as a function of protein concentration to 30 g/liter. Experiments were conducted under the following conditions: pH 4-7 and ionic strength 0.05-5.0 M. Diffusivity data for ionic strengths up to 0.5 M were interpreted in the context of a two-body interaction model for monomers. From this analysis, two potential-of-mean-force parameters, the effective monomer charge, and the Hamaker constant were obtained. At higher ionic strength, the data were analyzed using a model that describes the diffusion coefficient of a polydisperse system of interacting protein aggregates in terms of an isodesmic, indefinite aggregation equilibrium constant. Data analysis incorporated multicomponent virial and hydrodynamic effects. The resulting equilibrium constants indicate that lysozyme does not aggregate significantly as ionic strength increases, even at salt concentrations near the point of salting-out precipitation. PMID:9414232

No tillage effect on water retention characteristics of soil aggregates in rainfed semiarid conditions.

NASA Astrophysics Data System (ADS)

Blanco-Moure, Nuria; López, M. Victoria; Moret, David

2010-05-01

The evaluation of changes in soil moisture retention characteristics associated to alterations in soil structure is of great interest in tillage studies. Most of these studies have evaluated soil properties in samples of total soil but not in individual aggregates. However, soil behavior at a macroscale level depends on the aggregate properties. A better knowledge of aggregate characteristics, as the water retention properties, will help to explain, for example, the response of soil to tillage, compaction and crop growth, and hence, to plan adequate soil management practices. In this study we determine the water retention curve of soil aggregates of different sizes from a soil under two tillage systems (conventional and no tillage). The study was carried out in a silty clay loam soil of semiarid Aragon (NE Spain). Two tillage systems were compared: no tillage (NT) and conventional tillage with mouldboard plough (CT). Water retention curves (WRC) were determined for soil surface aggregates (0-5 cm) of three different sizes (8-4, 4-2 and 2-1 mm in diameter) by using the TDR-pressure cell (Moret et al. 2008. Soil Till. Res, 100, 114-119). The TDR-pressure cell is a non-destructive method which permits determining WRC with the only one and same soil sample. Thus, the pressure cell was filled with aggregates up to 4 cm height, weighted and wetted to saturation from the bottom. Pressure steps were sequentially applied at -0.5, -1.5, -3, -5, -10, -33, -100, -300 kPa, and water content of each aggregate sample was measured gravimetrically and by TDR 24 h after starting each pressure head step. The volume of the sample within the cell was also determined at this moment in order to obtain the bulk density and thus calculate the volumetric water content. A good relationship was obtained between the volumetric water content calculated from the gravimetric water content and the corresponding values measured by TDR (r2=0.907; p≤0.05). Within the same tillage treatment, no significant differences in WRC were found among soil aggregate sizes. Soil aggregates under CT retained more water at lower pressure heads in all aggregate sizes; in contrast the retention was more effective in those from NT at high pressure level. The extensive structural degradation of the CT aggregates observed during wetting with the consequent decrease in the soil volume within the transparent cell, can help to explain the different behaviour of both soils. The CT aggregates were probably disintegrated by slaking, causing a reduction in water drainage and, therefore, an increase in soil water content at low pressure heads. This idea was also confirmed with the application of the double exponential function proposed by Dexter et al. (2008. Geoderma 173, 243-253). The WRC curves measured by TDR were successfully fitted to the theoretical model proposed by Dexter (r2=0.986; p≤0.05). Thus, the model estimated that the large porosity between aggregates retain slightly more water under CT (0.36-0.39 m3 m-3) than under NT (0.31-0.35 m3 m-3). On the contrary, pores inside the aggregates tend to storage more water in NT (0.16-0.20 m3 m-3vs. 0.13-0.17 m3 m-3 in CT). These results show the suitability of NT to reduce the risk of soil crusting and compaction in agricultural lands of Aragón.

Rate-limiting step analysis of the microbial desulfurization of dibenzothiophene in a model oil system

PubMed Central

Abin-Fuentes, Andres; Leung, James C.; Mohamed, Magdy El-Said; Wang, Daniel IC; Prather, Kristala LJ

2014-01-01

A mechanistic analysis of the various mass transport and kinetic steps in the microbial desulfurization of dibenzothiophene (DBT) by Rhodococcus erythropolis IGTS8 in a model biphasic (oil-water), small-scale system was performed. The biocatalyst was distributed into three populations, free cells in the aqueous phase, cell aggregates and oil-adhered cells, and the fraction of cells in each population was measured. The power input per volume (P/V) and the impeller tip speed (vtip) were identified as key operating parameters in determining whether the system is mass transport controlled or kinetically controlled. Oil-water DBT mass transport was found to not be limiting under the conditions tested. Experimental results at both the 100 mL and 4L (bioreactor) scales suggest that agitation leading to P/V greater than 10,000 W/ m3 and/or vtip greater than 0.67 m/s is sufficient to overcome the major mass transport limitation in the system, which was the diffusion of DBT within the biocatalyst aggregates. PMID:24284557

Initial stages of aggregation in aqueous solutions of ionic liquids: molecular dynamics studies.

PubMed

Bhargava, B L; Klein, Michael L

2009-07-16

Structures formed by 1-alkyl-3-methylimidazolium bromide aqueous solutions with decyl, dodecyl, tetradecyl, and hexadecyl chains have been studied using molecular dynamics (MD) simulations. Spontaneous self-assembly of the amphiphilic cations to form quasi-spherical polydisperse aggregates has been observed in all of the systems, with the size and nature of the aggregates varying with chain length. In all systems, the cation alkyl tails are buried deep inside the aggregates with the polar imidazolium group exposed to exploit the favorable interactions with water. Aggregation numbers steadily increase with the chain length. The hexadecyl aggregates have the most ordered internal structure of the systems studied, and the alkyl chains in these cations show the least number of gauche defects.

47 CFR 10.300 - Alert aggregator. [Reserved

Code of Federal Regulations, 2010 CFR

2010-10-01

... 47 Telecommunication 1 2010-10-01 2010-10-01 false Alert aggregator. [Reserved] 10.300 Section 10.300 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL COMMERCIAL MOBILE ALERT SYSTEM System Architecture § 10.300 Alert aggregator. [Reserved] ...

47 CFR 10.300 - Alert aggregator. [Reserved

Code of Federal Regulations, 2012 CFR

2012-10-01

... 47 Telecommunication 1 2012-10-01 2012-10-01 false Alert aggregator. [Reserved] 10.300 Section 10.300 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL COMMERCIAL MOBILE ALERT SYSTEM System Architecture § 10.300 Alert aggregator. [Reserved] ...

47 CFR 10.300 - Alert aggregator. [Reserved

Code of Federal Regulations, 2011 CFR

2011-10-01

... 47 Telecommunication 1 2011-10-01 2011-10-01 false Alert aggregator. [Reserved] 10.300 Section 10.300 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL COMMERCIAL MOBILE ALERT SYSTEM System Architecture § 10.300 Alert aggregator. [Reserved] ...

Behavioral transitions induced by speed and noise in animal aggregates

NASA Astrophysics Data System (ADS)

Cambui, Dorílson S.; Iliass, Tarras

2017-04-01

In this paper, we used a self-propelled particle model to study the transition between phases of collective behavior observed in animal aggregates. In these systems, transitions occur when individuals shift from one collective state to another. We investigated transitions induced by both the speed and the noise. Statistical quantities that characterize the phase transition driven by noise, such as order parameter, the Binder cumulant and the susceptibility were analyzed, and we used the finite-size scaling theory to estimate the critical exponent ratios β/ν and γ/ν.

LACIE performance predictor final operational capability program description, volume 3

NASA Technical Reports Server (NTRS)

1976-01-01

The requirements and processing logic for the LACIE Error Model program (LEM) are described. This program is an integral part of the Large Area Crop Inventory Experiment (LACIE) system. LEM is that portion of the LPP (LACIE Performance Predictor) which simulates the sample segment classification, strata yield estimation, and production aggregation. LEM controls repetitive Monte Carlo trials based on input error distributions to obtain statistical estimates of the wheat area, yield, and production at different levels of aggregation. LEM interfaces with the rest of the LPP through a set of data files.

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.

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.

Disaggregation and Refinement of System Dynamics Models via Agent-based Modeling

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

Nutaro, James J; Ozmen, Ozgur; Schryver, Jack C

System dynamics models are usually used to investigate aggregate level behavior, but these models can be decomposed into agents that have more realistic individual behaviors. Here we develop a simple model of the STEM workforce to illuminate the impacts that arise from the disaggregation and refinement of system dynamics models via agent-based modeling. Particularly, alteration of Poisson assumptions, adding heterogeneity to decision-making processes of agents, and discrete-time formulation are investigated and their impacts are illustrated. The goal is to demonstrate both the promise and danger of agent-based modeling in the context of a relatively simple model and to delineate themore » importance of modeling decisions that are often overlooked.« less

Micelle-induced depletion interaction and resultant structure in charged colloidal nanoparticle system

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

Ray, D.; Aswal, V. K., E-mail: vkaswal@barc.gov.in; Kohlbrecher, J.

2015-04-28

The evolution of the interaction and the resultant structure in the mixed system of anionic silica nanoparticles (Ludox LS30) and non-ionic surfactant decaethylene glycol monododecylether (C12E10), undergoing phase separation, have been studied using small-angle neutron scattering and dynamic light scattering. The measurements have been carried out for a fixed concentration of nanoparticle (1 wt. %) with varying concentration of surfactant (0 to 1 wt. %), in the absence and presence of an electrolyte. It is found that the micelles of non-ionic surfactant adsorb on the nanoparticle in the absence of electrolyte (form stable system), whereas these micelles become non-adsorbing in the presence of electrolytemore » (show phase separation). The phase separation arises because of C12E10 micelles, causing depletion interaction between nanoparticles and leading to their aggregation. The interaction is modeled by double Yukawa potential accounting for attractive depletion as well as repulsive electrostatic forces. Both the interactions (attraction and repulsion) are found to be of long-range. The nanoparticle aggregation (phase separation) is governed by the increase in the magnitude and the range of the depletion attraction with the increase in the surfactant concentration. The nanoparticle aggregates formed are quite large in size (order of micron) and are characterized by the surface fractal having simple cubic packing of nanoparticles within the aggregates.« less

Evaluation of the effect on aggregate properties of samples extracted using the ignition furnace.

DOT National Transportation Integrated Search

2000-04-01

The Superpave mix design system includes four consensus aggregate properties to ensure aggregate quality: coarse aggregate angularity, flat and elongated particles, fine aggregate angularity, and sand equivalent. In addition to determining these cons...

Nonrotating Convective Self-Aggregation in a Limited Area AGCM

NASA Astrophysics Data System (ADS)

Arnold, Nathan P.; Putman, William M.

2018-04-01

We present nonrotating simulations with the Goddard Earth Observing System (GEOS) atmospheric general circulation model (AGCM) in a square limited area domain over uniform sea surface temperature. As in previous studies, convection spontaneously aggregates into humid clusters, driven by a combination of radiative and moisture-convective feedbacks. The aggregation is qualitatively independent of resolution, with horizontal grid spacing from 3 to 110 km, with both explicit and parameterized deep convection. A budget for the spatial variance of column moist static energy suggests that longwave radiative and surface flux feedbacks help establish aggregation, while the shortwave feedback contributes to its maintenance. Mechanism-denial experiments confirm that aggregation does not occur without interactive longwave radiation. Ice cloud radiative effects help support the humid convecting regions but are not essential for aggregation, while liquid clouds have a negligible effect. Removing the dependence of parameterized convection on tropospheric humidity reduces the intensity of aggregation but does not prevent the formation of dry regions. In domain sizes less than (5,000 km)2, the aggregation forms a single cluster, while larger domains develop multiple clusters. Larger domains initialized with a single large cluster are unable to maintain them, suggesting an upper size limit. Surface wind speed increases with domain size, implying that maintenance of the boundary layer winds may limit cluster size. As cluster size increases, large boundary layer temperature anomalies develop to maintain the surface pressure gradient, leading to an increase in the depth of parameterized convective heating and an increase in gross moist stability.

Data Aggregation Issues in the Application of the MOBILE Emissions Factor Model

DOT National Transportation Integrated Search

1999-09-01

This is one of seven studies exploring processes for developing Intelligent Transportation Systems (ITS) architectures for regional, statewide, or commercial vehicle applications. This study was prepared for a broad-based, non-technical audience. The...

On defense strategies for system of systems using aggregated correlations

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

Rao, Nageswara S.; Imam, Neena; Ma, Chris Y. T.

2017-04-01

We consider a System of Systems (SoS) wherein each system Si, i = 1; 2; ... ;N, is composed of discrete cyber and physical components which can be attacked and reinforced. We characterize the disruptions using aggregate failure correlation functions given by the conditional failure probability of SoS given the failure of an individual system. We formulate the problem of ensuring the survival of SoS as a game between an attacker and a provider, each with a utility function composed of asurvival probability term and a cost term, both expressed in terms of the number of components attacked and reinforced.more » The survival probabilities of systems satisfy simple product-form, first-order differential conditions, which simplify the Nash Equilibrium (NE) conditions. We derive the sensitivity functions that highlight the dependence of SoS survival probability at NE on cost terms, correlation functions, and individual system survival probabilities.We apply these results to a simplified model of distributed cloud computing infrastructure.« less

Rheological and fractal characteristics of unconditioned and conditioned water treatment residuals.

PubMed

Dong, Y J; Wang, Y L; Feng, J

2011-07-01

The rheological and fractal characteristics of raw (unconditioned) and conditioned water treatment residuals (WTRs) were investigated in this study. Variations in morphology, size, and image fractal dimensions of the flocs/aggregates in these WTR systems with increasing polymer doses were analyzed. The results showed that when the raw WTRs were conditioned with the polymer CZ8688, the optimum polymer dosage was observed at 24 kg/ton dry sludge. The average diameter of irregularly shaped flocs/aggregates in the WTR suspensions increased from 42.54 μm to several hundred micrometers with increasing polymer doses. Furthermore, the aggregates in the conditioned WTR system displayed boundary/surface and mass fractals. At the optimum polymer dosage, the aggregates formed had a volumetric average diameter of about 820.7 μm, with a one-dimensional fractal dimension of 1.01 and a mass fractal dimension of 2.74 on the basis of the image analysis. Rheological tests indicated that the conditioned WTRs at the optimum polymer dosage showed higher levels of shear-thinning behavior than the raw WTRs. Variations in the limiting viscosity (η(∞)) of conditioned WTRs with sludge content could be described by a linear equation, which were different from the often-observed empirical exponential relationship for most municipal sludge. With increasing temperature, the η(∞) of the raw WTRs decreased more rapidly than that of the raw WTRs. Good fitting results for the relationships between lgη(∞)∼T using the Arrhenius equation indicate that the WTRs had a much higher activation energy for viscosity of about 17.86-26.91 J/mol compared with that of anaerobic granular sludge (2.51 J/mol) (Mu and Yu, 2006). In addition, the Bingham plastic model adequately described the rheological behavior of the conditioned WTRs, whereas the rheology of the raw WTRs fit the Herschel-Bulkley model well at only certain sludge contents. Considering the good power-law relationships between the limiting viscosity and sludge content of the conditioned WTRs, their mass fractal dimensions were calculated through the models proposed by Shih et al. (1990), which were 2.48 for these conditioned WTR aggregates. The results demonstrate that conditioned WTRs behave like weak-link flocs/aggregates. Copyright © 2011 Elsevier Ltd. All rights reserved.

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

PubMed

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

2016-12-15

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

Direct comparisons of X-ray scattering and atomistic molecular dynamics simulations for precise acid copolymers and ionomers

DOE PAGES

Buitrago, C. Francisco; Bolintineanu, Dan; Seitz, Michelle E.; ...

2015-02-09

Designing acid- and ion-containing polymers for optimal proton, ion, or water transport would benefit profoundly from predictive models or theories that relate polymer structures with ionomer morphologies. Recently, atomistic molecular dynamics (MD) simulations were performed to study the morphologies of precise poly(ethylene-co-acrylic acid) copolymer and ionomer melts. Here, we present the first direct comparisons between scattering profiles, I(q), calculated from these atomistic MD simulations and experimental X-ray data for 11 materials. This set of precise polymers has spacers of exactly 9, 15, or 21 carbons between acid groups and has been partially neutralized with Li, Na, Cs, or Zn. Inmore » these polymers, the simulations at 120 °C reveal ionic aggregates with a range of morphologies, from compact, isolated aggregates (type 1) to branched, stringy aggregates (type 2) to branched, stringy aggregates that percolate through the simulation box (type 3). Excellent agreement is found between the simulated and experimental scattering peak positions across all polymer types and aggregate morphologies. The shape of the amorphous halo in the simulated I(q) profile is in excellent agreement with experimental I(q). We found that the modified hard-sphere scattering model fits both the simulation and experimental I(q) data for type 1 aggregate morphologies, and the aggregate sizes and separations are in agreement. Given the stringy structure in types 2 and 3, we develop a scattering model based on cylindrical aggregates. Both the spherical and cylindrical scattering models fit I(q) data from the polymers with type 2 and 3 aggregates equally well, and the extracted aggregate radii and inter- and intra-aggregate spacings are in agreement between simulation and experiment. Furthermore, these dimensions are consistent with real-space analyses of the atomistic MD simulations. By combining simulations and experiments, the ionomer scattering peak can be associated with the average distance between branches of type 2 or 3 aggregates. Furthermore, this direct comparison of X-ray scattering data to the atomistic MD simulations is a substantive step toward providing a comprehensive, predictive model for ionomer morphology, gives substantial support for this atomistic MD model, and provides new credibility to the presence of stringy, branched, and percolated ionic aggregates in precise ionomer melts.« less

Plant-soil-microbe interactions regulating soil C storage

NASA Astrophysics Data System (ADS)

Hofmockel, K. S.; Bach, E.; Williams, R.

2016-12-01

Integration across disciplines is required to identify the emergent microbial scale properties that regulate the release or occlusion of plant inputs in soil organic matter. To investigate how micro-scale processes influence soil carbon cycling, we measured microbial community composition and activity within soil aggregates monthly over two growing seasons of a long-term bioenergy field experiment. Using a biologically sensitive sieving technique, soil aggregates were isolated and microbial community activity and composition were measured. This aggregate approach revealed biogeochemical processes regulating C cycling that are not detected using whole soil approaches. Soil aggregation influenced microbe-substrate interactions, where diversified perennial grassland systems supported greater aggregation and reduced severity of aggregate turnover compared to corn systems. Aggregate turnover and concurrent increases in activity resulted in greater microbial biomass and physical protection of soil organic matter in prairie systems, especially fertilized prairies. Fertilized prairie enhanced microbial biomass, enzyme activity, and soil aggregation despite greater root biomass in unfertilized prairie. Independent of ecosystem or sampling date, N-acetyl-glucosaminidase activity and Nitrospirae abundance was greatest in large macroaggregates (>2000 µm), which harbored the highest C:N; cellobiohydrolase activity and Acidobacteria abundance was greatest in microaggregates (<250 µm) which had the lowest C:N. Aggregate fractions differed in microbial community composition (bacteria, archaea, and fungi) and potential enzyme activity, independent of cropping system. Microaggregates harbored significantly greater microbial diversity and richness across all bioenergy cropping systems. Together these results suggest that by mediating access to substrates, soil structure (aggregates) can influence the microbial community composition and extracellular enzyme activity to regulate ecosystem scale decomposition of soil organic matter.

Structure-activity relationships for a series of compounds that inhibit aggregation of the Alzheimer's peptide, Aβ42.

PubMed

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

2014-11-01

Inhibiting aggregation of the amyloid-beta (Aβ) peptide may be an effective strategy for combating Alzheimer's disease. As the high-resolution structure of the toxic Aβ aggregate is unknown, rational design of small molecule inhibitors is not possible, and inhibitors are best isolated by high-throughput screening. We applied high-throughput screening to a collection of 65,000 compounds to identify compound D737 as an inhibitor of Aβ aggregation. D737 diminished the formation of oligomers and fibrils, and reduced Aβ42-induced cytotoxicity. Most importantly, D737 increased the life span and locomotive ability of transgenic flies in a Drosophila melanogaster model of Alzheimer's disease (J Biol Chem, 287, 2012, 38992). To explore the chemical features that make D737 an effective inhibitor of Aβ42 aggregation and toxicity, we tested a small collection of eleven analogues of D737. Overall, the ability of a compound to inhibit Aβ aggregation was a good predictor of its efficacy in prolonging the life span and locomotive ability of transgenic flies expressing human Aβ42 in the central nervous system. Two compounds (D744 and D830) with fluorine substitutions on an aromatic ring were effective inhibitors of Aβ42 aggregation and increased the longevity of transgenic flies beyond that observed for the parent compound, D737. © 2014 John Wiley & Sons A/S.

Aggregated Recombinant Human Interferon Beta Induces Antibodies but No Memory in Immune-Tolerant Transgenic Mice

PubMed Central

Sauerborn, Melody; Gilli, Francesca; Brinks, Vera; Schellekens, Huub; Jiskoot, Wim

2010-01-01

ABSTRACT Purpose To study the influence of protein aggregation on the immunogenicity of recombinant human interferon beta (rhIFNβ) in wild-type mice and transgenic, immune-tolerant mice, and to evaluate the induction of immunological memory. Methods RhIFNβ-1b and three rhIFNβ-1a preparations with different aggregate levels were injected intraperitoneally in mice 15× during 3 weeks, and the mice were rechallenged with rhIFNβ-1a. The formation of binding (BABs) and neutralizing antibodies (NABs) was monitored. Results Bulk rhIFNβ-1a contained large, mainly non-covalent aggregates and stressed rhIFNβ-1a mainly covalent, homogeneous (ca. 100 nm) aggregates. Reformulated rhIFNβ-1a was essentially aggregate-free. All products induced BABs and NABs in wild-type mice. Immunogenicity in the transgenic mice was product dependent. RhIFNβ-1b showed the highest and reformulated rhIFNβ-1a the lowest immunogenicity. In contrast with wild-type mice, transgenic mice did not show NABs, nor did they respond to the rechallenge. Conclusions The immunogenicity of the products in transgenic mice, unlike in wild-type mice, varied. In the transgenic mice, neither NABs nor immunological memory developed. The immunogenicity of rhIFNβ in a model reflecting the human immune system depends on the presence and the characteristics of aggregates. PMID:20499141

MODELING AGGREGATE CHLORPYRIFOS EXPOSURE AND DOSE TO CHILDREN

EPA Science Inventory

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

Biochemical nature of Russell Bodies

PubMed Central

Francesca Mossuto, Maria; Ami, Diletta; Anelli, Tiziana; Fagioli, Claudio; Maria Doglia, Silvia; Sitia, Roberto

2015-01-01

Professional secretory cells produce and release abundant proteins. Particularly in case of mutations and/or insufficient chaperoning, these can aggregate and become toxic within or amongst cells. Immunoglobulins (Ig) are no exception. In the extracellular space, certain Ig-L chains form fibrils causing systemic amyloidosis. On the other hand, Ig variants lacking the first constant domain condense in dilated cisternae of the early secretory compartment, called Russell Bodies (RB), frequently observed in plasma cell dyscrasias, autoimmune diseases and chronic infections. RB biogenesis can be recapitulated in lymphoid and non-lymphoid cells by expressing mutant Ig-μ, providing powerful models to investigate the pathophysiology of endoplasmic reticulum storage disorders. Here we analyze the aggregation propensity and the biochemical features of the intra- and extra-cellular Ig deposits in human cells, revealing β-aggregated features for RB. PMID:26223695

Biochemical nature of Russell Bodies.

PubMed

Mossuto, Maria Francesca; Ami, Diletta; Anelli, Tiziana; Fagioli, Claudio; Doglia, Silvia Maria; Sitia, Roberto

2015-07-30

Professional secretory cells produce and release abundant proteins. Particularly in case of mutations and/or insufficient chaperoning, these can aggregate and become toxic within or amongst cells. Immunoglobulins (Ig) are no exception. In the extracellular space, certain Ig-L chains form fibrils causing systemic amyloidosis. On the other hand, Ig variants lacking the first constant domain condense in dilated cisternae of the early secretory compartment, called Russell Bodies (RB), frequently observed in plasma cell dyscrasias, autoimmune diseases and chronic infections. RB biogenesis can be recapitulated in lymphoid and non-lymphoid cells by expressing mutant Ig-μ, providing powerful models to investigate the pathophysiology of endoplasmic reticulum storage disorders. Here we analyze the aggregation propensity and the biochemical features of the intra- and extra-cellular Ig deposits in human cells, revealing β-aggregated features for RB.

IEEE 802.15.4 Frame Aggregation Enhancement to Provide High Performance in Life-Critical Patient Monitoring Systems

PubMed Central

Akbar, Muhammad Sajjad; Yu, Hongnian; Cang, Shuang

2017-01-01

In wireless body area sensor networks (WBASNs), Quality of Service (QoS) provision for patient monitoring systems in terms of time-critical deadlines, high throughput and energy efficiency is a challenging task. The periodic data from these systems generates a large number of small packets in a short time period which needs an efficient channel access mechanism. The IEEE 802.15.4 standard is recommended for low power devices and widely used for many wireless sensor networks applications. It provides a hybrid channel access mechanism at the Media Access Control (MAC) layer which plays a key role in overall successful transmission in WBASNs. There are many WBASN’s MAC protocols that use this hybrid channel access mechanism in variety of sensor applications. However, these protocols are less efficient for patient monitoring systems where life critical data requires limited delay, high throughput and energy efficient communication simultaneously. To address these issues, this paper proposes a frame aggregation scheme by using the aggregated-MAC protocol data unit (A-MPDU) which works with the IEEE 802.15.4 MAC layer. To implement the scheme accurately, we develop a traffic patterns analysis mechanism to understand the requirements of the sensor nodes in patient monitoring systems, then model the channel access to find the performance gap on the basis of obtained requirements, finally propose the design based on the needs of patient monitoring systems. The mechanism is initially verified using numerical modelling and then simulation is conducted using NS2.29, Castalia 3.2 and OMNeT++. The proposed scheme provides the optimal performance considering the required QoS. PMID:28134853

IEEE 802.15.4 Frame Aggregation Enhancement to Provide High Performance in Life-Critical Patient Monitoring Systems.

PubMed

Akbar, Muhammad Sajjad; Yu, Hongnian; Cang, Shuang

2017-01-28

In wireless body area sensor networks (WBASNs), Quality of Service (QoS) provision for patient monitoring systems in terms of time-critical deadlines, high throughput and energy efficiency is a challenging task. The periodic data from these systems generates a large number of small packets in a short time period which needs an efficient channel access mechanism. The IEEE 802.15.4 standard is recommended for low power devices and widely used for many wireless sensor networks applications. It provides a hybrid channel access mechanism at the Media Access Control (MAC) layer which plays a key role in overall successful transmission in WBASNs. There are many WBASN's MAC protocols that use this hybrid channel access mechanism in variety of sensor applications. However, these protocols are less efficient for patient monitoring systems where life critical data requires limited delay, high throughput and energy efficient communication simultaneously. To address these issues, this paper proposes a frame aggregation scheme by using the aggregated-MAC protocol data unit (A-MPDU) which works with the IEEE 802.15.4 MAC layer. To implement the scheme accurately, we develop a traffic patterns analysis mechanism to understand the requirements of the sensor nodes in patient monitoring systems, then model the channel access to find the performance gap on the basis of obtained requirements, finally propose the design based on the needs of patient monitoring systems. The mechanism is initially verified using numerical modelling and then simulation is conducted using NS2.29, Castalia 3.2 and OMNeT++. The proposed scheme provides the optimal performance considering the required QoS.

Functional Evaluation and Characterization of a Newly Developed Silicone Oil-Free Prefillable Syringe System

PubMed Central

Yoshino, Keisuke; Nakamura, Koji; Yamashita, Arisa; Abe, Yoshihiko; Iwasaki, Kazuhiro; Kanazawa, Yukie; Funatsu, Kaori; Yoshimoto, Tsuyoshi; Suzuki, Shigeru

2014-01-01

The functionality of a newly developed silicone oil-free (SOF) syringe system, of which the plunger stopper is coated by a novel coating technology (i-coating™), was assessed. By scanning electron microscopy observations and other analysis, it was confirmed that the plunger stopper surface was uniformly covered with the designed chemical composition. A microflow imaging analysis showed that the SOF system drastically reduced both silicone oil (SO) doplets and oil-induced aggregations in a model protein formulation, whereas a large number of subvisible particles and protein aggregations were formed when a SO system was used. Satisfactory container closure integrity (CCI) was confirmed by means of dye and microorganism penetration studies. Furthermore, no significant difference between the break loose and gliding forces was observed in the former, and stability studies revealed that the SOF system could perfectly show the aging independence in break loose force observed in the SO system. The results suggest that the introduced novel SOF system has a great potential and represents an alternative that can achieve very low subvisible particles, secure CCI, and the absence of a break loose force. In particular, no risk of SO-induced aggregation can bring additional value in the highly sensitive biotech drug market. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association J Pharm Sci 103:1520–1528, 2014 PMID:24643749

Non-Linear Dynamics of Saturn’s Rings

NASA Astrophysics Data System (ADS)

Esposito, Larry W.

2015-11-01

Non-linear processes can explain why Saturn’s rings are so active and dynamic. Ring systems differ from simple linear systems in two significant ways: 1. They are systems of granular material: where particle-to-particle collisions dominate; thus a kinetic, not a fluid description needed. We find that stresses are strikingly inhomogeneous and fluctuations are large compared to equilibrium. 2. They are strongly forced by resonances: which drive a non-linear response, pushing the system across thresholds that lead to persistent states.Some of this non-linearity is captured in a simple Predator-Prey Model: Periodic forcing from the moon causes streamline crowding; This damps the relative velocity, and allows aggregates to grow. About a quarter phase later, the aggregates stir the system to higher relative velocity and the limit cycle repeats each orbit.Summary of Halo Results: A predator-prey model for ring dynamics produces transient structures like ‘straw’ that can explain the halo structure and spectroscopy: This requires energetic collisions (v ≈ 10m/sec, with throw distances about 200km, implying objects of scale R ≈ 20km).Transform to Duffing Eqn : With the coordinate transformation, z = M2/3, the Predator-Prey equations can be combined to form a single second-order differential equation with harmonic resonance forcing.Ring dynamics and history implications: Moon-triggered clumping at perturbed regions in Saturn’s rings creates both high velocity dispersion and large aggregates at these distances, explaining both small and large particles observed there. We calculate the stationary size distribution using a cell-to-cell mapping procedure that converts the phase-plane trajectories to a Markov chain. Approximating the Markov chain as an asymmetric random walk with reflecting boundaries allows us to determine the power law index from results of numerical simulations in the tidal environment surrounding Saturn. Aggregates can explain many dynamic aspects of the rings and can renew rings by shielding and recycling the material within them, depending on how long the mass is sequestered. We can ask: Are Saturn’s rings a chaotic non-linear driven system?

A549 lung epithelial cells grown as three-dimensional aggregates: alternative tissue culture model for Pseudomonas aeruginosa pathogenesis.

PubMed

Carterson, A J; Höner zu Bentrup, K; Ott, C M; Clarke, M S; Pierson, D L; Vanderburg, C R; Buchanan, K L; Nickerson, C A; Schurr, M J

2005-02-01

A three-dimensional (3-D) lung aggregate model was developed from A549 human lung epithelial cells by using a rotating-wall vessel bioreactor to study the interactions between Pseudomonas aeruginosa and lung epithelial cells. The suitability of the 3-D aggregates as an infection model was examined by immunohistochemistry, adherence and invasion assays, scanning electron microscopy, and cytokine and mucoglycoprotein production. Immunohistochemical characterization of the 3-D A549 aggregates showed increased expression of epithelial cell-specific markers and decreased expression of cancer-specific markers compared to their monolayer counterparts. Immunohistochemistry of junctional markers on A549 3-D cells revealed that these cells formed tight junctions and polarity, in contrast to the cells grown as monolayers. Additionally, the 3-D aggregates stained positively for the production of mucoglycoprotein while the monolayers showed no indication of staining. Moreover, mucin-specific antibodies to MUC1 and MUC5A bound with greater affinity to 3-D aggregates than to the monolayers. P. aeruginosa attached to and penetrated A549 monolayers significantly more than the same cells grown as 3-D aggregates. Scanning electron microscopy of A549 cells grown as monolayers and 3-D aggregates infected with P. aeruginosa showed that monolayers detached from the surface of the culture plate postinfection, in contrast to the 3-D aggregates, which remained attached to the microcarrier beads. In response to infection, proinflammatory cytokine levels were elevated for the 3-D A549 aggregates compared to monolayer controls. These findings suggest that A549 lung cells grown as 3-D aggregates may represent a more physiologically relevant model to examine the interactions between P. aeruginosa and the lung epithelium during infection.

Structural characterization of astaxanthin aggregates as revealed by analysis and simulation of optical spectra

NASA Astrophysics Data System (ADS)

Lu, Liping; Hu, Taoping; Xu, Zhigang

2017-10-01

Carotenoids can self-assemble in hydrated polar solvents to form J- or H-type aggregates, inducing dramatic changes in photophysical properties. Here, we measured absorption and emission spectra of astaxanthin in ethanol-water solution using ultraviolet-visible and fluorescence spectrometers. Two types of aggregates were distinguished in mixed solution at different water contents by absorption spectra. After addition of water, all probed samples immediately formed H-aggregates with maximum blue shift of 31 nm. In addition, J-aggregate was formed in 1:3 ethanol-water solution measured after an hour. Based on Frenkel exciton model, we calculated linear absorption and emission spectra of these aggregates to describe aggregate structures in solution. For astaxanthin, experimental results agreed well with the fitted spectra of H-aggregate models, which consisted of tightly packed stacks of individual molecules, including hexamers, trimers, and dimers. Transition moment of single astaxanthin in ethanol was obtained by Gaussian 09 program package to estimate the distance between molecules in aggregates. Intermolecular distance of astaxanthin aggregates ranges from 0.45 nm to 0.9 nm. Fluorescence analysis showed that between subbands, strong exciton coupling induced rapid relaxation of H-aggregates. This coupling generated larger Stokes shift than monomers and J-aggregates.

The Aggregate Demand Curve and Its Proper Interpretation.

ERIC Educational Resources Information Center

Hansen, Richard B.; And Others

1985-01-01

Textbook authors, presenting aggregate demand-aggregate supply (AD-AS), are admonished to set their houses in order. The traditional Keynesian cross model should continue to be used as a pedagogical device. A version superior to the AD-AS models found in many texts is presented. (Author/RM)

A settling curve modeling method for quantitative description of the dispersion stability of carbon nanotubes in aquatic environments.

PubMed

Zhou, Lixia; Zhu, Dunxue; Zhang, Shujuan; Pan, Bingcai

2015-03-01

Understanding the aggregation and deposition behavior of carbon nanotubes (CNTs) is of great significance in terms of their fate and transport in the environment. Attachment efficiency is a widely used index for well-dispersed CNT solutions. However, in natural waters, CNTs are usually heterogeneous in particle size. The attachment efficiency method is not applicable to such systems. Describing the dispersion stability of CNTs in natural aquatic systems is still a challenge. In this work, a settling curve modeling (SCM) method was developed for the description of the aggregation and deposition behavior of CNTs in aqueous solutions. The effects of water chemistry (natural organic matter, pH, and ionic strength) on the aggregation and deposition behavior of pristine and surface-functionalized multi-walled carbon nanotubes (MWCNTs) were systematically studied to evaluate the reliability of the SCM method. The results showed that, as compared to particle size and optical density, the centrifugal sedimentation rate constant (ks) from the settling curve profile is a practical, useful and reliable index for the description of heterogeneous CNT suspensions. The SCM method was successfully applied to MWCNT in three natural waters. The constituents in water, especially organic matter, determine the dispersion stability of MWCNTs in natural water bodies. Copyright © 2015. Published by Elsevier B.V.

Maillard-reaction-induced modification and aggregation of proteins and hardening of texture in protein bar model systems.

PubMed

Zhou, Peng; Guo, Mufan; Liu, Dasong; Liu, Xiaoming; Labuza, Teodore P

2013-03-01

The hardening of high-protein bars causes problems in their acceptability to consumers. The objective of this study was to determine the progress of the Maillard reaction in model systems of high-protein nutritional bars containing reducing sugars, and to illustrate the influences of the Maillard reaction on the modification and aggregation of proteins and the hardening of bar matrices during storage. The progress of the Maillard reaction, glycation, and aggregation of proteins, and textural changes in bar matrices were investigated during storage at 25, 35, and 45 °C. The initial development of the Maillard reaction caused little changes in hardness; however, further storage resulted in dramatic modification of protein with formation of high-molecular-weight polymers, resulting in the hardening in texture. The replacement of reducing sugars with nonreducing ingredients such as sugar alcohols in the formula minimized the changes in texture. The hardening of high-protein bars causes problems in their acceptability to consumers. Maillard reaction is one of the mechanisms contributing to the hardening of bar matrix, particularly for the late stage of storage. The replacement of reducing sugars with nonreducing ingredients such as sugar alcohols in the formula will minimize the changes in texture. © 2013 Institute of Food Technologists®

A Materials Approach to Collective Behavior

NASA Astrophysics Data System (ADS)

Ouellette, Nicholas

Aggregations of social animals, such as flocks of birds, schools of fish, or swarms of insects, are beautiful, natural examples of self-organized behavior far from equilibrium. Understanding these systems, however, has proved to be quite challenging. Determining the rules of interaction from empirical measurements of animals is a difficult inverse problem. Thus, researchers tend to focus on the macroscopic behavior of the group instead. Because so many of these systems display large-scale ordered patterns, it has become the norm in modeling animal aggregations to focus on this order. Large-scale patterns alone, however, are not sufficient information to characterize all the dynamics of animal aggregations, and do not provide stringent enough conditions to benchmark models. Instead, I will argue that we should borrow ideas from materials characterization to describe the macroscopic state of an animal group in terms of its response to external stimuli. I will illustrate these ideas with recent experiments on mating swarms of the non-biting midge Chironomus riparius, where we have developed methods to apply controlled perturbations and measure the detailed swarm response. Our results allow us to begin to describe swarms in terms of state variables and response functions, bringing them into the purview of theories of active matter. These results also point towards new, more detailed ways of characterizing and hopefully comparing collective behavior in animal groups.

Effects of osmolytes on Pelodiscus sinensis creatine kinase: a study on thermal denaturation and aggregation.

PubMed

Wang, Wei; Lee, Jinhyuk; Jin, Qin-Xin; Fang, Nai-Yun; Si, Yue-Xiu; Yin, Shang-Jun; Qian, Guo-Ying; Park, Yong-Doo

2013-09-01

The protective effect of osmolytes on the thermal denaturation and aggregation of Pelodiscus sinensis muscle creatine kinase (PSCK) was investigated by a combination of spectroscopic methods and thermodynamic analysis. Our results demonstrated that the addition of osmolytes, such as glycine and proline, could prevent thermal denaturation and aggregation of PSCK in a concentration-dependent manner. When the concentration of glycine and proline increased in the denatured system, the relative activation was significantly enhanced; meanwhile, the aggregation of PSCK during thermal denaturation was decreased. Spectrofluorometer results showed that glycine and proline significantly decreased the tertiary structural changes of PSCK and that thermal denaturation directly induced PSCK aggregation. In addition, we also built the 3D structure of PSCK and osmolytes by homology models. The results of computational docking simulations showed that the docking energy was relatively low and that the clustering groups were spread to the surface of PSCK, indicating that osmolytes directly protect the surface of the protein. P. sinensis are poikilothermic and quite sensitive to the change of ambient temperature; however, there were few studies on the thermal denaturation of reptile CK. Our study provides important insight into the protective effects of osmolytes on thermal denaturation and aggregation of PSCK. Copyright © 2013 Elsevier B.V. All rights reserved.

On the importance of considering heterogeneity in witnesses' competence levels when reconstructing crimes from multiple witness testimonies.

PubMed

Waubert de Puiseau, Berenike; Greving, Sven; Aßfalg, André; Musch, Jochen

2017-09-01

Aggregating information across multiple testimonies may improve crime reconstructions. However, different aggregation methods are available, and research on which method is best suited for aggregating multiple observations is lacking. Furthermore, little is known about how variance in the accuracy of individual testimonies impacts the performance of competing aggregation procedures. We investigated the superiority of aggregation-based crime reconstructions involving multiple individual testimonies and whether this superiority varied as a function of the number of witnesses and the degree of heterogeneity in witnesses' ability to accurately report their observations. Moreover, we examined whether heterogeneity in competence levels differentially affected the relative accuracy of two aggregation procedures: a simple majority rule, which ignores individual differences, and the more complex general Condorcet model (Romney et al., Am Anthropol 88(2):313-338, 1986; Batchelder and Romney, Psychometrika 53(1):71-92, 1988), which takes into account differences in competence between individuals. 121 participants viewed a simulated crime and subsequently answered 128 true/false questions about the crime. We experimentally generated groups of witnesses with homogeneous or heterogeneous competences. Both the majority rule and the general Condorcet model provided more accurate reconstructions of the observed crime than individual testimonies. The superiority of aggregated crime reconstructions involving multiple individual testimonies increased with an increasing number of witnesses. Crime reconstructions were most accurate when competences were heterogeneous and aggregation was based on the general Condorcet model. We argue that a formal aggregation should be considered more often when eyewitness testimonies have to be assessed and that the general Condorcet model provides a good framework for such aggregations.

Estimating Bulk Entrainment With Unaggregated and Aggregated Convection

NASA Astrophysics Data System (ADS)

Becker, Tobias; Bretherton, Christopher S.; Hohenegger, Cathy; Stevens, Bjorn

2018-01-01

To investigate how entrainment is influenced by convective organization, we use the ICON (ICOsahedral Nonhydrostatic) model in a radiative-convective equilibrium framework, with a 1 km spatial grid mesh covering a 600 by 520 km2 domain. We analyze two simulations, with unaggregated and aggregated convection, and find that, in the lower free troposphere, the bulk entrainment rate increases when convection aggregates. The increase of entrainment rate with aggregation is caused by a strong increase of turbulence in the close environment of updrafts, masking other effects like the increase of updraft size and of static stability with aggregation. Even though entrainment rate increases with aggregation, updraft buoyancy reduction through entrainment decreases because aggregated updrafts are protected by a moist shell. Parameterizations that wish to represent mesoscale convective organization would need to model this moist shell.

GENERAL: Kinetic Behaviors of Catalysis-Driven Growth of Three-Species Aggregates on Base of Exchange-Driven Aggregations

NASA Astrophysics Data System (ADS)

Sun, Yun-Fei; Chen, Dan; Lin, Zhen-Quan; Ke, Jian-Hong

2009-06-01

We propose a solvable aggregation model to mimic the evolution of population A, asset B, and the quantifiable resource C in a society. In this system, the population and asset aggregates themselves grow through self-exchanges with the rate kernels K1(k, j) = K1kj and K2(k, j) = K2kj, respectively. The actions of the population and asset aggregations on the aggregation evolution of resource aggregates are described by the population-catalyzed monomer death of resource aggregates and asset-catalyzed monomer birth of resource aggregates with the rate kernels J1(k, j) = J1k and J2(k, j) = J2k, respectively. Meanwhile, the asset and resource aggregates conjunctly catalyze the monomer birth of population aggregates with the rate kernel I1(k, i, j) = I1kiμjη, and population and resource aggregates conjunctly catalyze the monomer birth of asset aggregates with the rate kernel I2(k, i, j) = I2kivjη. The kinetic behaviors of species A, B, and C are investigated by means of the mean-field rate equation approach. The effects of the population-catalyzed death and asset-catalyzed birth on the evolution of resource aggregates based on the self-exchanges of population and asset appear in effective forms. The coefficients of the effective population-catalyzed death and the asset-catalyzed birth are expressed as J1e = J1/K1 and J2e = J2/K2, respectively. The aggregate size distribution of C species is found to be crucially dominated by the competition between the effective death and the effective birth. It satisfies the conventional scaling form, generalized scaling form, and modified scaling form in the cases of J1e < J2e, J1e = J2e, and J1e > J2e, respectively. Meanwhile, we also find the aggregate size distributions of populations and assets both fall into two distinct categories for different parameters μ, ν, and η: (i) When μ = ν = η = 0 and μ = ν = 0, η = 1, the population and asset aggregates obey the generalized scaling forms; and (ii) When μ = ν = 1, η = 0, and μ = ν = η = 1, the population and asset aggregates experience gelation transitions at finite times and the scaling forms break down.

Effect of particulate aggregation in aquatic environments on the beam attenuation and its utility as a proxy for particulate mass.

PubMed

Boss, Emmanuel; Slade, Wayne; Hill, Paul

2009-05-25

Marine aggregates, agglomerations of particles and dissolved materials, are an important particulate pool in aquatic environments, but their optical properties are not well understood. To improve understanding of the optical properties of aggregates, two related studies are presented. In the first, an in situ manipulation experiment is described, in which beam attenuation of undisturbed and sheared suspensions are compared. Results show that in the sheared treatment bulk particle size decreases and beam attenuation increases, consistent with the hypothesis that a significant fraction of mass in suspension is contained in fragile aggregates. Interestingly, the magnitude of increase in beam attenuation is less than expected if the aggregates are modeled as solid spheres. Motivated by this result, a second study is presented, in which marine aggregates are modeled to assess how the beam attenuation of aggregates differs from that of their constituent particles and from solid particles of the same mass. The model used is based on that of Latimer [Appl. Opt. 24, 3231 (1985)] and mass specific attenuation is compared with that based on homogeneous and solid particles, the standard model for aquatic particles. In the modeling we use recent research relating size and solid fraction of aquatic aggregates. In contrast with Mie theory, this model provides a rather size-insensitive mass specific attenuation for most relevant sizes. This insensitivity is consistent with the observations that mass specific beam-attenuation of marine particles is in the range 0.2-0.6m(2)/gr despite large variability in size distribution and composition across varied aquatic environments.

Rigid aggregates: theory and applications

NASA Astrophysics Data System (ADS)

Richardson, D. C.

2005-08-01

Numerical models employing ``perfect'' self-gravitating rubble piles that consist of monodisperse rigid spheres with configurable contact dissipation have been used to explore collisional and rotational disruption of gravitational aggregates. Applications of these simple models include numerical simulations of planetesimal evolution, asteroid family formation, tidal disruption, and binary asteroid formation. These studies may be limited by the idealized nature of the rubble pile model, since perfect identical spheres stack and shear in a very specific, possibly over-idealized way. To investigate how constituent properties affect the overall characteristics of a gravitational aggregate, particularly its failure modes, we have generalized our numerical code to model colliding, self-gravitating, rigid aggregates made up of variable-size spheres. Euler's equation of rigid-body motion in the presence of external torques are implemented, along with a self-consistent prescription for handling non-central impacts. Simple rules for sticking and breaking are also included. Preliminary results will be presented showing the failure modes of gravitational aggregates made up of smaller, rigid, non-idealized components. Applications of this new capability include more realistic aggregate models, convenient modeling of arbitrary rigid shapes for studies of the stability of orbiting companions (replacing one or both bodies with rigid aggregates eliminates expensive interparticle collisions while preserving the shape, spin, and gravity field of the bodies), and sticky particle aggregation in dense planetary rings. This material is based upon work supported by the National Aeronautics and Space Administration under Grant No. NAG511722 issued through the Office of Space Science and by the National Science Foundation under Grant No. AST0307549.

Microcanonical thermostatistics of coarse-grained proteins with amyloidogenic propensity

NASA Astrophysics Data System (ADS)

Frigori, Rafael B.; Rizzi, Leandro G.; Alves, Nelson A.

2013-01-01

The formation of fibrillar aggregates seems to be a common characteristic of polypeptide chains, although the observation of these aggregates may depend on appropriate experimental conditions. Partially folded intermediates seem to have an important role in the generation of protein aggregates, and a mechanism for this fibril formation considers that these intermediates also correspond to metastable states with respect to the fibrillar ones. Here, using a coarse-grained (CG) off-lattice model, we carry out a comparative analysis of the thermodynamic aspects characterizing the folding transition with respect to the propensity for aggregation of four different systems: two isoforms of the amyloid β-protein, the Src SH3 domain, and the human prion proteins (hPrP). Microcanonical analysis of the data obtained from replica exchange method is conducted to evaluate the free-energy barrier and latent heat in these models. The simulations of the amyloid β isoforms and Src SH3 domain indicated that the folding process described by this CG model is related to a negative specific heat, a phenomenon that can only be verified in the microcanonical ensemble in first-order phase transitions. The CG simulation of the hPrP heteropolymer yielded a continuous folding transition. The absence of a free-energy barrier and latent heat favors the presence of partially unfolded conformations, and in this context, this thermodynamic aspect could explain the reason why the hPrP heteropolymer is more aggregation-prone than the other heteropolymers considered in this study. We introduced the hydrophobic radius of gyration as an order parameter and found that it can be used to obtain reliable information about the hydrophobic packing and the transition temperatures in the folding process.

GFP-Mutant Human Tau Transgenic Mice Develop Tauopathy Following CNS Injections of Alzheimer's Brain-Derived Pathological Tau or Synthetic Mutant Human Tau Fibrils.

PubMed

Gibbons, Garrett S; Banks, Rachel A; Kim, Bumjin; Xu, Hong; Changolkar, Lakshmi; Leight, Susan N; Riddle, Dawn M; Li, Chi; Gathagan, Ronald J; Brown, Hannah J; Zhang, Bin; Trojanowski, John Q; Lee, Virginia M-Y

2017-11-22

Neurodegenerative proteinopathies characterized by intracellular aggregates of tau proteins, termed tauopathies, include Alzheimer's disease (AD), frontotemporal lobar degeneration (FTLD) with tau pathology (FTLD-tau), and related disorders. Pathological tau proteins derived from human AD brains (AD-tau) act as proteopathic seeds that initiate the templated aggregation of soluble tau upon intracerebral injection into tau transgenic (Tg) and wild-type mice, thereby modeling human tau pathology. In this study, we found that aged Tg mice of both sexes expressing human tau proteins harboring a pathogenic P301L MAPT mutation labeled with green fluorescent protein (T40PL-GFP Tg mouse line) exhibited hyperphosphorylated tau mislocalized to the somatodentritic domain of neurons, but these mice did not develop de novo insoluble tau aggregates, which are characteristic of human AD and related tauopathies. However, intracerebral injections of either T40PL preformed fibrils (PFFs) or AD-tau seeds into T40PL-GFP mice induced abundant intraneuronal pathological inclusions of hyperphosphorylated T40PL-GFP. These injections of pathological tau resulted in the propagation of tau pathology from the injection site to neuroanatomically connected brain regions, and these tau inclusions consisted of both T40PL-GFP and WT endogenous mouse tau. Primary neurons cultured from the brains of neonatal T40PL-GFP mice provided an informative in vitro model for examining the uptake and localization of tau PFFs. These findings demonstrate the seeded aggregation of T40PL-GFP in vivo by synthetic PFFs and human AD-tau and the utility of this system to study the neuropathological spread of tau aggregates. SIGNIFICANCE STATEMENT The stereotypical spread of pathological tau protein aggregates have recently been attributed to the transmission of proteopathic seeds. Despite the extensive use of transgenic mouse models to investigate the propagation of tau pathology in vivo , details of the aggregation process such as the early seeding events leading to new tau pathology have remained elusive. This study validates the use of GFP-labeled tau expressed by neurons in vivo and in vitro as models for investigating mechanisms underlying the seeded transmission of tau pathology as well as tau-focused drug discovery to identify disease-modifying therapies for AD and related tauopathies. Copyright © 2017 the authors 0270-6474/17/3711485-10$15.00/0.

GFP-Mutant Human Tau Transgenic Mice Develop Tauopathy Following CNS Injections of Alzheimer's Brain-Derived Pathological Tau or Synthetic Mutant Human Tau Fibrils

PubMed Central

Banks, Rachel A.; Kim, Bumjin; Xu, Hong; Changolkar, Lakshmi; Leight, Susan N.; Riddle, Dawn M.; Li, Chi; Brown, Hannah J.; Zhang, Bin

2017-01-01

Neurodegenerative proteinopathies characterized by intracellular aggregates of tau proteins, termed tauopathies, include Alzheimer's disease (AD), frontotemporal lobar degeneration (FTLD) with tau pathology (FTLD-tau), and related disorders. Pathological tau proteins derived from human AD brains (AD-tau) act as proteopathic seeds that initiate the templated aggregation of soluble tau upon intracerebral injection into tau transgenic (Tg) and wild-type mice, thereby modeling human tau pathology. In this study, we found that aged Tg mice of both sexes expressing human tau proteins harboring a pathogenic P301L MAPT mutation labeled with green fluorescent protein (T40PL-GFP Tg mouse line) exhibited hyperphosphorylated tau mislocalized to the somatodentritic domain of neurons, but these mice did not develop de novo insoluble tau aggregates, which are characteristic of human AD and related tauopathies. However, intracerebral injections of either T40PL preformed fibrils (PFFs) or AD-tau seeds into T40PL-GFP mice induced abundant intraneuronal pathological inclusions of hyperphosphorylated T40PL-GFP. These injections of pathological tau resulted in the propagation of tau pathology from the injection site to neuroanatomically connected brain regions, and these tau inclusions consisted of both T40PL-GFP and WT endogenous mouse tau. Primary neurons cultured from the brains of neonatal T40PL-GFP mice provided an informative in vitro model for examining the uptake and localization of tau PFFs. These findings demonstrate the seeded aggregation of T40PL-GFP in vivo by synthetic PFFs and human AD-tau and the utility of this system to study the neuropathological spread of tau aggregates. SIGNIFICANCE STATEMENT The stereotypical spread of pathological tau protein aggregates have recently been attributed to the transmission of proteopathic seeds. Despite the extensive use of transgenic mouse models to investigate the propagation of tau pathology in vivo, details of the aggregation process such as the early seeding events leading to new tau pathology have remained elusive. This study validates the use of GFP-labeled tau expressed by neurons in vivo and in vitro as models for investigating mechanisms underlying the seeded transmission of tau pathology as well as tau-focused drug discovery to identify disease-modifying therapies for AD and related tauopathies. PMID:28986461

Statistical, economic and other tools for assessing natural aggregate

USGS Publications Warehouse

Bliss, J.D.; Moyle, P.R.; Bolm, K.S.

2003-01-01

Quantitative aggregate resource assessment provides resource estimates useful for explorationists, land managers and those who make decisions about land allocation, which may have long-term implications concerning cost and the availability of aggregate resources. Aggregate assessment needs to be systematic and consistent, yet flexible enough to allow updating without invalidating other parts of the assessment. Evaluators need to use standard or consistent aggregate classification and statistic distributions or, in other words, models with geological, geotechnical and economic variables or interrelationships between these variables. These models can be used with subjective estimates, if needed, to estimate how much aggregate may be present in a region or country using distributions generated by Monte Carlo computer simulations.

Public Opinion as Collective Coorientation.

ERIC Educational Resources Information Center

Tipton, Leonard; And Others

To conceptualize public opinion as something other than "mere aggregation" of individual opinions requires systemic models that identify component parts of public opinion and their structural/functional relationships. Operationalization requires asking respondents not only their individual opinion, but also their perception of public…

Measuring Changes in Energy Efficiency for the Annual Energy Outlook 2002

EIA Publications

2002-01-01

This paper describes the methodology used to develop the National Energy Modeling System estimate of projected aggregate energy efficiency and to describe the results of applying it to the Annual Energy Outlook 2002 (AEO2002) reference case.

Application of imaging techniques to evaluate polishing characteristics of aggregates : final report.

DOT National Transportation Integrated Search

2016-12-01

Previous research conducted at the University of Florida (UF) to investigate the use of the Aggregate Image Measurement System (AIMS) and Micro-Deval (MD) to evaluate frictional performance of aggregates concluded that the current AIMS system cannot ...

Alternative complement pathway activation increases mortality in a model of burn injury in mice.

PubMed Central

Gelfand, J A; Donelan, M; Hawiger, A; Burke, J F

1982-01-01

We have studied the role of the complement system in burn injury in an experimental model in mice. A 25% body surface area, full-thickness scald wound was produced in anesthetized animals. Massive activation of the alternative complement pathway, but not the classical pathway, was seen. This activation was associated with the generation of neutrophil aggregating activity in the plasma, neutrophil aggregates in the lungs, increased pulmonary vascular permeability, and increased lung edema formation. Decomplementation with cobra venom factor (CVF) or genetic C5 deficiency diminished these pathologic changes, and CVF pretreatment substantially reduced burn mortality in the first 24 h. Preliminary data show that human burn patients have a similar pattern of complement activation involving predominantly the alternative pathway, indicating the possible relevance of the murine model to human disease. Images PMID:7174787

A versatile model for soft patchy particles with various patch arrangements.

PubMed

Li, Zhan-Wei; Zhu, You-Liang; Lu, Zhong-Yuan; Sun, Zhao-Yan

2016-01-21

We propose a simple and general mesoscale soft patchy particle model, which can felicitously describe the deformable and surface-anisotropic characteristics of soft patchy particles. This model can be used in dynamics simulations to investigate the aggregation behavior and mechanism of various types of soft patchy particles with tunable number, size, direction, and geometrical arrangement of the patches. To improve the computational efficiency of this mesoscale model in dynamics simulations, we give the simulation algorithm that fits the compute unified device architecture (CUDA) framework of NVIDIA graphics processing units (GPUs). The validation of the model and the performance of the simulations using GPUs are demonstrated by simulating several benchmark systems of soft patchy particles with 1 to 4 patches in a regular geometrical arrangement. Because of its simplicity and computational efficiency, the soft patchy particle model will provide a powerful tool to investigate the aggregation behavior of soft patchy particles, such as patchy micelles, patchy microgels, and patchy dendrimers, over larger spatial and temporal scales.

Aspects of spatial and temporal aggregation in estimating regional carbon dioxide fluxes from temperate forest soils

NASA Technical Reports Server (NTRS)

Kicklighter, David W.; Melillo, Jerry M.; Peterjohn, William T.; Rastetter, Edward B.; Mcguire, A. David; Steudler, Paul A.; Aber, John D.

1994-01-01

We examine the influence of aggregation errors on developing estimates of regional soil-CO2 flux from temperate forests. We find daily soil-CO2 fluxes to be more sensitive to changes in soil temperatures (Q(sub 10) = 3.08) than air temperatures (Q(sub 10) = 1.99). The direct use of mean monthly air temperatures with a daily flux model underestimates regional fluxes by approximately 4%. Temporal aggregation error varies with spatial resolution. Overall, our calibrated modeling approach reduces spatial aggregation error by 9.3% and temporal aggregation error by 15.5%. After minimizing spatial and temporal aggregation errors, mature temperate forest soils are estimated to contribute 12.9 Pg C/yr to the atmosphere as carbon dioxide. Georeferenced model estimates agree well with annual soil-CO2 fluxes measured during chamber studies in mature temperate forest stands around the globe.

A model for bacterial colonization of sinking aggregates.

PubMed

Bearon, R N

2007-01-01

Sinking aggregates provide important nutrient-rich environments for marine bacteria. Quantifying the rate at which motile bacteria colonize such aggregations is important in understanding the microbial loop in the pelagic food web. In this paper, a simple analytical model is presented to predict the rate at which bacteria undergoing a random walk encounter a sinking aggregate. The model incorporates the flow field generated by the sinking aggregate, the swimming behavior of the bacteria, and the interaction of the flow with the swimming behavior. An expression for the encounter rate is computed in the limit of large Péclet number when the random walk can be approximated by a diffusion process. Comparison with an individual-based numerical simulation is also given.

Potency of a tau fibrillization inhibitor is influenced by its aggregation state

PubMed Central

Congdon, Erin E.; Necula, Mihaela; Blackstone, Robert D.; Kuret, Jeff

2007-01-01

Tau fibrillization is a potential therapeutic target for Alzheimer’s and other neurodegenerative diseases. Several small molecule inhibitors of tau aggregation have been developed for this purpose. One of them, 3,3′-bis(β-hydroxyethyl)-9-ethyl-5,5′-dimethoxythiacarbocyanine iodide (N744), is a cationic thiacarbocyanine dye that inhibits recombinant tau filament formation when present at submicromolar concentrations. To prepare dosing regimens for testing N744 activity in biological models, its full concentration-effect relationship in the range 0.01 – 60 μM was examined in vitro by electron microscopy and laser light scattering methods. Results revealed that N744 concentration dependence was biphasic, with fibrillization inhibitory activity appearing at submicromolar concentration, but with relief of inhibition and increases in fibrillization apparent above 10 μM. Therefore, fibrillization was inhibited ≥50% only over a narrow concentration range, which was further reduced by filament stabilizing modifications such as tau pseudophosphorylation. N744 inhibitory activity also was paralleled by changes in its aggregation state, with dimer predominating at inhibitory concentrations and large dye aggregates appearing at high concentrations. Ligand dimerization was promoted by the presence of tau protein, which lowered the equilibrium dissociation constant for dimerization more than an order of magnitude relative to controls. The results suggest that ligand aggregation may play an important role in both inhibitory and disinhibitory phases of the concentration-effect curve, and may lead to complex dose response relationships in model systems. PMID:17559794

Aggregation Pheromone System: A Real-parameter Optimization Algorithm using Aggregation Pheromones as the Base Metaphor

NASA Astrophysics Data System (ADS)

Tsutsui, Shigeyosi

This paper proposes an aggregation pheromone system (APS) for solving real-parameter optimization problems using the collective behavior of individuals which communicate using aggregation pheromones. APS was tested on several test functions used in evolutionary computation. The results showed APS could solve real-parameter optimization problems fairly well. The sensitivity analysis of control parameters of APS is also studied.

A convergent model for distributed processing of Big Sensor Data in urban engineering networks

NASA Astrophysics Data System (ADS)

Parygin, D. S.; Finogeev, A. G.; Kamaev, V. A.; Finogeev, A. A.; Gnedkova, E. P.; Tyukov, A. P.

2017-01-01

The problems of development and research of a convergent model of the grid, cloud, fog and mobile computing for analytical Big Sensor Data processing are reviewed. The model is meant to create monitoring systems of spatially distributed objects of urban engineering networks and processes. The proposed approach is the convergence model of the distributed data processing organization. The fog computing model is used for the processing and aggregation of sensor data at the network nodes and/or industrial controllers. The program agents are loaded to perform computing tasks for the primary processing and data aggregation. The grid and the cloud computing models are used for integral indicators mining and accumulating. A computing cluster has a three-tier architecture, which includes the main server at the first level, a cluster of SCADA system servers at the second level, a lot of GPU video cards with the support for the Compute Unified Device Architecture at the third level. The mobile computing model is applied to visualize the results of intellectual analysis with the elements of augmented reality and geo-information technologies. The integrated indicators are transferred to the data center for accumulation in a multidimensional storage for the purpose of data mining and knowledge gaining.

PM10 emissions from aggregate fractions of an Entic Haplustoll under two contrasting tillage systems

NASA Astrophysics Data System (ADS)

Mendez, Mariano J.; Aimar, Silvia B.; Buschiazzo, Daniel E.

2015-12-01

Tillage systems affect physical and chemical properties of soils modifying its aggregation. How changes of the aggregate size distribution affect the capacity of the soil to emit fine particulate matter (PM10) to the atmosphere during wind erosion processes, is a less investigated issue. In order to answer this question, PM10 emissions from an Entic Haplustoll submitted to 25 years of continuous conventional tillage (LC) and no-till (NT) were analyzed. Soil samples were sieved with a rotary sieve in order to determine the aggregate size distribution (fractions : <0.42 mm, 0.42-0.84 mm, 0.84-2 mm, 2-6.4 mm, 6.4-19.2 mm, and >19.2 mm), the dry aggregate stability (DAS) and the erodible fraction (EF). The organic matter contents (OM), the particle size composition and the PM10 emission of each aggregate fraction were also measured. Results showed that NT promoted OM accumulations in all aggregate fractions which favored DAS and soil aggregation. The <0.42 mm sized aggregates (27%) predominated in CT and the >19.2 mm (41.7%) in NT, while the proportion of the other aggregate fractions was similar in both tillage systems. As a consequence of the smaller proportion of the <0.42 mm aggregates, the erodible fraction was lower in NT (EF: 17.3%) than in CT (30.8%). PM10 emissions of each aggregate fraction (AE) decreased exponentially with increasing size of the fractions in both tillage systems, mainly as a consequence of the smaller size and higher specific surface. AE was higher in CT than in NT for all aggregate fractions, but the higher differences were found in the <0.42 mm aggregates (18 μg g-1 in CT vs 8 μg g-1 in NT). The PM10 emission of the whole soil was three times higher in CT than in NT, while the emission of the erodible fraction (EFE) was in CT four times higher than in NT. PM10 emissions of the <0.42 mm aggregates represented over 50% of SE and 90% of EFE. We concluded that NT reduced the capacity of soils of the semiarid Pampas to emit PM10 because it produced a better aggregation that reduced the proportion and emission of the <0.42 mm aggregates. These aggregates had, by far, the highest emission potential.

Multiscale measurement error models for aggregated small area health data.

PubMed

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

2016-08-01

Spatial data are often aggregated from a finer (smaller) to a coarser (larger) geographical level. The process of data aggregation induces a scaling effect which smoothes the variation in the data. To address the scaling problem, multiscale models that link the convolution models at different scale levels via the shared random effect have been proposed. One of the main goals in aggregated health data is to investigate the relationship between predictors and an outcome at different geographical levels. In this paper, we extend multiscale models to examine whether a predictor effect at a finer level hold true at a coarser level. To adjust for predictor uncertainty due to aggregation, we applied measurement error models in the framework of multiscale approach. To assess the benefit of using multiscale measurement error models, we compare the performance of multiscale models with and without measurement error in both real and simulated data. We found that ignoring the measurement error in multiscale models underestimates the regression coefficient, while it overestimates the variance of the spatially structured random effect. On the other hand, accounting for the measurement error in multiscale models provides a better model fit and unbiased parameter estimates. © The Author(s) 2016.

Spatial and Temporal Uncertainty of Crop Yield Aggregations

NASA Technical Reports Server (NTRS)

Porwollik, Vera; Mueller, Christoph; Elliott, Joshua; Chryssanthacopoulos, James; Iizumi, Toshichika; Ray, Deepak K.; Ruane, Alex C.; Arneth, Almut; Balkovic, Juraj; Ciais, Philippe;

Multitarget Therapeutic Leads for Alzheimer's Disease: Quinolizidinyl Derivatives of Bi- and Tricyclic Systems as Dual Inhibitors of Cholinesterases and β-Amyloid (Aβ) Aggregation.

PubMed

Tonelli, Michele; Catto, Marco; Tasso, Bruno; Novelli, Federica; Canu, Caterina; Iusco, Giovanna; Pisani, Leonardo; Stradis, Angelo De; Denora, Nunzio; Sparatore, Anna; Boido, Vito; Carotti, Angelo; Sparatore, Fabio

2015-06-01

Multitarget therapeutic leads for Alzheimer's disease were designed on the models of compounds capable of maintaining or restoring cell protein homeostasis and of inhibiting β-amyloid (Aβ) oligomerization. Thirty-seven thioxanthen-9-one, xanthen-9-one, naphto- and anthraquinone derivatives were tested for the direct inhibition of Aβ(1-40) aggregation and for the inhibition of electric eel acetylcholinesterase (eeAChE) and horse serum butyrylcholinesterase (hsBChE). These compounds are characterized by basic side chains, mainly quinolizidinylalkyl moieties, linked to various bi- and tri-cyclic (hetero)aromatic systems. With very few exceptions, these compounds displayed inhibitory activity on both AChE and BChE and on the spontaneous aggregation of β-amyloid. In most cases, IC50 values were in the low micromolar and sub-micromolar range, but some compounds even reached nanomolar potency. The time course of amyloid aggregation in the presence of the most active derivative (IC50 =0.84 μM) revealed that these compounds might act as destabilizers of mature fibrils rather than mere inhibitors of fibrillization. Many compounds inhibited one or both cholinesterases and Aβ aggregation with similar potency, a fundamental requisite for the possible development of therapeutics exhibiting a multitarget mechanism of action. The described compounds thus represent interesting leads for the development of multitarget AD therapeutics. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Aggregation, sedimentation, dissolution and bioavailability of ...

EPA Pesticide Factsheets

Due to increasing use in flat screen applications, solar cells, ink–jet printing, and medical devices, cadmium-based quantum dots (QDs) are among the fastest growing classes of engineered nanomaterial. These wide-ranging consumer product applications and end of use disposal issues assure that QDs will eventually enter the marine environment. In an effort to understand the fate and transport of CdSe QDs in estuarine systems, the aggregation, sedimentation, dissolution, and bioavailability of CdSe QDs in seawater was investigated. The size of CdSe QDs increased from 40-60 nm to >1 mm within one hour once introduced to seawater, and the diffusion-limited aggregation led to highly polydispersed aggregates with loose structures. As a result, the sedimentation rate of CdSe QD aggregates in seawater was measured to be 4-10 mm/day, which was slow considering their relatively large size. Humic acid (HA), as a model natural organic matter, further increased the size and polydispersity of CdSe QDs, and slowed their sedimentation accordingly. Given the effect of light on CdSe QDs, natural sunlight and light filters were employed to simulate the photic conditions at different water depths in an estuarine system. It was observed that light played a vital role in promoting the dissolution of CdSe QDs and the release of dissolved Cd. The ZnS shell surrounding the CdSe core also significantly hindered the degradation of CdSe QDs into their ionic components. With sufficient

Effects in the network topology due to node aggregation: Empirical evidence from the domestic maritime transportation in Greece

NASA Astrophysics Data System (ADS)

Tsiotas, Dimitrios; Polyzos, Serafeim

2018-02-01

This article studies the topological consistency of spatial networks due to node aggregation, examining the changes captured between different network representations that result from nodes' grouping and they refer to the same socioeconomic system. The main purpose of this study is to evaluate what kind of topological information remains unalterable due to node aggregation and, further, to develop a framework for linking the data of an empirical network with data of its socioeconomic environment, when the latter are available for hierarchically higher levels of aggregation, in an effort to promote the interdisciplinary research in the field of complex network analysis. The research question is empirically tested on topological and socioeconomic data extracted from the Greek Maritime Network (GMN) that is modeled as a non-directed multilayer (bilayer) graph consisting of a port-layer, where nodes represent ports, and a prefecture-layer, where nodes represent coastal and insular prefectural groups of ports. The analysis highlights that the connectivity (degree) of the GMN is the most consistent aspect of this multilayer network, which preserves both the topological and the socioeconomic information through node aggregation. In terms of spatial analysis and regional science, such effects illustrate the effectiveness of the prefectural administrative division for the functionality of the Greek maritime transportation system. Overall, this approach proposes a methodological framework that can enjoy further applications about the grouping effects induced on the network topology, providing physical, technical, socioeconomic, strategic or political insights.

Solvent tuning configurational conversion of lycopene aggregates in organic-aqueous mixing solvent

NASA Astrophysics Data System (ADS)

Dong, Jia; Zhang, Di; Wang, Xin-Yue; Wang, Peng

2018-06-01

In general cases, carotenoid aggregates are prepared in organic-water mixing solvent depending on its hydrophobic character. It is well-known that one of carotenoids, lycopene, is more likely to form typical H-aggregates. In this study, new type lycopene J-aggregates were prepared in DMSO-water mixing solvent with small amount of toluene, which was observed for the first time. We proposed a potential structure model combining with exciton model to interpret the mechanism of spectra changes. Our finding has provided new methods and novel ideas for controlling carotenoid aggregates formation.

Lorentz microscopy sheds light on the role of dipolar interactions in magnetic hyperthermia

NASA Astrophysics Data System (ADS)

Campanini, M.; Ciprian, R.; Bedogni, E.; Mega, A.; Chiesi, V.; Casoli, F.; de Julián Fernández, C.; Rotunno, E.; Rossi, F.; Secchi, A.; Bigi, F.; Salviati, G.; Magén, C.; Grillo, V.; Albertini, F.

2015-04-01

Monodispersed Fe3O4 nanoparticles with comparable size distributions have been synthesized by two different synthesis routes, co-precipitation and thermal decomposition. Thanks to the different steric stabilizations, the described samples can be considered as a model system to investigate the effects of magnetic dipolar interactions on the aggregation states of the nanoparticles. Moreover, the presence of magnetic dipolar interactions can strongly affect the nanoparticle efficiency as a hyperthermic mediator. In this paper, we present a novel way to visualize and map the magnetic dipolar interactions in different kinds of nanoparticle aggregates by the use of Lorentz microscopy, an easy and reliable in-line electron holographic technique. By exploiting Lorentz microscopy, which is complementary to the magnetic measurements, it is possible to correlate the interaction degrees of magnetic nanoparticles with their magnetic behaviors. In particular, we demonstrate that Lorentz microscopy is successful in visualizing the magnetic configurations stabilized by dipolar interactions, thus paving the way to the comprehension of the power loss mechanisms for different nanoparticle aggregates.Monodispersed Fe3O4 nanoparticles with comparable size distributions have been synthesized by two different synthesis routes, co-precipitation and thermal decomposition. Thanks to the different steric stabilizations, the described samples can be considered as a model system to investigate the effects of magnetic dipolar interactions on the aggregation states of the nanoparticles. Moreover, the presence of magnetic dipolar interactions can strongly affect the nanoparticle efficiency as a hyperthermic mediator. In this paper, we present a novel way to visualize and map the magnetic dipolar interactions in different kinds of nanoparticle aggregates by the use of Lorentz microscopy, an easy and reliable in-line electron holographic technique. By exploiting Lorentz microscopy, which is complementary to the magnetic measurements, it is possible to correlate the interaction degrees of magnetic nanoparticles with their magnetic behaviors. In particular, we demonstrate that Lorentz microscopy is successful in visualizing the magnetic configurations stabilized by dipolar interactions, thus paving the way to the comprehension of the power loss mechanisms for different nanoparticle aggregates. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr00273g

Revisiting the flocculation kinetics of destabilized asphaltenes.

PubMed

Vilas Bôas Fávero, Cláudio; Maqbool, Tabish; Hoepfner, Michael; Haji-Akbari, Nasim; Fogler, H Scott

2017-06-01

A comprehensive review of the recently published work on asphaltene destabilization and flocculation kinetics is presented. Four different experimental techniques were used to study asphaltenes undergoing flocculation process in crude oils and model oils. The asphaltenes were destabilized by different n-alkanes and a geometric population balance with the Smoluchowski collision kernel was used to model the asphaltene aggregation process. Additionally, by postulating a relation between the aggregation collision efficiency and the solubility parameter of asphaltenes and the solution, a unified model of asphaltene aggregation model was developed. When the aggregation model is applied to the experimental data obtained from several different crude oil and model oils, the detection time curves collapsed onto a universal single line, indicating that the model successfully captures the underlying physics of the observed process. Copyright © 2016 Elsevier B.V. All rights reserved.

Light scattering method to measure red blood cell aggregation during incubation

NASA Astrophysics Data System (ADS)

Grzegorzewski, B.; Szołna-Chodór, A.; Baryła, J.; DreŻek, D.

2018-01-01

Red blood cell (RBC) aggregation can be observed both in vivo as well as in vitro. This process is a cause of alterations of blood flow in microvascular network. Enhanced RBC aggregation makes oxygen and nutrients delivery difficult. Measurements of RBC aggregation usually give a description of the process for a sample where the state of a solution and cells is well-defined and the system reached an equilibrium. Incubation of RBCs in various solutions is frequently used to study the effects of the solutions on the RBC aggregation. The aggregation parameters are compared before and after incubation while the detailed changes of the parameters during incubation remain unknown. In this paper we have proposed a method to measure red blood cell aggregation during incubation based on the well-known technique where backscattered light is used to assess the parameters of the RBC aggregation. Couette system consisting of two cylinders is adopted in the method. The incubation is observed in the Couette system. In the proposed method following sequence of rotations is adapted. Two minutes rotation is followed by two minutes stop. In this way we have obtained a time series of back scattered intensity consisting of signals respective for disaggregation and aggregation. It is shown that the temporal changes of the intensity manifest changes of RBC aggregation during incubation. To show the ability of the method to assess the effect of incubation time on RBC aggregation the results are shown for solutions that cause an increase of RBC aggregation as well as for the case where the aggregation is decreased.

A discrete mathematical model for the aggregation of β-Amyloid.

PubMed

Dayeh, Maher A; Livadiotis, George; Elaydi, Saber

2018-01-01

Dementia associated with the Alzheimer's disease is thought to be correlated with the conversion of the β - Amyloid (Aβ) peptides from soluble monomers to aggregated oligomers and insoluble fibrils. We present a discrete-time mathematical model for the aggregation of Aβ monomers into oligomers using concepts from chemical kinetics and population dynamics. Conditions for the stability and instability of the equilibria of the model are established. A formula for the number of monomers that is required for producing oligomers is also given. This may provide compound designers a mechanism to inhibit the Aβ aggregation.

A spring-matrix model for pigment translocation in the red ovarian chromatophores of the freshwater shrimp Macrobrachium olfersi (Crustacea, Decapoda).

PubMed

Boyle, Robert Tew; McNamara, John Campbell

2008-04-01

A model for intracellular transport of pigment granules in the red ovarian chromatophores of the freshwater shrimp Macrobrachium olfersi is proposed on the basis of shifts in the equilibrium of resting forces acting on an elastic pigment matrix. The model describes a pigment-transport mechanism in which mechanochemical protein motors like kinesin and myosin alternately stretch and compress a structurally unified, elastic pigment matrix. Quantifiable properties of the spring-matrix obey Hooke's Law during the rapid phases of pigment aggregation and dispersion. The spring-like response of the pigment mass is estimated from previous kinetic experiments on pigment translocation induced by red pigment concentrating hormone, or by the calcium ionophore A23187. Both translocation effectors trigger an initial phase of rapid pigment aggregation, and their removal or washout after complete aggregation produces a phase of rapid pigment dispersion, followed by slow pigment translocation. The rapid-phase kinetics of pigment transport are in reasonable agreement with Hooke's Law, suggesting that such phases represent the release of kinetic energy, probably produced by the mechanochemical protein motors and stored in the form of matrix deformation during the slow phases of translocation. This semiquantitative model should aid in analyzing intracellular transport systems that incorporate an elastic component.

Evaluation of the effects of amyloid β aggregation from seaweed extracts by a microliter-scale high-throughput screening system with a quantum dot nanoprobe.

PubMed

Ogara, Toshiki; Takahashi, Tomohito; Yasui, Hajime; Uwai, Koji; Tokuraku, Kiyotaka

2015-07-01

Inhibitors of amyloid β (Aβ) aggregation have the potential to serve as lead compounds for anti-Alzheimer's disease (AD) agents because Aβ aggregation is a key step in AD pathogenesis. Recently, we developed a novel microliter-scale high-throughput screening (MSHTS) system for Aβ aggregation inhibitors that applied fluorescence microscopic analysis with quantum dot nanoprobes, and attempted to comprehensively screen the inhibitors from spices using this system (Ishigaki et al., PLoS One, 8, e72992, 2013). In this study, we tried to evaluate the inhibitory activities of 11 seaweed extracts on Aβ aggregation using the MSHTS system. The half-maximal effective concentration (EC50) of the ethanolic extracts from all seaweeds exceeded 4.9 mg/ml, indicating that the extracts inhibit Aβ aggregation although this activity was significantly lower than that displayed by members of the Lamiaceae, a family of herbal spices that showed highest activity among 52 spices tested in our 2013 study. On the other hand, the EC50 of boiling water extracts was 0.013-0.42 mg/ml which was comparable with the EC50 of the extracts from the Lamiaceae family. These results suggest that the extraction efficiency of the inhibitors by boiling water extraction was higher than that by ethanolic extraction. Moreover, analysis of fluorescence micrographs, which were obtained from the MSHTS system, revealed that the morphology of the Aβ aggregates coincubated with boiling water extracts differed from control aggregates, suggesting that the MSHTS system is also useful for screening substances that affect the morphology of aggregates. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Collective Intelligence: Aggregation of Information from Neighbors in a Guessing Game.

PubMed

Pérez, Toni; Zamora, Jordi; Eguíluz, Víctor M

2016-01-01

Complex systems show the capacity to aggregate information and to display coordinated activity. In the case of social systems the interaction of different individuals leads to the emergence of norms, trends in political positions, opinions, cultural traits, and even scientific progress. Examples of collective behavior can be observed in activities like the Wikipedia and Linux, where individuals aggregate their knowledge for the benefit of the community, and citizen science, where the potential of collectives to solve complex problems is exploited. Here, we conducted an online experiment to investigate the performance of a collective when solving a guessing problem in which each actor is endowed with partial information and placed as the nodes of an interaction network. We measure the performance of the collective in terms of the temporal evolution of the accuracy, finding no statistical difference in the performance for two classes of networks, regular lattices and random networks. We also determine that a Bayesian description captures the behavior pattern the individuals follow in aggregating information from neighbors to make decisions. In comparison with other simple decision models, the strategy followed by the players reveals a suboptimal performance of the collective. Our contribution provides the basis for the micro-macro connection between individual based descriptions and collective phenomena.

Collective Intelligence: Aggregation of Information from Neighbors in a Guessing Game

PubMed Central

Pérez, Toni; Zamora, Jordi; Eguíluz, Víctor M.

2016-01-01

Complex systems show the capacity to aggregate information and to display coordinated activity. In the case of social systems the interaction of different individuals leads to the emergence of norms, trends in political positions, opinions, cultural traits, and even scientific progress. Examples of collective behavior can be observed in activities like the Wikipedia and Linux, where individuals aggregate their knowledge for the benefit of the community, and citizen science, where the potential of collectives to solve complex problems is exploited. Here, we conducted an online experiment to investigate the performance of a collective when solving a guessing problem in which each actor is endowed with partial information and placed as the nodes of an interaction network. We measure the performance of the collective in terms of the temporal evolution of the accuracy, finding no statistical difference in the performance for two classes of networks, regular lattices and random networks. We also determine that a Bayesian description captures the behavior pattern the individuals follow in aggregating information from neighbors to make decisions. In comparison with other simple decision models, the strategy followed by the players reveals a suboptimal performance of the collective. Our contribution provides the basis for the micro-macro connection between individual based descriptions and collective phenomena. PMID:27093274

An in vitro model of Mycobacterium leprae induced granuloma formation

PubMed Central

2013-01-01

Background Leprosy is a contagious and chronic systemic granulomatous disease caused by Mycobacterium leprae. In the pathogenesis of leprosy, granulomas play a key role, however, the mechanisms of the formation and maintenance of M. leprae granulomas are still not clearly understood. Methods To better understand the molecular physiology of M. leprae granulomas and the interaction between the bacilli and human host cells, we developed an in vitro model of human granulomas, which mimicked the in vivo granulomas of leprosy. Macrophages were differentiated from human monocytes, and infected with M. leprae, and then cultured with autologous human peripheral blood mononuclear cells (PBMCs). Results Robust granuloma-like aggregates were obtained only when the M. leprae infected macrophages were co-cultured with PBMCs. Histological examination showed M. leprae within the cytoplasmic center of the multinucleated giant cells, and these bacilli were metabolically active. Macrophages of both M1 and M2 types co-existed in the granuloma like aggregates. There was a strong relationship between the formation of granulomas and changes in the expression levels of cell surface antigens on macrophages, cytokine production and the macrophage polarization. The viability of M. leprae isolated from granulomas indicated that the formation of host cell aggregates benefited the host, but the bacilli also remained metabolically active. Conclusions A simple in vitro model of human M. leprae granulomas was established using human monocyte-derived macrophages and PBMCs. This system may be useful to unravel the mechanisms of disease progression, and subsequently develop methods to control leprosy. PMID:23782413

An in vitro model of Mycobacterium leprae induced granuloma formation.

PubMed

Wang, Hongsheng; Maeda, Yumi; Fukutomi, Yasuo; Makino, Masahiko

2013-06-20

Leprosy is a contagious and chronic systemic granulomatous disease caused by Mycobacterium leprae. In the pathogenesis of leprosy, granulomas play a key role, however, the mechanisms of the formation and maintenance of M. leprae granulomas are still not clearly understood. To better understand the molecular physiology of M. leprae granulomas and the interaction between the bacilli and human host cells, we developed an in vitro model of human granulomas, which mimicked the in vivo granulomas of leprosy. Macrophages were differentiated from human monocytes, and infected with M. leprae, and then cultured with autologous human peripheral blood mononuclear cells (PBMCs). Robust granuloma-like aggregates were obtained only when the M. leprae infected macrophages were co-cultured with PBMCs. Histological examination showed M. leprae within the cytoplasmic center of the multinucleated giant cells, and these bacilli were metabolically active. Macrophages of both M1 and M2 types co-existed in the granuloma like aggregates. There was a strong relationship between the formation of granulomas and changes in the expression levels of cell surface antigens on macrophages, cytokine production and the macrophage polarization. The viability of M. leprae isolated from granulomas indicated that the formation of host cell aggregates benefited the host, but the bacilli also remained metabolically active. A simple in vitro model of human M. leprae granulomas was established using human monocyte-derived macrophages and PBMCs. This system may be useful to unravel the mechanisms of disease progression, and subsequently develop methods to control leprosy.

Flocculation of Clay Colloids Induced by Model Polyelectrolytes: Effects of Relative Charge Density and Size.

PubMed

Sakhawoth, Yasine; Michot, Laurent J; Levitz, Pierre; Malikova, Natalie

2017-10-06

Flocculation and its tuning are of utmost importance in the optimization of several industrial protocols in areas such as purification of waste water and civil engineering. Herein, we studied the polyelectrolyte-induced flocculation of clay colloids on a model system consisting of purified clay colloids of well-defined size fractions and ionene polyelectrolytes presenting regular and tunable chain charge density. To characterize ionene-induced clay flocculation, we turned to the combination of light absorbance (turbidity) and ζ-potential measurements, as well as adsorption isotherms. Our model system allowed us to identify the exact ratio of positive and negative charges in clay-ionene mixtures, the (c+/c-) ratio. For all samples studied, the onset of efficient flocculation occurred consistently at c+/c- ratios significantly below 1, which indicated the formation of highly ionene-deficient aggregates. At the same time, the ζ-potential measurements indicated an apparent zero charge on such aggregates. Thus, the ζ-potential values could not provide the stoichiometry inside the clay-ionene aggregates. The early onset of flocculation in clay-ionene mixtures is reminiscent of the behavior of multivalent salts and contrasts that of monovalent salts, for which a large excess amount of ions is necessary to achieve flocculation. Clear differences in the flocculation behavior are visible as a function of the ionene charge density, which governs the conformation of the ionene chains on the clay surface. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dielectric spectroscopy platform to measure MCF10A epithelial cell aggregation as a model for spheroidal cell cluster analysis.

PubMed

Heileman, K L; Tabrizian, M

2017-05-02

3-Dimensional cell cultures are more representative of the native environment than traditional cell cultures on flat substrates. As a result, 3-dimensional cell cultures have emerged as a very valuable model environment to study tumorigenesis, organogenesis and tissue regeneration. Many of these models encompass the formation of cell aggregates, which mimic the architecture of tumor and organ tissue. Dielectric impedance spectroscopy is a non-invasive, label free and real time technique, overcoming the drawbacks of established techniques to monitor cell aggregates. Here we introduce a platform to monitor cell aggregation in a 3-dimensional extracellular matrix using dielectric spectroscopy. The MCF10A breast epithelial cell line serves as a model for cell aggregation. The platform maintains sterile conditions during the multi-day assay while allowing continuous dielectric spectroscopy measurements. The platform geometry optimizes dielectric measurements by concentrating cells within the electrode sensing region. The cells show a characteristic dielectric response to aggregation which corroborates with finite element analysis computer simulations. By fitting the experimental dielectric spectra to the Cole-Cole equation, we demonstrated that the dispersion intensity Δε and the characteristic frequency f c are related to cell aggregate growth. In addition, microscopy can be performed directly on the platform providing information about cell position, density and morphology. This platform could yield many applications for studying the electrophysiological activity of cell aggregates.

Physicochemical study of mixed systems composed by bovine caseinate and the galactomannan from Gleditsia amorphoides.

PubMed

López, Débora N; Galante, Micaela; Alvarez, Estela M; Risso, Patricia H; Boeris, Valeria

2017-10-01

Model systems formed by sodium caseinate (NaCAS) and espina corona gum (ECG) were studied. There was no evidence of attractive interactions between NaCAS and ECG macromolecules. Aqueous mixtures of NaCAS and ECG phase-separate segregatively over a wide range of concentrations. According to the images obtained by confocal laser scanning microscopy, NaCAS particles form larger protein aggregates when ECG is present in the system. An increase in the hydrodynamic diameter of NaCAS particles, as a result of ECG addition, was also observed by light scattering in diluted systems. A depletion-flocculation phenomenon, in which ECG is excluded from NaCAS surface, is proposed to occur in the concentrated mixed systems, resulting in NaCAS aggregation. ECG raises the viscosity of NaCAS dispersions without affecting the Newtonian flow behaviour of NaCAS. These results contribute to improve the knowledge of a barely-studied hydrocolloid which may be useful in the development of innovative food systems. Copyright © 2017 Elsevier Ltd. All rights reserved.

Practical problems in aggregating expert opinions

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

Booker, J.M.; Picard, R.R.; Meyer, M.A.

1993-11-01

Expert opinion is data given by a qualified person in response to a technical question. In these analyses, expert opinion provides information where other data are either sparse or non-existent. Improvements in forecasting result from the advantageous addition of expert opinion to observed data in many areas, such as meteorology and econometrics. More generally, analyses of large, complex systems often involve experts on various components of the system supplying input to a decision process; applications include such wide-ranging areas as nuclear reactor safety, management science, and seismology. For large or complex applications, no single expert may be knowledgeable enough aboutmore » the entire application. In other problems, decision makers may find it comforting that a consensus or aggregation of opinions is usually better than a single opinion. Many risk and reliability studies require a single estimate for modeling, analysis, reporting, and decision making purposes. For problems with large uncertainties, the strategy of combining as diverse a set of experts as possible hedges against underestimation of that uncertainty. Decision makers are frequently faced with the task of selecting the experts and combining their opinions. However, the aggregation is often the responsibility of an analyst. Whether the decision maker or the analyst does the aggregation, the input for it, such as providing weights for experts or estimating other parameters, is imperfect owing to a lack of omniscience. Aggregation methods for expert opinions have existed for over thirty years; yet many of the difficulties with their use remain unresolved. The bulk of these problem areas are summarized in the sections that follow: sensitivities of results to assumptions, weights for experts, correlation of experts, and handling uncertainties. The purpose of this paper is to discuss the sources of these problems and describe their effects on aggregation.« less

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

Depletion of E. coli in permeable pavement mineral aggregate storage and reuse systems.

PubMed

Myers, B R; Beecham, S; van Leeuwen, J A; Keegan, A

2009-01-01

Permeable pavement reservoirs provide an important opportunity for the harvesting and storage of stormwater for reuse. This research aims to determine whether storage in dolomite, calcite and quartzite mineral aggregates in the base course of a permeable pavement impacts on the survival of the pathogen indicator organism Escherichia coli (E. coli) in storage. The reasons for depletion were also investigated. Twelve model permeable pavement storage reservoirs were filled, in triplicate, with dolomite, calcite and quartzite. Three reservoirs contained no aggregate. After filling with pathogen spiked rainwater, the concentration of E. coli was examined for 22 days in the reservoirs. The reservoirs were then agitated to determine if there was E. coli present which was not in aqueous suspension. The results of the experiments show that there is no significant difference in the depletion of E. coli found in reservoirs without aggregate, and those filled with dolomite or calcite. The rate of depletion was found to be significantly lower in the quartzite filled reservoirs. Agitation of the reservoirs yielded increases in the aqueous concentration of E. coli in all reservoir types, suggesting that the bacteria are adhering to the surface of the mineral aggregate and to the reservoir walls.

Reduction and degradation of amyloid aggregates by a pulsed radio-frequency cold atmospheric plasma jet

NASA Astrophysics Data System (ADS)

Bayliss, D. L.; Walsh, J. L.; Shama, G.; Iza, F.; Kong, M. G.

2009-11-01

Surface-borne amyloid aggregates with mature fibrils are used as a non-infectious prion model to evaluate cold atmospheric plasmas (CAPs) as a prion inactivation strategy. Using a helium-oxygen CAP jet with pulsed radio-frequency (RF) excitation, amyloid aggregates deposited on freshly cleaved mica discs are reduced substantially leaving only a few spherical fragments of sub-micrometer sizes in areas directly treated by the CAP jet. Outside the light-emitting part of the CAP jet, plasma treatment results in a 'skeleton' of much reduced amyloid stacks with clear evidence of fibril fragmentation. Analysis of possible plasma species and the physical configuration of the jet-sample interaction suggests that the skeleton structures observed are unlikely to have arisen as a result of physical forces of detachment, but instead by progressive diffusion of oxidizing plasma species into porous amyloid aggregates. Composition of chemical bonds of this reduced amyloid sample is very different from that of intact amyloid aggregates. These suggest the possibility of on-site degradation by CAP treatment with little possibility of spreading contamination elsewhere , thus offering a new reaction chemistry route to protein infectivity control with desirable implications for the practical implementation of CAP-based sterilization systems.

The self-association of acebutolol: Conductometry and light scattering

NASA Astrophysics Data System (ADS)

Ruso, Juan M.; López-Fontán, José L.; Prieto, Gerardo; Sarmiento, Félix

2003-04-01

The association characteristics of an amphiphilic beta-blocker drug, acebutolol hydrochloride, in aqueous solution containing high concentrations of electrolyte and at different temperatures have been examined by static and dynamic light scattering and electrical conductivity. Time averaged light scattering measurements on aqueous solutions of acebutolol at 298.15 K in the presence of added electrolyte (0.4-1.0 mol kg-1 NaCl) have shown discontinuities which reflect the appearance of aggregates. The critical micelle concentration, aggregation numbers, effective micelle charges, and degree of micellar ionization were calculated. Dynamic light scattering has shown an increase in micellar size with increase in concentration of added electrolyte. Data have been interpreted using the DLVO theory to quantify the interaction between the drug aggregates and the colloidal stability. Critical micelle concentrations in water have been calculated from conductivity measurements over the temperature range 288.15-313.15 K. The variation in critical concentration with temperature passes through a minimum close to 294 K. Thermodynamic parameters of aggregate formation (ΔGm0,ΔHm0,ΔSm0) were obtained from a variation of the mass action model applicable to systems of low aggregation number.

Deducing dust emission mechanisms from field measurements

USDA-ARS?s Scientific Manuscript database

Field observations are needed to both develop and test theories on dust emission for use in global modeling systems. The mechanism of dust emission (aerodynamic entrainment, saltation bombardment, aggregate disintegration) and the amount and particle-size distribution of emitted dust may vary under ...

Aggregation of asbestos fibers in water: role of solution chemistry

NASA Astrophysics Data System (ADS)

Wu, L.; Ortiz, C. P.; Jerolmack, D. J.

2016-12-01

Aggregation kinetics and stability of colloidal particles have been extensively studied using bulk techniques such as dynamic light scattering; these techniques involve large ensembles of particles and interpretation of results is difficult when particles are non-spherical and poorly characterized, as is always the case with non-ideal natural hazardous materials such as asbestos fibers. These difficulties hinder greatly progress on fundamental understanding of whether the classic colloidal aggregation theories can be applied to natural materials and how the heterogeneity of particles (e.g., shape) affects the colloidal aggregation kinetics and structure. By using in-situ microscopy and particle tracking techniques, we were able to observe the particle-by-particle growth of aggregated formed by elongated particles (synthetic glass rods and natural asbestos fibers) and demonstrated the rod-shaped geometry induced novel structures and growth dynamics that challenge existing theory. In this study, we continue to use asbestos as model system of elongated colloidal contaminant, and investigate the effects of changing solution chemistry (e.g., ionic strength, pH, and natural organic matter (NOM)), on growth dynamics and aggregates structure. The results show that aggregate growth curves are self-similar with a characteristic timescale that increases with increasing pH. By varying ionic strength for fixed pH values, we determine that the ccc is sensitive to pH. Fractal dimension decreases slightly with increasing pH and decreasing ionic strength, indicating that stronger inter-particle repulsion create sparser aggregates; however, the magnitude of the solution chemistry effects is much smaller than that of colloid shape. In monovalent solutions, regardless of their concentration, HA drastically reduces the aggregation kinetics of asbestos fiber. This work may lead to enhanced prediction of the colloidal contaminants' mobility in the environment, bioavailability, and toxicity to organisms.

A discrete three-layer stack aggregate of a linear porphyrin tetramer: solution-phase structure elucidation by NMR and X-ray scattering.

PubMed

Hutin, Marie; Sprafke, Johannes K; Odell, Barbara; Anderson, Harry L; Claridge, Tim D W

2013-08-28

Formation of stacked aggregates can dramatically alter the properties of aromatic π-systems, yet the solution-phase structure elucidation of these aggregates is often impossible because broad distributions of species are formed, giving uninformative spectroscopic data. Here, we show that a butadiyne-linked zinc porphyrin tetramer forms a remarkably well-defined aggregate, consisting of exactly three molecules, in a parallel stacked arrangement (in chloroform at room temperature; concentration 1 mM-0.1 μM). The aggregate has a mass of 14.7 kDa. Unlike most previously reported aggregates, it gives sharp NMR resonances and aggregation is in slow exchange on the NMR time scale. The structure was elucidated using a range of NMR techniques, including diffusion-editing, (1)H-(29)Si HMBC, (1)H-(1)H COSY, TOCSY and NOESY, and (1)H-(13)C edited HSQC spectroscopy. Surprisingly, the (1)H-(1)H COSY spectrum revealed many long-range residual dipolar couplings (RDCs), and detailed analysis of magnetic field-induced (1)H-(13)C RDCs provided further evidence for the structural model. The size and shape of the aggregate is supported by small-angle X-ray scattering (SAXS) data. It adopts a geometry that maximizes van der Waals contact between the porphyrins, while avoiding clashes between side chains. The need for interdigitation of the side chains prevents formation of stacks consisting of more than three layers. Although a detailed analysis has only been carried out for one compound (the tetramer), comparison with the NMR spectra of other oligomers indicates that they form similar three-layer stacks. In all cases, aggregation can be prevented by addition of pyridine, although at low pyridine concentrations, disaggregation takes many hours to reach equilibrium.

Micro- and meso-scale pore structure in mortar in relation to aggregate content

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

Gao, Yun, E-mail: yun.gao@ugent.be; De Schutter, Geert; Ye, Guang

2013-10-15

Mortar is often viewed as a three-phase composite consisting of aggregate, bulk paste, and an interfacial transition zone (ITZ). However, this description is inconsistent with experimental findings because of the basic assumption that larger pores are only present within the ITZ. In this paper, we use backscattered electron (BSE) imaging to investigate the micro- and meso-scale structure of mortar with varying aggregate content. The results indicate that larger pores are present not only within the ITZ but also within areas far from aggregates. This phenomenon is discussed in detail based on a series of analytical calculations, such as the effectivemore » water binder ratio and the inter-aggregate spacing. We developed a modified computer model that includes a two-phase structure for bulk paste. This model interprets previous mercury intrusion porosimetry data very well. -- Highlights: •Based on BSE, we examine the HCSS model. •We develop the HCSS-DBLB model. •We use the modified model to interpret the MIP data.« less

Exciton-vibrational coupling in the dynamics and spectroscopy of Frenkel excitons in molecular aggregates

NASA Astrophysics Data System (ADS)

Schröter, M.; Ivanov, S. D.; Schulze, J.; Polyutov, S. P.; Yan, Y.; Pullerits, T.; Kühn, O.

2015-03-01

The influence of exciton-vibrational coupling on the optical and transport properties of molecular aggregates is an old problem that gained renewed interest in recent years. On the experimental side, various nonlinear spectroscopic techniques gave insight into the dynamics of systems as complex as photosynthetic antennae. Striking evidence was gathered that in these protein-pigment complexes quantum coherence is operative even at room temperature conditions. Investigations were triggered to understand the role of vibrational degrees of freedom, beyond that of a heat bath characterized by thermal fluctuations. This development was paralleled by theory, where efficient methods emerged, which could provide the proper frame to perform non-Markovian and non-perturbative simulations of exciton-vibrational dynamics and spectroscopy. This review summarizes the state of affairs of the theory of exciton-vibrational interaction in molecular aggregates and photosynthetic antenna complexes. The focus is put on the discussion of basic effects of exciton-vibrational interaction from the stationary and dynamics points of view. Here, the molecular dimer plays a prominent role as it permits a systematic investigation of absorption and emission spectra by numerical diagonalization of the exciton-vibrational Hamiltonian in a truncated Hilbert space. An extension to larger aggregates, having many coupled nuclear degrees of freedom, becomes possible with the Multi-Layer Multi-Configuration Time-Dependent Hartree (ML-MCTDH) method for wave packet propagation. In fact it will be shown that this method allows one to approach the limit of almost continuous spectral densities, which is usually the realm of density matrix theory. Real system-bath situations are introduced for two models, which differ in the way strongly coupled nuclear coordinates are treated, as a part of the relevant system or the bath. A rather detailed exposition of the Hierarchy Equations Of Motion (HEOM) method will be given in terms of a stochastic decoupling ansatz. This method has become the standard in exciton-vibrational theory and illustrative examples will be presented as well as a comparison with ML-MCTDH. Applications will be shown for generic model systems as well as for small aggregates mimicking those formed by perylene bisimide dyes. Further, photosynthetic antenna complexes will be discussed, including spectral densities and the role of exciton-vibrational coupling in two-dimensional electronic spectroscopy.

An Investigation of Aggregation in Synergistic Solvent Extraction Systems

NASA Astrophysics Data System (ADS)

Jackson, Andy Steven

With an increasing focus on anthropogenic climate change, nuclear reactors present an attractive option for base load power generation with regard to air pollution and carbon emissions, especially when compared with traditional fossil fuel based options. However, used nuclear fuel (UNF) is highly radiotoxic and contains minor actinides (americium and curium) which remain more radiotoxic than natural uranium ore for hundreds of thousands of years, presenting a challenge for long-term storage . Advanced nuclear fuel recycling can reduce this required storage time to thousands of years by removing the highly radiotoxic minor actinides. Many advanced separation schemes have been proposed to achieve this separation but none have been implemented to date. A key feature among many proposed schemes is the use of more than one extraction reagent in a single extraction phase, which can lead to the phenomenon known as "synergism" in which the extraction efficiency for a combination of the reagents is greater than that of the individual extractants alone. This feature is not well understood for many systems and a comprehensive picture of the mechanism behind synergism does not exist. There are several proposed mechanisms for synergism though none have been used to model multiple extraction systems. This work examines several proposed advanced extractant combinations which exhibit synergism: 2-bromodecanoic acid (BDA) with 2,2':6',2"-terpyridine (TERPY), tri-n-butylphosphine oxide (TPBO) with 2-thenoyltrifluoro acetone (HTTA), and dinonylnaphthalene sulfonic acid (HDNNS) with 5,8-diethyl-7-hydroxy-dodecan-6-oxime (LIX). We examine two proposed synergistic mechanisms involving and attempt to verify the ability of these mechanisms to predict the extraction behavior of the chosen systems. These are a reverse micellar catalyzed extraction model and a mixed complex formation model. Neither was able to effectively predict the synergistic behavior of the systems. We further examine these systems for the presence of large reverse micellar aggregates and thermodynamic signatures of aggregation. Behaviors differed widely from system to system, suggesting the possibility of more than one mechanism being responsible for similar observed extraction trends.

The specific role of fungal community structure on soil aggregation and carbon sequestration: results from long-term field study in a paddy soil

NASA Astrophysics Data System (ADS)

Murugan, Rajasekaran; Kumar, Sanjay

2015-04-01

Soil aggregate stability is a crucial soil property that affects soil biota, biogeochemical processes and C sequestration. The relationship between soil aggregate stability and soil C cycling is well known but the influence of specific fungal community structure on this relationship is largely unknown in paddy soils. The aim of the present study was to evaluate the long-term fertilisation (mineral fertiliser-MIN; farmyard manure-FYM; groundnut oil cake-GOC) effects on soil fungal community shifts associated with soil aggregates under rice-monoculture (RRR) and rice-legume-rice (RLR) systems. Fungal and bacterial communities were characterized using phospholipid fatty acids, and glucosamine and muramic acid were used as biomarkers for fungal and bacterial residues, respectively. Microbial biomass C and N, fungal biomass and residues were significantly higher in the organic fertiliser treatments than in the MIN treatment, for all aggregate sizes under both crop rotation systems. In general, fungal/bacterial biomass ratio and fungal residue C/bacterial residue C ratio were significantly higher in macroaggregate fractions (> 2000 and 250-2000 μm) than in microaggregate fractions (53-250 and <53 μm). In both crop rotation systems, the long-term application of FYM and GOC led to increased accumulation of saprotrophic fungi (SF) in aggregate fractions > 2000 μm. In contrast, we found that arbuscular mycorrhizal fungi (AMF) was surprisingly higher in aggregate fractions > 2000 μm than in aggregate fraction 250-2000 μm under MIN treatment. The RLR system showed significantly higher AMF biomass and fungal residue C/ bacterial residue C ratio in both macroaggregate fractions compared to the RRR system. The strong relationships between SF, AMF and water stable aggregates shows the specific contribution of fungi community on soil aggregate stability. Our results highlight the fact that changes within fungal community structure play an important role in shaping the soil aggregate stability and C sequestration in tropical agricultural ecosystems.

Particle-based simulations of self-motile suspensions

NASA Astrophysics Data System (ADS)

Hinz, Denis F.; Panchenko, Alexander; Kim, Tae-Yeon; Fried, Eliot

2015-11-01

A simple model for simulating flows of active suspensions is investigated. The approach is based on dissipative particle dynamics. While the model is potentially applicable to a wide range of self-propelled particle systems, the specific class of self-motile bacterial suspensions is considered as a modeling scenario. To mimic the rod-like geometry of a bacterium, two dissipative particle dynamics particles are connected by a stiff harmonic spring to form an aggregate dissipative particle dynamics molecule. Bacterial motility is modeled through a constant self-propulsion force applied along the axis of each such aggregate molecule. The model accounts for hydrodynamic interactions between self-propelled agents through the pairwise dissipative interactions conventional to dissipative particle dynamics. Numerical simulations are performed using a customized version of the open-source software package LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) software package. Detailed studies of the influence of agent concentration, pairwise dissipative interactions, and Stokes friction on the statistics of the system are provided. The simulations are used to explore the influence of hydrodynamic interactions in active suspensions. For high agent concentrations in combination with dominating pairwise dissipative forces, strongly correlated motion patterns and a fluid-like spectral distributions of kinetic energy are found. In contrast, systems dominated by Stokes friction exhibit weaker spatial correlations of the velocity field. These results indicate that hydrodynamic interactions may play an important role in the formation of spatially extended structures in active suspensions.

Laboratory light scattering measurements on "natural" particles with the PROGRA2 experiment: an overview

NASA Astrophysics Data System (ADS)

Hadamcik, E.; Rrenard, J.; Levasseur-Regourd, A. C.; Worms, J. C.

Polarimetric phase curves were obtained with the PROGRA2 instrument for different particles: glass beads, polyhedral solids, rough particles, dense aggregates and aggregates with porosity higher than 90 %. The main purpose of these measurements is to build a large database, which allows interpreting remote sensing observations of solar system bodies. For some samples numerical or experimental models (i.e. DDA, stochastically built particles, microwave analogue) and laboratory experiments are compared to better disentangle the involved physical properties. This paper gives some main results of the experiment, and their applications to Earth atmosphere, comets and asteroids.

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

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

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

2014-03-01

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

A GIS analysis of suitability for construction aggregate recycling sites using regional transportation network and population density features

USGS Publications Warehouse

Robinson, G.R.; Kapo, K.E.

2004-01-01

Aggregate is used in road and building construction to provide bulk, strength, support, and wear resistance. Reclaimed asphalt pavement (RAP) and reclaimed Portland cement concrete (RPCC) are abundant and available sources of recycled aggregate. In this paper, current aggregate production operations in Virginia, Maryland, and the District of Columbia are used to develop spatial association models for the recycled aggregate industry with regional transportation network and population density features. The cost of construction aggregate to the end user is strongly influenced by the cost of transporting processed aggregate from the production site to the construction site. More than 60% of operations recycling aggregate in the mid-Atlantic study area are located within 4.8 km (3 miles) of an interstate highway. Transportation corridors provide both sites of likely road construction where aggregate is used and an efficient means to move both materials and on-site processing equipment back and forth from various work sites to the recycling operations. Urban and developing areas provide a high market demand for aggregate and a ready source of construction debris that may be processed into recycled aggregate. Most aggregate recycling operators in the study area are sited in counties with population densities exceeding 77 people/km2 (200 people/mile 2). No aggregate recycling operations are sited in counties with less than 19 people/km2 (50 people/mile2), reflecting the lack of sufficient long-term sources of construction debris to be used as an aggregate source, as well as the lack of a sufficient market demand for aggregate in most rural areas to locate a recycling operation there or justify the required investment in the equipment to process and produce recycled aggregate. Weights of evidence analyses (WofE), measuring correlation on an area-normalized basis, and weighted logistic regression (WLR), are used to model the distribution of RAP and RPCC operations relative to transportation network and population distribution data. The models can be used on a regional scale to quickly map the relative site suitability for a RAP or RPCC aggregate recycling operation in a particular area based on transportation network and population parameters. The results can be used to identify general areas to be further evaluated on a site-specific basis using more detailed marketplace information. As transportation or population features change due to planning or actual development, the models can be easily revised to reflect these changes. ?? 2004 Elsevier B.V. All rights reserved.

Understanding amyloid aggregation by statistical analysis of atomic force microscopy images

NASA Astrophysics Data System (ADS)

Adamcik, Jozef; Jung, Jin-Mi; Flakowski, Jérôme; de Los Rios, Paolo; Dietler, Giovanni; Mezzenga, Raffaele

2010-06-01

The aggregation of proteins is central to many aspects of daily life, including food processing, blood coagulation, eye cataract formation disease and prion-related neurodegenerative infections. However, the physical mechanisms responsible for amyloidosis-the irreversible fibril formation of various proteins that is linked to disorders such as Alzheimer's, Creutzfeldt-Jakob and Huntington's diseases-have not yet been fully elucidated. Here, we show that different stages of amyloid aggregation can be examined by performing a statistical polymer physics analysis of single-molecule atomic force microscopy images of heat-denatured β-lactoglobulin fibrils. The atomic force microscopy analysis, supported by theoretical arguments, reveals that the fibrils have a multistranded helical shape with twisted ribbon-like structures. Our results also indicate a possible general model for amyloid fibril assembly and illustrate the potential of this approach for investigating fibrillar systems.

Tuning aggregation of microemulsion droplets and silica nanoparticles using solvent mixtures.

PubMed

Salabat, Alireza; Eastoe, Julian; Mutch, Kevin J; Tabor, Rico F

2008-02-15

The effect of solvent on stability of water-in-oil microemulsions has been studied with AOT (sodium bis(2-ethylhexyl)sulfosuccinate) and different solvent mixtures of n-heptane, toluene and dodecane. Dynamic light scattering DLS was used to monitor the apparent diffusion coefficient D(A) and effective microemulsion droplet diameter on changing composition of the solvent. Interdroplet attractive interactions, as indicated by variations in D(A), can be tuned by formulation of appropriate solvent mixtures using heptane, toluene, and dodecane. In extreme cases, solvent mixtures can be used to induce phase transitions in the microemulsions. Aggregation and stability of model AOT-stabilized silica nanoparticles in different solvents were also investigated to explore further these solvent effects. For both systems the state of aggregation can be correlated with the effective molecular volume of the solvent V(mol)(eff) mixture.

DDA Computations of Porous Aggregates with Forsterite Crystals: Effects of Crystal Shape and Crystal Mass Fraction

NASA Technical Reports Server (NTRS)

Wooden, Diane H.; Lindsay, Sean S.; Harker, David; Woodward, Charles; Kelley, Michael S.; Kolokolova, Ludmilla

2015-01-01

Porous aggregate grains are commonly found in cometary dust samples and are needed to model cometary IR spectral energy distributions (SEDs). Models for thermal emissions from comets require two forms of silicates: amorphous and crystalline. The dominant crystal resonances observed in comet SEDs are from Forsterite (Mg2SiO4). The mass fractions that are crystalline span a large range from 0.0 < or = fcrystal < or = 0.74. Radial transport models that predict the enrichment of the outer disk (>25 AU at 1E6 yr) by inner disk materials (crystals) are challenged to yield the highend-range of cometary crystal mass fractions. However, in current thermal models, Forsterite crystals are not incorporated into larger aggregate grains but instead only are considered as discrete crystals. A complicating factor is that Forsterite crystals with rectangular shapes better fit the observed spectral resonances in wavelength (11.0-11.15 microns, 16, 19, 23.5, 27, and 33 microns), feature asymmetry and relative height (Lindley et al. 2013) than spherically or elliptically shaped crystals. We present DDA-DDSCAT computations of IR absorptivities (Qabs) of 3 micron-radii porous aggregates with 0.13 < or = fcrystal < or = 0.35 and with polyhedral-shaped Forsterite crystals. We can produce crystal resonances with similar appearance to the observed resonances of comet Hale- Bopp. Also, a lower mass fraction of crystals in aggregates can produce the same spectral contrast as a higher mass fraction of discrete crystals; the 11micron and 23 micron crystalline resonances appear amplified when crystals are incorporated into aggregates composed otherwise of spherically shaped amorphous Fe-Mg olivines and pyroxenes. We show that the optical properties of a porous aggregate is not linear combination of its monomers, so aggregates need to be computed. We discuss the consequence of lowering comet crystal mass fractions by modeling IR SEDs with aggregates with crystals, and the implications for radial transport models of our protoplanetary disk.

A Psychological Model for Aggregating Judgments of Magnitude

NASA Astrophysics Data System (ADS)

Merkle, Edgar C.; Steyvers, Mark

In this paper, we develop and illustrate a psychologically-motivated model for aggregating judgments of magnitude across experts. The model assumes that experts' judgments are perturbed from the truth by both systematic biases and random error, and it provides aggregated estimates that are implicitly based on the application of nonlinear weights to individual judgments. The model is also easily extended to situations where experts report multiple quantile judgments. We apply the model to expert judgments concerning flange leaks in a chemical plant, illustrating its use and comparing it to baseline measures.

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

Thomas, Reshmi; Thomas, Anoop; Pullanchery, Saranya

Strong coupling interactions between plasmon and exciton-based excitations have been proposed to be useful in the design of optoelectronic systems. However, the role of various optical parameters dictating the plasmon-exciton (plexciton) interactions is less understood. Herein, we propose an inequality for achieving strong coupling between plasmons and excitons through appropriate variation of their oscillator strengths and spectral widths. These aspects are found to be consistent with experiments on two sets of free-standing plexcitonic systems obtained by (i) linking fluorescein isothiocyanate on Ag nanoparticles of varying sizes through silane coupling and (ii) electrostatic binding of cyanine dyes on polystyrenesulfonate-coated Au nanorodsmore » of varying aspect ratios. Being covalently linked on Ag nanoparticles, fluorescein isothiocyanate remains in monomeric state, and its high oscillator strength and narrow spectral width enable us to approach the strong coupling limit. In contrast, in the presence of polystyrenesulfonate, monomeric forms of cyanine dyes exist in equilibrium with their aggregates: Coupling is not observed for monomers and H-aggregates whose optical parameters are unfavorable. The large aggregation number, narrow spectral width, and extremely high oscillator strength of J-aggregates of cyanines permit effective delocalization of excitons along the linear assembly of chromophores, which in turn leads to efficient coupling with the plasmons. Further, the results obtained from experiments and theoretical models are jointly employed to describe the plexcitonic states, estimate the coupling strengths, and rationalize the dispersion curves. The experimental results and the theoretical analysis presented here portray a way forward to the rational design of plexcitonic systems attaining the strong coupling limits.« less

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

PubMed

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

2016-03-01

Aggregates of amyloid-β (Aβ) peptide are known to be the key pathological agents in Alzheimer disease (AD). Aβ aggregates to form large, insoluble fibrils that deposit as senile plaques in AD brains. The process of aggregation is nucleation-dependent in which the formation of a nucleus is the rate-limiting step, and controls the physiochemical fate of the aggregates formed. Therefore, understanding the properties of nucleus and pre-nucleation events will be significant in reducing the existing knowledge-gap in AD pathogenesis. In this report, we have determined the plausible range of critical nucleation number (n(*)), the number of monomers associated within the nucleus for a homogenous aggregation model with single unique nucleation event, by two independent methods: A reduced-order stability analysis and ordinary differential equation based numerical analysis, supported by experimental biophysics. The results establish that the most likely range of n(*) is between 7 and 14 and within, this range, n(*) = 12 closely supports the experimental data. These numbers are in agreement with those previously reported, and importantly, the report establishes a new modeling framework using two independent approaches towards a convergent solution in modeling complex aggregation reactions. Our model also suggests that the formation of large protofibrils is dependent on the nature of n(*), further supporting the idea that pre-nucleation events are significant in controlling the fate of larger aggregates formed. This report has re-opened an old problem with a new perspective and holds promise towards revealing the molecular events in amyloid pathologies in the future. Copyright © 2015 Elsevier Inc. All rights reserved.

Development of Extended Period Pressure-Dependent Demand Water Distribution Models

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

Judi, David R.; Mcpherson, Timothy N.

2015-03-20

Los Alamos National Laboratory (LANL) has used modeling and simulation of water distribution systems for N-1 contingency analyses to assess criticality of water system assets. Critical components considered in these analyses include pumps, tanks, and supply sources, in addition to critical pipes or aqueducts. A contingency represents the complete removal of the asset from system operation. For each contingency, an extended period simulation (EPS) is run using EPANET. An EPS simulates water system behavior over a time period, typically at least 24 hours. It assesses the ability of a system to respond and recover from asset disruption through distributed storagemore » in tanks throughout the system. Contingencies of concern are identified as those in which some portion of the water system has unmet delivery requirements. A delivery requirement is defined as an aggregation of water demands within a service area, similar to an electric power demand. The metric used to identify areas of unmet delivery requirement in these studies is a pressure threshold of 15 pounds per square inch (psi). This pressure threshold is used because it is below the required pressure for fire protection. Any location in the model with pressure that drops below this threshold at any time during an EPS is considered to have unmet service requirements and is used to determine cascading consequences. The outage area for a contingency is the aggregation of all service areas with a pressure below the threshold at any time during the EPS.« less

Physical soil architectural traits are functionally linked to carbon decomposition and bacterial diversity.

PubMed

Rabbi, S M F; Daniel, H; Lockwood, P V; Macdonald, C; Pereg, L; Tighe, M; Wilson, B R; Young, I M

2016-09-12

Aggregates play a key role in protecting soil organic carbon (SOC) from microbial decomposition. The objectives of this study were to investigate the influence of pore geometry on the organic carbon decomposition rate and bacterial diversity in both macro- (250-2000 μm) and micro-aggregates (53-250 μm) using field samples. Four sites of contrasting land use on Alfisols (i.e. native pasture, crop/pasture rotation, woodland) were investigated. 3D Pore geometry of the micro-aggregates and macro-aggregates were examined by X-ray computed tomography (μCT). The occluded particulate organic carbon (oPOC) of aggregates was measured by size and density fractionation methods. Micro-aggregates had 54% less μCT observed porosity but 64% more oPOC compared with macro-aggregates. In addition, the pore connectivity in micro-aggregates was lower than macro-aggregates. Despite both lower μCT observed porosity and pore connectivity in micro-aggregates, the organic carbon decomposition rate constant (Ksoc) was similar in both aggregate size ranges. Structural equation modelling showed a strong positive relationship of the concentration of oPOC with bacterial diversity in aggregates. We use these findings to propose a conceptual model that illustrates the dynamic links between substrate, bacterial diversity, and pore geometry that suggests a structural explanation for differences in bacterial diversity across aggregate sizes.

Physical soil architectural traits are functionally linked to carbon decomposition and bacterial diversity

PubMed Central

Rabbi, S. M. F.; Daniel, H.; Lockwood, P. V.; Macdonald, C.; Pereg, L.; Tighe, M.; Wilson, B. R.; Young, I. M.

2016-01-01

Aggregates play a key role in protecting soil organic carbon (SOC) from microbial decomposition. The objectives of this study were to investigate the influence of pore geometry on the organic carbon decomposition rate and bacterial diversity in both macro- (250–2000 μm) and micro-aggregates (53–250 μm) using field samples. Four sites of contrasting land use on Alfisols (i.e. native pasture, crop/pasture rotation, woodland) were investigated. 3D Pore geometry of the micro-aggregates and macro-aggregates were examined by X-ray computed tomography (μCT). The occluded particulate organic carbon (oPOC) of aggregates was measured by size and density fractionation methods. Micro-aggregates had 54% less μCT observed porosity but 64% more oPOC compared with macro-aggregates. In addition, the pore connectivity in micro-aggregates was lower than macro-aggregates. Despite both lower μCT observed porosity and pore connectivity in micro-aggregates, the organic carbon decomposition rate constant (Ksoc) was similar in both aggregate size ranges. Structural equation modelling showed a strong positive relationship of the concentration of oPOC with bacterial diversity in aggregates. We use these findings to propose a conceptual model that illustrates the dynamic links between substrate, bacterial diversity, and pore geometry that suggests a structural explanation for differences in bacterial diversity across aggregate sizes. PMID:27615807

The response of aggregated Pseudomonas putida CP1 cells to UV-C and UV-A/B disinfection.

PubMed

Maganha de Almeida, Ana C; Quilty, Bríd

2016-11-01

UV radiation is a spread method used worldwide for the disinfection of water. However, much of the research on the disinfection of bacterial cells by UV has focused on planktonic cells. Many bacterial cells in nature are present in clumps or aggregates, and these aggregates, which are more resistant to disinfection than their planktonic counterparts, can be problematic in engineered water systems. The current research used Pseudomonas putida (P. putida) CP1, an environmental and non-pathogenic microorganism which autoaggregates when grown under certain conditions, as a model organism to simulate aggregated cells. The study investigated the response of both the planktonic and the aggregated forms of the bacterium to UV-C (λ = 253.7 nm) and UV-A/B (λ > 300 nm) disinfection at laboratory scale in a minimal medium. The planktonic cells of P. putida CP1 were inactivated within 60 s by UV-C and in 60 min by UV-A/B; however, the aggregated cells required 120 min of UV-C treatment and 240 min of UV-A/B radiation to become inactive. The size of the aggregate was reduced following UV treatment. Although all the cells had lost culturability, viability as measured by the LIVE/DEAD ® stain and epifluorescence microscopy was not completely lost and the cells all demonstrated regrowth after overnight incubation in the dark.

Stand-level growth and yield component models for red oak-sweetgum forests on Mid-South minor stream bottoms

Treesearch

Emily B. Schultz; J. Clint Iles; Thomas G. Matney; Andrew W. Ezell; James S. Meadows; Theodor D. Leininger; al. et.

2010-01-01

Greater emphasis is being placed on Southern bottomland hardwood management, but relatively few growth and yield prediction systems exist that are based on sufficient measurements. We present the aggregate stand-level expected yield and structural component equations for a red oak (Quercus section Lobatae)-sweetgum (Liquidambar styraciflua L.) growth and yield model....

TDP-43 and ubiquitinated cytoplasmic aggregates in sporadic ALS are low frequency and widely distributed in the lower motor neuron columns independent of disease spread

PubMed Central

Bodansky, Aaron; Kim, Jae Mun ‘Hugo’; Tempest, Lynne; Velagapudi, Amit; Libby, Ryan; Ravits, John

2010-01-01

Abstract Ubiqitinated and TDP-43 immunoreactive cytoplasmic aggregates are hallmark features of ALS molecular pathology. Since clinically most ALS begins focally and advances contiguously, it is important to characterize their distribution. Our objective was to determine the extent and distribution of TDP-43 immunoreactive aggregates in the lower motor neuron columns as a function of disease onset, and to correlate ubiquitinated with TDP-43 aggregates in the lumbar region. We examined TDP-43 cytoplasmic aggregates at four separate neuraxis levels – hypoglossal nucleus and cervical, thoracic, and lumbar anterior horns – in five controls and 20 sporadic ALS nervous systems from patients whose disease began in various sites, i.e. five bulbar, five arm, five trunk, and five leg onsets. We correlated ubiquitinated to TDP-43 aggregates on adjacent histological sections for the lumbar regions. We found that TDP-43 cytoplasmic aggregates are seen in about 8% of motor neurons but there is marked variability between nervous systems, ranging from 0.4% to 20.6%. The aggregates are uniformly distributed within individual nervous systems. There is no obvious correlation between site of disease onset and rate of spread. Almost all ubiquitinated aggregates correlate to TDP-43 aggregates. Thus, TDP-43 immunoreactive cytoplasmic aggregates have a low overall average frequency that does not correlate with either disease course or clinical spread and is the prime ubiquitinated protein. PMID:20225928

Model for fluorescence quenching in light harvesting complex II in different aggregation states.

PubMed

Andreeva, Atanaska; Abarova, Silvia; Stoitchkova, Katerina; Busheva, Mira

2009-02-01

Low-temperature (77 K) steady-state fluorescence emission spectroscopy and dynamic light scattering were applied to the main chlorophyll a/b protein light harvesting complex of photosystem II (LHC II) in different aggregation states to elucidate the mechanism of fluorescence quenching within LHC II oligomers. Evidences presented that LHC II oligomers are heterogeneous and consist of large and small particles with different fluorescence yield. At intermediate detergent concentrations the mean size of the small particles is similar to that of trimers, while the size of large particles is comparable to that of aggregated trimers without added detergent. It is suggested that in small particles and trimers the emitter is monomeric chlorophyll, whereas in large aggregates there is also another emitter, which is a poorly fluorescing chlorophyll associate. A model, describing populations of antenna chlorophyll molecules in small and large aggregates in their ground and first singlet excited states, is considered. The model enables us to obtain the ratio of the singlet excited-state lifetimes in small and large particles, the relative amount of chlorophyll molecules in large particles, and the amount of quenchers as a function of the degree of aggregation. These dependencies reveal that the quenching of the chl a fluorescence upon aggregation is due to the formation of large aggregates and the increasing of the amount of chlorophyll molecules forming these aggregates. As a consequence, the amount of quenchers, located in large aggregates, is increased, and their singlet excited-state lifetimes steeply decrease.

Localization of Protein Aggregation in Escherichia coli Is Governed by Diffusion and Nucleoid Macromolecular Crowding Effect

PubMed Central

Coquel, Anne-Sophie; Jacob, Jean-Pascal; Primet, Mael; Demarez, Alice; Dimiccoli, Mariella; Julou, Thomas; Moisan, Lionel

2013-01-01

Aggregates of misfolded proteins are a hallmark of many age-related diseases. Recently, they have been linked to aging of Escherichia coli (E. coli) where protein aggregates accumulate at the old pole region of the aging bacterium. Because of the potential of E. coli as a model organism, elucidating aging and protein aggregation in this bacterium may pave the way to significant advances in our global understanding of aging. A first obstacle along this path is to decipher the mechanisms by which protein aggregates are targeted to specific intercellular locations. Here, using an integrated approach based on individual-based modeling, time-lapse fluorescence microscopy and automated image analysis, we show that the movement of aging-related protein aggregates in E. coli is purely diffusive (Brownian). Using single-particle tracking of protein aggregates in live E. coli cells, we estimated the average size and diffusion constant of the aggregates. Our results provide evidence that the aggregates passively diffuse within the cell, with diffusion constants that depend on their size in agreement with the Stokes-Einstein law. However, the aggregate displacements along the cell long axis are confined to a region that roughly corresponds to the nucleoid-free space in the cell pole, thus confirming the importance of increased macromolecular crowding in the nucleoids. We thus used 3D individual-based modeling to show that these three ingredients (diffusion, aggregation and diffusion hindrance in the nucleoids) are sufficient and necessary to reproduce the available experimental data on aggregate localization in the cells. Taken together, our results strongly support the hypothesis that the localization of aging-related protein aggregates in the poles of E. coli results from the coupling of passive diffusion-aggregation with spatially non-homogeneous macromolecular crowding. They further support the importance of “soft” intracellular structuring (based on macromolecular crowding) in diffusion-based protein localization in E. coli. PMID:23633942

Fractal Aggregates in Tennis Ball Systems

ERIC Educational Resources Information Center

Sabin, J.; Bandin, M.; Prieto, G.; Sarmiento, F.

2009-01-01

We present a new practical exercise to explain the mechanisms of aggregation of some colloids which are otherwise not easy to understand. We have used tennis balls to simulate, in a visual way, the aggregation of colloids under reaction-limited colloid aggregation (RLCA) and diffusion-limited colloid aggregation (DLCA) regimes. We have used the…

Implementation of AIMS in measuring aggregate resistance to polishing, abrasion, and breakage.

DOT National Transportation Integrated Search

2014-05-01

The feasibility of using the Micro-Deval apparatus along with the second-generation Aggregate Imaging System : (AIMS) to develop a procedure for measuring aggregate polishing resistance, and to measure aggregate shape : properties was investigated. E...

Electrical interactions in the cell: Asymmetric screening in a watery antiverse.

PubMed

Doerr, T P; Yu, Yi-Kuo

2014-05-01

The problem of electrostatics in biomolecular systems presents an excellent opportunity for cross-disciplinary science and a context in which fundamental physics is called for to answer complex questions. Due to the large density in biological cells of charged biomacromolecules such as protein factors and DNA, it is challenging to understand quantitatively the electric forces in these systems. Two questions are especially puzzling. First, how is it that such a dense system of charged molecules does not simply aggregate in random and non-functional ways? Second, since some mechanism apparently prevents such aggregation, how is it that binding of biomolecules still occurs so reliably? Recognizing the role of water as a universal solvent in living systems is key to understanding these questions. We present a simplified physical model in which water is regarded as a medium of high dielectric constant that nevertheless exhibits the key features essential for answering the two questions presented. The answer to the first question lies in the strong screening ability of water, which reduces the energy scale of the electrostatic interactions. Furthermore, our model reveals the existence of asymmetric screening, a pronounced asymmetry between the screening for a system with like charges and that for a system with opposite charges, and this provides an answer to the second question.

Electrical interactions in the cell: Asymmetric screening in a watery antiverse

PubMed Central

Doerr, T. P.; Yu, Yi-Kuo

2014-01-01

The problem of electrostatics in biomolecular systems presents an excellent opportunity for cross-disciplinary science and a context in which fundamental physics is called for to answer complex questions. Due to the large density in biological cells of charged biomacromolecules such as protein factors and DNA, it is challenging to understand quantitatively the electric forces in these systems. Two questions are especially puzzling. First, how is it that such a dense system of charged molecules does not simply aggregate in random and non-functional ways? Second, since some mechanism apparently prevents such aggregation, how is it that binding of biomolecules still occurs so reliably? Recognizing the role of water as a universal solvent in living systems is key to understanding these questions. We present a simplified physical model in which water is regarded as a medium of high dielectric constant that nevertheless exhibits the key features essential for answering the two questions presented. The answer to the first question lies in the strong screening ability of water, which reduces the energy scale of the electrostatic interactions. Furthermore, our model reveals the existence of asymmetric screening, a pronounced asymmetry between the screening for a system with like charges and that for a system with opposite charges, and this provides an answer to the second question. PMID:25125701

Discrete stochastic charging of aggregate grains

NASA Astrophysics Data System (ADS)

Matthews, Lorin S.; Shotorban, Babak; Hyde, Truell W.

2018-05-01

Dust particles immersed in a plasma environment become charged through the collection of electrons and ions at random times, causing the dust charge to fluctuate about an equilibrium value. Small grains (with radii less than 1 μm) or grains in a tenuous plasma environment are sensitive to single additions of electrons or ions. Here we present a numerical model that allows examination of discrete stochastic charge fluctuations on the surface of aggregate grains and determines the effect of these fluctuations on the dynamics of grain aggregation. We show that the mean and standard deviation of charge on aggregate grains follow the same trends as those predicted for spheres having an equivalent radius, though aggregates exhibit larger variations from the predicted values. In some plasma environments, these charge fluctuations occur on timescales which are relevant for dynamics of aggregate growth. Coupled dynamics and charging models show that charge fluctuations tend to produce aggregates which are much more linear or filamentary than aggregates formed in an environment where the charge is stationary.

Characterizing the mechanical behavior of the zebrafish germ layers

NASA Astrophysics Data System (ADS)

Kealhofer, David; Serwane, Friedhelm; Mongera, Alessandro; Rowghanian, Payam; Lucio, Adam; Campàs, Otger

Organ morphogenesis and the development of the animal body plan involve complex spatial and temporal control of tissue- and cell-level mechanics. A prime example is the generation of stresses by individual cells to reorganize the tissue. These processes have remained poorly understood due to a lack of techniques to characterize the local constitutive law of the material, which relates local cellular forces to the resulting tissue flows. We have developed a method for quantitative, local in vivo study of material properties in living tissue using magnetic droplet probes. We use this technique to study the material properties of the different zebrafish germ layers using aggregates of zebrafish mesendodermal and ectodermal cells as a model system. These aggregates are ideal for controlled studies of the mechanics of individual germ layers because of the homogeneity of the cell type and the simple spherical geometry. Furthermore, the numerous molecular tools and transgenic lines already developed for this model organism can be applied to these aggregates, allowing us to characterize the contributions of cell cortex tension and cell adhesion to the mechanical properties of the zebrafish germ layers.

Biomarkers for ragwort poisoning in horses: identification of protein targets

PubMed Central

Moore, Rowan E; Knottenbelt, Derek; Matthews, Jacqueline B; Beynon, Robert J; Whitfield, Phillip D

2008-01-01

Background Ingestion of the poisonous weed ragwort (Senecio jacobea) by horses leads to irreversible liver damage. The principal toxins of ragwort are the pyrrolizidine alkaloids that are rapidly metabolised to highly reactive and cytotoxic pyrroles, which can escape into the circulation and bind to proteins. In this study a non-invasive in vitro model system has been developed to investigate whether pyrrole toxins induce specific modifications of equine blood proteins that are detectable by proteomic methods. Results One dimensional gel electrophoresis revealed a significant alteration in the equine plasma protein profile following pyrrole exposure and the formation of a high molecular weight protein aggregate. Using mass spectrometry and confirmation by western blotting the major components of this aggregate were identified as fibrinogen, serum albumin and transferrin. Conclusion These findings demonstrate that pyrrolic metabolites can modify equine plasma proteins. The high molecular weight aggregate may result from extensive inter- and intra-molecular cross-linking of fibrinogen with the pyrrole. This model has the potential to form the basis of a novel proteomic strategy aimed at identifying surrogate protein biomarkers of ragwort exposure in horses and other livestock. PMID:18691403

Aggregation, sedimentation, dissolution and bioavailability of quantum dots in estuarine systems.

EPA Science Inventory

To understand their fate and transport in estuarine systems, the aggregation, sedimentation, and dissolution of CdSe quantum dots (QDs) in seawater were investigated. Hydrodynamic size increased from 40 to 60 nm to >1 mm within 1 h in seawater, and the aggregates were highly p...

Using JEDI Data | Jobs and Economic Development Impact Models | NREL

Science.gov Websites

tool; Purchase the necessary aggregated multiplier and consumer commodity demand data from someone skilled in input-output modeling (IMPLAN or another modeling tool); or Purchase the necessary aggregated

Network aggregation in transportation planning models

DOT National Transportation Integrated Search

1979-06-01

This report contains six papers addressed at mathematical and computation aspects of an extraction aggregation model often employed in transportation planning studies. This model concerns the optimal flowing of an extracted subnetwork of a given netw...

GIS Learning Objects: An Approach to Content Aggregation

ERIC Educational Resources Information Center

Govorov, Michael; Gienko, Gennady

2013-01-01

Content development and maintenance of geographic information systems (GIS) related courses, especially designed for distance and online delivery, could be a tedious task even for an experienced instructor. The paper outlines application of abstract instructional design techniques for modeling course structure and developing corresponding course…

Can dust emission mechanisms be determined from field measurements?

USDA-ARS?s Scientific Manuscript database

Field observations are needed to develop and test theories on dust emission for use in dust modeling systems. The dust emission mechanism (aerodynamic entrainment, saltation bombardment, aggregate disintegration) as well as the amount and particle-size distribution of emitted dust may vary under sed...

Disentangling dust emission mechanisms – a field study

USDA-ARS?s Scientific Manuscript database

Field observations are needed to both develop and test theories on dust emission for use in global modeling systems. The dust emission mechanism (aerodynamic entrainment, saltation bombardment, aggregate disintegration) as well as the amount and particle-size distribution of emitted dust may vary un...

Experimental Studies on Geocells and Mat Systems for Stabilization of Unpaved Shoulders and Temporary Roads

NASA Astrophysics Data System (ADS)

Guo, Jun

Geosynthetics have been used to improve the performance of geomaterials, especially when weak soil exists in roadway applications. In this study, two types of geosynthetic materials, geocell and a mat system, were studied for their applications for unpaved roads and shoulders. The study of geocell was focused on its application for unpaved shoulders. The ability of geocell to improve different geomaterials over intermediate strength subgrade and its possible effect on vegetation were investigated. The study of the mat system was focused on investigating the performance of the mat system over soft and intermediate subgrade with different strengths under cyclic loading to simulate temporary roadway conditions. In the study of geocell for the application for unpaved shoulders, six large scale plate loading tests were conducted on a single type of geocell on target 5% CBR subgrade to investigate the benefits of geocell reinforcement on different base course and topsoil combinations. Different base course and topsoil combinations were investigated including: 200-mm thick unreinforced aggregate, 200-mm thick soil-aggregate mixture (50% aggregate and 50% top soil) with and without geocell reinforcement, 200-mm thick geocell-reinforced topsoil, 50-mm thick aggregate over 150-mm soil-aggregate mixture (50% aggregate and 50% top soil), and 50-mm thick top soil over 150-mm thick geocell-reinforced soil-aggregate mixture (50% aggregate and 50% top soil). Earth pressure cells were install at the interface between subgrade and base course to monitor the load distribution. The cyclic plate loading tests showed that geocell effectively reduced the permanent deformation and the geocell-reinforced soil-aggregate mixture slightly outperformed the unreinforced aggregate at the same thickness. The plate loading tests also suggested the topsoil cover resulted in large permanent deformations. A one-year long outdoor field vegetation test was conducted on base courses with different combinations of aggregate and topsoil including: 200-mm thick unreinforced topsoil, 200-mm thick soil-aggregate mixture (50% aggregate and 50% topsoil), 50-mm thick aggregate over 150-mm soil-aggregate mixture (50% aggregate and 50% topsoil), and 50-mm thick topsoil over 150-mm reinforced soil-aggregate mixture (50% aggregate and 50% topsoil) to investigate the possible effect of geocell on shoulder vegetation established mainly by tall fescue grass and perennial ryegrass. One control (unreinforced) section and one geocell-reinforced section were prepared for each base course combination with a surface area of 1.5 m by 1.5 m. During the one-year test period, soil moisture temperature and volumetric moisture content were monitored. Weather data, such as precipitation and air temperature, were obtain from the nearby weather station at the Lawrence airport. Vegetation growth was evaluated by grass leaf blade length, root length, and grass density. Vegetation biomass was obtained at the end of the test. The test results showed no definite evidence of geocell influencing the vegetation in unpaved shoulders. In the study of the mat system, six large-scale cyclic plate loading tests were conducted on a single type of polyethylene mat system with anchorage to study its performance over soft and intermediate subgrade with the CBR ranging from 1% to 4%. For the comparison purposes, test sections with and without the mat system were prepared and evaluated. For the test section with 1% CBR subgrade, an aggregate base course was used for the test section without the mat system to enable the cyclic plate loading test. The size of the mat system under the investigation was 1.92 m by 1.92 m. A cyclic load at the magnitude of 40 kN was applied through a 300 mm diameter loading plate with a thin rubber pad to simulate a vehicle tire. Earth pressure cells were installed at the interface between the mat system and the subgrade to monitor the load distribution. Loading plate displacements were measured by the displacement transducer inside the actuator. Test results concluded that the mat system was more effective over the intermediate subgrade than the soft subgrade and when large permanent deformations were allowed.

Role of Multicellular Aggregates in Biofilm Formation

PubMed Central

Kragh, Kasper N.; Hutchison, Jaime B.; Melaugh, Gavin; Rodesney, Chris; Roberts, Aled E. L.; Irie, Yasuhiko; Jensen, Peter Ø.; Diggle, Stephen P.; Allen, Rosalind J.

2016-01-01

ABSTRACT In traditional models of in vitro biofilm development, individual bacterial cells seed a surface, multiply, and mature into multicellular, three-dimensional structures. Much research has been devoted to elucidating the mechanisms governing the initial attachment of single cells to surfaces. However, in natural environments and during infection, bacterial cells tend to clump as multicellular aggregates, and biofilms can also slough off aggregates as a part of the dispersal process. This makes it likely that biofilms are often seeded by aggregates and single cells, yet how these aggregates impact biofilm initiation and development is not known. Here we use a combination of experimental and computational approaches to determine the relative fitness of single cells and preformed aggregates during early development of Pseudomonas aeruginosa biofilms. We find that the relative fitness of aggregates depends markedly on the density of surrounding single cells, i.e., the level of competition for growth resources. When competition between aggregates and single cells is low, an aggregate has a growth disadvantage because the aggregate interior has poor access to growth resources. However, if competition is high, aggregates exhibit higher fitness, because extending vertically above the surface gives cells at the top of aggregates better access to growth resources. Other advantages of seeding by aggregates, such as earlier switching to a biofilm-like phenotype and enhanced resilience toward antibiotics and immune response, may add to this ecological benefit. Our findings suggest that current models of biofilm formation should be reconsidered to incorporate the role of aggregates in biofilm initiation. PMID:27006463

Multifrequency acoustic observations of zooplankton in Knight Inlet, B.C

NASA Astrophysics Data System (ADS)

Trevorrow, Mark V.; Mackas, David L.; Benfield, Mark C.

2004-05-01

A collaborative investigation of midwater zooplankton aggregations in a coastal fjord was conducted in November 2002. Midwater aggregations of zooplankton in a coastal fjord were sampled and mapped using a calibrated, three-frequency (38, 120, and 200 kHz) vessel-based echo-sounder system, a multinet towed zooplankton net (BIONESS), and a high-resolution in situ camera system (ZOOVIS). Dense daytime layers of euphausiids and amphipods near 70- to 90-m depth were found in the lower reaches of the inlet, especially concentrated by tidal flows around a sill which rises above the layer. Quantitative euphausiid and amphipod backscattering measurements, combined with in situ species, size, and abundance estimates, were found to agree closely with recent size- and orientation-averaged fluid-cylinder scattering models produced by Stanton et al. Also, in situ scattering measurements of physonect siphonophores were found to have a much stronger low-frequency (38 kHz) scattering strength, in agreement with a simple bubble scattering model. [Work supported by Dr. J. Eckman, ONR code 322BC.

Impacts of Cropping Systems on Aggregates Associated Organic Carbon and Nitrogen in a Semiarid Highland Agroecosystem

PubMed Central

Chu, Jiashu; Zhang, Tianzhe; Chang, Weidong; Zhang, Dan; Zulfiqar, Saman; Fu, Aigen; Hao, Yaqi

2016-01-01

The effect of cropping system on the distribution of organic carbon (OC) and nitrogen (N) in soil aggregates has not been well addressed, which is important for understanding the sequestration of OC and N in agricultural soils. We analyzed the distribution of OC and N associated with soil aggregates in three unfertilized cropping systems in a 27-year field experiment: continuously cropped alfalfa, continuously cropped wheat and a legume-grain rotation. The objectives were to understand the effect of cropping system on the distribution of OC and N in aggregates and to examine the relationships between the changes in OC and N stocks in total soils and in aggregates. The cropping systems increased the stocks of OC and N in total soils (0–40 cm) at mean rates of 15.6 g OC m-2 yr-1 and 1.2 g N m-2 yr-1 relative to a fallow control. The continuous cropping of alfalfa produced the largest increases at the 0–20 cm depth. The OC and N stocks in total soils were significantly correlated with the changes in the >0.053 mm aggregates. 27-year of cropping increased OC stocks in the >0.053 mm size class of aggregates and N stocks in the >0.25 mm size class but decreased OC stocks in the <0.053 mm size class and N stocks in the <0.25 mm size class. The increases in OC and N stocks in these aggregates accounted for 99.5 and 98.7% of the total increases, respectively, in the continuous alfalfa system. The increases in the OC and N stocks associated with the >0.25 mm aggregate size class accounted for more than 97% of the total increases in the continuous wheat and the legume-grain rotation systems. These results suggested that long-term cropping has the potential to sequester OC and N in soils and that the increases in soil OC and N stocks were mainly due to increases associated with aggregates >0.053 mm. PMID:27764209

Total organic carbon in aggregates as a soil recovery indicator

NASA Astrophysics Data System (ADS)

Luciene Maltoni, Katia; Rodrigues Cassiolato, Ana Maria; Amorim Faria, Glaucia; Dubbin, William

2015-04-01

The soil aggregation promotes physical protection of organic matter, preservation of which is crucial to improve soil structure, fertility and ensure the agro-ecosystems sustainability. The no-tillage cultivation system has been considered as one of the strategies to increase total soil organic carbono (TOC) contents and soil aggregation, both are closely related and influenced by soil management systems. The aim of this study was to evaluate the distribution of soil aggregates and the total organic carbon inside aggregates, with regard to soil recovery, under 3 different soil management systems, i.e. 10 and 20 years of no-tillage cultivation as compared with soil under natural vegetation (Cerrado). Undisturbed soils (0-5; 5-10; and 10-20 cm depth) were collected from Brazil, Central Region. The soils, Oxisols from Cerrado, were collected from a field under Natural Vegetation-Cerrado (NV), and from fields that were under conventional tillage since 1970s, and 10 and 20 years ago were changed to no-tillage cultivation system (NT-10; NT-20 respectively). The undisturbed samples were sieved (4mm) and the aggregates retained were further fractionated by wet sieving through five sieves (2000, 1000, 500, 250, and 50 μm) with the aggregates distribution expressed as percentage retained by each sieve. The TOC was determined, for each aggregate size, by combustion (Thermo-Finnigan). A predominance of aggregates >2000 μm was observed under NV treatment (92, 91, 82 %), NT-10 (64, 73, 61 %), and NT-20 (71, 79, 63 %) for all three depths (0-5; 5-10; 10-20 cm). In addition greater quantities of aggregates in sizes 1000, 500, 250 and 50 μm under NT-10 and NT-20 treatments, explain the lower aggregate stability under these treatments compared to the soil under NV. The organic C concentration for NV in aggregates >2000 μm was 24,4; 14,2; 8,7 mg/g for each depth (0-5; 5-10; 10-20 cm, respectively), higher than in aggregates sized 250-50 μm (7,2; 5,5; 4,4 mg/g) for all depths. Although, with lower organic C contents, NT-10 and NT-20 presented the same behavior, i.e., greater amounts of organic C in bigger aggregates, (NT-10: 10,7; 9,5; 9,0 mg/g and NT-20: 18,8; 15,7; 8,6 mg/g, for each depth respectively 0-5; 5-10; 10-20 cm), and lower C contents in smaller aggregates (NT-10: 5,7; 6,1; 5,6 mg/g and NT-20: 8,2; 7,9; 6,3 mg/g , for each depth respectively 0-5; 5-10; 10-20 cm). The aggregates > 2000 μm, at 10-20 cm depth, showed similar C contents for NV, NT-10 and NT-20 (8,7; 9,0; 8,6 mg/g, respectively) suggesting that the C supply, even in natural environment, is not enough to increase organic C at 10-20 cm depth. The organic C concentration for aggregates sized 250-50 μm, in all three evaluated depths, is similar. Therefore, under NT-10 and NT-20 the smaller aggregates are not influenced by cultivation system, suggesting that the organic C inside the smaller aggregates can be retained for longer time in soil system. The results suggest, with regard to aggregate distribution and organic carbon content under NV, that soil under NT-20 is recovering. Acknowledgement: This study received financial support from CNPq

Anti-aging treatments slow propagation of synucleinopathy by restoring lysosomal function.

PubMed

Kim, Dong-Kyu; Lim, Hee-Sun; Kawasaki, Ichiro; Shim, Yhong-Hee; Vaikath, Nishant N; El-Agnaf, Omar M A; Lee, He-Jin; Lee, Seung-Jae

2016-10-02

Aging is the major risk factor for neurodegenerative diseases that are also associated with impaired proteostasis, resulting in abnormal accumulation of protein aggregates. However, the role of aging in development and progression of disease remains elusive. Here, we used Caenorhabditis elegans models to show that aging-promoting genetic variations accelerated the rate of cell-to-cell transmission of SNCA/α-synuclein aggregates, hallmarks of Parkinson disease, and the progression of disease phenotypes, such as nerve degeneration, behavioral deficits, and reduced life span. Genetic and pharmacological anti-aging manipulations slowed the spread of aggregates and the associated phenotypes. Lysosomal degradation was significantly impaired in aging models, while anti-aging treatments reduced the impairment. Transgenic expression of hlh-30p::hlh-30, the master controller of lysosomal biogenesis, alleviated intercellular transmission of aggregates in the aging model. Our results demonstrate that the rate of aging closely correlates with the rate of aggregate propagation and that general anti-aging treatments can slow aggregate propagation and associated disease progression by restoring lysosomal function.

``Just Another Distribution Channel?''

NASA Astrophysics Data System (ADS)

Lemstra, Wolter; de Leeuw, Gerd-Jan; van de Kar, Els; Brand, Paul

The telecommunications-centric business model of mobile operators is under attack due to technological convergence in the communication and content industries. This has resulted in a plethora of academic contributions on the design of new business models and service platform architectures. However, a discussion of the challenges that operators are facing in adopting these models is lacking. We assess these challenges by considering the mobile network as part of the value system of the content industry. We will argue that from the perspective of a content provider the mobile network is ‘just another’ distribution channel. Strategic options available for the mobile communication operators are to deliver an excellent distribution channel for content delivery or to move upwards in the value chain by becoming a content aggregator. To become a mobile content aggregator operators will have to develop or acquire complementary resources and capabilities. Whether this strategic option is sustainable remains open.

Aggregation-fragmentation-diffusion model for trail dynamics

DOE PAGES

Kawagoe, Kyle; Huber, Greg; Pradas, Marc; ...

2017-07-21

We investigate statistical properties of trails formed by a random process incorporating aggregation, fragmentation, and diffusion. In this stochastic process, which takes place in one spatial dimension, two neighboring trails may combine to form a larger one, and also one trail may split into two. In addition, trails move diffusively. The model is defined by two parameters which quantify the fragmentation rate and the fragment size. In the long-time limit, the system reaches a steady state, and our focus is the limiting distribution of trail weights. We find that the density of trail weight has power-law tail P(w)~w –γ formore » small weight w. We obtain the exponent γ analytically and find that it varies continuously with the two model parameters. In conclusion, the exponent γ can be positive or negative, so that in one range of parameters small-weight trails are abundant and in the complementary range they are rare.« less

Mitochondrial enzymes are protected from stress-induced aggregation by mitochondrial chaperones and the Pim1/LON protease

PubMed Central

Bender, Tom; Lewrenz, Ilka; Franken, Sebastian; Baitzel, Catherina; Voos, Wolfgang

2011-01-01

Proteins in a natural environment are constantly challenged by stress conditions, causing their destabilization, unfolding, and, ultimately, aggregation. Protein aggregation has been associated with a wide variety of pathological conditions, especially neurodegenerative disorders, stressing the importance of adequate cellular protein quality control measures to counteract aggregate formation. To secure protein homeostasis, mitochondria contain an elaborate protein quality control system, consisting of chaperones and ATP-dependent proteases. To determine the effects of protein aggregation on the functional integrity of mitochondria, we set out to identify aggregation-prone endogenous mitochondrial proteins. We could show that major metabolic pathways in mitochondria were affected by the aggregation of key enzyme components, which were largely inactivated after heat stress. Furthermore, treatment with elevated levels of reactive oxygen species strongly influenced the aggregation behavior, in particular in combination with elevated temperatures. Using specific chaperone mutant strains, we showed a protective effect of the mitochondrial Hsp70 and Hsp60 chaperone systems. Moreover, accumulation of aggregated polypeptides was strongly decreased by the AAA-protease Pim1/LON. We therefore propose that the proteolytic breakdown of aggregation-prone polypeptides represents a major protective strategy to prevent the in vivo formation of aggregates in mitochondria. PMID:21209324

Statistical physics approaches to Alzheimer's disease

NASA Astrophysics Data System (ADS)

Peng, Shouyong

Alzheimer's disease (AD) is the most common cause of late life dementia. In the brain of an AD patient, neurons are lost and spatial neuronal organizations (microcolumns) are disrupted. An adequate quantitative analysis of microcolumns requires that we automate the neuron recognition stage in the analysis of microscopic images of human brain tissue. We propose a recognition method based on statistical physics. Specifically, Monte Carlo simulations of an inhomogeneous Potts model are applied for image segmentation. Unlike most traditional methods, this method improves the recognition of overlapped neurons, and thus improves the overall recognition percentage. Although the exact causes of AD are unknown, as experimental advances have revealed the molecular origin of AD, they have continued to support the amyloid cascade hypothesis, which states that early stages of aggregation of amyloid beta (Abeta) peptides lead to neurodegeneration and death. X-ray diffraction studies reveal the common cross-beta structural features of the final stable aggregates-amyloid fibrils. Solid-state NMR studies also reveal structural features for some well-ordered fibrils. But currently there is no feasible experimental technique that can reveal the exact structure or the precise dynamics of assembly and thus help us understand the aggregation mechanism. Computer simulation offers a way to understand the aggregation mechanism on the molecular level. Because traditional all-atom continuous molecular dynamics simulations are not fast enough to investigate the whole aggregation process, we apply coarse-grained models and discrete molecular dynamics methods to increase the simulation speed. First we use a coarse-grained two-bead (two beads per amino acid) model. Simulations show that peptides can aggregate into multilayer beta-sheet structures, which agree with X-ray diffraction experiments. To better represent the secondary structure transition happening during aggregation, we refine the model to four beads per amino acid. Typical essential interactions, such as backbone hydrogen bond, hydrophobic and electrostatic interactions, are incorporated into our model. We study the aggregation of Abeta16-22, a peptide that can aggregate into a well-ordered fibrillar structure in experiments. Our results show that randomly-oriented monomers can aggregate into fibrillar subunits, which agree not only with X-ray diffraction experiments but also with solid-state NMR studies. Our findings demonstrate that coarse-grained models and discrete molecular dynamics simulations can help researchers understand the aggregation mechanism of amyloid peptides.

Evaluating the agreement between measurements and models of net ecosystem exchange at different times and timescales using wavelet coherence: an example using data from the North American Carbon Program Site-Level Interim Synthesis

Treesearch

P.C. Stoy; M.C. Dietze; A.D. Richardson; R. Vargas; A.G. Barr; R.S. Anderson; M.A. Arain; I.T. Baker; T.A. Black; J.M. Chen; R.B. Cook; C.M. Gough; R.F. Grant; D.Y. Hollinger; R.C. Izaurralde; C.J. Kucharik; P. Lafleur; B.E. Law; S. Liu; E. Lokupitiya; Y. Luo; J. W. Munger; C. Peng; B. Poulter; D.T. Price; D. M. Ricciuto; W. J. Riley; A. K. Sahoo; K. Schaefer; C.R. Schwalm; H. Tian; H. Verbeeck; E. Weng

2013-01-01

Earth system processes exhibit complex patterns across time, as do the models that seek to replicate these processes. Model output may or may not be significantly related to observations at different times and on different frequencies. Conventional model diagnostics provide an aggregate view of model-data agreement, but usually do not identify the time and frequency...

Multilayer network modeling of integrated biological systems. Comment on "Network science of biological systems at different scales: A review" by Gosak et al.

NASA Astrophysics Data System (ADS)

De Domenico, Manlio

2018-03-01

Biological systems, from a cell to the human brain, are inherently complex. A powerful representation of such systems, described by an intricate web of relationships across multiple scales, is provided by complex networks. Recently, several studies are highlighting how simple networks - obtained by aggregating or neglecting temporal or categorical description of biological data - are not able to account for the richness of information characterizing biological systems. More complex models, namely multilayer networks, are needed to account for interdependencies, often varying across time, of biological interacting units within a cell, a tissue or parts of an organism.

A study of the aggregation of cyclodextrins: Determination of the critical aggregation concentration, size of aggregates and thermodynamics using isodesmic and K2-K models.

PubMed

Do, Thao Thi; Van Hooghten, Rob; Van den Mooter, Guy

2017-04-15

The aggregation of three different cyclodextrins (CDs): 2-hydroxypropyl-β-cyclodextrin (HP-β-CD), 2-hydroxypropyl-γ-cyclodextrin (HP-γ-CD) and sulfobutylether-β-cyclodextrin (SBE-β-CD) was studied. The critical aggregation concentration (cac) of these three CDs is quite similar and is situated at ca. 2% (m/v). There was only a small difference in the cac values determined by DLS and 1 H NMR. DLS measurements revealed that CDs in solution have three size populations wherein one of them is that of a single CD molecule. The size of aggregates determined by TEM appears to be similar to the size of the aggregates in the second size distribution determined by DLS. Isodesmic and K 2 -K self-assembly models were used for studying the aggregation process of HP-β-CD, HP-γ-CD and SBE-β-CD. The results showed that the aggregation process of these CDs is a cooperative one, where the first step of aggregation is less favorable than the next steps. The determined thermodynamic parameters showed that the aggregation process of all three CDs is spontaneous and exothermic and it is driven by an increase of the entropy of the environment. Copyright © 2017 Elsevier B.V. All rights reserved.

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

PubMed Central

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

2014-01-01

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

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

PubMed Central

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

2015-01-01

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

Multiagent intelligent systems

NASA Astrophysics Data System (ADS)

Krause, Lee S.; Dean, Christopher; Lehman, Lynn A.

2003-09-01

This paper will discuss a simulation approach based upon a family of agent-based models. As the demands placed upon simulation technology by such applications as Effects Based Operations (EBO), evaluations of indicators and warnings surrounding homeland defense and commercial demands such financial risk management current single thread based simulations will continue to show serious deficiencies. The types of "what if" analysis required to support these types of applications, demand rapidly re-configurable approaches capable of aggregating large models incorporating multiple viewpoints. The use of agent technology promises to provide a broad spectrum of models incorporating differing viewpoints through a synthesis of a collection of models. Each model would provide estimates to the overall scenario based upon their particular measure or aspect. An agent framework, denoted as the "family" would provide a common ontology in support of differing aspects of the scenario. This approach permits the future of modeling to change from viewing the problem as a single thread simulation, to take into account multiple viewpoints from different models. Even as models are updated or replaced the agent approach permits rapid inclusion in new or modified simulations. In this approach a variety of low and high-resolution information and its synthesis requires a family of models. Each agent "publishes" its support for a given measure and each model provides their own estimates on the scenario based upon their particular measure or aspect. If more than one agent provides the same measure (e.g. cognitive) then the results from these agents are combined to form an aggregate measure response. The objective would be to inform and help calibrate a qualitative model, rather than merely to present highly aggregated statistical information. As each result is processed, the next action can then be determined. This is done by a top-level decision system that communicates to the family at the ontology level without any specific understanding of the processes (or model) behind each agent. The increasingly complex demands upon simulation for the necessity to incorporate the breadth and depth of influencing factors makes a family of agent based models a promising solution. This paper will discuss that solution with syntax and semantics necessary to support the approach.

A Multi-Scale Energy Food Systems Modeling Framework For Climate Adaptation

NASA Astrophysics Data System (ADS)

Siddiqui, S.; Bakker, C.; Zaitchik, B. F.; Hobbs, B. F.; Broaddus, E.; Neff, R.; Haskett, J.; Parker, C.

2016-12-01

Our goal is to understand coupled system dynamics across scales in a manner that allows us to quantify the sensitivity of critical human outcomes (nutritional satisfaction, household economic well-being) to development strategies and to climate or market induced shocks in sub-Saharan Africa. We adopt both bottom-up and top-down multi-scale modeling approaches focusing our efforts on food, energy, water (FEW) dynamics to define, parameterize, and evaluate modeled processes nationally as well as across climate zones and communities. Our framework comprises three complementary modeling techniques spanning local, sub-national and national scales to capture interdependencies between sectors, across time scales, and on multiple levels of geographic aggregation. At the center is a multi-player micro-economic (MME) partial equilibrium model for the production, consumption, storage, and transportation of food, energy, and fuels, which is the focus of this presentation. We show why such models can be very useful for linking and integrating across time and spatial scales, as well as a wide variety of models including an agent-based model applied to rural villages and larger population centers, an optimization-based electricity infrastructure model at a regional scale, and a computable general equilibrium model, which is applied to understand FEW resources and economic patterns at national scale. The MME is based on aggregating individual optimization problems for relevant players in an energy, electricity, or food market and captures important food supply chain components of trade and food distribution accounting for infrastructure and geography. Second, our model considers food access and utilization by modeling food waste and disaggregating consumption by income and age. Third, the model is set up to evaluate the effects of seasonality and system shocks on supply, demand, infrastructure, and transportation in both energy and food.

The Requirements and Design of the Rapid Prototyping Capabilities System

NASA Astrophysics Data System (ADS)

Haupt, T. A.; Moorhead, R.; O'Hara, C.; Anantharaj, V.

2006-12-01

The Rapid Prototyping Capabilities (RPC) system will provide the capability to rapidly evaluate innovative methods of linking science observations. To this end, the RPC will provide the capability to integrate the software components and tools needed to evaluate the use of a wide variety of current and future NASA sensors, numerical models, and research results, model outputs, and knowledge, collectively referred to as "resources". It is assumed that the resources are geographically distributed, and thus RPC will provide the support for the location transparency of the resources. The RPC system requires providing support for: (1) discovery, semantic understanding, secure access and transport mechanisms for data products available from the known data provides; (2) data assimilation and geo- processing tools for all data transformations needed to match given data products to the model input requirements; (3) model management including catalogs of models and model metadata, and mechanisms for creation environments for model execution; and (4) tools for model output analysis and model benchmarking. The challenge involves developing a cyberinfrastructure for a coordinated aggregate of software, hardware and other technologies, necessary to facilitate RPC experiments, as well as human expertise to provide an integrated, "end-to-end" platform to support the RPC objectives. Such aggregation is to be achieved through a horizontal integration of loosely coupled services. The cyberinfrastructure comprises several software layers. At the bottom, the Grid fabric encompasses network protocols, optical networks, computational resources, storage devices, and sensors. At the top, applications use workload managers to coordinate their access to physical resources. Applications are not tightly bounded to a single physical resource. Instead, they bind dynamically to resources (i.e., they are provisioned) via a common grid infrastructure layer. For the RPC system, the cyberinfrastructure must support organizing computations (or "data transformations" in general) into complex workflows with resource discovery, automatic resource allocation, monitoring, preserving provenance as well as to aggregate heterogeneous, distributed data into knowledge databases. Such service orchestration is the responsibility of the "collective services" layer. For RPC, this layer will be based on Java Business Integration (JBI, [JSR-208]) specification which is a standards-based integration platform that combines messaging, web services, data transformation, and intelligent routing to reliably connect and coordinate the interaction of significant numbers of diverse applications (plug-in components) across organizational boundaries. JBI concept is a new approach to integration that can provide the underpinnings for loosely coupled, highly distributed integration network that can scale beyond the limits of currently used hub-and-spoke brokers. This presentation discusses the requirements, design and early prototype of the NASA-sponsored RPC system under development at Mississippi State University, demonstrating the integration of data provisioning mechanisms, data transformation tools and computational models into a single interoperable system enabling rapid execution of RPC experiments.

Coupling population dynamics with earth system models: the POPEM model.

PubMed

Navarro, Andrés; Moreno, Raúl; Jiménez-Alcázar, Alfonso; Tapiador, Francisco J

2017-09-16

Precise modeling of CO 2 emissions is important for environmental research. This paper presents a new model of human population dynamics that can be embedded into ESMs (Earth System Models) to improve climate modeling. Through a system dynamics approach, we develop a cohort-component model that successfully simulates historical population dynamics with fine spatial resolution (about 1°×1°). The population projections are used to improve the estimates of CO 2 emissions, thus transcending the bulk approach of existing models and allowing more realistic non-linear effects to feature in the simulations. The module, dubbed POPEM (from Population Parameterization for Earth Models), is compared with current emission inventories and validated against UN aggregated data. Finally, it is shown that the module can be used to advance toward fully coupling the social and natural components of the Earth system, an emerging research path for environmental science and pollution research.

Some methodological issues in the longitudinal analysis of demographic data.

PubMed

Krishinan, P

1982-12-01

Most demographic data are macro (or aggregate) in nature. Some relevant methodological issues are presented here in a time series study using aggregate data. The micro-macro distinction is relative. Time enters into the micro and macro variables in different ways. A simple micro model of rural-urban migration is given. Method 1 is to assume homogeneity in behavior. Method 2 is a Bayesian estimation. A discusssion of the results follows. Time series models of aggregate data are given. The nature of the model--predictive or explanatory--must be decided on. Explanatory models in longitudinal studies have been developed. Ways to go to the micro level from the macro are discussed. The aggregation-disaggregation problem in demography is not similar to that in econometrics. To understand small populations, separate micro level data have to be collected and analyzed and appropriate models developed. Both types of models have their uses.

A Multiagent System for Dynamic Data Aggregation in Medical Research

PubMed Central

Urovi, Visara; Barba, Imanol; Aberer, Karl; Schumacher, Michael Ignaz

2016-01-01

The collection of medical data for research purposes is a challenging and long-lasting process. In an effort to accelerate and facilitate this process we propose a new framework for dynamic aggregation of medical data from distributed sources. We use agent-based coordination between medical and research institutions. Our system employs principles of peer-to-peer network organization and coordination models to search over already constructed distributed databases and to identify the potential contributors when a new database has to be built. Our framework takes into account both the requirements of a research study and current data availability. This leads to better definition of database characteristics such as schema, content, and privacy parameters. We show that this approach enables a more efficient way to collect data for medical research. PMID:27975063

Stability of binaries. Part 1: Rigid binaries

NASA Astrophysics Data System (ADS)

Sharma, Ishan

2015-09-01

We consider the stability of binary asteroids whose members are possibly granular aggregates held together by self-gravity alone. A binary is said to be stable whenever each member is orbitally and structurally stable to both orbital and structural perturbations. To this end, we extend the stability test for rotating granular aggregates introduced by Sharma (Sharma, I. [2012]. J. Fluid Mech., 708, 71-99; Sharma, I. [2013]. Icarus, 223, 367-382; Sharma, I. [2014]. Icarus, 229, 278-294) to the case of binary systems comprised of rubble members. In part I, we specialize to the case of a binary with rigid members subjected to full three-dimensional perturbations. Finally, we employ the stability test to critically appraise shape models of four suspected binary systems, viz., 216 Kleopatra, 25143 Itokawa, 624 Hektor and 90 Antiope.

An insight into the complex prion-prion interaction network in the budding yeast Saccharomyces cerevisiae.

PubMed

Du, Zhiqiang; Valtierra, Stephanie; Li, Liming

2014-01-01

The budding yeast Saccharomyces cerevisiae is a valuable model system for studying prion-prion interactions as it contains multiple prion proteins. A recent study from our laboratory showed that the existence of Swi1 prion ([SWI(+)]) and overproduction of Swi1 can have strong impacts on the formation of 2 other extensively studied yeast prions, [PSI(+)] and [PIN(+)] ([RNQ(+)]) (Genetics, Vol. 197, 685-700). We showed that a single yeast cell is capable of harboring at least 3 heterologous prion elements and these prions can influence each other's appearance positively and/or negatively. We also showed that during the de novo [PSI(+)] formation process upon Sup35 overproduction, the aggregation patterns of a preexisting inducer ([RNQ(+)] or [SWI(+)]) can undergo significant remodeling from stably transmitted dot-shaped aggregates to aggregates that co-localize with the newly formed Sup35 aggregates that are ring/ribbon/rod- shaped. Such co-localization disappears once the newly formed [PSI(+)] prion stabilizes. Our finding provides strong evidence supporting the "cross-seeding" model for prion-prion interactions and confirms earlier reports that the interactions among different prions and their prion proteins mostly occur at the initiation stages of prionogenesis. Our results also highlight a complex prion interaction network in yeast. We believe that elucidating the mechanism underlying the yeast prion-prion interaction network will not only provide insight into the process of prion de novo generation and propagation in yeast but also shed light on the mechanisms that govern protein misfolding, aggregation, and amyloidogenesis in higher eukaryotes.

Misfolded Polyglutamine, Polyalanine, and Superoxide Dismutase 1 Aggregate via Distinct Pathways in the Cell*

PubMed Central

Polling, Saskia; Mok, Yee-Foong; Ramdzan, Yasmin M.; Turner, Bradley J.; Yerbury, Justin J.; Hill, Andrew F.; Hatters, Danny M.

2014-01-01

Protein aggregation into intracellular inclusions is a key feature of many neurodegenerative disorders. A common theme has emerged that inappropriate self-aggregation of misfolded or mutant polypeptide sequences is detrimental to cell health. Yet protein quality control mechanisms may also deliberately cluster them together into distinct inclusion subtypes, including the insoluble protein deposit (IPOD) and the juxtanuclear quality control (JUNQ). Here we investigated how the intrinsic oligomeric state of three model systems of disease-relevant mutant protein and peptide sequences relates to the IPOD and JUNQ patterns of aggregation using sedimentation velocity analysis. Two of the models (polyalanine (37A) and superoxide dismutase 1 (SOD1) mutants A4V and G85R) accumulated into the same JUNQ-like inclusion whereas the other, polyglutamine (72Q), formed spatially distinct IPOD-like inclusions. Using flow cytometry pulse shape analysis (PulSA) to separate cells with inclusions from those without revealed the SOD1 mutants and 37A to have abruptly altered oligomeric states with respect to the nonaggregating forms, regardless of whether cells had inclusions or not, whereas 72Q was almost exclusively monomeric until inclusions formed. We propose that mutations leading to JUNQ inclusions induce a constitutively “misfolded” state exposing hydrophobic side chains that attract and ultimately overextend protein quality capacity, which leads to aggregation into JUNQ inclusions. Poly(Q) is not misfolded in this same sense due to universal polar side chains, but is highly prone to forming amyloid fibrils that we propose invoke a different engagement mechanism with quality control. PMID:24425868

Misfolded polyglutamine, polyalanine, and superoxide dismutase 1 aggregate via distinct pathways in the cell.

PubMed

Polling, Saskia; Mok, Yee-Foong; Ramdzan, Yasmin M; Turner, Bradley J; Yerbury, Justin J; Hill, Andrew F; Hatters, Danny M

2014-03-07

Protein aggregation into intracellular inclusions is a key feature of many neurodegenerative disorders. A common theme has emerged that inappropriate self-aggregation of misfolded or mutant polypeptide sequences is detrimental to cell health. Yet protein quality control mechanisms may also deliberately cluster them together into distinct inclusion subtypes, including the insoluble protein deposit (IPOD) and the juxtanuclear quality control (JUNQ). Here we investigated how the intrinsic oligomeric state of three model systems of disease-relevant mutant protein and peptide sequences relates to the IPOD and JUNQ patterns of aggregation using sedimentation velocity analysis. Two of the models (polyalanine (37A) and superoxide dismutase 1 (SOD1) mutants A4V and G85R) accumulated into the same JUNQ-like inclusion whereas the other, polyglutamine (72Q), formed spatially distinct IPOD-like inclusions. Using flow cytometry pulse shape analysis (PulSA) to separate cells with inclusions from those without revealed the SOD1 mutants and 37A to have abruptly altered oligomeric states with respect to the nonaggregating forms, regardless of whether cells had inclusions or not, whereas 72Q was almost exclusively monomeric until inclusions formed. We propose that mutations leading to JUNQ inclusions induce a constitutively "misfolded" state exposing hydrophobic side chains that attract and ultimately overextend protein quality capacity, which leads to aggregation into JUNQ inclusions. Poly(Q) is not misfolded in this same sense due to universal polar side chains, but is highly prone to forming amyloid fibrils that we propose invoke a different engagement mechanism with quality control.