Convective Self-Aggregation in Numerical Simulations: A Review
NASA Astrophysics Data System (ADS)
Wing, Allison A.; Emanuel, Kerry; Holloway, Christopher E.; Muller, Caroline
2017-11-01
Organized convection in the tropics occurs across a range of spatial and temporal scales and strongly influences cloud cover and humidity. One mode of organization found is "self-aggregation," in which moist convection spontaneously organizes into one or several isolated clusters despite spatially homogeneous boundary conditions and forcing. Self-aggregation is driven by interactions between clouds, moisture, radiation, surface fluxes, and circulation, and occurs in a wide variety of idealized simulations of radiative-convective equilibrium. Here we provide a review of convective self-aggregation in numerical simulations, including its character, causes, and effects. We describe the evolution of self-aggregation including its time and length scales and the physical mechanisms leading to its triggering and maintenance, and we also discuss possible links to climate and climate change.
Convective Self-Aggregation in Numerical Simulations: A Review
NASA Astrophysics Data System (ADS)
Wing, Allison A.; Emanuel, Kerry; Holloway, Christopher E.; Muller, Caroline
Organized convection in the tropics occurs across a range of spatial and temporal scales and strongly influences cloud cover and humidity. One mode of organization found is ``self-aggregation,'' in which moist convection spontaneously organizes into one or several isolated clusters despite spatially homogeneous boundary conditions and forcing. Self-aggregation is driven by interactions between clouds, moisture, radiation, surface fluxes, and circulation, and occurs in a wide variety of idealized simulations of radiative-convective equilibrium. Here we provide a review of convective self-aggregation in numerical simulations, including its character, causes, and effects. We describe the evolution of self-aggregation including its time and length scales and the physical mechanisms leading to its triggering and maintenance, and we also discuss possible links to climate and climate change.
Melittin Aggregation in Aqueous Solutions: Insight from Molecular Dynamics Simulations.
Liao, Chenyi; Esai Selvan, Myvizhi; Zhao, Jun; Slimovitch, Jonathan L; Schneebeli, Severin T; Shelley, Mee; Shelley, John C; Li, Jianing
2015-08-20
Melittin is a natural peptide that aggregates in aqueous solutions with paradigmatic monomer-to-tetramer and coil-to-helix transitions. Since little is known about the molecular mechanisms of melittin aggregation in solution, we simulated its self-aggregation process under various conditions. After confirming the stability of a melittin tetramer in solution, we observed—for the first time in atomistic detail—that four separated melittin monomers aggregate into a tetramer. Our simulated dependence of melittin aggregation on peptide concentration, temperature, and ionic strength is in good agreement with prior experiments. We propose that melittin mainly self-aggregates via a mechanism involving the sequential addition of monomers, which is supported by both qualitative and quantitative evidence obtained from unbiased and metadynamics simulations. Moreover, by combining computer simulations and a theory of the electrical double layer, we provide evidence to suggest why melittin aggregation in solution likely stops at the tetramer, rather than forming higher-order oligomers. Overall, our study not only explains prior experimental results at the molecular level but also provides quantitative mechanistic information that may guide the engineering of melittin for higher efficacy and safety.
Multiscale simulation of red blood cell aggregation
NASA Astrophysics Data System (ADS)
Bagchi, P.; Popel, A. S.
2004-11-01
In humans and other mammals, aggregation of red blood cells (RBC) is a major determinant to blood viscosity in microcirculation under physiological and pathological conditions. Elevated levels of aggregation are often related to cardiovascular diseases, bacterial infection, diabetes, and obesity. Aggregation is a multiscale phenomenon that is governed by the molecular bond formation between adjacent cells, morphological and rheological properties of the cells, and the motion of the extra-cellular fluid in which the cells circulate. We have developed a simulation technique using front tracking methods for multiple fluids that includes the multiscale characteristics of aggregation. We will report the first-ever direct computer simulation of aggregation of deformable cells in shear flows. We will present results on the effect of shear rate, strength of the cross-bridging bonds, and the cell rheological properties on the rolling motion, deformation and subsequent breakage of an aggregate.
Simulation of Ionic Aggregation and Ion Dynamics in Model Ionomers
NASA Astrophysics Data System (ADS)
Frischknecht, Amalie L.
2012-02-01
Ionomers, polymers containing a small fraction of covalently bound ionic groups, are of interest as possible electrolytes in batteries. A single-ion conducting polymer electrolyte would be safer and have higher efficiency than the currently-used liquid electrolytes. However, to date ionomeric materials do not have sufficiently high conductivities for practical application. This is most likely because the ions tend to form aggregates, leading to slow ion transport. A key question is therefore how molecular structure affects the ionic aggregation and ion dynamics. To probe these structure-property relationships, we have performed molecular simulations of a set of recently synthesized poly(ethylene-co-acrylic acid) copolymers and ionomers, with a focus on the morphology of the ionic aggregates. The ionomers have a precise, constant spacing of charged groups, making them ideal for direct comparisons with simulations. Ab initio calculations give insight into the expected coordination of cations with fragments of the ionomers. All-atom molecular dynamics (MD) simulations of the ionomer melt show aggregation of the ionic groups into extended string-like clusters. An extensive set of coarse-grained molecular dynamics simulations extend the results to longer times and larger length scales. The structure factors calculated from the MD simulations compare favorably with x-ray scattering data. Furthermore, the simulations give a detailed picture of the sizes, shapes, and composition of the ionic aggregates, and how they depend on polymer architecture. Implications for ion transport will be discussed. [Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.
Aggregation increases prey survival time in group chase and escape
NASA Astrophysics Data System (ADS)
Yang, Sicong; Jiang, Shijie; Jiang, Li; Li, Geng; Han, Zhangang
2014-08-01
Recently developed chase-and-escape models have addressed a fascinating pursuit-and-evasion problem that may have both theoretical significance and potential applications. We introduce three aggregation strategies for the prey in a group chase model on a lattice. Simulation results show that aggregation dramatically increases the group survival time, even allowing immortal prey. The average survival time τ and the aggregation probability P have a power-law dependence of \\tau \\sim {{(1-P)}^{-1}} for P\\in [0.9,0.997]. With increasing numbers of predators, there is still a phase transition. When the number of predators is less than the critical point value, the prey group survival time increases significantly.
Protein aggregate turbidity: Simulation of turbidity profiles for mixed-aggregation reactions.
Hall, Damien; Zhao, Ran; Dehlsen, Ian; Bloomfield, Nathaniel; Williams, Steven R; Arisaka, Fumio; Goto, Yuji; Carver, John A
2016-04-01
Due to their colloidal nature, all protein aggregates scatter light in the visible wavelength region when formed in aqueous solution. This phenomenon makes solution turbidity, a quantity proportional to the relative loss in forward intensity of scattered light, a convenient method for monitoring protein aggregation in biochemical assays. Although turbidity is often taken to be a linear descriptor of the progress of aggregation reactions, this assumption is usually made without performing the necessary checks to provide it with a firm underlying basis. In this article, we outline utilitarian methods for simulating the turbidity generated by homogeneous and mixed-protein aggregation reactions containing fibrous, amorphous, and crystalline structures. The approach is based on a combination of Rayleigh-Gans-Debye theory and approximate forms of the Mie scattering equations. Crown Copyright © 2015. Published by Elsevier Inc. All rights reserved.
NASA Astrophysics Data System (ADS)
Nasri, Mohamed Aziz; Robert, Camille; Ammar, Amine; El Arem, Saber; Morel, Franck
2018-02-01
The numerical modelling of the behaviour of materials at the microstructural scale has been greatly developed over the last two decades. Unfortunately, conventional resolution methods cannot simulate polycrystalline aggregates beyond tens of loading cycles, and they do not remain quantitative due to the plasticity behaviour. This work presents the development of a numerical solver for the resolution of the Finite Element modelling of polycrystalline aggregates subjected to cyclic mechanical loading. The method is based on two concepts. The first one consists in maintaining a constant stiffness matrix. The second uses a time/space model reduction method. In order to analyse the applicability and the performance of the use of a space-time separated representation, the simulations are carried out on a three-dimensional polycrystalline aggregate under cyclic loading. Different numbers of elements per grain and two time increments per cycle are investigated. The results show a significant CPU time saving while maintaining good precision. Moreover, increasing the number of elements and the number of time increments per cycle, the model reduction method is faster than the standard solver.
Convective aggregation in realistic convective-scale simulations
NASA Astrophysics Data System (ADS)
Holloway, Christopher E.
2017-06-01
To investigate the real-world relevance of idealized-model convective self-aggregation, five 15 day cases of real organized convection in the tropics are simulated. These include multiple simulations of each case to test sensitivities of the convective organization and mean states to interactive radiation, interactive surface fluxes, and evaporation of rain. These simulations are compared to self-aggregation seen in the same model configured to run in idealized radiative-convective equilibrium. Analysis of the budget of the spatial variance of column-integrated frozen moist static energy shows that control runs have significant positive contributions to organization from radiation and negative contributions from surface fluxes and transport, similar to idealized runs once they become aggregated. Despite identical lateral boundary conditions for all experiments in each case, systematic differences in mean column water vapor (CWV), CWV distribution shape, and CWV autocorrelation length scale are found between the different sensitivity runs, particularly for those without interactive radiation, showing that there are at least some similarities in sensitivities to these feedbacks in both idealized and realistic simulations (although the organization of precipitation shows less sensitivity to interactive radiation). The magnitudes and signs of these systematic differences are consistent with a rough equilibrium between (1) equalization due to advection from the lateral boundaries and (2) disaggregation due to the absence of interactive radiation, implying disaggregation rates comparable to those in idealized runs with aggregated initial conditions and noninteractive radiation. This points to a plausible similarity in the way that radiation feedbacks maintain aggregated convection in both idealized simulations and the real world.
All-atom Simulation of Amyloid Aggregates
NASA Astrophysics Data System (ADS)
Berhanu, Workalemahu M.; Alred, Erik J.; Bernhardt, Nathan A.; Hansmann, Ulrich H. E.
Molecular simulations are now commonly used to complement experiments in the investigation of amyloid formation and their role in human diseases. While various simulations based on enhanced sampling techniques are used in amyloid formation simulations, this article will focus on those using standard atomistic simulations to evaluate the stability of fibril models. Such studies explore the limitations that arise from the choice of force field or polymorphism; and explore the stability of in vivo and in vitro forms of Aβ fibril aggregates, and the role of heterologous seeding as a link between different amyloid diseases.
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.
NASA Astrophysics Data System (ADS)
Danesh-Yazdi, Mohammad; Botter, Gianluca; Foufoula-Georgiou, Efi
2017-05-01
Lack of hydro-bio-chemical data at subcatchment scales necessitates adopting an aggregated system approach for estimating water and solute transport properties, such as residence and travel time distributions, at the catchment scale. In this work, we show that within-catchment spatial heterogeneity, as expressed in spatially variable discharge-storage relationships, can be appropriately encapsulated within a lumped time-varying stochastic Lagrangian formulation of transport. This time (variability) for space (heterogeneity) substitution yields mean travel times (MTTs) that are not significantly biased to the aggregation of spatial heterogeneity. Despite the significant variability of MTT at small spatial scales, there exists a characteristic scale above which the MTT is not impacted by the aggregation of spatial heterogeneity. Extensive simulations of randomly generated river networks reveal that the ratio between the characteristic scale and the mean incremental area is on average independent of river network topology and the spatial arrangement of incremental areas.
Impact of Spatial Soil and Climate Input Data Aggregation on Regional Yield Simulations
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.
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.
NASA Astrophysics Data System (ADS)
López-López, J. M.; Moncho-Jordá, A.; Schmitt, A.; Hidalgo-Álvarez, R.
2005-09-01
Binary diffusion-limited cluster-cluster aggregation processes are studied as a function of the relative concentration of the two species. Both, short and long time behaviors are investigated by means of three-dimensional off-lattice Brownian Dynamics simulations. At short aggregation times, the validity of the Hogg-Healy-Fuerstenau approximation is shown. At long times, a single large cluster containing all initial particles is found to be formed when the relative concentration of the minority particles lies above a critical value. Below that value, stable aggregates remain in the system. These stable aggregates are composed by a few minority particles that are highly covered by majority ones. Our off-lattice simulations reveal a value of approximately 0.15 for the critical relative concentration. A qualitative explanation scheme for the formation and growth of the stable aggregates is developed. The simulations also explain the phenomenon of monomer discrimination that was observed recently in single cluster light scattering experiments.
Atomistic Structure of Mineral Nano-aggregates from Simulated Compaction and Dewatering.
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.
Srivastava, Alka; Balaji, Petety V
2015-12-01
This study probes the early events during lag phase of aggregation of GNNQQNY using all atom MD simulations in explicit solvent. Simulations were performed by varying system size, temperature and starting configuration. Peptides dispersed randomly in the simulation box come together early on in the simulation and form aggregates. These aggregates are dynamic implying the absence of stabilizing interactions. This facilitates the exploration of alternate arrangements. The constituent peptides sample a variety of conformations, frequently re-orient and re-arrange with respect to each other and dissociate from/re-associate with the aggregate. The size and lifetime of aggregates vary depending upon the number of inter-peptide backbone H-bonds. Most of the aggregates formed are amorphous but crystalline aggregates of smaller size (mainly 2-mers) do appear and sustain for varying durations of time. The peptides in crystalline 2-mers are mostly anti-parallel. The largest crystalline aggregate that appears is a 4-mer in a single sheet and a 4-, 5-, or 6-mer in double layered arrangement. Crystalline aggregates grow either by the sequential addition of peptides, or by the head-on or lateral collision-adhesion of 2-mers. The formation of various smaller aggregates suggests the polymorphic nature of oligomers and heterogeneity in the lag phase. Copyright © 2015 Elsevier Inc. All rights reserved.
Atomistic Structure of Mineral Nano-aggregates from Simulated Compaction and Dewatering
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 REBOUND CONDITION OF DUST AGGREGATES REVEALED BY NUMERICAL SIMULATION OF THEIR COLLISIONS
DOE Office of Scientific and Technical Information (OSTI.GOV)
Wada, Koji; Tanaka, Hidekazu; Yamamoto, Tetsuo
2011-08-10
Collisional growth of dust aggregates is a plausible root of planetesimals forming in protoplanetary disks. However, a rebound of colliding dust aggregates prevents dust from growing into planetesimals. In fact, rebounding aggregates are observed in laboratory experiments but not in previous numerical simulations. Therefore, the condition of rebound between dust aggregates should be clarified to better understand the processes of dust growth and planetesimal formation. We have carried out numerical simulations of aggregate collisions for various types of aggregates and succeeded in reproducing a rebound of colliding aggregates under specific conditions. Our finding is that in the rebound process, themore » key factor of the aggregate structure is the coordination number, namely, the number of particles in contact with a particle. A rebound is governed by the energy dissipation along with restructuring of the aggregates and a large coordination number inhibits the restructuring at collisions. Results of our numerical simulation for various aggregates indicate that they stick to each other when the mean coordination number is less than 6, regardless of their materials and structures, as long as their collision velocity is less than the critical velocity for fragmentation. This criterion of the coordination number would correspond to a filling factor of {approx}0.3, which is somewhat larger than that reported in laboratory experiments. In protoplanetary disks, dust aggregates are expected to have low bulk densities (<0.1 g cm{sup -3}) during their growth, which would prevent dust aggregates from rebounding. This result supports the formation of planetesimals with direct dust growth in protoplanetary disks.« less
NASA Astrophysics Data System (ADS)
Michel, Patrick; Richardson, D. C.
2007-10-01
We have made major improvements in simulations of asteroid disruption by computing explicitly aggregate formations during the gravitational reaccumulation of small fragments, allowing us to obtain information on their spin and shape. First results will be presented taking as examples asteroid families that we reproduced successfully with previous less sophisticated simulations. In the last years, we have simulated successfully the formation of asteroid families using a SPH hydrocode to compute the fragmentation following the impact of a projectile on the parent body, and the N-body code pkdgrav to compute the mutual interactions of the fragments. We found that fragments generated by the disruption of a km-size asteroid can have large enough masses to be attracted by each other during their ejection. Consequently, many reaccumulations take place. Eventually most large fragments correspond to gravitational aggregates formed by reaccumulation of smaller ones. Moreover, formation of satellites occurs around the largest and other big remnants. In these previous simulations, when fragments reaccumulate, they merge into a single sphere whose mass is the sum of their masses. Thus, no information is obtained on the actual shape of the aggregates, their spin, ... For the first time, we have now simulated the disruption of a family parent body by computing explicitly the formation of aggregates, along with the above-mentioned properties. Once formed these aggregates can interact and/or collide with each other and break up during their evolution. We will present these first simulations and their possible implications on properties of asteroids generated by disruption. Results can for instance be compared with data provided by the Japanese space mission Hayabusa of the asteroid Itokawa, a body now understood to be a reaccumulated fragment from a larger parent body. Acknowledgments: PM and DCR acknowledge supports from the French Programme National de Planétologie and grants
Gething, Peter W; Patil, Anand P; Hay, Simon I
2010-04-01
Risk maps estimating the spatial distribution of infectious diseases are required to guide public health policy from local to global scales. The advent of model-based geostatistics (MBG) has allowed these maps to be generated in a formal statistical framework, providing robust metrics of map uncertainty that enhances their utility for decision-makers. In many settings, decision-makers require spatially aggregated measures over large regions such as the mean prevalence within a country or administrative region, or national populations living under different levels of risk. Existing MBG mapping approaches provide suitable metrics of local uncertainty--the fidelity of predictions at each mapped pixel--but have not been adapted for measuring uncertainty over large areas, due largely to a series of fundamental computational constraints. Here the authors present a new efficient approximating algorithm that can generate for the first time the necessary joint simulation of prevalence values across the very large prediction spaces needed for global scale mapping. This new approach is implemented in conjunction with an established model for P. falciparum allowing robust estimates of mean prevalence at any specified level of spatial aggregation. The model is used to provide estimates of national populations at risk under three policy-relevant prevalence thresholds, along with accompanying model-based measures of uncertainty. By overcoming previously unchallenged computational barriers, this study illustrates how MBG approaches, already at the forefront of infectious disease mapping, can be extended to provide large-scale aggregate measures appropriate for decision-makers.
Computer simulations of structural transitions in large ferrofluid aggregates
NASA Astrophysics Data System (ADS)
Yoon, Mina; Tomanek, David
2003-03-01
We have developed a quaternion molecular dynamics formalism to study structural transitions in systems of ferrofluid particles in colloidal suspensions. Our approach takes advantage of the viscous damping provided by the surrounding liquid and enables us to study the time evolution of these systems over milli-second time periods as a function of the number of particles, initial geometry, and an externally applied magnetic field. Our computer simulations for aggregates containing tens to hundreds of ferrofluid particles suggest that these systems relax to the global optimum structure in a step-wise manner. During the relaxation process, the potential energy decreases by two mechanisms, which occur on different time scales. Short time periods associated with structural relaxations within a given morphology are followed by much slower processes that generally lead to a simpler morphology. We discuss possible applications of these externally driven structural transitions for targeted medication delivery.
NASA Astrophysics Data System (ADS)
Patrizio, Casey
A three-dimensional cloud-resolving model (CRM) was used to investigate the preferred separation distance between humid, rainy regions formed by convective aggregation in radiative-convective equilibrium without rotation. We performed the simulations with doubly-periodic square domains of widths 768 km, 1536 km and 3072 km over a time period of about 200 days. The simulations in the larger domains were initialized using multiple copies of the results in the small domain at day 90, plus a small perturbation. With all three domain sizes, the simulations evolved to a single statistically steady convective cluster surrounded by a broader region of dry, subsiding air by about day 150. In the largest domain case, however, we found that an additional convective cluster formed when we the simulation was run for an extended period of time. Specifically, a smaller convective cluster formed at around day 185 at a maximum radial distance from the larger cluster and then re-merged with the larger cluster after about 10 days. We explored how the aggregated state was different in each domain case, before the smaller cluster formed in the large domain. In particular, we investigated changes in the radial structure of the aggregated state by calculating profiles for the water, dynamics and radiation as a function of distance from the center of the convective region. Changes in the vertical structure were also investigated by compositing on the convective region and dry, subsiding region at each height. We found that, with increasing domain size, the convective region boundary layer became more buoyant, the convective cores reached deeper into the troposphere, the mesoscale convective updraft became weaker, and the mesoscale convective region spread out. Additionally, as the domain size was increased, conditions in the remote environment became favorable for convection. We describe a physical mechanism for the weakening of the mesoscale convective updraft and associated broadening
Middleton, L. Robert; Tarver, Jacob D.; Cordaro, Joseph; ...
2016-11-10
Melt state dynamics for a series of strictly linear polyethylenes with precisely spaced associating functional groups were investigated. The periodic pendant acrylic acid groups form hydrogen-bonded acid aggregates within the polyethylene (PE) matrix. The dynamics of these nanoscale heterogeneous morphologies were investigated from picosecond to nanosecond timescales by both quasi-elastic neutron scattering (QENS) measurements and fully atomistic molecular dynamics (MD) simulations. Two dynamic processes were observed. The faster dynamic processes which occur at the picosecond timescales are compositionally insensitive and indicative of spatially restricted local motions. The slower dynamic processes are highly composition dependent and indicate the structural relaxation ofmore » the polymer backbone. Higher acid contents, or shorter PE spacers between pendant acid groups, slow the structural relaxation timescale and increase the stretching parameter (β) of the structural relaxation. Additionally, the dynamics of specific hydrogen atom positions along the backbone correlate structural heterogeneity imposed by the associating acid groups with a mobility gradient along the polymer backbone. At time intervals (<2 ns), the mean-squared displacements for the four methylene groups closest to the acid groups are up to 10 times smaller than those of methylene groups further from the acid groups. At longer timescales acid aggregates rearrange and the chain dynamics of the slow, near-aggregate regions and the faster bridge regions converge, implying a characteristic timescale for the passage of chains between aggregates. As a result, the characterization of the nanoscale chain dynamics in these associating polymer systems both provides validation of simulation force fields and provides understanding of heterogeneous chain dynamics in associating polymers.« less
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;
2016-01-01
The aggregation of simulated gridded crop yields to national or regional scale requires information on temporal and spatial patterns of crop-specific harvested areas. This analysis estimates the uncertainty of simulated gridded yield time series related to the aggregation with four different harvested area data sets. We compare aggregated yield time series from the Global Gridded Crop Model Inter-comparison project for four crop types from 14 models at global, national, and regional scale to determine aggregation-driven differences in mean yields and temporal patterns as measures of uncertainty. The quantity and spatial patterns of harvested areas differ for individual crops among the four datasets applied for the aggregation. Also simulated spatial yield patterns differ among the 14 models. These differences in harvested areas and simulated yield patterns lead to differences in aggregated productivity estimates, both in mean yield and in the temporal dynamics. Among the four investigated crops, wheat yield (17% relative difference) is most affected by the uncertainty introduced by the aggregation at the global scale. The correlation of temporal patterns of global aggregated yield time series can be as low as for soybean (r = 0.28).For the majority of countries, mean relative differences of nationally aggregated yields account for10% or less. The spatial and temporal difference can be substantial higher for individual countries. Of the top-10 crop producers, aggregated national multi-annual mean relative difference of yields can be up to 67% (maize, South Africa), 43% (wheat, Pakistan), 51% (rice, Japan), and 427% (soybean, Bolivia).Correlations of differently aggregated yield time series can be as low as r = 0.56 (maize, India), r = 0.05*Corresponding (wheat, Russia), r = 0.13 (rice, Vietnam), and r = -0.01 (soybean, Uruguay). The aggregation to sub-national scale in comparison to country scale shows that spatial uncertainties can cancel out in countries with
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.
Observing Convective Aggregation
NASA Astrophysics Data System (ADS)
Holloway, Christopher E.; Wing, Allison A.; Bony, Sandrine; Muller, Caroline; Masunaga, Hirohiko; L'Ecuyer, Tristan S.; Turner, David D.; Zuidema, Paquita
2017-11-01
Convective self-aggregation, the spontaneous organization of initially scattered convection into isolated convective clusters despite spatially homogeneous boundary conditions and forcing, was first recognized and studied in idealized numerical simulations. While there is a rich history of observational work on convective clustering and organization, there have been only a few studies that have analyzed observations to look specifically for processes related to self-aggregation in models. Here we review observational work in both of these categories and motivate the need for more of this work. We acknowledge that self-aggregation may appear to be far-removed from observed convective organization in terms of time scales, initial conditions, initiation processes, and mean state extremes, but we argue that these differences vary greatly across the diverse range of model simulations in the literature and that these comparisons are already offering important insights into real tropical phenomena. Some preliminary new findings are presented, including results showing that a self-aggregation simulation with square geometry has too broad distribution of humidity and is too dry in the driest regions when compared with radiosonde records from Nauru, while an elongated channel simulation has realistic representations of atmospheric humidity and its variability. We discuss recent work increasing our understanding of how organized convection and climate change may interact, and how model discrepancies related to this question are prompting interest in observational comparisons. We also propose possible future directions for observational work related to convective aggregation, including novel satellite approaches and a ground-based observational network.
Aggregated Indexing of Biomedical Time Series Data
Woodbridge, Jonathan; Mortazavi, Bobak; Sarrafzadeh, Majid; Bui, Alex A.T.
2016-01-01
Remote and wearable medical sensing has the potential to create very large and high dimensional datasets. Medical time series databases must be able to efficiently store, index, and mine these datasets to enable medical professionals to effectively analyze data collected from their patients. Conventional high dimensional indexing methods are a two stage process. First, a superset of the true matches is efficiently extracted from the database. Second, supersets are pruned by comparing each of their objects to the query object and rejecting any objects falling outside a predetermined radius. This pruning stage heavily dominates the computational complexity of most conventional search algorithms. Therefore, indexing algorithms can be significantly improved by reducing the amount of pruning. This paper presents an online algorithm to aggregate biomedical times series data to significantly reduce the search space (index size) without compromising the quality of search results. This algorithm is built on the observation that biomedical time series signals are composed of cyclical and often similar patterns. This algorithm takes in a stream of segments and groups them to highly concentrated collections. Locality Sensitive Hashing (LSH) is used to reduce the overall complexity of the algorithm, allowing it to run online. The output of this aggregation is used to populate an index. The proposed algorithm yields logarithmic growth of the index (with respect to the total number of objects) while keeping sensitivity and specificity simultaneously above 98%. Both memory and runtime complexities of time series search are improved when using aggregated indexes. In addition, data mining tasks, such as clustering, exhibit runtimes that are orders of magnitudes faster when run on aggregated indexes. PMID:27617298
A novel weight determination method for time series data aggregation
NASA Astrophysics Data System (ADS)
Xu, Paiheng; Zhang, Rong; Deng, Yong
2017-09-01
Aggregation in time series is of great importance in time series smoothing, predicting and other time series analysis process, which makes it crucial to address the weights in times series correctly and reasonably. In this paper, a novel method to obtain the weights in time series is proposed, in which we adopt induced ordered weighted aggregation (IOWA) operator and visibility graph averaging (VGA) operator and linearly combine the weights separately generated by the two operator. The IOWA operator is introduced to the weight determination of time series, through which the time decay factor is taken into consideration. The VGA operator is able to generate weights with respect to the degree distribution in the visibility graph constructed from the corresponding time series, which reflects the relative importance of vertices in time series. The proposed method is applied to two practical datasets to illustrate its merits. The aggregation of Construction Cost Index (CCI) demonstrates the ability of proposed method to smooth time series, while the aggregation of The Taiwan Stock Exchange Capitalization Weighted Stock Index (TAIEX) illustrate how proposed method maintain the variation tendency of original data.
Molecular Dynamics Simulations to Clarify the Concentration Dependency of Protein Aggregation
NASA Astrophysics Data System (ADS)
Nishikawa, Naohiro; Sakae, Yoshitake; Okamoto, Yuko
We examined the concentration dependency of amyloid protein aggregation by using several molecular dynamics simulations, which were performed with different concentrations for each system. For these simulations, we used a fragment of amyloid-β, which is believed to be the cause of Alzheimer's disease, as our simulation system. We found that high concentration of amyloid peptides promotes the formation of β-structures which is the origin of amyloid fibrils.
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.
di Stasio, Stefano; Konstandopoulos, Athanasios G; Kostoglou, Margaritis
2002-03-01
The agglomeration kinetics of growing soot generated in a diffusion atmospheric flame are here studied in situ by light scattering technique to infer cluster morphology and size (fractal dimension D(f) and radius of gyration R(g)). SEM analysis is used as a standard reference to obtain primary particle size D(P) at different residence times. The number N(P) of primary particles per aggregate and the number concentration n(A) of clusters are evaluated on the basis of the measured angular patterns of the scattered light intensity. The major finding is that the kinetics of the coagulation process that yields to the formation of chain-like aggregates by soot primary particles (size 10 to 40 nm) can be described with a constant coagulation kernel beta(c,exp)=2.37x10(-9) cm3/s (coagulation constant tau(c) approximately = 0.28 ms). This result is in nice accord with the Smoluchowski coagulation equation in the free molecular regime, and, vice versa, it is in contrast with previous studies conducted by invasive (ex situ) techniques, which claimed the evidence in flames of coagulation rates much larger than the kinetic theory predictions. Thereafter, a number of numerical simulations is implemented to compare with the experimental results on primary particle growth rate and on the process of aggregate reshaping that is observed by light scattering at later residence times. The restructuring process is conjectured to occur, for not well understood reasons, as a direct consequence of the atomic rearrangement in the solid phase carbon due to the prolonged residence time within the flame. Thus, on one side, it is shown that the numerical simulations of primary size history compare well with the values of primary size from SEM experiment with a growth rate constant of primary diameter about 1 nm/s. On the other side, the evolution of aggregate morphology is found to be predictable by the numerical simulations when the onset of a first-order "thermal" restructuring mechanism is
NASA Astrophysics Data System (ADS)
Townsend, B.; Peyronel, F.; Callaghan-Patrachar, N.; Quinn, B.; Marangoni, A. G.; Pink, D. A.
2017-12-01
The effects of shear upon the aggregation of solid objects formed from solid triacylglycerols (TAGs) immersed in liquid TAG oils were modeled using Dissipative Particle Dynamics (DPD) and the predictions compared to experimental data using Ultra-Small Angle X-ray Scattering (USAXS). The solid components were represented by spheres interacting via attractive van der Waals forces and short range repulsive forces. A velocity was applied to the liquid particles nearest to the boundary, and Lees-Edwards boundary conditions were used to transmit this motion to non-boundary layers via dissipative interactions. The shear was created through the dissipative forces acting between liquid particles. Translational diffusion was simulated, and the Stokes-Einstein equation was used to relate DPD length and time scales to SI units for comparison with USAXS results. The SI values depended on how large the spherical particles were (250 nm vs. 25 nm). Aggregation was studied by (a) computing the Structure Function and (b) quantifying the number of pairs of solid spheres formed. Solid aggregation was found to be enhanced by low shear rates. As the shear rate was increased, a transition shear region was manifested in which aggregation was inhibited and shear banding was observed. Aggregation was inhibited, and eventually eliminated, by further increases in the shear rate. The magnitude of the transition region shear, γ˙ t, depended on the size of the solid particles, which was confirmed experimentally.
Real-time imaging of Huntingtin aggregates diverting target search and gene transcription
Li, Li; Liu, Hui; Dong, Peng; Li, Dong; Legant, Wesley R; Grimm, Jonathan B; Lavis, Luke D; Betzig, Eric; Tjian, Robert; Liu, Zhe
2016-01-01
The presumptive altered dynamics of transient molecular interactions in vivo contributing to neurodegenerative diseases have remained elusive. Here, using single-molecule localization microscopy, we show that disease-inducing Huntingtin (mHtt) protein fragments display three distinct dynamic states in living cells – 1) fast diffusion, 2) dynamic clustering and 3) stable aggregation. Large, stable aggregates of mHtt exclude chromatin and form 'sticky' decoy traps that impede target search processes of key regulators involved in neurological disorders. Functional domain mapping based on super-resolution imaging reveals an unexpected role of aromatic amino acids in promoting protein-mHtt aggregate interactions. Genome-wide expression analysis and numerical simulation experiments suggest mHtt aggregates reduce transcription factor target site sampling frequency and impair critical gene expression programs in striatal neurons. Together, our results provide insights into how mHtt dynamically forms aggregates and disrupts the finely-balanced gene control mechanisms in neuronal cells. DOI: http://dx.doi.org/10.7554/eLife.17056.001 PMID:27484239
Real-Time Charging Strategies for an Electric Vehicle Aggregator to Provide Ancillary Services
Wenzel, George; Negrete-Pincetic, Matias; Olivares, Daniel E.; ...
2017-03-13
Real-time charging strategies, in the context of vehicle to grid (V2G) technology, are needed to enable the use of electric vehicle (EV) fleets batteries to provide ancillary services (AS). Here, we develop tools to manage charging and discharging in a fleet to track an Automatic Generation Control (AGC) signal when aggregated. We also propose a real-time controller that considers bidirectional charging efficiency and extend it to study the effect of looking ahead when implementing Model Predictive Control (MPC). Simulations show that the controller improves tracking error as compared with benchmark scheduling algorithms, as well as regulation capacity and battery cycling.
Real-Time Charging Strategies for an Electric Vehicle Aggregator to Provide Ancillary Services
DOE Office of Scientific and Technical Information (OSTI.GOV)
Wenzel, George; Negrete-Pincetic, Matias; Olivares, Daniel E.
Real-time charging strategies, in the context of vehicle to grid (V2G) technology, are needed to enable the use of electric vehicle (EV) fleets batteries to provide ancillary services (AS). Here, we develop tools to manage charging and discharging in a fleet to track an Automatic Generation Control (AGC) signal when aggregated. We also propose a real-time controller that considers bidirectional charging efficiency and extend it to study the effect of looking ahead when implementing Model Predictive Control (MPC). Simulations show that the controller improves tracking error as compared with benchmark scheduling algorithms, as well as regulation capacity and battery cycling.
NASA Astrophysics Data System (ADS)
Boek, Edo S.; Ladva, Hemant K.; Crawshaw, John P.; Padding, Johan T.
2008-07-01
The aggregation and deposition of colloidal asphaltene in reservoir rock is a significant problem in the oil industry. To obtain a fundamental understanding of this phenomenon, we have studied the deposition and aggregation of colloidal asphaltene in capillary flow by experiment and simulation. For the simulation, we have used the stochastic rotation dynamics (SRD) method, in which the solvent hydrodynamic emerges from the collisions between the solvent particles, while the Brownian motion emerges naturally from the interactions between the colloidal asphaltene particles and the solvent. The asphaltene colloids interact through a screened Coulomb potential. We vary the well depth ɛ∝ and the flow rate v to obtain Peflow≫1 (hydrodynamic interactions dominate) and Re≪1 (Stokes flow). In the simulations, we impose a pressure drop over the capillary length and measure the corresponding solvent flow rate. We observe that the transient solvent flow rate decreases when the asphaltene particles become more "sticky". For a well depth ɛ∝ = 2kBT, a monolayer deposits on the capillary wall. With an increasing well depth, the capillary becomes totally blocked. The clogging is transient for ɛ∝ = 5kBT, but appears to be permanent for ɛ∝ = 10-20 kBT. We compare our simulation results with flow experiments in glass capillaries, where we use extracted asphaltenes in toluene, reprecipitated with n-heptane. In the experiments, the dynamics of asphaltene precipitation and deposition were monitored in a slot capillary using optical microscopy under flow conditions similar to those used in the simulation. Maintaining a constant flow rate of 5 μL min-1, we found that the pressure drop across the capillary first increased slowly, followed by a sharp increase, corresponding to a complete local blockage of the capillary. Doubling the flow rate to 10 μL min-1, we observe that the initial deposition occurs faster but the deposits are subsequently entrained by the flow. We
First-principles calculation of the optical properties of an amphiphilic cyanine dye aggregate.
Haverkort, Frank; Stradomska, Anna; de Vries, Alex H; Knoester, Jasper
2014-02-13
Using a first-principles approach, we calculate electronic and optical properties of molecular aggregates of the dye amphi-pseudoisocyanine, whose structures we obtained from molecular dynamics (MD) simulations of the self-aggregation process. Using quantum chemistry methods, we translate the structural information into an effective time-dependent Frenkel exciton Hamiltonian for the dominant optical transitions in the aggregate. This Hamiltonian is used to calculate the absorption spectrum. Detailed analysis of the dynamic fluctuations in the molecular transition energies and intermolecular excitation transfer interactions in this Hamiltonian allows us to elucidate the origin of the relevant time scales; short time scales, on the order of up to a few hundreds of femtoseconds, result from internal motions of the dye molecules, while the longer (a few picosecond) time scales we ascribe to environmental motions. The absorption spectra of the aggregate structures obtained from MD feature a blue-shifted peak compared to that of the monomer; thus, our aggregates can be classified as H-aggregates, although considerable oscillator strength is carried by states along the entire exciton band. Comparison to the experimental absorption spectrum of amphi-PIC aggregates shows that the simulated line shape is too wide, pointing to too much disorder in the internal structure of the simulated aggregates.
Riccardi, Laura; Nguyen, Phuong H; Stock, Gerhard
2012-04-10
To describe the structure and dynamics of oligomers during peptide aggregation, a method is proposed that considers both the intramolecular and intermolecular structures of the multimolecule system and correctly accounts for its degeneracy. The approach is based on the "by-parts" strategy, which partitions a complex molecular system into parts, determines the metastable conformational states of each part, and describes the overall conformational state of the system in terms of a product basis of the states of the parts. Starting from a molecular dynamics simulation of n molecules, the method consists of three steps: (i) characterization of the intramolecular structure, that is, of the conformational states of a single molecule in the presence of the other molecules (e.g., β-strand or random coil); (ii) characterization of the intermolecular structure through the identification of all occurring aggregate states of the peptides (dimers, trimers, etc.); and (iii) construction of the overall conformational states of the system in terms of a product basis of the n "single-molecule" states and the aggregate states. Considering the Alzheimer β-amyloid peptide fragment Aβ16-22 as a first application, about 700 overall conformational states of the trimer (Aβ16-22)3 were constructed from all-atom molecular dynamics simulation in explicit water. Based on these states, a transition network reflecting the free energy landscape of the aggregation process can be constructed that facilitates the identification of the aggregation pathways.
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.
Stafford, Richard; Williams, Gray A; Davies, Mark S
2011-01-01
Group or population level self-organised systems comprise many individuals displaying group-level emergent properties. Current theory indicates that individual-level behaviours have an effect on the final group-level behaviour; that is, self-organised systems are sensitive to small changes in individual behaviour. Here we examine a self-organised behaviour in relation to environmentally-driven individual-level changes in behaviour, using both natural systems and computer simulations. We demonstrate that aggregations of intertidal snails slightly decrease in size when, owing to hotter and more desiccating conditions, individuals forage for shorter periods--a seemingly non-adaptive behaviour for the snails since aggregation reduces desiccation stress. This decrease, however, only occurs in simple experimental systems (and simulations of these systems). When studied in their natural and more complex environment, and simulations of such an environment, using the same reduced foraging time, no difference in aggregation behaviour was found between hot and cool days. These results give an indication of how robust self-organised systems are to changes in individual-level behaviour. The complexity of the natural environment and the interactions of individuals with this environment, therefore, can result in self-organised systems being more resilient to individual-level changes than previously assumed.
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
Fu, Yunhai; Ma, Lin; Xu, Yubin
2015-01-01
In spectrum aggregation (SA), two or more component carriers (CCs) of different bandwidths in different bands can be aggregated to support a wider transmission bandwidth. The scheduling delay is the most important design constraint for the broadband wireless trunking (BWT) system, especially in the cognitive radio (CR) condition. The current resource scheduling schemes for spectrum aggregation become questionable and are not suitable for meeting the challenge of the delay requirement. Consequently, the authors propose a novel component carrier configuration and switching scheme for real-time traffic (RT-CCCS) to satisfy the delay requirement in the CR-based SA system. In this work, the authors consider a sensor-network-assisted CR network. The authors first introduce a resource scheduling structure for SA in the CR condition. Then the proposed scheme is analyzed in detail. Finally, simulations are carried out to verify the analysis on the proposed scheme. Simulation results prove that our proposed scheme can satisfy the delay requirement in the CR-based SA system. PMID:26393594
NASA Astrophysics Data System (ADS)
Wüster, S.; Rost, J.-M.
2018-02-01
We review Rydberg aggregates, assemblies of a few Rydberg atoms exhibiting energy transport through collective eigenstates, considering isolated atoms or assemblies embedded within clouds of cold ground-state atoms. We classify Rydberg aggregates, and provide an overview of their possible applications as quantum simulators for phenomena from chemical or biological physics. Our main focus is on flexible Rydberg aggregates, in which atomic motion is an essential feature. In these, simultaneous control over Rydberg-Rydberg interactions, external trapping and electronic energies, allows Born-Oppenheimer surfaces for the motion of the entire aggregate to be tailored as desired. This is illustrated with theory proposals towards the demonstration of joint motion and excitation transport, conical intersections and non-adiabatic effects. Additional flexibility for quantum simulations is enabled by the use of dressed dipole-dipole interactions or the embedding of the aggregate in a cold gas or Bose-Einstein condensate environment. Finally we provide some guidance regarding the parameter regimes that are most suitable for the realization of either static or flexible Rydberg aggregates based on Li or Rb atoms. The current status of experimental progress towards enabling Rydberg aggregates is also reviewed.
Kamgar-Parsi, Kian; Hong, Liu; Naito, Akira; Brooks, Charles L; Ramamoorthy, Ayyalusamy
2017-09-08
The role of the peptide hormone calcitonin in skeletal protection has led to its use as a therapeutic for osteoporosis. However, calcitonin aggregation into amyloid fibrils limits its therapeutic efficacy, necessitating a modification of calcitonin's aggregation kinetics. Here, we report a direct relationship between human calcitonin (hCT) concentration and aggregation lag time. This kinetic trend was contrary to the conventional understanding of amyloid aggregation and persisted over a range of aggregation conditions, as confirmed by thioflavin-T kinetics assays, CD spectroscopy, and transmission EM. Dynamic light scattering, 1 H NMR experiments, and seeded thioflavin-T assay results indicated that differences in initial peptide species contribute to this trend more than variations in the primary nucleus formation rate. On the basis of kinetics modeling results, we propose a mechanism whereby a structural conversion of hCT monomers is needed before incorporation into the fibril. Our kinetic mechanism recapitulates the experimentally observed relationship between peptide concentration and lag time and represents a novel mechanism in amyloid aggregation. Interestingly, hCT at low pH and salmon calcitonin (sCT) exhibited the canonical inverse relationship between concentration and lag time. Comparative studies of hCT and sCT with molecular dynamics simulations and CD indicated an increased α-helical structure in sCT and low-pH hCT monomers compared with neutral-pH hCT, suggesting that α-helical monomers represent a growth-competent species, whereas unstructured random coil monomers represent a growth-incompetent species. Our finding that initial monomer concentration is positively correlated with lag time in hCT aggregation could help inform future efforts for improving therapeutic applications of CT. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.
On Time/Space Aggregation of Fine-Scale Error Estimates (Invited)
NASA Astrophysics Data System (ADS)
Huffman, G. J.
2013-12-01
Estimating errors inherent in fine time/space-scale satellite precipitation data sets is still an on-going problem and a key area of active research. Complicating features of these data sets include the intrinsic intermittency of the precipitation in space and time and the resulting highly skewed distribution of precipitation rates. Additional issues arise from the subsampling errors that satellites introduce, the errors due to retrieval algorithms, and the correlated error that retrieval and merger algorithms sometimes introduce. Several interesting approaches have been developed recently that appear to make progress on these long-standing issues. At the same time, the monthly averages over 2.5°x2.5° grid boxes in the Global Precipitation Climatology Project (GPCP) Satellite-Gauge (SG) precipitation data set follow a very simple sampling-based error model (Huffman 1997) with coefficients that are set using coincident surface and GPCP SG data. This presentation outlines the unsolved problem of how to aggregate the fine-scale errors (discussed above) to an arbitrary time/space averaging volume for practical use in applications, reducing in the limit to simple Gaussian expressions at the monthly 2.5°x2.5° scale. Scatter diagrams with different time/space averaging show that the relationship between the satellite and validation data improves due to the reduction in random error. One of the key, and highly non-linear, issues is that fine-scale estimates tend to have large numbers of cases with points near the axes on the scatter diagram (one of the values is exactly or nearly zero, while the other value is higher). Averaging 'pulls' the points away from the axes and towards the 1:1 line, which usually happens for higher precipitation rates before lower rates. Given this qualitative observation of how aggregation affects error, we observe that existing aggregation rules, such as the Steiner et al. (2003) power law, only depend on the aggregated precipitation rate
Protein Aggregation and Molecular Crowding: Perspectives From Multiscale Simulations.
Musiani, F; Giorgetti, A
2017-01-01
Cells are extremely crowded environments, thus the use of diluted salted aqueous solutions containing a single protein is too simplistic to mimic the real situation. Macromolecular crowding might affect protein structure, folding, shape, conformational stability, binding of small molecules, enzymatic activity, interactions with cognate biomolecules, and pathological aggregation. The latter phenomenon typically leads to the formation of amyloid fibrils that are linked to several lethal neurodegenerative diseases, but that can also play a functional role in certain organisms. The majority of molecular simulations performed before the last few years were conducted in diluted solutions and were restricted both in the timescales and in the system dimensions by the available computational resources. In recent years, several computational solutions were developed to get close to physiological conditions. In this review we summarize the main computational techniques used to tackle the issue of protein aggregation both in a diluted and in a crowded environment. © 2017 Elsevier Inc. All rights reserved.
Real-time amyloid aggregation monitoring with a photonic crystal-based approach.
Santi, Sara; Musi, Valeria; Descrovi, Emiliano; Paeder, Vincent; Di Francesco, Joab; Hvozdara, Lubos; van der Wal, Peter; Lashuel, Hilal A; Pastore, Annalisa; Neier, Reinhard; Herzig, Hans Peter
2013-10-21
We propose the application of a new label-free optical technique based on photonic nanostructures to real-time monitor the amyloid-beta 1-42 (Aβ(1-42)) fibrillization, including the early stages of the aggregation process, which are related to the onset of the Alzheimer's Disease (AD). The aggregation of Aβ peptides into amyloid fibrils has commonly been associated with neuronal death, which culminates in the clinical features of the incurable degenerative AD. Recent studies revealed that cell toxicity is determined by the formation of soluble oligomeric forms of Aβ peptides in the early stages of aggregation. At this phase, classical amyloid detection techniques lack in sensitivity. Upon a chemical passivation of the sensing surface by means of polyethylene glycol, the proposed approach allows an accurate, real-time monitoring of the refractive index variation of the solution, wherein Aβ(1-42) peptides are aggregating. This measurement is directly related to the aggregation state of the peptide throughout oligomerization and subsequent fibrillization. Our findings open new perspectives in the understanding of the dynamics of amyloid formation, and validate this approach as a new and powerful method to screen aggregation at early stages. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
NASA Astrophysics Data System (ADS)
Xu, Yuanwei; Rodger, P. Mark
2017-03-01
We study the effect of helical structure on the aggregation of proteins using a simplified lattice protein model with an implicit membrane environment. A recently proposed Monte Carlo approach, which exploits the proven statistical optimality of the MBAR estimator in order to improve simulation efficiency, was used. The results show that with both two and four proteins present, the tendency to aggregate is strongly expedited by the presence of amphipathic helix (APH), whereas a transmembrane helix (TMH) slightly disfavours aggregation. When four protein molecules are present, partially aggregated states (dimers and trimers) were more common when the APH was present, compared with the cases where no helices or only the TMH is present.
Berhanu, Workalemahu Mikre; Masunov, Artëm E
2014-01-01
Amyloid oligomers are considered to play essential roles in the pathogenesis of amyloid-related degenerative diseases including type 2 diabetes. Using an explicit solvent all atomic MD simulation, we explored the stability, conformational dynamics and association force of different single-layer models of the full-length wild-type and glycine mutants of amylin (pentamer) obtained from a recent high resolution fibril model. The RMSF profile shows enhanced flexibility in the disorder (Lys1-Cys7) and turn region (Ser19-Gly23), along with smallest fluctuation at the residues (Asn14-Phe15-Leu16-Val17-His18) of β1 region and (Ala25-Ile26-Leu27-Ser28-Ser29) of the β2 region. We obtained a significant difference in backbone RMSD between the wild-type and the mutants, indicating that mutations affected the stability of the peptide. The RMSD and RMSF profiles indicate the edge and loop residues are the primary contributors to the overall conformational changes. The degree of structural similarity between the oligomers in the simulation and the fibril conformation is proposed as the possible explanation for experimentally observed shortening of the nucleation lag phase of amylin with oligomer seeding. On the basis of structure-stability findings, the β1 and β2 portions are optimal target for further anti-amyloid drug design. The MM-PBSA binding energy calculation reveals the binding of amylin: amylin strands in single layer is dominated by contributions from van der Waals interactions. The non-polar solvation term is also found to be favorable. While the electrostatic interactions and polar solvation energy was found to be favorable for the interaction for the larger aggregate and unfavorable for the smaller aggregates. A per-residue decomposition of the binding free energy has been performed to identify the residues contributing most to the self-association free energy. Residues found in the β-sheet regions were found to be key residue making the largest favorable
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.
Parallel algorithms for simulating continuous time Markov chains
NASA Technical Reports Server (NTRS)
Nicol, David M.; Heidelberger, Philip
1992-01-01
We have previously shown that the mathematical technique of uniformization can serve as the basis of synchronization for the parallel simulation of continuous-time Markov chains. This paper reviews the basic method and compares five different methods based on uniformization, evaluating their strengths and weaknesses as a function of problem characteristics. The methods vary in their use of optimism, logical aggregation, communication management, and adaptivity. Performance evaluation is conducted on the Intel Touchstone Delta multiprocessor, using up to 256 processors.
Molecular dynamics simulations of aggregation of copper nanoparticles with different heating rates
NASA Astrophysics Data System (ADS)
Li, Qibin; Wang, Meng; Liang, Yunpei; Lin, Liyang; Fu, Tao; Wei, Peitang; Peng, Tiefeng
2017-06-01
Molecular dynamics simulations were employed to investigate the heating rates' effect on aggregation of two copper nanoparticles. The aggregation can be distinguished into three distinct regimes by the contacting and melting of nanoparticles. The nanoparticles contacting at a lower temperature during the sintering with lower heating rate, meanwhile, some temporary stacking fault exists at the contacting neck. The aggregation properties of the system, i.e. neck diameter, shrinkage ratio, potential energy, mean square displacement (MSD) and relative gyration radius, experience drastic changes due to the free surface annihilation. After the nanoparticles coalesced for a stable period, the shrinkage ratio, MSD, relative gyration radius and neck diameter of the system are dramatically changed during the melting process. It is shown that the shrinkage ratio and MSD have relative larger increasing ratio for a lower heating rate. While the evolution of the relative gyration radius and neck diameter is only sensitive to the temperature.
Detecting beta-amyloid aggregation from time-resolved emission spectra
NASA Astrophysics Data System (ADS)
Alghamdi, A.; Vyshemirsky, V.; Birch, D. J. S.; Rolinski, O. J.
2018-04-01
The aggregation of beta-amyloids is one of the key processes responsible for the development of Alzheimer’s disease. Early molecular-level detection of beta-amyloid oligomers may help in early diagnosis and in the development of new intervention therapies. Our previous studies on the changes in beta-amyloid’s single tyrosine intrinsic fluorescence response during aggregation demonstrated a four-exponential fluorescence intensity decay, and the ratio of the pre-exponential factors indicated the extent of the aggregation in the early stages of the process before the beta-sheets were formed. Here we present a complementary approach based on the time-resolved emission spectra (TRES) of amyloid’s tyrosine excited at 279 nm and fluorescence in the window 240-450 nm. TRES have been used to demonstrate sturctural changes occuring on the nanosecond time scale after excitation which has significant advantages over using steady-state spectra. We demonstrate this by resolving the fluorescent species and revealing that beta-amyloid’s monomers show very fast dielectric relaxation, and its oligomers display a substantial spectral shift due to dielectric relaxation, which gradually decreases when the oligomers become larger.
NASA Technical Reports Server (NTRS)
Huntington, J. L.; Schwartz, D. E.; Marshall, J. R.
1991-01-01
The Gas-Grain Simulation Facility (GGSF) will provide a microgravity environment where undesirable environmental effects are reduced, and thus, experiments involving interactions between small particles and grains can be more suitably performed. Slated for flight aboard the Shuttle in 1992, the ESA glovebox will serve as a scientific and technological testbed for GGSF exobiology experiments as well as generating some basic scientific data. Initial glovebox experiments will test a method of generating a stable, mono-dispersed cloud of fine particles using a vibrating sprinkler system. In the absence of gravity and atmospheric turbulence, it will be possible to determine the influence of interparticle forces in controlling the rate and mode of aggregation. The experimental chamber can be purged of suspended matter to enable multiple repetitions of the experiments. Of particular interest will be the number of particles per unit volume of the chamber, because it is suspected that aggregation will occur extremely rapidly if the number exceeds a critical value. All aggregation events will be recorded on high-resolution video film. Changes in the experimental procedure as a result of surprise events will be accompanied by real-time interaction with the mission specialist during the Shuttle flight.
Aggregation of flexible polyelectrolytes: Phase diagram and dynamics.
Tom, Anvy Moly; Rajesh, R; Vemparala, Satyavani
2017-10-14
Similarly charged polymers in solution, known as polyelectrolytes, are known to form aggregated structures in the presence of oppositely charged counterions. Understanding the dependence of the equilibrium phases and the dynamics of the process of aggregation on parameters such as backbone flexibility and charge density of such polymers is crucial for insights into various biological processes which involve biological polyelectrolytes such as protein, DNA, etc. Here, we use large-scale coarse-grained molecular dynamics simulations to obtain the phase diagram of the aggregated structures of flexible charged polymers and characterize the morphology of the aggregates as well as the aggregation dynamics, in the presence of trivalent counterions. Three different phases are observed depending on the charge density: no aggregation, a finite bundle phase where multiple small aggregates coexist with a large aggregate and a fully phase separated phase. We show that the flexibility of the polymer backbone causes strong entanglement between charged polymers leading to additional time scales in the aggregation process. Such slowing down of the aggregation dynamics results in the exponent, characterizing the power law decay of the number of aggregates with time, to be dependent on the charge density of the polymers. These results are contrary to those obtained for rigid polyelectrolytes, emphasizing the role of backbone flexibility.
Task-Driven Evaluation of Aggregation in Time Series Visualization
Albers, Danielle; Correll, Michael; Gleicher, Michael
2014-01-01
Many visualization tasks require the viewer to make judgments about aggregate properties of data. Recent work has shown that viewers can perform such tasks effectively, for example to efficiently compare the maximums or means over ranges of data. However, this work also shows that such effectiveness depends on the designs of the displays. In this paper, we explore this relationship between aggregation task and visualization design to provide guidance on matching tasks with designs. We combine prior results from perceptual science and graphical perception to suggest a set of design variables that influence performance on various aggregate comparison tasks. We describe how choices in these variables can lead to designs that are matched to particular tasks. We use these variables to assess a set of eight different designs, predicting how they will support a set of six aggregate time series comparison tasks. A crowd-sourced evaluation confirms these predictions. These results not only provide evidence for how the specific visualizations support various tasks, but also suggest using the identified design variables as a tool for designing visualizations well suited for various types of tasks. PMID:25343147
NASA Astrophysics Data System (ADS)
Chen, Zhiming; Feng, Yuncheng
1988-08-01
This paper describes an algorithmic structure for combining simulation and optimization techniques both in theory and practice. Response surface methodology is used to optimize the decision variables in the simulation environment. A simulation-optimization software has been developed and successfully implemented, and its application to an aggregate production planning simulation-optimization model is reported. The model's objective is to minimize the production cost and to generate an optimal production plan and inventory control strategy for an aircraft factory.
Lou, Zhichao; Wang, Bin; Guo, Cunlan; Wang, Kun; Zhang, Haiqian; Xu, Bingqian
2015-11-01
By in situ time-lapse AFM, we investigated early-stage aggregates of PrP formed at low concentration (100 ng/mL) on mica and Au(111) surfaces in acetate buffer (pH 4.5). Remarkably different PrP assemblies were observed. Oligomeric structures of PrP aggregates were observed on mica surface, which was in sharp contrast to the multi-layer PrP aggregates yielding parallel linear patterns observed Au(111) surface. Combining molecular dynamics and docking simulations, PrP monomers, dimers and trimers were revealed as the basic units of the observed aggregates. Besides, the mechanisms of the observed PrP aggregations and the corresponding molecular-substrate and intermolecular interactions were suggested. These interactions involved gold-sulfur interaction, electrostatic interaction, hydrophobic interaction, and hydrogen binding interaction. In contrast, the PrP aggregates observed in pH 7.2 PBS buffer demonstrated similar large ball-like structures on both mica and Au(111) surfaces. The results indicate that the pH of a solution and the surface of the system can have strong effects on supramolecular assemblies of prion proteins. This study provides in-depth understanding on the structural and mechanistic nature of PrP aggregation, and can be used to study the aggregation mechanisms of other proteins with similar misfolding properties. Copyright © 2015 Elsevier B.V. All rights reserved.
NASA Astrophysics Data System (ADS)
Van Liedekerke, P.; Ghysels, P.; Tijskens, E.; Samaey, G.; Smeedts, B.; Roose, D.; Ramon, H.
2010-06-01
This paper is concerned with addressing how plant tissue mechanics is related to the micromechanics of cells. To this end, we propose a mesh-free particle method to simulate the mechanics of both individual plant cells (parenchyma) and cell aggregates in response to external stresses. The model considers two important features in the plant cell: (1) the cell protoplasm, the interior liquid phase inducing hydrodynamic phenomena, and (2) the cell wall material, a viscoelastic solid material that contains the protoplasm. In this particle framework, the cell fluid is modeled by smoothed particle hydrodynamics (SPH), a mesh-free method typically used to address problems with gas and fluid dynamics. In the solid phase (cell wall) on the other hand, the particles are connected by pairwise interactions holding them together and preventing the fluid to penetrate the cell wall. The cell wall hydraulic conductivity (permeability) is built in as well through the SPH formulation. Although this model is also meant to be able to deal with dynamic and even violent situations (leading to cell wall rupture or cell-cell debonding), we have concentrated on quasi-static conditions. The results of single-cell compression simulations show that the conclusions found by analytical models and experiments can be reproduced at least qualitatively. Relaxation tests revealed that plant cells have short relaxation times (1 µs-10 µs) compared to mammalian cells. Simulations performed on cell aggregates indicated an influence of the cellular organization to the tissue response, as was also observed in experiments done on tissues with a similar structure.
Wang, Jiang; Gayatri, Mohit A; Ferguson, Andrew L
2017-05-11
Asphaltenes constitute the heaviest fraction of the aromatic group in crude oil. Aggregation and precipitation of asphaltenes during petroleum processing costs the petroleum industry billions of dollars each year due to downtime and production inefficiencies. Asphaltene aggregation proceeds via a hierarchical self-assembly process that is well-described by the Yen-Mullins model. Nevertheless, the microscopic details of the emergent cluster morphologies and their relative stability under different processing conditions remain poorly understood. We perform coarse-grained molecular dynamics simulations of a prototypical asphaltene molecule to establish a phase diagram mapping the self-assembled morphologies as a function of temperature, pressure, and n-heptane:toluene solvent ratio informing how to control asphaltene aggregation by regulating external processing conditions. We then combine our simulations with graph matching and nonlinear manifold learning to determine low-dimensional free energy surfaces governing asphaltene self-assembly. In doing so, we introduce a variant of diffusion maps designed to handle data sets with large local density variations, and report the first application of many-body diffusion maps to molecular self-assembly to recover a pseudo-1D free energy landscape. Increasing pressure only weakly affects the landscape, serving only to destabilize the largest aggregates. Increasing temperature and toluene solvent fraction stabilizes small cluster sizes and loose bonding arrangements. Although the underlying molecular mechanisms differ, the strikingly similar effect of these variables on the free energy landscape suggests that toluene acts upon asphaltene self-assembly as an effective temperature.
Multilevel Space-Time Aggregation for Bright Field Cell Microscopy Segmentation and Tracking
Inglis, Tiffany; De Sterck, Hans; Sanders, Geoffrey; Djambazian, Haig; Sladek, Robert; Sundararajan, Saravanan; Hudson, Thomas J.
2010-01-01
A multilevel aggregation method is applied to the problem of segmenting live cell bright field microscope images. The method employed is a variant of the so-called “Segmentation by Weighted Aggregation” technique, which itself is based on Algebraic Multigrid methods. The variant of the method used is described in detail, and it is explained how it is tailored to the application at hand. In particular, a new scale-invariant “saliency measure” is proposed for deciding when aggregates of pixels constitute salient segments that should not be grouped further. It is shown how segmentation based on multilevel intensity similarity alone does not lead to satisfactory results for bright field cells. However, the addition of multilevel intensity variance (as a measure of texture) to the feature vector of each aggregate leads to correct cell segmentation. Preliminary results are presented for applying the multilevel aggregation algorithm in space time to temporal sequences of microscope images, with the goal of obtaining space-time segments (“object tunnels”) that track individual cells. The advantages and drawbacks of the space-time aggregation approach for segmentation and tracking of live cells in sequences of bright field microscope images are presented, along with a discussion on how this approach may be used in the future work as a building block in a complete and robust segmentation and tracking system. PMID:20467468
Stabilizing Off-pathway Oligomers by Polyphenol Nanoassemblies for IAPP Aggregation Inhibition
NASA Astrophysics Data System (ADS)
Nedumpully-Govindan, Praveen; Kakinen, Aleksandr; Pilkington, Emily H.; Davis, Thomas P.; Chun Ke, Pu; Ding, Feng
2016-01-01
Experimental studies have shown that many naturally occurring polyphenols have inhibitory effect on the aggregation of several proteins. Here, we use discrete molecular dynamics (DMD) simulations and high-throughput dynamic light scattering (DLS) experiments to study the anti-aggregation effects of two polyphenols, curcumin and resveratrol, on the aggregation of islet amyloid polypeptide (IAPP or amylin). Our DMD simulations suggest that the aggregation inhibition is caused by stabilization of small molecular weight IAPP off-pathway oligomers by the polyphenols. Our analysis indicates that IAPP-polyphenol hydrogen bonds and π-π stacking combined with hydrophobic interactions are responsible for the stabilization of oligomers. The presence of small oligomers is confirmed with DLS measurements in which nanometer-sized oligomers are found to be stable for up to 7.5 hours, the time frame within which IAPP aggregates in the absence of polyphenols. Our study offers a general anti-aggregation mechanism for polyphenols, and further provides a computational framework for the future design of anti-amyloid aggregation therapeutics.
NASA Astrophysics Data System (ADS)
Castellanos, Maria Monica
Aggregation of therapeutic proteins is currently one of the major challenges in the bio-pharmaceutical industry, because aggregates could induce immunogenic responses and compromise the quality of the product. Current scientific efforts, both in industry and academia, are focused on developing rational approaches to screen different drug candidates and predict their stability under different conditions. Moreover, aggregation is promoted in highly concentrated protein solutions, which are typically required for subcutaneous injection. In order to gain further understanding about the mechanisms that lead to aggregation, an approach that combined rheology, neutron scattering, and molecular simulations was undertaken. Two model systems were studied in this work: Bovine Serum Albumin in surfactant-free Phosphate Buffered Saline at pH = 7.4 at concentrations from 11 mg/mL up to ˜519 mg/mL, and a monoclonal antibody in 20 mM Histidine/Histidine Hydrochloride at pH = 6.0 with 60 mg/mL trehalose and 0.2 mg/mL polysorbate-80 at concentrations from 53 mg/mL up to ˜220 mg/mL. The antibody used here has three mutations in the CH2 domain, which result in lower stability upon incubation at 40 °C with respect to the wild-type protein, based on size-exclusion chromatography assays. This temperature is below 49 °C, where unfolding of the least stable, CH2 domain occurs, according to differential scanning calorimetry. This dissertation focuses on identifying the role of aggregation on the viscosity of protein solutions. The protein solutions of this work show an increase in the low shear viscosity in the absence of surfactants, because proteins adsorb at the air/water interface forming a viscoelastic film that affects the measured rheology. Stable surfactant-laden protein solutions behave as simple Newtonian fluids. However, the surfactant-laden antibody solution also shows an increase in the low shear viscosity from bulk aggregation, after prolonged incubation at 40 °C. Small
Trusova, Valeriya M; Gorbenko, Galyna P
2017-07-10
Using the molecular dynamics simulation, the role of lipids in the lysozyme transition into the aggregation-competent conformation has been clarified. Analysis of the changes of lysozyme secondary structure upon its interactions with the model bilayer membranes composed of phosphatidylcholine and its mixtures with phosphatidylglycerol (10, 40, and 80 mol%) within the time interval of 100 ns showed that lipid-bound protein is characterized by the increased content of β-structures. Along with this, the formation of protein-lipid complexes was accompanied by the increase in the gyration radius and the decrease in RMSD of polypeptide chain. The results obtained were interpreted in terms of the partial unfolding of lysozyme molecule on the lipid matrix, with the magnitude of this effect being increased with increasing the fraction of anionic lipids. Based on the results of molecular dynamics simulation, a hypothetical model of the nucleation of lysozyme amyloid fibrils in a membrane environment was suggested.
Synchrony between reanalysis-driven RCM simulations and observations: variation with time scale
NASA Astrophysics Data System (ADS)
de Elía, Ramón; Laprise, René; Biner, Sébastien; Merleau, James
2017-04-01
Unlike coupled global climate models (CGCMs) that run in a stand-alone mode, nested regional climate models (RCMs) are driven by either a CGCM or a reanalysis dataset. This feature makes high correlations between the RCM simulation and its driver possible. When the driving dataset is a reanalysis, time correlations between RCM output and observations are also common and to be expected. In certain situations time correlation between driver and driven RCM is of particular interest and techniques have been developed to increase it (e.g. large-scale spectral nudging). For such cases, a question that remains open is whether aggregating in time increases the correlation between RCM output and observations. That is, although the RCM may be unable to reproduce a given daily event, whether it will still be able to satisfactorily simulate an anomaly on a monthly or annual basis. This is a preconception that the authors of this work and others in the community have held, perhaps as a natural extension of the properties of upscaling or aggregating other statistics such as the mean squared error. Here we explore analytically four particular cases that help us partially answer this question. In addition, we use observations datasets and RCM-simulated data to illustrate our findings. Results indicate that time upscaling does not necessarily increase time correlations, and that those interested in achieving high monthly or annual time correlations between RCM output and observations may have to do so by increasing correlation as much as possible at the shortest time scale. This may indicate that even when only concerned with time correlations at large temporal scale, large-scale spectral nudging acting at the time-step level may have to be used.
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.
Coherent and incoherent ultrasound backscatter from cell aggregates.
de Monchy, Romain; Destrempes, François; Saha, Ratan K; Cloutier, Guy; Franceschini, Emilie
2016-09-01
The effective medium theory (EMT) was recently developed to model the ultrasound backscatter from aggregating red blood cells [Franceschini, Metzger, and Cloutier, IEEE Trans. Ultrason. Ferroelectr. Freq. Control 58, 2668-2679 (2011)]. The EMT assumes that aggregates can be treated as homogeneous effective scatterers, which have effective properties determined by the aggregate compactness and the acoustical characteristics of the cells and the surrounding medium. In this study, the EMT is further developed to decompose the differential backscattering cross section of a single cell aggregate into coherent and incoherent components. The coherent component corresponds to the squared norm of the average scattering amplitude from the effective scatterer, and the incoherent component considers the variance of the scattering amplitude (i.e., the mean squared norm of the fluctuation of the scattering amplitude around its mean) within the effective scatterer. A theoretical expression for the incoherent component based on the structure factor is proposed and compared with another formulation based on the Gaussian direct correlation function. This theoretical improvement is assessed using computer simulations of ultrasound backscatter from aggregating cells. The consideration of the incoherent component based on the structure factor allows us to approximate the simulations satisfactorily for a product of the wavenumber times the aggregate radius kr ag around 2.
Nakano, Miki; Ebina, Kuniyoshi; Tanaka, Shigenori
2013-04-01
Polyglutamine (polyQ, a peptide) with an abnormal repeat length is the causative agent of polyQ diseases, such as Huntington's disease. Although glutamine is a polar residue, polyQ peptides form insoluble aggregates in water, and the mechanism for this aggregation is still unclear. To elucidate the detailed mechanism for the nucleation and aggregation of polyQ peptides, replica exchange molecular dynamics simulations were performed for monomers and dimers of polyQ peptides with several chain lengths. Furthermore, to determine how the aggregation mechanism of polyQ differs from those of other peptides, we compared the results for polyQ with those of polyasparagine and polyleucine. The energy barrier between the monomeric and dimeric states of polyQ was found to be relatively low, and it was observed that polyQ dimers strongly favor the formation of antiparallel β-sheet structures. We also found a characteristic behavior of the monomeric polyQ peptide: a turn at the eighth residue is always present, even when the chain length is varied. We previously showed that a structure including more than two sets of β-turns is stable, so a long monomeric polyQ chain can act as an aggregation nucleus by forming several pairs of antiparallel β-sheet structures within a single chain. Since the aggregation of polyQ peptides has some features in common with an amyloid fibril, our results shed light on the mechanism for the aggregation of polyQ peptides as well as the mechanism for the formation of general amyloid fibrils, which cause the onset of amyloid diseases.
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.
Bouncing behavior of microscopic dust aggregates
NASA Astrophysics Data System (ADS)
Seizinger, A.; Kley, W.
2013-03-01
Context. Bouncing collisions of dust aggregates within the protoplanetary disk may have a significant impact on the growth process of planetesimals. Yet, the conditions that result in bouncing are not very well understood. Existing simulations studying the bouncing behavior used aggregates with an artificial, very regular internal structure. Aims: Here, we study the bouncing behavior of sub-mm dust aggregates that are constructed applying different sample preparation methods. We analyze how the internal structure of the aggregate alters the collisional outcome and we determine the influence of aggregate size, porosity, collision velocity, and impact parameter. Methods: We use molecular dynamics simulations where the individual aggregates are treated as spheres that are made up of several hundred thousand individual monomers. The simulations are run on graphic cards (GPUs). Results: Statistical bulk properties and thus bouncing behavior of sub-mm dust aggregates depend heavily on the preparation method. In particular, there is no unique relation between the average volume filling factor and the coordination number of the aggregate. Realistic aggregates bounce only if their volume filling factor exceeds 0.5 and collision velocities are below 0.1 ms-1. Conclusions: For dust particles in the protoplanetary nebula we suggest that the bouncing barrier may not be such a strong handicap in the growth phase of dust agglomerates, at least in the size range of ≈100 μm.
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
NASA Astrophysics Data System (ADS)
Wakamatsu, Takashi; Onoda, Takashi; Ogata, Makoto
2018-05-01
An in situ measurement method of monitoring protein aggregation in precrystalline solutions is presented. The method is based on a small-angle forward static light scattering (F-SLS) technique. This technique uses an accurate optical arrangement of a combination of a collimating lens and a CCD to obtain an F-SLS pattern from an aggregate-containing protein solution in one shot. The real-time observation of a crystallizing lysozyme captured the formation of fractal aggregates in the initial formation stage.
NASA Astrophysics Data System (ADS)
Peter, Emanuel K.
2017-12-01
In this article, we present a novel adaptive enhanced sampling molecular dynamics (MD) method for the accelerated simulation of protein folding and aggregation. We introduce a path-variable L based on the un-biased momenta p and displacements dq for the definition of the bias s applied to the system and derive 3 algorithms: general adaptive bias MD, adaptive path-sampling, and a hybrid method which combines the first 2 methodologies. Through the analysis of the correlations between the bias and the un-biased gradient in the system, we find that the hybrid methodology leads to an improved force correlation and acceleration in the sampling of the phase space. We apply our method on SPC/E water, where we find a conservation of the average water structure. We then use our method to sample dialanine and the folding of TrpCage, where we find a good agreement with simulation data reported in the literature. Finally, we apply our methodologies on the initial stages of aggregation of a hexamer of Alzheimer's amyloid β fragment 25-35 (Aβ 25-35) and find that transitions within the hexameric aggregate are dominated by entropic barriers, while we speculate that especially the conformation entropy plays a major role in the formation of the fibril as a rate limiting factor.
Peter, Emanuel K
2017-12-07
In this article, we present a novel adaptive enhanced sampling molecular dynamics (MD) method for the accelerated simulation of protein folding and aggregation. We introduce a path-variable L based on the un-biased momenta p and displacements dq for the definition of the bias s applied to the system and derive 3 algorithms: general adaptive bias MD, adaptive path-sampling, and a hybrid method which combines the first 2 methodologies. Through the analysis of the correlations between the bias and the un-biased gradient in the system, we find that the hybrid methodology leads to an improved force correlation and acceleration in the sampling of the phase space. We apply our method on SPC/E water, where we find a conservation of the average water structure. We then use our method to sample dialanine and the folding of TrpCage, where we find a good agreement with simulation data reported in the literature. Finally, we apply our methodologies on the initial stages of aggregation of a hexamer of Alzheimer's amyloid β fragment 25-35 (Aβ 25-35) and find that transitions within the hexameric aggregate are dominated by entropic barriers, while we speculate that especially the conformation entropy plays a major role in the formation of the fibril as a rate limiting factor.
Signature of an aggregation-prone conformation of tau
NASA Astrophysics Data System (ADS)
Eschmann, Neil A.; Georgieva, Elka R.; Ganguly, Pritam; Borbat, Peter P.; Rappaport, Maxime D.; Akdogan, Yasar; Freed, Jack H.; Shea, Joan-Emma; Han, Songi
2017-03-01
The self-assembly of the microtubule associated tau protein into fibrillar cell inclusions is linked to a number of devastating neurodegenerative disorders collectively known as tauopathies. The mechanism by which tau self-assembles into pathological entities is a matter of much debate, largely due to the lack of direct experimental insights into the earliest stages of aggregation. We present pulsed double electron-electron resonance measurements of two key fibril-forming regions of tau, PHF6 and PHF6*, in transient as aggregation happens. By monitoring the end-to-end distance distribution of these segments as a function of aggregation time, we show that the PHF6(*) regions dramatically extend to distances commensurate with extended β-strand structures within the earliest stages of aggregation, well before fibril formation. Combined with simulations, our experiments show that the extended β-strand conformational state of PHF6(*) is readily populated under aggregating conditions, constituting a defining signature of aggregation-prone tau, and as such, a possible target for therapeutic interventions.
Aggregation of alpha-synuclein by a coarse-grained Monte Carlo simulation
NASA Astrophysics Data System (ADS)
Farmer, Barry; Pandey, Ras
Alpha-synuclein, an intrinsic protein abundant in neurons, is believed to be a major cause of neurodegenerative diseases (e.g. Alzheimer, Parkinson's disease). Abnormal aggregation of ASN leads to Lewy bodies with specific morphologies. We investigate the self-organizing structures in a crowded environment of ASN proteins by a coarse-grained Monte Carlo simulation. ASN is a chain of 140 residues. Structure detail of residues is neglected but its specificity is captured via unique knowledge-based residue-residue interactions. Large-scale simulations are performed to analyze a number local and global physical quantities (e.g. mobility profile, contact map, radius of gyration, structure factor) as a function of temperature and protein concentration. Trend in multi-scale structural variations of the protein in a crowded environment is compared with that of a free protein chain.
Progranulin inhibits platelet aggregation and prolongs bleeding time in rats.
Al-Yahya, A M; Al-Masri, A A; El Eter, E A; Hersi, A; Lateef, R; Mawlana, O
2018-05-01
Several adipokines secreted by adipose tissue have an anti-thrombotic and anti-atherosclerotic function. Recently identified adipokine progranulin was found to play a protective role in atherosclerosis. Bearing in mind the central role of platelets in inflammation and atherosclerosis, we aimed, in this study, to examine the effect of progranulin on platelet function and coagulation profile in rats. Healthy male albino Wistar rats weighing (250-300 g) were divided into 4 groups. Three groups were given increasing doses of progranulin (0.001 µg, 0.01 µg, and 0.1 µg) intraperitoneally, while the control group received phosphate-buffered saline (PBS). Bleeding time, prothrombin time, activated partial thromboplastin time and platelet aggregation responses to adenosine diphosphate and arachidonic acid were assessed. Administration of progranulin resulted in a significant inhibition of platelet aggregation in response to both adenosine diphosphate, and arachidonic acid. Bleeding time, prothrombin time and activated partial thromboplastin time were significantly prolonged in all groups that received progranulin, in particular, the 0.1 µg dose, in comparison to the control group. This preliminary data is first suggesting that the antiplatelet and anticoagulant action of progranulin could have a physiological protective function against thrombotic disorders associated with obesity and atherosclerosis. However, these results merit further exploration.
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…
Lapelosa, Mauro; Patapoff, Thomas W; Zarraga, Isidro E
2016-06-01
Micellar aggregation behavior of polysorbate 20 (PS20) has generated significant interest because of the wide use of PS20 as a surfactant to minimize protein surface adsorption and mitigate protein aggregation. Thus, there is a need for better molecular understanding of what drives the biophysical behavior of PS20 in solution. We observe that a complex amphipathic PS20 molecule, which contains both hydrophobic tail and relatively large hydrophilic head, self-associates strongly within the course of a molecular dynamics simulation performed with a fully atomistic representation of the molecule and an explicit water solvent model. The in silico behavior is consistent with micellar models of PS20 in solution. The dynamics of this self-association is rather complex involving both internal reorganization of the molecule and diffusion to form stable micelle-like aggregates. The micellar aggregates of PS20 are long-lived and are formed by the balance between the large hydrophobic interactions associated with the aliphatic tail of PS20, and the steric repulsion of the hydrophilic sorbitan head structure. In the present work, molecular models of PS20 that represent naturally occurring PS20 fractions were produced and characterized in silico. The study investigated the monoester and diester fractions: PS20M, and PS20D. These fractions present differences in the strength of their hydrophobic effect, which influences the aggregation behavior. Adaptive biasing force (ABF) simulations were carried out with the PS20M and PS20D molecular constructs to calculate the free energy of their pairwise interaction. The free energy barrier for the dissociation is higher for PS20D compared with PS20M. The results show that hydrogen bonds can form when head groups are in close proximity, such as in the PS20 aggregate assembly, and the free energy of interaction can be used to predict the morphology of the micellar aggregate for the different PS20 fractions. We were also able to simulate PS20
NASA Astrophysics Data System (ADS)
Chaudhury, Susmitnarayan; Dutta, Anirudha; Bag, Sudipta; Biswas, Pranandita; Das, Amit Kumar; Dasgupta, Swagata
2018-03-01
Aggregation of human ocular lens proteins, the crystallins is believed to be one of the key reasons for age-onset cataract. Previous studies have shown that human γD-crystallin forms amyloid like fibres under conditions of low pH and elevated temperature. In this article, we have investigated the aggregation propensity of human γB-crystallin in absence and presence of epigallocatechin gallate (EGCG), in vitro, when exposed to stressful conditions. We have used different spectroscopic and microscopic techniques to elucidate the inhibitory effect of EGCG towards aggregation. The experimental results have been substantiated by molecular dynamics simulation studies. We have shown that EGCG possesses inhibitory potency against the aggregation of human γB-crystallin at low pH and elevated temperature.
Gadi, Dounia; Bnouham, Mohamed; Aziz, Mohammed; Ziyyat, Abderrahim; Legssyer, Abdelkhaleq; Legrand, Chantal; Lafeve, Françoise Fauvel; Mekhfi, Hassane
2009-08-17
Many cardiovascular diseases are associated with an increase in blood platelet activity. In Morocco, parsley (Petroselinum crispum, Apiaceae) is one of the medicinal herbs used to treat cardiovascular diseases such as arterial hypertension. In this study, crude aqueous extract (CAE) of parsley was evaluated for its anti-platelet activity in experimental animals on platelet aggregation in vitro and ex vivo; and on bleeding time in vivo. The in vitro aggregation was monitored after pre-incubation of platelets with CAE. The bleeding time and ex vivo aggregation were performed after oral treatment. CAE inhibited dose dependently platelet aggregation in vitro induced by thrombin, ADP, collagen and epinephrine. The oral administration of CAE (3g/kg) inhibited significantly (p<0.001) platelet aggregation ex vivo and prolonged bleeding time (p<0.001) without changes in the platelet amount. The prolongation of bleeding time by CAE may be attributed to the observed inhibition of platelet aggregation. These effects could be related in part to the polyphenolic compounds present in the extract. These results support the hypothesis that the dietary intake of parsley may be benefit in the normalization of platelet hyperactivation, in the nutritional prevention of cardiovascular diseases and are potentially interesting in the development of new prevention strategies.
Aggregation of Sentinel-2 time series classifications as a solution for multitemporal analysis
NASA Astrophysics Data System (ADS)
Lewiński, Stanislaw; Nowakowski, Artur; Malinowski, Radek; Rybicki, Marcin; Kukawska, Ewa; Krupiński, Michał
2017-10-01
The general aim of this work was to elaborate efficient and reliable aggregation method that could be used for creating a land cover map at a global scale from multitemporal satellite imagery. The study described in this paper presents methods for combining results of land cover/land use classifications performed on single-date Sentinel-2 images acquired at different time periods. For that purpose different aggregation methods were proposed and tested on study sites spread on different continents. The initial classifications were performed with Random Forest classifier on individual Sentinel-2 images from a time series. In the following step the resulting land cover maps were aggregated pixel by pixel using three different combinations of information on the number of occurrences of a certain land cover class within a time series and the posterior probability of particular classes resulting from the Random Forest classification. From the proposed methods two are shown superior and in most cases were able to reach or outperform the accuracy of the best individual classifications of single-date images. Moreover, the aggregations results are very stable when used on data with varying cloudiness. They also enable to reduce considerably the number of cloudy pixels in the resulting land cover map what is significant advantage for mapping areas with frequent cloud coverage.
Measuring Aggregation of Events about a Mass Using Spatial Point Pattern Methods
Smith, Michael O.; Ball, Jackson; Holloway, Benjamin B.; Erdelyi, Ferenc; Szabo, Gabor; Stone, Emily; Graham, Jonathan; Lawrence, J. Josh
2017-01-01
We present a methodology that detects event aggregation about a mass surface using 3-dimensional study regions with a point pattern and a mass present. The Aggregation about a Mass function determines aggregation, randomness, or repulsion of events with respect to the mass surface. Our method closely resembles Ripley’s K function but is modified to discern the pattern about the mass surface. We briefly state the definition and derivation of Ripley’s K function and explain how the Aggregation about a Mass function is different. We develop the novel function according to the definition: the Aggregation about a Mass function times the intensity is the expected number of events within a distance h of a mass. Special consideration of edge effects is taken in order to make the function invariant to the location of the mass within the study region. Significance of aggregation or repulsion is determined using simulation envelopes. A simulation study is performed to inform researchers how the Aggregation about a Mass function performs under different types of aggregation. Finally, we apply the Aggregation about a Mass function to neuroscience as a novel analysis tool by examining the spatial pattern of neurotransmitter release sites as events about a neuron. PMID:29046865
Fractal aggregates in tennis ball systems
NASA Astrophysics Data System (ADS)
Sabin, J.; Bandín, M.; Prieto, G.; Sarmiento, F.
2009-09-01
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 images of the cluster of balls, following Forrest and Witten's pioneering studies on the aggregation of smoke particles, to estimate their fractal dimension.
Mechanical Dissociation of Platelet Aggregates in Blood Stream
NASA Astrophysics Data System (ADS)
Hoore, Masoud; Fedosov, Dmitry A.; Gompper, Gerhard; Complex; Biological Fluids Group Team
2017-11-01
von Willebrand factor (VWF) and platelet aggregation is a key phenomenon in blood clotting. These aggregates form critically in high shear rates and dissolve reversibly in low shear rates. The emergence of a critical shear rate, beyond which aggregates form and below which they dissolve, has an interesting impact on aggregation in blood flow. As red blood cells (RBCs) migrate to the center of the vessel in blood flow, a RBC free layer (RBC-FL) is left close to the walls into which the platelets and VWFs are pushed back from the bulk flow. This margination process provides maximal VWF-platelet aggregation probability in the RBC-FL. Using mesoscale hydrodynamic simulations of aggregate dynamics in blood flow, it is shown that the aggregates form and grow in RBC-FL wherein shear rate is high for VWF stretching. By growing, the aggregates penetrate to the bulk flow and get under order of magnitude lower shear rates. Consequently, they dissolve and get back into the RBC-FL. This mechanical limitation for aggregates prohibits undesired thrombosis and vessel blockage by aggregates, while letting the VWFs and platelets to aggregate close to the walls where they are actually needed. The support by the DFG Research Unit FOR 1543 SHENC and CPU time Grant by the Julich Supercomputing Center are acknowledged.
Real-time protein aggregation monitoring with a Bloch surface wave-based approach
NASA Astrophysics Data System (ADS)
Santi, Sara; Barakat, Elsie; Descrovi, Emiliano; Neier, Reinhard; Herzig, Hans Peter
2014-05-01
The misfolding and aggregation of amyloid proteins has been associated with incurable diseases such as Alzheimer's or Parkinson's disease. In the specific case of Alzheimer's disease, recent studies have shown that cell toxicity is caused by soluble oligomeric forms of aggregates appearing in the early stages of aggregation, rather than by insoluble fibrils. Research on new strategies of diagnosis is imperative to detect the disease prior to the onset of clinical symptoms. Here, we propose the use of an optical method for protein aggregation dynamic studies using a Bloch surface wave based approach. A one dimension photonic crystal made of a periodic stack of silicon oxide and silicon nitride layers is used to excite a Bloch surface wave, which is sensitive to variation of the refractive index of an aqueous solution. The aim is to detect the early dynamic events of protein aggregation and fibrillogenesis of the amyloid-beta peptide Aβ42, which plays a central role in the onset of the Alzheimer's disease. The detection principle relies on the refractive index changes caused by the depletion of the Aβ42 monomer concentration during oligomerization and fibrillization. We demonstrate the efficacy of the Bloch surface wave approach by monitoring in real-time the first crucial steps of Aβ42 oligomerization.
Nath, Suman C; Horie, Masanobu; Nagamori, Eiji; Kino-Oka, Masahiro
2017-10-01
Aggregate culture of human induced pluripotent stem cells (hiPSCs) is a promising method to obtain high number of cells for cell therapy applications. This study quantitatively evaluated the effects of initial cell number and culture time on the growth of hiPSCs in the culture of single aggregate. Small size aggregates ((1.1 ± 0.4) × 10 1 -(2.8 ± 0.5) × 10 1 cells/aggregate) showed a lower growth rate in comparison to medium size aggregates ((8.8 ± 0.8) × 10 1 -(6.8 ± 1.1) × 10 2 cells/aggregate) during early-stage of culture (24-72 h). However, when small size aggregates were cultured in conditioned medium, their growth rate increased significantly. On the other hand, large size aggregates ((1.1 ± 0.2) × 10 3 -(3.5 ± 1.1) × 10 3 cells/aggregate) showed a lower growth rate and lower expression level of proliferation marker (ki-67) in the center region of aggregate in comparison to medium size aggregate during early-stage of culture. Medium size aggregates showed the highest growth rate during early-stage of culture. Furthermore, hiPSCs proliferation was dependent on culture time because the growth rate decreased significantly during late-stage of culture (72-120 h) at which point collagen type I accumulated on the periphery of aggregate, suggesting blockage of diffusive transport of nutrients, oxygen and metabolites into and out of the aggregates. Consideration of initial cell number and culture time are important to maintain balance between autocrine factors secretion and extracellular matrix accumulation on the aggregate periphery to achieve optimal growth of hiPSCs in the culture of single aggregate. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.
Kinetic behaviours of aggregate growth driven by time-dependent migration, birth and death
NASA Astrophysics Data System (ADS)
Zhu, Sheng-Qing; Yang, Shun-You; Ke, Jianhong; Lin, Zhenquan
2008-12-01
We propose a dynamic growth model to mimic some social phenomena, such as the evolution of cities' population, in which monomer migrations occur between any two aggregates and monomer birth/death can simultaneously occur in each aggregate. Considering the fact that the rate kernels of migration, birth and death processes may change with time, we assume that the migration rate kernel is ijf(t), and the self-birth and death rate kernels are ig1(t) and ig2(t), respectively. Based on the mean-field rate equation, we obtain the exact solution of this model and then discuss semi-quantitatively the scaling behaviour of the aggregate size distribution at large times. The results show that in the long-time limit, (i) if ∫t0g1(t') dt'/∫t0g2(t') dt' >= 1 or exp{∫t0[g2(t') - g1(t')] dt'}/∫t0f(t') dt' → 0, the aggregate size distribution ak(t) can obey a generalized scaling form; (ii) if ∫t0g1(t') dt'/∫t0g2(t') dt' → 0 and exp ∫t0[g2(t') - g1(t') dt'/∫t0f(t') dt' → ∞, ak(t) can take a scale-free form and decay exponentially in size k; (iii) ak(t) will satisfy a modified scaling law in the remaining cases. Moreover, the total mass of aggregates depends strongly on the net birth rate g1(t) - g2(t) and evolves exponentially as exp{∫t0[g1(t') - g2(t')] dt'}, which is in qualitative agreement with the evolution of the total population of a country in real world.
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
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
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
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
Location Isn’t Everything: Timing of Spawning Aggregations Optimizes Larval Replenishment
Donahue, Megan J.; Karnauskas, Mandy; Toews, Carl; Paris, Claire B.
2015-01-01
Many species of reef fishes form large spawning aggregations that are highly predictable in space and time. Prior research has suggested that aggregating fish derive fitness benefits not just from mating at high density but, also, from oceanographic features of the spatial locations where aggregations occur. Using a probabilistic biophysical model of larval dispersal coupled to a fine resolution hydrodynamic model of the Florida Straits, we develop a stochastic landscape of larval fitness. Tracking virtual larvae from release to settlement and incorporating changes in larval behavior through ontogeny, we found that larval success was sensitive to the timing of spawning. Indeed, propagules released during the observed spawning period had higher larval success rates than those released outside the observed spawning period. In contrast, larval success rates were relatively insensitive to the spatial position of the release site. In addition, minimum (rather than mean) larval survival was maximized during the observed spawning period, indicating a reproductive strategy that minimizes the probability of recruitment failure. Given this landscape of larval fitness, we take an inverse optimization approach to define a biological objective function that reflects a tradeoff between the mean and variance of larval success in a temporally variable environment. Using this objective function, we suggest that the length of the spawning period can provide insight into the tradeoff between reproductive risk and reward. PMID:26103162
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
NASA Astrophysics Data System (ADS)
Jiang, Yiyue; Lei, Cheng; Yasumoto, Atsushi; Ito, Takuro; Guo, Baoshan; Kobayashi, Hirofumi; Ozeki, Yasuyuki; Yatomi, Yutaka; Goda, Keisuke
2017-02-01
According to WHO, approximately 10 million new cases of thrombotic disorders are diagnosed worldwide every year. In the U.S. and Europe, their related diseases kill more people than those from AIDS, prostate cancer, breast cancer and motor vehicle accidents combined. Although thrombotic disorders, especially arterial ones, mainly result from enhanced platelet aggregability in the vascular system, visual detection of platelet aggregates in vivo is not employed in clinical settings. Here we present a high-throughput label-free platelet aggregate detection method, aiming at the diagnosis and monitoring of thrombotic disorders in clinical settings. With optofluidic time-stretch microscopy with a spatial resolution of 780 nm and an ultrahigh linear scanning rate of 75 MHz, it is capable of detecting aggregated platelets in lysed blood which flows through a hydrodynamic-focusing microfluidic device at a high throughput of 10,000 particles/s. With digital image processing and statistical analysis, we are able to distinguish them from single platelets and other blood cells via morphological features. The detection results are compared with results of fluorescence-based detection (which is slow and inaccurate, but established). Our results indicate that the method holds promise for real-time, low-cost, label-free, and minimally invasive detection of platelet aggregates, which is potentially applicable to detection of platelet aggregates in vivo and to the diagnosis and monitoring of thrombotic disorders in clinical settings. This technique, if introduced clinically, may provide important clinical information in addition to that obtained by conventional techniques for thrombotic disorder diagnosis, including ex vivo platelet aggregation tests.
NASA Astrophysics Data System (ADS)
Okada, Kazuya; Satoh, Akira
2017-09-01
In the present study, we address a suspension composed ferromagnetic rod-like particles to elucidate a regime change in the aggregate structures and the magneto-rheological characteristics. Monte Carlo simulations have been employed for investigating the aggregate structures in thermodynamic equilibrium, and Brownian dynamics simulations for magneto-rheological features in a simple shear flow. The main results obtained here are summarized as follows. For the case of thermodynamic equilibrium, the rod-like particles aggregate to form thick chain-like clusters and the neighboring clusters incline in opposite directions. If the external magnetic field is increased, the thick chain-like clusters in the magnetic field direction grow thicker by adsorbing the neighboring clusters that incline in the opposite direction. Hence, a significant phase change in the particle aggregates is not induced by an increase in the magnetic field strength. For the case of a simple shear flow, even a weak shear flow induces a significant regime change from the thick chain-like clusters of thermodynamic equilibrium into wall-like aggregates composed of short raft-like clusters. A strong external magnetic field drastically changes these aggregates into wall-like aggregates composed of thick chain-like clusters rather than the short raft-like clusters. The internal structure of these aggregates is not strongly influenced by a shear flow, and the formation of the short raft-like clusters is maintained inside the aggregates. The main contribution to the net viscosity is the viscosity component due to magnetic particle-particle interaction forces in relation to the present volumetric fraction. Hence, a larger magnetic interaction strength and also a stronger external magnetic field give rise to a larger magneto-rheological effect. However, the dependence of the viscosity on these factors is governed in a complex manner by whether or not the wall-like aggregates are composed mainly of short raft
Detergent-mediated protein aggregation
Neale, Chris; Ghanei, Hamed; Holyoake, John; Bishop, Russell E.; Privé, Gilbert G.; Pomès, Régis
2016-01-01
Because detergents are commonly used to solvate membrane proteins for structural evaluation, much attention has been devoted to assessing the conformational bias imparted by detergent micelles in comparison to the native environment of the lipid bilayer. Here, we conduct six 500-ns simulations of a system with >600,000 atoms to investigate the spontaneous self assembly of dodecylphosphocholine detergent around multiple molecules of the integral membrane protein PagP. This detergent formed equatorial micelles in which acyl chains surround the protein’s hydrophobic belt, confirming existing models of the detergent solvation of membrane proteins. In addition, unexpectedly, the extracellular and periplasmic apical surfaces of PagP interacted with the headgroups of detergents in other micelles 85 and 60% of the time, respectively, forming complexes that were stable for hundreds of nanoseconds. In some cases, an apical surface of one molecule of PagP interacted with an equatorial micelle surrounding another molecule of PagP. In other cases, the apical surfaces of two molecules of PagP simultaneously bound a neat detergent micelle. In these ways, detergents mediated the non-specific aggregation of folded PagP. These simulation results are consistent with dynamic light scattering experiments, which show that, at detergent concentrations ≥600 mM, PagP induces the formation of large scattering species that are likely to contain many copies of the PagP protein. Together, these simulation and experimental results point to a potentially generic mechanism of detergent-mediated protein aggregation. PMID:23466535
Acceleration of tropical cyclogenesis by self-aggregation feedbacks
NASA Astrophysics Data System (ADS)
Muller, Caroline J.; Romps, David M.
2018-03-01
Idealized simulations of tropical moist convection have revealed that clouds can spontaneously clump together in a process called self-aggregation. This results in a state where a moist cloudy region with intense deep convection is surrounded by extremely dry subsiding air devoid of deep convection. Because of the idealized settings of the simulations where it was discovered, the relevance of self-aggregation to the real world is still debated. Here, we show that self-aggregation feedbacks play a leading-order role in the spontaneous genesis of tropical cyclones in cloud-resolving simulations. Those feedbacks accelerate the cyclogenesis process by a factor of 2, and the feedbacks contributing to the cyclone formation show qualitative and quantitative agreement with the self-aggregation process. Once the cyclone is formed, wind-induced surface heat exchange (WISHE) effects dominate, although we find that self-aggregation feedbacks have a small but nonnegligible contribution to the maintenance of the mature cyclone. Our results suggest that self-aggregation, and the framework developed for its study, can help shed more light into the physical processes leading to cyclogenesis and cyclone intensification. In particular, our results point out the importance of the longwave radiative cooling outside the cyclone.
Jiang, Yiyue; Lei, Cheng; Yasumoto, Atsushi; Kobayashi, Hirofumi; Aisaka, Yuri; Ito, Takuro; Guo, Baoshan; Nitta, Nao; Kutsuna, Natsumaro; Ozeki, Yasuyuki; Nakagawa, Atsuhiro; Yatomi, Yutaka; Goda, Keisuke
2017-07-11
According to WHO, about 10 million new cases of thrombotic disorders are diagnosed worldwide every year. Thrombotic disorders, including atherothrombosis (the leading cause of death in the US and Europe), are induced by occlusion of blood vessels, due to the formation of blood clots in which aggregated platelets play an important role. The presence of aggregated platelets in blood may be related to atherothrombosis (especially acute myocardial infarction) and is, hence, useful as a potential biomarker for the disease. However, conventional high-throughput blood analysers fail to accurately identify aggregated platelets in blood. Here we present an in vitro on-chip assay for label-free, single-cell image-based detection of aggregated platelets in human blood. This assay builds on a combination of optofluidic time-stretch microscopy on a microfluidic chip operating at a high throughput of 10 000 blood cells per second with machine learning, enabling morphology-based identification and enumeration of aggregated platelets in a short period of time. By performing cell classification with machine learning, we differentiate aggregated platelets from single platelets and white blood cells with a high specificity and sensitivity of 96.6% for both. Our results indicate that the assay is potentially promising as predictive diagnosis and therapeutic monitoring of thrombotic disorders in clinical settings.
Molecular Dynamics Simulation Studies of Caffeine Aggregation in Aqueous Solution
Tavagnacco, Letizia; Schnupf, Udo; Mason, Philip E.; Saboungi, Marie-Louise; Cesàro, Attilio; Brady, John W.
2011-01-01
Molecular dynamics simulations were carried out on a system of eight independent caffeine molecules in a periodic box of water at 300 K, representing a solution near the solubility limit for caffeine at room temperature, using a newly-developed CHARMM-type force field for caffeine in water. Simulations were also conducted for single caffeine molecules in water using two different water models (TIP3P and TIP4P). Water was found to structure in a complex fashion around the planar caffeine molecules, which was not sensitive to the water model used. As expected, extensive aggregation of the caffeine molecules was observed, with the molecules stacking their flat faces against one another like coins, with their methylene groups staggered to avoid steric clashes. A dynamic equilibrum was observed between large n-mers, including stacks with all eight solute molecules, and smaller clusters, with the calculated osmotic coefficient being in acceptable agreement with the experimental value. The insensitivity of the results to water model and the congruence with experimental thermodynamic data suggest that the observed stacking interactions are a realistic representation of the actual association mechanism in aqueous caffeine solutions. PMID:21812485
Molecular dynamics simulation studies of caffeine aggregation in aqueous solution.
Tavagnacco, Letizia; Schnupf, Udo; Mason, Philip E; Saboungi, Marie-Louise; Cesàro, Attilio; Brady, John W
2011-09-22
Molecular dynamics simulations were carried out on a system of eight independent caffeine molecules in a periodic box of water at 300 K, representing a solution near the solubility limit for caffeine at room temperature, using a newly developed CHARMM-type force field for caffeine in water. Simulations were also conducted for single caffeine molecules in water using two different water models (TIP3P and TIP4P). Water was found to structure in a complex fashion around the planar caffeine molecules, which was not sensitive to the water model used. As expected, extensive aggregation of the caffeine molecules was observed, with the molecules stacking their flat faces against one another like coins, with their methylene groups staggered to avoid steric clashes. A dynamic equilibrum was observed between large n-mers, including stacks with all eight solute molecules, and smaller clusters, with the calculated osmotic coefficient being in acceptable agreement with the experimental value. The insensitivity of the results to water model and the congruence with experimental thermodynamic data suggest that the observed stacking interactions are a realistic representation of the actual association mechanism in aqueous caffeine solutions.
The infrared spectral transmittance of Aspergillus niger spore aggregated particle swarm
NASA Astrophysics Data System (ADS)
Zhao, Xinying; Hu, Yihua; Gu, Youlin; Li, Le
2015-10-01
Microorganism aggregated particle swarm, which is quite an important composition of complex media environment, can be developed as a new kind of infrared functional materials. Current researches mainly focus on the optical properties of single microorganism particle. As for the swarm, especially the microorganism aggregated particle swarm, a more accurate simulation model should be proposed to calculate its extinction effect. At the same time, certain parameters deserve to be discussed, which helps to better develop the microorganism aggregated particle swarm as a new kind of infrared functional materials. In this paper, take Aspergillus Niger spore as an example. On the one hand, a new calculation model is established. Firstly, the cluster-cluster aggregation (CCA) model is used to simulate the structure of Aspergillus Niger spore aggregated particle. Secondly, the single scattering extinction parameters for Aspergillus Niger spore aggregated particle are calculated by using the discrete dipole approximation (DDA) method. Thirdly, the transmittance of Aspergillus Niger spore aggregated particle swarm is simulated by using Monte Carlo method. On the other hand, based on the model proposed above, what influences can wavelength causes has been studied, including the spectral distribution of scattering intensity of Aspergillus Niger spore aggregated particle and the infrared spectral transmittance of the aggregated particle swarm within the range of 8-14μm incident infrared wavelengths. Numerical results indicate that the scattering intensity of Aspergillus Niger spore aggregated particle reduces with the increase of incident wavelengths at each scattering angle. Scattering energy mainly concentrates on the scattering angle between 0-40°, forward scattering has an obvious effect. In addition, the infrared transmittance of Aspergillus Niger spore aggregated particle swarm goes up with the increase of incident wavelengths. However, some turning points of the trend are
NASA Astrophysics Data System (ADS)
Lorite, I. J.; Mateos, L.; Fereres, E.
2005-01-01
SummaryThe simulations of dynamic, spatially distributed non-linear models are impacted by the degree of spatial and temporal aggregation of their input parameters and variables. This paper deals with the impact of these aggregations on the assessment of irrigation scheme performance by simulating water use and crop yield. The analysis was carried out on a 7000 ha irrigation scheme located in Southern Spain. Four irrigation seasons differing in rainfall patterns were simulated (from 1996/1997 to 1999/2000) with the actual soil parameters and with hypothetical soil parameters representing wider ranges of soil variability. Three spatial aggregation levels were considered: (I) individual parcels (about 800), (II) command areas (83) and (III) the whole irrigation scheme. Equally, five temporal aggregation levels were defined: daily, weekly, monthly, quarterly and annually. The results showed little impact of spatial aggregation in the predictions of irrigation requirements and of crop yield for the scheme. The impact of aggregation was greater in rainy years, for deep-rooted crops (sunflower) and in scenarios with heterogeneous soils. The highest impact on irrigation requirement estimations was in the scenario of most heterogeneous soil and in 1999/2000, a year with frequent rainfall during the irrigation season: difference of 7% between aggregation levels I and III was found. Equally, it was found that temporal aggregation had only significant impact on irrigation requirements predictions for time steps longer than 4 months. In general, simulated annual irrigation requirements decreased as the time step increased. The impact was greater in rainy years (specially with abundant and concentrated rain events) and in crops which cycles coincide in part with the rainy season (garlic, winter cereals and olive). It is concluded that in this case, average, representative values for the main inputs of the model (crop, soil properties and sowing dates) can generate results
Bedrov, Dmitry; Smith, Grant D; Li, Liwei
2005-06-07
The aggregation behavior of C60 fullerenes and C60 fullerenes with six symmetrically tethered poly(ethylene oxide) oligomers [(PEO)-6-C60] in aqueous solutions has been studied using implicit solvent molecular dynamics simulations. Our simulations reveal that while the attraction between two (PEO)-6-C60 fullerenes in aqueous solution is stronger and longer range than that between two bare C60 fullerenes, the (PEO)-6-C60 fullerenes do not phase-separate in water but rather aggregate in chain-like clusters at concentrations where unmodified fullerenes completely phase-separate.
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
Ren, Hao; Zhang, Yu; Guo, Sibei; ...
2017-10-31
The aggregation of amyloid beta (Aβ) peptides plays a crucial role in the pathology and etiology of Alzheimer's disease. Experimental evidence shows that copper ion is an aggregation-prone species with the ability to coordinately bind to Aβ and further induce the formation of neurotoxic Aβ oligomers. However, the detailed structures of Cu(II)–Aβ complexes have not been illustrated, and the kinetics and dynamics of the Cu(II) binding are not well understood. Two Cu(II)–Aβ complexes have been proposed to exist under physiological conditions, and another two might exist at higher pH values. By using ab initio simulations for the spontaneous resonance Ramanmore » and time domain stimulated resonance Raman spectroscopy signals, we obtained the characteristic Raman vibronic features of each complex. Finally, these signals contain rich structural information with high temporal resolution, enabling the characterization of transient states during the fast Cu–Aβ binding and interconversion processes.« less
Describing Myxococcus xanthus Aggregation Using Ostwald Ripening Equations for Thin Liquid Films
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
Folding and Aggregation of Mucin Domains.
NASA Astrophysics Data System (ADS)
Urbanc, Brigita; Bansil, Rama; Turner, Bradley
2007-03-01
Mucin glycoproteins consist of tandem repeating glycosylated regions flanked by non-repetitive protein domains with little glycosylation. These non-repetitive domains are involved in polymerization of mucin via disulfide bonds and play an important role in the pH dependent gelation of gastric mucin, which is essential to protecting the stomach from autodigestion. We have examined the folding and aggregation of the non-repetitive sequence of von Willebrand factor vWF-C1 domain (67 amino acids) and PGM 2X (242 amino acids) using Discrete Molecular Dynamics (four-bead protein model with hydrogen bonding and amino acid-specific hydrophobic/hydrophilic and electrostatic interactions of side chains). Simulations of vWF C1 show 4-6 β-strands separated by turns/loops with more loops at lower pH. A simulation of several vWF C1 proteins at low pH shows aggregates still with a high content of β-strands and enhanced turn/loop regions. For the PGM 2X simulation the contact map shows several salt bridges enclosing hairpin turns. The implications of these simulations for describing the aggregation/gelation of PGM will be discussed.
NASA Astrophysics Data System (ADS)
Chaiyarit, Sakdithep; Thongboonkerd, Visith
2017-12-01
Crystal aggregation is one of the most crucial steps in kidney stone pathogenesis. However, previous studies of crystal aggregation were rarely done and quantitative analysis of aggregation degree was handicapped by a lack of the standard measurement. We thus performed an in vitro assay to generate aggregation of calcium oxalate monohydrate (COM) crystals with various concentrations (25-800 µg/ml) in saturated aggregation buffer. The crystal aggregates were analyzed by microscopic examination, UV-visible spectrophotometry, and GraphPad Prism6 software to define a total of 12 aggregation indices (including number of aggregates, aggregated mass index, optical density, aggregation coefficient, span, number of aggregates at plateau time-point, aggregated area index, aggregated diameter index, aggregated symmetry index, time constant, half-life, and rate constant). The data showed linear correlation between crystal concentration and almost all of these indices, except only for rate constant. Among these, number of aggregates provided the greatest regression coefficient (r=0.997; p<0.001), whereas the equally second rank included aggregated mass index and optical density (r=0.993; p<0.001 and r=‑0.993; p<0.001, respectively) and the equally forth were aggregation coefficient and span (r=0.991; p<0.001 for both). These five indices are thus recommended as the most appropriate indices for quantitative analysis of COM crystal aggregation in vitro.
Structure and aggregation in model tetramethylurea solutions
DOE Office of Scientific and Technical Information (OSTI.GOV)
Gupta, Rini; Patey, G. N., E-mail: patey@chem.ubc.ca
The structure of model aqueous tetramethylurea (TMU) solutions is investigated employing large-scale (32 000, 64 000 particles) molecular dynamics simulations. Results are reported for TMU mole fractions, X{sub t}, ranging from infinite dilution up to 0.07, and for two temperatures, 300 and 330 K. Two existing force fields for TMU-water solutions are considered. These are the GROMOS 53A6 united-atom TMU model combined with SPC/E water [TMU(GROMOS-UA)/W(SPC/E)], and the more frequently employed AMBER03 all-atom force field for TMU combined with the TIP3P water model [TMU(AMBER-AA)/W(TIP3P)]. It is shown that TMU has a tendency towards aggregation for both models considered, but the tendency ismore » significantly stronger for the [TMU(AMBER-AA)/W(TIP3P)] force field. For this model signs of aggregation are detected at X{sub t} = 0.005, aggregation is a well established feature of the solution at X{sub t} = 0.02, and the aggregates increase further in size with increasing concentration. This is in agreement with at least some experimental studies, which report signals of aggregation in the low concentration regime. The TMU aggregates exhibit little structure and are simply loosely ordered, TMU-rich regions of solution. The [TMU(GROMOS-UA)/W(SPC/E)] model shows strong signs of aggregation only at higher concentrations (X{sub t} ≳ 0.04), and the aggregates appear more loosely ordered, and less well-defined than those occurring in the [TMU(AMBER-AA)/W(TIP3P)] system. For both models, TMU aggregation increases when the temperature is increased from 300 to 330 K, consistent with an underlying entropy driven, hydrophobic interaction mechanism. At X{sub t} = 0.07, the extra-molecular correlation length expected for microheterogeneous solutions has become comparable with the size of the simulation cell for both models considered, indicating that even the systems simulated here are sufficiently large only at low concentrations.« less
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…
Microscopic mechanism of nanocrystal formation from solution by cluster aggregation and coalescence
Hassan, Sergio A.
2011-01-01
Solute-cluster aggregation and particle fusion have recently been suggested as alternative routes to the classical mechanism of nucleation from solution. The role of both processes in the crystallization of an aqueous electrolyte under controlled salt addition is here elucidated by molecular dynamics simulation. The time scale of the simulation allows direct observation of the entire crystallization pathway, from early events in the prenucleation stage to the formation of a nanocrystal in equilibrium with concentrated solution. The precursor originates in a small amorphous aggregate stabilized by hydration forces. The core of the nucleus becomes crystalline over time and grows by coalescence of the amorphous phase deposited at the surface. Imperfections of ion packing during coalescence promote growth of two conjoint crystallites. A parameter of order and calculated cohesive energies reflect the increasing crystalline order and stress relief at the grain boundary. Cluster aggregation plays a major role both in the formation of the nucleus and in the early stages of postnucleation growth. The mechanism identified shares common features with nucleation of solids from the melt and of liquid droplets from the vapor. PMID:21428633
NASA Astrophysics Data System (ADS)
Tulip, P. R.; Bates, S. P.
2009-07-01
We investigate the structure of the glycyl-l-alanine dipeptide in aqueous solution at a 1:20 peptide:water concentration via classical, atomistic molecular dynamics simulations using the CHARMM22 force field, and compare to recent neutron diffraction data [S. E. McLain, A. K. Soper, and A. Watts, Eur. Biophys. J. 37, 647 (2008); S. E. McLain, A. K. Soper, I. Diadone, J. C. Smith, and A. Watts, Angew. Chem. Int. Ed. 47, 9059 (2008)]. Comparison between simulations and experiments is made using the static structure factor S (Q ) . The effect of water model (TIP3P, TIP4P, and SPC/E) upon the solution structure is investigated. Agreement between experiment and simulation is generally good across the entire Q range, although some model-dependent variation is observed, particularly in the predicted intensities of features in S (Q ) . Peptide aggregation is found to be driven by "hydrophilic" (often bifurcated) hydrogen bonds formed between carboxy and amine functional groups, although simulations suggest that the degree of aggregation is less than that observed experimentally. It is found that hydrophobic association is not significant, with hydrophobic hydration being preferred to association. Detailed examination of the solute structural motifs reveals the existence of bifurcated motifs that are suggested to be an artifact of the CHARMM force field, and may imply that classical force fields provide a flawed structural and dynamical description of such molecular fluids. Investigation of the water structure reveals the presence of an electrostrictive effect which manifests itself as an increase in the number of interstitial molecules in the water second coordination shell, in contradiction to suggestions that this phenomenon arises owing to hydrogen bond bending. Detailed analysis based upon two-dimensional distribution functions suggests an intimate link between the phenomenon of electrostriction and the behavior of water under high-pressure compression. We find the
What favors convective aggregation and why?
NASA Astrophysics Data System (ADS)
Muller, Caroline; Bony, Sandrine
2015-07-01
The organization of convection is ubiquitous, but its physical understanding remains limited. One particular type of organization is the spatial self-aggregation of convection, taking the form of cloud clusters, or tropical cyclones in the presence of rotation. We show that several physical processes can give rise to self-aggregation and highlight the key features responsible for it, using idealized simulations. Longwave radiative feedbacks yield a "radiative aggregation." In that case, sufficient spatial variability of radiative cooling rates yields a low-level circulation, which induces the upgradient energy transport and radiative-convective instability. Not only do vertically integrated radiative budgets matter but the vertical profile of cooling is also crucial. Convective aggregation is facilitated when downdrafts below clouds are weak ("moisture-memory aggregation"), and this is sufficient to trigger aggregation in the absence of longwave radiative feedbacks. These results shed some light on the sensitivity of self-aggregation to various parameters, including resolution or domain size.
Graph Theory and Ion and Molecular Aggregation in Aqueous Solutions
NASA Astrophysics Data System (ADS)
Choi, Jun-Ho; Lee, Hochan; Choi, Hyung Ran; Cho, Minhaeng
2018-04-01
In molecular and cellular biology, dissolved ions and molecules have decisive effects on chemical and biological reactions, conformational stabilities, and functions of small to large biomolecules. Despite major efforts, the current state of understanding of the effects of specific ions, osmolytes, and bioprotecting sugars on the structure and dynamics of water H-bonding networks and proteins is not yet satisfactory. Recently, to gain deeper insight into this subject, we studied various aggregation processes of ions and molecules in high-concentration salt, osmolyte, and sugar solutions with time-resolved vibrational spectroscopy and molecular dynamics simulation methods. It turns out that ions (or solute molecules) have a strong propensity to self-assemble into large and polydisperse aggregates that affect both local and long-range water H-bonding structures. In particular, we have shown that graph-theoretical approaches can be used to elucidate morphological characteristics of large aggregates in various aqueous salt, osmolyte, and sugar solutions. When ion and molecular aggregates in such aqueous solutions are treated as graphs, a variety of graph-theoretical properties, such as graph spectrum, degree distribution, clustering coefficient, minimum path length, and graph entropy, can be directly calculated by considering an ensemble of configurations taken from molecular dynamics trajectories. Here we show percolating behavior exhibited by ion and molecular aggregates upon increase in solute concentration in high solute concentrations and discuss compelling evidence of the isomorphic relation between percolation transitions of ion and molecular aggregates and water H-bonding networks. We anticipate that the combination of graph theory and molecular dynamics simulation methods will be of exceptional use in achieving a deeper understanding of the fundamental physical chemistry of dissolution and in describing the interplay between the self-aggregation of solute
Graph Theory and Ion and Molecular Aggregation in Aqueous Solutions.
Choi, Jun-Ho; Lee, Hochan; Choi, Hyung Ran; Cho, Minhaeng
2018-04-20
In molecular and cellular biology, dissolved ions and molecules have decisive effects on chemical and biological reactions, conformational stabilities, and functions of small to large biomolecules. Despite major efforts, the current state of understanding of the effects of specific ions, osmolytes, and bioprotecting sugars on the structure and dynamics of water H-bonding networks and proteins is not yet satisfactory. Recently, to gain deeper insight into this subject, we studied various aggregation processes of ions and molecules in high-concentration salt, osmolyte, and sugar solutions with time-resolved vibrational spectroscopy and molecular dynamics simulation methods. It turns out that ions (or solute molecules) have a strong propensity to self-assemble into large and polydisperse aggregates that affect both local and long-range water H-bonding structures. In particular, we have shown that graph-theoretical approaches can be used to elucidate morphological characteristics of large aggregates in various aqueous salt, osmolyte, and sugar solutions. When ion and molecular aggregates in such aqueous solutions are treated as graphs, a variety of graph-theoretical properties, such as graph spectrum, degree distribution, clustering coefficient, minimum path length, and graph entropy, can be directly calculated by considering an ensemble of configurations taken from molecular dynamics trajectories. Here we show percolating behavior exhibited by ion and molecular aggregates upon increase in solute concentration in high solute concentrations and discuss compelling evidence of the isomorphic relation between percolation transitions of ion and molecular aggregates and water H-bonding networks. We anticipate that the combination of graph theory and molecular dynamics simulation methods will be of exceptional use in achieving a deeper understanding of the fundamental physical chemistry of dissolution and in describing the interplay between the self-aggregation of solute
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
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
Early-Aggregation Studies of Polyglutamine in Solution
NASA Astrophysics Data System (ADS)
Fluitt, Aaron; de Pablo, Juan
2012-02-01
Several neurodegenerative diseases, notably Huntington's disease, are associated with certain proteins containing extended polyglutamine tracts. In all polyglutamine diseases, the age of onset is inversely correlated with the length of the polyglutamine domain beyond some pathological threshold. Diseased cells are characterized by intranuclear inclusions rich in aggregated polyglutamine. Experimental evidence suggests that oligomeric aggregate species, not mature amyloid fibrils, are the species most toxic to the cell. Little is known about the structures and aggregation dynamics of polyglutamine oligomers due to their short lifetimes. A better understanding of the pathway through which polyglutamine peptides form oligomeric aggregates will aid the design of therapies to inhibit their toxic activity. In this work, we report structural characterization of polyglutamine monomers and dimers from atomistic molecular dynamics simulations in explicit water. Umbrella sampling simulations reveal that the stability of the dimer species with respect to the disassociated monomers is an increasing function of the chain length.
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.
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.
Decentralized real-time simulation of forest machines
NASA Astrophysics Data System (ADS)
Freund, Eckhard; Adam, Frank; Hoffmann, Katharina; Rossmann, Juergen; Kraemer, Michael; Schluse, Michael
2000-10-01
To develop realistic forest machine simulators is a demanding task. A useful simulator has to provide a close- to-reality simulation of the forest environment as well as the simulation of the physics of the vehicle. Customers demand a highly realistic three dimensional forestry landscape and the realistic simulation of the complex motion of the vehicle even in rough terrain in order to be able to use the simulator for operator training under close-to- reality conditions. The realistic simulation of the vehicle, especially with the driver's seat mounted on a motion platform, greatly improves the effect of immersion into the virtual reality of a simulated forest and the achievable level of education of the driver. Thus, the connection of the real control devices of forest machines to the simulation system has to be supported, i.e. the real control devices like the joysticks or the board computer system to control the crane, the aggregate etc. Beyond, the fusion of the board computer system and the simulation system is realized by means of sensors, i.e. digital and analog signals. The decentralized system structure allows several virtual reality systems to evaluate and visualize the information of the control devices and the sensors. So, while the driver is practicing, the instructor can immerse into the same virtual forest to monitor the session from his own viewpoint. In this paper, we are describing the realized structure as well as the necessary software and hardware components and application experiences.
Borana, Mohanish S; Mishra, Pushpa; Pissurlenkar, Raghuvir R S; Hosur, Ramakrishna V; Ahmad, Basir
2014-03-01
Interaction of small molecule inhibitors with protein aggregates has been studied extensively, but how these inhibitors modulate aggregation kinetic parameters is little understood. In this work, we investigated the ability of two potential aggregation inhibiting drugs, curcumin and kaempferol, to control the kinetic parameters of aggregation reaction. Using thioflavin T fluorescence and static light scattering, the kinetic parameters such as amplitude, elongation rate constant and lag time of guanidine hydrochloride-induced aggregation reactions of hen egg white lysozyme were studied. We observed a contrasting effect of inhibitors on the kinetic parameters when aggregation reactions were measured by these two probes. The interactions of these inhibitors with hen egg white lysozyme were investigated using fluorescence quench titration method and molecular dynamics simulations coupled with binding free energy calculations. We conclude that both the inhibitors prolong nucleation of amyloid aggregation through binding to region of the protein which is known to form the core of the protein fibril, but once the nucleus is formed the rate of elongation is not affected by the inhibitors. This work would provide insight into the mechanism of aggregation inhibition by these potential drug molecules. Copyright © 2014 Elsevier B.V. All rights reserved.
Zhao, Ying; Liu, Dongmei; Tang, Huan; Lu, Jing; Cui, Fuyi
2014-01-01
With the development of nanotechnology, more nanomaterials will enter into water environment system. Studying the existing form of nanomaterials in water environment will help people benefit from the correct use of them and to reduce the harm to human caused by them for some nanomaterials can bring polluting effect. Aggregation is a main behavior for nanoparticle in water environment. NZVI are used widely in many fields resulting in more NZVI in water environment. Molecular dynamics simulations and Materials Studio software are used to investigate the microaggregation behaviors of NZVI particles. Two scenes are involved: (1) particle size of NZVI in each simulation system is the same, but initial distance of two NZVI particles is different; (2) initial distance of two NZVI particles in each simulation system is the same, but particle size of NZVI is different. Atomistic trajectory, NP activity, total energy, and adsorption of H2O are analyzed with MS. The method provides new quantitative insight into the structure, energy, and dynamics of the aggregation behaviors of NZVI particles in water. It is necessary to understand microchange of NPs in water because it can provide theoretical research that is used to reduce polluting effect of NPs on water environment.
Liu, Dongmei; Tang, Huan; Lu, Jing; Cui, Fuyi
2014-01-01
With the development of nanotechnology, more nanomaterials will enter into water environment system. Studying the existing form of nanomaterials in water environment will help people benefit from the correct use of them and to reduce the harm to human caused by them for some nanomaterials can bring polluting effect. Aggregation is a main behavior for nanoparticle in water environment. NZVI are used widely in many fields resulting in more NZVI in water environment. Molecular dynamics simulations and Materials Studio software are used to investigate the microaggregation behaviors of NZVI particles. Two scenes are involved: (1) particle size of NZVI in each simulation system is the same, but initial distance of two NZVI particles is different; (2) initial distance of two NZVI particles in each simulation system is the same, but particle size of NZVI is different. Atomistic trajectory, NP activity, total energy, and adsorption of H2O are analyzed with MS. The method provides new quantitative insight into the structure, energy, and dynamics of the aggregation behaviors of NZVI particles in water. It is necessary to understand microchange of NPs in water because it can provide theoretical research that is used to reduce polluting effect of NPs on water environment. PMID:25250388
Gustafsson, Leif; Sternad, Mikael
2007-10-01
Population models concern collections of discrete entities such as atoms, cells, humans, animals, etc., where the focus is on the number of entities in a population. Because of the complexity of such models, simulation is usually needed to reproduce their complete dynamic and stochastic behaviour. Two main types of simulation models are used for different purposes, namely micro-simulation models, where each individual is described with its particular attributes and behaviour, and macro-simulation models based on stochastic differential equations, where the population is described in aggregated terms by the number of individuals in different states. Consistency between micro- and macro-models is a crucial but often neglected aspect. This paper demonstrates how the Poisson Simulation technique can be used to produce a population macro-model consistent with the corresponding micro-model. This is accomplished by defining Poisson Simulation in strictly mathematical terms as a series of Poisson processes that generate sequences of Poisson distributions with dynamically varying parameters. The method can be applied to any population model. It provides the unique stochastic and dynamic macro-model consistent with a correct micro-model. The paper also presents a general macro form for stochastic and dynamic population models. In an appendix Poisson Simulation is compared with Markov Simulation showing a number of advantages. Especially aggregation into state variables and aggregation of many events per time-step makes Poisson Simulation orders of magnitude faster than Markov Simulation. Furthermore, you can build and execute much larger and more complicated models with Poisson Simulation than is possible with the Markov approach.
Effect of aggregate graining compositions on skid resistance of Exposed Aggregate Concrete pavement
NASA Astrophysics Data System (ADS)
Wasilewska, Marta; Gardziejczyk, Wladysław; Gierasimiuk, Pawel
2018-05-01
The paper presents the evaluation of skid resistance of EAC (Exposed Aggregate Concrete) pavements which differ in aggregate graining compositions. The tests were carried out on concrete mixes with a maximum aggregate size of 8 mm. Three types of coarse aggregates were selected depending on their resistance to polishing which was determined on the basis of the PSV (Polished Stone Value). Basalt (PSV 48), gabbro (PSV 50) and trachybasalt (PSV 52) aggregates were chosen. For each type of aggregate three graining compositions were designed, which differed in the content of coarse aggregate > 4mm. Their content for each series was as follows: A - 38%, B - 50% and C - 68%. Evaluation of the skid resistance has been performed using the FAP (Friction After Polishing) test equipment also known as the Wehner/Schulze machine. Laboratory method enables to compare the skid resistance of different types of wearing course under specified conditions simulating polishing processes. In addition, macrotexture measurements were made on the surface of each specimen using the Elatexure laser profile. Analysis of variance showed that at significance level α = 0.05, aggregate graining compositions as well as the PSV have a significant influence on the obtained values of the friction coefficient μm of the tested EAC pavements. The highest values of the μm have been obtained for EAC with the lowest amount of coarse aggregates (compositions A). In these cases the resistance to polishing of the aggregate does not significantly affect the friction coefficients. This is related to the large areas of cement mortar between the exposed coarse grains. Based on the analysis of microscope images, it was observed that the coarse aggregates were not sufficiently exposed. It has been proved that PSV significantly affected the coefficient of friction in the case of compositions B and C. This is caused by large areas of exposed coarse aggregate. The best parameters were achieved for the EAC pavements
NASA Astrophysics Data System (ADS)
Matsui, Toshi; Zhang, Sara Q.; Lang, Stephen E.; Tao, Wei-Kuo; Ichoku, Charles; Peters-Lidard, Christa D.
2018-03-01
In this study, the impact of different configurations of the Goddard radiation scheme on convection-permitting simulations (CPSs) of the West African monsoon (WAM) is investigated using the NASA-Unified WRF (NU-WRF). These CPSs had 3 km grid spacing to explicitly simulate the evolution of mesoscale convective systems (MCSs) and their interaction with radiative processes across the WAM domain and were able to reproduce realistic precipitation and energy budget fields when compared with satellite data, although low clouds were overestimated. Sensitivity experiments reveal that (1) lowering the radiation update frequency (i.e., longer radiation update time) increases precipitation and cloudiness over the WAM region by enhancing the monsoon circulation, (2) deactivation of precipitation radiative forcing suppresses cloudiness over the WAM region, and (3) aggregating radiation columns reduces low clouds over ocean and tropical West Africa. The changes in radiation configuration immediately modulate the radiative heating and low clouds over ocean. On the 2nd day of the simulations, patterns of latitudinal air temperature profiles were already similar to the patterns of monthly composites for all radiation sensitivity experiments. Low cloud maintenance within the WAM system is tightly connected with radiation processes; thus, proper coupling between microphysics and radiation processes must be established for each modeling framework.
Dielectric aggregation kinetics of cells in a uniform AC electric field.
Tada, Shigeru; Natsuya, Tomoyuki; Tsukamoto, Akira
2014-01-01
Cell manipulation and separation technologies have potential biological and medical applications, including advanced clinical protocols such as tissue engineering. An aggregation model was developed for a human carcinoma (HeLa) cell suspension exposed to a uniform AC electric field, in order to explore the field-induced structure formation and kinetics of cell aggregates. The momentum equations of cells under the action of the dipole-dipole interaction were solved theoretically and the total time required to form linear string-like cluster was derived. The results were compared with those of a numerical simulation. Experiments using HeLa cells were also performed for comparison. The total time required to form linear string-like clusters was derived from a simple theoretical model of the cell cluster kinetics. The growth rates of the average string length of cell aggregates showed good agreement with those of the numerical simulation. In the experiment, cells were found to form massive clusters on the bottom of a chamber. The results imply that the string-like cluster grows rapidly by longitudinal attraction when the electric field is first applied and that this process slows at later times and is replaced by lateral coagulation of short strings. The findings presented here are expected to enable design of methods for the organization of three-dimensional (3D) cellular structures without the use of micro-fabricated substrates, such as 3D biopolymer scaffolds, to manipulate cells into spatial arrangement.
Role of streams in myxobacteria aggregate formation
NASA Astrophysics Data System (ADS)
Kiskowski, Maria A.; Jiang, Yi; Alber, Mark S.
2004-10-01
Cell contact, movement and directionality are important factors in biological development (morphogenesis), and myxobacteria are a model system for studying cell-cell interaction and cell organization preceding differentiation. When starved, thousands of myxobacteria cells align, stream and form aggregates which later develop into round, non-motile spores. Canonically, cell aggregation has been attributed to attractive chemotaxis, a long range interaction, but there is growing evidence that myxobacteria organization depends on contact-mediated cell-cell communication. We present a discrete stochastic model based on contact-mediated signaling that suggests an explanation for the initialization of early aggregates, aggregation dynamics and final aggregate distribution. Our model qualitatively reproduces the unique structures of myxobacteria aggregates and detailed stages which occur during myxobacteria aggregation: first, aggregates initialize in random positions and cells join aggregates by random walk; second, cells redistribute by moving within transient streams connecting aggregates. Streams play a critical role in final aggregate size distribution by redistributing cells among fewer, larger aggregates. The mechanism by which streams redistribute cells depends on aggregate sizes and is enhanced by noise. Our model predicts that with increased internal noise, more streams would form and streams would last longer. Simulation results suggest a series of new experiments.
An atomistic simulation scheme for modeling crystal formation from solution.
Kawska, Agnieszka; Brickmann, Jürgen; Kniep, Rüdiger; Hochrein, Oliver; Zahn, Dirk
2006-01-14
We present an atomistic simulation scheme for investigating crystal growth from solution. Molecular-dynamics simulation studies of such processes typically suffer from considerable limitations concerning both system size and simulation times. In our method this time-length scale problem is circumvented by an iterative scheme which combines a Monte Carlo-type approach for the identification of ion adsorption sites and, after each growth step, structural optimization of the ion cluster and the solvent by means of molecular-dynamics simulation runs. An important approximation of our method is based on assuming full structural relaxation of the aggregates between each of the growth steps. This concept only holds for compounds of low solubility. To illustrate our method we studied CaF2 aggregate growth from aqueous solution, which may be taken as prototypes for compounds of very low solubility. The limitations of our simulation scheme are illustrated by the example of NaCl aggregation from aqueous solution, which corresponds to a solute/solvent combination of very high salt solubility.
Price Formation Based on Particle-Cluster Aggregation
NASA Astrophysics Data System (ADS)
Wang, Shijun; Zhang, Changshui
In the present work, we propose a microscopic model of financial markets based on particle-cluster aggregation on a two-dimensional small-world information network in order to simulate the dynamics of the stock markets. "Stylized facts" of the financial market time series, such as fat-tail distribution of returns, volatility clustering and multifractality, are observed in the model. The results of the model agree with empirical data taken from historical records of the daily closures of the NYSE composite index.
NASA Astrophysics Data System (ADS)
Alves, S. G.; Martins, M. L.
2010-09-01
Aggregation of animal cells in culture comprises a series of motility, collision and adhesion processes of basic relevance for tissue engineering, bioseparations, oncology research and in vitro drug testing. In the present paper, a cluster-cluster aggregation model with stochastic particle replication and chemotactically driven motility is investigated as a model for the growth of animal cells in culture. The focus is on the scaling laws governing the aggregation kinetics. Our simulations reveal that in the absence of chemotaxy the mean cluster size and the total number of clusters scale in time as stretched exponentials dependent on the particle replication rate. Also, the dynamical cluster size distribution functions are represented by a scaling relation in which the scaling function involves a stretched exponential of the time. The introduction of chemoattraction among the particles leads to distribution functions decaying as power laws with exponents that decrease in time. The fractal dimensions and size distributions of the simulated clusters are qualitatively discussed in terms of those determined experimentally for several normal and tumoral cell lines growing in culture. It is shown that particle replication and chemotaxy account for the simplest cluster size distributions of cellular aggregates observed in culture.
Theoretical deposition of carcinogenic particle aggregates in the upper respiratory tract.
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
de Jesus Mendes, Pedro A; Thomsen, Laurenz
2012-01-01
The dissolution of CaCO(3) is one of the ways ocean acidification can, potentially, greatly affect the ballast of aggregates. A diminution of the ballast could reduce the settling speed of aggregates, resulting in a change in the carbon flux to the deep sea. This would mean lower amounts of more refractory organic matter reaching the ocean floor. This work aimed to determine the effect of ocean acidification on the ballast of sinking surface aggregates. Our hypothesis was that the decrease of pH will increase the dissolution of particulate inorganic carbon ballasting the aggregates, consequently reducing their settling velocity and increasing their residence time in the upper twilight zone. Using a new methodology for simulation of aggregate settling, our results suggest that future pCO(2) conditions can significantly change the ballast composition of sinking aggregates. The change in aggregate composition had an effect on the size distribution of the aggregates, with a shift to smaller aggregates. A change also occurred in the settling velocity of the particles, which would lead to a higher residence time in the water column, where they could be continuously degraded. In the environment, such an effect would result in a reduction of the carbon flux to the deep-sea. This reduction would impact those benthic communities, which rely on the vertical flow of carbon as primary source of energy.
Yielding in a strongly aggregated colloidal gel: 2D simulations and theory
NASA Astrophysics Data System (ADS)
Roy, Saikat; Tirumkudulu, Mahesh
2015-11-01
We investigated the micro-structural details and the mechanical response under uniaxial compression of the strongly aggregating gel starting from low to high packing fraction.The numerical simulations account for short-range inter-particle attractions, normal and tangential deformation at particle contacts,sliding and rolling friction, and preparation history. It is observed that in the absence of rolling resistance(RR),the average coordination number varies only slightly with compaction whereas it is significant in the presence of RR. The particle contact distribution is isotropic throughout the consolidation process. In both cases, the yield strain is constant with the volume fraction. The modulus values are very similar at different attraction, and with and without RR implying that the elastic modulus does not scale with attraction.The modulus was found to be a weak function of the preparation history. The increase in yield stress with volume fraction is a consequence of the increased elastic modulus of the network. However, the yield stress scales similarly both with and without RR. The power law exponent of 5.4 is in good agreement with previous simulation results. A micromechanical theory is also proposed to describe the stress versus strain relation for the gelled network.
Tolpekin, V A; Duits, M H G; van den Ende, D; Mellema, J
2004-03-30
We used video microscopy to study the behavior of aggregating suspensions in shear flow. Suspensions consisted of 920 nm diameter silica spheres, dispersed in a methanol/bromoform solvent, to which poly(ethylene glycol) (M = 35.000 g) was added to effect weak particle aggregation. With our solvent mixture, the refractive index of the particles could be closely matched, to allow microscopic observations up to 80 microm deep into the suspension. Also the mass density is nearly equal to that of the particles, thus allowing long observation times without problems due to aggregate sedimentation. Particles were visualized via fluorescent molecules incorporated into their cores. Using a fast confocal scanning laser microscope made it possible to characterize the (flowing) aggregates via their contour-area distributions as observed in the focal plane. The aggregation process was monitored from the initial state (just after adding the polymer), until a steady state was reached. The particle volume fraction was chosen at 0.001, to obtain a characteristic aggregation time of a few hundred seconds. On variation of polymer concentration, cP (2.2-12.0 g/L), and shear rate, gamma (3-6/s), it was observed that the volume-averaged size, Dv, in the steady state became larger with polymer concentration and smaller with shear rate. This demonstrates that the aggregate size is set by a competition between cohesive forces caused by the polymer and rupture forces caused by the flow. Also aggregate size distributions were be measured (semiquantitatively). Together with a description for the internal aggregate structure they allowed a modeling of the complete aggregation curve, from t = 0 up to the steady state. A satisfactory description could be obtained by describing the aggregates as fractal objects, with Df = 2.0, as measured from CSLM images after stopping the flow. In this modeling, the fitted characteristic breakup time was found to increase with cP.
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.
Molecular simulations of conformation change and aggregation of HIV-1 Vpr13-33 on graphene oxide
NASA Astrophysics Data System (ADS)
Zeng, Songwei; Zhou, Guoquan; Guo, Jianzhong; Zhou, Feng; Chen, Junlang
2016-04-01
Recent experiments have reported that the fragment of viral protein R (Vpr), Vpr13-33, can assemble and change its conformation after adsorbed on graphene oxide (GO) and then reduce its cytotoxicity. This discovery is of great importance, since the mutation of Vpr13-33 can decrease the viral replication, viral load and delay the disease progression. However, the interactions between Vpr13-33 and GO at atomic level are still unclear. In this study, we performed molecular dynamics simulation to investigate the dynamic process of the adsorption of Vpr13-33 onto GO and the conformation change after aggregating on GO surface. We found that Vpr13-33 was adsorbed on GO surface very quickly and lost its secondary structure. The conformation of peptides-GO complex was highly stable because of π-π stacking and electrostatic interactions. When two peptides aggregated on GO, they did not dimerize, since the interactions between the two peptides were much weaker than those between each peptide and GO.
Remsing, Richard C; Liu, Zhiwei; Sergeyev, Ivan; Moyna, Guillermo
2008-06-26
The solvation and aggregation of the ionic liquid (IL) 1-n-butyl-3-methylimidazolium chloride ([C4mim]Cl) in water and dimethylsulfoxide (DMSO) were examined by analysis of (1)H and (35/37)Cl chemical shift perturbations and molecular dynamics (MD) simulations. Evidence of aggregation of the IL n-butyl chains in aqueous environments at IL concentrations of 75-80 wt% was observed both in the NMR experiments and in the MD simulations. The studies also show that [C4mim]Cl behaves as a typical electrolyte in water, with both ions completely solvated at low concentrations. On the other hand, the data reveal that the interactions between the [C4mim](+) and Cl(-) ions strengthen as the DMSO content of the solutions increases, and IL-rich clusters persist in this solvent even at concentrations below 10 wt%. These results provide an experimentally supported atomistic explanation of the effects that these two solvents have on some of the macroscopic properties of [C4mim]Cl. The implications that these findings could have on the design of IL-based solvent systems are briefly discussed.
Enhanced Luminescent Stability through Particle Interactions in Silicon Nanocrystal Aggregates
DOE Office of Scientific and Technical Information (OSTI.GOV)
Miller, Joseph B.; Dandu, Naveen; Velizhanin, Kirill A.
2015-10-27
Close-packed assemblies of ligand-passivated colloidal nanocrystals can exhibit enhanced photoluminescent stability, but the origin of this effect is unclear. Here, we use experiment, simulation, and ab initio computation to examine the influence of interparticle interactions on the photoluminescent stability of silicon nanocrystal aggregates. The time-dependent photoluminescence emitted by structures ranging in size from a single quantum dot to agglomerates of more than a thousand is compared with Monte Carlo simulations of noninteracting ensembles using measured single-particle blinking data as input. In contrast to the behavior typically exhibited by the metal chalcogenides, the measured photoluminescent stability shows an enhancement with respectmore » to the noninteracting scenario with increasing aggregate size. We model this behavior using time-dependent density functional theory calculations of energy transfer between neighboring nanocrystals as a function of nanocrystal size, separation, and the presence of charge and/or surface-passivation defects. Our results suggest that rapid exciton transfer from “bright” nanocrystals to surface trap states in nearest-neighbors can efficiently fill such traps and enhance the stability of emission by promoting the radiative recombination of slowly diffusing excited electrons.« less
The excel file contains time series data of flow rates, concentrations of alachlor , atrazine, ammonia, total phosphorus, and total suspended solids observed in two watersheds in Indiana from 2002 to 2007. The aggregate time series data corresponding or representative to all these parameters was obtained using a specialized, data-driven technique. The aggregate data is hypothesized in the published paper to represent the overall health of both watersheds with respect to various potential water quality impairments. The time series data for each of the individual water quality parameters were used to compute corresponding risk measures (Rel, Res, and Vul) that are reported in Table 4 and 5. The aggregation of the risk measures, which is computed from the aggregate time series and water quality standards in Table 1, is also reported in Table 4 and 5 of the published paper. Values under column heading uncertainty reports uncertainties associated with reconstruction of missing records of the water quality parameters. Long-term records of the water quality parameters were reconstructed in order to estimate the (R-R-V) and corresponding aggregate risk measures. This dataset is associated with the following publication:Hoque, Y., S. Tripathi, M. Hantush , and R. Govindaraju. Aggregate Measures of Watershed Health from Reconstructed Water Quality Data with Uncertainty. Ed Gregorich JOURNAL OF ENVIRONMENTAL QUALITY. American Society of Agronomy, MADISON, WI,
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.
Spontaneous chiral symmetry breaking in two-dimensional aggregation
NASA Astrophysics Data System (ADS)
Sandler, Ilya Moiseevich
Recently, unusual and strikingly beautiful seahorse-like growth patterns have been discovered. These patterns possess a spontaneously broken chiral (left/right) symmetry. To explain this spontaneous chiral symmetry breaking, we develop a model for the growth of the aggregate, assuming that the latter is charged, and that the incoming particles are polarizable, and hence drawn preferentially to regions of strong electric field. This model is used both for numerical simulation and theoretical analysis of the aggregation process. We find that the broken symmetry (typically, an 'S' shape) appears in our simulations for some parameter values. Its origin is the long-range interaction (competition and repulsion) among growing branches of the aggregate, such that a right or left side consistently dominates the growth process. We show that the electrostatic interaction may account for the other geometrical properties of the aggregates, such as the existence of only 2 main arms, and the "finned" external edge of the main arms. The results of our simulations of growth in the presence of the external electric field are also in a good agreement with the results of new experiments, motivated by our ideas. Thus, we believe that our growth model provides a plausible explanation of the origin of the broken symmetry in the experimental patterns.
Macroeconomic susceptibility, inflation, and aggregate supply
NASA Astrophysics Data System (ADS)
Hawkins, Raymond J.
2017-03-01
We unify aggregate-supply dynamics as a time-dependent susceptibility-mediated relationship between inflation and aggregate economic output. In addition to representing well various observations of inflation-output dynamics this parsimonious formalism provides a straightforward derivation of popular representations of aggregate-supply dynamics and a natural basis for economic-agent expectations as an element of inflation formation. Our formalism also illuminates questions of causality and time-correlation that challenge central banks for whom aggregate-supply dynamics is a key constraint in their goal of achieving macroeconomic stability.
Self-organization of intertidal snails facilitates evolution of aggregation behavior.
Stafford, Richard; Davies, Mark S; Williams, Gray A
2008-01-01
Many intertidal snails form aggregations during emersion to minimize desiccation stress. Here we investigate possible mechanisms for the evolution of such behavior. Two behavioral traits (following of mucus trails, and crevice occupation), which both provide selective advantages to individuals that possess the traits over individuals that do not, result in self-organization of aggregations in crevices in the rock surface. We suggest that the existence of self-organizing aggregations provides a mechanism by which aggregation behavior can evolve. The inclusion of an explicitly coded third behavior, aggregation, in a simulated population produces patterns statistically similar to those found on real rocky shores. Allowing these three behaviors to evolve using an evolutionary algorithm, however, results in aggregation behavior being selected against on shores with high crevice density. The inclusion of broadcast spawning dispersal mechanisms in the simulation, however, results in aggregation behavior evolving as predicted on shores with both high crevice density and low crevice density (evolving in crevices first, and then both in crevices and on flat rock), indicating the importance of environmental interactions in understanding evolutionary processes. We propose that self-organization can be an important factor in the evolution of group behaviors.
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.
NASA Astrophysics Data System (ADS)
Choi, Jun-Ho; Choi, Hyung Ran; Jeon, Jonggu; Cho, Minhaeng
2017-10-01
Ions in high salt solutions have a strong propensity to form polydisperse ion aggregates with broad size and shape distributions. In a series of previous comparative investigations using femtosecond IR pump-probe spectroscopy, molecular dynamics simulation, and graph theoretical analysis, we have shown that there exists a morphological difference in the structures of ion aggregates formed in various salt solutions. As salt concentration increases, the ions in high salt solutions form either cluster-like structures excluding water molecules or network-like structures entwined with water hydrogen-bonding networks. Interestingly, such morphological characteristics of the ion aggregates have been found to be in correlation with the solubility limits of salts. An important question that still remains unexplored is why certain salts with different cations have notably different solubility limits in water. Here, carrying out a series of molecular dynamics simulations of aqueous salt solutions and analyzing the distributions and connectivity patterns of ion aggregates with a spectral graph analysis method, we establish the relationship between the salt solubility and the ion aggregate morphology with a special emphasis on the cationic effects on water structures and ion aggregation. We anticipate that the understanding of large scale ion aggregate structures revealed in this study will be critical for elucidating the specific ion effects on the solubility and conformational stability of co-solute molecules such as proteins in water.
NASA Astrophysics Data System (ADS)
Dobronets, Boris S.; Popova, Olga A.
2018-05-01
The paper considers a new approach of regression modeling that uses aggregated data presented in the form of density functions. Approaches to Improving the reliability of aggregation of empirical data are considered: improving accuracy and estimating errors. We discuss the procedures of data aggregation as a preprocessing stage for subsequent to regression modeling. An important feature of study is demonstration of the way how represent the aggregated data. It is proposed to use piecewise polynomial models, including spline aggregate functions. We show that the proposed approach to data aggregation can be interpreted as the frequency distribution. To study its properties density function concept is used. Various types of mathematical models of data aggregation are discussed. For the construction of regression models, it is proposed to use data representation procedures based on piecewise polynomial models. New approaches to modeling functional dependencies based on spline aggregations are proposed.
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.
Grabowski, T.B.; Isely, J.J.
2008-01-01
Little is known about the behavior of individual fish in a spawning aggregation, specifically how long an individual remains in an aggregation. We monitored Moxostoma robustum (Cope) (Robust Redhorse) in a Savannah River spawning aggregation during spring 2004 and 2005 to provide an estimate of the total number of adults and the number of males comprising the aggregation and to determine male residence time and movements within a spawning aggregation. Robust Redhorse were captured using prepostioned grid electrofishers, identified to sex, weighed, measured, and implanted with a passive integrated transponder. Spawning aggregation size was estimated using a multiple census mark-and-recapture procedure. The spawning aggregation seemed to consist of approximately the same number of individuals (82-85) and males (50-56) during both years of this study. Individual males were present for a mean of 3.6 ?? 0.24 days (?? SE) during the 12-day spawning period. The mean distance between successive recaptures of individual males was 15.9 ?? 1.29 m (?? SE). We conclude that males establish spawning territories on a daily basis and are present within the spawning aggregation for at least 3-4 days. The relatively short duration of the aggregation may be the result of an extremely small population of adults. However, the behavior of individuals has the potential to influence population estimates made while fish are aggregated for spawning.
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.
A phase field approach for multicellular aggregate fusion in biofabrication.
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.
A microfabricated platform to form three-dimensional toroidal multicellular aggregate.
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.
NASA Astrophysics Data System (ADS)
Furuki, Makoto; Tian, Minquan; Sato, Yasuhiro; Pu, Lyong Sun; Tatsuura, Satoshi; Wada, Osamu
2000-07-01
We applied time-to-space conversion using femtosecond nonlinear-optical response of squarylium-dye (SQ) J-aggregates film. A pump pulse and a train of four probe pulses were illuminated on the same area (10 mm φ) of the film in direction of oblique and normal to the film plane, respectively. Due to the oblique illumination, the pump pulse met probe pulses (interval time: 1 ps) at separate places. The film picked out part of each probe pulse by its transmittance change, which was observed for a transmitted image of spatially separated four lines. Response time of the SQ J aggregates is enough for the single-shot 1 THz demultiplexing.
Aeolian comminution experiments revealing surprising sandball mineral aggregates
NASA Astrophysics Data System (ADS)
Nørnberg, P.; Bak, E.; Finster, K.; Gunnlaugsson, H. P.; Iversen, J. J.; Jensen, S. Knak; Merrison, J. P.
2014-06-01
We have undertaken a set of wind erosion experiments on a simple and well defined mineral, quartz. In these experiments wind action is simulated by end over end tumbling of quartz grains in a sealed quartz flask. The tumbling induces collisions among the quartz grains and the walls of the flask. This process simulates wind action impact speed of ∼1.2 m/s. After several months of tumbling we observed the formation of a large number of spherical sand aggregates, which resemble small snowballs under optical microscopy. Upon mechanical load the aggregates are seen to be more elastic than quartz and their mechanical strength is comparable, though slightly lower than that of sintered silica aerogels. Aggregates of this kind have not been reported from field sites or from closed circulation systems. However, sparse occurrence might explain this, or in nature the concentration of the aggregate building particles is so low that they never meet and just appear as the most fine grained tail of the sediment particle size distribution.
Real time digital propulsion system simulation for manned flight simulators
NASA Technical Reports Server (NTRS)
Mihaloew, J. R.; Hart, C. E.
1978-01-01
A real time digital simulation of a STOL propulsion system was developed which generates significant dynamics and internal variables needed to evaluate system performance and aircraft interactions using manned flight simulators. The simulation ran at a real-to-execution time ratio of 8.8. The model was used in a piloted NASA flight simulator program to evaluate the simulation technique and the propulsion system digital control. The simulation is described and results shown. Limited results of the flight simulation program are also presented.
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.
VERSE - Virtual Equivalent Real-time Simulation
NASA Technical Reports Server (NTRS)
Zheng, Yang; Martin, Bryan J.; Villaume, Nathaniel
2005-01-01
Distributed real-time simulations provide important timing validation and hardware in the- loop results for the spacecraft flight software development cycle. Occasionally, the need for higher fidelity modeling and more comprehensive debugging capabilities - combined with a limited amount of computational resources - calls for a non real-time simulation environment that mimics the real-time environment. By creating a non real-time environment that accommodates simulations and flight software designed for a multi-CPU real-time system, we can save development time, cut mission costs, and reduce the likelihood of errors. This paper presents such a solution: Virtual Equivalent Real-time Simulation Environment (VERSE). VERSE turns the real-time operating system RTAI (Real-time Application Interface) into an event driven simulator that runs in virtual real time. Designed to keep the original RTAI architecture as intact as possible, and therefore inheriting RTAI's many capabilities, VERSE was implemented with remarkably little change to the RTAI source code. This small footprint together with use of the same API allows users to easily run the same application in both real-time and virtual time environments. VERSE has been used to build a workstation testbed for NASA's Space Interferometry Mission (SIM PlanetQuest) instrument flight software. With its flexible simulation controls and inexpensive setup and replication costs, VERSE will become an invaluable tool in future mission development.
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 .
Statistical, economic and other tools for assessing natural aggregate
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.
Turbulent breakage of ductile aggregates.
Marchioli, Cristian; Soldati, Alfredo
2015-05-01
In this paper we study breakage rate statistics of small colloidal aggregates in nonhomogeneous anisotropic turbulence. We use pseudospectral direct numerical simulation of turbulent channel flow and Lagrangian tracking to follow the motion of the aggregates, modeled as sub-Kolmogorov massless particles. We focus specifically on the effects produced by ductile rupture: This rupture is initially activated when fluctuating hydrodynamic stresses exceed a critical value, σ>σ(cr), and is brought to completion when the energy absorbed by the aggregate meets the critical breakage value. We show that ductile rupture breakage rates are significantly reduced with respect to the case of instantaneous brittle rupture (i.e., breakage occurs as soon as σ>σ(cr)). These discrepancies are due to the different energy values at play as well as to the statistical features of energy distribution in the anisotropic turbulence case examined.
Active matter model of Myxococcus xanthus aggregation
NASA Astrophysics Data System (ADS)
Patch, Adam; Bahar, Fatmagul; Liu, Guannan; Thutupalli, Shashi; Welch, Roy; Yllanes, David; Shaevitz, Joshua; Marchetti, M. Cristina
Myxococcus xanthus is a soil-dwelling bacterium that exhibits several fascinating collective behaviors including streaming, swarming, and generation of fruiting bodies. A striking feature of M. xanthus is that it periodically reverses its motility direction. The first stage of fruiting body formation is characterized by the aggregation of cells on a surface into round mesoscopic structures. Experiments have shown that this aggregation relies heavily on regulation of the reversal rate and local mechanical interactions, suggesting motility-induced phase separation may play an important role. We have adapted self-propelled particle models to include cell reversal and motility suppression resulting from sporulation observed in aggregates. Using 2D molecular dynamics simulations, we map the phase behavior in the space of Péclet number and local density and examine the kinetics of aggregation for comparison to experiments.
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.
Hydrogen-bonded aggregates in precise acid copolymers
DOE Office of Scientific and Technical Information (OSTI.GOV)
Lueth, Christopher A.; Bolintineanu, Dan S.; Stevens, Mark J., E-mail: msteve@sandia.gov
2014-02-07
We perform atomistic molecular dynamics simulations of melts of four precise acid copolymers, two poly(ethylene-co-acrylic acid) (PEAA) copolymers, and two poly(ethylene-co-sulfonic acid) (PESA) copolymers. The acid groups are spaced by either 9 or 21 carbons along the polymer backbones. Hydrogen bonding causes the acid groups to form aggregates. These aggregates give rise to a low wavevector peak in the structure factors, in agreement with X-ray scattering data for the PEAA materials. The structure factors for the PESA copolymers are very similar to those for the PEAA copolymers, indicating a similar distance between aggregates which depends on the spacer length butmore » not on the nature of the acid group. The PEAA copolymers are found to form more dimers and other small aggregates than do the PESA copolymers, while the PESA copolymers have both more free acid groups and more large aggregates.« less
Structural study of aggregated β-carotene by absorption spectroscopy
NASA Astrophysics Data System (ADS)
Lu, Li Ping; Wei, Liang Shu
2017-10-01
By UV-visible absorption spectroscope, the aggregated β-carotene in hydrated ethanol was studied in the temperature range of 5 55°C, with different ethanol/water ratio. And the structural evolutions of these aggregates with time were detected. The spectrophotometric analysis showed that the aggregate of β-carotene formed in 1:1 ethanol/water solution transfered from H-type to J-type with temperature increase. In 2:1 ethanol/water solution a new type of aggregate with strong coupling was predicated by the appearing absorption peak located at about 550 nm. In the time scales of 48 houses all the aggregated structures were stable, but the absorption intensity decreased with time. It was concluded that the types of aggregated β-carotene which wouldn't change with time depended on the solvent composition and temperature.
Monitoring Insulin Aggregation via Capillary Electrophoresis
Pryor, Elizabeth; Kotarek, Joseph A.; Moss, Melissa A.; Hestekin, Christa N.
2011-01-01
Early stages of insulin aggregation, which involve the transient formation of oligomeric aggregates, are an important aspect in the progression of Type II diabetes and in the quality control of pharmaceutical insulin production. This study is the first to utilize capillary electrophoresis (CE) with ultraviolet (UV) detection to monitor insulin oligomer formation at pH 8.0 and physiological ionic strength. The lag time to formation of the first detected species in the aggregation process was evaluated by UV-CE and thioflavin T (ThT) binding for salt concentrations from 100 mM to 250 mM. UV-CE had a significantly shorter (5–8 h) lag time than ThT binding (15–19 h). In addition, the lag time to detection of the first aggregated species via UV-CE was unaffected by salt concentration, while a trend toward an increased lag time with increased salt concentration was observed with ThT binding. This result indicates that solution ionic strength impacts early stages of aggregation and β-sheet aggregate formation differently. To observe whether CE may be applied for the analysis of biological samples containing low insulin concentrations, the limit of detection using UV and laser induced fluorescence (LIF) detection modes was determined. The limit of detection using LIF-CE, 48.4 pM, was lower than the physiological insulin concentration, verifying the utility of this technique for monitoring biological samples. LIF-CE was subsequently used to analyze the time course for fluorescein isothiocyanate (FITC)-labeled insulin oligomer formation. This study is the first to report that the FITC label prevented incorporation of insulin into oligomers, cautioning against the use of this fluorescent label as a tag for following early stages of insulin aggregation. PMID:22272138
Lehrer, Roni; Schumacher, Gijs
2018-01-01
The policy positions parties choose are central to both attracting voters and forming coalition governments. How then should parties choose positions to best represent voters? Laver and Sergenti show that in an agent-based model with boundedly rational actors a decision rule (Aggregator) that takes the mean policy position of its supporters is the best rule to achieve high congruence between voter preferences and party positions. But this result only pertains to representation by the legislature, not representation by the government. To evaluate this we add a coalition formation procedure with boundedly rational parties to the Laver and Sergenti model of party competition. We also add two new decision rules that are sensitive to government formation outcomes rather than voter positions. We develop two simulations: a single-rule one in which parties with the same rule compete and an evolutionary simulation in which parties with different rules compete. In these simulations we analyze party behavior under a large number of different parameters that describe real-world variance in political parties' motives and party system characteristics. Our most important conclusion is that Aggregators also produce the best match between government policy and voter preferences. Moreover, even though citizens often frown upon politicians' interest in the prestige and rents that come with winning political office (office pay-offs), we find that citizens actually receive better representation by the government if politicians are motivated by these office pay-offs in contrast to politicians with ideological motivations (policy pay-offs). Finally, we show that while more parties are linked to better political representation, how parties choose policy positions affects political representation as well. Overall, we conclude that to understand variation in the quality of political representation scholars should look beyond electoral systems and take into account variation in party
2018-01-01
The policy positions parties choose are central to both attracting voters and forming coalition governments. How then should parties choose positions to best represent voters? Laver and Sergenti show that in an agent-based model with boundedly rational actors a decision rule (Aggregator) that takes the mean policy position of its supporters is the best rule to achieve high congruence between voter preferences and party positions. But this result only pertains to representation by the legislature, not representation by the government. To evaluate this we add a coalition formation procedure with boundedly rational parties to the Laver and Sergenti model of party competition. We also add two new decision rules that are sensitive to government formation outcomes rather than voter positions. We develop two simulations: a single-rule one in which parties with the same rule compete and an evolutionary simulation in which parties with different rules compete. In these simulations we analyze party behavior under a large number of different parameters that describe real-world variance in political parties’ motives and party system characteristics. Our most important conclusion is that Aggregators also produce the best match between government policy and voter preferences. Moreover, even though citizens often frown upon politicians’ interest in the prestige and rents that come with winning political office (office pay-offs), we find that citizens actually receive better representation by the government if politicians are motivated by these office pay-offs in contrast to politicians with ideological motivations (policy pay-offs). Finally, we show that while more parties are linked to better political representation, how parties choose policy positions affects political representation as well. Overall, we conclude that to understand variation in the quality of political representation scholars should look beyond electoral systems and take into account variation in party
Self-aggregation and coaggregation of the p53 core fragment with its aggregation gatekeeper variant.
Lei, Jiangtao; Qi, Ruxi; Wei, Guanghong; Nussinov, Ruth; Ma, Buyong
2016-03-21
Recent studies suggested that p53 aggregation can lead to loss-of-function (LoF), dominant-negative (DN) and gain-of-function (GoF) effects, with adverse cancer consequences. The p53 aggregation-nucleating (251)ILTIITL(257) fragment is a key segment in wild-type p53 aggregation; however, an I254R mutation can prevent it. It was suggested that self-assembly of wild-type p53 and its cross-interaction with mutants differ from the classical amyloid nucleation-growth mechanism. Here, using replica exchange molecular dynamics (REMD) simulations, we studied the cross-interactions of this p53 core fragment and its aggregation rescue I254R mutant. We found that the core fragment displays strong aggregation propensity, whereas the gatekeeper I254R mutant tends to be disordered, consistent with experiments. Our cross-interaction results reveal that the wild-type p53 fragment promotes β-sheet formation of the I254R mutant by shifting the disordered mutant peptides into aggregating states. As a result, the system has similar oligomeric structures, inter-peptide interactions and free energy landscape as the wild type fragment does, revealing a prion-like process. We also found that in the cross-interaction system, the wild-type species has higher tendency to interact with the mutant than with itself. This phenomenon illustrates synergistic effects between the p53 (251)ILTIITL(257) fragment and the mutant resembling prion cross-species propagation, cautioning against exploiting it in drug discovery.
A model for bacterial colonization of sinking aggregates.
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.
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.
Building aggregate timber supply models from individual harvest choice
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...
Aggregate breakdown of nanoparticulate titania
NASA Astrophysics Data System (ADS)
Venugopal, Navin
Six nanosized titanium dioxide powders synthesized from a sulfate process were investigated. The targeted end-use of this powder was for a de-NOx catalyst honeycomb monolith. Alteration of synthesis parameters had resulted principally in differences in soluble ion level and specific surface area of the powders. The goal of this investigation was to understand the role of synthesis parameters in the aggregation behavior of these powders. Investigation via scanning electron microscopy of the powders revealed three different aggregation iterations at specific length scales. Secondary and higher order aggregate strength was investigated via oscillatory stress rheometry as a means of simulating shear conditions encountered during extrusion. G' and G'' were measured as a function of the applied oscillatory stress. Oscillatory rheometry indicated a strong variation as a function of the sulfate level of the particles in the viscoelastic yield strengths. Powder yield stresses ranged from 3.0 Pa to 24.0 Pa of oscillatory stress. Compaction curves to 750 MPa found strong similarities in extrapolated yield point of stage I and II compaction for each of the powders (at approximately 500 MPa) suggesting that the variation in sulfate was greatest above the primary aggregate level. Scanning electron microscopy of samples at different states of shear in oscillatory rheometry confirmed the variation in the linear elastic region and the viscous flow regime. A technique of this investigation was to approach aggregation via a novel perspective: aggregates are distinguished as being loose open structures that are highly disordered and stochastic in nature. The methodology used was to investigate the shear stresses required to rupture the various aggregation stages encountered and investigate the attempt to realign the now free-flowing constituents comprising the aggregate into a denser configuration. Mercury porosimetry was utilized to measure the pore size of the compact resulting from
A new efficient method for calculation of Frenkel exciton parameters in molecular aggregates
NASA Astrophysics Data System (ADS)
Plötz, Per-Arno; Niehaus, Thomas; Kühn, Oliver
2014-05-01
The Frenkel exciton Hamiltonian is at the heart of many simulations of excitation energy transfer in molecular aggregates. It separates the aggregate into Coulomb-coupled monomers. Here it is shown that the respective parameters, i.e., monomeric excitation energies and Coulomb couplings between transition densities can be efficiently calculated using time-dependent tight-binding-based density functional theory (TD-DFTB). Specifically, Coulomb couplings are expressed in terms of self-consistently determined Mulliken transition charges. The approach is applied to two dimer systems. First, formaldehyde oxime for which a detailed comparison with standard DFT using the B3LYP and the PBE functionals as well as with SCS-CC2 is provided. Second, the Coulomb coupling is explored in dependence on the intermolecular coordinates for a perylene bisimide dimer. This provides structural evidence for the previously observed biphasic aggregation behavior of this dye.
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.
Optimum Aggregation and Control of Spatially Distributed Flexible Resources in Smart Grid
Bhattarai, Bishnu; Mendaza, Iker Diaz de Cerio; Myers, Kurt S.; ...
2017-03-24
This paper presents an algorithm to optimally aggregate spatially distributed flexible resources at strategic microgrid/smart-grid locations. The aggregation reduces a distribution network having thousands of nodes to an equivalent network with a few aggregated nodes, thereby enabling distribution system operators (DSOs) to make faster operational decisions. Moreover, the aggregation enables flexibility from small distributed flexible resources to be traded to different power and energy markets. A hierarchical control architecture comprising a combination of centralized and decentralized control approaches is proposed to practically deploy the aggregated flexibility. The proposed method serves as a great operational tool for DSOs to decide themore » exact amount of required flexibilities from different network section(s) for solving grid constraint violations. The effectiveness of the proposed method is demonstrated through simulation of three operational scenarios in a real low voltage distribution system having high penetrations of electric vehicles and heat pumps. Finally, the simulation results demonstrated that the aggregation helps DSOs not only in taking faster operational decisions, but also in effectively utilizing the available flexibility.« less
Optimum Aggregation and Control of Spatially Distributed Flexible Resources in Smart Grid
DOE Office of Scientific and Technical Information (OSTI.GOV)
Bhattarai, Bishnu; Mendaza, Iker Diaz de Cerio; Myers, Kurt S.
This paper presents an algorithm to optimally aggregate spatially distributed flexible resources at strategic microgrid/smart-grid locations. The aggregation reduces a distribution network having thousands of nodes to an equivalent network with a few aggregated nodes, thereby enabling distribution system operators (DSOs) to make faster operational decisions. Moreover, the aggregation enables flexibility from small distributed flexible resources to be traded to different power and energy markets. A hierarchical control architecture comprising a combination of centralized and decentralized control approaches is proposed to practically deploy the aggregated flexibility. The proposed method serves as a great operational tool for DSOs to decide themore » exact amount of required flexibilities from different network section(s) for solving grid constraint violations. The effectiveness of the proposed method is demonstrated through simulation of three operational scenarios in a real low voltage distribution system having high penetrations of electric vehicles and heat pumps. Finally, the simulation results demonstrated that the aggregation helps DSOs not only in taking faster operational decisions, but also in effectively utilizing the available flexibility.« less
ERIC Educational Resources Information Center
Yamaguchi, Yusuke; Sakamoto, Wataru; Goto, Masashi; Staessen, Jan A.; Wang, Jiguang; Gueyffier, Francois; Riley, Richard D.
2014-01-01
When some trials provide individual patient data (IPD) and the others provide only aggregate data (AD), meta-analysis methods for combining IPD and AD are required. We propose a method that reconstructs the missing IPD for AD trials by a Bayesian sampling procedure and then applies an IPD meta-analysis model to the mixture of simulated IPD and…
Formation and Growth of Stacking Fault Tetrahedra in Ni via Vacancy Aggregation Mechanism
Aidhy, Dilpuneet S.; Lu, Chenyang; Jin, Ke; ...
2015-12-29
Using molecular dynamics simulations, the formation and growth of stacking fault tetrahedra (SFT) are captured by vacancy cluster diffusion and aggregation mechanisms in Ni. The vacancytetrahedron acts as a nucleation point for SFT formation. Simulations show that perfect SFT can grow to the next size perfect SFT via a vacancy aggregation mechanism. The stopping and range of ions in matter (SRIM) calculations and transmission electron microscopy (TEM) observations reveal that SFT can form farther away from the initial cascade-event locations, indicating the operation of diffusion-based vacancy-aggregation mechanism.
Formation and Growth of Stacking Fault Tetrahedra in Ni via Vacancy Aggregation Mechanism
DOE Office of Scientific and Technical Information (OSTI.GOV)
Aidhy, Dilpuneet S.; Lu, Chenyang; Jin, Ke
Using molecular dynamics simulations, the formation and growth of stacking fault tetrahedra (SFT) are captured by vacancy cluster diffusion and aggregation mechanisms in Ni. The vacancytetrahedron acts as a nucleation point for SFT formation. Simulations show that perfect SFT can grow to the next size perfect SFT via a vacancy aggregation mechanism. The stopping and range of ions in matter (SRIM) calculations and transmission electron microscopy (TEM) observations reveal that SFT can form farther away from the initial cascade-event locations, indicating the operation of diffusion-based vacancy-aggregation mechanism.
Ishii, Tomohiro; Kawakami, Emiko; Endo, Kentaro; Misawa, Hidemi; Watabe, Kazuhiko
2017-01-01
TAR DNA-binding protein 43 (TDP-43) is a main constituent of cytoplasmic aggregates in neuronal and glial cells in cases of amyotrophic lateral sclerosis and frontotemporal lobar degeneration. We have previously demonstrated that adenovirus-transduced artificial TDP-43 cytoplasmic aggregates formation is enhanced by proteasome inhibition in vitro and in vivo. However, the relationship between cytoplasmic aggregate formation and cell death remains unclear. In the present study, rat neural stem cell lines stably transfected with EGFP- or Sirius-expression vectors under the control of tubulin beta III, glial fibrillary acidic protein, or 2′,3′-cyclic nucleotide 3′-phosphodiesterase promoter were differentiated into neurons, astrocytes, and oligodendrocytes, respectively, in the presence of retinoic acid. The differentiated cells were then transduced with adenoviruses expressing DsRed-tagged human wild type and C-terminal fragment TDP-43 under the condition of proteasome inhibition. Time-lapse imaging analyses revealed growing cytoplasmic aggregates in the transduced neuronal and glial cells, followed by collapse of the cell. The aggregates remained insoluble in culture media, consisted of sarkosyl-insoluble granular materials, and contained phosphorylated TDP-43. Moreover, the released aggregates were incorporated into neighboring neuronal cells, suggesting cell-to-cell spreading. The present study provides a novel tool for analyzing the detailed molecular mechanisms of TDP-43 proteinopathy in vitro. PMID:28599005
NASA Technical Reports Server (NTRS)
1997-01-01
Coryphaeus Software, founded in 1989 by former NASA electronic engineer Steve Lakowske, creates real-time 3D software. Designer's Workbench, the company flagship product, is a modeling and simulation tool for the development of both static and dynamic 3D databases. Other products soon followed. Activation, specifically designed for game developers, allows developers to play and test the 3D games before they commit to a target platform. Game publishers can shorten development time and prove the "playability" of the title, maximizing their chances of introducing a smash hit. Another product, EasyT, lets users create massive, realistic representation of Earth terrains that can be viewed and traversed in real time. Finally, EasyScene software control the actions among interactive objects within a virtual world. Coryphaeus products are used on Silican Graphics workstation and supercomputers to simulate real-world performance in synthetic environments. Customers include aerospace, aviation, architectural and engineering firms, game developers, and the entertainment industry.
Longhi, Giovanna; Fornili, Sandro L; Turco Liveri, Vincenzo
2015-07-07
Experimental investigations using mass spectrometry have established that surfactant molecules are able to form aggregates in the gas phase. However, there is no general consensus on the organization of these aggregates and how it depends on the aggregation number and surfactant molecular structure. In the present paper we investigate the structural organization of some surfactants in vacuo by molecular dynamics and well-tempered metadynamics simulations to widely explore the space of their possible conformations in vacuo. To study how the specific molecular features of such compounds affect their organization, we have considered as paradigmatic surfactants, the anionic single-chain sodium dodecyl sulfate (SDS), the anionic double-chain sodium bis(2-ethylhexyl) sulfosuccinate (AOT) and the zwitterionic single-chain dodecyl phosphatidyl choline (DPC) within a wide aggregation number range (from 5 to 100). We observe that for low aggregation numbers the aggregates show in vacuo the typical structure of reverse micelles, while for large aggregation numbers a variety of globular aggregates occur that are characterized by the coexistence of interlaced domains formed by the polar or ionic heads and by the alkyl chains of the surfactants. Well-tempered metadynamics simulations allows us to confirm that the structural organizations obtained after 50 ns of molecular dynamics simulations are practically the equilibrium ones. Similarities and differences of surfactant aggregates in vacuo and in apolar media are also discussed.
Aggregate Size Dependence of Amyloid Adsorption onto Charged Interfaces
2017-01-01
Amyloid aggregates are associated with a range of human neurodegenerative disorders, and it has been shown that neurotoxicity is dependent on aggregate size. Combining molecular simulation with analytical theory, a predictive model is proposed for the adsorption of amyloid aggregates onto oppositely charged surfaces, where the interaction is governed by an interplay between electrostatic attraction and entropic repulsion. Predictions are experimentally validated against quartz crystal microbalance–dissipation experiments of amyloid beta peptides and fragmented fibrils in the presence of a supported lipid bilayer. Assuming amyloids as rigid, elongated particles, we observe nonmonotonic trends for the extent of adsorption with respect to aggregate size and preferential adsorption of smaller aggregates over larger ones. Our findings describe a general phenomenon with implications for stiff polyions and rodlike particles that are electrostatically attracted to a surface. PMID:29284092
Pandey, R B; Farmer, B L
2014-11-07
Multi-scale aggregation to network formation of interacting proteins (H3.1) are examined by a knowledge-based coarse-grained Monte Carlo simulation as a function of temperature and the number of protein chains, i.e., the concentration of the protein. Self-assembly of corresponding homo-polymers of constitutive residues (Cys, Thr, and Glu) with extreme residue-residue interactions, i.e., attractive (Cys-Cys), neutral (Thr-Thr), and repulsive (Glu-Glu), are also studied for comparison with the native protein. Visual inspections show contrast and similarity in morphological evolutions of protein assembly, aggregation of small aggregates to a ramified network from low to high temperature with the aggregation of a Cys-polymer, and an entangled network of Glu and Thr polymers. Variations in mobility profiles of residues with the concentration of the protein suggest that the segmental characteristic of proteins is altered considerably by the self-assembly from that in its isolated state. The global motion of proteins and Cys polymer chains is enhanced by their interacting network at the low temperature where isolated chains remain quasi-static. Transition from globular to random coil transition, evidenced by the sharp variation in the radius of gyration, of an isolated protein is smeared due to self-assembly of interacting networks of many proteins. Scaling of the structure factor S(q) with the wave vector q provides estimates of effective dimension D of the mass distribution at multiple length scales in self-assembly. Crossover from solid aggregates (D ∼ 3) at low temperature to a ramified fibrous network (D ∼ 2) at high temperature is observed for the protein H3.1 and Cys polymers in contrast to little changes in mass distribution (D ∼ 1.6) of fibrous Glu- and Thr-chain configurations.
NASA Astrophysics Data System (ADS)
Pandey, R. B.; Farmer, B. L.
2014-11-01
Multi-scale aggregation to network formation of interacting proteins (H3.1) are examined by a knowledge-based coarse-grained Monte Carlo simulation as a function of temperature and the number of protein chains, i.e., the concentration of the protein. Self-assembly of corresponding homo-polymers of constitutive residues (Cys, Thr, and Glu) with extreme residue-residue interactions, i.e., attractive (Cys-Cys), neutral (Thr-Thr), and repulsive (Glu-Glu), are also studied for comparison with the native protein. Visual inspections show contrast and similarity in morphological evolutions of protein assembly, aggregation of small aggregates to a ramified network from low to high temperature with the aggregation of a Cys-polymer, and an entangled network of Glu and Thr polymers. Variations in mobility profiles of residues with the concentration of the protein suggest that the segmental characteristic of proteins is altered considerably by the self-assembly from that in its isolated state. The global motion of proteins and Cys polymer chains is enhanced by their interacting network at the low temperature where isolated chains remain quasi-static. Transition from globular to random coil transition, evidenced by the sharp variation in the radius of gyration, of an isolated protein is smeared due to self-assembly of interacting networks of many proteins. Scaling of the structure factor S(q) with the wave vector q provides estimates of effective dimension D of the mass distribution at multiple length scales in self-assembly. Crossover from solid aggregates (D ˜ 3) at low temperature to a ramified fibrous network (D ˜ 2) at high temperature is observed for the protein H3.1 and Cys polymers in contrast to little changes in mass distribution (D ˜ 1.6) of fibrous Glu- and Thr-chain configurations.
Agent Based Simulation Design for Aggregation and Disaggregation
2011-12-01
of law, no person shall be subject to a penalty for failing to comply with a collection of information if it does not display a currently valid OMB... PERSON a. REPORT unclassified b. ABSTRACT unclassified c. THIS PAGE unclassified Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std Z39-18...theo- retical analysis) finding conditions under which aggregation equations might be reasonably valid (requires theo- retical analysis
Kinetics of Aggregation with Choice
Ben-Naim, Eli; Krapivsky, Paul
2016-12-01
Here we generalize the ordinary aggregation process to allow for choice. In ordinary aggregation, two random clusters merge and form a larger aggregate. In our implementation of choice, a target cluster and two candidate clusters are randomly selected and the target cluster merges with the larger of the two candidate clusters.We study the long-time asymptotic behavior and find that as in ordinary aggregation, the size density adheres to the standard scaling form. However, aggregation with choice exhibits a number of different features. First, the density of the smallest clusters exhibits anomalous scaling. Second, both the small-size and the large-size tailsmore » of the density are overpopulated, at the expense of the density of moderate-size clusters. Finally, we also study the complementary case where the smaller candidate cluster participates in the aggregation process and find an abundance of moderate clusters at the expense of small and large clusters. Additionally, we investigate aggregation processes with choice among multiple candidate clusters and a symmetric implementation where the choice is between two pairs of clusters.« less
Surface and mass fractals in vapor-phase aggregates
NASA Astrophysics Data System (ADS)
Hurd, Alan J.; Schaefer, Dale W.; Martin, James E.
1987-03-01
Several types of fumed-silica aggregates with differing surface areas were studied over a wide range of spatial resolution by employing both light and neutron scattering. At intermediate length scales, between 100 and 1000 Å, the aggregates are mass fractals with Dm~=1.7-2.0, in basic agreement with simulations of aggregating clusters. At short length scales below 100 Å where the nature of the surfaces of the primary particles dominates the scattering, some of the samples appear to be fractally rough. In particular, a higher surface area seems to be correlated not with smaller primary particles in the aggregates, as previously assumed, but with fractally rough surfaces having Ds as high as 2.5. These may be the first materials discovered to have both mass and surface fractal structure.
Time-Variable Transit Time Distributions in the Hyporheic Zone of a Headwater Mountain Stream
NASA Astrophysics Data System (ADS)
Ward, Adam S.; Schmadel, Noah M.; Wondzell, Steven M.
2018-03-01
Exchange of water between streams and their hyporheic zones is known to be dynamic in response to hydrologic forcing, variable in space, and to exist in a framework with nested flow cells. The expected result of heterogeneous geomorphic setting, hydrologic forcing, and between-feature interaction is hyporheic transit times that are highly variable in both space and time. Transit time distributions (TTDs) are important as they reflect the potential for hyporheic processes to impact biogeochemical transformations and ecosystems. In this study we simulate time-variable transit time distributions based on dynamic vertical exchange in a headwater mountain stream with observed, heterogeneous step-pool morphology. Our simulations include hyporheic exchange over a 600 m river corridor reach driven by continuously observed, time-variable hydrologic conditions for more than 1 year. We found that spatial variability at an instance in time is typically larger than temporal variation for the reach. Furthermore, we found reach-scale TTDs were marginally variable under all but the most extreme hydrologic conditions, indicating that TTDs are highly transferable in time. Finally, we found that aggregation of annual variation in space and time into a "master TTD" reasonably represents most of the hydrologic dynamics simulated, suggesting that this aggregation approach may provide a relevant basis for scaling from features or short reaches to entire networks.
A look at construction aggregates production
Willett, Jason Christopher
2009-01-01
Construction aggregates are defined as the combination of crushed stone and construction sand and gravel. Aggregates are one of the most accessible natural resources on Earth and one of the fundamental building blocks of our society. They have been used from the earliest times of our civilization for a variety of applications that have increased in number and complexity with time and technological progress. Despite the relatively low but increasing unit value of its basic products, the construction aggregates industry is a major contributor to and an indicator of the economic well-being of the nation.
Estácio, Sílvia G.; Krobath, Heinrich; Vila-Viçosa, Diogo; Machuqueiro, Miguel; Shakhnovich, Eugene I.; Faísca, Patrícia F. N.
2014-01-01
A major component of ex vivo amyloid plaques of patients with dialysis-related amyloidosis (DRA) is a cleaved variant of β2-microglobulin (ΔN6) lacking the first six N-terminal residues. Here we perform a computational study on ΔN6, which provides clues to understand the amyloidogenicity of the full-length β2-microglobulin. Contrary to the wild-type form, ΔN6 is able to efficiently nucleate fibrillogenesis in vitro at physiological pH. This behavior is enhanced by a mild acidification of the medium such as that occurring in the synovial fluid of DRA patients. Results reported in this work, based on molecular simulations, indicate that deletion of the N-terminal hexapeptide triggers the formation of an intermediate state for folding and aggregation with an unstructured strand A and a native-like core. Strand A plays a pivotal role in aggregation by acting as a sticky hook in dimer assembly. This study further predicts that the detachment of strand A from the core is maximized at pH 6.2 resulting into higher aggregation efficiency. The structural mapping of the dimerization interface suggests that Tyr10, His13, Phe30 and His84 are hot-spot residues in ΔN6 amyloidogenesis. PMID:24809460
Global optimization of cholic acid aggregates
NASA Astrophysics Data System (ADS)
Jójárt, Balázs; Viskolcz, Béla; Poša, Mihalj; Fejer, Szilard N.
2014-04-01
In spite of recent investigations into the potential pharmaceutical importance of bile acids as drug carriers, the structure of bile acid aggregates is largely unknown. Here, we used global optimization techniques to find the lowest energy configurations for clusters composed between 2 and 10 cholate molecules, and evaluated the relative stabilities of the global minima. We found that the energetically most preferred geometries for small aggregates are in fact reverse micellar arrangements, and the classical micellar behaviour (efficient burial of hydrophobic parts) is achieved only in systems containing more than five cholate units. Hydrogen bonding plays a very important part in keeping together the monomers, and among the size range considered, the most stable structure was found to be the decamer, having 17 hydrogen bonds. Molecular dynamics simulations showed that the decamer has the lowest dissociation propensity among the studied aggregation numbers.
NASA Astrophysics Data System (ADS)
Lee, Shiann-Jong; Liu, Qinya; Tromp, Jeroen; Komatitsch, Dimitri; Liang, Wen-Tzong; Huang, Bor-Shouh
2014-06-01
We developed a Real-time Online earthquake Simulation system (ROS) to simulate regional earthquakes in Taiwan. The ROS uses a centroid moment tensor solution of seismic events from a Real-time Moment Tensor monitoring system (RMT), which provides all the point source parameters including the event origin time, hypocentral location, moment magnitude and focal mechanism within 2 min after the occurrence of an earthquake. Then, all of the source parameters are automatically forwarded to the ROS to perform an earthquake simulation, which is based on a spectral-element method (SEM). A new island-wide, high resolution SEM mesh model is developed for the whole Taiwan in this study. We have improved SEM mesh quality by introducing a thin high-resolution mesh layer near the surface to accommodate steep and rapidly varying topography. The mesh for the shallow sedimentary basin is adjusted to reflect its complex geometry and sharp lateral velocity contrasts. The grid resolution at the surface is about 545 m, which is sufficient to resolve topography and tomography data for simulations accurate up to 1.0 Hz. The ROS is also an infrastructural service, making online earthquake simulation feasible. Users can conduct their own earthquake simulation by providing a set of source parameters through the ROS webpage. For visualization, a ShakeMovie and ShakeMap are produced during the simulation. The time needed for one event is roughly 3 min for a 70 s ground motion simulation. The ROS is operated online at the Institute of Earth Sciences, Academia Sinica (http://ros.earth.sinica.edu.tw/). Our long-term goal for the ROS system is to contribute to public earth science outreach and to realize seismic ground motion prediction in real-time.
Version 4.0 of code Java for 3D simulation of the CCA model
NASA Astrophysics Data System (ADS)
Fan, Linyu; Liao, Jianwei; Zuo, Junsen; Zhang, Kebo; Li, Chao; Xiong, Hailing
2018-07-01
This paper presents a new version Java code for the three-dimensional simulation of Cluster-Cluster Aggregation (CCA) model to replace the previous version. Many redundant traverses of clusters-list in the program were totally avoided, so that the consumed simulation time is significantly reduced. In order to show the aggregation process in a more intuitive way, we have labeled different clusters with varied colors. Besides, a new function is added for outputting the particle's coordinates of aggregates in file to benefit coupling our model with other models.
Arnold, L.R.; Mladinich, C.S.; Langer, W.H.; Daniels, J.S.
2010-01-01
Land use in the South Platte River valley between the cities of Brighton and Fort Lupton, Colo., is undergoing change as urban areas expand, and the extent of aggregate mining in the Brighton-Fort Lupton area is increasing as the demand for aggregate grows in response to urban development. To improve understanding of land-use change and the potential effects of land-use change and aggregate mining on groundwater flow, the U.S. Geological Survey, in cooperation with the cities of Brighton and Fort Lupton, analyzed socioeconomic and land-use trends and constructed a numerical groundwater flow model of the South Platte alluvial aquifer in the Brighton-Fort Lupton area. The numerical groundwater flow model was used to simulate (1) steady-state hydrologic effects of predicted land-use conditions in 2020 and 2040, (2) transient cumulative hydrologic effects of the potential extent of reclaimed aggregate pits in 2020 and 2040, (3) transient hydrologic effects of actively dewatered aggregate pits, and (4) effects of different hypothetical pit spacings and configurations on groundwater levels. The SLEUTH (Slope, Land cover, Exclusion, Urbanization, Transportation, and Hillshade) urban-growth modeling program was used to predict the extent of urban area in 2020 and 2040. Wetlands in the Brighton-Fort Lupton area were mapped as part of the study, and mapped wetland locations and areas of riparian herbaceous vegetation previously mapped by the Colorado Division of Wildlife were compared to simulation results to indicate areas where wetlands or riparian herbaceous vegetation might be affected by groundwater-level changes resulting from land-use change or aggregate mining. Analysis of land-use conditions in 1957, 1977, and 2000 indicated that the general distribution of irrigated land and non-irrigated land remained similar from 1957 to 2000, but both land uses decreased as urban area increased. Urban area increased about 165 percent from 1957 to 1977 and about 56 percent from
Hempel, Judith; Fischer, Anja; Fischer, Monique; Högel, Josef; Bosy-Westphal, Anja; Carle, Reinhold; Schweiggert, Ralf M
2017-11-01
Carotenoid bioavailability from plant and animal food is highly variable depending on numerous factors such as the physical deposition form of carotenoids. As the carotenoid zeaxanthin is believed to play an important role in eye and brain health, we sought to compare the human bioavailability of an H-aggregated with that of a J-aggregated deposition form of zeaxanthin encapsulated into identical formulation matrices. A randomised two-way cross-over study with sixteen participants was designed to compare the post-prandial bioavailability of an H-aggregated zeaxanthin and a J-aggregated zeaxanthin dipalmitate formulation, both delivering 10 mg of free zeaxanthin. Carotenoid levels in TAG-rich lipoprotein fractions were analysed over 9·5 h after test meal consumption. Bioavailability from the J-aggregated formulation (AUC=55·9 nmol h/l) was 23 % higher than from the H-aggregated one (AUC=45·5 nmol h/l), although being only marginally significant (P=0·064). Furthermore, the same formulations were subjected to an internationally recognised in vitro digestion protocol to reveal potential strengths and weaknesses of simulated digestions. In agreement with our human study, liberation of zeaxanthin from the J-aggregated formulation into the simulated duodenal fluids was superior to that from the H-aggregated form. However, micellization rate (bioaccessibility) of the J-aggregated zeaxanthin dipalmitate was lower than that of the H-aggregated zeaxanthin, being contradictory to our in vivo results. An insufficient ester cleavage during simulated digestion was suggested to be the root cause for these observations. In brief, combining our in vitro and in vivo observations, the effect of the different aggregation forms on human bioavailability was lower than expected.
Toward real-time Monte Carlo simulation using a commercial cloud computing infrastructure.
Wang, Henry; Ma, Yunzhi; Pratx, Guillem; Xing, Lei
2011-09-07
Monte Carlo (MC) methods are the gold standard for modeling photon and electron transport in a heterogeneous medium; however, their computational cost prohibits their routine use in the clinic. Cloud computing, wherein computing resources are allocated on-demand from a third party, is a new approach for high performance computing and is implemented to perform ultra-fast MC calculation in radiation therapy. We deployed the EGS5 MC package in a commercial cloud environment. Launched from a single local computer with Internet access, a Python script allocates a remote virtual cluster. A handshaking protocol designates master and worker nodes. The EGS5 binaries and the simulation data are initially loaded onto the master node. The simulation is then distributed among independent worker nodes via the message passing interface, and the results aggregated on the local computer for display and data analysis. The described approach is evaluated for pencil beams and broad beams of high-energy electrons and photons. The output of cloud-based MC simulation is identical to that produced by single-threaded implementation. For 1 million electrons, a simulation that takes 2.58 h on a local computer can be executed in 3.3 min on the cloud with 100 nodes, a 47× speed-up. Simulation time scales inversely with the number of parallel nodes. The parallelization overhead is also negligible for large simulations. Cloud computing represents one of the most important recent advances in supercomputing technology and provides a promising platform for substantially improved MC simulation. In addition to the significant speed up, cloud computing builds a layer of abstraction for high performance parallel computing, which may change the way dose calculations are performed and radiation treatment plans are completed.
Toward real-time Monte Carlo simulation using a commercial cloud computing infrastructure
NASA Astrophysics Data System (ADS)
Wang, Henry; Ma, Yunzhi; Pratx, Guillem; Xing, Lei
2011-09-01
Monte Carlo (MC) methods are the gold standard for modeling photon and electron transport in a heterogeneous medium; however, their computational cost prohibits their routine use in the clinic. Cloud computing, wherein computing resources are allocated on-demand from a third party, is a new approach for high performance computing and is implemented to perform ultra-fast MC calculation in radiation therapy. We deployed the EGS5 MC package in a commercial cloud environment. Launched from a single local computer with Internet access, a Python script allocates a remote virtual cluster. A handshaking protocol designates master and worker nodes. The EGS5 binaries and the simulation data are initially loaded onto the master node. The simulation is then distributed among independent worker nodes via the message passing interface, and the results aggregated on the local computer for display and data analysis. The described approach is evaluated for pencil beams and broad beams of high-energy electrons and photons. The output of cloud-based MC simulation is identical to that produced by single-threaded implementation. For 1 million electrons, a simulation that takes 2.58 h on a local computer can be executed in 3.3 min on the cloud with 100 nodes, a 47× speed-up. Simulation time scales inversely with the number of parallel nodes. The parallelization overhead is also negligible for large simulations. Cloud computing represents one of the most important recent advances in supercomputing technology and provides a promising platform for substantially improved MC simulation. In addition to the significant speed up, cloud computing builds a layer of abstraction for high performance parallel computing, which may change the way dose calculations are performed and radiation treatment plans are completed. This work was presented in part at the 2010 Annual Meeting of the American Association of Physicists in Medicine (AAPM), Philadelphia, PA.
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.
NASA Astrophysics Data System (ADS)
Enzenhoefer, R.; Binning, P. J.; Nowak, W.
2015-09-01
Risk is often defined as the product of probability, vulnerability and value. Drinking water supply from groundwater abstraction is often at risk due to multiple hazardous land use activities in the well catchment. Each hazard might or might not introduce contaminants into the subsurface at any point in time, which then affects the pumped quality upon transport through the aquifer. In such situations, estimating the overall risk is not trivial, and three key questions emerge: (1) How to aggregate the impacts from different contaminants and spill locations to an overall, cumulative impact on the value at risk? (2) How to properly account for the stochastic nature of spill events when converting the aggregated impact to a risk estimate? (3) How will the overall risk and subsequent decision making depend on stakeholder objectives, where stakeholder objectives refer to the values at risk, risk attitudes and risk metrics that can vary between stakeholders. In this study, we provide a STakeholder-Objective Risk Model (STORM) for assessing the total aggregated risk. Or concept is a quantitative, probabilistic and modular framework for simulation-based risk estimation. It rests on the source-pathway-receptor concept, mass-discharge-based aggregation of stochastically occuring spill events, accounts for uncertainties in the involved flow and transport models through Monte Carlo simulation, and can address different stakeholder objectives. We illustrate the application of STORM in a numerical test case inspired by a German drinking water catchment. As one may expect, the results depend strongly on the chosen stakeholder objectives, but they are equally sensitive to different approaches for risk aggregation across different hazards, contaminant types, and over time.
Molecular dynamics analysis of the aggregation propensity of polyglutamine segments
Wen, Jingran; Scoles, Daniel R.
2017-01-01
Protein misfolding and aggregation is a pathogenic feature shared among at least ten polyglutamine (polyQ) neurodegenerative diseases. While solvent-solution interaction is a key factor driving protein folding and aggregation, the solvation properties of expanded polyQ tracts are not well understood. By using GPU-enabled all-atom molecular dynamics simulations of polyQ monomers in an explicit solvent environment, this study shows that solvent-polyQ interaction propensity decreases as the lengths of polyQ tract increases. This study finds a predominance in long-distance interactions between residues far apart in polyQ sequences with longer polyQ segments, that leads to significant conformational differences. This study also indicates that large loops, comprised of parallel β-structures, appear in long polyQ tracts and present new aggregation building blocks with aggregation driven by long-distance intra-polyQ interactions. Finally, consistent with previous observations using coarse-grain simulations, this study demonstrates that there is a gain in the aggregation propensity with increased polyQ length, and that this gain is correlated with decreasing ability of solvent-polyQ interaction. These results suggest the modulation of solvent-polyQ interactions as a possible therapeutic strategy for treating polyQ diseases. PMID:28542401
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.
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.
Molecular dynamics studies of protein folding and aggregation
NASA Astrophysics Data System (ADS)
Ding, Feng
This thesis applies molecular dynamics simulations and statistical mechanics to study: (i) protein folding; and (ii) protein aggregation. Most small proteins fold into their native states via a first-order-like phase transition with a major free energy barrier between the folded and unfolded states. A set of protein conformations corresponding to the free energy barrier, Delta G >> kBT, are the folding transition state ensemble (TSE). Due to their evasive nature, TSE conformations are hard to capture (probability ∝ exp(-DeltaG/k BT)) and characterize. A coarse-grained discrete molecular dynamics model with realistic steric constraints is constructed to reproduce the experimentally observed two-state folding thermodynamics. A kinetic approach is proposed to identify the folding TSE. A specific set of contacts, common to the TSE conformations, is identified as the folding nuclei which are necessary to be formed in order for the protein to fold. Interestingly, the amino acids at the site of the identified folding nuclei are highly conserved for homologous proteins sharing the same structures. Such conservation suggests that amino acids that are important for folding kinetics are under selective pressure to be preserved during the course of molecular evolution. In addition, studies of the conformations close to the transition states uncover the importance of topology in the construction of order parameter for protein folding transition. Misfolded proteins often form insoluble aggregates, amyloid fibrils, that deposit in the extracellular space and lead to a type of disease known as amyloidosis. Due to its insoluble and non-crystalline nature, the aggregation structure and, thus the aggregation mechanism, has yet to be uncovered. Discrete molecular dynamics studies reveal an aggregate structure with the same structural signatures as in experimental observations and show a nucleation aggregation scenario. The simulations also suggest a generic aggregation mechanism
Veloso, D
2003-01-01
Many in vitro studies have shown that activation of prekallikrein (PK) to kallikrein (KAL) in normal plasma triggers rapid activation of the coagulation cascade. In agreement, the coagulation activation is impaired in PK-deficient plasma. Paradoxically, PK-deficient patients show a tendency to thrombosis. To investigate the discrepancy between the in vitro and in vivo findings, we analyzed the effect of KAL on the rate of platelet aggregation. For this research, physiologic concentrations of washed human platelets were incubated for 5 and/or 10 min with approximately 2.2 to 88 nM human plasma KAL (< 1/100 to approximately 1/3 of PK concentrations in plasma) prior to the addition of high concentrations of alpha-thrombin (54 nM) or fibrinogen plus ADP. KAL concentrations were arbitrarily selected on the assumption that concentrations of free KAL (the enzymatically active species) were minute in normal plasma and higher when KAL production was enhanced, and/or inhibitors were depleted. Full platelet aggregation was that seen in the absence of KAL or PK. Inhibition of platelet aggregation stimulated by thrombin was markedly increased with increased KAL concentrations and incubation times. The degree of inhibition by KAL was smaller when ADP was the agonist. The data suggest that KAL may play a role in the modulation of platelet aggregation in vivo under normal conditions as well as when prolonged, high concentrations of KAL occur in blood. The data may also help to explain the intriguing observation that PK-deficient patients show a tendency to thrombotic episodes and myocardial infarction whereas in vitro assays predict bleeding.
Convective aggregation in idealised models and realistic equatorial cases
NASA Astrophysics Data System (ADS)
Holloway, Chris
2015-04-01
Idealised explicit convection simulations of the Met Office Unified Model are shown to exhibit spontaneous self-aggregation in radiative-convective equilibrium, as seen previously in other models in several recent studies. This self-aggregation is linked to feedbacks between radiation, surface fluxes, and convection, and the organization is intimately related to the evolution of the column water vapour (CWV) field. To investigate the relevance of this behaviour to the real world, these idealized simulations are compared with five 15-day cases of real organized convection in the tropics, including multiple simulations of each case testing sensitivities of the convective organization and mean states to interactive radiation, interactive surface fluxes, and evaporation of rain. Despite similar large-scale forcing via lateral boundary conditions, systematic differences in mean CWV, CWV distribution shape, and the length scale of CWV features are found between the different sensitivity runs, showing that there are at least some similarities in sensitivities to these feedbacks in both idealized and realistic simulations.
Convective aggregation in idealised models and realistic equatorial cases
NASA Astrophysics Data System (ADS)
Holloway, C. E.
2014-12-01
Idealised explicit convection simulations of the Met Office Unified Model are shown to exhibit spontaneous self-aggregation in radiative-convective equilibrium, as seen previously in other models in several recent studies. This self-aggregation is linked to feedbacks between radiation, surface fluxes, and convection, and the organization is intimately related to the evolution of the column water vapor (CWV) field. To investigate the relevance of this behavior to the real world, these idealized simulations are compared with five 15-day cases of real organized convection in the tropics, including multiple simulations of each case testing sensitivities of the convective organization and mean states to interactive radiation, interactive surface fluxes, and evaporation of rain. Despite similar large-scale forcing via lateral boundary conditions, systematic differences in mean CWV, CWV distribution shape, and the length scale of CWV features are found between the different sensitivity runs, showing that there are at least some similarities in sensitivities to these feedbacks in both idealized and realistic simulations.
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.
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.
Fractal-like Tar Ball Aggregates from Wildfire Smoke
DOE Office of Scientific and Technical Information (OSTI.GOV)
Girotto, Giulia; China, Swarup; Bhandari, Janarjan
Tar balls are atmospheric particles abundant in slightly aged biomass burning smoke and have a significant, but highly uncertain, role on Earth's radiative balance. Tar balls are typically detected using electron microscopy; they are resistant to the electron beam, and generally, they are observed as individual spheres. Here, we report new observations of a significant fraction of tar ball aggregates (~27% by number) from samples collected in a plume of the Whitewater-Baldy Complex fire in New Mexico. The structure of these aggregates is fractal-like and follows a scale invariant power law similar to that of soot particles, despite the considerablymore » larger size and smaller number of monomers. We also present observations of tar ball aggregates from four other geographical locations, including from a remote high elevation site in the North Atlantic Ocean. Aggregation affects the particle optical properties and therefore, their climatic impact. We performed numerical simulations based on the observed morphology and estimated the effects of aggregation on the tar balls optical properties. We find that aggregation can enhance single scattering albedo by up to 41%.« less
Exciton Level Structure and Dynamics in Tubular Porphyrin Aggregates
DOE Office of Scientific and Technical Information (OSTI.GOV)
Wan, Yan; Stradomska, Anna; Fong, Sarah
2014-10-30
We present an account of the optical properties of the Frenkel excitons in self-assembled porphyrin tubular aggregates that represent an analog to natural photosynthetic antennae. Using a combination of ultrafast optical spectroscopy and stochastic exciton modeling, we address both linear and nonlinear exciton absorption, relaxation pathways, and the role of disorder. The static disorder-dominated absorption and fluorescence line widths show little temperature dependence for the lowest excitons (Q band), which we successfully simulate using a model of exciton scattering on acoustic phonons in the host matrix. Temperature-dependent transient absorption of and fluorescence from the excitons in the tubular aggregates aremore » marked by nonexponential decays with time scales ranging from a few picoseconds to a few nanoseconds, reflecting complex relaxation mechanisms. Combined experimental and theoretical investigations indicate that nonradiative pathways induced by traps and defects dominate the relaxation of excitons in the tubular aggregates. We model the pumpprobe spectra and ascribe the excited-state absorption to transitions from one-exciton states to a manifold of mixed one- and two-exciton states. Our results demonstrate that while the delocalized Frenkel excitons (over 208 (1036) molecules for the optically dominant excitons in the Q (B) band) resulting from strong intermolecular coupling in these aggregates could potentially facilitate efficient energy transfer, fast relaxation due to defects and disorder probably present a major limitation for exciton transport over large distances.« less
Early-stage aggregation in three-dimensional charged granular gas.
Singh, Chamkor; Mazza, Marco G
2018-02-01
Neutral grains made of the same dielectric material can attain considerable charges due to collisions and generate long-range interactions. We perform molecular dynamic simulations in three dimensions for a dilute, freely cooling granular gas of viscoelastic particles that exchange charges during collisions. As compared to the case of clustering of viscoelastic particles solely due to dissipation, we find that the electrostatic interactions due to collisional charging alter the characteristic size, morphology, and growth rate of the clusters. The average cluster size grows with time as a power law, whose exponent is relatively larger in the charged gas than the neutral case. The growth of the average cluster size is found to be independent of the ratio of characteristic Coulomb to kinetic energy, or equivalently, of the typical Bjerrum length. However, this ratio alters the crossover time of the growth. Both simulations and mean-field calculations based on Smoluchowski's equation suggest that a suppression of particle diffusion due to the electrostatic interactions helps in the aggregation process.
Early-stage aggregation in three-dimensional charged granular gas
NASA Astrophysics Data System (ADS)
Singh, Chamkor; Mazza, Marco G.
2018-02-01
Neutral grains made of the same dielectric material can attain considerable charges due to collisions and generate long-range interactions. We perform molecular dynamic simulations in three dimensions for a dilute, freely cooling granular gas of viscoelastic particles that exchange charges during collisions. As compared to the case of clustering of viscoelastic particles solely due to dissipation, we find that the electrostatic interactions due to collisional charging alter the characteristic size, morphology, and growth rate of the clusters. The average cluster size grows with time as a power law, whose exponent is relatively larger in the charged gas than the neutral case. The growth of the average cluster size is found to be independent of the ratio of characteristic Coulomb to kinetic energy, or equivalently, of the typical Bjerrum length. However, this ratio alters the crossover time of the growth. Both simulations and mean-field calculations based on Smoluchowski's equation suggest that a suppression of particle diffusion due to the electrostatic interactions helps in the aggregation process.
Aggregates and Superaggregates of Soot with Four Distinct Fractal Morphologies
NASA Technical Reports Server (NTRS)
Sorensen, C. M.; Kim, W.; Fry, D.; Chakrabarti, A.
2004-01-01
Soot formed in laminar diffusion flames of heavily sooting fuels evolves through four distinct growth stages which give rise to four distinct aggregate fractal morphologies. These results were inferred from large and small angle static light scattering from the flames, microphotography of the flames, and analysis of soot sampled from the flames. The growth stages occur approximately over four successive orders of magnitude in aggregate size. Comparison to computer simulations suggests that these four growth stages involve either diffusion limited cluster aggregation or percolation in either three or two dimensions.
Cooperative structural transitions in amyloid-like aggregation
NASA Astrophysics Data System (ADS)
Steckmann, Timothy; Bhandari, Yuba R.; Chapagain, Prem P.; Gerstman, Bernard S.
2017-04-01
Amyloid fibril aggregation is associated with several horrific diseases such as Alzheimer's, Creutzfeld-Jacob, diabetes, Parkinson's, and others. Although proteins that undergo aggregation vary widely in their primary structure, they all produce a cross-β motif with the proteins in β-strand conformations perpendicular to the fibril axis. The process of amyloid aggregation involves forming myriad different metastable intermediate aggregates. To better understand the molecular basis of the protein structural transitions and aggregation, we report on molecular dynamics (MD) computational studies on the formation of amyloid protofibrillar structures in the small model protein ccβ, which undergoes many of the structural transitions of the larger, naturally occurring amyloid forming proteins. Two different structural transition processes involving hydrogen bonds are observed for aggregation into fibrils: the breaking of intrachain hydrogen bonds to allow β-hairpin proteins to straighten, and the subsequent formation of interchain H-bonds during aggregation into amyloid fibrils. For our MD simulations, we found that the temperature dependence of these two different structural transition processes results in the existence of a temperature window that the ccβ protein experiences during the process of forming protofibrillar structures. This temperature dependence allows us to investigate the dynamics on a molecular level. We report on the thermodynamics and cooperativity of the transformations. The structural transitions that occurred in a specific temperature window for ccβ in our investigations may also occur in other amyloid forming proteins but with biochemical parameters controlling the dynamics rather than temperature.
The Conformation and Aggregation of Proline-Rich Surfactant-Like Peptides.
Hamley, Ian W; Castelletto, Valeria; Dehsorkhi, Ashkan; Torras, Juan; Aleman, Carlos; Portnaya, Irina; Danino, Dganit
2018-02-15
The secondary structure of proline-rich surfactant-like peptides is examined for the first time and is found to be influenced by charged end groups in peptides P 6 K, P 6 E, and KP 6 E and an equimolar mixture of P 6 K and P 6 E. The peptides exhibit a conformational transition from unordered to polyproline II (PPII) above a critical concentration, detected from circular dichroism (CD) measurements and unexpectedly from fluorescence dye probe measurements. Isothermal titration calorimetry (ITC) measurements provided the Gibbs energies of hydration of P 6 K and P 6 E, which correspond essentially to the hydration energies of the terminal charged residues. A detailed analysis of peptide conformation for these peptides was performed using density functional theory calculations, and this was used as a basis for hybrid quantum mechanics/molecular mechanics molecular dynamics (QM/MM MD) simulations. Quantum mechanics simulations in implicit water show both peptides (and their 1:1 mixture) exhibit PPII conformations. However, hybrid QM/MM MD simulations suggest that some deviations from this conformation are present for P 6 K and P 6 E in peptide bonds close to the charged residue, whereas in the 1:1 mixture a PPII structure is observed. Finally, aggregation of the peptides was investigated using replica exchange molecular dynamics simulations. These reveal a tendency for the average aggregate size (as measured by the radius of gyration) to increase with increasing temperature, which is especially marked for P 6 K, although the fraction of the most populated clusters is larger for P 6 E.
Exploring the early steps of amyloid peptide aggregation by computers.
Mousseau, Normand; Derreumaux, Philippe
2005-11-01
The assembly of normally soluble proteins into amyloid fibrils is a hallmark of neurodegenerative diseases. Because protein aggregation is very complex, involving a variety of oligomeric metastable intermediates, the detailed aggregation paths and structural characterization of the intermediates remain to be determined. Yet, there is strong evidence that these oligomers, which form early in the process of fibrillogenesis, are cytotoxic. In this paper, we review our current understanding of the underlying factors that promote the aggregation of peptides into amyloid fibrils. We focus here on the structural and dynamic aspects of the aggregation as observed in state-of-the-art computer simulations of amyloid-forming peptides with an emphasis on the activation-relaxation technique.
Connell, Jodi L; Kim, Jiyeon; Shear, Jason B; Bard, Allen J; Whiteley, Marvin
2014-12-23
Microbes frequently live in nature as small, densely packed aggregates containing ∼10(1)-10(5) cells. These aggregates not only display distinct phenotypes, including resistance to antibiotics, but also, serve as building blocks for larger biofilm communities. Aggregates within these larger communities display nonrandom spatial organization, and recent evidence indicates that this spatial organization is critical for fitness. Studying single aggregates as well as spatially organized aggregates remains challenging because of the technical difficulties associated with manipulating small populations. Micro-3D printing is a lithographic technique capable of creating aggregates in situ by printing protein-based walls around individual cells or small populations. This 3D-printing strategy can organize bacteria in complex arrangements to investigate how spatial and environmental parameters influence social behaviors. Here, we combined micro-3D printing and scanning electrochemical microscopy (SECM) to probe quorum sensing (QS)-mediated communication in the bacterium Pseudomonas aeruginosa. Our results reveal that QS-dependent behaviors are observed within aggregates as small as 500 cells; however, aggregates larger than 2,000 bacteria are required to stimulate QS in neighboring aggregates positioned 8 μm away. These studies provide a powerful system to analyze the impact of spatial organization and aggregate size on microbial behaviors.
Biological framework for soil aggregation: Implications for ecological functions.
NASA Astrophysics Data System (ADS)
Ghezzehei, Teamrat; Or, Dani
2016-04-01
Soil aggregation is heuristically understood as agglomeration of primary particles bound together by biotic and abiotic cementing agents. The organization of aggregates is believed to be hierarchical in nature; whereby primary particles bond together to form secondary particles and subsequently merge to form larger aggregates. Soil aggregates are not permanent structures, they continuously change in response to internal and external forces and other drivers, including moisture, capillary pressure, temperature, biological activity, and human disturbances. Soil aggregation processes and the resulting functionality span multiple spatial and temporal scales. The intertwined biological and physical nature of soil aggregation, and the time scales involved precluded a universally applicable and quantifiable framework for characterizing the nature and function of soil aggregation. We introduce a biophysical framework of soil aggregation that considers the various modes and factors of the genesis, maturation and degradation of soil aggregates including wetting/drying cycles, soil mechanical processes, biological activity and the nature of primary soil particles. The framework attempts to disentangle mechanical (compaction and soil fragmentation) from in-situ biophysical aggregation and provides a consistent description of aggregate size, hierarchical organization, and life time. It also enables quantitative description of biotic and abiotic functions of soil aggregates including diffusion and storage of mass and energy as well as role of aggregates as hot spots of nutrient accumulation, biodiversity, and biogeochemical cycles.
Trust-aware recommendation for improving aggregate diversity
NASA Astrophysics Data System (ADS)
Liu, Haifeng; Bai, Xiaomei; Yang, Zhuo; Tolba, Amr; Xia, Feng
2015-10-01
Recommender systems are becoming increasingly important and prevalent because of the ability of solving information overload. In recent years, researchers are paying increasing attention to aggregate diversity as a key metric beyond accuracy, because improving aggregate recommendation diversity may increase long tails and sales diversity. Trust is often used to improve recommendation accuracy. However, how to utilize trust to improve aggregate recommendation diversity is unexplored. In this paper, we focus on solving this problem and propose a novel trust-aware recommendation method by incorporating time factor into similarity computation. The rationale underlying the proposed method is that, trustees with later creation time of trust relation can bring more diverse items to recommend to their trustors than other trustees with earlier creation time of trust relation. Through relevant experiments on publicly available dataset, we demonstrate that the proposed method outperforms the baseline method in terms of aggregate diversity while maintaining almost the same recall.
NASA Astrophysics Data System (ADS)
Nasehnejad, Maryam; Nabiyouni, G.; Gholipour Shahraki, Mehran
2018-03-01
In this study a 3D multi-particle diffusion limited aggregation method is employed to simulate growth of rough surfaces with fractal behavior in electrodeposition process. A deposition model is used in which the radial motion of the particles with probability P, competes with random motions with probability 1 - P. Thin films growth is simulated for different values of probability P (related to the electric field) and thickness of the layer(related to the number of deposited particles). The influence of these parameters on morphology, kinetic of roughening and the fractal dimension of the simulated surfaces has been investigated. The results show that the surface roughness increases with increasing the deposition time and scaling exponents exhibit a complex behavior which is called as anomalous scaling. It seems that in electrodeposition process, radial motion of the particles toward the growing seeds may be an important mechanism leading to anomalous scaling. The results also indicate that the larger values of probability P, results in smoother topography with more densely packed structure. We have suggested a dynamic scaling ansatz for interface width has a function of deposition time, scan length and probability. Two different methods are employed to evaluate the fractal dimension of the simulated surfaces which are "cube counting" and "roughness" methods. The results of both methods show that by increasing the probability P or decreasing the deposition time, the fractal dimension of the simulated surfaces is increased. All gained values for fractal dimensions are close to 2.5 in the diffusion limited aggregation model.
NASA Astrophysics Data System (ADS)
Yuan, Xiang-Ai; Wen, Jin; Zheng, Dong; Ma, Jing
2018-04-01
This Review highlights the structure/property relationship underlying the morphology modulation through various factors towards the exploration of light-absorbing materials for efficient utilisation of solar power. Theoretical study using a combination of molecular dynamics imulations and the time-dependent density functional theory demonstrated that the planarity plays an important role in tuning spectral properties of oligomer aggregates. The aggregation-induced blue-shift in absorption spectra of oligothiophenes and the red-shift for oligofluorenols were rationalised in a unified way from the reduced (and increased) content of planar conformations in molecular aggregates. The planarity versus non-planarity of oligomers can be modulated by introduction of alkyl side chain or steric bulky substituents. The substitution with various groups in the ortho-position of azobenzene leads to the distorted backbone, breaking symmetry, and hence the red-shift in spectra, expanding the application in biological systems with visible light absorption. The donor-acceptor substituent groups in conjugated oligomers can increase the degree of planarity, electron delocalisation and polarisation, and charge separation, giving rise to the red-shift in spectra and enhancement in polarisability and charge mobility for device applications. The solvent dependent and pH-sensitive properties and intramolecular hydrogen bonds also caused the shift of absorption spectra with the appearance of planar conformers.
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.
Chapman, Kent; Favaloro, Emmanuel J
2018-05-01
The Multiplate is a popular instrument that measures platelet function using whole blood. Potentially considered a point of care instrument, it is also used by hemostasis laboratories. The instrument is usually utilized to assess antiplatelet medication or as a screen of platelet function. According to the manufacturer, testing should be performed within 0.5-3 hours of blood collection, and preferably using manufacturer provided hirudin tubes. We report time-associated reduction in platelet aggregation using the Multiplate and hirudin blood collection tubes, for all the major employed agonists. Blood for Multiplate analysis was collected into manufacturer supplied hirudin tubes, and 21 consecutive samples assessed using manufacturer supplied agonists (ADP, arachidonic acid, TRAP, collagen and ristocetin), at several time-points post-sample collection within the recommended test time period. Blood was also collected into EDTA as a reference method for platelet counts, with samples collected into sodium citrate and hirudin used for comparative counts. All platelet agonists showed a diminution of response with time. Depending on the agonist, the reduction caused 5-20% and 22-47% of responses initially in the normal reference range to fall below the reference range at 120min and 180min, respectively. Considering any agonist, 35% and 67% of initially "normal" responses became 'abnormal' at 120 min and 180 min, respectively. Platelet counts showed generally minimal changes in EDTA blood, but were markedly reduced over time in both citrate and hirudin blood, with up to 40% and 60% reduction, respectively, at 240 min. The presence of platelet clumping (micro-aggregate formation) was also observed in a time dependent manner, especially for hirudin. In conclusion, considering any platelet agonist, around two-thirds of samples can, within the recommended 0.5-3 hour testing window post-blood collection, yield a reduction in platelet aggregation that may lead to a change in
Tensile strength and fracture of cemented granular aggregates.
Affes, R; Delenne, J-Y; Monerie, Y; Radjaï, F; Topin, V
2012-11-01
Cemented granular aggregates include a broad class of geomaterials such as sedimentary rocks and some biomaterials such as the wheat endosperm. We present a 3D lattice element method for the simulation of such materials, modeled as a jammed assembly of particles bound together by a matrix partially filling the interstitial space. From extensive simulation data, we analyze the mechanical properties of aggregates subjected to tensile loading as a function of matrix volume fraction and particle-matrix adhesion. We observe a linear elastic behavior followed by a brutal failure along a fracture surface. The effective stiffness before failure increases almost linearly with the matrix volume fraction. We show that the tensile strength of the aggregates increases with both the increasing tensile strength at the particle-matrix interface and decreasing stress concentration as a function of matrix volume fraction. The proportion of broken bonds in the particle phase reveals a range of values of the particle-matrix adhesion and matrix volume fraction for which the cracks bypass the particles and hence no particle damage occurs. This limit is shown to depend on the relative toughness of the particle-matrix interface with respect to the particles.
Self-folding and aggregation of amyloid nanofibrils
NASA Astrophysics Data System (ADS)
Paparcone, Raffaella; Cranford, Steven W.; Buehler, Markus J.
2011-04-01
Amyloids are highly organized protein filaments, rich in β-sheet secondary structures that self-assemble to form dense plaques in brain tissues affected by severe neurodegenerative disorders (e.g. Alzheimer's Disease). Identified as natural functional materials in bacteria, in addition to their remarkable mechanical properties, amyloids have also been proposed as a platform for novel biomaterials in nanotechnology applications including nanowires, liquid crystals, scaffolds and thin films. Despite recent progress in understanding amyloid structure and behavior, the latent self-assembly mechanism and the underlying adhesion forces that drive the aggregation process remain poorly understood. On the basis of previous full atomistic simulations, here we report a simple coarse-grain model to analyze the competition between adhesive forces and elastic deformation of amyloid fibrils. We use simple model system to investigate self-assembly mechanisms of fibrils, focused on the formation of self-folded nanorackets and nanorings, and thereby address a critical issue in linking the biochemical (Angstrom) to micrometre scales relevant for larger-scale states of functional amyloid materials. We investigate the effect of varying the interfibril adhesion energy on the structure and stability of self-folded nanorackets and nanorings and demonstrate that these aggregated amyloid fibrils are stable in such states even when the fibril-fibril interaction is relatively weak, given that the constituting amyloid fibril length exceeds a critical fibril length-scale of several hundred nanometres. We further present a simple approach to directly determine the interfibril adhesion strength from geometric measures. In addition to providing insight into the physics of aggregation of amyloid fibrils our model enables the analysis of large-scale amyloid plaques and presents a new method for the estimation and engineering of the adhesive forces responsible of the self-assembly process of
7 CFR 1.6 - Aggregating requests.
Code of Federal Regulations, 2011 CFR
2011-01-01
... 7 Agriculture 1 2011-01-01 2011-01-01 false Aggregating requests. 1.6 Section 1.6 Agriculture Office of the Secretary of Agriculture ADMINISTRATIVE REGULATIONS Official Records § 1.6 Aggregating... be considered in determining whether such a belief would be reasonable is the brevity of the time...
7 CFR 1.6 - Aggregating requests.
Code of Federal Regulations, 2010 CFR
2010-01-01
... 7 Agriculture 1 2010-01-01 2010-01-01 false Aggregating requests. 1.6 Section 1.6 Agriculture Office of the Secretary of Agriculture ADMINISTRATIVE REGULATIONS Official Records § 1.6 Aggregating... be considered in determining whether such a belief would be reasonable is the brevity of the time...
7 CFR 1.6 - Aggregating requests.
Code of Federal Regulations, 2012 CFR
2012-01-01
... 7 Agriculture 1 2012-01-01 2012-01-01 false Aggregating requests. 1.6 Section 1.6 Agriculture Office of the Secretary of Agriculture ADMINISTRATIVE REGULATIONS Official Records § 1.6 Aggregating... be considered in determining whether such a belief would be reasonable is the brevity of the time...
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
A Secure-Enhanced Data Aggregation Based on ECC in Wireless Sensor Networks
Zhou, Qiang; Yang, Geng; He, Liwen
2014-01-01
Data aggregation is an important technique for reducing the energy consumption of sensor nodes in wireless sensor networks (WSNs). However, compromised aggregators may forge false values as the aggregated results of their child nodes in order to conduct stealthy attacks or steal other nodes' privacy. This paper proposes a Secure-Enhanced Data Aggregation based on Elliptic Curve Cryptography (SEDA-ECC). The design of SEDA-ECC is based on the principles of privacy homomorphic encryption (PH) and divide-and-conquer. An aggregation tree disjoint method is first adopted to divide the tree into three subtrees of similar sizes, and a PH-based aggregation is performed in each subtree to generate an aggregated subtree result. Then the forged result can be identified by the base station (BS) by comparing the aggregated count value. Finally, the aggregated result can be calculated by the BS according to the remaining results that have not been forged. Extensive analysis and simulations show that SEDA-ECC can achieve the highest security level on the aggregated result with appropriate energy consumption compared with other asymmetric schemes. PMID:24732099
NASA Astrophysics Data System (ADS)
Magno, Andrea; Pellarin, Riccardo; Caflisch, Amedeo
Amyloid fibrils are ordered polypeptide aggregates that have been implicated in several neurodegenerative pathologies, such as Alzheimer's, Parkinson's, Huntington's, and prion diseases, [1, 2] and, more recently, also in biological functionalities. [3, 4, 5] These findings have paved the way for a wide range of experimental and computational studies aimed at understanding the details of the fibril-formation mechanism. Computer simulations using low-resolution models, which employ a simplified representation of protein geometry and energetics, have provided insights into the basic physical principles underlying protein aggregation in general [6, 7, 8] and ordered amyloid aggregation. [9, 10, 11, 12, 13, 14, 15] For example, Dokholyan and coworkers have used the Discrete Molecular Dynamics method [16, 17] to shed light on the mechanisms of protein oligomerization [18] and the conformational changes that take place in proteins before the aggregation onset. [19, 20] One challenging observation, which is difficult to observe by computer simulations, is the wide range of aggregation scenarios emerging from a variety of biophysical measurements. [21, 22] Atomistic models have been employed to study the conformational space of amyloidogenic polypeptides in the monomeric state, [23, 24, 25] the very initial steps of amyloid formation, [26, 27, 28, 29, 30, 31, 32] and the structural stability of fibril models. [33, 34, 35) However, all-atom simulations of the kinetics of fibril formation are beyond what can be done with modern computers.
A Scheme to Smooth Aggregated Traffic from Sensors with Periodic Reports
Oh, Sungmin; Jang, Ju Wook
2017-01-01
The possibility of smoothing aggregated traffic from sensors with varying reporting periods and frame sizes to be carried on an access link is investigated. A straightforward optimization would take O(pn) time, whereas our heuristic scheme takes O(np) time where n, p denote the number of sensors and size of periods, respectively. Our heuristic scheme performs local optimization sensor by sensor, starting with the smallest to largest periods. This is based on an observation that sensors with large offsets have more choices in offsets to avoid traffic peaks than the sensors with smaller periods. A MATLAB simulation shows that our scheme excels the known scheme by M. Grenier et al. in a similar situation (aggregating periodic traffic in a controller area network) for almost all possible permutations. The performance of our scheme is very close to the straightforward optimization, which compares all possible permutations. We expect that our scheme would greatly contribute in smoothing the traffic from an ever-increasing number of IoT sensors to the gateway, reducing the burden on the access link to the Internet. PMID:28273831
A Scheme to Smooth Aggregated Traffic from Sensors with Periodic Reports.
Oh, Sungmin; Jang, Ju Wook
2017-03-03
The possibility of smoothing aggregated traffic from sensors with varying reporting periods and frame sizes to be carried on an access link is investigated. A straightforward optimization would take O(pn) time, whereas our heuristic scheme takes O(np) time where n, p denote the number of sensors and size of periods, respectively. Our heuristic scheme performs local optimization sensor by sensor, starting with the smallest to largest periods. This is based on an observation that sensors with large offsets have more choices in offsets to avoid traffic peaks than the sensors with smaller periods. A MATLAB simulation shows that our scheme excels the known scheme by M. Grenier et al. in a similar situation (aggregating periodic traffic in a controller area network) for almost all possible permutations. The performance of our scheme is very close to the straightforward optimization, which compares all possible permutations. We expect that our scheme would greatly contribute in smoothing the traffic from an ever-increasing number of IoT sensors to the gateway, reducing the burden on the access link to the Internet.
Kelbauskas, L; Dietel, W
2002-12-01
Amphiphilic sensitizers self-associate in aqueous environments and form aggregated species that exhibit no or only negligible photodynamic activity. However, amphiphilic photosensitizers number among the most potent agents of photodynamic therapy. The processes by which these sensitizers are internalized into tumor cells have yet to be fully elucidated and thus remain the subject of debate. In this study the uptake of photosensitizer aggregates into tumor cells was examined directly using subcellular time-resolved fluorescence spectroscopy with a high temporal resolution (20-30 ps) and high sensitivity (time-correlated single-photon counting). The investigations were performed on selected sensitizers that exhibit short fluorescence decay times (< 50 ps) in aggregated form. Derivatives of pyropheophorbide-a ether and chlorin e6 with varying lipophilicity were used for the study. The characteristic fluorescence decay times and spectroscopic features of the sensitizer aggregates measured in aqueous solution also could be observed in A431 human endothelial carcinoma cells administered with these photosensitizers. This shows that tumor cells can internalize sensitizers in aggregated form. Uptake of aggregates and their monomerization inside cells were demonstrated directly for the first time by means of fluorescence lifetime imaging with a high temporal resolution. Internalization of the aggregates seems to be endocytosis mediated. The degree of their monomerization in tumor cells is strongly influenced by the lipophilicity of the compounds.
Narang, Simranjeet S; Shuaib, Suniba; Goyal, Deepti; Goyal, Bhupesh
2018-01-01
Dialysis-related amyloidosis (DRA) is a severe condition characterized by the accumulation of amyloidogenic β2-microglobulin (β2m) protein around skeletal joints and bones. The recent studies highlighted a critical role of the DE loop region for β2m stability and amyloid aggregation propensity. Despite significant efforts, the molecular mechanism of enhanced aggregation due to D59P mutation in the DE loop region remain elusive. In the present study, explicit-solvent molecular dynamics (MD) simulations were performed to examine the key changes in the structural and dynamic properties of wild type (wt) β2m upon D59P mutation. MD simulations reveal a decrease in the average number of hydrogen bonds in the loop regions on D59P mutation that enhances conformational flexibility, which lead to higher aggregation propensity of D59P as compare to wt β2m. The principal component analysis (PCA) highlight that D59P covers a larger region of phase space and display a higher trace value than wt β2m, which suggest an overall enhancement in the conformational flexibility. D59P display two minimum energy basins in the free energy landscape (FEL) that are associated with thermodynamically less stable conformational states as compare to single minimum energy basin in wt β2m. The present study provides theoretical insights into the molecular mechanism behind the higher aggregation propensity of D59P as compare to wt β2m. © 2017 Wiley Periodicals, Inc.
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.
Mamme, Mesfin Haile; Köhn, Christoph; Deconinck, Johan; Ustarroz, Jon
2018-04-19
Fundamental understanding of the early stages of electrodeposition at the nanoscale is key to address the challenges in a wide range of applications. Despite having been studied for decades, a comprehensive understanding of the whole process is still out of reach. In this work, we introduce a novel modelling approach that couples a finite element method (FEM) with a random walk algorithm, to study the early stages of nanocluster formation, aggregation and growth, during electrochemical deposition. This approach takes into account not only electrochemical kinetics and transport of active species, but also the surface diffusion and aggregation of adatoms and small nanoclusters. The simulation results reveal that the relative surface mobility of the nanoclusters compared to that of the adatoms plays a crucial role in the early growth stages. The number of clusters, their size and their size dispersion are influenced more significantly by nanocluster mobility than by the applied overpotential itself. Increasing the overpotential results in shorter induction times and leads to aggregation prevalence at shorter times. A higher mobility results in longer induction times, a delayed transition from nucleation to aggregation prevalence, and as a consequence, a larger surface coverage of smaller clusters with a smaller size dispersion. As a consequence, it is shown that a classical first-order nucleation kinetics equation cannot describe the evolution of the number of clusters with time, N(t), in potentiostatic electrodeposition. Instead, a more accurate representation of N(t) is provided. We show that an evaluation of N(t), which neglects the effect of nanocluster mobility and aggregation, can induce errors of several orders of magnitude in the determination of nucleation rate constants. These findings are extremely important towards evaluating the elementary electrodeposition processes, considering not only adatoms, but also nanoclusters as building blocks.
Enrichment Ratio and Aggregate Stability Dynamics in Intensely Managed Landscapes
NASA Astrophysics Data System (ADS)
Wacha, K.; Papanicolaou, T.; Filley, T. R.; Hou, T.; Abban, B. K.; Wilson, C. G.; Boys, J.
2015-12-01
Challenges in understanding the soil carbon dynamics within intensely managed landscapes (IMLs), found throughout much the US Midwest, is highly complex due to the presence of heterogeneous landscape features and properties, as well as a mosaic of physical and biogeochemical processes occurring at different time scales. In addition, rainfall events exacerbate the effects of tillage by the impact of raindrops, which break down aggregates that encase carbon and dislodge and entrain soil particles and aggregates along the downslope. The redistribution of soil and carbon can have huge implications on biogeochemical cycling and overall carbon budgeting. In this study, we provide some rare field data on the mechanisms impacting aggregate stability, enrichment ratio values to estimate fluxes of carbon, as well as lignin chemistry to see influences on oxidation/mineralization rates. Rainfall simulation experiments were conducted within agricultural fields. Experiments were performed on the midslope (eroding) and toeslope (depositional) sections of representative hillslopes, under a variety of land managements, including row crop (conventional and conservation) and restored grasslands. Sensors were utilized to capture the evolution of soil moisture, temperature, microbial respiration pulses, and discharge rates to identify pseudo-steady state conditions. Samples collected at the weir outlet were tested for sediment concentrations and size fractions, as well as carbon and lignin fluxes. Preliminary findings show that conservation management practices have higher aggregate stability and decreased mass fluxes of carbon in the downslope than conventional tillage techniques.
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.
A real-time simulator of a turbofan engine
NASA Technical Reports Server (NTRS)
Litt, Jonathan S.; Delaat, John C.; Merrill, Walter C.
1989-01-01
A real-time digital simulator of a Pratt and Whitney F100 engine has been developed for real-time code verification and for actuator diagnosis during full-scale engine testing. This self-contained unit can operate in an open-loop stand-alone mode or as part of closed-loop control system. It can also be used for control system design and development. Tests conducted in conjunction with the NASA Advanced Detection, Isolation, and Accommodation program show that the simulator is a valuable tool for real-time code verification and as a real-time actuator simulator for actuator fault diagnosis. Although currently a small perturbation model, advances in microprocessor hardware should allow the simulator to evolve into a real-time, full-envelope, full engine simulation.
Early-Stage Aggregation of Human Islet Amyloid Polypeptide
NASA Astrophysics Data System (ADS)
Guo, Ashley; de Pablo, Juan
Human islet amyloid polypeptide (hIAPP, or human amylin) is implicated in the development of type II diabetes. hIAPP is known to aggregate into amyloid fibrils; however, it is prefibrillar oligomeric species, rather than mature fibrils, that are proposed to be cytotoxic. In order to better understand the role of hIAPP aggregation in the onset of disease, as well as to design effective diagnostics and therapeutics, it is crucial to understand the mechanism of early-stage hIAPP aggregation. In this work, we use atomistic molecular dynamics simulations combined with multiple advanced sampling techniques to examine the formation of the hIAPP dimer and trimer. Metadynamics calculations reveal a free energy landscape for the hIAPP dimer, which suggest multiple possible transition pathways. We employ finite temperature string method calculations to identify favorable pathways for dimer and trimer formation, along with relevant free energy barriers and intermediate structures. Results provide valuable insights into the mechanisms and energetics of hIAPP aggregation. In addition, this work demonstrates that the finite temperature string method is an effective tool in the study of protein aggregation. Funded by National Institute of Standards and Technology.
Rainfall continuous time stochastic simulation for a wet climate in the Cantabric Coast
NASA Astrophysics Data System (ADS)
Rebole, Juan P.; Lopez, Jose J.; Garcia-Guzman, Adela
2010-05-01
Rain is the result of a series of complex atmospheric processes which are influenced by numerous factors. This complexity makes its simulation practically unfeasible from a physical basis, advising the use of stochastic diagrams. These diagrams, which are based on observed characteristics (Todorovic and Woolhiser, 1975), allow the introduction of renewal alternating processes, that account for the occurrence of rainfall at different time lapses (Markov chains are a particular case, where lapses can be described by exponential distributions). Thus, a sequential rainfall process can be defined as a temporal series in which rainfall events (periods in which rainfall is recorded) alternate with non rain events (periods in which no rainfall is recorded). The variables of a temporal rain sequence have been characterized (duration of the rainfall event, duration of the non rainfall event, average intensity of the rain in the rain event, and a temporal distribution of the amount of rain in the rain event) in a wet climate such as that of the coastal area of Guipúzcoa. The study has been performed from two series recorded at the meteorological stations of Igueldo-San Sebastián and Fuenterrabia / Airport (data every ten minutes and for its hourly aggregation). As a result of this work, the variables satisfactorily fitted the following distribution functions: the duration of the rain event to a exponential function; the duration of the dry event to a truncated exponential mixed distribution; the average intensity to a Weibull distribution; and the distribution of the rain fallen to the Beta distribution. The characterization was made for an hourly aggregation of the recorded interval of ten minutes. The parameters of the fitting functions were better obtained by means of the maximum likelihood method than the moment method. The parameters obtained from the characterization were used to develop a stochastic rainfall process simulation model by means of a three states Markov
Geographically distributed real-time digital simulations using linear prediction
Liu, Ren; Mohanpurkar, Manish; Panwar, Mayank; ...
2016-07-04
Real time simulation is a powerful tool for analyzing, planning, and operating modern power systems. For analyzing the ever evolving power systems and understanding complex dynamic and transient interactions larger real time computation capabilities are essential. These facilities are interspersed all over the globe and to leverage unique facilities geographically-distributed real-time co-simulation in analyzing the power systems is pursued and presented. However, the communication latency between different simulator locations may lead to inaccuracy in geographically distributed real-time co-simulations. In this paper, the effect of communication latency on geographically distributed real-time co-simulation is introduced and discussed. In order to reduce themore » effect of the communication latency, a real-time data predictor, based on linear curve fitting is developed and integrated into the distributed real-time co-simulation. Two digital real time simulators are used to perform dynamic and transient co-simulations with communication latency and predictor. Results demonstrate the effect of the communication latency and the performance of the real-time data predictor to compensate it.« less
Geographically distributed real-time digital simulations using linear prediction
DOE Office of Scientific and Technical Information (OSTI.GOV)
Liu, Ren; Mohanpurkar, Manish; Panwar, Mayank
Real time simulation is a powerful tool for analyzing, planning, and operating modern power systems. For analyzing the ever evolving power systems and understanding complex dynamic and transient interactions larger real time computation capabilities are essential. These facilities are interspersed all over the globe and to leverage unique facilities geographically-distributed real-time co-simulation in analyzing the power systems is pursued and presented. However, the communication latency between different simulator locations may lead to inaccuracy in geographically distributed real-time co-simulations. In this paper, the effect of communication latency on geographically distributed real-time co-simulation is introduced and discussed. In order to reduce themore » effect of the communication latency, a real-time data predictor, based on linear curve fitting is developed and integrated into the distributed real-time co-simulation. Two digital real time simulators are used to perform dynamic and transient co-simulations with communication latency and predictor. Results demonstrate the effect of the communication latency and the performance of the real-time data predictor to compensate it.« less
Adaptive Aggregation Routing to Reduce Delay for Multi-Layer Wireless Sensor Networks
Li, Xujing; Xie, Mande; Zeng, Zhiwen; Cai, Zhiping
2018-01-01
The quality of service (QoS) regarding delay, lifetime and reliability is the key to the application of wireless sensor networks (WSNs). Data aggregation is a method to effectively reduce the data transmission volume and improve the lifetime of a network. In the previous study, a common strategy required that data wait in the queue. When the length of the queue is greater than or equal to the predetermined aggregation threshold (Nt) or the waiting time is equal to the aggregation timer (Tt), data are forwarded at the expense of an increase in the delay. The primary contributions of the proposed Adaptive Aggregation Routing (AAR) scheme are the following: (a) the senders select the forwarding node dynamically according to the length of the data queue, which effectively reduces the delay. In the AAR scheme, the senders send data to the nodes with a long data queue. The advantages are that first, the nodes with a long data queue need a small amount of data to perform aggregation; therefore, the transmitted data can be fully utilized to make these nodes aggregate. Second, this scheme balances the aggregating and data sending load; thus, the lifetime increases. (b) An improved AAR scheme is proposed to improve the QoS. The aggregation deadline (Tt) and the aggregation threshold (Nt) are dynamically changed in the network. In WSNs, nodes far from the sink have residual energy because these nodes transmit less data than the other nodes. In the improved AAR scheme, the nodes far from the sink have a small value of Tt and Nt to reduce delay, and the nodes near the sink are set to a large value of Tt and Nt to reduce energy consumption. Thus, the end to end delay is reduced, a longer lifetime is achieved, and the residual energy is fully used. Simulation results demonstrate that compared with the previous scheme, the performance of the AAR scheme is improved. This scheme reduces the delay by 14.91%, improves the lifetime by 30.91%, and increases energy efficiency by 76
Reduction in soil aggregation in response to dust emission processes
NASA Astrophysics Data System (ADS)
Swet, Nitzan; Katra, Itzhak
2016-09-01
Dust emission by aeolian (wind) soil erosion depends on the topsoil properties of the source area, especially on the nature of the aggregates where most dust particles are held. Although the key role of soil aggregates in dust emission, the response of soil aggregation to aeolian processes and its implications for dust emission remain unknown. This study focuses on aggregate size distribution (ASD) analyses before and after in-situ aeolian experiments in semiarid loess soils that are associated with dust emission. Wind tunnel simulations show that particulate matter (PM) emission and saltation rates depend on the initial ASD and shear velocity. Under all initial ASD conditions, the content of saltator-sized aggregates (63-250 μm) increased by 10-34% due to erosion of macro-aggregates (> 500 μm), resulting in a higher size ratio (SR) between the saltators and macro-aggregates following the aeolian erosion. The results revealed that the saltator production increases significantly for soils that are subjected to short-term (anthropogenic) disturbance of the topsoil. The findings highlight a decrease in soil aggregation for all initial ASD's in response to aeolian erosion, and consequently its influence on the dust emission potential. Changes in ASD should be considered as a key parameter in dust emission models of complex surfaces.
Kinetic roughening and porosity scaling in film growth with subsurface lateral aggregation.
Reis, F D A Aarão
2015-06-01
We study surface and bulk properties of porous films produced by a model in which particles incide perpendicularly to a substrate, interact with deposited neighbors in its trajectory, and aggregate laterally with probability of order a at each position. The model generalizes ballisticlike models by allowing attachment to particles below the outer surface. For small values of a, a crossover from uncorrelated deposition (UD) to correlated growth is observed. Simulations are performed in 1+1 and 2+1 dimensions. Extrapolation of effective exponents and comparison of roughness distributions confirm Kardar-Parisi-Zhang roughening of the outer surface for a>0. A scaling approach for small a predicts crossover times as a(-2/3) and local height fluctuations as a(-1/3) at the crossover, independent of substrate dimension. These relations are different from all previously studied models with crossovers from UD to correlated growth due to subsurface aggregation, which reduces scaling exponents. The same approach predicts the porosity and average pore height scaling as a(1/3) and a(-1/3), respectively, in good agreement with simulation results in 1+1 and 2+1 dimensions. These results may be useful for modeling samples with desired porosity and long pores.
Stability of Iowa mutant and wild type Aβ-peptide aggregates
NASA Astrophysics Data System (ADS)
Alred, Erik J.; Scheele, Emily G.; Berhanu, Workalemahu M.; Hansmann, Ulrich H. E.
2014-11-01
Recent experiments indicate a connection between the structure of amyloid aggregates and their cytotoxicity as related to neurodegenerative diseases. Of particular interest is the Iowa Mutant, which causes early-onset of Alzheimer's disease. While wild-type Amyloid β-peptides form only parallel beta-sheet aggregates, the mutant also forms meta-stable antiparallel beta sheets. Since these structural variations may cause the difference in the pathological effects of the two Aβ-peptides, we have studied in silico the relative stability of the wild type and Iowa mutant in both parallel and antiparallel forms. We compare regular molecular dynamics simulations with such where the viscosity of the samples is reduced, which, we show, leads to higher sampling efficiency. By analyzing and comparing these four sets of all-atom molecular dynamics simulations, we probe the role of the various factors that could lead to the structural differences. Our analysis indicates that the parallel forms of both wild type and Iowa mutant aggregates are stable, while the antiparallel aggregates are meta-stable for the Iowa mutant and not stable for the wild type. The differences result from the direct alignment of hydrophobic interactions in the in-register parallel oligomers, making them more stable than the antiparallel aggregates. The slightly higher thermodynamic stability of the Iowa mutant fibril-like oligomers in its parallel organization over that in antiparallel form is supported by previous experimental measurements showing slow inter-conversion of antiparallel aggregates into parallel ones. Knowledge of the mechanism that selects between parallel and antiparallel conformations and determines their relative stability may open new avenues for the development of therapies targeting familial forms of early-onset Alzheimer's disease.
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.
Real-time simulation of thermal shadows with EMIT
NASA Astrophysics Data System (ADS)
Klein, Andreas; Oberhofer, Stefan; Schätz, Peter; Nischwitz, Alfred; Obermeier, Paul
2016-05-01
Modern missile systems use infrared imaging for tracking or target detection algorithms. The development and validation processes of these missile systems need high fidelity simulations capable of stimulating the sensors in real-time with infrared image sequences from a synthetic 3D environment. The Extensible Multispectral Image Generation Toolset (EMIT) is a modular software library developed at MBDA Germany for the generation of physics-based infrared images in real-time. EMIT is able to render radiance images in full 32-bit floating point precision using state of the art computer graphics cards and advanced shader programs. An important functionality of an infrared image generation toolset is the simulation of thermal shadows as these may cause matching errors in tracking algorithms. However, for real-time simulations, such as hardware in the loop simulations (HWIL) of infrared seekers, thermal shadows are often neglected or precomputed as they require a thermal balance calculation in four-dimensions (3D geometry in one-dimensional time up to several hours in the past). In this paper we will show the novel real-time thermal simulation of EMIT. Our thermal simulation is capable of simulating thermal effects in real-time environments, such as thermal shadows resulting from the occlusion of direct and indirect irradiance. We conclude our paper with the practical use of EMIT in a missile HWIL simulation.
Time-Spectral Rotorcraft Simulations on Overset Grids
NASA Technical Reports Server (NTRS)
Leffell, Joshua I.; Murman, Scott M.; Pulliam, Thomas H.
2014-01-01
The Time-Spectral method is derived as a Fourier collocation scheme and applied to NASA's overset Reynolds-averaged Navier-Stokes (RANS) solver OVERFLOW. The paper outlines the Time-Spectral OVERFLOWimplementation. Successful low-speed laminar plunging NACA 0012 airfoil simulations demonstrate the capability of the Time-Spectral method to resolve the highly-vortical wakes typical of more expensive three-dimensional rotorcraft configurations. Dealiasing, in the form of spectral vanishing viscosity (SVV), facilitates the convergence of Time-Spectral calculations of high-frequency flows. Finally, simulations of the isolated V-22 Osprey tiltrotor for both hover and forward (edgewise) flight validate the three-dimensional Time-Spectral OVERFLOW implementation. The Time-Spectral hover simulation matches the time-accurate calculation using a single harmonic. Significantly more temporal modes and SVV are required to accurately compute the forward flight case because of its more active, high-frequency wake.
Spatial aggregation query in dynamic geosensor networks
NASA Astrophysics Data System (ADS)
Yi, Baolin; Feng, Dayang; Xiao, Shisong; Zhao, Erdun
2007-11-01
Wireless sensor networks have been widely used for civilian and military applications, such as environmental monitoring and vehicle tracking. In many of these applications, the researches mainly aim at building sensor network based systems to leverage the sensed data to applications. However, the existing works seldom exploited spatial aggregation query considering the dynamic characteristics of sensor networks. In this paper, we investigate how to process spatial aggregation query over dynamic geosensor networks where both the sink node and sensor nodes are mobile and propose several novel improvements on enabling techniques. The mobility of sensors makes the existing routing protocol based on information of fixed framework or the neighborhood infeasible. We present an improved location-based stateless implicit geographic forwarding (IGF) protocol for routing a query toward the area specified by query window, a diameter-based window aggregation query (DWAQ) algorithm for query propagation and data aggregation in the query window, finally considering the location changing of the sink node, we present two schemes to forward the result to the sink node. Simulation results show that the proposed algorithms can improve query latency and query accuracy.
Initial stages of aggregation in aqueous solutions of ionic liquids: molecular dynamics studies.
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.
Tremblay, Yannick D N; Labrie, Josée; Chénier, Sonia; Jacques, Mario
2017-07-01
Actinobacillus pleuropneumoniae causes porcine pleuropneumonia and forms biofilms in vitro on abiotic surfaces; however, presence of biofilms during infections has not been documented. The aim of this study was to use a species-specific fluorescent oligonucleotide probe and confocal microscopy to localize A. pleuropneumoniae in the lungs of two naturally infected pigs. Actinobacillus pleuropneumoniae was detected by fluorescence in situ hybridization and observed to grow as aggregates (~30-45 μm) during a natural infection. As the A. pleuropneumoniae aggregates observed in porcine lungs differed from the biofilms grown on a solid surface obtained in vitro, we designed a new biofilm assay using agarose, a porous substrate, favouring the formation of aggregates. In this study, we described for the first time the mode of growth of A. pleuropneumoniae during a natural infection in pigs. We also propose an in vitro biofilm assay for A. pleuropneumoniae using a porous substrate which allows the formation of aggregates. This assay might be more representative of the in vivo situation, at least in terms of the size of the bacterial aggregates and the presence of a porous matrix, and could potentially be used to test the susceptibility of A. pleuropneumoniae aggregates to antibiotics and disinfectants. © 2016 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.
Spherical and hyperspherical harmonics representation of van der Waals aggregates
NASA Astrophysics Data System (ADS)
Lombardi, Andrea; Palazzetti, Federico; Aquilanti, Vincenzo; Grossi, Gaia; Albernaz, Alessandra F.; Barreto, Patricia R. P.; Cruz, Ana Claudia P. S.
2016-12-01
The representation of the potential energy surfaces of atom-molecule or molecular dimers interactions should account faithfully for the symmetry properties of the systems, preserving at the same time a compact analytical form. To this aim, the choice of a proper set of coordinates is a necessary precondition. Here we illustrate a description in terms of hyperspherical coordinates and the expansion of the intermolecular interaction energy in terms of hypersherical harmonics, as a general method for building potential energy surfaces suitable for molecular dynamics simulations of van der Waals aggregates. Examples for the prototypical case diatomic-molecule-diatomic-molecule interactions are shown.
Tavagnacco, Letizia; Gerelli, Yuri; Cesàro, Attilio; Brady, John W
2016-09-22
The dynamical and structural properties of caffeine solutions at the solubility limit have been investigated as a function of temperature by means of MD simulations, static and dynamic light scattering, and small angle neutron scattering experiments. A clear picture unambiguously supported by both experiment and simulation emerges: caffeine self-aggregation promotes the formation of two distinct types of clusters: linear aggregates of stacked molecules, formed by 2-14 caffeine molecules depending on the thermodynamic conditions and disordered branched aggregates with a size in the range 1000-3000 Å. While the first type of association is well-known to occur under room temperature conditions for both caffeine and other purine systems, such as nucleotides, the presence of the supramolecular aggregates has not been reported previously. MD simulations indicate that branched structures are formed by caffeine molecules in a T-shaped arrangement. An increase of the solubility limit (higher temperature but also higher concentration) broadens the distribution of cluster sizes, promoting the formation of stacked aggregates composed by a larger number of caffeine molecules. Surprisingly, the effect on the branched aggregates is rather limited. Their internal structure and size do not change considerably in the range of solubility limits investigated.
On the fractal morphology of combustion-generated soot aggregates
DOE Office of Scientific and Technical Information (OSTI.GOV)
Koylu, U.O.
1995-12-31
The fractal properties of soot aggregates were investigated using ex-situ and in-situ experimental methods as well as computer simulations. Ex-situ experiments involved thermophoretic sampling and analysis by transmission electron microscopy (TEM), while in-situ measurements employed angular static light scattering and data inversion based on Rayleigh-Debye-Gans (RDG) approximation. Computer simulations used a sequential algorithm which mimics mass fractal-like structures. So from a variety of hydrocarbon-fueled laminar and turbulent nonpremixed flame environments were considered in the present study. The TEM analysis of projected soot images sampled from fuel-rich conditions of buoyant and weakly-buoyant laminar flames indicated that the fractal dimension of sootmore » was relatively independent of position in flames, fuel type and flame condition. These measurements yielded an average fractal dimension of 1.8, although other structure parameters such as the primary particle diameters and number of primary particles in aggregates had wide range of values. Fractal prefactor (lacunarity) was also measured for soot sampled from the fuel-lean conditions of turbulent flames, considering the actual morphology by tilting the samples during TEM analysis. These measurements yielded a fractal dimension of 1.65 and a lacunarity of 8.5, with experimental uncertainties (95% confidence) of 0.08 and 0.5, respectively. Relationships between the actual and projected structure properties of soot were also developed by combining TEM observations with numerical simulations. Practical approximate formulae were suggested to find radius of gyration of an aggregate from its maximum dimension, and number of primary particles in an aggregate from projected area. Finally, the fractal dimension and lacunarity of soot were obtained using light scattering for the same conditions of the above TEM measurements.« less
Aggregate Measures of Watershed Health from Reconstructed ...
Risk-based indices such as reliability, resilience, and vulnerability (R-R-V), have the potential to serve as watershed health assessment tools. Recent research has demonstrated the applicability of such indices for water quality (WQ) constituents such as total suspended solids and nutrients on an individual basis. However, the calculations can become tedious when time-series data for several WQ constituents have to be evaluated individually. Also, comparisons between locations with different sets of constituent data can prove difficult. In this study, data reconstruction using relevance vector machine algorithm was combined with dimensionality reduction via variational Bayesian noisy principal component analysis to reconstruct and condense sparse multidimensional WQ data sets into a single time series. The methodology allows incorporation of uncertainty in both the reconstruction and dimensionality-reduction steps. The R-R-V values were calculated using the aggregate time series at multiple locations within two Indiana watersheds. Results showed that uncertainty present in the reconstructed WQ data set propagates to the aggregate time series and subsequently to the aggregate R-R-V values as well. serving as motivating examples. Locations with different WQ constituents and different standards for impairment were successfully combined to provide aggregate measures of R-R-V values. Comparisons with individual constituent R-R-V values showed that v
Role of small oligomers on the amyloidogenic aggregation free-energy landscape.
He, Xianglan; Giurleo, Jason T; Talaga, David S
2010-01-08
We combine atomic-force-microscopy particle-size-distribution measurements with earlier measurements on 1-anilino-8-naphthalene sulfonate, thioflavin T, and dynamic light scattering to develop a quantitative kinetic model for the aggregation of beta-lactoglobulin into amyloid. We directly compare our simulations to the population distributions provided by dynamic light scattering and atomic force microscopy. We combine species in the simulation according to structural type for comparison with fluorescence fingerprint results. The kinetic model of amyloidogenesis leads to an aggregation free-energy landscape. We define the roles of and propose a classification scheme for different oligomeric species based on their location in the aggregation free-energy landscape. We relate the different types of oligomers to the amyloid cascade hypothesis and the toxic oligomer hypothesis for amyloid-related diseases. We discuss existing kinetic mechanisms in terms of the different types of oligomers. We provide a possible resolution to the toxic oligomer-amyloid coincidence.
Kee, Kerk F; Sparks, Lisa; Struppa, Daniele C; Mannucci, Mirco A; Damiano, Alberto
2016-01-01
By integrating the simplicial model of social aggregation with existing research on opinion leadership and diffusion networks, this article introduces the constructs of simplicial diffusers (mathematically defined as nodes embedded in simplexes; a simplex is a socially bonded cluster) and simplicial diffusing sets (mathematically defined as minimal covers of a simplicial complex; a simplicial complex is a social aggregation in which socially bonded clusters are embedded) to propose a strategic approach for information diffusion of cancer screenings as a health intervention on Facebook for community cancer prevention and control. This approach is novel in its incorporation of interpersonally bonded clusters, culturally distinct subgroups, and different united social entities that coexist within a larger community into a computational simulation to select sets of simplicial diffusers with the highest degree of information diffusion for health intervention dissemination. The unique contributions of the article also include seven propositions and five algorithmic steps for computationally modeling the simplicial model with Facebook data.
Modelling parasite aggregation: disentangling statistical and ecological approaches.
Yakob, Laith; Soares Magalhães, Ricardo J; Gray, Darren J; Milinovich, Gabriel; Wardrop, Nicola; Dunning, Rebecca; Barendregt, Jan; Bieri, Franziska; Williams, Gail M; Clements, Archie C A
2014-05-01
The overdispersion in macroparasite infection intensity among host populations is commonly simulated using a constant negative binomial aggregation parameter. We describe an alternative to utilising the negative binomial approach and demonstrate important disparities in intervention efficacy projections that can come about from opting for pattern-fitting models that are not process-explicit. We present model output in the context of the epidemiology and control of soil-transmitted helminths due to the significant public health burden imposed by these parasites, but our methods are applicable to other infections with demonstrable aggregation in parasite numbers among hosts. Copyright © 2014. Published by Elsevier Ltd.
Pradhan, Nibedita; Shekhar, Shashi; Jana, Nihar R; Jana, Nikhil R
2017-03-29
Sugar-based osmolyte molecules are known to stabilize proteins under stress, but usually they have poor chaperone performance in inhibiting protein aggregation. Here, we show that the nanoparticle form of sugars molecule can enhance their chaperone performance typically by 10 2 -10 5 times, compared to molecular sugar. Sugar-based plate-like nanoparticles of 20-40 nm hydrodynamic size have been synthesized by simple heating of acidic aqueous solution of glucose/sucrose/maltose/trehalose. These nanoparticles have excitation-dependent green/yellow/orange emission and surface chemistry identical to the respective sugar molecule. Fibrillation of lysozyme/insulin/amyloid beta in extracellular space, aggregation of mutant huntingtin protein inside model neuronal cell, and cytotoxic effect of fibrils are investigated in the presence of these sugar nanoparticles. We found that sugar nanoparticles are 10 2 -10 5 times efficient than respective sugar molecules in inhibiting protein fibrillation and preventing cytotoxicity arising of fibrils. We propose that better performance of the nanoparticle form is linked to its stronger binding with fibril structure and enhanced cell uptake. This result suggests that nanoparticle form of osmolyte can be an attractive option in prevention and curing of protein aggregation-derived diseases.
High performance real-time flight simulation at NASA Langley
NASA Technical Reports Server (NTRS)
Cleveland, Jeff I., II
1994-01-01
In order to meet the stringent time-critical requirements for real-time man-in-the-loop flight simulation, computer processing operations must be deterministic and be completed in as short a time as possible. This includes simulation mathematical model computational and data input/output to the simulators. In 1986, in response to increased demands for flight simulation performance, personnel at NASA's Langley Research Center (LaRC), working with the contractor, developed extensions to a standard input/output system to provide for high bandwidth, low latency data acquisition and distribution. The Computer Automated Measurement and Control technology (IEEE standard 595) was extended to meet the performance requirements for real-time simulation. This technology extension increased the effective bandwidth by a factor of ten and increased the performance of modules necessary for simulator communications. This technology is being used by more than 80 leading technological developers in the United States, Canada, and Europe. Included among the commercial applications of this technology are nuclear process control, power grid analysis, process monitoring, real-time simulation, and radar data acquisition. Personnel at LaRC have completed the development of the use of supercomputers for simulation mathematical model computational to support real-time flight simulation. This includes the development of a real-time operating system and the development of specialized software and hardware for the CAMAC simulator network. This work, coupled with the use of an open systems software architecture, has advanced the state of the art in real time flight simulation. The data acquisition technology innovation and experience with recent developments in this technology are described.
Detection and characterization of red blood cell (RBC) aggregation with photoacoustics
NASA Astrophysics Data System (ADS)
Hysi, Eno; Saha, Ratan K.; Rui, Min; Kolios, Michael C.
2012-02-01
Red blood cells (RBCs) aggregate in the presence of increased plasma fibrinogen and low shear forces during blood flow. RBC aggregation has been observed in deep vein thrombosis, sepsis and diabetes. We propose using photoacoustics (PA) as a non-invasive imaging modality to detect RBC aggregation. The theoretical and experimental feasibility of PA for detecting and characterizing aggregation was assessed. A simulation study was performed to generate PA signals from non-aggregated and aggregated RBCs using a frequency domain approach and to study the PA signals' dependence on hematocrit and aggregate size. The effect of the finite bandwidth nature of transducers on the PA power spectra was also investigated. Experimental confirmation of theoretical results was conducted using porcine RBC samples exposed to 1064 nm optical wavelength using the Imagio Small Animal PA imaging system (Seno Medical Instruments, Inc., San Antonio, TX). Aggregation was induced with Dextran-70 (Sigma-Aldrich, St. Louis, MO) and the effect of hematocrit and aggregation level was investigated. The theoretical and experimental PA signal amplitude increased linearly with increasing hematocrit. The theoretical dominant frequency content of PA signals shifted towards lower frequencies (<30 MHz) and 9 dB enhancements in spectral power were observed as the size of aggregates increased compared to non-aggregating RBCs. Calibration of the PA spectra with the transducer response obtained from a 200 nm gold film was performed to remove system dependencies. Analysis of the spectral parameters from the calibrated spectra suggested that PA can assess the degree of aggregation at multiple hematocrit and aggregation levels.
Calcium oxalate monohydrate aggregation induced by aggregation of desialylated Tamm-Horsfall protein
Viswanathan, Pragasam; Rimer, Jeffrey D.; Kolbach, Ann M.; Kleinman, Jack G.
2011-01-01
Tamm-Horsfall protein (THP) is thought to protect against calcium oxalate monohydrate (COM) stone formation by inhibiting COM aggregation. Several studies reported that stone formers produce THP with reduced levels of glycosylation, particularly sialic acid levels, which leads to reduced negative charge. In this study, normal THP was treated with neuraminidase to remove sialic acid residues, confirmed by an isoelectric point shift to higher pH. COM aggregation assays revealed that desialylated THP (ds-THP) promoted COM aggregation, while normal THP inhibited aggregation. The appearance of protein aggregates in solutions at ds-THP concentrations ≥1 µg/mL in 150 mM NaCl correlated with COM aggregation promotion, implying that ds-THP aggregation induced COM aggregation. The aggregation-promoting effect of the ds-THP was independent of pH above its isoelectric point, but was substantially reduced at low ionic strength, where protein aggregation was much reduced. COM aggregation promotion was maximized at a ds-THP to COM mass ratio of ~0.025, which can be explained by a model wherein partial COM surface coverage by ds-THP aggregates promotes crystal aggregation by bridging opposing COM surfaces, whereas higher surface coverage leads to repulsion between adsorbed ds-THP aggregates. Thus, desialylation of THP apparently abrogates a normal defensive action of THP by inducing protein aggregation, and subsequently COM aggregation, a condition that favors kidney stone formation. PMID:21229239
Production of lightweight aggregates from washing aggregate sludge and fly ash
NASA Astrophysics Data System (ADS)
González-Corrochano, Beatriz; Alonso-Azcárate, Jacinto; Rodas, Magdalena
2010-05-01
Increasing generation of wastes is one of the main environmental problems in industrialised countries. Heat treatment at high temperatures can convert some types of wastes into ceramic products with a wide range of microstructural features and properties (Bethanis et al., 2004). A lightweight aggregate (LWA) is a granular material with a bulk density (bd) not exceeding 1.20 g/cm3 or with a particle density not exceeding 2.00 g/cm3 (UNE-EN-13055-1, 2003). They have become a focus of interest because the low particle density and the low bulk density entail a decrease in the load transmitted to the ground, and less work and effort are required to transport them (De' Gennaro et al., 2004). The benefits associated with these low densities, which are due to the formation of voids and pores, are very good thermal and acoustic insulation and materials with a good resistance to fire (Benbow, 1987; Fakhfakh et al., 2007). The objective was to recycle fly ash, used motor oil from cars and mineral wastes from washing aggregate sludge, in order to obtain a usable material such as lightweight aggregates, and also to ensure that they are of good quality for different applications. Raw materials have been physically, chemically and mineralogically characterized. On the basis of the results obtained, they were mixed, milled to a grain size of less than 200 μm (Yasuda, 1991), formed into pellets, pre-heated for 5 min and sintered in a rotary kiln at 1150°C, 1175°C, 1200°C and 1225°C for 10 and 15 min at each temperature (Theating). Effects of raw material characteristics, heating temperature and dwell time on the following LWAs properties were determined: loss on ignition (LOI), bloating index (BI), loose bulk density (bd), apparent and dry particle density (ad, dd), voids (H), water absorption (WA24h) and compressive strength (S). The products obtained were lightweight aggregates in accordance with norm UNE-EN-13055-1 (bd ≤1.20 g/cm3 or particle density ≤2.00 g/cm3). LWAs
Generating survival times to simulate Cox proportional hazards models with time-varying covariates.
Austin, Peter C
2012-12-20
Simulations and Monte Carlo methods serve an important role in modern statistical research. They allow for an examination of the performance of statistical procedures in settings in which analytic and mathematical derivations may not be feasible. A key element in any statistical simulation is the existence of an appropriate data-generating process: one must be able to simulate data from a specified statistical model. We describe data-generating processes for the Cox proportional hazards model with time-varying covariates when event times follow an exponential, Weibull, or Gompertz distribution. We consider three types of time-varying covariates: first, a dichotomous time-varying covariate that can change at most once from untreated to treated (e.g., organ transplant); second, a continuous time-varying covariate such as cumulative exposure at a constant dose to radiation or to a pharmaceutical agent used for a chronic condition; third, a dichotomous time-varying covariate with a subject being able to move repeatedly between treatment states (e.g., current compliance or use of a medication). In each setting, we derive closed-form expressions that allow one to simulate survival times so that survival times are related to a vector of fixed or time-invariant covariates and to a single time-varying covariate. We illustrate the utility of our closed-form expressions for simulating event times by using Monte Carlo simulations to estimate the statistical power to detect as statistically significant the effect of different types of binary time-varying covariates. This is compared with the statistical power to detect as statistically significant a binary time-invariant covariate. Copyright © 2012 John Wiley & Sons, Ltd.
Features of the use of time-frequency distributions for controlling the mixture-producing aggregate
NASA Astrophysics Data System (ADS)
Fedosenkov, D. B.; Simikova, A. A.; Fedosenkov, B. A.
2018-05-01
The paper submits and argues the information on filtering properties of the mixing unit as a part of the mixture-producing aggregate. Relevant theoretical data concerning a channel transfer function of the mixing unit and multidimensional material flow signals are adduced here. Note that ordinary one-dimensional material flow signals are defined in terms of time-frequency distributions of Cohen’s class representations operating with Gabor wavelet functions. Two time-frequencies signal representations are written about in the paper to show how one can solve controlling problems as applied to mixture-producing systems: they are the so-called Rihaczek and Wigner-Ville distributions. In particular, the latter illustrates low-pass filtering properties that are practically available in any of low-pass elements of a physical system.
Secure data aggregation in wireless sensor networks using homomorphic encryption
NASA Astrophysics Data System (ADS)
Kumar, Manish; Verma, Shekhar; Lata, Kusum
2015-04-01
In a Wireless Sensor Network (WSN), aggregation exploits the correlation between spatially and temporally proximate sensor data to reduce the total data volume to be transmitted to the sink. Mobile agents (MAs) fit into this paradigm, and data can be aggregated and collected by an MA from different sensor nodes using context specific codes. The MA-based data collection suffers due to large size of a typical WSN and is prone to security problems. In this article, homomorphic encryption in a clustered WSN has been proposed for secure and efficient data collection using MAs. The nodes keep encrypted data that are given to an MA for data aggregation tasks. The MA performs all the data aggregation operations upon encrypted data as it migrates between nodes in a tree-like structure in which the nodes are leafs and the cluster head is the root of the tree. It returns and deposits the encrypted aggregated data to the cluster head after traversing through all the intra cluster nodes over a shortest path route. The homomorphic encryption and aggregation processing in encrypted domain makes the data collection process secure. Simulation results confirm the effectiveness of the proposed secure data aggregation mechanism. In addition to security, MA-based mechanism leads to lesser delay and bandwidth requirements.
NASA Astrophysics Data System (ADS)
Nam, Hoang Bao; Kouza, Maksim; Zung, Hoang; Li, Mai Suan
2010-04-01
Despite much progress in understanding the aggregation process of biomolecules, the factors that govern its rates have not been fully understood. This problem is of particular importance since many conformational diseases such as Alzheimer, Parkinson, and type-II diabetes are associated with the protein oligomerization. Having performed all-atom simulations with explicit water and various force fields for two short peptides KFFE and NNQQ, we show that their oligomer formation times are strongly correlated with the population of the fibril-prone conformation in the monomeric state. The larger the population the faster the aggregation process. Our result not only suggests that this quantity plays a key role in the self-assembly of polypeptide chains but also opens a new way to understand the fibrillogenesis of biomolecules at the monomeric level. The nature of oligomer ordering of NNQQ is studied in detail.
Asphaltene aggregation and impact of alkylphenols.
Goual, Lamia; Sedghi, Mohammad; Wang, Xiaoxiao; Zhu, Ziming
2014-05-20
The main objective of this study was to provide novel insights into the mechanism of asphaltene aggregation in toluene/heptane (Heptol) solutions and the effect of alkylphenols on asphaltene dispersion through the integration of advanced experimental and modeling methods. High-resolution transmission electron microscope (HRTEM) images revealed that the onset of asphaltene flocculation occurs near a toluene/heptane volume ratio of 70:30 and that flocculates are well below 1 μm in size. To assess the impact of alkylphenols on asphaltene aggregation, octylphenol (OP) and dodecylphenol (DP) were evaluated by impedance analysis based on their ability to delay the precipitation onset and to reduce the size of nonflocculated asphaltene aggregates in 80:20 toluene/heptane solutions. Although a longer dispersant chain length did not affect the precipitation onset, it reduced the size of the aggregates. Molecular dynamics simulations were then performed to understand the mechanism of interaction between a model asphaltene and OP in heptane. OP molecules saturated the H-bonding sites of asphaltenes and prevented them from interacting laterally between themselves. This explained why OP favored the formation of flocculates with filamentary rather than globular structures, which were clearly observed by HRTEM. Although OP proved to be an effective dispersant, its effectiveness was hindered by its self-association and the fact that it interacted at the periphery of asphaltenes, leaving their aromatic cores uncovered.
Automated Data Aggregation for Time-Series Analysis: Study Case on Anaesthesia Data Warehouse.
Lamer, Antoine; Jeanne, Mathieu; Ficheur, Grégoire; Marcilly, Romaric
2016-01-01
Data stored in operational databases are not reusable directly. Aggregation modules are necessary to facilitate secondary use. They decrease volume of data while increasing the number of available information. In this paper, we present four automated engines of aggregation, integrated into an anaesthesia data warehouse. Four instances of clinical questions illustrate the use of those engines for various improvements of quality of care: duration of procedure, drug administration, assessment of hypotension and its related treatment.
Microbial aggregates in anaerobic wastewater treatment.
Kosaric, N; Blaszczyk, R
1990-01-01
The phenomenon aggregation of anaerobic bacteria gives an opportunity to speed up the digestion rate during methanogenesis. The aggregates are mainly composed of methanogenic bacteria which convert acetate and H2/CO2 into methane. Other bacteria are also included in the aggregates but their concentration is rather small. The aggregates may also be formed during acetogenesis or even hydrolysis but such aggregates are not stable and disrupt quickly when not fed. A two stage process seems to be suitable when high concentrated solid waste must be treated. Special conditions are necessary to promote aggregate formation from methanogenic bacteria but aggregates once formed are stable without feeding even for a few years. The structure, texture and activity of bacterial aggregates depend on several parameters: (1)--temperature and pH, (2)--wastewater composition and (3)--hydrodynamic conditions within the reactor. The common influence of all these parameters is still rather unknown but some recommendations may be given. Temperature and pH should be maintained in the range which is optimal for methanogenic bacteria e.g. a temperature between 32 and 50 degrees C and a value pH between 6.5 and 7.5. Wastewaters should contain soluble wastes and the specific loading rate should be around one kgCOD(kgVSS)-1 d-1. The concentration of the elements influences aggregate composition and probably structure and texture. At high calcium concentration a change in the colour of the granules has been observed. Research is necessary to investigate the influence of other elements and organic toxicants on maintenance of the aggregates. Hydrodynamic conditions seem to influence the stability of the granules over long time periods. At low liquid stream rates, aggregates may starve and lysis within the aggregates is possible which results in hollowing of aggregates and their floating. At high liquid stream rates the aggregates may be disrupted and washed out of the reactor as a flocculent
Real-time simulation of large-scale floods
NASA Astrophysics Data System (ADS)
Liu, Q.; Qin, Y.; Li, G. D.; Liu, Z.; Cheng, D. J.; Zhao, Y. H.
2016-08-01
According to the complex real-time water situation, the real-time simulation of large-scale floods is very important for flood prevention practice. Model robustness and running efficiency are two critical factors in successful real-time flood simulation. This paper proposed a robust, two-dimensional, shallow water model based on the unstructured Godunov- type finite volume method. A robust wet/dry front method is used to enhance the numerical stability. An adaptive method is proposed to improve the running efficiency. The proposed model is used for large-scale flood simulation on real topography. Results compared to those of MIKE21 show the strong performance of the proposed model.
Orientation of surfactant self-assembled aggregates on graphite
NASA Astrophysics Data System (ADS)
Sammalkorpi, Maria; Hynninen, Antti-Pekka; Panagiotopoulos, Athanassios Z.; Haataja, Mikko
2007-03-01
Micellar aggregates on surfaces can provide a self-healing corrosion protection or lubrication layer. It has been observed experimentally that on a single crystal surface this layer often consists of oriented hemi-cylindrical micelles which are aligned with the underlying crystal lattice (``orientation effect''). A key feature of this self-assembly process is the interplay between detergent--detergent and detergent--surface interactions. Since the dimensions of the detergent molecules and the unit cell of the surface are typically quite different, the origins of this orientation effect remain unclear. Here we address the question and present the results of Molecular Dynamics simulations of sodium dodecyl sulfate (SDS) self-aggregation on graphite. We employ both single-molecule and multi-molecule simulations of SDS to unravel the origins of the orientation effect. We report that the underlying graphite surface is sufficient to impose orientational bias on individual SDS molecules diffusing on the surface. This produces collective effects that give rise to the oriented hemi-micelles.
Dynamic Fluctuations of Protein-Carbohydrate Interactions Promote Protein Aggregation
Voynov, Vladimir; Chennamsetty, Naresh; Kayser, Veysel; Helk, Bernhard; Forrer, Kurt; Zhang, Heidi; Fritsch, Cornelius; Heine, Holger; Trout, Bernhardt L.
2009-01-01
Protein-carbohydrate interactions are important for glycoprotein structure and function. Antibodies of the IgG class, with increasing significance as therapeutics, are glycosylated at a conserved site in the constant Fc region. We hypothesized that disruption of protein-carbohydrate interactions in the glycosylated domain of antibodies leads to the exposure of aggregation-prone motifs. Aggregation is one of the main problems in protein-based therapeutics because of immunogenicity concerns and decreased efficacy. To explore the significance of intramolecular interactions between aromatic amino acids and carbohydrates in the IgG glycosylated domain, we utilized computer simulations, fluorescence analysis, and site-directed mutagenesis. We find that the surface exposure of one aromatic amino acid increases due to dynamic fluctuations. Moreover, protein-carbohydrate interactions decrease upon stress, while protein-protein and carbohydrate-carbohydrate interactions increase. Substitution of the carbohydrate-interacting aromatic amino acids with non-aromatic residues leads to a significantly lower stability than wild type, and to compromised binding to Fc receptors. Our results support a mechanism for antibody aggregation via decreased protein-carbohydrate interactions, leading to the exposure of aggregation-prone regions, and to aggregation. PMID:20037630
Protein aggregation and misfolding: good or evil?
NASA Astrophysics Data System (ADS)
Pastore, Annalisa; Temussi, Pierandrea
2012-06-01
Protein aggregation and misfolding have important implications in an increasing number of fields ranging from medicine to biology to nanotechnology and material science. The interest in understanding this field has accordingly increased steadily over the last two decades. During this time the number of publications that have been dedicated to protein aggregation has increased exponentially, tackling the problem from several different and sometime contradictory perspectives. This review is meant to summarize some of the highlights that come from these studies and introduce this topical issue on the subject. The factors that make a protein aggregate and the cellular strategies that defend from aggregation are discussed together with the perspectives that the accumulated knowledge may open.
Protein aggregation and misfolding: good or evil?
Pastore, Annalisa; Temussi, Pierandrea
2012-06-20
Protein aggregation and misfolding have important implications in an increasing number of fields ranging from medicine to biology to nanotechnology and material science. The interest in understanding this field has accordingly increased steadily over the last two decades. During this time the number of publications that have been dedicated to protein aggregation has increased exponentially, tackling the problem from several different and sometime contradictory perspectives. This review is meant to summarize some of the highlights that come from these studies and introduce this topical issue on the subject. The factors that make a protein aggregate and the cellular strategies that defend from aggregation are discussed together with the perspectives that the accumulated knowledge may open.
Computational study of aggregation mechanism in human lysozyme[D67H
Patel, Dharmeshkumar
2017-01-01
Aggregation of proteins is an undesired phenomena that affects both human health and bioengineered products such as therapeutic proteins. Finding preventative measures could be facilitated by a molecular-level understanding of dimer formation, which is the first step in aggregation. Here we present a molecular dynamics (MD) study of dimer formation propensity in human lysozyme and its D67H variant. Because the latter protein aggregates while the former does not, they offer an ideal system for testing the feasibility of the proposed MD approach which comprises three stages: i) partially unfolded conformers involved in dimer formation are generated via high-temperature MD simulations, ii) potential dimer structures are searched using docking and refined with MD, iii) free energy calculations are performed to find the most stable dimer structure. Our results provide a detailed explanation for how a single mutation (D67H) turns human lysozyme from non-aggregating to an aggregating protein. Conversely, the proposed method can be used to identify the residues causing aggregation in a protein, which can be mutated to prevent it. PMID:28467454
NASA Astrophysics Data System (ADS)
Sun, Yun-Fei; Chen, Dan; Lin, Zhen-Quan; Ke, Jian-Hong
2009-06-01
, and μ = ν = η = 1, the population and asset aggregates experience gelation transitions at finite times and the scaling forms break down.
Real-Time-Simulation of IEEE-5-Bus Network on OPAL-RT-OP4510 Simulator
NASA Astrophysics Data System (ADS)
Atul Bhandakkar, Anjali; Mathew, Lini, Dr.
2018-03-01
The Real-Time Simulator tools have high computing technologies, improved performance. They are widely used for design and improvement of electrical systems. The advancement of the software tools like MATLAB/SIMULINK with its Real-Time Workshop (RTW) and Real-Time Windows Target (RTWT), real-time simulators are used extensively in many engineering fields, such as industry, education, and research institutions. OPAL-RT-OP4510 is a Real-Time Simulator which is used in both industry and academia. In this paper, the real-time simulation of IEEE-5-Bus network is carried out by means of OPAL-RT-OP4510 with CRO and other hardware. The performance of the network is observed with the introduction of fault at various locations. The waveforms of voltage, current, active and reactive power are observed in the MATLAB simulation environment and on the CRO. Also, Load Flow Analysis (LFA) of IEEE-5-Bus network is computed using MATLAB/Simulink power-gui load flow tool.
NASA Astrophysics Data System (ADS)
Szabó, Judit Alexandra; Jakab, Gergely; Szabó, Boglárka
2015-04-01
Soil structure degradation has effect through the soil water balance and nutrient supply on the agricultural potential of an area. The soil erosion process comprises two phases: detachment and transport by water. To study the transport phase nozzle type laboratory-scale rainfall simulator was used with constant 80 mmhr-1 intensity on an arable haplic Cambisol. Measuring the aggregate and particle size distribution of the soil loss gives a good approach the erosion process. The primary objective of this study was to examine the sediment concentration, and detect the quality and quantity change of the soil loss during a single precipitation under six treatment combinations (recently tilled and crusty soil surface on two different slope steepness, inland inundation and drought soil conditions). Soil loss were collected continually, and separated per aggregate size fractions with sieves in three rounds during a rain to measure the weights. The particle size distribution was measured with Horiba LA-950 particle size analyzer. In general the ratio of the macro aggregates decreases and the ratio of the micro aggregates and clay fraction increases in the sediment with time during the precipitation due to the raindrop impact. Sediment concentration depends on the slope steepness, as from steeper slopes the runoff can transport bigger amount of sediment, but from the tilled surface bigger aggregates were washing down. Micro aggregate fraction is one of the indicators of good soil structure. The degradation of micro aggregates occurs in steeper slopes and the most erosive time period depends on the micromorphology of the surface. And while the aggregate size distribution of the soil loss of the treatments shows high variety of distribution and differs from the original soil, the particle size distribution of each aggregate size fraction shows similar trends except the 50-250 µm fraction where the fine sand fraction is dominating instead of the loam. This anomaly may be
Simulation study of 2D spectrum of molecular aggregates coupled to correlated vibrations
NASA Astrophysics Data System (ADS)
Abramavicius, Darius; Butkus, Vytautas; Valkunas, Leonas; Mukamel, Shaul
2011-03-01
Oscillatory dynamics of two-dimensional (2D) spectra of photosynthetic pigment-protein complexes raise the questions of how to disentangle various origins of these oscillations, which may include quantum beats, quantum transport, or molecular vibrations. We study the effects of correlated overdamped fluctuations and under-damped vibrations on the 2D spectra of Fenna-Matthews-Olson (FMO) aggregate, which has well-resolved exciton resonances, and a circular porphyrin aggregate (P6), whose absorption shows vibrational progression. We use a generic exciton Hamiltonian coupled to a bath, characterized by a spectral density. Fluctuations have smooth, while vibtations have δ -type spectral densities. We show how various scenarios of correlated molecular fluctuations lead to some highly oscillatory crosspeaks. Molecular vibrations cause progression of diagonal peaks in the 2D spectrum and make their corresponding cross-peaks highly oscillatory. We, thus, demonstrate that bath fluctuations and molecular vibrations of realistic molecular aggregates are highly entangled in 2D spectroscopy. DA acknowledges grant VP1-3.1-SMM-07-V, SM - the grants CHE0745892 (NSF), DRPA BAA-10-40 QUBE.
Opportunistic tri-band carrier aggregation in licensed spectrum for multi-operator 5G hetnet
NASA Astrophysics Data System (ADS)
Maksymuk, Taras; Kyryk, Maryan; Klymash, Mykhailo; Jo, Minho; Romaniuk, Ryszard; Kotyra, Andrzej; Zhanpeisova, Aizhan; Kozbekova, Ainur
2017-08-01
Increasing capacity of mobile networks is a real challenge due to rapid increasing of traffic demands and spectrum scarcity. Carrier aggregation technology is aimed to increase the user data rate by combining the throughput of few spectrum bands, even if they are not physically collocated. Utilization of unlicensed Wi-Fi 5 GHz band for mobile transmission opens new perspectives for carrier aggregation due to vast amount of spectrum range, which can be available for aggregation to supplement data rates for end users. There are many solutions proposed to enable mobile data transmission in unlicensed band without disturbing interference for the existing Wi-Fi users. The paper presents a new approach for opportunistic carrier aggregation in licensed and unlicensed band for multi-operator 5G network. It allows multiple network operators to utilize unlicensed spectrum opportunistically if it is not currently used by Wi-Fi or other mobile network operators. Performance of the proposed approach has been simulated in case of two competing operators. Simulation results reveal that applying the proposed method ensures achieving satisfactory performance of carrier aggregation for the case of two network operators.
A physical description of the adhesion and aggregation of platelets
NASA Astrophysics Data System (ADS)
Chopard, Bastien; de Sousa, Daniel Ribeiro; Lätt, Jonas; Mountrakis, Lampros; Dubois, Frank; Yourassowsky, Catherine; Van Antwerpen, Pierre; Eker, Omer; Vanhamme, Luc; Perez-Morga, David; Courbebaisse, Guy; Lorenz, Eric; Hoekstra, Alfons G.; Boudjeltia, Karim Zouaoui
2017-04-01
The early stages of clot formation in blood vessels involve platelet adhesion-aggregation. Although these mechanisms have been extensively studied, gaps in their understanding still persist. We have performed detailed in vitro experiments, using the well-known Impact-R device, and developed a numerical model to better describe and understand this phenomenon. Unlike previous studies, we took into account the differential role of pre-activated and non-activated platelets, as well as the three-dimensional nature of the aggregation process. Our investigation reveals that blood albumin is a major parameter limiting platelet aggregate formation in our experiment. Simulations are in very good agreement with observations and provide quantitative estimates of the adhesion and aggregation rates that are hard to measure experimentally. They also provide a value of the effective diffusion of platelets in blood subject to the shear rate produced by the Impact-R.
An Aß concatemer with altered aggregation propensities.
Giehm, L; Dal Degan, F; Fraser, P; Klysner, S; Otzen, Daniel E
2010-10-01
We present an analysis of the conformational and aggregative properties of an Aß concatemer (Con-Alz) of interest for vaccine development against Alzheimer's disease. Con-Alz consists of 3 copies of the 43 residues of the Aß peptide separated by the P2 and P30 T-cell epitopes from the tetanus toxin. Even in the presence of high concentrations of denaturants or fluorinated alcohols, Con-Alz has a very high propensity to form aggregates which slowly coalesce over time with changes in secondary, tertiary and quaternary structure. Only micellar concentrations of SDS were able to inhibit aggregation. The increase in the ability to bind the fibril-binding dye ThT increases without lag time, which is characteristic of relatively amorphous aggregates. Confirming this, electron microscopy reveals that Con-Alz adopts a morphology resembling truncated protofibrils after prolonged incubation, but it is unable to assemble into classical amyloid fibrils. Despite its high propensity to aggregate, Con-Alz does not show any significant ability to permeabilize vesicles, which for fibrillating proteins is taken to be a key factor in aggregate cytotoxicity and is attributed to oligomers formed at an early stage in the fibrillation process. Physically linking multiple copies of the Aß-peptide may thus sterically restrict Con-Alz against forming cytotoxic oligomers, forcing it instead to adopt a less well-organized assembly of intermeshed polypeptide chains. Copyright © 2010 Elsevier B.V. All rights reserved.
Action simulation: time course and representational mechanisms
Springer, Anne; Parkinson, Jim; Prinz, Wolfgang
2013-01-01
The notion of action simulation refers to the ability to re-enact foreign actions (i.e., actions observed in other individuals). Simulating others' actions implies a mirroring of their activities, based on one's own sensorimotor competencies. Here, we discuss theoretical and experimental approaches to action simulation and the study of its representational underpinnings. One focus of our discussion is on the timing of internal simulation and its relation to the timing of external action, and a paradigm that requires participants to predict the future course of actions that are temporarily occluded from view. We address transitions between perceptual mechanisms (referring to action representation before and after occlusion) and simulation mechanisms (referring to action representation during occlusion). Findings suggest that action simulation runs in real-time; acting on newly created action representations rather than relying on continuous visual extrapolations. A further focus of our discussion pertains to the functional characteristics of the mechanisms involved in predicting other people's actions. We propose that two processes are engaged, dynamic updating and static matching, which may draw on both semantic and motor information. In a concluding section, we discuss these findings in the context of broader theoretical issues related to action and event representation, arguing that a detailed functional analysis of action simulation in cognitive, neural, and computational terms may help to further advance our understanding of action cognition and motor control. PMID:23847563
Aggregated particles caused by instrument artifact
NASA Astrophysics Data System (ADS)
Pierce, Ashley M.; Loría-Salazar, S. Marcela; Arnott, W. Patrick; Edwards, Grant C.; Miller, Matthieu B.; Gustin, Mae S.
2018-04-01
Previous studies have indicated that superaggregates, clusters of aggregates of soot primary particles, can be formed in large-scale turbulent fires. Due to lower effective densities, higher porosity, and lower aerodynamic diameters, superaggregates may pass through inlets designed to remove particles < 2.5 µm in aerodynamic diameter (PM2.5). Ambient particulate matter samples were collected at Peavine Peak, NV, USA (2515 m) northwest of Reno, NV, USA from June to November 2014. The Teledyne Advanced Pollution Instrumentation (TAPI) 602 BetaPlus particulate monitor was used to collect PM2.5 on two filter types. During this time, aggregated particles > 2.5 µm in aerodynamic diameter were collected on 36 out of 158 sample days. On preliminary analysis, it was thought that these aggregated particles were superaggregates, depositing past PM10 (particles < 10 µm in aerodynamic diameter) pre-impactors and PM2.5 cyclones. However, further analysis revealed that these aggregated particles were dissimilar to superaggregates observed in previous studies, both in morphology and in elemental composition. To determine if the aggregated particles were superaggregates or an instrument artifact, samples were investigated for the presence of certain elements, the occurrence of fires, high relative humidity and wind speeds, as well as the use of generators on site. Samples with aggregated particles, referred to as aggregates, were analyzed using a scanning electron microscope for size and shape and energy dispersive X-ray spectroscopy was used for elemental analysis. It was determined, based on the high amounts of aluminum present in the aggregate samples, that a sampling artifact associated with the sample inlet and prolonged, high wind events was the probable reason for the observed aggregates.
Development and operation of a real-time simulation at the NASA Ames Vertical Motion Simulator
NASA Technical Reports Server (NTRS)
Sweeney, Christopher; Sheppard, Shirin; Chetelat, Monique
1993-01-01
The Vertical Motion Simulator (VMS) facility at the NASA Ames Research Center combines the largest vertical motion capability in the world with a flexible real-time operating system allowing research to be conducted quickly and effectively. Due to the diverse nature of the aircraft simulated and the large number of simulations conducted annually, the challenge for the simulation engineer is to develop an accurate real-time simulation in a timely, efficient manner. The SimLab facility and the software tools necessary for an operating simulation will be discussed. Subsequent sections will describe the development process through operation of the simulation; this includes acceptance of the model, validation, integration and production phases.
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.
Adaptive Aggregation Routing to Reduce Delay for Multi-Layer Wireless Sensor Networks.
Li, Xujing; Liu, Anfeng; Xie, Mande; Xiong, Neal N; Zeng, Zhiwen; Cai, Zhiping
2018-04-16
The quality of service (QoS) regarding delay, lifetime and reliability is the key to the application of wireless sensor networks (WSNs). Data aggregation is a method to effectively reduce the data transmission volume and improve the lifetime of a network. In the previous study, a common strategy required that data wait in the queue. When the length of the queue is greater than or equal to the predetermined aggregation threshold ( N t ) or the waiting time is equal to the aggregation timer ( T t ), data are forwarded at the expense of an increase in the delay. The primary contributions of the proposed Adaptive Aggregation Routing (AAR) scheme are the following: (a) the senders select the forwarding node dynamically according to the length of the data queue, which effectively reduces the delay. In the AAR scheme, the senders send data to the nodes with a long data queue. The advantages are that first, the nodes with a long data queue need a small amount of data to perform aggregation; therefore, the transmitted data can be fully utilized to make these nodes aggregate. Second, this scheme balances the aggregating and data sending load; thus, the lifetime increases. (b) An improved AAR scheme is proposed to improve the QoS. The aggregation deadline ( T t ) and the aggregation threshold ( N t ) are dynamically changed in the network. In WSNs, nodes far from the sink have residual energy because these nodes transmit less data than the other nodes. In the improved AAR scheme, the nodes far from the sink have a small value of T t and N t to reduce delay, and the nodes near the sink are set to a large value of T t and N t to reduce energy consumption. Thus, the end to end delay is reduced, a longer lifetime is achieved, and the residual energy is fully used. Simulation results demonstrate that compared with the previous scheme, the performance of the AAR scheme is improved. This scheme reduces the delay by 14.91%, improves the lifetime by 30.91%, and increases energy
Early aggregation studies of diabetic amyloid in solution
NASA Astrophysics Data System (ADS)
Singh, Sadanand; de Pablo, Juan
2011-03-01
Islet amyloid polypeptide (IAPP, also known as amylin) is responsible for pancreatic amyloid deposits in type II diabetes. The deposits, as well as intermediates in their assembly, are cytotoxic to pancreatic β -cells and contribute to the loss of β -cell mass associated with type II diabetes. To better understand the mechanism and cause of such aggregation, molecular simulations with explicit solvent models were used to compare monomer structure and early aggregation mechanism. Using free-energy maps generated~through~a variety of novel, enhanced sampling free-energy calculation techniques, we have found that, in water, the peptide adopts three major structures. One has a small α -helix at the N-terminus and a small β -hairpin at the other end. The second and the most stable one, is a complete β -hairpin, and the third is a random coil structure. Transition Path Sampling simulations along with reaction coordinate analysis reveal that the peptide follows a ``zipping mechanism'' in folding from α -helical to β -hairpin state. From studies of the dimerization of monomers in water, we have found that the early aggregation proceeds by conversion of all α -helical configurations to β -hairpins, and by two β -hairpins coming together to form a parallel β -sheet. Several aspects of the proposed mechanism have been verified by concerted 2D IR experimental measurements, thereby adding credence to the validity of our predictions.
Real-time simulations for automated rendezvous and capture
NASA Technical Reports Server (NTRS)
Cuseo, John A.
1991-01-01
Although the individual technologies for automated rendezvous and capture (AR&C) exist, they have not yet been integrated to produce a working system in the United States. Thus, real-time integrated systems simulations are critical to the development and pre-flight demonstration of an AR&C capability. Real-time simulations require a level of development more typical of a flight system compared to purely analytical methods, thus providing confidence in derived design concepts. This presentation will describe Martin Marietta's Space Operations Simulation (SOS) Laboratory, a state-of-the-art real-time simulation facility for AR&C, along with an implementation for the Satellite Servicer System (SSS) Program.
Insulin aggregation tracked by its intrinsic TRES
NASA Astrophysics Data System (ADS)
Chung, Li Hung C.; Birch, David J. S.; Vyshemirsky, Vladislav; Ryadnov, Maxim G.; Rolinski, Olaf J.
2017-12-01
Time-resolved emission spectra (TRES) have been used to detect conformational changes of intrinsic tyrosines within bovine insulin at a physiological pH. The approach offers the ability to detect the initial stages of insulin aggregation at the molecular level. The data analysis has revealed the existence of at least three fluorescent species undergoing dielectric relaxation and significant spectral changes due to insulin aggregation. The results indicate the suitability of the intrinsic TRES approach for insulin studies and for monitoring its stability during storage and aggregation in insulin delivery devices.
A brief review of the construction aggregates market
Willett, Jason Christopher
2012-01-01
The U.S. Geological Survey defines the construction aggregates industry as those companies that mine and process crushed stone and/or construction sand and gravel. Aggregates have been used from the earliest times of our civilization for a variety of purposes - construction being the major use. As construction aggregates, crushed stone and construction sand and gravel are the basic raw materials used to build the foundation for modern society. The widespread use of construction aggregates is the result of their general availability throughout the country and around the world along with their relatively low cost. Although construction aggregates have a low unit value, their widespread use makes them major contributors to, and indicators of, the economic well-being of the nation.
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.
Kampf, G; Ritter, J M
1994-01-01
Glyceryl trinitrate is a weak inhibitor of platelet aggregation in vitro. Its effect on platelet aggregation in response to U46619 (a thromboxane/endoperoxide receptor agonist) was studied turbidometrically in platelet-rich plasma from healthy volunteers. The object was to determine whether inhibition was influenced by a period of preincubation between preparation of platelet-rich plasma and addition of glyceryl trinitrate. Incubation was performed at 37 degrees C and 22 degrees C. Samples were removed at intervals and transferred to an aggregometer cuvette at 37 degrees C. Glyceryl trinitrate (100 microM) or an equal volume of distilled water was added 5 min before U46619 (2 microM), and aggregation recorded as change in light transmission. Inhibition by glyceryl trinitrate was markedly time and temperature dependent, with a progressive increase in inhibitory potency between 120 and 300 min preincubation at 37 degrees C but not at 22 degrees C. The explanation of this is unknown but the effect was not influenced by lipopolysaccharide or by cycloheximide, so it does not appear to be due to exposure to endotoxin or to enzyme induction in vitro. PMID:7946941
NASA Astrophysics Data System (ADS)
Hoshiar, Ali Kafash; Le, Tuan-Anh; Amin, Faiz Ul; Kim, Myeong Ok; Yoon, Jungwon
2017-04-01
Magnetic-guided targeted drug delivery (TDD) systems can enhance the treatment of diverse diseases. Despite the potential and promising results of nanoparticles, aggregation prevents precise particle guidance in the vasculature. In this study, we developed a simulation platform to investigate aggregation during steering of nanoparticles using a magnetic field function. The magnetic field function (MFF) comprises a positive and negative pulsed magnetic field generated by electromagnetic coils, which prevents adherence of particles to the vessel wall during magnetic guidance. A commonly used Y-shaped vessel was simulated and the performance of the MFF analyzed; the experimental data were in agreement with the simulation results. Moreover, the effects of various parameters on magnetic guidance were evaluated and the most influential identified. The simulation results presented herein will facilitate more precise guidance of nanoparticles in vivo.
NASA Astrophysics Data System (ADS)
Fagan, T. J.; Komatsu, M.; Nishijima, E.; Fukushima, H.; Yasuda, T.
2016-08-01
Coarse low-Ca pyroxene has been identified in two amoeboid olivine aggregates in the CV3 Allende. The pyroxene crystals appear to be relict chondrule phenocrysts. If so, the texture indicates overlapping formation times of AOAs and chondrules.
Raschke, Tanya M.; Tsai, Jerry; Levitt, Michael
2001-01-01
The hydrophobic interaction, the tendency for nonpolar molecules to aggregate in solution, is a major driving force in biology. In a direct approach to the physical basis of the hydrophobic effect, nanosecond molecular dynamics simulations were performed on increasing numbers of hydrocarbon solute molecules in water-filled boxes of different sizes. The intermittent formation of solute clusters gives a free energy that is proportional to the loss in exposed molecular surface area with a constant of proportionality of 45 ± 6 cal/mol⋅Å2. The molecular surface area is the envelope of the solute cluster that is impenetrable by solvent and is somewhat smaller than the more traditional solvent-accessible surface area, which is the area transcribed by the radius of a solvent molecule rolled over the surface of the cluster. When we apply a factor relating molecular surface area to solvent-accessible surface area, we obtain 24 cal/mol⋅Å2. Ours is the first direct calculation, to our knowledge, of the hydrophobic interaction from molecular dynamics simulations; the excellent qualitative and quantitative agreement with experiment proves that simple van der Waals interactions and atomic point-charge electrostatics account for the most important driving force in biology. PMID:11353861
Design of a microfluidic system for red blood cell aggregation investigation.
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.
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.
The influence of ion content on mobility and ion aggregation in PEO-based single-ion conductors
NASA Astrophysics Data System (ADS)
Caldwell, David; Maranas, Janna
2013-03-01
PEO-based ionomers reduce concentration polarization in solid polymer electrolytes by binding the anion to the polymer backbone. Ionomers have significant ion aggregation compared to PEO/salt systems, and the influence of these aggregates is unclear. When ion transport is coupled to the segmental dynamics of the polymer, aggregation will always reduce ion motion and conductivity. However, the conductivity of PEO ionomers is not sensitive to the degree of aggregation. We present results of molecular dynamics simulations where ion content is systematically varied. We consider the influence of ion content on ion aggregation, polymer mobility and cation motion.
Convection-driven aggregation of micron sized capsules
NASA Astrophysics Data System (ADS)
Shklyaev, Oleg; Shum, Henry; Balazs, Anna
Collective dynamics of microcapsules often serve as a model for understanding behavior observed in colonies of biological cells. Using computer simulations, we explore the capability of chemically generated convection to assemble microcapsules into a colony with neighbors close enough to facilitate chemical communication. The microcapsules are assumed to carry a supply of chemical fuel. When this fuel, leaking out of the capsules, reacts at enzyme-covered sites of the chamber, the reaction generates fluid density variations driving flows. These flows carry the microcapsules, which tend to aggregate into colonies on and near the enzyme-covered sites. This aggregation continues until the reagent has been depleted and convection stops. We show that capsule colonies of predesigned shapes can be assembled by patterning the enzyme-covered surface.
β-sheet propensity controls the kinetic pathways and morphologies of seeded peptide aggregation
NASA Astrophysics Data System (ADS)
Morriss-Andrews, Alex; Bellesia, Giovanni; Shea, Joan-Emma
2012-10-01
The effect of seeds in templating the morphology of peptide aggregates is examined using molecular dynamics simulations and a coarse-grained peptide representation. Varying the nature of the aggregate seed between β-sheet, amorphous, and β-barrel seeds leads to different aggregation pathways and to morphologically different aggregates. Similar effects are seen by varying the β-sheet propensity of the free peptides. For a fibrillar seed and free peptides of high β-sheet propensity, fibrillar growth occurred by means of direct attachment (without structural rearrangement) of free individual peptides and small ordered oligomers onto the seed. For a fibrillar seed and free peptides of low β-sheet propensity, fibrillar growth occurred through a dock-lock mechanism, in which the free peptides first docked onto the seed, and then locked on, extending and aligning to join the fibril. Amorphous seeds absorbed free peptides into themselves indiscriminately, with any fibrillar rearrangement subsequent to this absorption by means of a condensation-ordering transition. Although the mechanisms observed by varying peptide β-sheet propensity are diverse, the initial pathways can always be broken down into the following steps: (i) the free peptides diffuse in the bulk and attach individually to the seed; (ii) the free peptides diffuse and aggregate among themselves; (iii) the free peptide oligomers collide with the seed; and (iv) the free oligomers merge with the seed and rearrange in a manner dependent on the backbone flexibility of both the free and seed peptides. Our simulations indicate that it is possible to sequester peptides from amorphous aggregates into fibrils, and also that aggregate morphology (and thus cytoxicity) can be controlled by introducing seeds of aggregate-compatible peptides with differing β-sheet propensities into the system.
Aggregation, sedimentation, dissolution and bioavailability of ...
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
Behavior-based aggregation of land categories for temporal change analysis
NASA Astrophysics Data System (ADS)
Aldwaik, Safaa Zakaria; Onsted, Jeffrey A.; Pontius, Robert Gilmore, Jr.
2015-03-01
Comparison between two time points of the same categorical variable for the same study extent can reveal changes among categories over time, such as transitions among land categories. If many categories exist, then analysis can be difficult to interpret. Category aggregation is the procedure that combines two or more categories to create a single broader category. Aggregation can simplify interpretation, and can also influence the sizes and types of changes. Some classifications have an a priori hierarchy to facilitate aggregation, but an a priori aggregation might make researchers blind to important category dynamics. We created an algorithm to aggregate categories in a sequence of steps based on the categories' behaviors in terms of gross losses and gross gains. The behavior-based algorithm aggregates net gaining categories with net gaining categories and aggregates net losing categories with net losing categories, but never aggregates a net gaining category with a net losing category. The behavior-based algorithm at each step in the sequence maintains net change and maximizes swap change. We present a case study where data from 2001 and 2006 for 64 land categories indicate change on 17% of the study extent. The behavior-based algorithm produces a set of 10 categories that maintains nearly the original amount of change. In contrast, an a priori aggregation produces 10 categories while reducing the change to 9%. We offer a free computer program to perform the behavior-based aggregation.
Controlling ion aggregation and conduction in PEO-based ionomers.
NASA Astrophysics Data System (ADS)
Caldwell, David, II; Maranas, Janna
2015-03-01
PEO-based ionomers are ideal for reducing concentration polarization found in typical solid polymer electrolytes. This is achieved by binding the anion to the polymer backbone, significantly reducing the anions mobility. Ion aggregation is prevalent in these systems, but their influence on SPE performance is difficult to study experimentally. We present results of molecular dynamics simulations that explore the relationship between ion content and temperature on ion aggregation, polymer motion, and ion conduction. An unforeseen result of ionomers is the creation of string like aggregates that form conduction pathways in the amorphous region. These conduction pathways allow for a partial decoupling of ion conduction with polymer dynamics. The improvement in conductivity through the use of ion aggregates can be quantified by calculating the inverse of the Haven Ratio, dubbed f-value. Typical SPEs have an f-value less than 0.2, while the ionomers of study exhibit f-values near unity or higher. Understanding what properties influence the development and use of these conduction pathways will provide insight for further development of solid polymer electrolytes.
Real-time Simulation of Turboprop Engine Control System
NASA Astrophysics Data System (ADS)
Sheng, Hanlin; Zhang, Tianhong; Zhang, Yi
2017-05-01
On account of the complexity of turboprop engine control system, real-time simulation is the technology, under the prerequisite of maintaining real-time, to effectively reduce development cost, shorten development cycle and avert testing risks. The paper takes RT-LAB as a platform and studies the real-time digital simulation of turboprop engine control system. The architecture, work principles and external interfaces of RT-LAB real-time simulation platform are introduced firstly. Then based on a turboprop engine model, the control laws of propeller control loop and fuel control loop are studied. From that and on the basis of Matlab/Simulink, an integrated controller is designed which can realize the entire process control of the engine from start-up to maximum power till stop. At the end, on the basis of RT-LAB platform, the real-time digital simulation of the designed control system is studied, different regulating plans are tried and more ideal control effects have been obtained.
An intelligent processing environment for real-time simulation
NASA Technical Reports Server (NTRS)
Carroll, Chester C.; Wells, Buren Earl, Jr.
1988-01-01
The development of a highly efficient and thus truly intelligent processing environment for real-time general purpose simulation of continuous systems is described. Such an environment can be created by mapping the simulation process directly onto the University of Alamba's OPERA architecture. To facilitate this effort, the field of continuous simulation is explored, highlighting areas in which efficiency can be improved. Areas in which parallel processing can be applied are also identified, and several general OPERA type hardware configurations that support improved simulation are investigated. Three direct execution parallel processing environments are introduced, each of which greatly improves efficiency by exploiting distinct areas of the simulation process. These suggested environments are candidate architectures around which a highly intelligent real-time simulation configuration can be developed.
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.
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.
Adaptive time steps in trajectory surface hopping simulations
DOE Office of Scientific and Technical Information (OSTI.GOV)
Spörkel, Lasse, E-mail: spoerkel@kofo.mpg.de; Thiel, Walter, E-mail: thiel@kofo.mpg.de
2016-05-21
Trajectory surface hopping (TSH) simulations are often performed in combination with active-space multi-reference configuration interaction (MRCI) treatments. Technical problems may arise in such simulations if active and inactive orbitals strongly mix and switch in some particular regions. We propose to use adaptive time steps when such regions are encountered in TSH simulations. For this purpose, we present a computational protocol that is easy to implement and increases the computational effort only in the critical regions. We test this procedure through TSH simulations of a GFP chromophore model (OHBI) and a light-driven rotary molecular motor (F-NAIBP) on semiempirical MRCI potential energymore » surfaces, by comparing the results from simulations with adaptive time steps to analogous ones with constant time steps. For both test molecules, the number of successful trajectories without technical failures rises significantly, from 53% to 95% for OHBI and from 25% to 96% for F-NAIBP. The computed excited-state lifetime remains essentially the same for OHBI and increases somewhat for F-NAIBP, and there is almost no change in the computed quantum efficiency for internal rotation in F-NAIBP. We recommend the general use of adaptive time steps in TSH simulations with active-space CI methods because this will help to avoid technical problems, increase the overall efficiency and robustness of the simulations, and allow for a more complete sampling.« less
Adaptive time steps in trajectory surface hopping simulations
NASA Astrophysics Data System (ADS)
Spörkel, Lasse; Thiel, Walter
2016-05-01
Trajectory surface hopping (TSH) simulations are often performed in combination with active-space multi-reference configuration interaction (MRCI) treatments. Technical problems may arise in such simulations if active and inactive orbitals strongly mix and switch in some particular regions. We propose to use adaptive time steps when such regions are encountered in TSH simulations. For this purpose, we present a computational protocol that is easy to implement and increases the computational effort only in the critical regions. We test this procedure through TSH simulations of a GFP chromophore model (OHBI) and a light-driven rotary molecular motor (F-NAIBP) on semiempirical MRCI potential energy surfaces, by comparing the results from simulations with adaptive time steps to analogous ones with constant time steps. For both test molecules, the number of successful trajectories without technical failures rises significantly, from 53% to 95% for OHBI and from 25% to 96% for F-NAIBP. The computed excited-state lifetime remains essentially the same for OHBI and increases somewhat for F-NAIBP, and there is almost no change in the computed quantum efficiency for internal rotation in F-NAIBP. We recommend the general use of adaptive time steps in TSH simulations with active-space CI methods because this will help to avoid technical problems, increase the overall efficiency and robustness of the simulations, and allow for a more complete sampling.
Arfuso, F; Giannetto, C; Giudice, E; Fazio, F; Piccione, G
2016-02-01
The effect of exercise on platelet aggregation, albumin and nonesterified fatty acids (NEFAs) values and the correlation among these parameters were evaluated in ten clinically healthy and regularly trained Thoroughbred horses. All horses were subjected to two simulated races. Blood samples were collected by jugular venipuncture before and after the first simulated race (T0PRE and T0POST), every 7 days at rest condition for a month (T1R-T2R-T3R), and before and after the second simulated race (T4PRE and T4POST) in order to assess platelet aggregation, albumin and nonesterified fatty acids (NEFAs) levels. One-way analysis of variance showed a significant effect of exercise (P<0.01) on platelet aggregation, albumin and NEFAs values. A negative correlation between platelet aggregation and albumin or NEFAs values, and a positive correlation between albumin and NEFAs values, were found both at T0POST and T4POST (P<0.05). These findings are likely related to dynamic physiological adaptations to exercise that allow re-establishment of the homeostatic equilibrium of the organism. Copyright © 2015 Elsevier Ltd. All rights reserved.
Azaphilones inhibit tau aggregation and dissolve tau aggregates in vitro.
Paranjape, Smita R; Riley, Andrew P; Somoza, Amber D; Oakley, C Elizabeth; Wang, Clay C C; Prisinzano, Thomas E; Oakley, Berl R; Gamblin, T Chris
2015-05-20
The aggregation of the microtubule-associated protein tau is a seminal event in many neurodegenerative diseases, including Alzheimer's disease. The inhibition or reversal of tau aggregation is therefore a potential therapeutic strategy for these diseases. Fungal natural products have proven to be a rich source of useful compounds having wide varieties of biological activities. We have previously screened Aspergillus nidulans secondary metabolites for their ability to inhibit tau aggregation in vitro using an arachidonic acid polymerization protocol. One aggregation inhibitor identified was asperbenzaldehyde, an intermediate in azaphilone biosynthesis. We therefore tested 11 azaphilone derivatives to determine their tau assembly inhibition properties in vitro. All compounds tested inhibited tau filament assembly to some extent, and four of the 11 compounds had the advantageous property of disassembling preformed tau aggregates in a dose-dependent fashion. The addition of these compounds to the tau aggregates reduced both the total length and number of tau polymers. The most potent compounds were tested in in vitro reactions to determine whether they interfere with tau's normal function of stabilizing microtubules (MTs). We found that they did not completely inhibit MT assembly in the presence of tau. These derivatives are very promising lead compounds for tau aggregation inhibitors and, more excitingly, for compounds that can disassemble pre-existing tau filaments. They also represent a new class of anti-tau aggregation compounds with a novel structural scaffold.
DOE Office of Scientific and Technical Information (OSTI.GOV)
Hong, Jiyun; Jeon, SuKyung; Kim, Janice J.
2014-07-24
Oligomeric thiophenes are commonly-used components in organic electronics and solar cells. These molecules stack and/or aggregate readily under the processing conditions used to form thin films for these applications, significantly altering their optical and charge-transport properties. To determine how these effects depend on the substitution pattern of the thiophene main chains, nano-aggregates of three sexi-thiophene (6T) oligomers having different alkyl substitution patterns were formed using solvent poisoning techniques and studied using steady-state and time-resolved emission spectroscopy. The results indicate the substantial role played by the side-chain substituents in determining the emissive properties of these species. Both the measured spectral changesmore » and their dependence on substitution are well modeled by combined quantum chemistry and molecular dynamics simulations. The simulations connect the side-chain-induced disorder, which determines the favorable chain packing configurations within the aggregates, with their measured electronic spectra.« less
Real-time hierarchically distributed processing network interaction simulation
NASA Technical Reports Server (NTRS)
Zimmerman, W. F.; Wu, C.
1987-01-01
The Telerobot Testbed is a hierarchically distributed processing system which is linked together through a standard, commercial Ethernet. Standard Ethernet systems are primarily designed to manage non-real-time information transfer. Therefore, collisions on the net (i.e., two or more sources attempting to send data at the same time) are managed by randomly rescheduling one of the sources to retransmit at a later time interval. Although acceptable for transmitting noncritical data such as mail, this particular feature is unacceptable for real-time hierarchical command and control systems such as the Telerobot. Data transfer and scheduling simulations, such as token ring, offer solutions to collision management, but do not appropriately characterize real-time data transfer/interactions for robotic systems. Therefore, models like these do not provide a viable simulation environment for understanding real-time network loading. A real-time network loading model is being developed which allows processor-to-processor interactions to be simulated, collisions (and respective probabilities) to be logged, collision-prone areas to be identified, and network control variable adjustments to be reentered as a means of examining and reducing collision-prone regimes that occur in the process of simulating a complete task sequence.
Theoretical insights into aggregation-induced helicity modulation of a perylene bisimide derivative.
Liang, Lijun; Li, Xin
2018-02-12
Formation of helical chiroptical self-assemblies via noncovalent interaction is a widely observed phenomenon in nature, the mechanism of which remains insufficiently understood. Employing an amphiphilic perylene-sugar dyad molecule (PBI-HAG) as an example, we report that the modulatable supramolecular helicity may emerge from an aggregating process that is dominated by competition between two types of noncovalent interaction: hydrogen bonding and π-π stacking. The interplay between these two driving forces, which is greatly affected by the solvent environment, determines the morphology the supramolecular assembly of PBI-HAGs. In particular, a non-layered supramolecular structure was formed in octane owing to stabilization effects of intermolecular hydrogen bonds, whereas a layered supramolecular structure was formed in water because of energetically favorable π-π stacking of aromatic rings. The formation of distinct supramolecular architectures in different solvents was reinforced by simulated circular dichroism spectra, which show opposite signals consistent with experimental observations. The results of this study could help us understand aggregation-induced supramolecular chirality of noncovalent self-assemblies. Graphical abstract Left Typical structures of amphiphilic perylene-sugar dyad (PBI-HAG) aggregates in different octane and water. Right Simulated CD and UV-Vis spectra of core PBIs aggregates in octane and water.
Boat, wake, and wave real-time simulation
NASA Astrophysics Data System (ADS)
Świerkowski, Leszek; Gouthas, Efthimios; Christie, Chad L.; Williams, Owen M.
2009-05-01
We describe the extension of our real-time scene generation software VIRSuite to include the dynamic simulation of small boats and their wakes within an ocean environment. Extensive use has been made of the programmabilty available in the current generation of GPUs. We have demonstrated that real-time simulation is feasible, even including such complexities as dynamical calculation of the boat motion, wake generation and calculation of an FFTgenerated sea state.
Parallelizing Timed Petri Net simulations
NASA Technical Reports Server (NTRS)
Nicol, David M.
1993-01-01
The possibility of using parallel processing to accelerate the simulation of Timed Petri Nets (TPN's) was studied. It was recognized that complex system development tools often transform system descriptions into TPN's or TPN-like models, which are then simulated to obtain information about system behavior. Viewed this way, it was important that the parallelization of TPN's be as automatic as possible, to admit the possibility of the parallelization being embedded in the system design tool. Later years of the grant were devoted to examining the problem of joint performance and reliability analysis, to explore whether both types of analysis could be accomplished within a single framework. In this final report, the results of our studies are summarized. We believe that the problem of parallelizing TPN's automatically for MIMD architectures has been almost completely solved for a large and important class of problems. Our initial investigations into joint performance/reliability analysis are two-fold; it was shown that Monte Carlo simulation, with importance sampling, offers promise of joint analysis in the context of a single tool, and methods for the parallel simulation of general Continuous Time Markov Chains, a model framework within which joint performance/reliability models can be cast, were developed. However, very much more work is needed to determine the scope and generality of these approaches. The results obtained in our two studies, future directions for this type of work, and a list of publications are included.
Aggregation of montmorillonite and organic matter in aqueous media containing artificial seawater.
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.
Time-reversed, flow-reversed ballistics simulations
DOE Office of Scientific and Technical Information (OSTI.GOV)
Zernow, L.; Chapyak, E. J.; Scheffler, D. R.
2001-01-01
Two-dimensional simulations of planar sheet jet formation are studied to examine the hydrodynamic issues involved when simulations are carried out in the inverse direction, that is, with reversed time and flow. Both a realistic copper equation of state and a shockless equation of state were used. These studies are an initial step in evaluating this technique as a ballistics design tool.
Marine Synechococcus Aggregation
NASA Astrophysics Data System (ADS)
Neuer, S.; Deng, W.; Cruz, B. N.; Monks, L.
2016-02-01
Cyanobacteria are considered to play an important role in the oceanic biological carbon pump, especially in oligotrophic regions. But as single cells are too small to sink, their carbon export has to be mediated by aggregate formation and possible consumption by zooplankton producing sinking fecal pellets. Here we report results on the aggregation of the ubiquitous marine pico-cyanobacterium Synechococcus as a model organism. We first investigated the mechanism behind such aggregation by studying the potential role of transparent exopolymeric particles (TEP) and the effects of nutrient (nitrogen or phosphorus) limitation on the TEP production and aggregate formation of these pico-cyanobacteria. We further studied the aggregation and subsequent settling in roller tanks and investigated the effects of the clays kaolinite and bentonite in a series of concentrations. Our results show that despite of the lowered growth rates, Synechococcus in nutrient limited cultures had larger cell-normalized TEP production, formed a greater volume of aggregates, and resulted in higher settling velocities compared to results from replete cultures. In addition, we found that despite their small size and lack of natural ballasting minerals, Synechococcus cells could still form aggregates and sink at measureable velocities in seawater. Clay minerals increased the number and reduced the size of aggregates, and their ballasting effects increased the sinking velocity and carbon export potential of aggregates. In comparison with the Synechococcus, we will also present results of the aggregation of the pico-cyanobacterium Prochlorococcus in roller tanks. These results contribute to our understanding in the physiology of marine Synechococcus as well as their role in the ecology and biogeochemistry in oligotrophic oceans.
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.
Quantifying Aggregation Dynamics during Myxococcus xanthus Development▿†
Zhang, Haiyang; Angus, Stuart; Tran, Michael; Xie, Chunyan; Igoshin, Oleg A.; Welch, Roy D.
2011-01-01
Under starvation conditions, a swarm of Myxococcus xanthus cells will undergo development, a multicellular process culminating in the formation of many aggregates called fruiting bodies, each of which contains up to 100,000 spores. The mechanics of symmetry breaking and the self-organization of cells into fruiting bodies is an active area of research. Here we use microcinematography and automated image processing to quantify several transient features of developmental dynamics. An analysis of experimental data indicates that aggregation reaches its steady state in a highly nonmonotonic fashion. The number of aggregates rapidly peaks at a value 2- to 3-fold higher than the final value and then decreases before reaching a steady state. The time dependence of aggregate size is also nonmonotonic, but to a lesser extent: average aggregate size increases from the onset of aggregation to between 10 and 15 h and then gradually decreases thereafter. During this process, the distribution of aggregates transitions from a nearly random state early in development to a more ordered state later in development. A comparison of experimental results to a mathematical model based on the traffic jam hypothesis indicates that the model fails to reproduce these dynamic features of aggregation, even though it accurately describes its final outcome. The dynamic features of M. xanthus aggregation uncovered in this study impose severe constraints on its underlying mechanisms. PMID:21784940
Secure Data Aggregation Protocol for M2M Communications
2015-03-24
networking and collaboration among various devices has experienced tremendous growth. To adapt to the trend, the concept of Internet of Things ( IoT ... IoTs ): Models, Algorithms, and Implementations, accepted Title: “Privacy-Preserving Time-Series Data Aggregation for Internet of Things ” Date...public release; distribution is unlimited. (5) Privacy-Preserving Time-Series Data Aggregation for Internet of Things Abstract In recent years, the
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.
Toward a Time-Domain Fractal Lightning Simulation
NASA Astrophysics Data System (ADS)
Liang, C.; Carlson, B. E.; Lehtinen, N. G.; Cohen, M.; Lauben, D.; Inan, U. S.
2010-12-01
Electromagnetic simulations of lightning are useful for prediction of lightning properties and exploration of the underlying physical behavior. Fractal lightning models predict the spatial structure of the discharge, but thus far do not provide much information about discharge behavior in time and therefore cannot predict electromagnetic wave emissions or current characteristics. Here we develop a time-domain fractal lightning simulation from Maxwell's equations, the method of moments with the thin wire approximation, an adaptive time-stepping scheme, and a simplified electrical model of the lightning channel. The model predicts current pulse structure and electromagnetic wave emissions and can be used to simulate the entire duration of a lightning discharge. The model can be used to explore the electrical characteristics of the lightning channel, the temporal development of the discharge, and the effects of these characteristics on observable electromagnetic wave emissions.
Enhanced DNA Sensing via Catalytic Aggregation of Gold Nanoparticles
Huttanus, Herbert M.; Graugnard, Elton; Yurke, Bernard; Knowlton, William B.; Kuang, Wan; Hughes, William L.; Lee, Jeunghoon
2014-01-01
A catalytic colorimetric detection scheme that incorporates a DNA-based hybridization chain reaction into gold nanoparticles was designed and tested. While direct aggregation forms an inter-particle linkage from only ones target DNA strand, the catalytic aggregation forms multiple linkages from a single target DNA strand. Gold nanoparticles were functionalized with thiol-modified DNA strands capable of undergoing hybridization chain reactions. The changes in their absorption spectra were measured at different times and target concentrations and compared against direct aggregation. Catalytic aggregation showed a multifold increase in sensitivity at low target concentrations when compared to direct aggregation. Gel electrophoresis was performed to compare DNA hybridization reactions in catalytic and direct aggregation schemes, and the product formation was confirmed in the catalytic aggregation scheme at low levels of target concentrations. The catalytic aggregation scheme also showed high target specificity. This application of a DNA reaction network to gold nanoparticle-based colorimetric detection enables highly-sensitive, field-deployable, colorimetric readout systems capable of detecting a variety of biomolecules. PMID:23891867
Pornamazeh, Tahereh; Yadegari, Zahra; Ghasemi, Amir; Sheykh-al-Eslamian, Seyedeh Mahsa; Shojaeian, Shiva
2017-01-01
Introduction: The present study sought to evaluate and compare biocompatibility and setting time of Retro mineral trioxide aggregate (MTA), calcium-enriched mixture (CEM) and Angelus MTA. Methods and Materials: CEM cement, Angelus MTA and Retro MTA were assessed in set and fresh states. Extracts transformed to each cavity of three 24-well plates in which 1×104 cell were seeded into each well 24 h earlier. All specimens were incubated in a humidified incubator with 5% CO2 at 37°C. Mosmann’s tetrazolium toxicity (MTT) assay was used to determine in vitro cytotoxicity on L929 mouse fibroblast cell line. Cell viability was determined at 1, 24, and 72 h after exposure. The initial setting time was measured by 113.4 g Gilmore needle testing. Then, final setting times were assessed by the 456.5 g Gilmore needle. Data comparisons were performed using the analysis of variance (ANOVA) and Tukey's post hoc test (α=0.05). Results: All groups in both forms indicated higher cell vitality compared to positive control group (P<0.001). After 24 h, the set Retro MTA showed better biocompatibility compared to set CEM and set Angelus MTA (P<0.001). Retro MTA showed significantly lower initial and final setting time compared to CEM and Angelus MTA (P<0.001). Conclusion: Our results indicated the good cell viability values of Retro MTA and relatively short period of setting time. It seems a promising alternative material in clinical situations where accelerated setting is required. However, more clinical and in vivo investigations are needed for a clear decision making. PMID:29225646
Time simulation of flutter with large stiffness changes
NASA Technical Reports Server (NTRS)
Karpel, M.; Wieseman, C. D.
1992-01-01
Time simulation of flutter, involving large local structural changes, is formulated with a state-space model that is based on a relatively small number of generalized coordinates. Free-free vibration modes are first calculated for a nominal finite-element model with relatively large fictitious masses located at the area of structural changes. A low-frequency subset of these modes is then transformed into a set of structural modal coordinates with which the entire simulation is performed. These generalized coordinates and the associated oscillatory aerodynamic force coefficient matrices are used to construct an efficient time-domain, state-space model for basic aeroelastic case. The time simulation can then be performed by simply changing the mass, stiffness and damping coupling terms when structural changes occur. It is shown that the size of the aeroelastic model required for time simulation with large structural changes at a few a priori known locations is similar to that required for direct analysis of a single structural case. The method is applied to the simulation of an aeroelastic wind-tunnel model. The diverging oscillations are followed by the activation of a tip-ballast decoupling mechanism that stabilizes the system but may cause significant transient overshoots.
Time simulation of flutter with large stiffness changes
NASA Technical Reports Server (NTRS)
Karpel, Mordechay; Wieseman, Carol D.
1992-01-01
Time simulation of flutter, involving large local structural changes, is formulated with a state-space model that is based on a relatively small number of generalized coordinates. Free-free vibration modes are first calculated for a nominal finite-element model with relatively large fictitious masses located at the area of structural changes. A low-frequency subset of these modes is then transformed into a set of structural modal coordinates with which the entire simulation is performed. These generalized coordinates and the associated oscillatory aerodynamic force coefficient matrices are used to construct an efficient time-domain, state-space model for a basic aeroelastic case. The time simulation can then be performed by simply changing the mass, stiffness, and damping coupling terms when structural changes occur. It is shown that the size of the aeroelastic model required for time simulation with large structural changes at a few apriori known locations is similar to that required for direct analysis of a single structural case. The method is applied to the simulation of an aeroelastic wind-tunnel model. The diverging oscillations are followed by the activation of a tip-ballast decoupling mechanism that stabilizes the system but may cause significant transient overshoots.
Persistent homology analysis of ion aggregations and hydrogen-bonding networks.
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
Growth and form of planetary seedlings: results from a microgravity aggregation experiment.
Blum, J; Wurm, G; Kempf, S; Poppe, T; Klahr, H; Kozasa, T; Rott, M; Henning, T; Dorschner, J; Schräpler, R; Keller, H U; Markiewicz, W J; Mann, I; Gustafson, B A; Giovane, F; Neuhaus, D; Fechtig, H; Grün, E; Feuerbacher, B; Kochan, H; Ratke, L; El Goresy, A; Morfill, G; Weidenschilling, S J; Schwehm, G; Metzler, K; Ip, W H
2000-09-18
The outcome of the first stage of planetary formation, which is characterized by ballistic agglomeration of preplanetary dust grains due to Brownian motion in the free molecular flow regime of the solar nebula, is still somewhat speculative. We performed a microgravity experiment flown onboard the space shuttle in which we simulated, for the first time, the onset of free preplanetary dust accumulation and revealed the structures and growth rates of the first dust agglomerates in the young solar system. We find that a thermally aggregating swarm of dust particles evolves very rapidly and forms unexpected open-structured agglomerates.
Andrzejaczek, Samantha; Meeuwig, Jessica; Rowat, David; Pierce, Simon; Davies, Tim; Fisher, Rebecca; Meekan, Mark
2016-11-01
Genetic and modelling studies suggest that seasonal aggregations of whale sharks ( Rhincodon typus ) at coastal sites in the tropics may be linked by migration. Here, we used photo-identification (photo-ID) data collected by both citizen scientists and researchers to assess the connectedness of five whale shark aggregation sites across the entire Indian Ocean at timescales of up to a decade. We used the semi-automated program I 3 S (Individual Interactive Identification System) to compare photographs of the unique natural marking patterns of individual whale sharks collected from aggregations at Mozambique, the Seychelles, the Maldives, Christmas Island (Australia) and Ningaloo Reef (Australia). From a total of 6519 photos, we found no evidence of connectivity of whale shark aggregations at ocean-basin scales within the time frame of the study and evidence for only limited connectivity at regional (hundreds to thousands of kilometres) scales. A male whale shark photographed in January 2010 at Mozambique was resighted eight months later in the Seychelles and was the only one of 1724 individuals in the database to be photographed at more than one site. On average, 35% of individuals were resighted at the same site in more than one year. A Monte Carlo simulation study showed that the power of this photo-ID approach to document patterns of emigration and immigration was strongly dependent on both the number of individuals identified in aggregations and the size of resident populations.
Meeuwig, Jessica; Rowat, David; Pierce, Simon; Davies, Tim; Fisher, Rebecca; Meekan, Mark
2016-01-01
Genetic and modelling studies suggest that seasonal aggregations of whale sharks (Rhincodon typus) at coastal sites in the tropics may be linked by migration. Here, we used photo-identification (photo-ID) data collected by both citizen scientists and researchers to assess the connectedness of five whale shark aggregation sites across the entire Indian Ocean at timescales of up to a decade. We used the semi-automated program I3S (Individual Interactive Identification System) to compare photographs of the unique natural marking patterns of individual whale sharks collected from aggregations at Mozambique, the Seychelles, the Maldives, Christmas Island (Australia) and Ningaloo Reef (Australia). From a total of 6519 photos, we found no evidence of connectivity of whale shark aggregations at ocean-basin scales within the time frame of the study and evidence for only limited connectivity at regional (hundreds to thousands of kilometres) scales. A male whale shark photographed in January 2010 at Mozambique was resighted eight months later in the Seychelles and was the only one of 1724 individuals in the database to be photographed at more than one site. On average, 35% of individuals were resighted at the same site in more than one year. A Monte Carlo simulation study showed that the power of this photo-ID approach to document patterns of emigration and immigration was strongly dependent on both the number of individuals identified in aggregations and the size of resident populations. PMID:28018629
Interactive real time flow simulations
NASA Technical Reports Server (NTRS)
Sadrehaghighi, I.; Tiwari, S. N.
1990-01-01
An interactive real time flow simulation technique is developed for an unsteady channel flow. A finite-volume algorithm in conjunction with a Runge-Kutta time stepping scheme was developed for two-dimensional Euler equations. A global time step was used to accelerate convergence of steady-state calculations. A raster image generation routine was developed for high speed image transmission which allows the user to have direct interaction with the solution development. In addition to theory and results, the hardware and software requirements are discussed.
Real-time inextensible surgical thread simulation.
Xu, Lang; Liu, Qian
2018-03-27
This paper discusses a real-time simulation method of inextensible surgical thread based on the Cosserat rod theory using position-based dynamics (PBD). The method realizes stable twining and knotting of surgical thread while including inextensibility, bending, twisting and coupling effects. The Cosserat rod theory is used to model the nonlinear elastic behavior of surgical thread. The surgical thread model is solved with PBD to achieve a real-time, extremely stable simulation. Due to the one-dimensional linear structure of surgical thread, the direct solution of the distance constraint based on tridiagonal matrix algorithm is used to enhance stretching resistance in every constraint projection iteration. In addition, continuous collision detection and collision response guarantee a large time step and high performance. Furthermore, friction is integrated into the constraint projection process to stabilize the twining of multiple threads and complex contact situations. Through comparisons with existing methods, the surgical thread maintains constant length under large deformation after applying the direct distance constraint in our method. The twining and knotting of multiple threads correspond to stable solutions to contact and friction forces. A surgical suture scene is also modeled to demonstrate the practicality and simplicity of our method. Our method achieves stable and fast simulation of inextensible surgical thread. Benefiting from the unified particle framework, the rigid body, elastic rod, and soft body can be simultaneously simulated. The method is appropriate for applications in virtual surgery that require multiple dynamic bodies.
Effects of Convective Aggregation on Radiative Cooling and Precipitation in a CRM
NASA Astrophysics Data System (ADS)
Naegele, A. C.; Randall, D. A.
2017-12-01
In the global energy budget, the atmospheric radiative cooling (ARC) is approximately balanced by latent heating, but on regional scales, the ARC and precipitation rates are inversely related. We use a cloud-resolving model to explore how the relationship between precipitation and the ARC is affected by convective aggregation, in which the convective activity is confined to a small portion of the domain that is surrounded by a much larger region of dry, subsiding air. Sensitivity tests show that the precipitation rate and ARC are highly sensitive to both SST and microphysics; a higher SST and 1-moment microphysics both act to increase the domain-averaged ARC and precipitation rates. In all simulations, both the domain-averaged ARC and precipitation rates increased due to convective aggregation, resulting in a positive temporal correlation. Furthermore, the radiative effect of clouds in these simulations is to decrease the ARC. This finding is consistent with our observational results of the cloud effect on the ARC, and has implications for convective aggregation and the geographic extent in which it can occur.
Random access with adaptive packet aggregation in LTE/LTE-A.
Zhou, Kaijie; Nikaein, Navid
While random access presents a promising solution for efficient uplink channel access, the preamble collision rate can significantly increase when massive number of devices simultaneously access the channel. To address this issue and improve the reliability of the random access, an adaptive packet aggregation method is proposed. With the proposed method, a device does not trigger a random access for every single packet. Instead, it starts a random access when the number of aggregated packets reaches a given threshold. This method reduces the packet collision rate at the expense of an extra latency, which is used to accumulate multiple packets into a single transmission unit. Therefore, the tradeoff between packet loss rate and channel access latency has to be carefully selected. We use semi-Markov model to derive the packet loss rate and channel access latency as functions of packet aggregation number. Hence, the optimal amount of aggregated packets can be found, which keeps the loss rate below the desired value while minimizing the access latency. We also apply for the idea of packet aggregation for power saving, where a device aggregates as many packets as possible until the latency constraint is reached. Simulations are carried out to evaluate our methods. We find that the packet loss rate and/or power consumption are significantly reduced with the proposed method.
Rheology of three-dimensional packings of aggregates: microstructure and effects of nonconvexity.
Azéma, Emilien; Radjaï, Farhang; Saint-Cyr, Baptiste; Delenne, Jean-Yves; Sornay, Philippe
2013-05-01
We use three-dimensional contact dynamics simulations to analyze the rheological properties of granular materials composed of rigid aggregates. The aggregates are made from four overlapping spheres and described by a nonconvexity parameter depending on the relative positions of the spheres. The macroscopic and microstructural properties of several sheared packings are analyzed as a function of the degree of nonconvexity of the aggregates. We find that the internal angle of friction increases with the nonconvexity. In contrast, the packing fraction first increases to a maximum value but declines as the nonconvexity increases further. At a high level of nonconvexity, the packings are looser but show a higher shear strength. At the microscopic scale, the fabric and force anisotropy, as well as the friction mobilization, are enhanced by multiple contacts between aggregates and interlocking, thus revealings the mechanical and geometrical origins of shear strength.
Dispersion of ferrofluid aggregates in steady flows
NASA Astrophysics Data System (ADS)
Williams, Alicia M.; Vlachos, Pavlos P.
2011-12-01
Using focused shadowgraphs, we investigate steady flows of a magnetically non-susceptible fluid interacting with ferrofluid aggregates comprised of superparamagnetic nanoparticles. The ferrofluid aggregate is retained at a specific site within the flow channel using two different applied magnetic fields. The bulk flow induces shear stresses on the aggregate, which give rise to the development of interfacial disturbances, leading to Kelvin-Helmholtz (K-H) instabilities and shedding of ferrofluid structures. Herein, the effects of bulk Reynolds number, ranging from 100 to 1000, and maximum applied magnetic fields of 1.2 × 105 and 2.4 × 105 A/m are investigated in the context of their impact on dispersion or removal of material from the core aggregate. The aggregate interaction with steady bulk flow reveals three regimes of aggregate dynamics over the span of Reynolds numbers studied: stable, transitional, and shedding. The first regime is characterized by slight aggregate stretching for low Reynolds numbers, with full aggregate retention. As the Reynolds number increases, the aggregate is in-transition between stable and shedding states. This second regime is characterized by significant initial stretching that gives way to small amplitude Kelvin-Helmholtz waves. Higher Reynolds numbers result in ferrofluid shedding, with Strouhal numbers initially between 0.2 and 0.3, wherein large vortical structures are shed from the main aggregate accompanied by precipitous decay of the accumulated ferrofluid aggregate. These behaviors are apparent for both magnetic field strengths, although the transitional Reynolds numbers are different between the cases, as are the characteristic shedding frequencies relative to the same Reynolds number. In the final step of this study, relevant parameters were extracted from the time series dispersion data to comprehensively quantify aggregate mechanics. The aggregate half-life is found to decrease as a function of the Reynolds number
Free energy landscapes for initiation and branching of protein aggregation.
Zheng, Weihua; Schafer, Nicholas P; Wolynes, Peter G
2013-12-17
Experiments on artificial multidomain protein constructs have probed the early stages of aggregation processes, but structural details of the species that initiate aggregation remain elusive. Using the associative-memory, water-mediated, structure and energy model known as AWSEM, a transferable coarse-grained protein model, we performed simulations of fused constructs composed of up to four copies of the Titin I27 domain or its mutant I27* (I59E). Free energy calculations enable us to quantify the conditions under which such multidomain constructs will spontaneously misfold. Consistent with experimental results, the dimer of I27 is found to be the smallest spontaneously misfolding construct. Our results show how structurally distinct misfolded states can be stabilized under different thermodynamic conditions, and this result provides a plausible link between the single-molecule misfolding experiments under native conditions and aggregation experiments under denaturing conditions. The conditions for spontaneous misfolding are determined by the interplay among temperature, effective local protein concentration, and the strength of the interdomain interactions. Above the folding temperature, fusing additional domains to the monomer destabilizes the native state, and the entropically stabilized amyloid-like state is favored. Because it is primarily energetically stabilized, the domain-swapped state is more likely to be important under native conditions. Both protofibril-like and branching structures are found in annealing simulations starting from extended structures, and these structures suggest a possible connection between the existence of multiple amyloidogenic segments in each domain and the formation of branched, amorphous aggregates as opposed to linear fibrillar structures.
A Note on the Incremental Validity of Aggregate Predictors.
ERIC Educational Resources Information Center
Day, H. D.; Marshall, David
Three computer simulations were conducted to show that very high aggregate predictive validity coefficients can occur when the across-case variability in absolute score stability occurring in both the predictor and criterion matrices is quite small. In light of the increase in internal consistency reliability achieved by the method of aggregation…
Social aggregation in pea aphids: experiment and random walk modeling.
Nilsen, Christa; Paige, John; Warner, Olivia; Mayhew, Benjamin; Sutley, Ryan; Lam, Matthew; Bernoff, Andrew J; Topaz, Chad M
2013-01-01
From bird flocks to fish schools and ungulate herds to insect swarms, social biological aggregations are found across the natural world. An ongoing challenge in the mathematical modeling of aggregations is to strengthen the connection between models and biological data by quantifying the rules that individuals follow. We model aggregation of the pea aphid, Acyrthosiphon pisum. Specifically, we conduct experiments to track the motion of aphids walking in a featureless circular arena in order to deduce individual-level rules. We observe that each aphid transitions stochastically between a moving and a stationary state. Moving aphids follow a correlated random walk. The probabilities of motion state transitions, as well as the random walk parameters, depend strongly on distance to an aphid's nearest neighbor. For large nearest neighbor distances, when an aphid is essentially isolated, its motion is ballistic with aphids moving faster, turning less, and being less likely to stop. In contrast, for short nearest neighbor distances, aphids move more slowly, turn more, and are more likely to become stationary; this behavior constitutes an aggregation mechanism. From the experimental data, we estimate the state transition probabilities and correlated random walk parameters as a function of nearest neighbor distance. With the individual-level model established, we assess whether it reproduces the macroscopic patterns of movement at the group level. To do so, we consider three distributions, namely distance to nearest neighbor, angle to nearest neighbor, and percentage of population moving at any given time. For each of these three distributions, we compare our experimental data to the output of numerical simulations of our nearest neighbor model, and of a control model in which aphids do not interact socially. Our stochastic, social nearest neighbor model reproduces salient features of the experimental data that are not captured by the control.
Sustainable aggregates production : green applications for aggregate by-products.
DOT National Transportation Integrated Search
2015-06-01
Increased emphasis in the construction industry on sustainability and recycling requires production of : aggregate gradations with lower dust (cleaner aggregates) and smaller maximum sizeshence, increased : amount of quarry by-products (QBs). QBs ...
Star Polymers Reduce Islet Amyloid Polypeptide Toxicity via Accelerated Amyloid Aggregation.
Pilkington, Emily H; Lai, May; Ge, Xinwei; Stanley, William J; Wang, Bo; Wang, Miaoyi; Kakinen, Aleksandr; Sani, Marc-Antonie; Whittaker, Michael R; Gurzov, Esteban N; Ding, Feng; Quinn, John F; Davis, Thomas P; Ke, Pu Chun
2017-12-11
Protein aggregation into amyloid fibrils is a ubiquitous phenomenon across the spectrum of neurodegenerative disorders and type 2 diabetes. A common strategy against amyloidogenesis is to minimize the populations of toxic oligomers and protofibrils by inhibiting protein aggregation with small molecules or nanoparticles. However, melanin synthesis in nature is realized by accelerated protein fibrillation to circumvent accumulation of toxic intermediates. Accordingly, we designed and demonstrated the use of star-shaped poly(2-hydroxyethyl acrylate) (PHEA) nanostructures for promoting aggregation while ameliorating the toxicity of human islet amyloid polypeptide (IAPP), the peptide involved in glycemic control and the pathology of type 2 diabetes. The binding of PHEA elevated the β-sheet content in IAPP aggregates while rendering a new morphology of "stelliform" amyloids originating from the polymers. Atomistic molecular dynamics simulations revealed that the PHEA arms served as rodlike scaffolds for IAPP binding and subsequently accelerated IAPP aggregation by increased local peptide concentration. The tertiary structure of the star nanoparticles was found to be essential for driving the specific interactions required to impel the accelerated IAPP aggregation. This study sheds new light on the structure-toxicity relationship of IAPP and points to the potential of exploiting star polymers as a new class of therapeutic agents against amyloidogenesis.
Operating system for a real-time multiprocessor propulsion system simulator
NASA Technical Reports Server (NTRS)
Cole, G. L.
1984-01-01
The success of the Real Time Multiprocessor Operating System (RTMPOS) in the development and evaluation of experimental hardware and software systems for real time interactive simulation of air breathing propulsion systems was evaluated. The Real Time Multiprocessor Operating System (RTMPOS) provides the user with a versatile, interactive means for loading, running, debugging and obtaining results from a multiprocessor based simulator. A front end processor (FEP) serves as the simulator controller and interface between the user and the simulator. These functions are facilitated by the RTMPOS which resides on the FEP. The RTMPOS acts in conjunction with the FEP's manufacturer supplied disk operating system that provides typical utilities like an assembler, linkage editor, text editor, file handling services, etc. Once a simulation is formulated, the RTMPOS provides for engineering level, run time operations such as loading, modifying and specifying computation flow of programs, simulator mode control, data handling and run time monitoring. Run time monitoring is a powerful feature of RTMPOS that allows the user to record all actions taken during a simulation session and to receive advisories from the simulator via the FEP. The RTMPOS is programmed mainly in PASCAL along with some assembly language routines. The RTMPOS software is easily modified to be applicable to hardware from different manufacturers.
Growth hormone aggregates in the rat adenohypophysis
NASA Technical Reports Server (NTRS)
Farrington, M.; Hymer, W. C.
1990-01-01
Although it has been known for some time that GH aggregates are contained within the rat anterior pituitary gland, the role that they might play in pituitary function is unknown. The present study examines this issue using the technique of Western blotting, which permitted visualization of 11 GH variants with apparent mol wt ranging from 14-88K. Electroelution of the higher mol wt variants from gels followed by their chemical reduction with beta-mercaptoethanol increased GH immunoassayability by about 5-fold. With the blot procedure we found 1) that GH aggregates greater than 44K were associated with a 40,000 x g sedimentable fraction; 2) that GH aggregates were not present in glands from thyroidectomized rats, but were in glands from the thyroidectomized rats injected with T4; 3) that GH aggregates were uniquely associated with a heavily granulated somatotroph subpopulation isolated by density gradient centrifugation; and 4) that high mol wt GH forms were released from the dense somatotrophs in culture, since treatment of the culture medium with beta-mercaptoethanol increased GH immunoassayability by about 5-fold. Taken together, the results show that high mol wt GH aggregates are contained in secretory granules of certain somatotrophs and are also released in aggregate form from these cells in vitro.
Aggregation of montmorillonite and organic matter in aqueous media containing artificial seawater
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
Laser characterization of fine aggregate.
DOT National Transportation Integrated Search
2012-12-01
This report describes the results of a research effort to establish the feasibility of using a laser monitoring system to provide real-time data to characterize aggregate properties in a laboratory or field environment. This was accomplished by using...
Cushing, Christopher C; Walters, Ryan W; Hoffman, Lesa
2014-03-01
Aggregated N-of-1 randomized controlled trials (RCTs) combined with multilevel modeling represent a methodological advancement that may help bridge science and practice in pediatric psychology. The purpose of this article is to offer a primer for pediatric psychologists interested in conducting aggregated N-of-1 RCTs. An overview of N-of-1 RCT methodology is provided and 2 simulated data sets are analyzed to demonstrate the clinical and research potential of the methodology. The simulated data example demonstrates the utility of aggregated N-of-1 RCTs for understanding the clinical impact of an intervention for a given individual and the modeling of covariates to explain why an intervention worked for one patient and not another. Aggregated N-of-1 RCTs hold potential for improving the science and practice of pediatric psychology.
Modeling the reversible kinetics of neutrophil aggregation under hydrodynamic shear.
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
Time-Domain Filtering for Spatial Large-Eddy Simulation
NASA Technical Reports Server (NTRS)
Pruett, C. David
1997-01-01
An approach to large-eddy simulation (LES) is developed whose subgrid-scale model incorporates filtering in the time domain, in contrast to conventional approaches, which exploit spatial filtering. The method is demonstrated in the simulation of a heated, compressible, axisymmetric jet, and results are compared with those obtained from fully resolved direct numerical simulation. The present approach was, in fact, motivated by the jet-flow problem and the desire to manipulate the flow by localized (point) sources for the purposes of noise suppression. Time-domain filtering appears to be more consistent with the modeling of point sources; moreover, time-domain filtering may resolve some fundamental inconsistencies associated with conventional space-filtered LES approaches.
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.
Boundary Layer Height and Buoyancy Determine the Horizontal Scale of Convective Self-Aggregation
Yang, Da
2018-01-24
Organized rainstorms and their associated overturning circulations can self-emerge over an ocean surface with uniform temperature in cloud-resolving simulations. This phenomenon is referred to as convective self-aggregation. Convective self-aggregation is argued to be an important building block for tropical weather systems and may help regulate tropical atmospheric humidity and thereby tropical climate stability. Here the author presents a boundary layer theory for the horizontal scale λ of 2D (x, z) convective self-aggregation by considering both the momentum and energy constraints for steady circulations. This theory suggests that λ scales with the product of the boundary layer height h and themore » square root of the amplitude of density variation between aggregated moist and dry regions in the boundary layer, and that this density variation mainly arises from the moisture variation due to the virtual effect of water vapor. Furthermore, this theory predicts the following: 1) the order of magnitude of λ is ~2000 km, 2) the aspect ratio of the boundary layer λ/h increases with surface warming, and 3) λ decreases when the virtual effect of water vapor is disabled. These predictions are confirmed using a sui te of cloud-resolving simulations spanning a wide range of climates.« less
Boundary Layer Height and Buoyancy Determine the Horizontal Scale of Convective Self-Aggregation
DOE Office of Scientific and Technical Information (OSTI.GOV)
Yang, Da
Organized rainstorms and their associated overturning circulations can self-emerge over an ocean surface with uniform temperature in cloud-resolving simulations. This phenomenon is referred to as convective self-aggregation. Convective self-aggregation is argued to be an important building block for tropical weather systems and may help regulate tropical atmospheric humidity and thereby tropical climate stability. Here the author presents a boundary layer theory for the horizontal scale λ of 2D (x, z) convective self-aggregation by considering both the momentum and energy constraints for steady circulations. This theory suggests that λ scales with the product of the boundary layer height h and themore » square root of the amplitude of density variation between aggregated moist and dry regions in the boundary layer, and that this density variation mainly arises from the moisture variation due to the virtual effect of water vapor. Furthermore, this theory predicts the following: 1) the order of magnitude of λ is ~2000 km, 2) the aspect ratio of the boundary layer λ/h increases with surface warming, and 3) λ decreases when the virtual effect of water vapor is disabled. These predictions are confirmed using a sui te of cloud-resolving simulations spanning a wide range of climates.« less
Real-Time Visualization of an HPF-based CFD Simulation
NASA Technical Reports Server (NTRS)
Kremenetsky, Mark; Vaziri, Arsi; Haimes, Robert; Chancellor, Marisa K. (Technical Monitor)
1996-01-01
Current time-dependent CFD simulations produce very large multi-dimensional data sets at each time step. The visual analysis of computational results are traditionally performed by post processing the static data on graphics workstations. We present results from an alternate approach in which we analyze the simulation data in situ on each processing node at the time of simulation. The locally analyzed results, usually more economical and in a reduced form, are then combined and sent back for visualization on a graphics workstation.
12 CFR 1402.27 - Aggregating requests.
Code of Federal Regulations, 2011 CFR
2011-01-01
... Information § 1402.27 Aggregating requests. A requester may not file multiple requests at the same time, each... in concert, is attempting to break a request down into a series of requests for the purpose of... reasonable is the time period over which the requests have occurred. ...
12 CFR 1402.27 - Aggregating requests.
Code of Federal Regulations, 2014 CFR
2014-01-01
... Information § 1402.27 Aggregating requests. A requester may not file multiple requests at the same time, each... in concert, is attempting to break a request down into a series of requests for the purpose of... reasonable is the time period over which the requests have occurred. ...
12 CFR 1402.27 - Aggregating requests.
Code of Federal Regulations, 2010 CFR
2010-01-01
... Information § 1402.27 Aggregating requests. A requester may not file multiple requests at the same time, each... in concert, is attempting to break a request down into a series of requests for the purpose of... reasonable is the time period over which the requests have occurred. ...
Distributed simulation using a real-time shared memory network
NASA Technical Reports Server (NTRS)
Simon, Donald L.; Mattern, Duane L.; Wong, Edmond; Musgrave, Jeffrey L.
1993-01-01
The Advanced Control Technology Branch of the NASA Lewis Research Center performs research in the area of advanced digital controls for aeronautic and space propulsion systems. This work requires the real-time implementation of both control software and complex dynamical models of the propulsion system. We are implementing these systems in a distributed, multi-vendor computer environment. Therefore, a need exists for real-time communication and synchronization between the distributed multi-vendor computers. A shared memory network is a potential solution which offers several advantages over other real-time communication approaches. A candidate shared memory network was tested for basic performance. The shared memory network was then used to implement a distributed simulation of a ramjet engine. The accuracy and execution time of the distributed simulation was measured and compared to the performance of the non-partitioned simulation. The ease of partitioning the simulation, the minimal time required to develop for communication between the processors and the resulting execution time all indicate that the shared memory network is a real-time communication technique worthy of serious consideration.
Estimating linear temporal trends from aggregated environmental monitoring data
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.
Kirchner, M K; Schulze Westerath, H; Knierim, U; Tessitore, E; Cozzi, G; Winckler, C
2014-03-01
Consistency over time of (on-farm) animal welfare assessment systems forms part of reliability, meaning that results of the assessment should be representative of the longer-term welfare state of the farm as long as the housing and management conditions have not changed considerably. This is especially important if assessments are to be used for certification purposes. It was the aim of the present study to investigate consistency over time of the Welfare Quality(®) (WQ(®)) assessment system for fattening cattle at single measure level, aggregated criterion and principle scores, and overall classification across short-term (1 month) and longer-term periods (6 months). We hypothesized that consistency over time of aggregated criterion and principle scores is higher than that of single measures. Consistency was also expected to be lower with longer intervals between assessments. Data were obtained using the WQ(®) protocol for fattening cattle during three visits (months 0, 1 and 7) on 63 beef farms in Austria, Germany and Italy. Only data from farms where no major changes in housing and management had taken place were considered for analysis. At the single measure level, Spearman rank correlations between visits were >0.7 and variance was lower within farms than between farms for six and two of 19 measures after 1 month and 6 months, respectively. After aggregation of single measures into criterion and principle scores, five and two of 10 criteria and three and one of four principles were found reliable after 1 and 6 months, respectively. At the WQ(®) principle level, this was the case for three and one of four principles. Seventy-nine per cent and 75% of the farms were allocated to the same overall welfare category after 1 month and 6 months. Possible reasons for a lack of consistency are seasonal effects or short-term fluctuations that occur under normal farm conditions, low prevalence of clinical measures and probably insufficient sample size, whereas poor
On the radiative properties of soot aggregates - Part 2: Effects of coating
NASA Astrophysics Data System (ADS)
Liu, Fengshan; Yon, Jérôme; Bescond, Alexandre
2016-03-01
The effects of weakly absorbing material coating on soot have attracted considerable research attention in recent years due to the significant influence of such coating on soot radiative properties and the large differences predicted by different numerical models. Soot aggregates were first numerically generated using the diffusion limited cluster aggregation algorithm to produce fractal aggregates formed by log-normally distributed polydisperse spherical primary particles in point-touch. These aggregates were then processed by adding a certain amount of primary particle overlapping and necking to simulate the soot morphology observed from transmission electron microscopy images. After this process, a layer of WAM coating of different thicknesses was added to these more realistic soot aggregates. The radiative properties of these coated soot aggregates over the spectral range of 266-1064 nm were calculated by the discrete dipole approximation (DDA) using the spectrally dependent refractive index of soot for four aggregates containing Np=1, 20, 51 and 96 primary particles. The considered coating thicknesses range from 0% (no coating) up to 100% coating in terms of the primary particle diameter. Coating enhances both the particle absorption and scattering cross sections, with much stronger enhancement to the scattering one, as well as the asymmetry factor and the single scattering albedo. The absorption enhancement is stronger in the UV than in the visible and the near infrared. The simple corrections to the Rayleigh-Debye-Gans fractal aggregates theory for uncoated soot aggregates are found not working for coated soot aggregates. The core-shell model significantly overestimates the absorption enhancement by coating in the visible and the near infrared compared to the DDA results of the coated soot particle. Treating an externally coated soot aggregate as an aggregate formed by individually coated primary particles significantly underestimates the absorption
The Nation's top 25 construction aggregates producers
Willett, Jason Christopher
2013-01-01
U.S. production of construction aggregates in 2011 was 2.17 billion short tons, valued at $17.2 billion, free on board (f.o.b.) at plant. Construction aggregates production decreased by 37 percent, and the associated value decreased by 25 percent, compared with the record highs reported in 2006. In 2011, construction aggregates production increased for the first time since 2006, owing to a very slight increase in the production of both construction sand and gravel and crushed stone. The average unit value, which is the f.o.b. at plant price of a ton of material, increased slightly, but is still less than the average unit value of two years prior.
Strong coupling-like phenomenon in single metallic nanoparticle embedded in molecular J-aggregates
NASA Astrophysics Data System (ADS)
Feng, Xin; Wang, Chen; Ma, Hongjing; Chen, Yuanyuan; Duan, Gaoyan; Zhang, Pengfei; Song, Gang
2018-02-01
Strong coupling-like phenomenon between plasmonic cavities and emitters provides a new way to realize the quantum-like effect controlling at microscale/nanoscale. We investigate the strong coupling-like phenomenon in the structure of single metallic nanoparticle embedded in molecular J-aggregates by the classical simulation method and show that the size of the metallic nanoparticle and the oscillator strength of molecular J-aggregates impact the strong coupling-like phenomenon. The strong coupling-like phenomenon is induced by the interactions between two dipoles formed by the metallic nanoparticle and molecular J-aggregates or the interactions between the dipole generated from molecular J-aggregates and the quadrupole generated from the metallic nanoparticle. The strong coupling-like phenomenon appears evidently with the increase in oscillator strength of molecular J-aggregates. The detuning energy linearly decreases with the increase in radius of the metallic nanoparticle. Our structure has potential applications in quantum networks, quantum key distributions and so on.
RiPPAS: A Ring-Based Privacy-Preserving Aggregation Scheme in Wireless Sensor Networks
Zhang, Kejia; Han, Qilong; Cai, Zhipeng; Yin, Guisheng
2017-01-01
Recently, data privacy in wireless sensor networks (WSNs) has been paid increased attention. The characteristics of WSNs determine that users’ queries are mainly aggregation queries. In this paper, the problem of processing aggregation queries in WSNs with data privacy preservation is investigated. A Ring-based Privacy-Preserving Aggregation Scheme (RiPPAS) is proposed. RiPPAS adopts ring structure to perform aggregation. It uses pseudonym mechanism for anonymous communication and uses homomorphic encryption technique to add noise to the data easily to be disclosed. RiPPAS can handle both sum() queries and min()/max() queries, while the existing privacy-preserving aggregation methods can only deal with sum() queries. For processing sum() queries, compared with the existing methods, RiPPAS has advantages in the aspects of privacy preservation and communication efficiency, which can be proved by theoretical analysis and simulation results. For processing min()/max() queries, RiPPAS provides effective privacy preservation and has low communication overhead. PMID:28178197
Neuroforecasting Aggregate Choice
Knutson, Brian; Genevsky, Alexander
2018-01-01
Advances in brain-imaging design and analysis have allowed investigators to use neural activity to predict individual choice, while emerging Internet markets have opened up new opportunities for forecasting aggregate choice. Here, we review emerging research that bridges these levels of analysis by attempting to use group neural activity to forecast aggregate choice. A survey of initial findings suggests that components of group neural activity might forecast aggregate choice, in some cases even beyond traditional behavioral measures. In addition to demonstrating the plausibility of neuroforecasting, these findings raise the possibility that not all neural processes that predict individual choice forecast aggregate choice to the same degree. We propose that although integrative choice components may confer more consistency within individuals, affective choice components may generalize more broadly across individuals to forecast aggregate choice. PMID:29706726
Duncan, James R; Kline, Benjamin; Glaiberman, Craig B
2007-04-01
To create and test methods of extracting efficiency data from recordings of simulated renal stent procedures. Task analysis was performed and used to design a standardized testing protocol. Five experienced angiographers then performed 16 renal stent simulations using the Simbionix AngioMentor angiographic simulator. Audio and video recordings of these simulations were captured from multiple vantage points. The recordings were synchronized and compiled. A series of efficiency metrics (procedure time, contrast volume, and tool use) were then extracted from the recordings. The intraobserver and interobserver variability of these individual metrics was also assessed. The metrics were converted to costs and aggregated to determine the fixed and variable costs of a procedure segment or the entire procedure. Task analysis and pilot testing led to a standardized testing protocol suitable for performance assessment. Task analysis also identified seven checkpoints that divided the renal stent simulations into six segments. Efficiency metrics for these different segments were extracted from the recordings and showed excellent intra- and interobserver correlations. Analysis of the individual and aggregated efficiency metrics demonstrated large differences between segments as well as between different angiographers. These differences persisted when efficiency was expressed as either total or variable costs. Task analysis facilitated both protocol development and data analysis. Efficiency metrics were readily extracted from recordings of simulated procedures. Aggregating the metrics and dividing the procedure into segments revealed potential insights that could be easily overlooked because the simulator currently does not attempt to aggregate the metrics and only provides data derived from the entire procedure. The data indicate that analysis of simulated angiographic procedures will be a powerful method of assessing performance in interventional radiology.
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.
NASA Astrophysics Data System (ADS)
Chen, Shaojin; Liu, Wei; Ge, Zhaohai; Zhang, Wenxuan; Wang, Kunpeng; Hu, Zhiqiang
2018-03-01
Axial chiral bisbenzocoumarins were synthesized for the first time by converting naphthanol units in 1,1‧-binaphthol (BINOL) molecule to the benzocoumarin rings. The substitute groups on 3,3‧-positions of bisbenzocoumarins showed significant influence on their aggregation-induced emission enhancement (AEE) properties. It was also found that BBzC1 with ester groups on 3,3‧-positions exhibit an abnormal aggregation-annihilation circular dichroism (AACD) phenomenon, which could be caused by the decrease of the dihedral angle between adjacent benzocoumarin rings in the aggregation state. The single crystal structure of BBzC1 showed that the large dihedral angle in molecule prohibited the strong π-π stacking interactions, which could be main factors for its AEE properties.
Controlled Aggregation of Ferritin to Modulate MRI Relaxivity
Bennett, Kevin M.; Shapiro, Erik M.; Sotak, Christopher H.; Koretsky, Alan P.
2008-01-01
Ferritin is an iron storage protein expressed in varying concentrations in mammalian cells. The deposition of ferric iron in the core of ferritin makes it a magnetic resonance imaging contrast agent, and ferritin has recently been proposed as a gene expression reporter protein for magnetic resonance imaging. To date, ferritin has been overexpressed in vivo and has been coexpressed with transferrin receptor to increase iron loading in cells. However, ferritin has a relatively low T2 relaxivity (R2 ≈ 1 mM−1s−1) at typical magnetic field strengths and so requires high levels of expression to be detected. One way to modulate the transverse relaxivity of a superparamagnetic agent is to cause it to aggregate, thereby manipulating the magnetic field gradients through which water diffuses. In this work, it is demonstrated by computer simulation and in vitro that aggregation of ferritin can alter relaxivity. The effects of aggregate size and intraaggregate perturber spacing on R2 are studied. Computer modeling indicates that the optimal spacing of the ferritin molecules in aggregate for increasing R2 is 100–200 nm for a typical range of water diffusion rates. Chemical cross-linking of ferritin at 12 Å spacing led to a 70% increase in R2 compared to uncross-linked ferritin controls. To modulate ferritin aggregation in a potentially biologically relevant manner, ferritin was attached to actin and polymerized in vitro. The polymerization of ferritin-F-actin caused a 20% increase in R2 compared to unpolymerized ferritin-G-actin. The R2-value was increased by another 10% by spacing the ferritin farther apart on the actin filaments. The modulation of ferritin aggregation by binding to cytoskeletal elements may be a useful strategy to make a functional reporter gene for magnetic resonance imaging. PMID:18326661
NASA Astrophysics Data System (ADS)
Kirchner, J. W.
2016-01-01
Environmental heterogeneity is ubiquitous, but environmental systems are often analyzed as if they were homogeneous instead, resulting in aggregation errors that are rarely explored and almost never quantified. Here I use simple benchmark tests to explore this general problem in one specific context: the use of seasonal cycles in chemical or isotopic tracers (such as Cl-, δ18O, or δ2H) to estimate timescales of storage in catchments. Timescales of catchment storage are typically quantified by the mean transit time, meaning the average time that elapses between parcels of water entering as precipitation and leaving again as streamflow. Longer mean transit times imply greater damping of seasonal tracer cycles. Thus, the amplitudes of tracer cycles in precipitation and streamflow are commonly used to calculate catchment mean transit times. Here I show that these calculations will typically be wrong by several hundred percent, when applied to catchments with realistic degrees of spatial heterogeneity. This aggregation bias arises from the strong nonlinearity in the relationship between tracer cycle amplitude and mean travel time. I propose an alternative storage metric, the young water fraction in streamflow, defined as the fraction of runoff with transit times of less than roughly 0.2 years. I show that this young water fraction (not to be confused with event-based "new water" in hydrograph separations) is accurately predicted by seasonal tracer cycles within a precision of a few percent, across the entire range of mean transit times from almost zero to almost infinity. Importantly, this relationship is also virtually free from aggregation error. That is, seasonal tracer cycles also accurately predict the young water fraction in runoff from highly heterogeneous mixtures of subcatchments with strongly contrasting transit-time distributions. Thus, although tracer cycle amplitudes yield biased and unreliable estimates of catchment mean travel times in heterogeneous
Kundu, Niloy; Banik, Debasis; Roy, Arpita; Kuchlyan, Jagannath; Sarkar, Nilmoni
2015-10-14
In this article, we have investigated the effect of a hydrophilic ionic liquid, 1-butyl-3-methylimidazolium tetrafluoroborate ([bmim]-BF4), on the aggregation properties of a biological surfactant, sodium deoxycholate (NaDC), in water. In solution, unlike conventional surfactants it shows stepwise aggregation and the effect of the conventional ionic liquid on the aggregation properties is rather interesting. We have observed concentration dependent dual role of the ionic liquid; at their low concentration, the aggregated structure of NaDC reorganizes itself into an elongated rod like structure. However, the aggregated network is disintegrated into small aggregates upon further addition of ionic liquid. TEM (Transmission Electron Microscopy), SEM (Scanning Electron Microscopy) and FLIM (Fluorescence Lifetime Imaging Microscopy) images also confirmed the structural alteration of NaDC upon varying the concentration of the ionic liquid. The proton NMR data indicate that hydrophobic as well as electrostatic interaction is solely responsible for such structural adaptation of NaDC in the presence of an ionic liquid. The host-guest interaction inside the aggregates is monitored using Coumarin-153 (C-153) and the location of C-153 is probed by varying the excitation wavelength from 375 nm to 440 nm and the two binding sites of the aggregates are affected in a different fashion in the presence of ionic liquid. Excitation in the blue region selects the fluorophores which preferably bind to the buried region of the aggregates, whereas 440 nm excitation corresponds to the guest molecules which are exposed to the solvent molecules. The average solvation time of C-153 is increased in the presence of 1.68 wt% [bmim]-BF4 at λexc = 440 nm i.e. the probe molecules relocate themselves to a more restricted region. However, the average solvation time became 2.6 times faster in the presence of 11.2 wt% [bmim]-BF4, which corresponds to a more polar and exposed region. The time resolved
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
In situ imaging of ultra-fast loss of nanostructure in nanoparticle aggregates
DOE Office of Scientific and Technical Information (OSTI.GOV)
Egan, Garth C.; Sullivan, Kyle T.; LaGrange, Thomas
2014-02-28
The word “nanoparticle” nominally elicits a vision of an isolated sphere; however, the vast bulk of nanoparticulate material exists in an aggregated state. This can have significant implications for applications such as combustion, catalysis, and optical excitation, where particles are exposed to high temperature and rapid heating conditions. In such environments, particles become susceptible to morphological changes which can reduce surface area, often to the detriment of functionality. Here, we report on thermally-induced coalescence which can occur in aluminum nanoparticle aggregates subjected to rapid heating (10{sup 6}–10{sup 11} K/s). Using dynamic transmission electron microscopy, we observed morphological changes in nanoparticle aggregatesmore » occurring in as little as a few nanoseconds after the onset of heating. The time-resolved probes reveal that the morphological changes initiate within 15 ns and are completed in less than 50 ns. The morphological changes were found to have a threshold temperature of about 1300 ± 50 K, as determined by millisecond-scale experiments with a calibrated heating stage. The temperature distribution of aggregates during laser heating was modeled with various simulation approaches. The results indicate that, under rapid heating conditions, coalescence occurs at an intermediate temperature between the melting points of aluminum and the aluminum oxide shell, and proceeds rapidly once this threshold temperature is reached.« less
Aggregation of Adenovirus 2 in Source Water and Impacts on Disinfection by Chlorine
Cromeans, Theresa L.; Metcalfe, Maureen G.; Humphrey, Charles D.; Hill, Vincent R.
2016-01-01
It is generally accepted that viral particles in source water are likely to be found as aggregates attached to other particles. For this reason, it is important to investigate the disinfection efficacy of chlorine on aggregated viruses. A method to produce adenovirus particle aggregation was developed for this study. Negative stain electron microscopy was used to measure aggregation before and after addition of virus particles to surface water at different pH and specific conductance levels. The impact of aggregation on the efficacy of chlorine disinfection was also examined. Disinfection experiments with human adenovirus 2 (HAdV2) in source water were conducted using 0.2 mg/L free chlorine at 5 °C. Aggregation of HAdV2 in source water (≥3 aggregated particles) remained higher at higher specific conductance and pH levels. However, aggregation was highly variable, with the percentage of particles present in aggregates ranging from 43 to 71 %. Upon addition into source water, the aggregation percentage dropped dramatically. On average, chlorination CT values (chlorine concentration in mg/L × time in min) for 3-log10 inactivation of aggregated HAdV2 were up to three times higher than those for dispersed HAdV2, indicating that aggregation reduced the disinfection rate. This information can be used by water utilities and regulators to guide decision making regarding disinfection of viruses in water. PMID:26910058
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.
Toward real-time regional earthquake simulation of Taiwan earthquakes
NASA Astrophysics Data System (ADS)
Lee, S.; Liu, Q.; Tromp, J.; Komatitsch, D.; Liang, W.; Huang, B.
2013-12-01
We developed a Real-time Online earthquake Simulation system (ROS) to simulate regional earthquakes in Taiwan. The ROS uses a centroid moment tensor solution of seismic events from a Real-time Moment Tensor monitoring system (RMT), which provides all the point source parameters including the event origin time, hypocentral location, moment magnitude and focal mechanism within 2 minutes after the occurrence of an earthquake. Then, all of the source parameters are automatically forwarded to the ROS to perform an earthquake simulation, which is based on a spectral-element method (SEM). We have improved SEM mesh quality by introducing a thin high-resolution mesh layer near the surface to accommodate steep and rapidly varying topography. The mesh for the shallow sedimentary basin is adjusted to reflect its complex geometry and sharp lateral velocity contrasts. The grid resolution at the surface is about 545 m, which is sufficient to resolve topography and tomography data for simulations accurate up to 1.0 Hz. The ROS is also an infrastructural service, making online earthquake simulation feasible. Users can conduct their own earthquake simulation by providing a set of source parameters through the ROS webpage. For visualization, a ShakeMovie and ShakeMap are produced during the simulation. The time needed for one event is roughly 3 minutes for a 70 sec ground motion simulation. The ROS is operated online at the Institute of Earth Sciences, Academia Sinica (http://ros.earth.sinica.edu.tw/). Our long-term goal for the ROS system is to contribute to public earth science outreach and to realize seismic ground motion prediction in real-time.
Patterns of [PSI+] aggregation allow insights into cellular organization of yeast prion aggregates
Tyedmers, Jens
2012-01-01
The yeast prion phenomenon is very widespread and mounting evidence suggests that it has an impact on cellular regulatory mechanisms related to phenotypic responses to changing environments. Studying the aggregation patterns of prion amyloids during different stages of the prion life cycle is a first key step to understand major principles of how and where cells generate, organize and turn-over prion aggregates. The induction of the [PSI+] state involves the actin cytoskeleton and quality control compartments such as the Insoluble Protein Deposit (IPOD). An initially unstable transitional induction state can be visualized by overexpression of the prion determinant and displays characteristic large ring- and ribbon-shaped aggregates consisting of poorly fragmented bundles of very long prion fibrils. In the mature prion state, the aggregation pattern is characterized by highly fragmented, shorter prion fibrils that form aggregates, which can be visualized through tagging with fluorescent proteins. The number of aggregates formed varies, ranging from a single large aggregate at the IPOD to multiple smaller ones, depending on several parameters discussed. Aggregate units below the resolution of light microscopy that are detectable by fluorescence correlation spectroscopy are in equilibrium with larger aggregates in this stage and can mediate faithful inheritance of the prion state. Loss of the prion state is often characterized by reduced fragmentation of prion fibrils and fewer, larger aggregates. PMID:22449721
Kinetics of Thermal Denaturation and Aggregation of Bovine Serum Albumin
Borzova, Vera A.; Markossian, Kira A.; Chebotareva, Natalia A.; Kleymenov, Sergey Yu.; Poliansky, Nikolay B.; Muranov, Konstantin O.; Stein-Margolina, Vita A.; Shubin, Vladimir V.; Markov, Denis I.; Kurganov, Boris I.
2016-01-01
Thermal aggregation of bovine serum albumin (BSA) has been studied using dynamic light scattering, asymmetric flow field-flow fractionation and analytical ultracentrifugation. The studies were carried out at fixed temperatures (60°C, 65°C, 70°C and 80°C) in 0.1 M phosphate buffer, pH 7.0, at BSA concentration of 1 mg/ml. Thermal denaturation of the protein was studied by differential scanning calorimetry. Analysis of the experimental data shows that at 65°C the stage of protein unfolding and individual stages of protein aggregation are markedly separated in time. This circumstance allowed us to propose the following mechanism of thermal aggregation of BSA. Protein unfolding results in the formation of two forms of the non-native protein with different propensity to aggregation. One of the forms (highly reactive unfolded form, Uhr) is characterized by a high rate of aggregation. Aggregation of Uhr leads to the formation of primary aggregates with the hydrodynamic radius (Rh,1) of 10.3 nm. The second form (low reactive unfolded form, Ulr) participates in the aggregation process by its attachment to the primary aggregates produced by the Uhr form and possesses ability for self-aggregation with formation of stable small-sized aggregates (Ast). At complete exhaustion of Ulr, secondary aggregates with the hydrodynamic radius (Rh,2) of 12.8 nm are formed. At 60°C the rates of unfolding and aggregation are commensurate, at 70°C the rates of formation of the primary and secondary aggregates are commensurate, at 80°C the registration of the initial stages of aggregation is complicated by formation of large-sized aggregates. PMID:27101281
Automatic analysis of microscopic images of red blood cell aggregates
NASA Astrophysics Data System (ADS)
Menichini, Pablo A.; Larese, Mónica G.; Riquelme, Bibiana D.
2015-06-01
Red blood cell aggregation is one of the most important factors in blood viscosity at stasis or at very low rates of flow. The basic structure of aggregates is a linear array of cell commonly termed as rouleaux. Enhanced or abnormal aggregation is seen in clinical conditions, such as diabetes and hypertension, producing alterations in the microcirculation, some of which can be analyzed through the characterization of aggregated cells. Frequently, image processing and analysis for the characterization of RBC aggregation were done manually or semi-automatically using interactive tools. We propose a system that processes images of RBC aggregation and automatically obtains the characterization and quantification of the different types of RBC aggregates. Present technique could be interesting to perform the adaptation as a routine used in hemorheological and Clinical Biochemistry Laboratories because this automatic method is rapid, efficient and economical, and at the same time independent of the user performing the analysis (repeatability of the analysis).
Das, Payel; King, Jonathan A.; Zhou, Ruhong
2011-01-01
The prevalent eye disease age-onset cataract is associated with aggregation of human γD-crystallins, one of the longest-lived proteins. Identification of the γ-crystallin precursors to aggregates is crucial for developing strategies to prevent and reverse cataract. Our microseconds of atomistic molecular dynamics simulations uncover the molecular structure of the experimentally detected aggregation-prone folding intermediate species of monomeric native γD-crystallin with a largely folded C-terminal domain and a mostly unfolded N-terminal domain. About 30 residues including a, b, and c strands from the Greek Key motif 4 of the C-terminal domain experience strong solvent exposure of hydrophobic residues as well as partial unstructuring upon N-terminal domain unfolding. Those strands comprise the domain–domain interface crucial for unusually high stability of γD-crystallin. We further simulate the intermolecular linkage of these monomeric aggregation precursors, which reveals domain-swapped dimeric structures. In the simulated dimeric structures, the N-terminal domain of one monomer is frequently found in contact with residues 135–164 encompassing the a, b, and c strands of the Greek Key motif 4 of the second molecule. The present results suggest that γD-crystallin may polymerize through successive domain swapping of those three C-terminal β-strands leading to age-onset cataract, as an evolutionary cost of its very high stability. Alanine substitutions of the hydrophobic residues in those aggregation-prone β-strands, such as L145 and M147, hinder domain swapping as a pathway toward dimerization. These findings thus provide critical molecular insights onto the initial stages of age-onset cataract, which is important for understanding protein aggregation diseases. PMID:21670251
Non-Arrhenius protein aggregation.
Wang, Wei; Roberts, Christopher J
2013-07-01
Protein aggregation presents one of the key challenges in the development of protein biotherapeutics. It affects not only product quality but also potentially impacts safety, as protein aggregates have been shown to be linked with cytotoxicity and patient immunogenicity. Therefore, investigations of protein aggregation remain a major focus in pharmaceutical companies and academic institutions. Due to the complexity of the aggregation process and temperature-dependent conformational stability, temperature-induced protein aggregation is often non-Arrhenius over even relatively small temperature windows relevant for product development, and this makes low-temperature extrapolation difficult based simply on accelerated stability studies at high temperatures. This review discusses the non-Arrhenius nature of the temperature dependence of protein aggregation, explores possible causes, and considers inherent hurdles for accurately extrapolating aggregation rates from conventional industrial approaches for selecting accelerated conditions and from conventional or more advanced methods of analyzing the resulting rate data.
Ayyadevara, Srinivas; Balasubramaniam, Meenakshisundaram; Kakraba, Samuel; Alla, Ramani; Mehta, Jawahar L; Shmookler Reis, Robert J
2017-12-10
Many progressive neurological disorders, including Alzheimer's disease (AD), Huntington's disease, and Parkinson's disease (PD), are characterized by accumulation of insoluble protein aggregates. In prospective trials, the cyclooxygenase inhibitor aspirin (acetylsalicylic acid) reduced the risk of AD and PD, as well as cardiovascular events and many late-onset cancers. Considering the role played by protein hyperphosphorylation in aggregation and neurodegenerative diseases, and aspirin's known ability to donate acetyl groups, we asked whether aspirin might reduce both phosphorylation and aggregation by acetylating protein targets. Aspirin was substantially more effective than salicylate in reducing or delaying aggregation in human neuroblastoma cells grown in vitro, and in Caenorhabditis elegans models of human neurodegenerative diseases in vivo. Aspirin acetylates many proteins, while reducing phosphorylation, suggesting that acetylation may oppose phosphorylation. Surprisingly, acetylated proteins were largely excluded from compact aggregates. Molecular-dynamic simulations indicate that acetylation of amyloid peptide energetically disfavors its association into dimers and octamers, and oligomers that do form are less compact and stable than those comprising unacetylated peptides. Hyperphosphorylation predisposes certain proteins to aggregate (e.g., tau, α-synuclein, and transactive response DNA-binding protein 43 [TDP-43]), and it is a critical pathogenic marker in both cardiovascular and neurodegenerative diseases. We present novel evidence that acetylated proteins are underrepresented in protein aggregates, and that aggregation varies inversely with acetylation propensity after diverse genetic and pharmacologic interventions. These results are consistent with the hypothesis that aspirin inhibits protein aggregation and the ensuing toxicity of aggregates through its acetyl-donating activity. This mechanism may contribute to the neuro-protective, cardio
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
Mechanical Properties of Steel Fiber Reinforced all Lightweight Aggregate Concrete
NASA Astrophysics Data System (ADS)
Yang, Y. M.; Li, J. Y.; Zhen, Y.; Nie, Y. N.; Dong, W. L.
2018-05-01
In order to study the basic mechanical properties and failure characteristics of all lightweight aggregate concrete with different volume of steel fiber (0%, 1%, 2%), shale ceramsite is used as light coarse aggregate. The shale sand is made of light fine aggregate and mixed with different volume of steel fiber, and the mix proportion design of all lightweight aggregate concrete is carried out. The cubic compressive strength, axial compressive strength, flexural strength, splitting strength and modulus of elasticity of steel fiber all lightweight aggregate concrete were studied. Test results show that the incorporation of steel fiber can restrict the cracking of concrete, improve crack resistance; at the same time, it shows good plastic deformation ability and failure morphology. It lays a theoretical foundation for further research on the application of all lightweight aggregate concrete in structural systems.
Physically-Based Modelling and Real-Time Simulation of Fluids.
NASA Astrophysics Data System (ADS)
Chen, Jim Xiong
1995-01-01
Simulating physically realistic complex fluid behaviors presents an extremely challenging problem for computer graphics researchers. Such behaviors include the effects of driving boats through water, blending differently colored fluids, rain falling and flowing on a terrain, fluids interacting in a Distributed Interactive Simulation (DIS), etc. Such capabilities are useful in computer art, advertising, education, entertainment, and training. We present a new method for physically-based modeling and real-time simulation of fluids in computer graphics and dynamic virtual environments. By solving the 2D Navier -Stokes equations using a CFD method, we map the surface into 3D using the corresponding pressures in the fluid flow field. This achieves realistic real-time fluid surface behaviors by employing the physical governing laws of fluids but avoiding extensive 3D fluid dynamics computations. To complement the surface behaviors, we calculate fluid volume and external boundary changes separately to achieve full 3D general fluid flow. To simulate physical activities in a DIS, we introduce a mechanism which uses a uniform time scale proportional to the clock-time and variable time-slicing to synchronize physical models such as fluids in the networked environment. Our approach can simulate many different fluid behaviors by changing the internal or external boundary conditions. It can model different kinds of fluids by varying the Reynolds number. It can simulate objects moving or floating in fluids. It can also produce synchronized general fluid flows in a DIS. Our model can serve as a testbed to simulate many other fluid phenomena which have never been successfully modeled previously.
DOE Office of Scientific and Technical Information (OSTI.GOV)
Dall-Anese, Emiliano; Bernstein, Andrey; Simonetto, Andrea
This paper develops an online optimization method to maximize operational objectives of distribution-level distributed energy resources (DERs), while adjusting the aggregate power generated (or consumed) in response to services requested by grid operators. The design of the online algorithm is based on a projected-gradient method, suitably modified to accommodate appropriate measurements from the distribution network and the DERs. By virtue of this approach, the resultant algorithm can cope with inaccuracies in the representation of the AC power flows, it avoids pervasive metering to gather the state of noncontrollable resources, and it naturally lends itself to a distributed implementation. Optimality claimsmore » are established in terms of tracking of the solution of a well-posed time-varying convex optimization problem.« less
An adaptive bias - hybrid MD/kMC algorithm for protein folding and aggregation.
Peter, Emanuel K; Shea, Joan-Emma
2017-07-05
In this paper, we present a novel hybrid Molecular Dynamics/kinetic Monte Carlo (MD/kMC) algorithm and apply it to protein folding and aggregation in explicit solvent. The new algorithm uses a dynamical definition of biases throughout the MD component of the simulation, normalized in relation to the unbiased forces. The algorithm guarantees sampling of the underlying ensemble in dependency of one average linear coupling factor 〈α〉 τ . We test the validity of the kinetics in simulations of dialanine and compare dihedral transition kinetics with long-time MD-simulations. We find that for low 〈α〉 τ values, kinetics are in good quantitative agreement. In folding simulations of TrpCage and TrpZip4 in explicit solvent, we also find good quantitative agreement with experimental results and prior MD/kMC simulations. Finally, we apply our algorithm to study growth of the Alzheimer Amyloid Aβ 16-22 fibril by monomer addition. We observe two possible binding modes, one at the extremity of the fibril (elongation) and one on the surface of the fibril (lateral growth), on timescales ranging from ns to 8 μs.
Floating ice-algal aggregates below melting arctic sea ice.
Assmy, Philipp; Ehn, Jens K; Fernández-Méndez, Mar; Hop, Haakon; Katlein, Christian; Sundfjord, Arild; Bluhm, Katrin; Daase, Malin; Engel, Anja; Fransson, Agneta; Granskog, Mats A; Hudson, Stephen R; Kristiansen, Svein; Nicolaus, Marcel; Peeken, Ilka; Renner, Angelika H H; Spreen, Gunnar; Tatarek, Agnieszka; Wiktor, Jozef
2013-01-01
During two consecutive cruises to the Eastern Central Arctic in late summer 2012, we observed floating algal aggregates in the melt-water layer below and between melting ice floes of first-year pack ice. The macroscopic (1-15 cm in diameter) aggregates had a mucous consistency and were dominated by typical ice-associated pennate diatoms embedded within the mucous matrix. Aggregates maintained buoyancy and accumulated just above a strong pycnocline that separated meltwater and seawater layers. We were able, for the first time, to obtain quantitative abundance and biomass estimates of these aggregates. Although their biomass and production on a square metre basis was small compared to ice-algal blooms, the floating ice-algal aggregates supported high levels of biological activity on the scale of the individual aggregate. In addition they constituted a food source for the ice-associated fauna as revealed by pigments indicative of zooplankton grazing, high abundance of naked ciliates, and ice amphipods associated with them. During the Arctic melt season, these floating aggregates likely play an important ecological role in an otherwise impoverished near-surface sea ice environment. Our findings provide important observations and measurements of a unique aggregate-based habitat during the 2012 record sea ice minimum year.
Floating Ice-Algal Aggregates below Melting Arctic Sea Ice
Assmy, Philipp; Ehn, Jens K.; Fernández-Méndez, Mar; Hop, Haakon; Katlein, Christian; Sundfjord, Arild; Bluhm, Katrin; Daase, Malin; Engel, Anja; Fransson, Agneta; Granskog, Mats A.; Hudson, Stephen R.; Kristiansen, Svein; Nicolaus, Marcel; Peeken, Ilka; Renner, Angelika H. H.; Spreen, Gunnar; Tatarek, Agnieszka; Wiktor, Jozef
2013-01-01
During two consecutive cruises to the Eastern Central Arctic in late summer 2012, we observed floating algal aggregates in the melt-water layer below and between melting ice floes of first-year pack ice. The macroscopic (1-15 cm in diameter) aggregates had a mucous consistency and were dominated by typical ice-associated pennate diatoms embedded within the mucous matrix. Aggregates maintained buoyancy and accumulated just above a strong pycnocline that separated meltwater and seawater layers. We were able, for the first time, to obtain quantitative abundance and biomass estimates of these aggregates. Although their biomass and production on a square metre basis was small compared to ice-algal blooms, the floating ice-algal aggregates supported high levels of biological activity on the scale of the individual aggregate. In addition they constituted a food source for the ice-associated fauna as revealed by pigments indicative of zooplankton grazing, high abundance of naked ciliates, and ice amphipods associated with them. During the Arctic melt season, these floating aggregates likely play an important ecological role in an otherwise impoverished near-surface sea ice environment. Our findings provide important observations and measurements of a unique aggregate-based habitat during the 2012 record sea ice minimum year. PMID:24204642
Reduced receptor aggregation and altered cytoskeleton in cultured myocytes after space-flight
NASA Technical Reports Server (NTRS)
Gruener, R.; Roberts, R.; Reitstetter, R.
1994-01-01
We carried out parallel experiments first on the slow clinostat and then in space-flight to examine the effects of altered gravity on the aggregation of the nicotinic acetylcholine receptors and the structure of the cytoskeleton in cultured Xenopus embryonic muscle cells. By examining the concordance between results from space flight and the clinostat, we tested whether the slow clinostat is a relevant simulation paradigm. Space-flown cells showed marked changes in the distribution and organization of actin filaments and had a reduced incidence of acetylcholine receptor aggregates at the site of contact with polystyrene beads. Similar effects were found after clinostat rotation. The sensitivity of synaptic receptor aggregation and cytoskeletal morphology suggests that in the microgravity of space cell behavior may be importantly altered.
The influence of ionic strength and organic compounds on nanoparticle TiO2 (n-TiO2) aggregation.
Lee, Jaewoong; Bartelt-Hunt, Shannon L; Li, Yusong; Gilrein, Erica Jeanne
2016-07-01
This study investigated the aggregation of n-TiO2 in the presence of humic acid (HA) and/or 17β-estradiol (E2) under high ionic strength conditions simulating levels detected in landfill leachate. Aggregation of n-TiO2 was strongly influenced by ionic strength as well as ionic valence in that divalent cations (Ca(2+)) were more effective than monovalent (Na(+)) at the surface modification. HA or E2 enhanced aggregation of n-TiO2 in 20 mM CaCl2, however little aggregation was observed in 100 mM NaCl. Similarly, we observed only the increased aggregation of n-TiO2 in the presence of HA/E2. These results showed the critical role of particles' surface charges on the aggregation behaviors of n-TiO2 that HA plays more significantly than E2. However, the slightly increased zeta potential and aggregation of n-TiO2 in the combination of HA and E2 at both 20 mM CaCl2 and 100 mM NaCl means that E2 has influenced on the surface modification of n-TiO2 by adsorption. Based on the aggregation of n-TiO2 under high ionic strength with HA and/or E2, we simulated the mobility of aggregated n-TiO2 in porous media. As a result, we observed that the mobility distance of aggregated n-TiO2 was dramatically influenced by the surface modification with both HA and/or E2 between particles and media. Furthermore, larger mobility distance was observed with larger aggregation of n-TiO2 particles that can be explained by clean bed filtration (CFT) theory. Copyright © 2016 Elsevier Ltd. All rights reserved.
ADA and multi-microprocessor real-time simulation
NASA Technical Reports Server (NTRS)
Feyock, S.; Collins, W. R.
1983-01-01
The selection of a high-order programming language for a real-time distributed network simulation is described. The additional problem of implementing a language on a possibly changing network is addressed. The recently designed language ADA (trademarked by DoD) was chosen since it provides the best model of the underlying application to be simulated.
Evaluation of Canadian unconfined aggregate freeze-thaw tests for identifying nondurable aggregates.
DOT National Transportation Integrated Search
2012-06-01
Concrete is the most widely used material in construction. Aggregates contribute 60% to 75% of the total volume : of concrete. The aggregates play a key role in concrete durability. The U.S. Midwest has many aggregates that can : show distress in the...
DOE Office of Scientific and Technical Information (OSTI.GOV)
Shapiro, B I; Tyshkunova, E S; Kondorskiy, A D
2015-12-31
Optical properties of hybrid rod-like nanoparticles, consisting of a gold core, an intermediate passive organic layer (spacer) and outer layer of ordered molecular cyanine dye aggregates, are experimentally and theoretically investigated. It is shown that these dyes can form not only ordered J-aggregates but also H-aggregates (differing by the packing angle of dye molecules in an aggregate and having other spectral characteristics) in the outer shell of the hybrid nanostructure. Absorption spectra of synthesised three-layer nanorods are recorded, and their sizes are determined. The optical properties of the composite nanostructures under study are found to differ significantly, depending on themore » type of the molecular aggregate formed in the outer shell. The experimental data are quantitatively explained based on computer simulation using the finite-difference time-domain (FDTD) method, and characteristic features of the plasmon – exciton interaction in the systems under study are revealed. (nanophotonics)« less
NASA Technical Reports Server (NTRS)
Jefferson, David; Beckman, Brian
1986-01-01
This paper describes the concept of virtual time and its implementation in the Time Warp Operating System at the Jet Propulsion Laboratory. Virtual time is a distributed synchronization paradigm that is appropriate for distributed simulation, database concurrency control, real time systems, and coordination of replicated processes. The Time Warp Operating System is targeted toward the distributed simulation application and runs on a 32-node JPL Mark II Hypercube.
Lin, Xiaorong; Gao, Xiong; Chen, Zhongzheng; Zhang, Yuanyuan; Luo, Wei; Li, Xiaofei; Li, Bin
2017-05-10
Tea nano-aggregates spontaneously assembled in clear tea infusions are considered as the precursors of tea cream, although their molecular basis remains obscure. Here, we characterized nano-aggregates in green tea infusions from Camellia ptilophylla, a peculiar tea variety with 6.0% of theobromine, and Camellia sinensis as the control for comparative purpose. Numerous negatively charged spherical colloidal particles of 50-100 nm in diameter were primarily found in both green tea infusions. Catechins, proteins, and carbohydrates were confirmed as the dominant components in green tea nano-aggregates. In addition, iron, copper, nickel, proteins, and gallated catechins exhibited higher aggregating affinity than other components, whereas methylxanthines and calcium contributed to the transformation of nano-aggregates into tea cream. Green tea nano-aggregates were partly destroyed by simulated gastrointestinal digestion, and removing theses peculiar particles dramatically attenuated the bioaccessibility of methylxanthines, theanine, and some catechin monomers in green tea infusions. This study enhanced our knowledge of molecular interactions in the formation of green tea cream and provided insight into physicochemical profiles, phytochemical nature, and functional effects of green tea nano-aggregates.
Photophysics of Zinc Porphyrin Aggregates in Dilute Water-Ethanol Solutions.
Stevens, Amy L; Joshi, Neeraj K; Paige, Matthew F; Steer, Ronald P
2017-12-14
Dimeric and multimeric aggregates of a model metalloporphyrin, zinc tetraphenylporphyrin (ZnTPP), have been produced in a controlled manner by incrementally increasing the water content of dilute aqueous ethanol solutions. Steady state absorption, fluorescence emission, and fluorescence excitation spectra have been measured to identify the aggregates present as a function of solvent composition. The dynamics of the excited states of the aggregates produced initially by excitation in the Soret region have been measured by ultrafast fluorescence upconversion techniques. Only the monomer produces measurable emission from S 2 with a picosecond lifetime; all Soret-excited aggregates, including the dimer, decay radiationlessly on a femtosecond time scale. The S 1 state is the only significant product of the radiationless decay of the S 2 state of the excited monomer, and the aggregates also produce substantial quantum yields of S 1 fluorescence when initially excited in the Soret region. The resulting fluorescent aggregates all decay on a subnanosecond time scale, likely by a mechanism that involves dissociation of the excited monomer from the excitonic multimer. The ZnTPP dimers excited at their ground state geometries in the Soret region exhibit a dynamic behavior that is quite different from those produced following noncoherent triplet-triplet annihilation under the same conditions. The important implications of these observations in determining the aggregation conditions promoting efficient photon upconversion by excitonic annihilation in a variety of media are thoroughly discussed.
Characterization of wet aggregate stability of soils by ¹H-NMR relaxometry.
Buchmann, C; Meyer, M; Schaumann, G E
2015-09-01
For the assessment of soil structural stability against hydraulic stress, wet sieving or constant head permeability tests are typically used but rather limited in their intrinsic information value. The multiple applications of several tests is the only possibility to assess important processes and mechanisms during soil aggregate breakdown, e.g. the influences of soil fragment release or differential swelling on the porous systems of soils or soil aggregate columns. Consequently, the development of new techniques for a faster and more detailed wet aggregate stability assessment is required. (1)H nuclear magnetic resonance relaxometry ((1)H-NMR relaxometry) might provide these requirements because it has already been successfully applied on soils. We evaluated the potential of (1)H-NMR relaxometry for the assessment of wet aggregate stability of soils, with more detailed information on occurring mechanisms at the same time. Therefore, we conducted single wet sieving and constant head permeability tests on untreated and 1% polyacrylic acid-treated soil aggregates of different textures and organic matter contents, subsequently measured by (1)H-NMR relaxometry after percolation. The stability of the soil aggregates were mainly depending on their organic matter contents and the type of aggregate stabilization, whereby additional effects of clay swelling on the measured wet aggregate stability were identified by the transverse relaxation time (T2) distributions. Regression analyses showed that only the percentage of water stable aggregates could be determined accurately from percolated soil aggregate columns by (1)H-NMR relaxometry measurements. (1)H-NMR relaxometry seems a promising technique for wet aggregate stability measurements but should be further developed for nonpercolated aggregate columns and real soil samples. Copyright © 2014 John Wiley & Sons, Ltd.
Aggregation of Adenovirus 2 in Source Water and Impacts on Disinfection by Chlorine.
Kahler, Amy M; Cromeans, Theresa L; Metcalfe, Maureen G; Humphrey, Charles D; Hill, Vincent R
2016-06-01
It is generally accepted that viral particles in source water are likely to be found as aggregates attached to other particles. For this reason, it is important to investigate the disinfection efficacy of chlorine on aggregated viruses. A method to produce adenovirus particle aggregation was developed for this study. Negative stain electron microscopy was used to measure aggregation before and after addition of virus particles to surface water at different pH and specific conductance levels. The impact of aggregation on the efficacy of chlorine disinfection was also examined. Disinfection experiments with human adenovirus 2 (HAdV2) in source water were conducted using 0.2 mg/L free chlorine at 5 °C. Aggregation of HAdV2 in source water (≥3 aggregated particles) remained higher at higher specific conductance and pH levels. However, aggregation was highly variable, with the percentage of particles present in aggregates ranging from 43 to 71 %. Upon addition into source water, the aggregation percentage dropped dramatically. On average, chlorination CT values (chlorine concentration in mg/L × time in min) for 3-log10 inactivation of aggregated HAdV2 were up to three times higher than those for dispersed HAdV2, indicating that aggregation reduced the disinfection rate. This information can be used by water utilities and regulators to guide decision making regarding disinfection of viruses in water.
Sunlight affects aggregation and deposition of graphene oxide in the aquatic environment.
In this study, we investigate the role of simulated sunlight on the physicochemical properties, aggregation, and deposition of graphene oxide (GO) in aquatic environments. Results show that light exposure under varied environmental conditions significantly impacts the physicochem...
Time-dependent magnetohydrodynamic simulations of the inner heliosphere
NASA Astrophysics Data System (ADS)
Merkin, V. G.; Lyon, J. G.; Lario, D.; Arge, C. N.; Henney, C. J.
2016-04-01
This paper presents results from a simulation study exploring heliospheric consequences of time-dependent changes at the Sun. We selected a 2 month period in the beginning of year 2008 that was characterized by very low solar activity. The heliosphere in the equatorial region was dominated by two coronal holes whose changing structure created temporal variations distorting the classical steady state picture of the heliosphere. We used the Air Force Data Assimilate Photospheric Flux Transport (ADAPT) model to obtain daily updated photospheric magnetograms and drive the Wang-Sheeley-Arge (WSA) model of the corona. This leads to a formulation of a time-dependent boundary condition for our three-dimensional (3-D) magnetohydrodynamic (MHD) model, LFM-helio, which is the heliospheric adaptation of the Lyon-Fedder-Mobarry MHD simulation code. The time-dependent coronal conditions were propagated throughout the inner heliosphere, and the simulation results were compared with the spacecraft located near 1 astronomical unit (AU) heliocentric distance: Advanced Composition Explorer (ACE), Solar Terrestrial Relations Observatory (STEREO-A and STEREO-B), and the MErcury Surface, Space ENvironment, GEochemistry, and Ranging (MESSENGER) spacecraft that was in cruise phase measuring the heliospheric magnetic field between 0.35 and 0.6 AU. In addition, during the selected interval MESSENGER and ACE aligned radially allowing minimization of the effects of temporal variation at the Sun versus radial evolution of structures. Our simulations show that time-dependent simulationsreproduce the gross-scale structure of the heliosphere with higher fidelity, while on smaller spatial and faster time scales (e.g., 1 day) they provide important insights for interpretation of the data. The simulations suggest that moving boundaries of slow-fast wind transitions at 0.1 AU may result in the formation of inverted magnetic fields near pseudostreamers which is an intrinsically time-dependent process
A high fidelity real-time simulation of a small turboshaft engine
NASA Technical Reports Server (NTRS)
Ballin, Mark G.
1988-01-01
A high-fidelity component-type model and real-time digital simulation of the General Electric T700-GE-700 turboshaft engine were developed for use with current generation real-time blade-element rotor helicopter simulations. A control system model based on the specification fuel control system used in the UH-60A Black Hawk helicopter is also presented. The modeling assumptions and real-time digital implementation methods particular to the simulation of small turboshaft engines are described. The validity of the simulation is demonstrated by comparison with analysis-oriented simulations developed by the manufacturer, available test data, and flight-test time histories.
Feature ranking and rank aggregation for automatic sleep stage classification: a comparative study.
Najdi, Shirin; Gharbali, Ali Abdollahi; Fonseca, José Manuel
2017-08-18
Nowadays, sleep quality is one of the most important measures of healthy life, especially considering the huge number of sleep-related disorders. Identifying sleep stages using polysomnographic (PSG) signals is the traditional way of assessing sleep quality. However, the manual process of sleep stage classification is time-consuming, subjective and costly. Therefore, in order to improve the accuracy and efficiency of the sleep stage classification, researchers have been trying to develop automatic classification algorithms. Automatic sleep stage classification mainly consists of three steps: pre-processing, feature extraction and classification. Since classification accuracy is deeply affected by the extracted features, a poor feature vector will adversely affect the classifier and eventually lead to low classification accuracy. Therefore, special attention should be given to the feature extraction and selection process. In this paper the performance of seven feature selection methods, as well as two feature rank aggregation methods, were compared. Pz-Oz EEG, horizontal EOG and submental chin EMG recordings of 22 healthy males and females were used. A comprehensive feature set including 49 features was extracted from these recordings. The extracted features are among the most common and effective features used in sleep stage classification from temporal, spectral, entropy-based and nonlinear categories. The feature selection methods were evaluated and compared using three criteria: classification accuracy, stability, and similarity. Simulation results show that MRMR-MID achieves the highest classification performance while Fisher method provides the most stable ranking. In our simulations, the performance of the aggregation methods was in the average level, although they are known to generate more stable results and better accuracy. The Borda and RRA rank aggregation methods could not outperform significantly the conventional feature ranking methods. Among
Multiscale measurement error models for aggregated small area health data.
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.
Snyder, S W; Ladror, U S; Wade, W S; Wang, G T; Barrett, L W; Matayoshi, E D; Huffaker, H J; Krafft, G A; Holzman, T F
1994-01-01
One of the clinical manifestations of Alzheimer's disease is the deposition of the 39-43 residue amyloid-beta (A beta) peptide in aggregated fibrils in senile plaques. Characterization of the aggregation behavior of A beta is one of the critical issues in understanding the role of A beta in the disease process. Using solution hydrodynamics, A beta was observed to form three types of species in phosphate-buffered saline: insoluble aggregates with sedimentation coefficients of approximately 50,000 S and molecular masses of approximately 10(9) Da, "soluble aggregates" with sedimentation coefficients of approximately 30 S and masses of approximately 10(6) Da, and monomer. When starting from monomer, the aggregation kinetics of A beta 1-40 (A beta 40) and A beta 1-42 (A beta 42), alone and in combination, reveal large differences in the tendency of these peptides to aggregate as a function of pH and other solution conditions. At pH 4.1 and 7.0-7.4, aggregation is significantly slower than at pH 5 and 6. Under all conditions, aggregation of the longer A beta 42 was more rapid than A beta 40. Oxidation of Met-35 to the sulfoxide in A beta 40 enhances the aggregation rate over that of the nonoxidized peptide. Aggregation was found to be dependent upon temperature and to be strongly dependent on peptide concentration and ionic strength, indicating that aggregation is driven by a hydrophobic effect. When A beta 40 and A beta 42 are mixed together, A beta 40 retards the aggregation of A beta 42 in a concentration-dependent manner. Shorter fragments have a decreasing ability to interfere with A beta 42 aggregation. Conversely, the rate of aggregation of A beta 40 can be significantly enhanced by seeding slow aggregating solutions with preformed aggregates of A beta 42. Taken together, the inhibition of A beta 42 aggregation by A beta 40, the seeding of A beta 40 aggregation by A beta 42 aggregates, and the chemical oxidation of A beta 40 suggest that the relative abundance and
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.
Low temperature exciton dynamics and structural changes in perylene bisimide aggregates
NASA Astrophysics Data System (ADS)
Wolter, Steffen; Magnus Westphal, Karl; Hempel, Magdalena; Würthner, Frank; Kühn, Oliver; Lochbrunner, Stefan
2017-09-01
The temperature dependent exciton dynamics of J-aggregates formed by a perylene bisimide dye is investigated down to liquid nitrogen temperature (77 K) by femtosecond pump-probe spectroscopy. The analysis of the transient absorption data using a diffusion model for the excitons does not only reveal an overall decrease of the exciton mobility, but also a change in the dimensionality of the exciton transport at low temperatures. This change in dimensionality is further investigated by kinetic Monte Carlo simulations, identifying weakly interlinked one-dimensional aggregate chains as the most likely structure at low temperatures. This causes the exciton transport to be highly anisotropic.
Hanuschkin, Alexander; Kunkel, Susanne; Helias, Moritz; Morrison, Abigail; Diesmann, Markus
2010-01-01
Traditionally, event-driven simulations have been limited to the very restricted class of neuronal models for which the timing of future spikes can be expressed in closed form. Recently, the class of models that is amenable to event-driven simulation has been extended by the development of techniques to accurately calculate firing times for some integrate-and-fire neuron models that do not enable the prediction of future spikes in closed form. The motivation of this development is the general perception that time-driven simulations are imprecise. Here, we demonstrate that a globally time-driven scheme can calculate firing times that cannot be discriminated from those calculated by an event-driven implementation of the same model; moreover, the time-driven scheme incurs lower computational costs. The key insight is that time-driven methods are based on identifying a threshold crossing in the recent past, which can be implemented by a much simpler algorithm than the techniques for predicting future threshold crossings that are necessary for event-driven approaches. As run time is dominated by the cost of the operations performed at each incoming spike, which includes spike prediction in the case of event-driven simulation and retrospective detection in the case of time-driven simulation, the simple time-driven algorithm outperforms the event-driven approaches. Additionally, our method is generally applicable to all commonly used integrate-and-fire neuronal models; we show that a non-linear model employing a standard adaptive solver can reproduce a reference spike train with a high degree of precision. PMID:21031031
Genetic variation in aggregation behaviour and interacting phenotypes in Drosophila.
Philippe, Anne-Sophie; Jeanson, Raphael; Pasquaretta, Cristian; Rebaudo, Francois; Sueur, Cedric; Mery, Frederic
2016-03-30
Aggregation behaviour is the tendency for animals to group together, which may have important consequences on individual fitness. We used a combination of experimental and simulation approaches to study how genetic variation and social environment interact to influence aggregation dynamics in Drosophila To do this, we used two different natural lines of Drosophila that arise from a polymorphism in the foraging gene (rovers and sitters). We placed groups of flies in a heated arena. Flies could freely move towards one of two small, cooler refuge areas. In groups of the same strain, sitters had a greater tendency to aggregate. The observed behavioural variation was based on only two parameters: the probability of entering a refuge and the likelihood of choosing a refuge based on the number of individuals present. We then directly addressed how different strains interact by mixing rovers and sitters within a group. Aggregation behaviour of each line was strongly affected by the presence of the other strain, without changing the decision rules used by each. Individuals obeying local rules shaped complex group dynamics via a constant feedback loop between the individual and the group. This study could help to identify the circumstances under which particular group compositions may improve individual fitness through underlying aggregation mechanisms under specific environmental conditions. © 2016 The Author(s).
Taxi Time Prediction at Charlotte Airport Using Fast-Time Simulation and Machine Learning Techniques
NASA Technical Reports Server (NTRS)
Lee, Hanbong
2016-01-01
Accurate taxi time prediction is required for enabling efficient runway scheduling that can increase runway throughput and reduce taxi times and fuel consumptions on the airport surface. Currently NASA and American Airlines are jointly developing a decision-support tool called Spot and Runway Departure Advisor (SARDA) that assists airport ramp controllers to make gate pushback decisions and improve the overall efficiency of airport surface traffic. In this presentation, we propose to use Linear Optimized Sequencing (LINOS), a discrete-event fast-time simulation tool, to predict taxi times and provide the estimates to the runway scheduler in real-time airport operations. To assess its prediction accuracy, we also introduce a data-driven analytical method using machine learning techniques. These two taxi time prediction methods are evaluated with actual taxi time data obtained from the SARDA human-in-the-loop (HITL) simulation for Charlotte Douglas International Airport (CLT) using various performance measurement metrics. Based on the taxi time prediction results, we also discuss how the prediction accuracy can be affected by the operational complexity at this airport and how we can improve the fast time simulation model before implementing it with an airport scheduling algorithm in a real-time environment.
Metamodeling Techniques to Aid in the Aggregation Process of Large Hierarchical Simulation Models
2008-08-01
Level Outputs Campaign Level Model Campaign Level Outputs Aggregation Metamodeling Complexity (Spatial, Temporal, etc.) Others? Apply VRT (type......reduction, are called variance reduction techniques ( VRT ) [Law, 2006]. The implementation of some type of VRT can prove to be a very valuable tool
Asphaltene Aggregation and Fouling Behavior
NASA Astrophysics Data System (ADS)
Derakhshesh, Marzie
. Analysis of the spectra of the whole asphaltene samples in toluene indicates that the absorbance of visible light with wavelengths > 600 nm follows a lambda--4 dependence. This functional dependence is consistent with Rayleigh scattering. Rayleigh scattering provides strong evidence that the apparent absorption of visible light by asphaltenes from 600-800 nm is not a molecular absorption phenomenon but rather a scattering mechanism. Rayleigh scattering equations were combined with experimental visible spectra to estimate the average nanoaggregate sizes, which were in a very good agreement with the sizes reported in the literature. The occlusion of two polynuclear aromatic hydrocarbons (PAHs) (pyrene and phenanthrene) in asphaltene precipitates was tested by adding PAHs to the asphaltene in toluene solutions, precipitating by n-pentane and determining the amount of PAHs in precipitates using simulated distillation instrument. Pyrene and phenanthrene, which are normally soluble in the toluene-n-pentane solutions, were detected in the asphaltene precipitates at up to 6 wt% concentration. Trapping of PAHs outside of the nanoaggregates during precipitation gave 7-14 times less of the PAHs in the solid precipitate. This study shows that asphaltene aggregates can interact significantly with PAHs. The results are consistent with the presence open porous asphaltene nanoaggregates in solutions such as toluene.
A Novel Method to Quantify Soil Aggregate Stability by Measuring Aggregate Bond Energies
NASA Astrophysics Data System (ADS)
Efrat, Rachel; Rawlins, Barry G.; Quinton, John N.; Watts, Chris W.; Whitmore, Andy P.
2016-04-01
Soil aggregate stability is a key indicator of soil quality because it controls physical, biological and chemical functions important in cultivated soils. Micro-aggregates are responsible for the long term sequestration of carbon in soil, therefore determine soils role in the carbon cycle. It is thus vital that techniques to measure aggregate stability are accurate, consistent and reliable, in order to appropriately manage and monitor soil quality, and to develop our understanding and estimates of soil as a carbon store to appropriately incorporate in carbon cycle models. Practices used to assess the stability of aggregates vary in sample preparation, operational technique and unit of results. They use proxies and lack quantification. Conflicting results are therefore drawn between projects that do not provide methodological or resultant comparability. Typical modern stability tests suspend aggregates in water and monitor fragmentation upon exposure to an un-quantified amount of ultrasonic energy, utilising a laser granulometer to measure the change in mean weight diameter. In this project a novel approach has been developed based on that of Zhu et al., (2009), to accurately quantify the stability of aggregates by specifically measuring their bond energies. The bond energies are measured operating a combination of calorimetry and a high powered ultrasonic probe, with computable output function. Temperature change during sonication is monitored by an array of probes which enables calculation of the energy spent heating the system (Ph). Our novel technique suspends aggregates in heavy liquid lithium heteropolytungstate, as opposed to water, to avoid exposing aggregates to an immeasurable disruptive energy source, due to cavitation, collisions and clay swelling. Mean weight diameter is measured by a laser granulometer to monitor aggregate breakdown after successive periods of calculated ultrasonic energy input (Pi), until complete dispersion is achieved and bond
Automation of aggregate characterization using laser profiling and digital image analysis
NASA Astrophysics Data System (ADS)
Kim, Hyoungkwan
2002-08-01
Particle morphological properties such as size, shape, angularity, and texture are key properties that are frequently used to characterize aggregates. The characteristics of aggregates are crucial to the strength, durability, and serviceability of the structure in which they are used. Thus, it is important to select aggregates that have proper characteristics for each specific application. Use of improper aggregate can cause rapid deterioration or even failure of the structure. The current standard aggregate test methods are generally labor-intensive, time-consuming, and subject to human errors. Moreover, important properties of aggregates may not be captured by the standard methods due to a lack of an objective way of quantifying critical aggregate properties. Increased quality expectations of products along with recent technological advances in information technology are motivating new developments to provide fast and accurate aggregate characterization. The resulting information can enable a real time quality control of aggregate production as well as lead to better design and construction methods of portland cement concrete and hot mix asphalt. This dissertation presents a system to measure various morphological characteristics of construction aggregates effectively. Automatic measurement of various particle properties is of great interest because it has the potential to solve such problems in manual measurements as subjectivity, labor intensity, and slow speed. The main efforts of this research are placed on three-dimensional (3D) laser profiling, particle segmentation algorithms, particle measurement algorithms, and generalized particle descriptors. First, true 3D data of aggregate particles obtained by laser profiling are transformed into digital images. Second, a segmentation algorithm and a particle measurement algorithm are developed to separate particles and process each particle data individually with the aid of various kinds of digital image
Impact of aggregation on scaling behavior of Internet backbone traffic
NASA Astrophysics Data System (ADS)
Zhang, Zhi-Li; Ribeiro, Vinay J.; Moon, Sue B.; Diot, Christophe
2002-07-01
We study the impact of aggregation on the scaling behavior of Internet backbone tra ffic, based on traces collected from OC3 and OC12 links in a tier-1 ISP. We make two striking observations regarding the sub-second small time scaling behaviors of Internet backbone traffic: 1) for a majority of these traces, the Hurst parameters at small time scales (1ms - 100ms) are fairly close to 0.5. Hence the traffic at these time scales are nearly uncorrelated; 2) the scaling behaviors at small time scales are link-dependent, and stay fairly invariant over changing utilization and time. To understand the scaling behavior of network traffic, we develop analytical models and employ them to demonstrate how traffic composition -- aggregation of traffic with different characteristics -- affects the small-time scalings of network traffic. The degree of aggregation and burst correlation structure are two major factors in traffic composition. Our trace-based data analysis confirms this. Furthermore, we discover that traffic composition on a backbone link stays fairly consistent over time and changing utilization, which we believe is the cause for the invariant small-time scalings we observe in the traces.
Real-Time Simulation of Ares I Launch Vehicle
NASA Technical Reports Server (NTRS)
Tobbe, Patrick; Matras, Alex; Wilson, Heath; Alday, Nathan; Walker, David; Betts, Kevin; Hughes, Ryan; Turbe, Michael
2009-01-01
The Ares Real-Time Environment for Modeling, Integration, and Simulation (ARTEMIS) has been developed for use by the Ares I launch vehicle System Integration Laboratory (SIL) at the Marshall Space Flight Center (MSFC). The primary purpose of the Ares SIL is to test the vehicle avionics hardware and software in a hardware-in-the-loop (HWIL) environment to certify that the integrated system is prepared for flight. ARTEMIS has been designed to be the real-time software backbone to stimulate all required Ares components through high-fidelity simulation. ARTEMIS has been designed to take full advantage of the advances in underlying computational power now available to support HWIL testing. A modular real-time design relying on a fully distributed computing architecture has been achieved. Two fundamental requirements drove ARTEMIS to pursue the use of high-fidelity simulation models in a real-time environment. First, ARTEMIS must be used to test a man-rated integrated avionics hardware and software system, thus requiring a wide variety of nominal and off-nominal simulation capabilities to certify system robustness. The second driving requirement - derived from a nationwide review of current state-of-the-art HWIL facilities - was that preserving digital model fidelity significantly reduced overall vehicle lifecycle cost by reducing testing time for certification runs and increasing flight tempo through an expanded operational envelope. These two driving requirements necessitated the use of high-fidelity models throughout the ARTEMIS simulation. The nature of the Ares mission profile imposed a variety of additional requirements on the ARTEMIS simulation. The Ares I vehicle is composed of multiple elements, including the First Stage Solid Rocket Booster (SRB), the Upper Stage powered by the J- 2X engine, the Orion Crew Exploration Vehicle (CEV) which houses the crew, the Launch Abort System (LAS), and various secondary elements that separate from the vehicle. At launch, the
Scaling in the aggregation dynamics of a magnetorheological fluid.
Domínguez-García, P; Melle, Sonia; Pastor, J M; Rubio, M A
2007-11-01
We present experimental results on the aggregation dynamics of a magnetorheological fluid, namely, an aqueous suspension of micrometer-sized superparamagnetic particles, under the action of a constant uniaxial magnetic field using video microscopy and image analysis. We find a scaling behavior in several variables describing the aggregation kinetics. The data agree well with the Family-Vicsek scaling ansatz for diffusion-limited cluster-cluster aggregation. The kinetic exponents z and z' are obtained from the temporal evolution of the mean cluster size S(t) and the number of clusters N(t), respectively. The crossover exponent Delta is calculated in two ways: first, from the initial slope of the scaling function; second, from the evolution of the nonaggregated particles, n1(t). We report on results of Brownian two-dimensional dynamics simulations and compare the results with the experiments. Finally, we discuss the differences obtained between the kinetic exponents in terms of the variation in the crossover exponent and relate this behavior to the physical interpretation of the crossover exponent.
NASA Technical Reports Server (NTRS)
Yuen, Vincent K.
1989-01-01
The Systems Engineering Simulator has addressed the major issues in providing visual data to its real-time man-in-the-loop simulations. Out-the-window views and CCTV views are provided by three scene systems to give the astronauts their real-world views. To expand the window coverage for the Space Station Freedom workstation a rotating optics system is used to provide the widest field of view possible. To provide video signals to as many viewpoints as possible, windows and CCTVs, with a limited amount of hardware, a video distribution system has been developed to time-share the video channels among viewpoints at the selection of the simulation users. These solutions have provided the visual simulation facility for real-time man-in-the-loop simulations for the NASA space program.
Curcumin Attenuates Amyloid-β Aggregate Toxicity and Modulates Amyloid-β Aggregation Pathway.
Thapa, Arjun; Jett, Stephen D; Chi, Eva Y
2016-01-20
The abnormal misfolding and aggregation of amyloid-β (Aβ) peptides into β-sheet enriched insoluble deposits initiates a cascade of events leading to pathological processes and culminating in cognitive decline in Alzheimer's disease (AD). In particular, soluble oligomeric/prefibrillar Aβ have been shown to be potent neurotoxins. The naturally occurring polyphenol curcumin has been shown to exert a neuroprotective effect against age-related neurodegenerative diseases such as AD. However, its protective mechanism remains unclear. In this study, we investigated the effects of curcumin on the aggregation of Aβ40 as well as Aβ40 aggregate induced neurotoxicity. Our results show that the curcumin does not inhibit Aβ fibril formation, but rather enriches the population of "off-pathway" soluble oligomers and prefibrillar aggregates that were nontoxic. Curcumin also exerted a nonspecific neuroprotective effect, reducing toxicities induced by a range of Aβ conformers, including monomeric, oligomeric, prefibrillar, and fibrillar Aβ. The neuroprotective effect is possibly membrane-mediated, as curcumin reduced the extent of cell membrane permeabilization induced by Aβ aggregates. Taken together, our study shows that curcumin exerts its neuroprotective effect against Aβ induced toxicity through at least two concerted pathways, modifying the Aβ aggregation pathway toward the formation of nontoxic aggregates and ameliorating Aβ-induced toxicity possibly through a nonspecific pathway.
The Effects of Time Advance Mechanism on Simple Agent Behaviors in Combat Simulations
2011-12-01
modeling packages that illustrate the differences between discrete-time simulation (DTS) and discrete-event simulation ( DES ) methodologies. Many combat... DES ) models , often referred to as “next-event” (Law and Kelton 2000) or discrete time simulation (DTS), commonly referred to as “time-step.” DTS...discrete-time simulation (DTS) and discrete-event simulation ( DES ) methodologies. Many combat models use DTS as their simulation time advance mechanism
A Fast-Time Simulation Tool for Analysis of Airport Arrival Traffic
NASA Technical Reports Server (NTRS)
Erzberger, Heinz; Meyn, Larry A.; Neuman, Frank
2004-01-01
The basic objective of arrival sequencing in air traffic control automation is to match traffic demand and airport capacity while minimizing delays. The performance of an automated arrival scheduling system, such as the Traffic Management Advisor developed by NASA for the FAA, can be studied by a fast-time simulation that does not involve running expensive and time-consuming real-time simulations. The fast-time simulation models runway configurations, the characteristics of arrival traffic, deviations from predicted arrival times, as well as the arrival sequencing and scheduling algorithm. This report reviews the development of the fast-time simulation method used originally by NASA in the design of the sequencing and scheduling algorithm for the Traffic Management Advisor. The utility of this method of simulation is demonstrated by examining the effect on delays of altering arrival schedules at a hub airport.
Users manual for linear Time-Varying Helicopter Simulation (Program TVHIS)
NASA Technical Reports Server (NTRS)
Burns, M. R.
1979-01-01
A linear time-varying helicopter simulation program (TVHIS) is described. The program is designed as a realistic yet efficient helicopter simulation. It is based on a linear time-varying helicopter model which includes rotor, actuator, and sensor models, as well as a simulation of flight computer logic. The TVHIS can generate a mean trajectory simulation along a nominal trajectory, or propagate covariance of helicopter states, including rigid-body, turbulence, control command, controller states, and rigid-body state estimates.
Dynamics of micelle formation from temperature-jump Monte Carlo simulations.
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.
Collisional disruption of gravitational aggregates in the tidal environment
DOE Office of Scientific and Technical Information (OSTI.GOV)
Hyodo, Ryuki; Ohtsuki, Keiji
2014-05-20
The degree of disruption in collisions in free space is determined by specific impact energy, and the mass fraction of the largest remnant is a monotonically decreasing function of impact energy. However, it has not been shown whether such a relationship is applicable to collisions under the influence of a planet's tidal force, which is important in ring dynamics and satellite accretion. Here we examine the collisional disruption of gravitational aggregates in the tidal environment by using local N-body simulations. We find that outcomes of such a collision largely depend on the impact velocity, the direction of impact, and themore » radial distance from the planet. In the case of a strong tidal field corresponding to Saturn's F ring, collisions in the azimuthal direction are much more destructive than those in the radial direction. Numerical results of collisions sensitively depend on the impact velocity, and a complete disruption of aggregates can occur even in impacts with velocity much lower than their escape velocity. In such low-velocity collisions, the deformation of colliding aggregates plays an essential role in determining collision outcomes, because the physical size of the aggregate is comparable to its Hill radius. On the other hand, the dependence of collision outcomes on impact velocity becomes similar to the case in free space when the distance from the planet is sufficiently large. Our results are consistent with Cassini observations of the F ring, which suggest ongoing creation and disruption of aggregates within the ring.« less
Nearest-Neighbor Distances and Aggregative Effects in Turbulence
NASA Astrophysics Data System (ADS)
Lanerolle, Lyon W. J.; Rothschild, B. J.; Yeung, P. K.
2000-11-01
The dispersive nature of turbulence which causes fluid elements to move apart (on average) is well known. Here we study another facet of turbulent mixing relevant to marine population dynamics - on how small organisms (approximated by fluid particles) are brought close to each other and allowed to interact. The crucial role played by the small scales in this process allows us to use direct numerical simulations of stationary isotropic turbulence, here with Taylor-scale Reynolds numbers (R_λ) from 38 to 91. We study the evolution of the Nearest-Neighbor Distances (NND) for collections of fluid particles initially located randomly in space satisfying Poisson-type distributions with mean values from 0.5 to 2.0 Kolmogorov length scales. Our results show that as particles begin to disperse on average, some also begin to aggregate in space. In particular, we find that (i) a significant proportion of particles are closer to each other than if their NNDs were randomly distributed, (ii) aggregative effects become stronger with R_λ, and (iii) although the mean value of NND grows monotonically with time in Kolmogorov variables, the growth rates are slower at higher R_λ. These results may assist in explaining the ``patchiness'' in plankton distributions observed in biological oceanography. Further details are given in B. J. Rothschild et al., The Biophysical Interpretation of Spatial Effects of Small-scale Turbulent Flow in the Ocean (paper in prep.).
NASA Astrophysics Data System (ADS)
Tay, J.; Hood, R. R.
2016-02-01
Although jellyfish exert strong control over marine plankton dynamics (Richardson et al. 2009, Robison et al. 2014) and negatively impact human commercial and recreational activities (Purcell et al. 2007, Purcell 2012), jellyfish biomass is not well quantified due primarily to sampling difficulties with plankton nets or fisheries trawls (Haddock 2004). As a result, some of the longest records of jellyfish are visual shore-based surveys, such as the fixed-station time series of Chrysaora quinquecirrha that began in 1960 in the Patuxent River in Chesapeake Bay, USA (Cargo and King 1990). Time series counts from fixed-station surveys capture two signals: 1) demographic change at timescales on the order of reproductive processes and 2) spatial patchiness at shorter timescales as different parcels of water move in and out of the survey area by tidal and estuarine advection and turbulent mixing (Lee and McAlice 1979). In this study, our goal was to separate these two signals using a 4-year time series of C. quinquecirrha medusa counts from a fixed-station in the Choptank River, Chesapeake Bay. Idealized modeling of tidal and estuarine advection was used to conceptualize the sampling scheme. Change point and time series analysis was used to detect demographic changes. Indices of aggregation (Negative Binomial coefficient, Taylor's Power Law coefficient, and Morisita's Index) were calculated to describe the spatial patchiness of the medusae. Abundance estimates revealed a bloom cycle that differed in duration and magnitude for each of the study years. Indices of aggregation indicated that medusae were aggregated and that patches grew in the number of individuals, and likely in size, as abundance increased. Further inference from the conceptual modeling suggested that medusae patch structure was generally homogenous over the tidal extent. This study highlights the benefits of using fixed-station shore-based surveys for understanding the biology and ecology of jellyfish.
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.
Real-time visual simulation of APT system based on RTW and Vega
NASA Astrophysics Data System (ADS)
Xiong, Shuai; Fu, Chengyu; Tang, Tao
2012-10-01
The Matlab/Simulink simulation model of APT (acquisition, pointing and tracking) system is analyzed and established. Then the model's C code which can be used for real-time simulation is generated by RTW (Real-Time Workshop). Practical experiments show, the simulation result of running the C code is the same as running the Simulink model directly in the Matlab environment. MultiGen-Vega is a real-time 3D scene simulation software system. With it and OpenGL, the APT scene simulation platform is developed and used to render and display the virtual scenes of the APT system. To add some necessary graphics effects to the virtual scenes real-time, GLSL (OpenGL Shading Language) shaders are used based on programmable GPU. By calling the C code, the scene simulation platform can adjust the system parameters on-line and get APT system's real-time simulation data to drive the scenes. Practical application shows that this visual simulation platform has high efficiency, low charge and good simulation effect.
NASA Astrophysics Data System (ADS)
Camilloni, Carlo; Sala, Benedetta Maria; Sormanni, Pietro; Porcari, Riccardo; Corazza, Alessandra; De Rosa, Matteo; Zanini, Stefano; Barbiroli, Alberto; Esposito, Gennaro; Bolognesi, Martino; Bellotti, Vittorio; Vendruscolo, Michele; Ricagno, Stefano
2016-05-01
A wide range of human diseases is associated with mutations that, destabilizing proteins native state, promote their aggregation. However, the mechanisms leading from folded to aggregated states are still incompletely understood. To investigate these mechanisms, we used a combination of NMR spectroscopy and molecular dynamics simulations to compare the native state dynamics of Beta-2 microglobulin (β2m), whose aggregation is associated with dialysis-related amyloidosis, and its aggregation-resistant mutant W60G. Our results indicate that W60G low aggregation propensity can be explained, beyond its higher stability, by an increased average protection of the aggregation-prone residues at its surface. To validate these findings, we designed β2m variants that alter the aggregation-prone exposed surface of wild-type and W60G β2m modifying their aggregation propensity. These results allowed us to pinpoint the role of dynamics in β2m aggregation and to provide a new strategy to tune protein aggregation by modulating the exposure of aggregation-prone residues.
Brownian aggregation rate of colloid particles with several active sites
DOE Office of Scientific and Technical Information (OSTI.GOV)
Nekrasov, Vyacheslav M.; Yurkin, Maxim A.; Chernyshev, Andrei V., E-mail: chern@ns.kinetics.nsc.ru
2014-08-14
We theoretically analyze the aggregation kinetics of colloid particles with several active sites. Such particles (so-called “patchy particles”) are well known as chemically anisotropic reactants, but the corresponding rate constant of their aggregation has not yet been established in a convenient analytical form. Using kinematic approximation for the diffusion problem, we derived an analytical formula for the diffusion-controlled reaction rate constant between two colloid particles (or clusters) with several small active sites under the following assumptions: the relative translational motion is Brownian diffusion, and the isotropic stochastic reorientation of each particle is Markovian and arbitrarily correlated. This formula was shownmore » to produce accurate results in comparison with more sophisticated approaches. Also, to account for the case of a low number of active sites per particle we used Monte Carlo stochastic algorithm based on Gillespie method. Simulations showed that such discrete model is required when this number is less than 10. Finally, we applied the developed approach to the simulation of immunoagglutination, assuming that the formed clusters have fractal structure.« less
NASA Astrophysics Data System (ADS)
Tang, F. K.; Cui, M.; Lu, Q.; Liu, Y. G.; Guo, H. Y.; Zhou, J. X.
2015-08-01
Changes in soil utilization significantly affect aggregate stability and aggregate-associated soil organic carbon (SOC). A field investigation and indoor analysis were conducted in order to study the soil aggregate stability and organic carbon distribution in the water-stable aggregates (WSA) of the bare land (BL), grassland (GL), shrubland (SL), and woodland (WL) in a typical karst gorge region. The results indicated that the BL, GL, SL, and WL were dominated by particles with sizes > 5 mm under dry sieving treatment, and that the soil aggregate contents of various sizes decreased as the particle size decreased. In addition, the BL, GL, SL, and WL were predominantly comprised of WSA < 0.25 mm under wet sieving treatment, and that the WSA contents initially increased, then decreased, and then increased again as the particle size decreased. Furthermore, at a soil depth of 0-60 cm, the mean weight diameter (MWD), geometrical mean diameter (GMD), and fractal dimensions (D) of the dry aggregates and water-stable aggregates in the different types of land were ranked, in descending order, as WL > GL > SL > BL. The contents of WSA > 0.25 mm, MWD and GMD increased significantly, in that order, and the percentage of aggregate destruction (PAD) and fractal dimensions decreased significantly as the soil aggregate stability improved. The results of this study indicated that, as the SOC contents increased after vegetation restoration, the average SOC content of WL was 2.35, 1.37, and 1.26 times greater than that in the BL, GL, and SL, respectively. The total SOC and SOC associated in WSA of various sizes were the highest at a soil depth of 0-20 cm. In addition, the SOC contents of the WSA increased as the soil aggregate sizes decreased. The SOC contents of the WSA < 0.25 mm were highest except in the bare land, and the SOC contents of the aggregates < 0.25 mm, which ranged from 18.85 to 41.08 %, comprised the majority of the total aggregate SOC contents. The woodland and
The procedure for determining the residual life of high-temperature aggregates
NASA Astrophysics Data System (ADS)
Nikiforov, A. S.; Prihodko, E. V.; Kinzhibekova, A. K.; Karmanov, A. E.
2018-01-01
One of the main reasons for the withdrawal of high-temperature aggregates for repairs is the destruction of enclosing structures due to the occurrence of temperature stresses. A wide range of refractory materials used, a large number of product names, a difference in the operation of even the same aggregates makes it impossible to apply general principles for determining the residual resource of high-temperature aggregates, which is based, as a rule, on the determination of temperature stresses. In the article there is suggested a technique based on the method of simulation modeling, allowing to estimate the remaining resource and reliability of the operating equipment. There are given data on the calculation of these indicators for a 25-ton steel-casting ladle. The values obtained make it possible to evaluate the rationality of the further operation of the high-temperature unit by the condition of reliability of the enclosing structures.
Computer considerations for real time simulation of a generalized rotor model
NASA Technical Reports Server (NTRS)
Howe, R. M.; Fogarty, L. E.
1977-01-01
Scaled equations were developed to meet requirements for real time computer simulation of the rotor system research aircraft. These equations form the basis for consideration of both digital and hybrid mechanization for real time simulation. For all digital simulation estimates of the required speed in terms of equivalent operations per second are developed based on the complexity of the equations and the required intergration frame rates. For both conventional hybrid simulation and hybrid simulation using time-shared analog elements the amount of required equipment is estimated along with a consideration of the dynamic errors. Conventional hybrid mechanization using analog simulation of those rotor equations which involve rotor-spin frequencies (this consititutes the bulk of the equations) requires too much analog equipment. Hybrid simulation using time-sharing techniques for the analog elements appears possible with a reasonable amount of analog equipment. All-digital simulation with affordable general-purpose computers is not possible because of speed limitations, but specially configured digital computers do have the required speed and consitute the recommended approach.
NASA Technical Reports Server (NTRS)
Fijany, A.; Roberts, J. A.; Jain, A.; Man, G. K.
1993-01-01
Part 1 of this paper presented the requirements for the real-time simulation of Cassini spacecraft along with some discussion of the DARTS algorithm. Here, in Part 2 we discuss the development and implementation of parallel/vectorized DARTS algorithm and architecture for real-time simulation. Development of the fast algorithms and architecture for real-time hardware-in-the-loop simulation of spacecraft dynamics is motivated by the fact that it represents a hard real-time problem, in the sense that the correctness of the simulation depends on both the numerical accuracy and the exact timing of the computation. For a given model fidelity, the computation should be computed within a predefined time period. Further reduction in computation time allows increasing the fidelity of the model (i.e., inclusion of more flexible modes) and the integration routine.
From particle condensation to polymer aggregation
NASA Astrophysics Data System (ADS)
Janke, Wolfhard; Zierenberg, Johannes
2018-01-01
We draw an analogy between droplet formation in dilute particle and polymer systems. Our arguments are based on finite-size scaling results from studies of a two-dimensional lattice gas to three-dimensional bead-spring polymers. To set the results in perspective, we compare with in part rigorous theoretical scaling laws for canonical condensation in a supersaturated gas at fixed temperature, and derive corresponding scaling predictions for an undercooled gas at fixed density. The latter allows one to efficiently employ parallel multicanonical simulations and to reach previously not accessible scaling regimes. While the asymptotic scaling can not be observed for the comparably small polymer system sizes, they demonstrate an intermediate scaling regime also observable for particle condensation. Altogether, our extensive results from computer simulations provide clear evidence for the close analogy between particle condensation and polymer aggregation in dilute systems.
DOE Office of Scientific and Technical Information (OSTI.GOV)
Mansbach, Rachael A.; Ferguson, Andrew L.
Self-assembled aggregates of peptides containing aromatic groups possess optoelectronic properties that make them attractive targets for the fabrication of biocompatible electronics. Molecular-level understanding of how the microscopic peptide chemistry influences the properties of the aggregates is vital for rational peptide design. We construct a coarse-grained model of Asp-Phe-Ala-Gly-OPV3-Gly-Ala-Phe-Asp (DFAG-OPV3-GAFD) peptides containing OPV3 (distyrylbenzene) π-conjugated cores explicitly parameterized against all-atom calculations and perform molecular dynamics simulations of the self-assembly of hundreds of molecules over hundreds of nanoseconds. We observe a hierarchical assembly mechanism wherein ~2-8 peptides assemble into stacks with aligned aromatic cores that subsequently form elliptical aggregates and ultimately amore » branched network with a fractal dimensionality of ~1.5. The assembly dynamics are well described by a Smoluchowski coagulation process for which we extract rate constants from the molecular simulations to both furnish insight into the microscopic assembly kinetics and extrapolate our aggregation predictions to time and length scales beyond the reach of molecular simulation. Lastly, this study presents new molecular-level understanding of the morphology and dynamics of the spontaneous self-assembly of DFAG-OPV3-GAFD peptides and establishes a systematic protocol to develop coarse-grained models of optoelectronic peptides for the exploration and design of π-conjugated peptides with tunable optoelectronic properties.« less
Mansbach, Rachael A.; Ferguson, Andrew L.
2017-02-10
Self-assembled aggregates of peptides containing aromatic groups possess optoelectronic properties that make them attractive targets for the fabrication of biocompatible electronics. Molecular-level understanding of how the microscopic peptide chemistry influences the properties of the aggregates is vital for rational peptide design. We construct a coarse-grained model of Asp-Phe-Ala-Gly-OPV3-Gly-Ala-Phe-Asp (DFAG-OPV3-GAFD) peptides containing OPV3 (distyrylbenzene) π-conjugated cores explicitly parameterized against all-atom calculations and perform molecular dynamics simulations of the self-assembly of hundreds of molecules over hundreds of nanoseconds. We observe a hierarchical assembly mechanism wherein ~2-8 peptides assemble into stacks with aligned aromatic cores that subsequently form elliptical aggregates and ultimately amore » branched network with a fractal dimensionality of ~1.5. The assembly dynamics are well described by a Smoluchowski coagulation process for which we extract rate constants from the molecular simulations to both furnish insight into the microscopic assembly kinetics and extrapolate our aggregation predictions to time and length scales beyond the reach of molecular simulation. Lastly, this study presents new molecular-level understanding of the morphology and dynamics of the spontaneous self-assembly of DFAG-OPV3-GAFD peptides and establishes a systematic protocol to develop coarse-grained models of optoelectronic peptides for the exploration and design of π-conjugated peptides with tunable optoelectronic properties.« less
Analysis of aggregated tick returns: Evidence for anomalous diffusion
NASA Astrophysics Data System (ADS)
Weber, Philipp
2007-01-01
In order to investigate the origin of large price fluctuations, we analyze stock price changes of ten frequently traded NASDAQ stocks in the year 2002. Though the influence of the trading frequency on the aggregate return in a certain time interval is important, it cannot alone explain the heavy-tailed distribution of stock price changes. For this reason, we analyze intervals with a fixed number of trades in order to eliminate the influence of the trading frequency and investigate the relevance of other factors for the aggregate return. We show that in tick time the price follows a discrete diffusion process with a variable step width while the difference between the number of steps in positive and negative direction in an interval is Gaussian distributed. The step width is given by the return due to a single trade and is long-term correlated in tick time. Hence, its mean value can well characterize an interval of many trades and turns out to be an important determinant for large aggregate returns. We also present a statistical model reproducing the cumulative distribution of aggregate returns. For an accurate agreement with the empirical distribution, we also take into account asymmetries of the step widths in different directions together with cross correlations between these asymmetries and the mean step width as well as the signs of the steps.
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
AGGRESCAN3D (A3D): server for prediction of aggregation properties of protein structures
Zambrano, Rafael; Jamroz, Michal; Szczasiuk, Agata; Pujols, Jordi; Kmiecik, Sebastian; Ventura, Salvador
2015-01-01
Protein aggregation underlies an increasing number of disorders and constitutes a major bottleneck in the development of therapeutic proteins. Our present understanding on the molecular determinants of protein aggregation has crystalized in a series of predictive algorithms to identify aggregation-prone sites. A majority of these methods rely only on sequence. Therefore, they find difficulties to predict the aggregation properties of folded globular proteins, where aggregation-prone sites are often not contiguous in sequence or buried inside the native structure. The AGGRESCAN3D (A3D) server overcomes these limitations by taking into account the protein structure and the experimental aggregation propensity scale from the well-established AGGRESCAN method. Using the A3D server, the identified aggregation-prone residues can be virtually mutated to design variants with increased solubility, or to test the impact of pathogenic mutations. Additionally, A3D server enables to take into account the dynamic fluctuations of protein structure in solution, which may influence aggregation propensity. This is possible in A3D Dynamic Mode that exploits the CABS-flex approach for the fast simulations of flexibility of globular proteins. The A3D server can be accessed at http://biocomp.chem.uw.edu.pl/A3D/. PMID:25883144
Effects of maximum aggregate size on UPV of brick aggregate concrete.
Mohammed, Tarek Uddin; Mahmood, Aziz Hasan
2016-07-01
Investigation was carried out to study the effects of maximum aggregate size (MAS) (12.5mm, 19.0mm, 25.0mm, 37.5mm, and 50.0mm) on ultrasonic pulse velocity (UPV) of concrete. For investigation, first class bricks were collected and broken to make coarse aggregate. The aggregates were tested for specific gravity, absorption capacity, unit weight, and abrasion resistance. Cylindrical concrete specimens were made with different sand to aggregate volume ratio (s/a) (0.40 and 0.45), W/C ratio (0.45, 0.50, and 0.55), and cement content (375kg/m(3) and 400kg/m(3)). The specimens were tested for compressive strength and Young's modulus. UPV through wet specimen was measured using Portable Ultrasonic Non-destructive Digital Indicating Tester (PUNDIT). Results indicate that the pulse velocity through concrete increases with an increase in MAS. Relationships between UPV and compressive strength; and UPV and Young's modulus of concrete are proposed for different maximum sizes of brick aggregate. Copyright © 2016 Elsevier B.V. All rights reserved.
Memantine inhibits β-amyloid aggregation and disassembles preformed β-amyloid aggregates.
Takahashi-Ito, Kaori; Makino, Mitsuhiro; Okado, Keiko; Tomita, Taisuke
2017-11-04
Memantine, an uncompetitive glutamatergic N-methyl-d-aspartate (NMDA) receptor antagonist, is widely used as a medication for the treatment of Alzheimer's disease (AD). We previously reported that chronic treatment of AD with memantine reduces the amount of insoluble β-amyloid (Aβ) and soluble Aβ oligomers in animal models of AD. The mechanisms by which memantine reduces Aβ levels in the brain were evaluated by determining the effect of memantine on Aβ aggregation using thioflavin T and transmission electron microscopy. Memantine inhibited the formation of Aβ(1-42) aggregates in a concentration-dependent manner, whereas amantadine, a structurally similar compound, did not affect Aβ aggregation at the same concentrations. Furthermore, memantine inhibited the formation of different types of Aβ aggregates, including Aβs carrying familial AD mutations, and disaggregated preformed Aβ(1-42) fibrils. These results suggest that the inhibition of Aβ aggregation and induction of Aβ disaggregation may be involved in the mechanisms by which memantine reduces Aβ deposition in the brain. Copyright © 2017 Elsevier Inc. All rights reserved.
Patel, Lara A; Kindt, James T
2017-03-14
We introduce a global fitting analysis method to obtain free energies of association of noncovalent molecular clusters using equilibrated cluster size distributions from unbiased constant-temperature molecular dynamics (MD) simulations. Because the systems simulated are small enough that the law of mass action does not describe the aggregation statistics, the method relies on iteratively determining a set of cluster free energies that, using appropriately weighted sums over all possible partitions of N monomers into clusters, produces the best-fit size distribution. The quality of these fits can be used as an objective measure of self-consistency to optimize the cutoff distance that determines how clusters are defined. To showcase the method, we have simulated a united-atom model of methyl tert-butyl ether (MTBE) in the vapor phase and in explicit water solution over a range of system sizes (up to 95 MTBE in the vapor phase and 60 MTBE in the aqueous phase) and concentrations at 273 K. The resulting size-dependent cluster free energy functions follow a form derived from classical nucleation theory (CNT) quite well over the full range of cluster sizes, although deviations are more pronounced for small cluster sizes. The CNT fit to cluster free energies yielded surface tensions that were in both cases lower than those for the simulated planar interfaces. We use a simple model to derive a condition for minimizing non-ideal effects on cluster size distributions and show that the cutoff distance that yields the best global fit is consistent with this condition.
Observations of diffusion-limited aggregation-like patterns by atmospheric plasma jet
NASA Astrophysics Data System (ADS)
Chiu, Ching-Yang; Chu, Hong-Yu
2017-11-01
We report on the observations of diffusion-limited aggregation-like patterns during the thin film removal process by an atmospheric plasma jet. The fractal patterns are found to have various structures like dense branching and tree-like patterns. The determination of surface morphology reveals that the footprints of discharge bursts are not as random as expected. We propose a diffusion-limited aggregation model with a few extra requirements by analogy with the experimental results, and thereby present the beauty of nature. We show that the model simulates not only the shapes of the patterns similar to the experimental observations, but also the growing sequences of fluctuating, oscillatory, and zigzag traces.
Design of teleoperation system with a force-reflecting real-time simulator
NASA Technical Reports Server (NTRS)
Hirata, Mitsunori; Sato, Yuichi; Nagashima, Fumio; Maruyama, Tsugito
1994-01-01
We developed a force-reflecting teleoperation system that uses a real-time graphic simulator. This system eliminates the effects of communication time delays in remote robot manipulation. The simulator provides the operator with predictive display and feedback of computed contact forces through a six-degree of freedom (6-DOF) master arm on a real-time basis. With this system, peg-in-hole tasks involving round-trip communication time delays of up to a few seconds were performed at three support levels: a real image alone, a predictive display with a real image, and a real-time graphic simulator with computed-contact-force reflection and a predictive display. The experimental results indicate the best teleoperation efficiency was achieved by using the force-reflecting simulator with two images. The shortest work time, lowest sensor maximum, and a 100 percent success rate were obtained. These results demonstrate the effectiveness of simulated-force-reflecting teleoperation efficiency.
NASA Technical Reports Server (NTRS)
Venkatachari, Balaji Shankar; Streett, Craig L.; Chang, Chau-Lyan; Friedlander, David J.; Wang, Xiao-Yen; Chang, Sin-Chung
2016-01-01
Despite decades of development of unstructured mesh methods, high-fidelity time-accurate simulations are still predominantly carried out on structured, or unstructured hexahedral meshes by using high-order finite-difference, weighted essentially non-oscillatory (WENO), or hybrid schemes formed by their combinations. In this work, the space-time conservation element solution element (CESE) method is used to simulate several flow problems including supersonic jet/shock interaction and its impact on launch vehicle acoustics, and direct numerical simulations of turbulent flows using tetrahedral meshes. This paper provides a status report for the continuing development of the space-time conservation element solution element (CESE) numerical and software framework under the Revolutionary Computational Aerosciences (RCA) project. Solution accuracy and large-scale parallel performance of the numerical framework is assessed with the goal of providing a viable paradigm for future high-fidelity flow physics simulations.
Use of high performance networks and supercomputers for real-time flight simulation
NASA Technical Reports Server (NTRS)
Cleveland, Jeff I., II
1993-01-01
In order to meet the stringent time-critical requirements for real-time man-in-the-loop flight simulation, computer processing operations must be consistent in processing time and be completed in as short a time as possible. These operations include simulation mathematical model computation and data input/output to the simulators. In 1986, in response to increased demands for flight simulation performance, NASA's Langley Research Center (LaRC), working with the contractor, developed extensions to the Computer Automated Measurement and Control (CAMAC) technology which resulted in a factor of ten increase in the effective bandwidth and reduced latency of modules necessary for simulator communication. This technology extension is being used by more than 80 leading technological developers in the United States, Canada, and Europe. Included among the commercial applications are nuclear process control, power grid analysis, process monitoring, real-time simulation, and radar data acquisition. Personnel at LaRC are completing the development of the use of supercomputers for mathematical model computation to support real-time flight simulation. This includes the development of a real-time operating system and development of specialized software and hardware for the simulator network. This paper describes the data acquisition technology and the development of supercomputing for flight simulation.
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)
DOE Office of Scientific and Technical Information (OSTI.GOV)
Wilcke, W.; Kretzschmar, S.; Bundt, M.
1999-10-01
In many temperate soils the preferential weathering and leaching of aggregate surfaces and the nonaggregated material between aggregates depletes geogenic metals. It also shifts metals from strongly to more weakly bound metal forms. Deposited metals are sorbed preferentially on aggregate surfaces and between aggregates. The authors examined whether preferential desilication under tropical climate causes an enrichment in the aggregate exteriors in oxidic forms of metals. They also studied where deposited metals are bound in these soils. Aggregates (2--20 mm) were selected manually from the A horizons of eight Oxisols, six Andisols, two Mollisols, and two Inceptisols in Costa Rica. Allmore » samples were fractionated into interior and exterior portions and treated with a seven-step sequence to extract Al, Cd, Cu, Fe, Mn, Pb, and Zn. Total concentrations of all metals except Zn were higher in the aggregate exteriors than in the interiors. The average Cd and Pb concentrations in easily extractable fractions were significantly higher in the aggregate exteriors. There were no significant differences in metal partitioning between interiors and exteriors except for Pb, which had higher proportions in extractable forms with NH{sub 2}OH {center{underscore}dot} HCl {gt} NH{sub 4} - acetate, pH 6.0 {gt} EDTA in the exteriors. There were few significant differences in metal concentrations and partitioning between bulk soil and whole aggregates. The results may be explained by (i) preferential desilication of the aggregate exteriors and (ii) preferential sorption of deposited heavy metals mainly in easily extractable forms.« less
Limited protection of macro-aggregate-occluded organic carbon in Siberian steppe soils
NASA Astrophysics Data System (ADS)
Bischoff, Norbert; Mikutta, Robert; Shibistova, Olga; Puzanov, Alexander; Silanteva, Marina; Grebennikova, Anna; Fuß, Roland; Guggenberger, Georg
2017-05-01
Macro-aggregates especially in agricultural steppe soils are supposed to play a vital role for soil organic carbon (OC) stabilization at a decadal timescale. While most research on soil OC stabilization in steppes focused on North American prairie soils of the Great Plains with information mainly provided by short-term incubation experiments, little is known about the agricultural steppes in southwestern Siberia, though they belong to the greatest conversion areas in the world and occupy an area larger than that in the Great Plains. To quantify the proportion of macro-aggregate-protected OC under different land use as function of land use intensity and time since land use change (LUC) from pasture to arable land in Siberian steppe soils, we determined OC mineralization rates of intact (250-2000 µm) and crushed (< 250 µm) macro-aggregates in long-term incubations over 401 days (20 °C; 60 % water holding capacity) along two agricultural chronosequences in the Siberian Kulunda steppe. Additionally, we incubated bulk soil (< 2000 µm) to determine the effect of LUC and subsequent agricultural use on a fast and a slow soil OC pool (labile vs. more stable OC), as derived from fitting exponential-decay models to incubation data. We hypothesized that (i) macro-aggregate crushing leads to increased OC mineralization due to an increasing microbial accessibility of a previously occluded labile macro-aggregate OC fraction, and (ii) bulk soil OC mineralization rates and the size of the fast OC pool are higher in pasture than in arable soils with decreasing bulk soil OC mineralization rates and size of the fast OC pool as land use intensity and time since LUC increase. Against our hypothesis, OC mineralization rates of crushed macro-aggregates were similar to those of intact macro-aggregates under all land use regimes. Macro-aggregate-protected OC was almost absent and accounted for < 1 % of the total macro-aggregate OC content and to a maximum of 8 ± 4 % of mineralized OC
Power estimation using simulations for air pollution time-series studies
2012-01-01
Background Estimation of power to assess associations of interest can be challenging for time-series studies of the acute health effects of air pollution because there are two dimensions of sample size (time-series length and daily outcome counts), and because these studies often use generalized linear models to control for complex patterns of covariation between pollutants and time trends, meteorology and possibly other pollutants. In general, statistical software packages for power estimation rely on simplifying assumptions that may not adequately capture this complexity. Here we examine the impact of various factors affecting power using simulations, with comparison of power estimates obtained from simulations with those obtained using statistical software. Methods Power was estimated for various analyses within a time-series study of air pollution and emergency department visits using simulations for specified scenarios. Mean daily emergency department visit counts, model parameter value estimates and daily values for air pollution and meteorological variables from actual data (8/1/98 to 7/31/99 in Atlanta) were used to generate simulated daily outcome counts with specified temporal associations with air pollutants and randomly generated error based on a Poisson distribution. Power was estimated by conducting analyses of the association between simulated daily outcome counts and air pollution in 2000 data sets for each scenario. Power estimates from simulations and statistical software (G*Power and PASS) were compared. Results In the simulation results, increasing time-series length and average daily outcome counts both increased power to a similar extent. Our results also illustrate the low power that can result from using outcomes with low daily counts or short time series, and the reduction in power that can accompany use of multipollutant models. Power estimates obtained using standard statistical software were very similar to those from the simulations
Power estimation using simulations for air pollution time-series studies.
Winquist, Andrea; Klein, Mitchel; Tolbert, Paige; Sarnat, Stefanie Ebelt
2012-09-20
Estimation of power to assess associations of interest can be challenging for time-series studies of the acute health effects of air pollution because there are two dimensions of sample size (time-series length and daily outcome counts), and because these studies often use generalized linear models to control for complex patterns of covariation between pollutants and time trends, meteorology and possibly other pollutants. In general, statistical software packages for power estimation rely on simplifying assumptions that may not adequately capture this complexity. Here we examine the impact of various factors affecting power using simulations, with comparison of power estimates obtained from simulations with those obtained using statistical software. Power was estimated for various analyses within a time-series study of air pollution and emergency department visits using simulations for specified scenarios. Mean daily emergency department visit counts, model parameter value estimates and daily values for air pollution and meteorological variables from actual data (8/1/98 to 7/31/99 in Atlanta) were used to generate simulated daily outcome counts with specified temporal associations with air pollutants and randomly generated error based on a Poisson distribution. Power was estimated by conducting analyses of the association between simulated daily outcome counts and air pollution in 2000 data sets for each scenario. Power estimates from simulations and statistical software (G*Power and PASS) were compared. In the simulation results, increasing time-series length and average daily outcome counts both increased power to a similar extent. Our results also illustrate the low power that can result from using outcomes with low daily counts or short time series, and the reduction in power that can accompany use of multipollutant models. Power estimates obtained using standard statistical software were very similar to those from the simulations when properly implemented
Suchorab, Zbigniew; Barnat-Hunek, Danuta; Franus, Małgorzata; Łagód, Grzegorz
2016-01-01
This article is focused on lightweight aggregate-concrete modified by municipal sewage sludge and lightweight aggregate-concrete obtained from light aggregates. The article presents laboratory examinations of material physical parameters. Water absorptivity of the examined material was decreased by the admixture of water emulsion of reactive polysiloxanes. Water transport properties were determined using Time Domain Reflectometry, an indirect technique for moisture detection in porous media. Together with basic physical parameters, the heat conductivity coefficient λ was determined for both types of lightweight aggregate-concrete. Analysis of moisture and heat properties of the examined materials confirmed the usefulness of light aggregates supplemented with sewage sludge for prospective production. PMID:28773442
Suchorab, Zbigniew; Barnat-Hunek, Danuta; Franus, Małgorzata; Łagód, Grzegorz
2016-04-27
This article is focused on lightweight aggregate-concrete modified by municipal sewage sludge and lightweight aggregate-concrete obtained from light aggregates. The article presents laboratory examinations of material physical parameters. Water absorptivity of the examined material was decreased by the admixture of water emulsion of reactive polysiloxanes. Water transport properties were determined using Time Domain Reflectometry, an indirect technique for moisture detection in porous media. Together with basic physical parameters, the heat conductivity coefficient λ was determined for both types of lightweight aggregate-concrete. Analysis of moisture and heat properties of the examined materials confirmed the usefulness of light aggregates supplemented with sewage sludge for prospective production.
Monte Carlo decision curve analysis using aggregate data.
Hozo, Iztok; Tsalatsanis, Athanasios; Djulbegovic, Benjamin
2017-02-01
Decision curve analysis (DCA) is an increasingly used method for evaluating diagnostic tests and predictive models, but its application requires individual patient data. The Monte Carlo (MC) method can be used to simulate probabilities and outcomes of individual patients and offers an attractive option for application of DCA. We constructed a MC decision model to simulate individual probabilities of outcomes of interest. These probabilities were contrasted against the threshold probability at which a decision-maker is indifferent between key management strategies: treat all, treat none or use predictive model to guide treatment. We compared the results of DCA with MC simulated data against the results of DCA based on actual individual patient data for three decision models published in the literature: (i) statins for primary prevention of cardiovascular disease, (ii) hospice referral for terminally ill patients and (iii) prostate cancer surgery. The results of MC DCA and patient data DCA were identical. To the extent that patient data DCA were used to inform decisions about statin use, referral to hospice or prostate surgery, the results indicate that MC DCA could have also been used. As long as the aggregate parameters on distribution of the probability of outcomes and treatment effects are accurately described in the published reports, the MC DCA will generate indistinguishable results from individual patient data DCA. We provide a simple, easy-to-use model, which can facilitate wider use of DCA and better evaluation of diagnostic tests and predictive models that rely only on aggregate data reported in the literature. © 2017 Stichting European Society for Clinical Investigation Journal Foundation.
DOE Office of Scientific and Technical Information (OSTI.GOV)
Desai, D; Turney, DE; Anantharaman, B
2014-04-24
The morphology of Zn electrodeposits is studied on carbon-coated transmission electron microscopy grids. At low over-potentials (eta = -50 mV), the morphology develops by aggregation at two distinct length scales: similar to 5 nm diameter monocrystalline nanoclusters form similar to 50 nm diameter polycrystalline aggregates, and the aggregates form a branched network. Epitaxial (00 (0) over bar2) growth above an overpotential of vertical bar eta(c)vertical bar > 125 mV leads to the formation of hexagonal single crystals up to 2 mu m in diameter. Potentiostatic current transients were used to calculate the nucleation rate from Scharifker et al.'s model. Themore » exp(eta) dependence of the nucleation rates indicates that atomistic nucleation theory explains the nucleation process better than Volmer-Weber theory. A kinetic model is provided using the rate equations of vapor solidification to simulate the evolution of the different morphologies. On solving these equations, we show that aggregation is attributed to cluster impingement and cluster diffusion while single-crystal formation is attributed to direct attachment.« less
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
NASA Astrophysics Data System (ADS)
Boakye-Boateng, Nasir Abdulai
The growing demand for wind power integration into the generation mix prompts the need to subject these systems to stringent performance requirements. This study sought to identify the required tools and procedures needed to perform real-time simulation studies of Doubly-Fed Induction Generator (DFIG) based wind generation systems as basis for performing more practical tests of reliability and performance for both grid-connected and islanded wind generation systems. The author focused on developing a platform for wind generation studies and in addition, the author tested the performance of two DFIG models on the platform real-time simulation model; an average SimpowerSystemsRTM DFIG wind turbine, and a detailed DFIG based wind turbine using ARTEMiSRTM components. The platform model implemented here consists of a high voltage transmission system with four integrated wind farm models consisting in total of 65 DFIG based wind turbines and it was developed and tested on OPAL-RT's eMEGASimRTM Real-Time Digital Simulator.
DOE Office of Scientific and Technical Information (OSTI.GOV)
Dall-Anese, Emiliano; Bernstein, Andrey; Simonetto, Andrea
This paper develops an online optimization method to maximize the operational objectives of distribution-level distributed energy resources (DERs) while adjusting the aggregate power generated (or consumed) in response to services requested by grid operators. The design of the online algorithm is based on a projected-gradient method, suitably modified to accommodate appropriate measurements from the distribution network and the DERs. By virtue of this approach, the resultant algorithm can cope with inaccuracies in the representation of the AC power, it avoids pervasive metering to gather the state of noncontrollable resources, and it naturally lends itself to a distributed implementation. Optimality claimsmore » are established in terms of tracking of the solution of a well-posed time-varying optimization problem.« less
A discrete mathematical model for the aggregation of β-Amyloid.
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.
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.
A Microprocessor-Based Real-Time Simulator of a Turbofan Engine
1988-01-01
NASA AVSCOM Technical Memorandum 100889 Technical Report 88-C-011 Lfl A Microprocessor-Based Real-Time Simulator of a Turbofan Engine CD I Jonathan S...Accession For NTIS GRA&I A MICROPROCESSOR-BASED REAL-TIME SIMULATOR DTIC TABUnannounced OF A TURBOFAN ENGINE Justifiaation, Jonathan S. Litt Propulsion...the F100 engine without augmentation (without afterburning). HYTESS is a simplified simulation written in FORTRAN of a generalized turbofan engine . To
Samson, Andre L.; Knaupp, Anja S.; Kass, Itamar; Kleifeld, Oded; Marijanovic, Emilia M.; Hughes, Victoria A.; Lupton, Chris J.; Buckle, Ashley M.; Bottomley, Stephen P.; Medcalf, Robert L.
2014-01-01
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a ubiquitous and abundant protein that participates in cellular energy production. GAPDH normally exists in a soluble form; however, following necrosis, GAPDH and numerous other intracellular proteins convert into an insoluble disulfide-cross-linked state via the process of “nucleocytoplasmic coagulation.” Here, free radical-induced aggregation of GAPDH was studied as an in vitro model of nucleocytoplasmic coagulation. Despite the fact that disulfide cross-linking is a prominent feature of GAPDH aggregation, our data show that it is not a primary rate-determining step. To identify the true instigating event of GAPDH misfolding, we mapped the post-translational modifications that arise during its aggregation. Solvent accessibility and energy calculations of the mapped modifications within the context of the high resolution native GAPDH structure suggested that oxidation of methionine 46 may instigate aggregation. We confirmed this by mutating methionine 46 to leucine, which rendered GAPDH highly resistant to free radical-induced aggregation. Molecular dynamics simulations suggest that oxidation of methionine 46 triggers a local increase in the conformational plasticity of GAPDH that likely promotes further oxidation and eventual aggregation. Hence, methionine 46 represents a “linchpin” whereby its oxidation is a primary event permissive for the subsequent misfolding, aggregation, and disulfide cross-linking of GAPDH. A critical role for linchpin residues in nucleocytoplasmic coagulation and other forms of free radical-induced protein misfolding should now be investigated. Furthermore, because disulfide-cross-linked aggregates of GAPDH arise in many disorders and because methionine 46 is irrelevant to native GAPDH function, mutation of methionine 46 in models of disease should allow the unequivocal assessment of whether GAPDH aggregation influences disease progression. PMID:25086035
Parameterizing Aggregation Rates: Results of cold temperature ice-ash hydrometeor experiments
NASA Astrophysics Data System (ADS)
Courtland, L. M.; Dufek, J.; Mendez, J. S.; McAdams, J.
2014-12-01
Recent advances in the study of tephra aggregation have indicated that (i) far-field effects of tephra sedimentation are not adequately resolved without accounting for aggregation processes that preferentially remove the fine ash fraction of volcanic ejecta from the atmosphere as constituent pieces of larger particles, and (ii) the environmental conditions (e.g. humidity, temperature) prevalent in volcanic plumes may significantly alter the types of aggregation processes at work in different regions of the volcanic plume. The current research extends these findings to explore the role of ice-ash hydrometeor aggregation in various plume environments. Laboratory experiments utilizing an ice nucleation chamber allow us to parameterize tephra aggregation rates under the cold (0 to -50 C) conditions prevalent in the upper regions of volcanic plumes. We consider the interaction of ice-coated tephra of variable thickness grown in a controlled environment. The ice-ash hydrometers interact collisionally and the interaction is recorded by a number of instruments, including high speed video to determine if aggregation occurs. The electric charge on individual particles is examined before and after collision to examine the role of electrostatics in the aggregation process and to examine the charge exchange process. We are able to examine how sticking efficiency is related to both the relative abundance of ice on a particle as well as to the magnitude of the charge carried by the hydrometeor. We here present preliminary results of these experiments, the first to constrain aggregation efficiency of ice-ash hydrometeors, a parameter that will allow tephra dispersion models to use near-real-time meteorological data to better forecast particle residence time in the atmosphere.
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.
Ning, Lulu; Pan, Dabo; Zhang, Yan; Wang, Shaopeng; Liu, Huanxiang; Yao, Xiaojun
2015-01-01
The fragment 106-126 of prion protein exhibits similar properties to full-length prion. Experiments have shown that the A117V mutation enhances the aggregation of PrP106-126, while the H111S mutation abolishes the assembly. However, the mechanism of the change in the aggregation behavior of PrP106-126 upon the two mutations is not fully understood. In this study, replica exchange molecular dynamics simulations were performed to investigate the conformational ensemble of the WT PrP106-126 and its two mutants A117V and H111S. The obtained results indicate that the three species are all intrinsically disordered but they have distinct morphological differences. The A117V mutant has a higher propensity to form β-hairpin structures than the WT, while the H111S mutant has a higher population of helical structures. Furthermore, the A117V mutation increases the hydrophobic solvent accessible surface areas of PrP106-126 and the H111S mutation reduces the exposure of hydrophobic residues. It can be concluded that the difference in populations of β-hairpin structures and the change of hydrophobic solvent accessible areas may induce the different aggregation behaviors of the A117V and the H111S mutated PrP106-126. Understanding why the two mutations have contrary effects on the aggregation of PrP106-126 is very meaningful for further elucidation of the mechanism underlying aggregation and design of inhibitor against aggregation process.
Ning, Lulu; Pan, Dabo; Zhang, Yan; Wang, Shaopeng; Liu, Huanxiang; Yao, Xiaojun
2015-01-01
The fragment 106-126 of prion protein exhibits similar properties to full-length prion. Experiments have shown that the A117V mutation enhances the aggregation of PrP106-126, while the H111S mutation abolishes the assembly. However, the mechanism of the change in the aggregation behavior of PrP106-126 upon the two mutations is not fully understood. In this study, replica exchange molecular dynamics simulations were performed to investigate the conformational ensemble of the WT PrP106-126 and its two mutants A117V and H111S. The obtained results indicate that the three species are all intrinsically disordered but they have distinct morphological differences. The A117V mutant has a higher propensity to form β-hairpin structures than the WT, while the H111S mutant has a higher population of helical structures. Furthermore, the A117V mutation increases the hydrophobic solvent accessible surface areas of PrP106-126 and the H111S mutation reduces the exposure of hydrophobic residues. It can be concluded that the difference in populations of β-hairpin structures and the change of hydrophobic solvent accessible areas may induce the different aggregation behaviors of the A117V and the H111S mutated PrP106-126. Understanding why the two mutations have contrary effects on the aggregation of PrP106-126 is very meaningful for further elucidation of the mechanism underlying aggregation and design of inhibitor against aggregation process. PMID:25993001
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.
NASA Astrophysics Data System (ADS)
Meng, Xuan-Yu; Li, Baoyu; Liu, Shengtang; Kang, Hongsuk; Zhao, Lin; Zhou, Ruhong
2016-02-01
As a major effective component in green tea, (-)-epigallocatechin-3-gallate (EGCG)’s potential benefits to human health have been widely investigated. Recent experimental evidences indicate that EGCG can induce the aggregation of HMGB1 protein, a late mediator of inflammation, which subsequently stimulates the autophagic degradation and thus provides protection from lethal endotoxemia and sepsis. In this study, we use molecular dynamics (MD) simulations to explore the underlying molecular mechanism of this aggregation of HMGB1 facilitated by EGCG. Our simulation results reveal that EGCG firmly binds to HMGB1 near Cys106, which supports previous preliminary experimental evidence. A large HMGB1 conformational change is observed, where Box A and Box B, two homogenous domains of HMGB1, are repositioned and packed together by EGCG. This new HMGB1 conformation has large molecular polarity and distinctive electrostatic potential surface. We suggest that the highly polarized charge distribution leads to the aggregation of HMGB1, which differs from the previous hypothesis that two HMGB1 monomers are linked by the dimer of EGCG. Possible aggregating modes have also been investigated with potential of mean force (PMF) calculations. Finally, we conclude that the conformation induced by EGCG is more aggregation-prone with higher binding free energies as compared to those without EGCG.
Black, Caitlin; Collen, Ben; Johnston, Daniel; Hart, Tom
2016-01-01
Aggregations of young animals are common in a range of endothermic and ectothermic species, yet the adaptive behavior may depend on social circumstance and local conditions. In penguins, many species form aggregations (aka. crèches) for a variety of purposes, whilst others have never been observed exhibiting this behavior. Those that do form aggregations do so for three known benefits: 1) reduced thermoregulatory requirements, 2) avoidance of unrelated-adult aggression, and 3) lower predation risk. In gentoo penguins, Pygoscelis papua, chick aggregations are known to form during the post-guard period, yet the cause of these aggregations is poorly understood. Here, for the first time, we study aggregation behavior in gentoo penguins, examining four study sites along a latitudinal gradient using time-lapse cameras to examine the adaptive benefit of aggregations to chicks. Our results support the idea that aggregations of gentoo chicks decrease an individual's energetic expenditure when wet, cold conditions are present. However, we found significant differences in aggregation behavior between the lowest latitude site, Maiviken, South Georgia, and two of the higher latitude sites on the Antarctic Peninsula, suggesting this behavior may be colony specific. We provide strong evidence that more chicks aggregate and a larger number of aggregations occur on South Georgia, while the opposite occurs at Petermann Island in Antarctica. Future studies should evaluate multiple seabird colonies within one species before generalizing behaviors based on one location, and past studies may need to be re-evaluated to determine whether chick aggregation and other behaviors are in fact exhibited species-wide.
Collen, Ben; Johnston, Daniel
2016-01-01
Aggregations of young animals are common in a range of endothermic and ectothermic species, yet the adaptive behavior may depend on social circumstance and local conditions. In penguins, many species form aggregations (aka. crèches) for a variety of purposes, whilst others have never been observed exhibiting this behavior. Those that do form aggregations do so for three known benefits: 1) reduced thermoregulatory requirements, 2) avoidance of unrelated-adult aggression, and 3) lower predation risk. In gentoo penguins, Pygoscelis papua, chick aggregations are known to form during the post-guard period, yet the cause of these aggregations is poorly understood. Here, for the first time, we study aggregation behavior in gentoo penguins, examining four study sites along a latitudinal gradient using time-lapse cameras to examine the adaptive benefit of aggregations to chicks. Our results support the idea that aggregations of gentoo chicks decrease an individual’s energetic expenditure when wet, cold conditions are present. However, we found significant differences in aggregation behavior between the lowest latitude site, Maiviken, South Georgia, and two of the higher latitude sites on the Antarctic Peninsula, suggesting this behavior may be colony specific. We provide strong evidence that more chicks aggregate and a larger number of aggregations occur on South Georgia, while the opposite occurs at Petermann Island in Antarctica. Future studies should evaluate multiple seabird colonies within one species before generalizing behaviors based on one location, and past studies may need to be re-evaluated to determine whether chick aggregation and other behaviors are in fact exhibited species-wide. PMID:26840252
Properties of Concrete with Tire Derived Aggregate Partially Replacing Coarse Aggregates.
Siringi, Gideon; Abolmaali, Ali; Aswath, Pranesh B
2015-01-01
Tire derived aggregate (TDA) has been proposed as a possible lightweight replacement for mineral aggregate in concrete. The role played by the amount of TDA replacing coarse aggregate as well as different treatment and additives in concrete on its properties is examined. Conventional concrete (without TDA) and concrete containing TDA are compared by examining their compressive strength based on ASTM C39, workability based on ASTM C143, splitting tensile strength based on ASTM C496, modulus of rupture (flexural strength) based on ASTM C78, and bond stress based on ASTM C234. Results indicate that while replacement of coarse aggregates with TDA results in reduction in strength, it may be mitigated with addition of silica fume to obtain the desired strength. The greatest benefit of using TDA is in the development of a higher ductile product while utilizing recycled TDA.
Irvine, M A; Reimer, L J; Njenga, S M; Gunawardena, S; Kelly-Hope, L; Bockarie, M; Hollingsworth, T D
2015-10-22
With ambitious targets to eliminate lymphatic filariasis over the coming years, there is a need to identify optimal strategies to achieve them in areas with different baseline prevalence and stages of control. Modelling can assist in identifying what data should be collected and what strategies are best for which scenarios. We develop a new individual-based, stochastic mathematical model of the transmission of lymphatic filariasis. We validate the model by fitting to a first time point and predicting future timepoints from surveillance data in Kenya and Sri Lanka, which have different vectors and different stages of the control programme. We then simulate different treatment scenarios in low, medium and high transmission settings, comparing once yearly mass drug administration (MDA) with more frequent MDA and higher coverage. We investigate the potential impact that vector control, systematic non-compliance and different levels of aggregation have on the dynamics of transmission and control. In all settings, increasing coverage from 65 to 80 % has a similar impact on control to treating twice a year at 65 % coverage, for fewer drug treatments being distributed. Vector control has a large impact, even at moderate levels. The extent of aggregation of parasite loads amongst a small portion of the population, which has been estimated to be highly variable in different settings, can undermine the success of a programme, particularly if high risk sub-communities are not accessing interventions. Even moderate levels of vector control have a large impact both on the reduction in prevalence and the maintenance of gains made during MDA, even when parasite loads are highly aggregated, and use of vector control is at moderate levels. For the same prevalence, differences in aggregation and adherence can result in very different dynamics. The novel analysis of a small amount of surveillance data and resulting simulations highlight the need for more individual level data to be
USDA-ARS?s Scientific Manuscript database
Watershed models are calibrated to simulate stream discharge as accurately as possible. Modelers will often calculate model validation statistics on aggregate (often monthly) time periods, rather than the daily step at which models typically operate. This is because daily hydrologic data exhibit lar...
Real-time electron dynamics for massively parallel excited-state simulations
NASA Astrophysics Data System (ADS)
Andrade, Xavier
The simulation of the real-time dynamics of electrons, based on time dependent density functional theory (TDDFT), is a powerful approach to study electronic excited states in molecular and crystalline systems. What makes the method attractive is its flexibility to simulate different kinds of phenomena beyond the linear-response regime, including strongly-perturbed electronic systems and non-adiabatic electron-ion dynamics. Electron-dynamics simulations are also attractive from a computational point of view. They can run efficiently on massively parallel architectures due to the low communication requirements. Our implementations of electron dynamics, based on the codes Octopus (real-space) and Qball (plane-waves), allow us to simulate systems composed of thousands of atoms and to obtain good parallel scaling up to 1.6 million processor cores. Due to the versatility of real-time electron dynamics and its parallel performance, we expect it to become the method of choice to apply the capabilities of exascale supercomputers for the simulation of electronic excited states.
NASA Astrophysics Data System (ADS)
Anantharaj, V. G.; Venzke, J.; Lingerfelt, E.; Messer, B.
2015-12-01
Climate model simulations are used to understand the evolution and variability of earth's climate. Unfortunately, high-resolution multi-decadal climate simulations can take days to weeks to complete. Typically, the simulation results are not analyzed until the model runs have ended. During the course of the simulation, the output may be processed periodically to ensure that the model is preforming as expected. However, most of the data analytics and visualization are not performed until the simulation is finished. The lengthy time period needed for the completion of the simulation constrains the productivity of climate scientists. Our implementation of near real-time data visualization analytics capabilities allows scientists to monitor the progress of their simulations while the model is running. Our analytics software executes concurrently in a co-scheduling mode, monitoring data production. When new data are generated by the simulation, a co-scheduled data analytics job is submitted to render visualization artifacts of the latest results. These visualization output are automatically transferred to Bellerophon's data server located at ORNL's Compute and Data Environment for Science (CADES) where they are processed and archived into Bellerophon's database. During the course of the experiment, climate scientists can then use Bellerophon's graphical user interface to view animated plots and their associated metadata. The quick turnaround from the start of the simulation until the data are analyzed permits research decisions and projections to be made days or sometimes even weeks sooner than otherwise possible! The supercomputer resources used to run the simulation are unaffected by co-scheduling the data visualization jobs, so the model runs continuously while the data are visualized. Our just-in-time data visualization software looks to increase climate scientists' productivity as climate modeling moves into exascale era of computing.
Connecting source aggregating areas with distributive regions via Optimal Transportation theory.
NASA Astrophysics Data System (ADS)
Lanzoni, S.; Putti, M.
2016-12-01
We study the application of Optimal Transport (OT) theory to the transfer of water and sediments from a distributed aggregating source to a distributing area connected by a erodible hillslope. Starting from the Monge-Kantorovich equations, We derive a global energy functional that nonlinearly combines the cost of constructing the drainage network over the entire domain and the cost of water and sediment transportation through the network. It can be shown that the minimization of this functional is equivalent to the infinite time solution of a system of diffusion partial differential equations coupled with transient ordinary differential equations, that closely resemble the classical conservation laws of water and sediments mass and momentum. We present several numerical simulations applied to realstic test cases. For example, the solution of the proposed model forms network configurations that share strong similiratities with rill channels formed on an hillslope. At a larger scale, we obtain promising results in simulating the network patterns that ensure a progressive and continuous transition from a drainage drainage area to a distributive receiving region.
Polylogarithmic equilibrium treatment of molecular aggregation and critical concentrations.
Michel, Denis; Ruelle, Philippe
2017-02-15
A full equilibrium treatment of molecular aggregation is presented for prototypes of 1D and 3D aggregates, with and without nucleation. By skipping complex kinetic parameters like aggregate size-dependent diffusion, the equilibrium treatment allows us to predict directly time-independent quantities such as critical concentrations. The relationships between the macroscopic equilibrium constants for different paths are first established by statistical corrections and so as to comply with the detailed balance constraints imposed by nucleation, and the composition of the mixture resulting from homogeneous aggregation is then analyzed using a polylogarithmic function. Several critical concentrations are distinguished: the residual monomer concentration at equilibrium (RMC) and the critical nucleation concentration (CNC), which is the threshold concentration of total subunits necessary for initiating aggregation. When increasing the concentration of total subunits, the RMC converges more strongly to its asymptotic value, the equilibrium constant of depolymerization, for 3D aggregates and in the case of nucleation. The CNC moderately depends on the number of subunits in the nucleus, but sharply increases with the difference between the equilibrium constants of polymerization and nucleation. As the RMC and CNC can be numerically but not analytically determined, ansatz equations connecting them to thermodynamic parameters are proposed.
NASA Astrophysics Data System (ADS)
Jordán López, Antonio; García-Moreno, Jorge; Gordillo-Rivero, Ángel J.; Zavala, Lorena M.; Cerdà, Artemi; Alanís, Nancy; Jiménez-Compán, Elizabeth
2015-04-01
Water repellency (WR) is a property of some soils that inhibits or delays water infiltration between a few seconds and days or weeks. Inhibited or delayed infiltration contributes to ponding and increases runoff flow generation, often increasing soil erosion risk. In water-repellent soils, water infiltrates preferentially through cracks or macropores, causing irregular soil wetting patterns, the development of preferential flow paths and accelerated leaching of nutrients. Although low inputs of hydrophobic organic substances and high mineralization rates lead to low degrees of WR in cropped soils, it has been reported that conservative agricultural practices may induce soil WR. Although there are many studies at catchment, slope or plot scales very few studies have been carried out at particle or aggregate scale. Intra-aggregate heterogeneity of physical, biological and chemical properties conditions the transport of substances, microbial activity and biochemical processes, including changes in the amount, distribution and chemical properties of organic matter. Some authors have reported positive relationships between soil WR and aggregate stability, since it may delay the entry of water into aggregates, increase structural stability and contribute to reduce soil erosion risk. Organic C (OC) content, aggregate stability and WR are therefore strongly related parameters. In the case of agricultural soils, where both the type of management as crops can influence all these parameters, it is important to evaluate the interactions among them and their consequences. Studies focused on the intra-aggregate distribution of OC and WR are necessary to shed light on the soil processes at a detailed scale. It is extremely important to understand how the spatial distribution of OC in soil aggregates can protect against rapid water entry and help stabilize larger structural units or lead to preferential flow. The objectives of this research are to study [i] the OC content and the
AGGRESCAN3D (A3D): server for prediction of aggregation properties of protein structures.
Zambrano, Rafael; Jamroz, Michal; Szczasiuk, Agata; Pujols, Jordi; Kmiecik, Sebastian; Ventura, Salvador
2015-07-01
Protein aggregation underlies an increasing number of disorders and constitutes a major bottleneck in the development of therapeutic proteins. Our present understanding on the molecular determinants of protein aggregation has crystalized in a series of predictive algorithms to identify aggregation-prone sites. A majority of these methods rely only on sequence. Therefore, they find difficulties to predict the aggregation properties of folded globular proteins, where aggregation-prone sites are often not contiguous in sequence or buried inside the native structure. The AGGRESCAN3D (A3D) server overcomes these limitations by taking into account the protein structure and the experimental aggregation propensity scale from the well-established AGGRESCAN method. Using the A3D server, the identified aggregation-prone residues can be virtually mutated to design variants with increased solubility, or to test the impact of pathogenic mutations. Additionally, A3D server enables to take into account the dynamic fluctuations of protein structure in solution, which may influence aggregation propensity. This is possible in A3D Dynamic Mode that exploits the CABS-flex approach for the fast simulations of flexibility of globular proteins. The A3D server can be accessed at http://biocomp.chem.uw.edu.pl/A3D/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
Platform-Independence and Scheduling In a Multi-Threaded Real-Time Simulation
NASA Technical Reports Server (NTRS)
Sugden, Paul P.; Rau, Melissa A.; Kenney, P. Sean
2001-01-01
Aviation research often relies on real-time, pilot-in-the-loop flight simulation as a means to develop new flight software, flight hardware, or pilot procedures. Often these simulations become so complex that a single processor is incapable of performing the necessary computations within a fixed time-step. Threads are an elegant means to distribute the computational work-load when running on a symmetric multi-processor machine. However, programming with threads often requires operating system specific calls that reduce code portability and maintainability. While a multi-threaded simulation allows a significant increase in the simulation complexity, it also increases the workload of a simulation operator by requiring that the operator determine which models run on which thread. To address these concerns an object-oriented design was implemented in the NASA Langley Standard Real-Time Simulation in C++ (LaSRS++) application framework. The design provides a portable and maintainable means to use threads and also provides a mechanism to automatically load balance the simulation models.
Properties of Concrete with Tire Derived Aggregate Partially Replacing Coarse Aggregates
Siringi, Gideon; Abolmaali, Ali; Aswath, Pranesh B.
2015-01-01
Tire derived aggregate (TDA) has been proposed as a possible lightweight replacement for mineral aggregate in concrete. The role played by the amount of TDA replacing coarse aggregate as well as different treatment and additives in concrete on its properties is examined. Conventional concrete (without TDA) and concrete containing TDA are compared by examining their compressive strength based on ASTM C39, workability based on ASTM C143, splitting tensile strength based on ASTM C496, modulus of rupture (flexural strength) based on ASTM C78, and bond stress based on ASTM C234. Results indicate that while replacement of coarse aggregates with TDA results in reduction in strength, it may be mitigated with addition of silica fume to obtain the desired strength. The greatest benefit of using TDA is in the development of a higher ductile product while utilizing recycled TDA. PMID:26161440
Ning, Lulu; Wang, Qianqian; Zheng, Yang; Liu, Huanxiang; Yao, Xiaojun
2015-02-01
The palindromic region AGAAAAGA (PrP113-120) in prion is highly amyloidogenic and very critical in the structural conversion of cellular prion protein to its pathogenetic form. In this region, there is an important point mutation A117V, which is closely related to the occurrence of Gerstmann-Straussler-Scheinker Syndrome. However, the detailed knowledge about the effects of the A117V mutation on the folding and aggregation of the palindromic sequences is still lacking. To investigate the impacts of A117V mutation on the earliest steps along the PrP113-120 aggregation pathway, replica exchange molecular dynamics simulations of the monomer, 2- and 4-peptide systems of PrP113-120 and its A117V mutant were carried out. The simulations of monomers indicate that both WT and the A117V mutated PrP113-120 are mostly random coils with helical structures transiently populated. Differently, the A117V mutation enhances the intrinsic disorder of PrP113-120. The simulations of 2- and 4-peptide systems of the two species show that the A117V mutation increases the sheet contents and the populations of oligomers, which may be attributed to the enhancement of inter-peptide backbone hydrogen bonding interactions and side chain hydrophobic interactions. Overall, the study provides structural insights into the impacts of the A117V mutation on the folding and assembly of the palindromic sequences, which might be helpful to elucidate the mechanism underlying prion disease and the origin of the Gerstmann-Straussler-Scheinker Syndrome.
Real-time simulation of hand motion for prosthesis control
Blana, Dimitra; Chadwick, Edward K.; van den Bogert, Antonie J.; Murray, Wendy M.
2016-01-01
Individuals with hand amputation suffer substantial loss of independence. Performance of sophisticated prostheses is limited by the ability to control them. To achieve natural and simultaneous control of all wrist and hand motions, we propose to use real-time biomechanical simulation to map between residual EMG and motions of the intact hand. Here we describe a musculoskeletal model of the hand using only extrinsic muscles to determine whether real-time performance is possible. Simulation is 1.3 times faster than real time, but the model is locally unstable. Methods are discussed to increase stability and make this approach suitable for prosthesis control. PMID:27868425
Experimental aggregation of volcanic ash: the role of liquid bonding
NASA Astrophysics Data System (ADS)
Mueller, S.; Kueppers, U.; Jacob, M.; Ayris, P. M.; Dingwell, D. B.
2015-12-01
Explosive volcanic eruptions may release vast quantities of ash. Because of its size, it has the greatest dispersal potential and can be distributed globally. Ash may pose severe risks for 1) air traffic, 2) human and animal health, 3) agriculture and 4) infrastructure. Such ash particles can however cluster and form ash aggregates that range in size from millimeters to centimeters. During their growth, weight and aerodynamic properties change. This leads to significantly changed transport and settling behavior. The physico-chemical processes involved in aggregation are quantitatively poorly constrained. We have performed laboratory ash aggregation experiments using the ProCell Lab System® of Glatt Ingenieurtechnik GmbH. Solid particles are set into motion in a fluidized bed over a range of well-controlled boundary conditions (e.g., air flow rate, gas temperature, humidity, liquid composition). In this manner we simulate the variable gas-particle flow conditions expected in eruption plumes and pyroclastic density currents. We have used 1) soda-lime glass beads as an analogue material and 2) natural volcanic ash from Laacher See Volcano (Germany). In order to influence form, size, stability and the production rate of aggregates, a range of experimental conditions (e.g., particle concentration, degree of turbulence, temperature and moisture in the process chamber and the composition of the liquid phase) have been employed. We have successfully reproduced several features of natural ash aggregates, including round, internally structured ash pellets up to 3 mm in diameter. These experimental results help to constrain the boundary conditions required for the generation of spherical, internally-structured ash aggregates that survive deposition and are preserved in the volcanological record. These results should also serve as input parameters for models of ash transport and ash mass distribution.
Object Orientated Simulation on Transputer Arrays Using Time Warp
1989-12-01
Transputer based Machines, Grenoble, Sept 14-16 1987, Ed. Traian Muntean. [ 3 ] Muntean T., "PARX operating system kernal; application to Minix ", Esprit P1085...Simulation 3 Time Warp Simulation 8 3.1 Rollback Mechanism ........ ............................. 8 3.2 Simulation Outp,,t...23 4.3.* Importan Noc .......... ............................ 23 5 Low Level Operations 24 • 3 IIiI 5.1 Global Virtual Timne Estimiation
Methods of predicting aggregate voids.
DOT National Transportation Integrated Search
2013-03-01
Percent voids in combined aggregates vary significantly. Simplified methods of predicting aggregate : voids were studied to determine the feasibility of a range of gradations using aggregates available in Kansas. : The 0.45 Power Curve Void Predictio...
Blended aggregate study : final report.
DOT National Transportation Integrated Search
1980-03-01
Louisiana produces no naturally occurring skid resistant aggregate and, therefore, must import these aggregates at great expense. : In an effort to extend the yield of these aggregates, a laboratory investigation was initiated to determine the feasib...
Real-time simulator for designing electron dual scattering foil systems.
Carver, Robert L; Hogstrom, Kenneth R; Price, Michael J; LeBlanc, Justin D; Pitcher, Garrett M
2014-11-08
The purpose of this work was to develop a user friendly, accurate, real-time com- puter simulator to facilitate the design of dual foil scattering systems for electron beams on radiotherapy accelerators. The simulator allows for a relatively quick, initial design that can be refined and verified with subsequent Monte Carlo (MC) calculations and measurements. The simulator also is a powerful educational tool. The simulator consists of an analytical algorithm for calculating electron fluence and X-ray dose and a graphical user interface (GUI) C++ program. The algorithm predicts electron fluence using Fermi-Eyges multiple Coulomb scattering theory with the reduced Gaussian formalism for scattering powers. The simulator also estimates central-axis and off-axis X-ray dose arising from the dual foil system. Once the geometry of the accelerator is specified, the simulator allows the user to continuously vary primary scattering foil material and thickness, secondary scat- tering foil material and Gaussian shape (thickness and sigma), and beam energy. The off-axis electron relative fluence or total dose profile and central-axis X-ray dose contamination are computed and displayed in real time. The simulator was validated by comparison of off-axis electron relative fluence and X-ray percent dose profiles with those calculated using EGSnrc MC. Over the energy range 7-20 MeV, using present foils on an Elekta radiotherapy accelerator, the simulator was able to reproduce MC profiles to within 2% out to 20 cm from the central axis. The central-axis X-ray percent dose predictions matched measured data to within 0.5%. The calculation time was approximately 100 ms using a single Intel 2.93 GHz processor, which allows for real-time variation of foil geometrical parameters using slider bars. This work demonstrates how the user-friendly GUI and real-time nature of the simulator make it an effective educational tool for gaining a better understanding of the effects that various system
The single scattering properties of soot aggregates with concentric core-shell spherical monomers
NASA Astrophysics Data System (ADS)
Wu, Yu; Cheng, Tianhai; Gu, Xingfa; Zheng, Lijuan; Chen, Hao; Xu, Hui
2014-03-01
Anthropogenic soot aerosols are shown as complex, fractal-like aggregated structures with high light absorption efficiency. In atmospheric environment, soot monomers may tend to acquire a weakly absorbing coating, such as an organic coating, which introduces further complexity to the optical properties of the aggregates. The single scattering properties of soot aggregates can be significantly influenced by the coated status of these kinds of aerosols. In this article, the monomers of fractal soot aggregates are modelled as semi-external mixtures (physical contact) with constant radius of soot core and variable sizes of the coating for specific soot volume fractions. The single scattering properties of these coated soot particles, such as phase function, the cross sections of extinction and absorption, single scattering albedo (SSA) and asymmetry parameter (ASY), are calculated using the numerically exact superposition T-matrix method. The random-orientation averaging results have shown that the single scattering properties of these coated soot aggregates are significantly different from the single volume-equivalent core-shell sphere approximation using the Mie theory and the homogeneous aggregates with uncoated monomers using the effective medium theory, such as Maxwell-Garnett and Bruggemann approximations, which overestimate backscattering of coated soot. It is found that the SSA and cross sections of extinction and absorption are increased for soot aggregates with thicker weakly absorbing coating on the monomers. Especially, the SSA values of these simulated aggregates with less soot core volume fractions are remarkably (~50% for core volume fraction of soot aggregates of 0.5, ~100% for a core volume fraction of 0.2, at 0.67 μm) larger than for uncoated soot particles without consideration of coating. Moreover, the cross sections of extinction and absorption are underestimated by the computation of equivalent homogeneous fractal aggregate approximation (within
Real-time, interactive, visually updated simulator system for telepresence
NASA Technical Reports Server (NTRS)
Schebor, Frederick S.; Turney, Jerry L.; Marzwell, Neville I.
1991-01-01
Time delays and limited sensory feedback of remote telerobotic systems tend to disorient teleoperators and dramatically decrease the operator's performance. To remove the effects of time delays, key components were designed and developed of a prototype forward simulation subsystem, the Global-Local Environment Telerobotic Simulator (GLETS) that buffers the operator from the remote task. GLETS totally immerses an operator in a real-time, interactive, simulated, visually updated artificial environment of the remote telerobotic site. Using GLETS, the operator will, in effect, enter into a telerobotic virtual reality and can easily form a gestalt of the virtual 'local site' that matches the operator's normal interactions with the remote site. In addition to use in space based telerobotics, GLETS, due to its extendable architecture, can also be used in other teleoperational environments such as toxic material handling, construction, and undersea exploration.