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Sample records for aggregate simulation time

  1. Aggregation of oligoarginines at phospholipid membranes: molecular dynamics simulations, time-dependent fluorescence shift, and biomimetic colorimetric assays.

    PubMed

    Vazdar, Mario; Wernersson, Erik; Khabiri, Morteza; Cwiklik, Lukasz; Jurkiewicz, Piotr; Hof, Martin; Mann, Ella; Kolusheva, Sofiya; Jelinek, Raz; Jungwirth, Pavel

    2013-10-01

    A time-dependent fluorescence shift method, biomimetic colorimetric assays, and molecular dynamics simulations have been performed in search of explanations why arginine rich peptides with intermediate lengths of about 10 amino acids translocate well through cellular membranes, while analogous lysine rich peptides do not. First, we demonstrate that an important factor for efficient peptide adsorption, as the first prerequisite for translocation across the membrane, is the presence of negatively charged phospholipids in the bilayer. Second, we observe a strong tendency of adsorbed arginine (but not lysine) containing peptides to aggregate at the bilayer surface. We suggest that this aggregation of oligoarginines leads to partial disruption of the bilayer integrity due to the accumulated large positive charge at its surface, which increases membrane-surface interactions due to the increased effective charge of the aggregates. As a result, membrane penetration and translocation of medium length oligoarginines becomes facilitated in comparison to single arginine and very long polyarginines, as well as to lysine containing peptides.

  2. 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.

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

    NASA Astrophysics Data System (ADS)

    Li, Chao; Xiong, Hailing

    2014-12-01

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

  4. Collision simulation of sintered dust aggregates

    NASA Astrophysics Data System (ADS)

    Sirono, Sin-iti; Ueno, Haruta

    Collisional evolution of dust aggregates is the initial process of the planet formation. Sticking velocity, below which collisional sticking of an aggregate happens, is a crucial quantity in the collisional evolution. In the standard model of protoplanetary nebula, the maximum collisional velocity is around 50m/s. Therefore, if a planetesimal is formed through direct collisional sticking, the sticking velocity should be higher than 50m/s. Even if a planetesimal is formed by other mechanism such as anticyclonic vortices, substantial growth of an aggregate is required because the motion of an aggregate should be decoupled from that of gas. Collisional simulation of icy dust aggregates (Wada et al. 2009, ApJ 702, 1490) showed that the sticking velocity was larger than 50m/s and planetesimal formation by collisional sticking was possible. However, sintering of ice proceeds in a wide area of a protoplanetary nebula (Sirono 2011, ApJ 765, 50). Sintering enlarges a neck, connection between adjacent dust grains, and changes the mechanical properties of a dust aggregate. Here we performed collisional simulations between sintered dust aggregates taking account of sintering. We found that the sticking velocity was decreased substantially down to 20m/s. This result suggests that a planetesimal is not formed by direct collisional sticking and that the planetesimal formation proceeded in particular regions in a protoplanetary nebula.

  5. Simulations of kinetically irreversible protein aggregate structure.

    PubMed Central

    Patro, S Y; Przybycien, T M

    1994-01-01

    We have simulated the structure of kinetically irreversible protein aggregates in two-dimensional space using a lattice-based Monte-Carlo routine. Our model specifically accounts for the intermolecular interactions between hydrophobic and hydrophilic protein surfaces and a polar solvent. The simulations provide information about the aggregate density, the types of inter-monomer contacts and solvent content within the aggregates, the type and extent of solvent exposed perimeter, and the short- and long-range order all as a function of (i) the extent of monomer hydrophobic surface area and its distribution on the model protein surface and (ii) the magnitude of the hydrophobic-hydrophobic contact energy. An increase in the extent of monomer hydrophobic surface area resulted in increased aggregate densities with concomitant decreased system free energies. These effects are accompanied by increases in the number of hydrophobic-hydrophobic contacts and decreases in the solvent-exposed hydrophobic surface area of the aggregates. Grouping monomer hydrophobic surfaces in a single contiguous stretch resulted in lower aggregate densities and lower short range order. More favorable hydrophobic-hydrophobic contact energies produced structures with higher densities but the number of unfavorable protein-protein contacts was also observed to increase; greater configurational entropy produced the opposite effect. Properties predicted by our model are in good qualitative agreement with available experimental observations. Images FIGURE 6 FIGURE 13 PMID:8061184

  6. Dynamics of cell aggregates fusion: Experiments and simulations

    NASA Astrophysics Data System (ADS)

    Thomas, Gilberto L.; Mironov, Vladimir; Nagy-Mehez, Agnes; Mombach, José C. M.

    2014-02-01

    Fusion of cell tissues is an ubiquitous phenomenon and has important technological applications including tissue biofabrication. In this work we present experimental results of aggregates fusion using adipose derived stem cells (ADSC) and a three dimensional computer simulation of the process using the cellular Potts model with aggregates reaching 10,000 cells. We consider fusion of round aggregates and monitor the dimensionless neck area of contact between the two aggregates to characterize the process, as done for the coalescence of liquid droplets and polymers. Both experiments and simulations show that the evolution of this quantity obeys a power law in time. We also study quantitatively individual cell motion with the simulation and it corresponds to an anomalous diffusion.

  7. 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.

  8. Aggregated Indexing of Biomedical Time Series Data

    PubMed Central

    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.

  9. Low-Velocity Aggregate Collisions Simulating Planetary Ring Dynamics

    NASA Astrophysics Data System (ADS)

    Dove, A.; Colwell, J. E.; Bradley, E. T.; Vamos, C.

    2012-12-01

    Proto-planetary and planetary ring system evolution is driven by collisions between small particles and aggregates that may be composed of dust, water ice, or a combination of materials. In these collisional systems, impacts between objects can occur at very low velocities, much less than 1 m/s. Low-velocity impacts can have competing effects: at the lowest velocities, collisions may play a critical role in growth into larger aggregates; at slightly higher velocities, collisions can cause break-up and release of material. In the Saturnian ring system, for instance, particles are excited to such "higher" velocities (10's of cm/s) in regions where density waves enhance particle concentrations. These conditions are present in the A ring, and it has been hypothesized that collisions have an additional effect of modifying the spectral properties of the ring particles, which are composed of a mix of ice and dust (Nicholson et al., 2008). This modification may occur when collisions cause ejection of material with different spectral characteristics, or by breaking particles apart to reveal more pristine interiors. We have designed and built an apparatus to simulate low-velocity collisions between aggregates in a laboratory vacuum environment. In our experiment, two aggregates are launched towards each other; the resulting impact velocities are controlled by the initial spring launch velocity, the masses of the aggregates, and timing of the collisions. Initially, we use lunar regolith simulant to create the aggregates; the simulant can be packed to different densities to control the mass and porosity of the impactors. We also create aggregates that are mixtures of materials, including icy components. A high-speed digital video camera is used to record the impacts to observe the behavior of both impactors and the resulting ejecta material. We observe over a range of velocities to identify the conditions under which aggregates shed only some material from the surface, or

  10. Simulation of J-aggregate microcavity photoluminescence

    NASA Astrophysics Data System (ADS)

    Michetti, Paolo; La Rocca, Giuseppe C.

    2008-05-01

    We have developed a model in order to account for the photoexcitation dynamics of J-aggregate films and strongly coupled J-aggregate microcavities. The J aggregates are described as a disordered Frenkel exciton system in which relaxation occurs due to the presence of a thermal bath of molecular vibrations. The correspondence between the photophysics in J-aggregate films and that in J-aggregate microcavities is obtained by introducing a model polariton wave function mixing cavity photon modes and J-aggregate super-radiant excitons. With the same description of the material properties, we have calculated both absorption and luminescence spectra for the J-aggregate film and the photoluminescence of strongly coupled organic microcavities. The model is able to account for the fast relaxation dynamics in organic microcavities following nonresonant pumping and explains the temperature dependence of the ratio between the upper polariton and the lower polariton luminescence.

  11. Molecular dynamics simulations of the straining of nanoparticle chain aggregates: the case of copper

    NASA Astrophysics Data System (ADS)

    Dalis, Adamos; Friedlander, Sheldon K.

    2005-07-01

    Previous studies in our laboratory have shown that individual nanoparticle chain aggregates (NCAs) exhibit unusual mechanical behaviour when under strain inside the transmission electron microscope. NCAs made of various materials (e.g. carbon, metal oxides and metals) were strained by as much as 100% under tension. The nanoparticles that compose the chains were 5-10 nm in diameter and the chains of the order of 1 µm in length. Such aggregates are of technological importance in the manufacture of nanocomposite materials (e.g. rubber), aggregate break-up (e.g. sampling diesel emissions) and chemical-mechanical planarization. The goal of this study was to simulate the mechanical behaviour of chain aggregates with morphological properties similar to those of technological interest. Molecular dynamics (MD) and energy minimization computer simulations are employed to investigate, at the atomic scale, the behaviour of short nanoparticle aggregates under strain and to obtain quantitative information on the forces involved in aggregate straining and fracturing. The interaction potential used is that of copper obtained with the embedded atom method (EAM). Two seven-nanoparticle aggregates are studied, one linear and the other kinked. The seven nanoparticles in both aggregates are single crystals and about 2.5 nm in diameter each. The aggregates are strained along their longest dimension, to the breaking point, at strain rates spanning from 2.5 × 107 to 8.0 × 108 s-1 (MD simulations). The linear aggregate yield strain is about 0.1. The kinked aggregate elastic limit is also about 0.1, but only one-third of the stress develops along the straining direction compared to the linear aggregate. The kinked aggregate breaks at a strain of about 0.5, five times higher than the breaking strain of the linear aggregate. The ability of the kinked aggregate to straighten through combined nanoparticle interface sliding and rotation accounts for the extra strain accommodation. Simulation

  12. Molecular dynamics simulations of the straining of nanoparticle chain aggregates: the case of copper.

    PubMed

    Dalis, Adamos; Friedlander, Sheldon K

    2005-07-01

    Previous studies in our laboratory have shown that individual nanoparticle chain aggregates (NCAs) exhibit unusual mechanical behaviour when under strain inside the transmission electron microscope. NCAs made of various materials (e.g. carbon, metal oxides and metals) were strained by as much as 100% under tension. The nanoparticles that compose the chains were 5-10 nm in diameter and the chains of the order of 1 µm in length. Such aggregates are of technological importance in the manufacture of nanocomposite materials (e.g. rubber), aggregate break-up (e.g. sampling diesel emissions) and chemical-mechanical planarization. The goal of this study was to simulate the mechanical behaviour of chain aggregates with morphological properties similar to those of technological interest. Molecular dynamics (MD) and energy minimization computer simulations are employed to investigate, at the atomic scale, the behaviour of short nanoparticle aggregates under strain and to obtain quantitative information on the forces involved in aggregate straining and fracturing. The interaction potential used is that of copper obtained with the embedded atom method (EAM). Two seven-nanoparticle aggregates are studied, one linear and the other kinked. The seven nanoparticles in both aggregates are single crystals and about 2.5 nm in diameter each. The aggregates are strained along their longest dimension, to the breaking point, at strain rates spanning from 2.5 × 10(7) to 8.0 × 10(8) s(-1) (MD simulations). The linear aggregate yield strain is about 0.1. The kinked aggregate elastic limit is also about 0.1, but only one-third of the stress develops along the straining direction compared to the linear aggregate. The kinked aggregate breaks at a strain of about 0.5, five times higher than the breaking strain of the linear aggregate. The ability of the kinked aggregate to straighten through combined nanoparticle interface sliding and rotation accounts for the extra strain accommodation

  13. Protein aggregate turbidity: Simulation of turbidity profiles for mixed-aggregation reactions.

    PubMed

    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.

  14. Protein aggregate turbidity: Simulation of turbidity profiles for mixed-aggregation reactions.

    PubMed

    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. PMID:26763936

  15. Simulating aggregate dynamics in ocean biogeochemical models

    NASA Astrophysics Data System (ADS)

    Jackson, George A.; Burd, Adrian B.

    2015-04-01

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

  16. In vivo amyloid aggregation kinetics tracked by time-lapse confocal microscopy in real-time.

    PubMed

    Villar-Piqué, Anna; Espargaró, Alba; Ventura, Salvador; Sabate, Raimon

    2016-01-01

    Amyloid polymerization underlies an increasing number of human diseases. Despite this process having been studied extensively in vitro, aggregation is a difficult process to track in vivo due to methodological limitations and the slow kinetics of aggregation reactions in cells and tissues. Herein we exploit the amyloid properties of the inclusions bodies (IBs) formed by amyloidogenic proteins in bacteria to address the kinetics of in vivo amyloid aggregation. To this aim we used time-lapse confocal microscopy and a fusion of the amyloid-beta peptide (A β42) with a fluorescent reporter. This strategy allowed us to follow the intracellular kinetics of amyloid-like aggregation in real-time and to discriminate between variants exhibiting different in vivo aggregation propensity. Overall, the approach opens the possibility to assess the impact of point mutations as well as potential anti-aggregation drugs in the process of amyloid formation in living cells.

  17. Task-Driven Evaluation of Aggregation in Time Series Visualization.

    PubMed

    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.

  18. Osmolyte Induced Changes in Peptide Conformational Ensemble Correlate with Slower Amyloid Aggregation: A Coarse-Grained Simulation Study.

    PubMed

    Sukenik, Shahar; Sapir, Liel; Harries, Daniel

    2015-12-01

    Stabilizing osmolytes are known to impact the process of amyloid aggregation, often altering aggregation kinetics. Recent evidence further suggests that osmolytes modify the peptide conformational dynamics, as well as change the physical characteristics of assembling amyloid fibrils. To resolve how these variations emerge on the molecular level, we simulated the initial aggregation steps of an amyloid-forming peptide in the presence and absence of the osmolyte sorbitol, a naturally occurring polyol. To this end, a coarse-grained force field was extended and implemented to access larger aggregate sizes and longer time scales. The force field optimization procedure placed emphasis on calibrating the solution thermodynamics of sorbitol, the aggregating peptide in its monomeric form, and the interaction of both of these components with each other and with water. Our simulations show a difference in aggregation kinetics and structural parameters in the presence of sorbitol compared to water, which qualitatively agree well with our experimentally resolved aggregation kinetics of the same peptide. The kinetic changes induced by sorbitol can be traced in our simulations to changes in monomer conformations resulting from osmolyte presence. These translate into changes in peptide conformations within the aggregated clusters and into differences in rates of monomer nucleation and of association to formed fibrils. We find that, compared to pure water as solvent, the presence of sorbitol induces formation of more aggregates each containing fewer peptides, with an increased tendency toward parallel interpeptide contacts. PMID:26587669

  19. Monte Carlo simulations of protein amyloid formation reveal origin of sigmoidal aggregation kinetics.

    PubMed

    Linse, Björn; Linse, Sara

    2011-07-01

    Severe conditions and lack of cure for many amyloid diseases make it highly desired to understand the underlying principles of formation of fibrillar aggregates (amyloid). Here, amyloid formation from peptides was studied using Monte Carlo simulations. Systems of 20, 50, 100, 200 or 500 hexapeptides were simulated. Association kinetics were modeled equal for fibrillar and other (inter- and intra-peptide) contacts and assumed to be faster the lower the effective contact order, which represents the distance in space. Attempts to form contacts were thus accepted with higher probability the lower the effective contact order, whereby formation of new contacts next to preexisting ones is favored by shorter physical separation. Kinetic discrimination was invoked by using two different life-times for formed contacts. Contacts within amyloid fibrils were assumed to have on average longer life-time than other contacts. We find that the model produces fibrillation kinetics with a distinct lag phase, and that the fibrillar contacts need to dissociate on average 5-20 times slower than all other contacts for the fibrillar structure to dominate at equilibrium. Analysis of the species distribution along the aggregation process shows that no other intermediate is ever more populated than the dimer. Instead of a single nucleation event there is a concomitant increase in average aggregate size over the whole system, and the occurrence of multiple parallel processes makes the process more reproducible the larger the simulated system. The sigmoidal shape of the aggregation curves arises from cooperativity among multiple interactions within each pair of peptides in a fibril. A governing factor is the increasing probability as the aggregation process proceeds of neighboring reinforcing contacts. The results explain the very strong bias towards cross β-sheet fibrils in which the possibilities for cooperativity among interactions involving neighboring residues and the repetitive use of

  20. Naratriptan aggregation in lipid bilayers: perspectives from molecular dynamics simulations.

    PubMed

    Wood, Irene; Pickholz, Mónica

    2016-09-01

    In order to understand the interaction between naratriptan and a fully hydrated bilayer of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidyl-choline (POPC), we carried out molecular dynamics simulations. The simulations were performed considering neutral and protonated ionization states, starting from different initial conditions. At physiological pH, the protonated state of naratriptan is predominant. It is expected that neutral compounds could have larger membrane partition than charged compounds. However, for the specific case of triptans, it is difficult to study neutral species in membranes experimentally, making computer simulations an interesting tool. When the naratriptan molecules were originally placed in water, they partitioned between the bilayer/water interface and water phase, as has been described for similar compounds. From this condition, the drugs displayed low access to the hydrophobic environment, with no significant effects on bilayer organization. The molecules anchored in the interface, due mainly to the barrier function of the polar and oriented lipid heads. On the other hand, when placed inside the bilayer, both neutral and protonated naratriptan showed self-aggregation in the lipid tail environment. In particular, the protonated species exhibited a pore-like structure, dragging water through this environment. Graphical Abstract Different behaviour of Naratriptan and Sumatriptan, when the drugs were originally placed in the lipid core. PMID:27558798

  1. Aggregate Building Simulator (ABS) Methodology Development, Application, and User Manual

    SciTech Connect

    Dirks, James A.; Gorrissen, Willy J.

    2011-11-30

    As the relationship between the national building stock and various global energy issues becomes a greater concern, it has been deemed necessary to develop a system of predicting the energy consumption of large groups of buildings. Ideally this system is to take advantage of the most advanced energy simulation software available, be able to execute runs quickly, and provide concise and useful results at a level of detail that meets the users needs without inundating them with data. The resulting methodology that was developed allows the user to quickly develop and execute energy simulations of many buildings simultaneously, taking advantage of parallel processing to greatly reduce total simulation times. The result of these simulations can then be rapidly condensed and presented in a useful and intuitive manner.

  2. Linking phase behavior and reversible colloidal aggregation at low concentrations: simulations and stochastic mean field theory.

    PubMed

    Puertas, Antonio M; Odriozola, Gerardo

    2007-05-24

    We have studied the link between the kinetics of clustering and the phase behavior of dilute colloids with short range attractions of moderate strength. This was done by means of computer simulations and a theoretical kinetic model originally developed to deal with reversible colloidal aggregation. Three different regions of the phase diagram were accessed. For weak attractions, a gas phase of small clusters in equilibrium forms in the system. For intermediate attractions, the system undergoes liquid-gas separation, which is signatured by the formation of a few large droplike aggregates, a gas phase of small clusters, and an overall kinetics where a few seeds succeed in explosively growing at long times, after a lag time. Finally, for very strong attractions, fractal unbreakable clusters form and grow following DLCA-like (diffusion limited cluster aggregation) kinetics; liquid-gas separation is prevented by the strength of the bonds, which do not allow restructuration. Good qualitative and quantitative agreement is found between the dynamic simulations and the kinetic model in all the three regions.

  3. Molecular dynamics simulations of interfacial interactions between small nanoparticles during diffusion-limited aggregation

    NASA Astrophysics Data System (ADS)

    Lu, Jing; Liu, Dongmei; Yang, Xiaonan; Zhao, Ying; Liu, Haixing; Tang, Huan; Cui, Fuyi

    2015-12-01

    Due to the limitations of experimental methods at the atomic level, research on the aggregation of small nanoparticles (D < 5 nm) in aqueous solutions is quite rare. The aggregation of small nanoparticles in aqueous solutions is very different than that of normal sized nanoparticles. The interfacial interactions play a dominant role in the aggregation of small nanoparticles. In this paper, molecular dynamics simulations, which can explore the microscopic behavior of nanoparticles during the diffusion-limited aggregation at an atomic level, were employed to reveal the aggregation mechanism of small nanoparticles in aqueous solutions. First, the aggregation processes and aggregate structure were depicted. Second, the particle-particle interaction and surface diffusion of nanoparticles during aggregation were investigated. Third, the water-mediated interactions during aggregation were ascertained. The results indicate that the aggregation of nanoparticle in aqueous solutions is affected by particle size. The strong particle-particle interaction and high surface diffusion result in the formation of particle-particle bonds of 2 nm TiO2 nanoparticles, and the water-mediated interaction plays an important role in the aggregation process of 3 and 4 nm TiO2 nanoparticles.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  8. Monte Carlo simulation of ramified aggregates on hetero-substrates

    NASA Astrophysics Data System (ADS)

    Qian, Chang-Ji; Li, Hong; Zhong, Rui; Luo, Meng-Bo; Ye, Gao-Xiang

    2009-05-01

    We have studied the aggregation of particles on a hetero-substrate consisting of two different substrates A and B with finite surface barriers EAB and EBA between the AB and BA boundaries, respectively. With the diffusion energy limited aggregation (DELA) model, we find that the number of clusters and the mean radius of gyration of the clusters are dependent on the surface barriers EAB and EBA. For the case with a constant of EBA, a series of minima are summarized as EAB = (E0 - kBAEBA)/kAB with kAB and kBA being two integers, for main minima (kBA = kAB - 1) and two local minima (kBA = kAB and kBA = kAB + 1) between two neighbouring main minima.

  9. 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.

  10. Platelets aggregation in pathological conditions: role of local shear rates and platelet activation delay time.

    NASA Astrophysics Data System (ADS)

    Li, He; Zarif Khalili Yazdani, Alireza; Karniadakis, George

    2015-11-01

    Platelets play an essential role in the initiation and formation of a thrombus, however their detailed motion in blood vessels with complex geometries, such as in the aneurysmal vessel or stenotic vessel in atherosclerosis, has not been studied systematically. Here, we perform spectral element simulations (NEKTAR code) to obtain the 3D flow field in blood vessel with cavities, and we apply the force coupling method (FCM) to simulate the motion of platelets in blood flow. Specifically, simulations of platelets are performed in a 0.25 mm diameter circular blood vessel with 1 mm length. Corresponding coarse-grained molecular dynamics simulations are employed to provide input to the NEKTAR-FCM code. Simulations are conducted at several different Reynolds numbers (Re). An ellipsoid-shaped cavity is selected to intersect with the middle part of the circular vessel to represent the aneurysmal part of the blood vessel. Based on the simulation results, we quantify how the platelets motion and aggregation in the blood vessel cavities depend on Re, platelet activation delay time, and the geometry of the cavities.

  11. Time-dependent behaviour of high performance concrete: influence of coarse aggregate characteristics

    NASA Astrophysics Data System (ADS)

    Makani, A.; Vidal, T.; Pons, G.; Escadeillas, G.

    2010-06-01

    This paper examines the influence of coarse aggregate characteristics on the time-dependent deformations of High Performances Concretes (HPC). Four concretes made using the same cement paste but incorporating different types of aggregate (rolled siliceous gravel, crushed granite, crushed limestone and crushed siliceous gravels) were studied in order to investigate the effect of aggregate properties on the compressive strength, modulus of elasticity, shrinkage and creep. The results indicate that the aggregate type has a significant effect on creep and shrinkage deformations of HPC. An influence of the shape of aggregate on time-dependent deformations has also been observed. On the basis of these results, long-term behaviour seems to be correlated to the characteristics of the Interfacial Transition Zone (ITZ) strongly depending on the mineralogical nature and properties of aggregates. The experimental results are compared with the values calculated using the current Eurocode 2 model in order to assess the accuracy of the predictions.

  12. The sensitivity of convective aggregation to diabatic processes in idealized radiative-convective equilibrium simulations

    NASA Astrophysics Data System (ADS)

    Holloway, C. E.; Woolnough, S. J.

    2016-03-01

    Idealized explicit convection simulations of the Met Office Unified Model exhibit spontaneous self-aggregation in radiative-convective equilibrium, as seen in other models in previous 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 field. Analysis of the budget of the spatial variance of column-integrated frozen moist static energy (MSE), following Wing and Emanuel (2014), reveals that the direct radiative feedback (including significant cloud longwave effects) is dominant in both the initial development of self-aggregation and the maintenance of an aggregated state. A low-level circulation at intermediate stages of aggregation does appear to transport MSE from drier to moister regions, but this circulation is mostly balanced by other advective effects of opposite sign and is forced by horizontal anomalies of convective heating (not radiation). Sensitivity studies with either fixed prescribed radiative cooling, fixed prescribed surface fluxes, or both do not show full self-aggregation from homogeneous initial conditions, though fixed surface fluxes do not disaggregate an initialized aggregated state. A sensitivity study in which rain evaporation is turned off shows more rapid self-aggregation, while a run with this change plus fixed radiative cooling still shows strong self-aggregation, supporting a "moisture-memory" effect found in Muller and Bony (2015). Interestingly, self-aggregation occurs even in simulations with sea surface temperatures (SSTs) of 295 and 290 K, with direct radiative feedbacks dominating the budget of MSE variance, in contrast to results in some previous studies.

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

    PubMed

    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=0.82nm, disorder of the system D=1500cm(-1) for H-type and r=1.04nm, D=1800cm(-1) for J-type. PMID:27348046

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

    NASA Astrophysics Data System (ADS)

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

    2016-12-01

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

  15. Molecular dynamic simulation of asphaltene co-aggregation with humic acid during oil spill.

    PubMed

    Zhu, Xinzhe; Chen, Daoyi; Wu, Guozhong

    2015-11-01

    Humic acid in water and sediment plays a key role in the fate and transport of the spilled oil, but little is known about its influence on the aggregation of heavy oil asphaltenes which is adverse for remediation. Molecular dynamic simulation was performed to characterize the co-aggregation of asphaltenes (continental model and Violanthrone-79 model) with Leonardite humic acid (LHA) at the toluene-water interface and in bulk water, respectively, to simulate the transport of asphaltenes from oil to water. At the toluene-water interface, a LHA layer tended to form and bind to the water by hydrogen bonding which provided a surface for the accumulation of asphaltenes by parallel or T-shape stacking. After entering the bulk water, asphaltene aggregates stacked in parallel were tightly sequestrated inside the inner cavity of LHA aggregates following surface adsorption and structure deformation. Asphaltene aggregation in water was 2-fold higher than at the toluene-water interface. The presence of LHA increased the intensity of asphaltene aggregation by up to 83% in bulk water while relatively less influence was observed at the toluene-water interface. Overall results suggested that the co-aggregation of asphaltene with humic acid should be incorporated to the current oil spill models for better interpreting the overall environmental risks of oil spill.

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

    PubMed

    Areepitak, Trachu; Ren, Jianhong

    2011-07-01

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

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

    PubMed

    Areepitak, Trachu; Ren, Jianhong

    2011-07-01

    Colloids found in natural streams have large reactive surface areas, which makes them significant absorbents and carriers for pollutants. Stream-subsurface exchange plays a critical role in regulating the transport of colloids and contaminants in natural streams. Previous process-based multiphase exchange models were developed without consideration of colloid-colloid interaction. However, many studies have indicated that aggregation is a significant process and needs to be considered in stream process analysis. Herein, a new colloid exchange model was developed by including particle aggregation in addition to colloid settling and filtration. Self-preserving size distribution concepts and classical aggregation theory were employed to model the aggregation process. Model simulations indicate that under conditions of low filtration and high degree of particle-particle interaction, aggregation could either decrease or increase the amount of colloids retained in streambeds, depending on the initial particle size. Thus, two possible cases may occur including enhanced colloid deposition and facilitated colloid transport. Also, when the aggregation rate is high and filtration increases, more particles are retained by bed sediments due to filtration, and fewer are aggregated, which reduces the extent of aggregation effect on colloid deposition. The work presented here will contribute to a better understanding and prediction of colloid transport phenomena in natural streams. PMID:21627165

  18. Influence of pH and sequence in peptide aggregation via molecular simulation

    SciTech Connect

    Enciso, Marta; Schütte, Christof; Delle Site, Luigi

    2015-12-28

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

  19. The role of metals in amyloid aggregation - Experiments and ab initio simulations

    NASA Astrophysics Data System (ADS)

    Minicozzi, V.; Morante, S.; Rossi, G. C.; Stellato, F.; Christian, N.; Jansen, K.

    With a combination of modern spectroscopic techniques and numerical first principle simulations it is possible to investigate the physico-chemical basis of the beta-amyloid aggregation phenomenon, which is suspected to be at the basis of the development of the Alzheimer disease. On the experimental side, in fact, X-ray absorption spectroscopy can be successfully used to determine the atomic structure around the metal binding site in samples where beta-amyloid peptides are complexed with either Cu2+ or Zn2+ ions. Exploiting spectroscopic information obtained on a selected set of fragments of the natural Abeta-peptide, the residues that along the sequence are coordinated to the metal are identified. Although copper data can be consistently interpreted assuming that oligopeptides encompassing the minimal 1-16 amino acidic sequence display a metal coordination mode which involves three Histidines (His6, His13, and His14), in complexes with zinc a four Histidines coordination mode is seen to be preferred. Lacking a fourth Histidine in the Abeta1-16 fragment, this geometrical arrangement hints to a Zn2+ promoted inter-peptide aggregation mode. On the theoretical side, first principle ab initio molecular dynamics simulations of the Car-Parrinello type, which have proved to be of invaluable help in understanding the microscopic mechanisms of chemical bonding both in solid-state physics and structural biophysics, have been employed in an effort to give a microscopic basis and find a phenomenological interpretation of the body of available experimental data on Abeta-peptides-metal complexes. Using medium size PC-clusters as well as larger parallel platforms, it is possible to deal with systems comprising 300-500 atoms and 1,000-2,000 electrons for simulation times as long as 2-3 ps. We present structural results that nicely compare with NMR and XAS data.

  20. Application of simulated annealing to solve multi-objectives for aggregate production planning

    NASA Astrophysics Data System (ADS)

    Atiya, Bayda; Bakheet, Abdul Jabbar Khudhur; Abbas, Iraq Tereq; Bakar, Mohd. Rizam Abu; Soon, Lee Lai; Monsi, Mansor Bin

    2016-06-01

    Aggregate production planning (APP) is one of the most significant and complicated problems in production planning and aim to set overall production levels for each product category to meet fluctuating or uncertain demand in future. and to set decision concerning hiring, firing, overtime, subcontract, carrying inventory level. In this paper, we present a simulated annealing (SA) for multi-objective linear programming to solve APP. SA is considered to be a good tool for imprecise optimization problems. The proposed model minimizes total production and workforce costs. In this study, the proposed SA is compared with particle swarm optimization (PSO). The results show that the proposed SA is effective in reducing total production costs and requires minimal time.

  1. 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.

  2. First principles Monte Carlo simulations of aggregation in the vapor phase of hydrogen fluoride

    SciTech Connect

    McGrath, Matthew J.; Ghogomu, Julius. N.; Mundy, Christopher J.; Kuo, I-F. Will; Siepmann, J. Ilja

    2010-01-01

    The aggregation of superheated hydrogen fluoride vapor is explored through the use of Monte Carlo simulations employing Kohn-Sham density functional theory with the exchange/correlation functional of Becke-Lee-Yang-Parr to describe the molecular interactions. Simulations were carried out in the canonical ensemble for a system consisting of ten molecules at constant density (2700 Å3/molecule) and at three different temperatures (T = 310, 350, and 390 K). Aggregation-volume-bias and configurational-bias Monte Carlo approaches (along with pre-sampling with an approximate potential) were employed to increase the sampling efficiency of cluster formation and destruction.

  3. Aggregation of 12-Hydroxystearic Acid and Its Lithium Salt in Hexane: Molecular Dynamics Simulations.

    PubMed

    Gordon, Ryan; Stober, Spencer T; Abrams, Cameron F

    2016-07-28

    12-Hydroxystearic acid (12HSA) is a well-known organogelator, and its metal salts and derivatives find roles in many important applications. The structures of aggregates of 12-hydroxysteric acid and its salts depend sensitively on cation type, but a fundamental understanding of this phenomenon is lacking. In this study, molecular dynamics simulations were conducted on the microsecond long time scales for (1) 12HSA and (2) its lithium salt, each at 12.5 wt % in explicit hexane solvent. Self-assembly was accelerated by using a modified potential to prohibit alkane chain dihedral gauche states (all-trans-12HSA) and then verified by continuation using standard force-field parameters. In three independent simulation, acceleration using "gauche-less" potentials resulted in self-assembled pseudocrystalline aggregates through formation of polarized five- and six-membered rings between inter-12-hydroxyl groups and head-to-head carboxylic acid dimerization. When subjected to the unmodified dihedral potential, two of the three structures remained stable after 1 μs of MD. Stable structures exhibited a "ring-of-rings" motif, composed of two six-membered acetic acid-dimerized ring bundles with six satellite rings, while the unstable structure did not. In strong contrast, the lithium salt produced a network of fibrils that spanned the volume of the sample. When lithium ions were substituted for carboxylic acid protons in the stable acid structures, they remained intact but lost their chiral nature. Both the acid and lithium structures displayed scattering peaks that agreed with experiment. Taken together, our results suggest that this ring-of-rings structure could be a primary feature of the self-assembly of 12HSA in organic solvents. PMID:27387154

  4. 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.

  5. Ethane adsorption on aggregates of dahlia-like nanohorns: experiments and computer simulations.

    PubMed

    Russell, Brice A; Migone, Aldo D; Petucci, Justin; Mercedes Calbi, M; Yudasaka, Masako; Iijima, Sumio

    2016-06-01

    This is a report on a study of the adsorption characteristics of ethane on aggregates of unopened dahlia-like carbon nanohorns. This sorbent presents two main groups of adsorption sites: the outside surface of individual nanohorns and deep, interstitial spaces between neighbouring nanohorns towards the interior of the aggregates. We have explored the equilibrium properties of the adsorbed ethane films by determining the adsorption isotherms and isosteric heat of adsorption. Computer simulations performed on different model structures indicate that the majority of ethane adsorption occurs on the outer region of the aggregates, near the ends of the nanohorns. We have also measured the kinetics of adsorption of ethane on this sorbent. The measurements and simulations were conducted along several isotherms spanning the range between 120 K and 220 K. PMID:27218414

  6. Difference in aggregation between functional and toxic amyloids studied by atomistic simulations

    NASA Astrophysics Data System (ADS)

    Carballo Pacheco, Martin; Ismail, Ahmed E.; Strodel, Birgit

    Amyloids are highly structured protein aggregates, normally associated with neurodegenerative diseases such as Alzheimer's disease. In recent years, a number of nontoxic amyloids with physiologically normal functions, called functional amyloids, have been found. It is known that soluble small oligomers are more toxic than large fibrils. Thus, we study with atomistic explicit-solvent molecular dynamics simulations the oligomer formation of the amyloid- β peptide Aβ25 - 35, associated with Alzheimer's disease, and two functional amyloid-forming tachykinin peptides: kassinin and neuromedin K. Our simulations show that monomeric peptides in extended conformations aggregate faster than those in collapsed hairpin-like conformations. In addition, we observe faster aggregation by functional amyloids than toxic amyloids, which could explain their lack of toxicity.

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  8. Simulation of the optical properties of plate aggregates for application to the remote sensing of cirrus clouds.

    PubMed

    Xie, Yu; Yang, Ping; Kattawar, George W; Baum, Bryan A; Hu, Yongxiang

    2011-03-10

    In regions of deep tropical convection, ice particles often undergo aggregation and form complex chains. To investigate the effect of the representation of aggregates on electromagnetic scattering calculations, we developed an algorithm to efficiently specify the geometries of aggregates and to compute some of their geometric parameters, such as the projected area. Based on in situ observations, ice aggregates are defined as clusters of hexagonal plates with a chainlike overall shape, which may have smooth or roughened surfaces. An aggregate representation is developed with 10 ensemble members, each consisting of between 4-12 hexagonal plates. The scattering properties of an individual aggregate ice particle are computed using either the discrete dipole approximation or an improved geometric optics method, depending upon the size parameters. Subsequently, the aggregate properties are averaged over all geometries. The scattering properties of the aggregate representation closely agree with those computed from 1000 different aggregate geometries. As a result, the aggregate representation provides an accurate and computationally efficient way to represent all aggregates occurring within ice clouds. Furthermore, the aggregate representation can be used to study the influence of these complex ice particles on the satellite-based remote sensing of ice clouds. The computed cloud reflectances for aggregates are different from those associated with randomly oriented individual hexagonal plates. When aggregates are neglected, simulated cloud reflectances are generally lower at visible and shortwave-infrared wavelengths, resulting in smaller effective particle sizes but larger optical thicknesses.

  9. Parsley extract inhibits in vitro and ex vivo platelet aggregation and prolongs bleeding time in rats.

    PubMed

    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.

  10. Aggregation in concentrated protein solutions: Insights from rheology, neutron scattering and molecular simulations

    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

  11. Platelet aggregation responses vary over a period of time in healthy controls.

    PubMed

    Refaai, Majed A; Frenkel, Eugene; Sarode, Ravi

    2010-01-01

    Platelet aggregation study is performed to investigate platelet function abnormality. A normal healthy control sample is usually run with the patient sample as a quality control measure. At our institution, we observed variations in platelet aggregation responses in our normal repeat controls. Therefore, we analysed aggregation parameters in these controls. Whole blood aggregation studies were performed with adenosine diphosphate (ADP), arachidonic acid (AA), collagen and ristocetin. Adenosine triphosphate (ATP) secretion was also measured simultaneously by leuciferin-leuciferase reaction. During a 5-year period, a total of 86 studies were performed on seven controls. Aggregations were within the acceptable range in 67% of the time. Collagen was the most affected agonist in our study. On five occasions, four controls had subnormal aggregations with two agonists. All abnormal responses were hypoaggregation except for two who had hyperaggregation with collagen and AA. Only one out of seven controls was always normal. In the presence of a subnormal control result, a new control was run before releasing the patient's platelet aggregation results. These findings suggest that many physiological factors, other than medications, may affect platelet function even in normal individuals. Therefore, a repeat study at a later date to demonstrate a reproducible abnormality would be prudent before labeling a patient's platelets abnormal.

  12. Temporal properties of diagnosis code time series in aggregate.

    PubMed

    Perotte, Adler; Hripcsak, George

    2013-03-01

    Time series are essential to health data research and data mining. We aim to study the properties of one of the more commonly available but historically unreliable types of data: administrative diagnoses in the form of the International Classification of Diseases, Ninth Revision (ICD9) codes. We use differential entropy of ICD9 code time series as a surrogate measure for disease time course and also explore Gaussian kernel smoothing to characterize the time course of diseases in a more fine-grained way. Compared to a gold standard created by a panel of clinicians, the first model classified diseases into acute and chronic groups with a receiver operating characteristic area under curve of 0.83. In the second model, several characteristic temporal profiles were observed including permanent, chronic, and acute. In addition, condition dynamics such as the refractory period for giving birth following childbirth were observed. These models demonstrate that ICD9 codes, despite well-documented concerns, contain valid and potentially valuable temporal information.

  13. Heme prevents amyloid beta peptide aggregation through hydrophobic interaction based on molecular dynamics simulation.

    PubMed

    Zhao, Li Na; Mu, Yuguang; Chew, Lock Yue

    2013-09-01

    Heme, which is abundant in hemoglobin and many other hemoproteins, is known to play an important role in electron transfer, oxygen transport, regulation of gene expression, and many other biological functions. With the belief that the aggregation of Aβ peptides forming higher order oligomers is one of the central pathological pathways in Alzheimer's disease, the formation of the Aβ-heme complex is essential as it inhibits Aβ aggregation and protects the neurons from degradation. In our studies, conventional molecular dynamics simulations were performed on the 1 Aβ + 1 heme and 2 Aβ + 4 hemes system, respectively, with the identification of several dominant binding motifs. We found that hydrophobic residues of the Aβ peptide have a high affinity to interact with heme instead of the histidine residue. We conclude that hydrophobic interaction plays a dominant role in the Aβ-heme complex formation which indirectly serves to physically prevent Aβ aggregation.

  14. Aggregation and resuspension of graphene oxide in simulated natural surface aquatic environments.

    PubMed

    Hua, Zulin; Tang, Zhiqiang; Bai, Xue; Zhang, Jianan; Yu, Lu; Cheng, Haomiao

    2015-10-01

    A series of experiments were performed to simulate the environmental behavior and fate of graphene oxide nanoparticles (GONPs) involved in the surface environment relating to divalent cations, natural organic matter (NOM), and hydraulics. The electrokinetic properties and hydrodynamic diameters of GONPs was systematically determined to characterize GONPs stability and the results indicated Ca(2+) (Mg(2+)) significantly destabilized GONPs with high aggregate strength factors (SF) and fractal dimension (FD), whereas NOM decreased aggregate SF with lower FD and improved GONPs stability primarily because of increasing steric repulsion and electrostatic repulsion. Furthermore, the GONPs resuspension from the sand bed into overlying water with shear flow confirmed that the release would be restricted by Ca(2+) (Mg(2+)), however, enhanced by NOM. The interaction energy based on Derjaguin-Landau-Verwey-Overbeek theory verifies the aggregation and resuspension well. Overall, these experiments provide an innovative look and more details to study the behavior and fate of GONPs. PMID:26071942

  15. 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.

  16. Effect of Aggregation on the Mechanical Properties of Ionomers from MD Simulations

    NASA Astrophysics Data System (ADS)

    Sampath, Janani; Hall, Lisa M.

    Ionomers are polymers with a small fraction of charged monomers; these bound ions, along with free counterions, tend to aggregate together strongly in the absence of solvent. Ionic aggregates can act like temporary cross-links, giving rise to interesting mechanical properties. We perform coarse-grained molecular dynamics simulations of ionomers with various spacings of charges along the chain, representing experimental precisely spaced, neutralized poly(ethylene-co-acrylic acid) materials. We calculate aggregate morphology, dynamics, and scattering profiles and study the systems during uniaxial tensile strain to understand how aggregate structure changes under deformation and affects mechanical properties. Anisotropic structure factors (parallel and perpendicular to the direction of pull) and visualization shows that the aggregates align, in qualitative agreement with experimental findings. Stress-strain curves at different strain rates are also obtained. A modification of the model to account for unneutralized acid groups by adjusting their Lennard-Jones interaction strengths with each other and with ionic groups will also be discussed. This material is based upon work supported by the National Science Foundation under Grant 1463103.

  17. How hydrophobic nanoparticles aggregate in the interior of membranes: A computer simulation

    NASA Astrophysics Data System (ADS)

    Tian, Falin; Zhang, Xianren; Dong, Wei

    2014-11-01

    Lipid-based dispersion of hydrophobic nanoparticles (NPs) not only gives fundamental insight into how nanomaterials distribute in live cells and organisms, but also provides a quite general route to designing nanocarrier agents in triggered drug delivery and medical imaging. It is not clearly understood how hydrophobic NPs arrange in the interior of a membrane. In this paper, with computer simulation techniques, we demonstrate that hydrophobic NPs having a diameter compared to the hydrophobic thickness of the membrane are capable of clustering in the hydrophobic interior of a cell membrane. Except from the isotropic aggregation, an unexpected linear arrangement of spherical NPs, which is still not found from experiments, is identified here. The free-energy costs associated with linear and isotropic aggregations are computed explicitly to interpret aggregation behavior and the obtained phase diagrams give us a comprehensive understanding of where linear aggregation is expected. In this work we also shows that NP size and membrane tension play key roles in determining the NP aggregate, while the effects of NP concentration and membrane curvature seem to be relatively weak.

  18. Real-time amyloid aggregation monitoring with a photonic crystal-based approach.

    PubMed

    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. PMID:24105966

  19. Aggregation in dilute aqueous tert-butyl alcohol solutions: Insights from large-scale simulations

    NASA Astrophysics Data System (ADS)

    Gupta, Rini; Patey, G. N.

    2012-07-01

    Molecular dynamics simulations employing up to 64 000 particles are used to investigate aggregation and microheterogeneity in aqueous tert-butyl alcohol (TBA) solutions for TBA mole fractions Xt ⩽ 0.1. Four different force fields are considered. It is shown that the results obtained can be strongly dependent on the particular force field employed, and can be significantly influenced by system size. Two of the force fields considered show TBA aggregation in the concentration range Xt ≈ 0.03 - 0.06. For these models, systems of 64 000 particles are minimally sufficient to accommodate the TBA aggregates. The structures resulting from TBA aggregation do not have a well-defined size and shape, as one might find in micellar systems, but are better described as TBA-rich and water-rich regions. All pair correlation functions exhibit long-range oscillatory behavior with wavelengths that are much larger than molecular length scales. The oscillations are not strongly damped and the correlations can easily exceed the size of the simulation cell, even for the low TBA concentrations considered here. We note that these long-range correlations pose a serious problem if one wishes to obtain certain physical properties such as Kirkwood-Buff integrals from simulation results. In contrast, two other force fields that we consider show little sign of aggregation for Xt ≲ 0.08. In our 64 000 particle simulations all four models considered show demixing-like behavior for Xt ≳ 0.1, although such behavior is not evident in smaller systems of 2000 particles. The meaning of the demixing-like behavior is unclear. Since real TBA-water solutions do not demix, it might be an indication that all four models we consider poorly represent the real system. Alternatively, it might be an artifact of finite system size. Possibly, the apparent demixing indicates that for Xt ≳ 0.1, the stable TBA aggregates are simply too large to fit into the simulation cell. Our results provide a view of the

  20. Polyalanine and Abeta Aggregation Kinetics: Probing Intermediate Oligomer Formation and Structure Using Computer Simulations

    NASA Astrophysics Data System (ADS)

    Phelps, Erin Melissa

    2011-12-01

    The aggregation of proteins into stable, well-ordered structures known as amyloid fibrils has been associated with many neurodegenerative diseases. Amyloid fibrils are long straight, and un-branched structures containing several proto-filaments, each of which exhibits "cross beta structure," -- ribbon-like layers of large beta sheets whose strands run perpendicular to the fibril axis. It has been suggested in the literature that the pathway to fibril formation has the following steps: unfolded monomers associate into transient unstable oligomers, the oligomers undergo a rearrangement into the cross-beta structure and form into proto-filaments, these proto-filaments then associate and grow into fully formed fibrils. Recent experimental studies have determined that the unstable intermediate structures are toxic to cells and that their presence may play a key role in the pathogenesis of the amyloid diseases. Many efforts have been made to determine the structure of intermediate oligomer aggregates that form during the fibrillization process. The goal of this work is to provide details about the structure and formation kinetics of the unstable oligomers that appear in the fibril formation pathway. The specific aims of this work are to determine the steps in the fibril formation pathway and how the kinetics of fibrillization changes with variations in temperature and concentration. The method used is the application of discontinuous molecular dynamics to large systems of peptides represented with an intermediate resolution model, PRIME, that was previously developed in our group. Three different peptide sequences are simulated: polyalanine (KA14K), Abeta17-40, and Abeta17-42; the latter two are truncated sequences of the Alzheimer's peptide. We simulate the spontaneous assembly of these peptide chains from a random initial configuration of random coils. We investigate aggregation kinetics and oligomer formation of a system of 192 polyalanine (KA14K) chains over a

  1. Molecular-level insights of early-stage prion protein aggregation on mica and gold surface determined by AFM imaging and molecular simulation.

    PubMed

    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.

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

    PubMed

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

    2002-03-01

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

  3. Feature activated molecular dynamics: an efficient approach for atomistic simulation of solid-state aggregation phenomena.

    PubMed

    Prasad, Manish; Sinno, Talid

    2004-11-01

    An efficient approach is presented for performing efficient molecular dynamics simulations of solute aggregation in crystalline solids. The method dynamically divides the total simulation space into "active" regions centered about each minority species, in which regular molecular dynamics is performed. The number, size, and shape of these regions is updated periodically based on the distribution of solute atoms within the overall simulation cell. The remainder of the system is essentially static except for periodic rescaling of the entire simulation cell in order to balance the pressure between the isolated molecular dynamics regions. The method is shown to be accurate and robust for the Environment-Dependant Interatomic Potential (EDIP) for silicon and an Embedded Atom Method potential (EAM) for copper. Several tests are performed beginning with the diffusion of a single vacancy all the way to large-scale simulations of vacancy clustering. In both material systems, the predicted evolutions agree closely with the results of standard molecular dynamics simulations. Computationally, the method is demonstrated to scale almost linearly with the concentration of solute atoms, but is essentially independent of the total system size. This scaling behavior allows for the full dynamical simulation of aggregation under conditions that are more experimentally realizable than would be possible with standard molecular dynamics.

  4. A New Simulated Plasma for Assessing the Solubility of Mineral Trioxide Aggregate

    PubMed Central

    Samiei, Mohammad; Shahi, Shahriar; Aslaminabadi, Naser; Valizadeh, Hadi; Aghazadeh, Zahra; Pakdel, Seyyed Mahdi Vahid

    2015-01-01

    Introduction: Solubility of mineral trioxide aggregate (MTA) is an important characteristic that affects other properties such as microleakage and biocompatibility. Distilled water (DW) has previously been used for solubility tests. This experimental study compared the solubility of MTA in DW, synthetic tissue fluid (STF) and new simulated plasma (SP). Methods and Materials: In this study, 36 samples of tooth-colored ProRoot MTA were prepared and divided into three groups (n=12) to be immersed in three different solutions (DW, STF, and SP). Solubility tests were conducted at 2, 5, 9, 14, 21, 30, 50, and 78-day intervals. The unequal variance F-test (Welch test) was utilized to determine the effect of solubility media and Games-Howell analysis was used for pairwise comparisons. The repeated-measures ANOVA was used to assess the importance of immersion duration. Results: Welch test showed significant differences in solubility rates of samples between all the different solubility media at all the study intervals (P<0.05) except for the 14-day interval (P=0.094). The mixed repeated-measures ANOVA revealed a significant difference in solubility rate of MTA in three different solutions at all time-intervals (P=0.000). Games-Howell post-hoc test revealed that all pairwise comparisons were statistically significant at all time-intervals (P=0.000). Conclusion: Based on the findings of this study, the long-term solubility of MTA in simulated plasma was less than that in synthetic tissue fluid and distilled water. PMID:25598806

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

    PubMed Central

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Loh, Yen Lee

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

  7. Real time flight simulation methodology

    NASA Technical Reports Server (NTRS)

    Parrish, E. A.; Cook, G.; Mcvey, E. S.

    1977-01-01

    Substitutional methods for digitization, input signal-dependent integrator approximations, and digital autopilot design were developed. The software framework of a simulator design package is described. Included are subroutines for iterative designs of simulation models and a rudimentary graphics package.

  8. Computer simulation of diffusion-limited cluster-cluster aggregation with an Epstein drag force.

    PubMed

    Pierce, F; Sorensen, C M; Chakrabarti, A

    2006-08-01

    The motion of particles, dispersed in a medium, between collisions with each other can, in limiting situations, be either ballistic (straight line) or diffusive (random walker). The diffusive regime can be divided into two distinct subregimes. The "continuum regime" exhibits Stokes-Einstein-type diffusion (no-slip surface boundary condition) with a frictional coefficient proportional to the particle size (linear dimension). The "Epstein regime," as we shall refer to it, is characterized by a frictional coefficient proportional to the particle cross-sectional area, hence an Epstein-type diffusion (slip surface). The purpose of the current study is to illuminate the dynamics of dilute-limit aggregation in the Epstein regime. We present results from low volume fraction Monte Carlo simulations of cluster-cluster aggregation in the Epstein regime with the particle motion based on each particle's cross-sectional area. Our findings indicate that aggregates grown under Epstein conditions have a fractal dimension of approximately 1.8, similar to that of diffusion-limited cluster-cluster aggregates (DLCA) in the continuum regime. The kinetic exponent z in the Epstein regime is found to be z approximately 0.8, lower than its value for both the continuum regime DLCA (z = 1) and for the ballistic cluster aggregation regime (z approximately 2). Cluster size distribution data for Epstein systems are found to scale at large cluster sizes with exponents consistent with the kinetic data. A scaling argument for predicting the kinetic exponent and kernel homogeneity based on the mass or size dependence of the particle velocity and collision cross section is presented and is seen to give accurate results for dilute and intermediate values of particle volume fractions not only for the current study, but also for work done by other researchers with various choices for the aggregation kernel. PMID:17025429

  9. Structure and dynamics of surfactant and hydrocarbon aggregates on graphite: a molecular dynamics simulation study.

    PubMed

    Sammalkorpi, Maria; Panagiotopoulos, Athanassios Z; Haataja, Mikko

    2008-03-13

    We have examined the structure and dynamics of sodium dodecyl sulfate (SDS) and dodecane (C12) molecular aggregates at varying surface coverages on the basal plane of graphite via classical molecular dynamics simulations. Our results suggest that graphite-hydrocarbon chain interactions favor specific molecular orientations at the single-molecule level via alignment of the tail along the crystallographic directions. This orientational bias is reduced greatly upon increasing the surface coverage for both molecules due to intermolecular interactions, leading to very weak bias at intermediate surface coverages. Interestingly, for complete monolayers, we find a re-emergent orientational bias. Furthermore, by comparing the SDS behavior with C12, we demonstrate that the charged head group plays a key role in the aggregate structures: SDS molecules display a tendency to form linear file-like aggregates while C12 forms tightly bound planar ones. The observed orientational bias for SDS molecules is in agreement with experimental observations of hemimicelle orientation and provides support for the belief that an initial oriented layer governs the orientation of hemimicellar aggregates.

  10. Time-dependent aggregation-induced enhanced emission, absorption spectral broadening, and aggregation morphology of a novel perylene derivative with a large D-π-A structure.

    PubMed

    Yang, Long; Yu, Yuyan; Zhang, Jin; Ge, Feijie; Zhang, Jianling; Jiang, Long; Gao, Fang; Dan, Yi

    2015-05-01

    Strong aggregation-caused quenching of perylene diimides (PDI) is changed successfully by simple chemical modification with two quinoline moieties through C=C at the bay positions to obtain aggregation-induced enhanced emission (AIEE) of a perylene derivative (Cya-PDI) with a large π-conjugation system. Cya-PDI is weakly luminescent in the well-dispersed CH(3)CN or THF solutions and exhibits an evident time-dependent AIEE and absorption spectra broadening in the aggregated state. In addition, morphological inspection demonstrates that the morphology of the aggregated form of Cya-PDI molecules changed from plate-shaped to rod-like aggregates under the co-effects of time and water. An edge-to-face arrangement of aggregation was proposed and discussed. The fact that the Cya-PDI aggregates show a broad absorption covering the whole visible-light range and strong intermolecular interaction through π-π stacking in the solid state makes them promising materials for optoelectric applications.

  11. 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.

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

    SciTech Connect

    Zakharov, Anatoly I.; Adzhemyan, Loran Ts.; Shchekin, Alexander K.

    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 take 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.

  13. Hierarchically Fourier-aggregated signals and generalized coherence of the noise in the GPS time series

    NASA Astrophysics Data System (ADS)

    Lyubushin, Alexey

    2016-04-01

    A new method for joint analysis of big number of time series is presented. The method is based on using of Fourier-aggregated signals and it has a purpose to detect time intervals and frequency bands when there is a coherence between noise components of all time series. An aggregated signal (AS) is constructed in two stages. At the 1st stage, initial multidimensional time series is substituted by time series of the same dimensionality but composed of so-called canonical components. The canonical components accumulate signals that are common for all initial components and are free of local variations that are specific for individual scalar time series only. At the 2nd stage, the common signals are amplified by constructing a single scalar time series, their first principal component. Thus, an AS is the first principal component of canonical components. In the case when there is a monitoring system with big number of recording stations all stations are split into a number of clusters with moderate number (10-20) of stations within each clusters. For all clusters AS are calculated which could be called AS of the 1st order. The technique of the 1st order AS computing provides estimating in moving time window and gives a possibility to take into account gaps in registration. If the number of the 1st order aggregation clusters is still big they could be split into 2nd order aggregation clusters and the 1st order AS could be aggregated more into 2nd order AS. At any stage of aggregation a multiple spectral coherence measures could be calculated which present time-frequency diagrams for evolution of coherence between noise components of time series. The elaborated method was applied to daily 3-components GPS time series from the networks in the USA (4512 stations) and in Europe (2122 stations). The multiple coherence measure estimated for different combinations of AS of the 1st and 2nd orders inside regions of USA and Europe and between them extracted essential peaks of

  14. Exobiological implications of dust aggregation in planetary atmospheres: An experiment for the gas-grain simulation facility

    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.

  15. Convective self-aggregation feedbacks in near-global cloud-resolving simulations of an aquaplanet

    NASA Astrophysics Data System (ADS)

    Bretherton, Christopher S.; Khairoutdinov, Marat F.

    2015-12-01

    Positive feedbacks between precipitable water, reduced radiative cooling and enhanced surface fluxes promote convective self-aggregation in limited-area cloud-resolving model (CRM) simulations over uniform sea-surface temperature (SST). Near-global aquaplanet simulations with 4 km horizontal grid spacing and no cumulus or boundary layer parameterization are used to test the importance of these feedbacks to realistically organized tropical convection. A 20,480 × 10,240 km equatorially centered channel with latitudinally varying SST is used. Realistic midlatitude and tropical cloud structures develop. The natural zonal variability of humidity and convection are studied in a 30 day control simulation. The temporal growth of a small white-noise humidity perturbation and intrinsic predictability implications are explored. Atmospheric column budgets of moist-static energy (MSE) quantify its covariation with precipitation, surface heat flux, and radiative energy loss. Zonal Fourier analysis partitions these budgets by length scale. Radiative feedbacks on MSE natural variability and perturbation growth are found to be positive, broadly similar across scales, and comparable to limited-area CRMs, capable of e-folding a column MSE perturbation in 6-14 days. Surface fluxes are highest in synoptic-scale dry intrusions, inhibiting aggregation by damping tropical MSE perturbations. Sub-4-day MSE variations are due mainly to advection. Both tropics and midlatitudes have large-scale intrinsic predictability horizons of 15-30 days. An identical simulation but with 20 km grid spacing has more mesoscale variability and low cloud.

  16. The role of side-chain interactions in the early steps of aggregation: Molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35

    NASA Astrophysics Data System (ADS)

    Gsponer, Jörg; Haberthür, Urs; Caflisch, Amedeo

    2003-04-01

    Understanding the early steps of aggregation at atomic detail might be crucial for the rational design of therapeutics preventing diseases associated with amyloid deposits. In this paper, aggregation of the heptapeptide GNNQQNY, from the N-terminal prion-determining domain of the yeast protein Sup35, was studied by 20 molecular dynamics runs for a total simulation time of 20 μs. The simulations generate in-register parallel packing of GNNQQNY -strands that is consistent with x-ray diffraction and Fourier transform infrared data. The statistically preferred aggregation pathway does not correspond to a purely downhill profile of the energy surface because of the presence of enthalpic barriers that originate from out-of-register interactions. The parallel -sheet arrangement is favored over the antiparallel because of side-chain contacts; in particular, stacking interactions of the tyrosine rings and hydrogen bonds between amide groups. No ordered aggregation was found in control simulations with the mutant sequence SQNGNQQRG in accord with experimental data and the strong sequence dependence of aggregation.

  17. Lipid raft aggregation during the formation of the immunological synapse: quantitative mapping and simulations

    NASA Astrophysics Data System (ADS)

    Amador Kane, Suzanne; Adelman, Joshua; Lee, Mark; Punt, Jennifer; Ebert, Peter

    2002-03-01

    Lipid raft aggregation during formation of the immunological synapse in T-cells was explored using both experimental results from immunofluorescence imaging and computer simulations. Profiles of lipid raft distributions in the capping region relative to other protein species are presented, and compared for various experimental approaches. We also discuss a model for the dynamical formation of the synapse which incorporates different methods of transport for the lipid rafts themselves as well as other important species, including T-cell receptors and the major histocompatibility complex (MHC)/peptide complex, and we relate these to experimental findings.

  18. Fractal aggregates in reduced gravity experiments and numerical simulations to characterize cometary material properties.

    NASA Astrophysics Data System (ADS)

    Lasue, Jeremie; Levasseur-Regourd, Anny-Chantal; Hadamcik, Edith; Botet, Robert; Renard, Jean-Baptiste

    In situ missions have shown that cometary dust particles have low densities and are easily fragmenting aggregates [1]. The linear polarization of the solar light scattered by cometary dust corresponds to bell-shaped (with a small negative branch and a maximum below 30%) phase curves with a quasi-linear increase with the wavelength between 30° and 50° phase angle [2]. Such physical properties of the cometary material are reconciled by a fractal model of cometary dust and comet nuclei as formed by aggregation in reduced gravity as studied by laboratory experiments and numerical simulations. Reduced gravity light scattering experiments: The CODAG-LSU experiment (1999) gave the first indication of the light scattering properties transition between single particles and low dimensions fractal aggregates (D 1.3) [3, 4]. Such studies will be pursued on board the ISS with the ICAPS precursor experiment. The PROGRA2 experiment is designed to study the light scattering properties of particles levitated during dedicated microgravity flights or with ground-based configurations [5]. The material properties are chosen so as to be relevant in the context of cosmic dust from cometary and asteroidal origins. It is especially useful to disentangle the effects of varying albedos of constitutive materials [6], shape and size of constitutive grains [7]. Some of the results are interpreted in terms of fractal aggregates growth. Light scattering numerical simulations Based on numerical simulations and in coherence with the experimental results, a model of cometary coma by a mixture of fractal aggregates of up to 256 sub-micron sized spheroidal grains and compact spheroidal particles is shown to reproduce the polarimetric observations of comets such as 1P/Halley or C/1995 O1 Hale-Bopp [8]. Physical parameters of the size distribution of particles (minimum and maximum size, shape of the size distribution and quantity and location of absorbing and non-absorbing particles) can be retrieved

  19. Real-time simulation clock

    NASA Technical Reports Server (NTRS)

    Bennington, Donald R. (Inventor); Crawford, Daniel J. (Inventor)

    1990-01-01

    The invention is a clock for synchronizing operations within a high-speed, distributed data processing network. The clock is actually a distributed system comprising a central clock and multiple site clock interface units (SCIUs) which are connected by means of a fiber optic star network and which operate under control of separate clock software. The presently preferred embodiment is a part of the flight simulation system now in current use at the NASA Langley Research Center.

  20. Real-time simulation clock

    NASA Astrophysics Data System (ADS)

    Bennington, Donald R.; Crawford, Daniel J.

    1990-04-01

    The invention is a clock for synchronizing operations within a high-speed, distributed data processing network. The clock is actually a distributed system comprising a central clock and multiple site clock interface units (SCIUs) which are connected by means of a fiber optic star network and which operate under control of separate clock software. The presently preferred embodiment is a part of the flight simulation system now in current use at the NASA Langley Research Center.

  1. Polyalanine and Abeta Aggregation Kinetics: Probing Intermediate Oligomer Formation and Structure Using Computer Simulations

    NASA Astrophysics Data System (ADS)

    Phelps, Erin Melissa

    2011-12-01

    The aggregation of proteins into stable, well-ordered structures known as amyloid fibrils has been associated with many neurodegenerative diseases. Amyloid fibrils are long straight, and un-branched structures containing several proto-filaments, each of which exhibits "cross beta structure," -- ribbon-like layers of large beta sheets whose strands run perpendicular to the fibril axis. It has been suggested in the literature that the pathway to fibril formation has the following steps: unfolded monomers associate into transient unstable oligomers, the oligomers undergo a rearrangement into the cross-beta structure and form into proto-filaments, these proto-filaments then associate and grow into fully formed fibrils. Recent experimental studies have determined that the unstable intermediate structures are toxic to cells and that their presence may play a key role in the pathogenesis of the amyloid diseases. Many efforts have been made to determine the structure of intermediate oligomer aggregates that form during the fibrillization process. The goal of this work is to provide details about the structure and formation kinetics of the unstable oligomers that appear in the fibril formation pathway. The specific aims of this work are to determine the steps in the fibril formation pathway and how the kinetics of fibrillization changes with variations in temperature and concentration. The method used is the application of discontinuous molecular dynamics to large systems of peptides represented with an intermediate resolution model, PRIME, that was previously developed in our group. Three different peptide sequences are simulated: polyalanine (KA14K), Abeta17-40, and Abeta17-42; the latter two are truncated sequences of the Alzheimer's peptide. We simulate the spontaneous assembly of these peptide chains from a random initial configuration of random coils. We investigate aggregation kinetics and oligomer formation of a system of 192 polyalanine (KA14K) chains over a

  2. Piecewise aggregate representations and lower-bound distance functions for multivariate time series

    NASA Astrophysics Data System (ADS)

    Li, Hailin

    2015-06-01

    Dimensionality reduction is one of the most important methods to improve the efficiency of the techniques that are applied to the field of multivariate time series data mining. Due to multivariate time series with the variable-based and time-based dimensions, the reduction techniques must take both of them into consideration. To achieve this goal, we use a center sequence to represent a multivariate time series so that the new sequence can be seen as a univariate time series. Thus two sophisticated piecewise aggregate representations, including piecewise aggregate approximation and symbolization applied to univariate time series, are used to further represent the extended sequence that is derived from the center one. Furthermore, some distance functions are designed to measure the similarity between two representations. Through being proven by some related mathematical analysis, the proposed functions are lower bound on Euclidean distance and dynamic time warping. In this way, false dismissals can be avoided when they are used to index the time series. In addition, multivariate time series with different lengths can be transformed into the extended sequences with equal length, and their corresponding distance functions can measure the similarity between two unequal-length multivariate time series. The experimental results demonstrate that the proposed methods can reduce the dimensionality, and their corresponding distance functions satisfy the lower-bound condition, which can speed up the calculation of similarity search and indexing in the multivariate time series datasets.

  3. Aggregation behavior of amphiphilic cyclodextrins in a nonpolar solvent: evidence of large-scale structures by atomistic molecular dynamics simulations and solution studies.

    PubMed

    Raffaini, Giuseppina; Ganazzoli, Fabio; Mazzaglia, Antonino

    2016-01-01

    Chemically modified cyclodextrins carrying both hydrophobic and hydrophilic substituents may form supramolecular aggregates or nanostructures of great interest. These systems have been usually investigated and characterized in water for their potential use as nanocarriers for drug delivery, but they can also aggregate in apolar solvents, as shown in the present paper through atomistic molecular dynamics simulations and dynamic light scattering measurements. The simulations, carried out with a large number of molecules in vacuo adopting an unbiased bottom-up approach, suggest the formation of bidimensional structures with characteristic length scales of the order of 10 nm, although some of these sizes are possibly affected by the assumed periodicity of the simulation cell, in particular at longer lengths. In any case, these nanostructures are stable at least from the kinetic viewpoint for relatively long times thanks to the large number of intermolecular interactions of dipolar and dispersive nature. The dynamic light scattering experiments indicate the presence of aggregates with a hydrodynamic radius of the order of 80 nm and a relatively modest polydispersity, even though smaller nanometer-sized aggregates cannot be fully ruled out. Taken together, these simulation and experimental results indicate that amphiphilically modified cyclodextrins do also form large-scale nanoaggregates even in apolar solvents. PMID:26877809

  4. Aggregation behavior of amphiphilic cyclodextrins in a nonpolar solvent: evidence of large-scale structures by atomistic molecular dynamics simulations and solution studies

    PubMed Central

    Ganazzoli, Fabio; Mazzaglia, Antonino

    2016-01-01

    Summary Chemically modified cyclodextrins carrying both hydrophobic and hydrophilic substituents may form supramolecular aggregates or nanostructures of great interest. These systems have been usually investigated and characterized in water for their potential use as nanocarriers for drug delivery, but they can also aggregate in apolar solvents, as shown in the present paper through atomistic molecular dynamics simulations and dynamic light scattering measurements. The simulations, carried out with a large number of molecules in vacuo adopting an unbiased bottom-up approach, suggest the formation of bidimensional structures with characteristic length scales of the order of 10 nm, although some of these sizes are possibly affected by the assumed periodicity of the simulation cell, in particular at longer lengths. In any case, these nanostructures are stable at least from the kinetic viewpoint for relatively long times thanks to the large number of intermolecular interactions of dipolar and dispersive nature. The dynamic light scattering experiments indicate the presence of aggregates with a hydrodynamic radius of the order of 80 nm and a relatively modest polydispersity, even though smaller nanometer-sized aggregates cannot be fully ruled out. Taken together, these simulation and experimental results indicate that amphiphilically modified cyclodextrins do also form large-scale nanoaggregates even in apolar solvents. PMID:26877809

  5. 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.

  6. Size of spawning population, residence time, and territory shifts of individuals in the spawning aggregation of a riverine catostomid

    USGS Publications Warehouse

    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.

  7. Location Isn't Everything: Timing of Spawning Aggregations Optimizes Larval Replenishment.

    PubMed

    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

  8. Location Isn’t Everything: Timing of Spawning Aggregations Optimizes Larval Replenishment

    PubMed Central

    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

  9. Molecular dynamics simulations of ionic aggregates in a coarse%3CU%2B2010%3Egrained ionomer melt.

    SciTech Connect

    Hall, Lisa Michelle; Frischknecht, Amalie Lucile; Stevens, Mark Jackson

    2010-11-01

    Ionomers--polymers containing a small fraction of covalently bound ionic groups--have potential application as solid electrolytes in batteries. Understanding ion transport in ionomers is essential for such applications. Due to strong electrostatic interactions in these materials, the ions form aggregates, tending to slow counterion diffusion. A key question is how ionomer properties affect ionic aggregation and counterion dynamics on a molecular level. Recent experimental advances have allowed synthesis and extensive characterization of ionomers with a precise, constant spacing of charged groups, making them ideal for controlled measurement and more direct comparison with molecular simulation. We have used coarse-grained molecular dynamics to simulate such ionomers with regularly spaced charged beads. The charged beads are placed either in the polymer backbone or as pendants on the backbone. The polymers, along with the counterions, are simulated at melt densities. The ionic aggregate structure was determined as a function of the dielectric constant, spacing of the charged beads on the polymer, and the sizes of the charged beads and counterions. The pendant ion architecture can yield qualitatively different aggregate structures from those of the linear polymers. For small pendant ions, roughly spherical aggregates have been found above the glass transition temperature. The implications of these aggregates for ion diffusion will be discussed.

  10. Red blood cell aggregation and dissociation in shear flows simulated by lattice Boltzmann method.

    PubMed

    Zhang, Junfeng; Johnson, Paul C; Popel, Aleksander S

    2008-01-01

    In this paper we develop a lattice Boltzmann algorithm to simulate red blood cell (RBC) behavior in shear flows. The immersed boundary method is employed to incorporate the fluid-membrane interaction between the flow field and deformable cells. The cell membrane is treated as a neo-Hookean viscoelastic material and a Morse potential is adopted to model the intercellular interaction. Utilizing the available mechanical properties of RBCs, multiple cells have been studied in shear flows using a two-dimensional approximation. These cells aggregate and form a rouleau under the action of intercellular interaction. The equilibrium configuration is related to the interaction strength. The end cells exhibit concave shapes under weak interaction and convex shapes under strong interaction. In shear flows, such a rouleau-like aggregate will rotate or be separated, depending on the relative strengths of the intercellular interaction and hydrodynamic viscous forces. These behaviors are qualitatively similar to experimental observations and show the potential of this numerical scheme for future studies of blood flow in microvessels. PMID:17888442

  11. Red Blood Cell Aggregation and Dissociation in Shear Flows Simulated by Lattice Boltzmann Method

    PubMed Central

    Zhang, Junfeng; Johnson, Paul C.; Popel, Aleksander S.

    2008-01-01

    In this paper we develop a lattice Boltzmann algorithm to simulate red blood cell (RBC) behavior in shear flows. The immersed boundary method is employed to incorporate the fluid-membrane interaction between the flow field and deformable cells. The cell membrane is treated as a neo-Hookean viscoelastic material and a Morse potential is adopted to model the intercellular interaction. Utilizing the available mechanical properties of RBCs, multiple cells have been studied in shear flows using a two-dimensional approximation. These cells aggregate and form a rouleau under the action of intercellular interaction. The equilibrium configuration is related to the interaction strength. The end cells exhibit concave shapes under weak interaction and convex shapes under strong interaction. In shear flows, such a rouleau-like aggregate will rotate or be separated, depending on the relative strengths of the intercellular interaction and hydrodynamic viscous forces. These behaviors are qualitatively similar to experimental observations and show the potential of this numerical scheme for future studies of blood flow in microvessels. PMID:17888442

  12. Aggregation dynamics of laminin-1 in a physiological solution: A time-resolved static light scattering study

    NASA Astrophysics Data System (ADS)

    Onuma, Kazuo; Kanzaki, Noriko

    2005-11-01

    The aggregation of laminin-1 in a physiological solution was observed using time-resolved static light scattering. In a solution containing 150 mM of NaCl and 1 mM of CaCl 2, with a pH of 7.2 buffered by 50 mM Tris, and maintained at 25 °C, the weight-averaged mass (molecular weight) Mw, and radius of gyration Rg, of the aggregate were measured at 10 s intervals. The aggregation kinetics changed from reaction-limited cluster aggregation (RLCA) to diffusion-limited cluster aggregation (DLCA) over time. The fractal dimension estimated in the DLCA regime was 1.71 from the M˜Rgd relationship, which is consistent with the df of 1.75 obtained from an R˜t plot. Direct calculation of df using the scattering intensity and scattering vector revealed that df gradually increased over time in the DLCA regime, suggesting that spontaneous restructuring of the aggregate had occurred. This restructuring would have been caused by hydrophobic contact in the aggregate. The form factor of the aggregate was well fitted by a linear random coil model and not by a simple spherical model.

  13. Investigating bile salt aggregation using coarse-grained molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Vila Verde, Ana; Frenkel, Daan

    2010-03-01

    Bile salts are necessary for fat digestion due to their unusual surfactant properties: they assemble into small, polydisperse micelles and easily form mixed micelles with poorly soluble amphiphiles. Understanding these properties requires molecular scale information about bile salt micelles, something challenging to obtain experimentally but amenable to computational modeling. To address this issue we build a coarse-grained model of bile salts. We investigate their aggregation behavior through molecular dynamics simulations in a grand-canonical parallel tempering scheme. We validate our model against available solubility and light scattering data. Our results indicate that at physiological bile salt and counter ion concentrations, bile salts pack in many different orientations in pure bile micelles, contrary to standard surfactants. This feature may be physiologically relevant, allowing bile salts to solubilize the heterogeneous blends of fats typical of digestion.

  14. Effects of macromolecular crowding on amyloid beta (16-22) aggregation using coarse-grained simulations.

    PubMed

    Latshaw, David C; Cheon, Mookyung; Hall, Carol K

    2014-11-26

    To examine the effect of crowding on protein aggregation, discontinuous molecular dynamics (DMD) simulations combined with an intermediate resolution protein model, PRIME20, were applied to a peptide/crowder system. The systems contained 192 Aβ(16-22) peptides and crowders of diameters 5, 20, and 40 Å, represented here by simple hard spheres, at crowder volume fractions of 0.00, 0.10, and 0.20. Results show that both crowder volume fraction and crowder diameter have a large impact on fibril and oligomer formation. The addition of crowders to a system of peptides increases the rate of oligomer formation, shifting from a slow ordered formation of oligomers in the absence of crowders, similar to nucleated polymerization, to a fast collapse of peptides and subsequent rearrangement characteristic of nucleated conformational conversion with a high maximum in the number of peptides in oligomers as the total crowder surface area increases. The rate of conversion from oligomers to fibrils also increases with increasing total crowder surface area, giving rise to an increased rate of fibril growth. In all cases, larger volume fractions and smaller crowders provide the greatest aggregation enhancement effects. We also show that the size of the crowders influences the formation of specific oligomer sizes. In our simulations, the 40 Å crowders enhance the number of dimers relative to the numbers of trimers, hexamers, pentamers, and hexamers, while the 5 Å crowders enhance the number of hexamers relative to the numbers of dimers, trimers, tetramers, and pentamers. These results are in qualitative agreement with previous experimental and theoretical work.

  15. Effects of Macromolecular Crowding on Amyloid Beta (16–22) Aggregation Using Coarse-Grained Simulations

    PubMed Central

    2015-01-01

    To examine the effect of crowding on protein aggregation, discontinuous molecular dynamics (DMD) simulations combined with an intermediate resolution protein model, PRIME20, were applied to a peptide/crowder system. The systems contained 192 Aβ(16–22) peptides and crowders of diameters 5, 20, and 40 Å, represented here by simple hard spheres, at crowder volume fractions of 0.00, 0.10, and 0.20. Results show that both crowder volume fraction and crowder diameter have a large impact on fibril and oligomer formation. The addition of crowders to a system of peptides increases the rate of oligomer formation, shifting from a slow ordered formation of oligomers in the absence of crowders, similar to nucleated polymerization, to a fast collapse of peptides and subsequent rearrangement characteristic of nucleated conformational conversion with a high maximum in the number of peptides in oligomers as the total crowder surface area increases. The rate of conversion from oligomers to fibrils also increases with increasing total crowder surface area, giving rise to an increased rate of fibril growth. In all cases, larger volume fractions and smaller crowders provide the greatest aggregation enhancement effects. We also show that the size of the crowders influences the formation of specific oligomer sizes. In our simulations, the 40 Å crowders enhance the number of dimers relative to the numbers of trimers, hexamers, pentamers, and hexamers, while the 5 Å crowders enhance the number of hexamers relative to the numbers of dimers, trimers, tetramers, and pentamers. These results are in qualitative agreement with previous experimental and theoretical work. PMID:25347801

  16. Chondrule Pyroxene Embedded in Cores of Amoeboid Olivine Aggregates from Allende: Evidence of Overlapping Formation Times of AOAs and Chondrules

    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.

  17. Perspective: Computer simulations of long time dynamics

    PubMed Central

    Elber, Ron

    2016-01-01

    Atomically detailed computer simulations of complex molecular events attracted the imagination of many researchers in the field as providing comprehensive information on chemical, biological, and physical processes. However, one of the greatest limitations of these simulations is of time scales. The physical time scales accessible to straightforward simulations are too short to address many interesting and important molecular events. In the last decade significant advances were made in different directions (theory, software, and hardware) that significantly expand the capabilities and accuracies of these techniques. This perspective describes and critically examines some of these advances. PMID:26874473

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

    PubMed

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

    2015-09-01

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

  19. 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.

  20. Action simulation: time course and representational mechanisms

    PubMed Central

    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

  1. Simulation in pediatrics: Is it about time?

    PubMed Central

    Shetty, Rakshay; Thyagarajan, Sujatha

    2016-01-01

    Pediatrics is a challenging field where “Time is Essence” and the interplay of time-bound dynamics has a huge influence on the outcomes, particularly in an acutely ill child. In this context, simulation based training appears to play a major role in training young Paediatricians to develop critical decision making skills and learning in a risk-free environment. In present times and in future, it is expected that simulation is used by practically every healthcare provider at some or multiple points in the training and certification process. PMID:27397456

  2. Data-driven aggregative schemes for multisource estimation fusion: a road travel time application

    NASA Astrophysics Data System (ADS)

    El Faouzi, Nour-Eddin

    2004-04-01

    The principal motivation for combining estimators has been to avoid the a priori choice of which estimation method to use, by attempting to aggregate all the information which each estimation model embodies. In selecting the "best" model, one is often discarding useful independent evidence in those models which are rejected. This paper deals with estimation fusion; that is, data fusion for the purpose of estimation. More specifically, estimation fusion is studied under heterogeneous data source configurations. Two estimation fusion schemes could be considered: projective and aggregative. An unified linear model and general framework for later schemes are established. Explicit optimal fusion strategies in the sense of the best linear estimation and weighted least squares are presented. The evaluation of the effectiveness of the proposed schemes was conducted on the traffic application, namely, travel time estimation in a given path of a road network. In this problem, data comes from sensors and other sources of information geographically distributed where communication limitations and other considerations often eliminate the possibility of transmitting the observations into a central node processing where computation is performed.

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  4. System Equivalent for Real Time Digital Simulator

    NASA Astrophysics Data System (ADS)

    Lin, Xi

    2011-07-01

    The purpose of this research is to develop a method of making system equivalents for the Real Time Digital Simulator (RTDS), which should enhance its capability of simulating large power systems. The proposed equivalent combines a Frequency Dependent Network Equivalent (FDNE) for the high frequency electromagnetic transients and a Transient Stability Analysis (TSA) type simulation block for the electromechanical transients. The frequency dependent characteristic for FDNE is obtained by curve-fitting frequency domain admittance characteristics using the Vector Fitting method. An approach for approximating the frequency dependent characteristic of large power networks from readily available typical power-flow data is also introduced. A new scheme of incorporating TSA solution in RTDS is proposed. This report shows how the TSA algorithm can be adapted to a real time platform. The validity of this method is confirmed with examples, including the study of a multi in-feed HVDC system based network.

  5. LHC RF System Time-Domain Simulation

    SciTech Connect

    Mastorides, T.; Rivetta, C.; /SLAC

    2010-09-14

    Non-linear time-domain simulations have been developed for the Positron-Electron Project (PEP-II) and the Large Hadron Collider (LHC). These simulations capture the dynamic behavior of the RF station-beam interaction and are structured to reproduce the technical characteristics of the system (noise contributions, non-linear elements, and more). As such, they provide useful results and insight for the development and design of future LLRF feedback systems. They are also a valuable tool for the study of diverse longitudinal beam dynamics effects such as coupled-bunch impedance driven instabilities and single bunch longitudinal emittance growth. Results from these studies and related measurements from PEP-II and LHC have been presented in multiple places. This report presents an example of the time-domain simulation implementation for the LHC.

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

    SciTech Connect

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

    2015-12-28

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

    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.

  8. Aggregation behaviour of amphiphilic cyclodextrins: the nucleation stage by atomistic molecular dynamics simulations.

    PubMed

    Raffaini, Giuseppina; Mazzaglia, Antonino; Ganazzoli, Fabio

    2015-01-01

    Amphiphilically modified cyclodextrins may form various supramolecular aggregates. Here we report a theoretical study of the aggregation of a few amphiphilic cyclodextrins carrying hydrophobic thioalkyl groups and hydrophilic ethylene glycol moieties at opposite rims, focusing on the initial nucleation stage in an apolar solvent and in water. The study is based on atomistic molecular dynamics methods with a "bottom up" approach that can provide important information about the initial aggregates of few molecules. The focus is on the interaction pattern of amphiphilic cyclodextrin (aCD), which may interact by mutual inclusion of the substituent groups in the hydrophobic cavity of neighbouring molecules or by dispersion interactions at their lateral surface. We suggest that these aggregates can also form the nucleation stage of larger systems as well as the building blocks of micelles, vesicle, membranes, or generally nanoparticles thus opening new perspectives in the design of aggregates correlating their structures with the pharmaceutical properties. PMID:26734094

  9. Aggregation behaviour of amphiphilic cyclodextrins: the nucleation stage by atomistic molecular dynamics simulations.

    PubMed

    Raffaini, Giuseppina; Mazzaglia, Antonino; Ganazzoli, Fabio

    2015-01-01

    Amphiphilically modified cyclodextrins may form various supramolecular aggregates. Here we report a theoretical study of the aggregation of a few amphiphilic cyclodextrins carrying hydrophobic thioalkyl groups and hydrophilic ethylene glycol moieties at opposite rims, focusing on the initial nucleation stage in an apolar solvent and in water. The study is based on atomistic molecular dynamics methods with a "bottom up" approach that can provide important information about the initial aggregates of few molecules. The focus is on the interaction pattern of amphiphilic cyclodextrin (aCD), which may interact by mutual inclusion of the substituent groups in the hydrophobic cavity of neighbouring molecules or by dispersion interactions at their lateral surface. We suggest that these aggregates can also form the nucleation stage of larger systems as well as the building blocks of micelles, vesicle, membranes, or generally nanoparticles thus opening new perspectives in the design of aggregates correlating their structures with the pharmaceutical properties.

  10. Aggregation behaviour of amphiphilic cyclodextrins: the nucleation stage by atomistic molecular dynamics simulations

    PubMed Central

    Mazzaglia, Antonino; Ganazzoli, Fabio

    2015-01-01

    Summary Amphiphilically modified cyclodextrins may form various supramolecular aggregates. Here we report a theoretical study of the aggregation of a few amphiphilic cyclodextrins carrying hydrophobic thioalkyl groups and hydrophilic ethylene glycol moieties at opposite rims, focusing on the initial nucleation stage in an apolar solvent and in water. The study is based on atomistic molecular dynamics methods with a “bottom up” approach that can provide important information about the initial aggregates of few molecules. The focus is on the interaction pattern of amphiphilic cyclodextrin (aCD), which may interact by mutual inclusion of the substituent groups in the hydrophobic cavity of neighbouring molecules or by dispersion interactions at their lateral surface. We suggest that these aggregates can also form the nucleation stage of larger systems as well as the building blocks of micelles, vesicle, membranes, or generally nanoparticles thus opening new perspectives in the design of aggregates correlating their structures with the pharmaceutical properties. PMID:26734094

  11. Flutter Boundary Identification From Simulation Time Histories

    NASA Technical Reports Server (NTRS)

    Baker, Myles; Goggin, P. J.

    1997-01-01

    While there has been much recent progress in simulating nonlinear aeroelastic systems, and in predicting many of the aeroelastic phenomena of concern in transport aircraft design (i.e. transonic flutter buckets), the utility of a simulation in generating an understanding of the flutter behavior is limited. This is due in part to the high cost of generating these simulations; and the implied limitation on the number of conditions that can be analyzed, but there are also some difficulties introduced by the very nature of a simulation. Flutter engineers have traditionally worked in the frequency domain, and are accustomed to describing the flutter behavior of an airplane in terms of its V-G and V-F (or Q-G and Q-F) plots and flutter mode shapes. While the V-G and V-F plots give information about how the dynamic response of an airplane changes as the airspeed is increased, the simulation only gives information about one isolated condition (Mach, airspeed, altitude, etc.). Therefore, where a traditional flutter analysis can let the engineer determine an airspeed at which an airplane becomes unstable, while a simulation only serves as a binary check: either the airplane is fluttering at this condition, or it is not. In this document, a new technique is described in which system identification is used to easily extract modal frequencies and damping ratios from simulation time histories, and shows how the identified parameters can be used to determine the variation in frequency and dampin,o ratio as the airspeed is changed. This technique not only provides the flutter engineer with added insight into the aeroelastic behavior of the airplane, but it allows calculation of flutter mode shapes, and allows estimation of flutter boundaries while minimizing the number of simulations required.

  12. Computer simulation of bridging flocculation processes: The role of colloid to polymer concentration ratio on aggregation kinetics

    SciTech Connect

    Stoll, S.; Buffle, J.

    1996-06-25

    The flocculation of colloidal particles by adsorbing polymers is one of the central issues of colloid science and a very important topic in many industrial, biological, and environmental processes. The authors report a computer simulation study of a 2- and 3-dimensional model for bridging flocculation between large linear polymer chains and comparatively small colloidal particles, where the structure and growth kinetics of cluster formation are investigated. This model was developed within the framework of the cluster-cluster aggregation model using mass and fractal dimension dependent diffusion constants, where bridging flocculation is seen as a case of heterocoagulation in which, in addition, macromolecule configurations and lengths play an important role. The simulation of aggregate structure and formation kinetics obtained at different (1) relative particle concentrations, (2) polymer chain conformations, and (3) sticking probabilities are described from a qualitatively and quantitative point of view. The results suggest that the formation of large aggregates is a slow process, controlled by the reactivity of the clusters, even when the reaction between microcolloids and macrochains is very fast. Aggregation kinetics are strongly dependent on the particle/chain concentration ratio and on the configurational properties of the chains. It is shown that the scaling laws which are valid for homocoagulation processes are also applicable to the kinetics of bridging flocculation. The corresponding scaling exponents have been calculated.

  13. Network meta-analysis of (individual patient) time to event data alongside (aggregate) count data

    PubMed Central

    2014-01-01

    Background Network meta-analysis methods extend the standard pair-wise framework to allow simultaneous comparison of multiple interventions in a single statistical model. Despite published work on network meta-analysis mainly focussing on the synthesis of aggregate data, methods have been developed that allow the use of individual patient-level data specifically when outcomes are dichotomous or continuous. This paper focuses on the synthesis of individual patient-level and summary time to event data, motivated by a real data example looking at the effectiveness of high compression treatments on the healing of venous leg ulcers. Methods This paper introduces a novel network meta-analysis modelling approach that allows individual patient-level (time to event with censoring) and summary-level data (event count for a given follow-up time) to be synthesised jointly by assuming an underlying, common, distribution of time to healing. Alternative model assumptions were tested within the motivating example. Model fit and adequacy measures were used to compare and select models. Results Due to the availability of individual patient-level data in our example we were able to use a Weibull distribution to describe time to healing; otherwise, we would have been limited to specifying a uniparametric distribution. Absolute effectiveness estimates were more sensitive than relative effectiveness estimates to a range of alternative specifications for the model. Conclusions The synthesis of time to event data considering individual patient-level data provides modelling flexibility, and can be particularly important when absolute effectiveness estimates, and not just relative effect estimates, are of interest. PMID:25209121

  14. Aggregation in environmental systems: catchment mean transit times and young water fractions under hydrologic nonstationarity

    NASA Astrophysics Data System (ADS)

    Kirchner, J. W.

    2015-03-01

    Methods for estimating mean transit times from chemical or isotopic tracers (such as Cl-, δ18O, or δ2H) commonly assume that catchments are stationary (i.e. time-invariant) and homogeneous. Real catchments are neither. In a companion paper, I showed that catchment mean transit times estimated from seasonal tracer cycles are highly vulnerable to aggregation error, exhibiting strong bias and large scatter in spatially heterogeneous catchments. I proposed a different measure of transit times, the young water fraction, and showed that it is virtually immune to aggregation error under spatial heterogeneity. Here I extend this analysis by exploring how nonstationarity affects mean transit times and young water fractions estimated from seasonal tracer cycles, using benchmark tests based on a simple two-box model. The model exhibits complex nonstationary behavior, with striking volatility in tracer concentrations, young water fractions, and mean transit times, driven by rapid shifts in the mixing ratios of fluxes from the upper and lower boxes. The transit-time distribution in streamflow becomes increasingly skewed at higher discharges, with marked increases in the young water fraction and decreases in the mean water age, reflecting the increased dominance of the upper box at higher flows. Even this simple two-box model exhibits strong equifinality; hydrograph calibration cannot constrain four of its five parameters. This equifinality problem can be partly resolved by simple parameter transformations. However, transit times are primarily determined by residual storage, which cannot be constrained through hydrograph calibration and must instead be estimated by tracer behavior. Seasonal tracer cycles in the two-box model are very poor predictors of mean transit times, with typical errors of several hundred percent. However, the same tracer cycles predict young water fractions within a few percent, even in model catchments that are both nonstationary and spatially

  15. Aggregation of nanoscale iron oxyhydroxides and corresponding effects on metal uptake, retention, and speciation: II. Temperature and time

    NASA Astrophysics Data System (ADS)

    Stegemeier, J. P.; Reinsch, B. C.; Lentini, C. J.; Dale, J. G.; Kim, C. S.

    2015-01-01

    The aggregation and growth of nanosized particles can greatly impact their capacity to sorb and retain dissolved metals, thus affecting metal fate and transport in contaminated systems. Aqueous suspensions of synthesized nanoscale iron oxyhydroxides were exposed to dissolved Zn(II) or Cu(II) and aged at room temperature (∼20 °C), 50 °C, and 75 °C for timeframes ranging from 0 to 96 h before sorbed metal ions were desorbed by lowering the suspension pH. Atomic absorption spectroscopic analysis of supernatants both before and after the desorption step determined how temperature and time affect macroscopic metal uptake and retention capacities. Extended X-ray absorption fine structure (EXAFS) spectroscopy analysis described the local binding environment of the sorbed/retained metals on the solid phase. With increasing aging temperature and time, the initial ∼5-nm oblong nanoparticles formed dense aggregates, lost reactive surface area, and retained progressively larger fractions of the initially-introduced Zn(II) and Cu(II) following the desorption step, with the copper species inhibiting the oriented aggregation of the nanoparticles into nanorods. Based on EXAFS analysis, the speciation of the sorbed metal species evolves with increasing time and temperature from surface-sorbed metal ions, which readily desorb and return to solution, to more strongly-bound, structurally-incorporated metal ions. These retained metals appear to associate intimately with the nanoparticle aggregates by substituting for iron in the nanoparticle lattice or by binding within nanoparticle aggregate pore spaces.

  16. A Novel Component Carrier Configuration and Switching Scheme for Real-Time Traffic in a Cognitive-Radio-Based Spectrum Aggregation System.

    PubMed

    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

  17. A Novel Component Carrier Configuration and Switching Scheme for Real-Time Traffic in a Cognitive-Radio-Based Spectrum Aggregation System

    PubMed Central

    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

  18. A Novel Component Carrier Configuration and Switching Scheme for Real-Time Traffic in a Cognitive-Radio-Based Spectrum Aggregation System.

    PubMed

    Fu, Yunhai; Ma, Lin; Xu, Yubin

    2015-09-17

    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.

  19. Real Time Simulation of Power Grid Disruptions

    SciTech Connect

    Chinthavali, Supriya; Dimitrovski, Aleksandar D; Fernandez, Steven J; Groer, Christopher S; Nutaro, James J; Olama, Mohammed M; Omitaomu, Olufemi A; Shankar, Mallikarjun; Spafford, Kyle L; Vacaliuc, Bogdan

    2012-11-01

    DOE-OE and DOE-SC workshops (Reference 1-3) identified the key power grid problem that requires insight addressable by the next generation of exascale computing is coupling of real-time data streams (1-2 TB per hour) as the streams are ingested to dynamic models. These models would then identify predicted disruptions in time (2-4 seconds) to trigger the smart grid s self healing functions. This project attempted to establish the feasibility of this approach and defined the scientific issues, and demonstrated example solutions to important smart grid simulation problems. These objectives were accomplished by 1) using the existing frequency recorders on the national grid to establish a representative and scalable real-time data stream; 2) invoking ORNL signature identification algorithms; 3) modeling dynamically a representative region of the Eastern interconnect using an institutional cluster, measuring the scalability and computational benchmarks for a national capability; and 4) constructing a prototype simulation for the system s concept of smart grid deployment. The delivered ORNL enduring capability included: 1) data processing and simulation metrics to design a national capability justifying exascale applications; 2) Software and intellectual property built around the example solutions; 3) demonstrated dynamic models to design few second self-healing.

  20. Effects of hydroxylated carbon nanotubes on the aggregation of Aβ16-22 peptides: a combined simulation and experimental study.

    PubMed

    Xie, Luogang; Lin, Dongdong; Luo, Yin; Li, Huiyu; Yang, Xinju; Wei, Guanghong

    2014-10-21

    The pathogenesis of Alzheimer's disease (AD) is associated with the aggregation of amyloid-β (Aβ) peptides into toxic aggregates with ?-sheet character. In a previous computational study, we showed that pristine single-walled carbon nanotubes (SWCNTs) can inhibit the formation of β-sheet-rich oligomers in the central hydrophobic core fragment of Aβ (Aβ16-22). However, the poor solubility of SWCNTs in water hinders their use in biomedical applications and nanomedicine. Here, we investigate the influence of hydroxylated SWCNT, a water-soluble SWCNT derivative, on the aggregation of Aβ16-22 peptides using all-atom explicit-water replica exchange molecular dynamics simulations. Our results show that hydroxylated SWCNTs can significantly inhibit β-sheet formation and shift the conformations of Aβ16-22 oligomers from ordered β-sheet-rich structures toward disordered coil aggregates. Detailed analyses of the SWCNT-Aβ interaction reveal that the inhibition of β-sheet formation by hydroxylated SWCNTs mainly results from strong electrostatic interactions between the hydroxyl groups of SWCNTs and the positively charged residue K16 of Aβ16-22 and hydrophobic and aromatic stacking interactions between SWCNTs and F19 and F20. In addition, our atomic force microscopy and thioflavin T fluorescence experiments confirm the inhibitory effect of both pristine and hydroxylated SWCNTs on Aβ16-22 fibrillization, in support of our previous and present replica exchange molecular dynamics simulation results. These results demonstrate that hydroxylated SWCNTs efficiently inhibit the aggregation of Aβ16-22; in addition, they offer molecular insight into the inhibition mechanism, thus providing new clues for the design of therapeutic drugs against amyloidosis.

  1. Time-Domain Simulation of RF Couplers

    SciTech Connect

    Smithe, David; Carlsson, Johan; Austin, Travis

    2009-11-26

    We have developed a finite-difference time-domain (FDTD) fluid-like approach to integrated plasma-and-coupler simulation [1], and show how it can be used to model LH and ICRF couplers in the MST and larger tokamaks.[2] This approach permits very accurate 3-D representation of coupler geometry, and easily includes non-axi-symmetry in vessel wall, magnetic equilibrium, and plasma density. The plasma is integrated with the FDTD Maxwell solver in an implicit solve that steps over electron time-scales, and permits tenuous plasma in the coupler itself, without any need to distinguish or interface between different regions of vacuum and/or plasma. The FDTD algorithm is also generalized to incorporate a time-domain sheath potential [3] on metal structures within the simulation, to look for situations where the sheath potential might generate local sputtering opportunities. Benchmarking of the time-domain sheath algorithm has been reported in the references. Finally, the time-domain software [4] permits the use of particles, either as field diagnostic (test particles) or to self-consistently compute plasma current from the applied RF power.

  2. Flow-induced aggregation of colloidal particles in viscoelastic fluids

    NASA Astrophysics Data System (ADS)

    Xie, Donglin; Qiao, Greg G.; Dunstan, Dave E.

    2016-08-01

    The flow-induced aggregation of dilute colloidal polystyrene nanoparticles suspended in Newtonian and viscoelastic solutions is reported. A rheo-optical method has been used to detect real-time aggregation processes via measuring optical absorption or scattering in a quartz Couette cell. The observed absorbance decreases over time are attributed to the flow-induced coagulation. Numerical simulations show that the aggregation processes still follow the Smoluchowski coagulation equation in a revised version. Suspensions in a series of media are studied to evaluate the effect of the media rheological properties on the particle aggregation. The data shows that elasticity reduces the aggregation while the solution viscosity enhances the aggregation processes.

  3. Residential Real-time Price Response Simulation

    SciTech Connect

    Widergren, Steven E.; Subbarao, Krishnappa; Chassin, David P.; Fuller, Jason C.; Pratt, Robert G.

    2011-10-10

    The electric industry is gaining experience with innovative price responsive demand pilots and limited roll-outs to customers. One of these pilots is investigating real-time pricing signals to engage end-use systems and local distributed generation and storage in a distributed optimization process. Attractive aspects about the approach include strong scalability characteristics, simplified interfaces between automation devices, and the adaptability to integrate a wide variety of devices and systems. Experience in this nascent field is revealing a rich array of for engineering decisions and the application of complexity theory. To test the decisions, computer simulations are used to reveal insights about design, demand elasticity, and the limits of response (including consumer fatigue). Agent-based approaches lend themselves well in the simulation to modeling the participation and interaction of each piece of equipment on a distribution feeder. This paper discusses rate design and simulation experiences at the distribution feeder level where consumers and their HVAC systems and water heaters on a feeder receive real-time pricing signals.

  4. Automated Data Aggregation for Time-Series Analysis: Study Case on Anaesthesia Data Warehouse.

    PubMed

    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.

  5. Automated Data Aggregation for Time-Series Analysis: Study Case on Anaesthesia Data Warehouse.

    PubMed

    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. PMID:27071886

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  7. A computer simulation study on self- and cross-aggregation of multiple polar species in supercritical carbon dioxide.

    PubMed

    Xu, Wenhao; Yang, Jichu

    2010-04-29

    The effect of hydrogen-bond cooperativity on self- and cross-aggregation of multiple polar species in supercritical carbon dioxide was investigated using both ab initio calculations and Monte Carlo simulations. Ab initio calculations indicate that hydrogen-bond cooperativity has a significant impact on the cluster size, but does not greatly influence the composition of clusters. The microscopic structures in the ethanol + CO(2) and acetic acid + CO(2) binary mixtures were first studied using Monte Carlo simulations with a strict set of criteria for hydrogen bonding, and a satisfactory agreement with experimental data was achieved. The state of microscopic phase separation in the ethanol + water + CO(2) and acetic acid + water + CO(2) ternary mixtures was then extensively investigated, indicating that the size and composition of aggregates are strongly dependent on the mixing ratio. Moreover, hydrogen-bond cooperativity must be considered to acquire more thorough understanding of the hydration process. On the basis of the detailed distributions of aggregate size and structure, a new two-staged hydration mechanism was finally proposed for the ternary solutions.

  8. Effects of black carbon on aggregate stability, runoff generation, splash erosion and slopewash of a clay loam under simulated rainfall

    NASA Astrophysics Data System (ADS)

    Aston, Steve; Doerr, Stefan; Street-Perrott, Alayne

    2013-04-01

    Black (pyrogenic) carbon (BC) was produced from native hardwoods pyrolysed in a ring kiln at ~400° C and ground and sieved to < 2 mm. The BC was then added to a clay loam (sieved to 3.35 mm remaining. After 200 days of incubation, the remainder of each sample was air-dried and sieved to < 5 mm. Each sample was then placed in a square plot and subjected to 40 minutes of simulated rainfall. Runoff and subsurface drainage were measured at 2 minute intervals and runoff was collected at 5 minute intervals to enable subsequent determination of sediment concentrations, sediment yields and erosion rates of soil and BC. Splash cups were placed on each side of the plot to allow measurement of overall splash detachment for each simulation. A BC content of 5g kg-1 did not affect the mean aggregate stability of the clay loam, but a content of 25 g kg-1 led to a decrease in mean aggregate stability of >40%, with a further significant reduction observed when the BC content was 50 g kg-1. There were no statistically significant changes in aggregate stability between 50, 100 and 150 days of incubation for any of the application rates. Results showing the effects of BC on runoff generation, splash erosion and slopewash will also be presented.

  9. The inhibitory mechanism of a fullerene derivative against amyloid-β peptide aggregation: an atomistic simulation study.

    PubMed

    Sun, Yunxiang; Qian, Zhenyu; Wei, Guanghong

    2016-05-14

    Alzheimer's disease (AD) is associated with the pathological self-assembly of amyloid-β (Aβ) peptides into β-sheet enriched fibrillar aggregates. Aβ dimers formed in the initial step of Aβ aggregation were reported to be the smallest toxic species. Inhibiting the formation of β-sheet-rich oligomers and fibrils is considered as the primary therapeutic strategy for AD. Previous studies reported that fullerene derivatives strongly inhibit Aβ fibrillation. However, the underlying inhibitory mechanism remains elusive. As a first step to understand fullerene-modulated full-length Aβ aggregation, we investigated the conformational ensemble of the Aβ1-42 dimer with and without 1,2-(dimethoxymethano)fullerene (DMF) - a more water-soluble fullerene derivative - by performing a 340 ns explicit-solvent replica exchange molecular dynamics simulation. Our simulations show that although disordered states are the most abundant conformations of the Aβ1-42 dimer, conformations containing diverse extended β-hairpins are also populated. The first most-populated β-hairpins involving residues L17-D23 and A30-V36 strongly resemble the engineered β-hairpin which is a building block of toxic Aβ oligomers. We find that the interaction of DMFs with Aβ peptides greatly impedes the formation of such β-hairpins and inter-peptide β-sheets. Binding energy analyses demonstrate that DMF preferentially binds not only to the central hydrophobic motif LVFFA of the Aβ peptide as suggested experimentally, but also to the aromatic residues including F4 and Y10 and the C-terminal hydrophobic region I31-V40. This study reveals a complete picture of the inhibitory mechanism of full-length Aβ1-42 aggregation by fullerenes, providing theoretical insights into the development of drug candidates against AD.

  10. Real-time virtual room acoustic simulation

    NASA Astrophysics Data System (ADS)

    Carneal, James P.; Johnson, Jan; Johnson, Troge; Johnson, Marty

    2003-10-01

    A realistic virtual room acoustic simulation has been implemented on a PC-based computer in near real-time. Room acoustics are calculated by the image source method using realistic absorption coefficients for a variety of realistic surfaces and programmed in MATLAB. The resulting impulse response filters are then applied in near real-time using fast convolution DSP techniques using data being read from a CD-ROM. The system was implemented in a virtual acoustic room facility. Optimizations have been performed to retain the realistic virtual room effect while minimizing computations through limited psycho-acoustic testing. In general, realistic anechoic to reverberant virtual rooms have been re-created with six 8192 coefficient filters. To provide realistic simulations, special care must be taken to accurately reproduce the low frequency acoustics. Since the virtual room acoustic facility was not totally anechoic (as are most anechoic chambers), inverse filters were applied to compensate for over-amplified acoustics at frequencies below 350 Hz.

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

    NASA Astrophysics Data System (ADS)

    Zaliapin, I.; Kovchegov, Y.

    2012-12-01

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

  12. A MD Simulation and Analysis for Aggregation Behaviors of Nanoscale Zero-Valent Iron Particles in Water via MS

    PubMed Central

    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

  13. A Simulated Intermediate State for Folding and Aggregation Provides Insights into ΔN6 β2-Microglobulin Amyloidogenic Behavior

    PubMed Central

    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

  14. Voids in cosmological simulations over cosmic time

    NASA Astrophysics Data System (ADS)

    Wojtak, Radosław; Powell, Devon; Abel, Tom

    2016-06-01

    We study evolution of voids in cosmological simulations using a new method for tracing voids over cosmic time. The method is based on tracking watershed basins (contiguous regions around density minima) of well-developed voids at low redshift, on a regular grid of density field. It enables us to construct a robust and continuous mapping between voids at different redshifts, from initial conditions to the present time. We discuss how the new approach eliminates strong spurious effects of numerical origin when voids' evolution is traced by matching voids between successive snapshots (by analogy to halo merger trees). We apply the new method to a cosmological simulation of a standard Λ-cold-dark-matter cosmological model and study evolution of basic properties of typical voids (with effective radii 6 h-1 Mpc < Rv < 20 h-1 Mpc at redshift z = 0) such as volumes, shapes, matter density distributions and relative alignments. The final voids at low redshifts appear to retain a significant part of the configuration acquired in initial conditions. Shapes of voids evolve in a collective way which barely modifies the overall distribution of the axial ratios. The evolution appears to have a weak impact on mutual alignments of voids implying that the present state is in large part set up by the primordial density field. We present evolution of dark matter density profiles computed on isodensity surfaces which comply with the actual shapes of voids. Unlike spherical density profiles, this approach enables us to demonstrate development of theoretically predicted bucket-like shape of the final density profiles indicating a wide flat core and a sharp transition to high-density void walls.

  15. Time-Dependent Simulations of Turbopump Flows

    NASA Technical Reports Server (NTRS)

    Kris, Cetin C.; Kwak, Dochan

    2001-01-01

    The objective of the current effort is to provide a computational framework for design and analysis of the entire fuel supply system of a liquid rocket engine, including high-fidelity unsteady turbopump flow analysis. This capability is needed to support the design of pump sub-systems for advanced space transportation vehicles that are likely to involve liquid propulsion systems. To date, computational tools for design/analysis of turbopump flows are based on relatively lower fidelity methods. An unsteady, three-dimensional viscous flow analysis tool involving stationary and rotational components for the entire turbopump assembly has not been available for real-world engineering applications. The present effort will provide developers with information such as transient flow phenomena at start up, impact of non-uniform inflows, system vibration and impact on the structure. In the proposed paper, the progress toward the capability of complete simulation of the turbo-pump for a liquid rocket engine is reported. The Space Shuttle Main Engine (SSME) turbo-pump is used as a test case for evaluation of the hybrid MPI/Open-MP and MLP versions of the INS3D code. The relative motion of the grid systems for the rotor-stator interaction was obtained using overset grid techniques. Time-accuracy of the scheme has been evaluated with simple test cases. Unsteady computations for the SSME turbo-pump, which contains 114 zones with 34.5 million grid points, are carried out on Origin 2000 systems at NASA Ames Research Center. Results from these time-accurate simulations with moving boundary capability will be presented along with the performance of parallel versions of the code.

  16. Real-Time Demonstration of Optimized Spectrum Usage with LSA Carrier Aggregation

    NASA Astrophysics Data System (ADS)

    Wirth, Thomas; Wieruch, Dennis; Holfeld, Bernd; Mehlhose, Matthias; Pilz, Jens; Haustein, Thomas; Halfmann, Rüdiger; Friederichs, Karl-Josef

    2016-07-01

    Mobile broadband networks will face a tremendous growth in data traffic demand over the next 20 years. A key requirement for the evolution of radio access networks is the increase in the amount of spectrum and optimized spectrum usage, in order to meet future service demands. More efficient spectrum use will come with evolving technology features and novel spectrum sharing models. Candidates for technology improvements are higher order and massive MIMO systems, cooperative base stations and CoMP techniques, highly optimized resource allocation algorithms, network densification with inter-cell interference management and highly flexible carrier aggregation techniques to extend spectrum. In this paper, we will highlight carrier aggregation combined with flexible spectrum assignment and use of spectrum databases following novel licensing schemes. We give an overview of LSA activities, present a 3CA demonstration platform enabling the LSA concept and discuss its implementation constraints.

  17. Thermodynamics of Protein Aggregation

    NASA Astrophysics Data System (ADS)

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

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

  18. Ultrabright organic dots with aggregation-induced emission characteristics for real-time two-photon intravital vasculature imaging.

    PubMed

    Ding, Dan; Goh, Chi Ching; Feng, Guangxue; Zhao, Zujin; Liu, Jie; Liu, Rongrong; Tomczak, Nikodem; Geng, Junlong; Tang, Ben Zhong; Ng, Lai Guan; Liu, Bin

    2013-11-13

    Ultrabright organic dots with aggregation-induced emission characteristics (AIE dots) are prepared and shown to exhibit a high quantum yield, a, large two-photon absorption cross-section, and low in vivo toxicity. Real-time two-photon intravital blood vascular imaging in various tissues substantiates that the AIE dots are effective probes for in vivo vasculature imaging in a deep and high-contrast manner.

  19. Aggregation in environmental systems: seasonal tracer cycles quantify young water fractions, but not mean transit times, in spatially heterogeneous catchments

    NASA Astrophysics Data System (ADS)

    Kirchner, J. W.

    2015-03-01

    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

  20. Impact of high hydrostatic pressure processing on individual cellular resuscitation times and protein aggregates in Escherichia coli.

    PubMed

    Govers, Sander K; Aertsen, Abram

    2015-11-20

    Live cell biology approaches can contribute to a more comprehensive understanding of heterogeneous injury and resuscitation phenomena in stressed populations of foodborne pathogens and spoilage microorganisms, and in turn lead to better insights in the mechanisms and dynamics of inactivation that can improve food safety and preservation measures. Especially in the context of designing minimal processing strategies, which depend on a synergistic combination of different mild stresses to ensure sufficient microbial reduction, a more profound understanding of the impact of each such stress or hurdle is mandatory. High hydrostatic pressure (HHP) stress is an interesting hurdle in this concept since cells that manage to survive this stress nevertheless tend to be injured and sensitized to subsequent stresses. In this study, populations of Escherichia coli were subjected to different HHP intensities and studied at the single-cell level with time-lapse fluorescence microscopy while monitoring resuscitation times and protein aggregate integrity at the single-cell level. This approach revealed that higher pressure intensities lead to longer and more variable resuscitation times of surviving cells as well as an increased dispersal of intracellular protein aggregates. Interestingly, at mild HHP exposure, cells within the population incurring less dispersion of protein aggregates appeared to have a higher probability of survival.

  1. Aggregation Processes on Networks: Deterministic Equations, Stochastic Model and Numerical Simulation

    SciTech Connect

    Guias, Flavius

    2008-09-01

    We introduce an infinite system of equations modeling the time evolution of the growth process of a network. The nodes are characterized by their degree k(set-membership sign)N and a fitness parameter f(set-membership sign)[0,h]. Every new node which emerges becomes a fitness f' according to a given distribution P and attaches to an existing node with fitness f and degree k at rate fA{sub k}, where A{sub k} are positive coefficients, growing sub-linearly in k. If the parameter f takes only one value, the dynamics of this process can be described by a variant of the Becker-Doering equations, where the l growth of the size of clusters of size k occurs only with increment 1. In contrast l to the established Becker-Doering equations, the system considered here is nonconservative, since mass (i.e. links) is continuously added. Nevertheless, it has the property of linearity, which is a natural consequence of the process which is being modeled. The purpose of this paper is to construct a solution of the system based on a stochastic approximation algorithm, which allows also a numerical simulation in order to get insight into its qualitative behaviour. In particular we show analytically and numerically the property of Bose-Einstein condensation, which was observed in the literature on random graphs and which can be described as an emergence of a huge cluster which captures a macroscopic fraction of the total link density.

  2. Simulations to save time, money, and lives

    SciTech Connect

    Sackett, D.E.

    1996-11-01

    The Laboratory`s Conflict Simulation Laboratory (CSL) has been developing computerized programs to simulate combat and other conflicts since 1974. All branches of the military use these systems for training purposes and to prepare for operations as diverse as the 1989 invasion of Panama and peacekeeping in Somalia. The CSL is presently continuing development of the Joint Tactical Simulation (JTS) and recently began work on the Joint Conflict and Tactical Simulation (JCATS) program for the Joint Chiefs of Staff. The Army is still using the CSL`s first model, Janus.

  3. 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.

  4. Molecular simulations of conformation change and aggregation of HIV-1 Vpr13-33 on graphene oxide

    PubMed Central

    Zeng, Songwei; Zhou, Guoquan; Guo, Jianzhong; Zhou, Feng; Chen, Junlang

    2016-01-01

    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. PMID:27097898

  5. Blood-brain barrier transport studies, aggregation, and molecular dynamics simulation of multiwalled carbon nanotube functionalized with fluorescein isothiocyanate.

    PubMed

    Shityakov, Sergey; Salvador, Ellaine; Pastorin, Giorgia; Förster, Carola

    2015-01-01

    In this study, the ability of a multiwalled carbon nanotube functionalized with fluorescein isothiocyanate (MWCNT-FITC) was assessed as a prospective central nervous system-targeting drug delivery system to permeate the blood-brain barrier. The results indicated that the MWCNT-FITC conjugate is able to penetrate microvascular cerebral endothelial monolayers; its concentrations in the Transwell(®) system were fully equilibrated after 48 hours. Cell viability test, together with phase-contrast and fluorescence microscopies, did not detect any signs of MWCNT-FITC toxicity on the cerebral endothelial cells. These microscopic techniques also revealed presumably the intracellular localization of fluorescent MWCNT-FITCs apart from their massive nonfluorescent accumulation on the cellular surface due to nanotube lipophilic properties. In addition, the 1,000 ps molecular dynamics simulation in vacuo discovered the phenomenon of carbon nanotube aggregation driven by van der Waals forces via MWCNT-FITC rapid dissociation as an intermediate phase.

  6. Blood–brain barrier transport studies, aggregation, and molecular dynamics simulation of multiwalled carbon nanotube functionalized with fluorescein isothiocyanate

    PubMed Central

    Shityakov, Sergey; Salvador, Ellaine; Pastorin, Giorgia; Förster, Carola

    2015-01-01

    In this study, the ability of a multiwalled carbon nanotube functionalized with fluorescein isothiocyanate (MWCNT–FITC) was assessed as a prospective central nervous system-targeting drug delivery system to permeate the blood–brain barrier. The results indicated that the MWCNT–FITC conjugate is able to penetrate microvascular cerebral endothelial monolayers; its concentrations in the Transwell® system were fully equilibrated after 48 hours. Cell viability test, together with phase-contrast and fluorescence microscopies, did not detect any signs of MWCNT–FITC toxicity on the cerebral endothelial cells. These microscopic techniques also revealed presumably the intracellular localization of fluorescent MWCNT–FITCs apart from their massive nonfluorescent accumulation on the cellular surface due to nanotube lipophilic properties. In addition, the 1,000 ps molecular dynamics simulation in vacuo discovered the phenomenon of carbon nanotube aggregation driven by van der Waals forces via MWCNT–FITC rapid dissociation as an intermediate phase. PMID:25784800

  7. Real time simulation using position sensing

    NASA Technical Reports Server (NTRS)

    Studor, George F. (Inventor); Womack, Robert W. (Inventor); Hilferty, Michael F. (Inventor); Isbell, William B. (Inventor); Taylor, Jason A. (Inventor); Bacon, Bruce R. (Inventor)

    2000-01-01

    An interactive exercise system including exercise equipment having a resistance system, a speed sensor, a controller that varies the resistance setting of the exercise equipment, and a playback device for playing pre-recorded video and audio. The controller, operating in conjunction with speed information from the speed sensor and terrain information from media table files, dynamically varies the resistance setting of the exercise equipment in order to simulate varying degrees of difficulty while the playback device concurrently plays back the video and audio to create the simulation that the user is exercising in a natural setting such as a real-world exercise course.

  8. Molecular dynamics simulation of rupture in glassy polymer bridges within filler aggregates

    NASA Astrophysics Data System (ADS)

    Froltsov, Vladimir A.; Klüppel, Manfred; Raos, Guido

    2012-10-01

    We present a series of nonequilibrium molecular dynamics simulations, investigating the rupture mechanisms in glassy polymer films confined between two solid surfaces. Such systems provide a useful model for the strong nonlinear reinforcement of rubber by colloidal filler particles. Depending on the degree of confinement three qualitatively different rupture modes have been found, which originate from the interplay of internal (polymer-polymer) and external (polymer-wall) interactions. In very thin films we observe the formation and stretching of many single-chain bridges between the confining surfaces. Progressing to thicker samples we observe fewer bridges, consisting of bundled polymer chains, and eventually just one large bridge in thick specimens. The yield stress and the elongational modulus of the polymer films have been calculated from the stress-strain curves at various temperatures and confinements and their behavior has been analyzed in terms of polymer-polymer and polymer-surface interaction energies. The thinnest films (5 monomer diameters) are always glassy in our simulations, while the others display a glass transition temperature around 0.50-0.55 (in units ɛ0/kB of the Lennard-Jones interaction energy), depending on their thickness. This range of values, which has been determined using both the nonequilibrium tensile simulations and equilibrium diffusion data, agrees with the transition temperature previously found by shear simulations [Baljon and Robbins, ScienceSCIEAS0036-807510.1126/science.271.5248.482 271, 482 (1996)].

  9. Molecular dynamics simulation of rupture in glassy polymer bridges within filler aggregates.

    PubMed

    Froltsov, Vladimir A; Klüppel, Manfred; Raos, Guido

    2012-10-01

    We present a series of nonequilibrium molecular dynamics simulations, investigating the rupture mechanisms in glassy polymer films confined between two solid surfaces. Such systems provide a useful model for the strong nonlinear reinforcement of rubber by colloidal filler particles. Depending on the degree of confinement three qualitatively different rupture modes have been found, which originate from the interplay of internal (polymer-polymer) and external (polymer-wall) interactions. In very thin films we observe the formation and stretching of many single-chain bridges between the confining surfaces. Progressing to thicker samples we observe fewer bridges, consisting of bundled polymer chains, and eventually just one large bridge in thick specimens. The yield stress and the elongational modulus of the polymer films have been calculated from the stress-strain curves at various temperatures and confinements and their behavior has been analyzed in terms of polymer-polymer and polymer-surface interaction energies. The thinnest films (5 monomer diameters) are always glassy in our simulations, while the others display a glass transition temperature around 0.50-0.55 (in units ε(0)/k(B) of the Lennard-Jones interaction energy), depending on their thickness. This range of values, which has been determined using both the nonequilibrium tensile simulations and equilibrium diffusion data, agrees with the transition temperature previously found by shear simulations [Baljon and Robbins, Science 271, 482 (1996)]. PMID:23214604

  10. Water adsorption around oxalic acid aggregates: a molecular dynamics simulation of water nucleation on organic aerosols.

    PubMed

    Darvas, Maria; Picaud, Sylvain; Jedlovszky, Pál

    2011-11-28

    The phase behaviour of binary oxalic acid-water mixtures has been investigated by means of computer simulation techniques. Such mixtures play an important role in atmospheric processes, since the hydrogen bonding ability of oxalic acid molecules allows them to form aerosol particles. Water can in turn be readily adsorbed on the surface of such aerosol particles, which results in the formation of small ice grains. These grains are thus considered to be acting as cloud condensation nuclei, giving rise to the formation of ice clouds.

  11. The role of Metals in Amyloid Aggregation: A Test Case for ab initio Simulations

    SciTech Connect

    Minicozzi, V.; Rossi, G. C.; Stellato, F.; Morante, S.

    2007-12-26

    First principle ab initio molecular dynamics simulations of the Car-Parrinello type have proved to be of invaluable help in understanding the microscopic mechanisms of chemical bonding both in solid state physics and in structural biophysics. In this work we present as test cases the study of the Cu coordination mode in two especially important examples: Prion protein and {beta}-amyloids. Using medium size PC-clusters as well as larger parallel platforms, we are able to deal with systems comprising 300 to 500 atoms and 1000 to 1500 electrons for as long as 2-3 ps. We present structural results which confirm indications coming from NMR and XAS data.

  12. 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

    2016-06-01

    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.

  13. Time Dependent Simulation of Turbopump Flows

    NASA Technical Reports Server (NTRS)

    Kiris, Cetin C.; Kwak, Dochan; Chan, William; Williams, Robert

    2001-01-01

    The objective of this viewgraph presentation is to enhance incompressible flow simulation capability for developing aerospace vehicle components, especially unsteady flow phenomena associated with high speed turbo pumps. Unsteady Space Shuttle Main Engine (SSME)-rig1 1 1/2 rotations are completed for the 34.3 million grid points model. The moving boundary capability is obtained by using the DCF module. MLP shared memory parallelism has been implemented and benchmarked in INS3D. The scripting capability from CAD geometry to solution is developed. Data compression is applied to reduce data size in post processing and fluid/structure coupling is initiated.

  14. Time-Dependent Simulations of Turbopump Flows

    NASA Technical Reports Server (NTRS)

    Kiris, Cetin; Kwak, Dochan; Chan, William; Williams, Robert

    2002-01-01

    Unsteady flow simulations for RLV (Reusable Launch Vehicles) 2nd Generation baseline turbopump for one and half impeller rotations have been completed by using a 34.3 Million grid points model. MLP (Multi-Level Parallelism) shared memory parallelism has been implemented in INS3D, and benchmarked. Code optimization for cash based platforms will be completed by the end of September 2001. Moving boundary capability is obtained by using DCF module. Scripting capability from CAD (computer aided design) geometry to solution has been developed. Data compression is applied to reduce data size in post processing. Fluid/Structure coupling has been initiated.

  15. Dissipative particle dynamics simulations of deformation and aggregation of healthy and diseased red blood cells in a tube flow

    SciTech Connect

    Ye, Ting; Phan-Thien, Nhan Khoo, Boo Cheong; Lim, Chwee Teck

    2014-11-15

    In this paper, we report simulation results assessing the deformation and aggregation of mixed healthy and malaria-infected red blood cells (RBCs) in a tube flow. A three dimensional particle model based on Dissipative Particle Dynamics (DPD) is developed to predict the tube flow containing interacting cells. The cells are also modelled by DPD, with a Morse potential to characterize the cell-cell interaction. As validation tests, a single RBC in a tube flow and two RBCs in a static flow are simulated to examine the cell deformation and intercellular interaction, respectively. The study of two cells, one healthy and the other malaria-infected RBCs in a tube flow demonstrates that the malaria-infected RBC (in the leading position along flow direction) has different effects on the healthy RBC (in the trailing position) at the different stage of parasite development or at the different capillary number. With parasitic development, the malaria-infected RBC gradually loses its deformability, and in turn the corresponding trailing healthy RBC also deforms less due to the intercellular interaction. With increasing capillary number, both the healthy and malaria-infected RBCs are likely to undergo an axisymmetric motion. The minimum intercellular distance becomes small enough so that rouleaux is easily formed, i.e., the healthy and malaria-infected RBCs are difficultly disaggregated.

  16. Hardware for a real-time multiprocessor simulator

    NASA Technical Reports Server (NTRS)

    Blech, R. A.; Arpasi, D. J.

    1984-01-01

    The hardware for a real time multiprocessor simulator (RTMPS) developed at the NASA Lewis Research Center is described. The RTMPS is a multiple microprocessor system used to investigate the application of parallel processing concepts to real time simulation. It is designed to provide flexible data exchange paths between processors by using off the shelf microcomputer boards and minimal customized interfacing. A dedicated operator interface allows easy setup of the simulator and quick interpreting of simulation data. Simulations for the RTMPS are coded in a NASA designed real time multiprocessor language (RTMPL). This language is high level and geared to the multiprocessor environment. A real time multiprocessor operating system (RTMPOS) has also been developed that provides a user friendly operator interface. The RTMPS and supporting software are currently operational and are being evaluated at Lewis. The results of this evaluation will be used to specify the design of an optimized parallel processing system for real time simulation of dynamic systems.

  17. Simulation of Ground Winds Time Series

    NASA Technical Reports Server (NTRS)

    Adelfang, S. I.

    2008-01-01

    A simulation process has been developed for generation of the longitudinal and lateral components of ground wind atmospheric turbulence as a function of mean wind speed, elevation, temporal frequency range and distance between locations. The distance between locations influences the spectral coherence between the simulated series at adjacent locations. Short distances reduce correlation only at high frequencies; as distances increase correlation is reduced over a wider range of frequencies. The choice of values for the constants d1 and d3 in the PSD model is the subject of work in progress. An improved knowledge of the values for zO as a function of wind direction at the ARES-1 launch pads is necessary for definition of d1. Results of other studies at other locations may be helpful as summarized in Fichtl's recent correspondence. Ideally, further research is needed based on measurements of ground wind turbulence with high resolution anemometers at a number of altitudes at a new KSC tower located closer to the ARES-1 launch pad .The proposed research would be based on turbulence measurements that may be influenced by surface terrain roughness that may be significantly different from roughness prior to 1970 in Fichtl's measurements. Significant improvements in instrumentation, data storage end processing will greatly enhance the capability to model ground wind profiles and ground wind turbulence.

  18. Object orientated simulation on transputer arrays using time warp

    NASA Astrophysics Data System (ADS)

    Simpson, P.

    1989-12-01

    The successful application of transputers to distributed event driven heterogeneous simulation using the time warp methodology is demonstrated with transputers and occam providing a natural vehicle for this class of simulation. The simulation technique basically comprises a number of communicating simulation object processes, with appropriate action being taken to ensure the correct chronological sequence of processed simulation events. Time warp is particularly attractive, since it permits all parts of a distributed processor network to operate in parallel (although some of the computation may later be undone). The need for hardware control of memory management has not been identified, although the requirement for a deadlock free, random point to point communications strategy has.

  19. Meta-Analysis of a Continuous Outcome Combining Individual Patient Data and Aggregate Data: A Method Based on Simulated Individual Patient Data

    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…

  20. Amyloid peptide Aβ40 inhibits aggregation of Aβ42: Evidence from molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Viet, Man Hoang; Li, Mai Suan

    2012-06-01

    Effects of amyloid beta (Aβ) peptide Aβ40 on secondary structures of Aβ42 are studied by all-atom simulations using the GROMOS96 43a1 force field with explicit water. It is shown that in the presence of Aβ40 the beta-content of monomer Aβ42 is reduced. Since the fibril-prone conformation N* of full-length Aβ peptides has the shape of beta strand-loop-beta strand this result suggests that Aβ40 decreases the probability of observing N* of Aβ42 in monomer state. Based on this and the hypothesis that the higher is the population of N* the higher fibril formation rates, one can expect that, in agreement with the recent experiment, Aβ40 inhibit fibril formation of Aβ42. It is shown that the presence of Aβ40 makes the salt bridge D23-K28 and fragment 18-33 of Aβ42 more flexible providing additional support for this experimental fact. Our estimation of the binding free energy by the molecular mechanics-Poisson-Boltzmann surface area method reveals the inhibition mechanism that Aβ40 binds to Aβ42 modifying its morphology.

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

    NASA Astrophysics Data System (ADS)

    Minton, Allen

    2014-08-01

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

  2. Development Cycle Time Simulation for Civil Aircraft

    NASA Technical Reports Server (NTRS)

    Spitz, William; Berardino, Frank; Golaszewski, Richard; Johnson, Jesse

    2001-01-01

    Cycle Time Reduction (CTR) will be one of the major factors affecting the future of the civil aerospace industry. This focus is the end reflection of the level of competition in the commercial large carrier aircraft industry. Aircraft manufacturer must minimize costs and pass a portion of those savings onto buyers. CTR is one strategy used to move the manufacturing firm down the cost curve. The current NASA Airframe Development Cycle Time Reduction Goal is 50% by year 2022. This goal is not achievable based on the program analysis done by the LMI/GRA team. This may mean that the current roster of NASA CTR programs needs to be reexamined or that the program technology progress factors, as determined by the NASA experts, were understated. Programs that duplicate the reductions of others should be replaced with non-duplicative programs. In addition, new programs targeting a specific part of the cycle can be developed.

  3. Combatting Ionic Aggregation using Dielectric Forces Combining Modeling/Simulation and Experimental Results to Explain End-capping of Primary Amine Functionalized Polystyrene

    SciTech Connect

    Messman, Jamie M; Goswami, Monojoy; Pickel, Deanna L; Uhrig, David; Sumpter, Bobby G; Mays, Jimmy

    2011-01-01

    Chain-end functionalization of living poly(styryl)lithium using 1-(3-bromopropyl)-2,2,5,5-tetramethyl-1-aza-2,5-disilacyclo-pentane (BTDP) to generate primary amine end-functionalized polystyrene was investigated using high vacuum anionic polymerization techniques. 13C NMR spectroscopy and Matrix Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) were used to evaluate polymer end-groups and demonstrated that quantitative amine functionalized polymer was attained under appropriate reaction conditions. In general, the polymerization of styrene was conducted in benzene and the end-capping reaction was performed by adding tetrahydrofuran (THF) to the reaction prior to the addition of BTDP in THF at room temperature. Results indicated that approximately 20% THF by volume is required to obtain 100% end-capping free from side reactions. When too little or no THF was present, side reactions such as lithium halogen exchange followed by Wurtz coupling resulted in unfunctionalized head-to-head dimer as well as other byproducts. Modeling and simulation of the solvent effects using hybrid methods (the so-called QM/MM method) suggest that THF effectively dissociated the anionic chain-end aggregation, thereby resulting in the desired primary amine functionalized polymer. Molecular dynamics (MD) simulations were conducted to develop an understanding of the physics of counterions involved in the end-functionalization process.

  4. 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.

  5. 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.

  6. Space logistics simulation: Launch-on-time

    NASA Technical Reports Server (NTRS)

    Nii, Kendall M.

    1990-01-01

    During 1989-1990 the Center for Space Construction developed the Launch-On-Time (L-O-T) Model to help asses and improve the likelihood of successfully supporting space construction requiring multi-logistic delivery flights. The model chose a reference by which the L-O-T probability and improvements to L-O-T probability can be judged. The measure of improvement was chosen as the percent reduction in E(S(sub N)), the total expected amount of unscheduled 'hold' time. We have also previously developed an approach to determining the reduction in E(S(sub N)) by reducing some of the causes of unscheduled holds and increasing the speed at which the problems causing the holds may be 'fixed.' We provided a mathematical (binary linear programming) model for measuring the percent reduction in E(S(sub N)) given such improvements. In this presentation we shall exercise the model which was developed and draw some conclusions about the following: methods used, data available and needed, and make suggestions for areas of improvement in 'real world' application of the model.

  7. Transport of commercial endosulfan through a column of aggregated vineyard soil by a water flux simulating field conditions.

    PubMed

    López-Blanco, M Carmen; Cancho-Grande, Beatriz; Simal-Gándara, Jesús; López-Periago, Eugenio; Arias-Estévez, Manuel

    2005-08-24

    Endosulfan is a potentially harmful, degradation resistant pesticide that is found in soils where it has been used. Despite being hydrophobic and having high affinity for soil matrix components, it has also been found in groundwater. To investigate this behavior, we studied the passage of a commercial emulsified formulation through a column of aggregated vineyard soil under simulated light rain. Breakthrough data were obtained using gas chromatography with electron capture detection to determine the concentration of endosulfan in samples extracted from the column periodically at several depths. These data, and analogous data obtained previously for the passage of bromide, were analyzed using the program CXTFIT v.2. Analysis of the bromide data strongly suggested the existence of preferential flow paths in the column. The endosulfan data were adequately accounted for by a model in which the preferential flow and nonpreferential flow regions are almost isolated from each other. These regions differ also as regards both the partition of endosulfan between soil and soil solution and the rate at which reversibly adsorbed endosulfan is transformed into irreversibly adsorbed endosulfan. The "irreversibility" sink term accounts also for biological and chemical degradation of endosulfan. The findings imply that soil humidity favors the transport of commercial endosulfan by the formation and maintenance of preferential flow paths in soil, controlling both the presence of endosulfan in groundwater and its high persistence in soil.

  8. 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.

  9. Time Domain Partitioning of Electricity Production Cost Simulations

    SciTech Connect

    Barrows, C.; Hummon, M.; Jones, W.; Hale, E.

    2014-01-01

    Production cost models are often used for planning by simulating power system operations over long time horizons. The simulation of a day-ahead energy market can take several weeks to compute. Tractability improvements are often made through model simplifications, such as: reductions in transmission modeling detail, relaxation of commitment variable integrality, reductions in cost modeling detail, etc. One common simplification is to partition the simulation horizon so that weekly or monthly horizons can be simulated in parallel. However, horizon partitions are often executed with overlap periods of arbitrary and sometimes zero length. We calculate the time domain persistence of historical unit commitment decisions to inform time domain partitioning of production cost models. The results are implemented using PLEXOS production cost modeling software in an HPC environment to improve the computation time of simulations while maintaining solution integrity.

  10. 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.

  11. Simulations on time-of-flight ERDA spectrometer performance

    NASA Astrophysics Data System (ADS)

    Julin, Jaakko; Arstila, Kai; Sajavaara, Timo

    2016-08-01

    The performance of a time-of-flight spectrometer consisting of two timing detectors and an ionization chamber energy detector has been studied using Monte Carlo simulations for the recoil creation and ion transport in the sample and detectors. The ionization chamber pulses have been calculated using Shockley-Ramo theorem and the pulse processing of a digitizing data acquisition setup has been modeled. Complete time-of-flight-energy histograms were simulated under realistic experimental conditions. The simulations were used to study instrumentation related effects in coincidence timing and position sensitivity, such as background in time-of-flight-energy histograms. Corresponding measurements were made and simulated results are compared with data collected using the digitizing setup.

  12. Simulations on time-of-flight ERDA spectrometer performance.

    PubMed

    Julin, Jaakko; Arstila, Kai; Sajavaara, Timo

    2016-08-01

    The performance of a time-of-flight spectrometer consisting of two timing detectors and an ionization chamber energy detector has been studied using Monte Carlo simulations for the recoil creation and ion transport in the sample and detectors. The ionization chamber pulses have been calculated using Shockley-Ramo theorem and the pulse processing of a digitizing data acquisition setup has been modeled. Complete time-of-flight-energy histograms were simulated under realistic experimental conditions. The simulations were used to study instrumentation related effects in coincidence timing and position sensitivity, such as background in time-of-flight-energy histograms. Corresponding measurements were made and simulated results are compared with data collected using the digitizing setup. PMID:27587115

  13. Mechanisms of large Stokes shift and aggregation-enhanced emission of osmapentalyne cations in solution: combined MD simulations and QM/MM calculations.

    PubMed

    Sun, Guang-Xu; Ju, Ming-Gang; Zang, Hang; Zhao, Yi; Liang, WanZhen

    2015-10-01

    Osmapentalyne cations synthesized recently show remarkable optical properties, such as near-infrared emission, unusual large Stokes shift and aggregation-enhanced emission. Here, the mechanisms behind those novel optical behaviors are revealed from the combined molecular dynamics simulations and hybrid quantum mechanics/molecular mechanics calculations. The results demonstrate that the large Stokes shift in the gas phase comes from a photoexcitation-induced deformation of the osmium plane, whereas in solution it corresponds to the variation of osmium ring symmetry. Although the central chromophore ring dominates the absorption and emission processes, the protecting groups PPh3 join the emission. As osmapentalyne cations are aggregated together in solution, the radical distribution functions of their mass-central distances display several peaks immersed in a broad envelope due to different aggregation pathways. However, the chromophore centers are protected by the PPh3 groups, the aggregation structures do not affect the Stokes shift too much, and the calculated aggregate-enhanced emission is consistent with experimental measurements. PMID:26339695

  14. Real-time complex cognitive surgical simulator with testing.

    PubMed

    Oliker, Aaron; Cutting, Court B

    2009-01-01

    One of the greatest challenges facing surgical education is the inability to effectively test a surgeon's cognitive knowledge of a complex open surgery procedure. Cognitive knowledge is tested by paper, and more recently, computer-based and oral exams. Although these tools are used for testing in surgical education, they have been limited by providing a two-dimensional static representation of complex and dynamic, three-dimensional procedures.A three-dimensional interactive surgical simulator that will engage the surgeon, ask questions, test competency and provide feedback has the potential to revolutionize surgical education. Internet connectivity allows for rapid deployment of surgical modules, networked testing formats, data aggregation, comparative analysis and guided tutorials. Combined with the approval of a surgical society, this platform has the potential to set measurable quantitative surgical standards.

  15. Line-of-sight determination in real-time simulations

    NASA Technical Reports Server (NTRS)

    Kull, Frederick G., Jr.; Fought, Donald E.

    1993-01-01

    This paper describes the selection of a method for determining line-of-sight in real-time simulations for the NASA Ames Vertical Motion Simulator (VMS) facility. Five different combinations of terrain representation and line-of-sight determination algorithms were tested. A gridpost terrain format, in conjunction with a Digital Differential Analyzer algorithm, was found to best meet the simulation criteria of high speed, low storage requirements, and accuracy.

  16. 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.

  17. 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.

  18. Time-reversed, flow-reversed ballistics simulations

    SciTech Connect

    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.

  19. Noise Simulation of Continuous-Time {sigma}{delta} Modulators

    SciTech Connect

    Arias, J.; Quintanilla, L.; Bisbal, D.; San Pablo, J.; Enriquez, L.; Vicente, J.; Barbolla, J.

    2005-08-25

    In this work, an approach for the simulation of the effect of noise sources in the performance of continuous-time {delta}{sigma} modulators is presented. Electrical noise including thermal noise, 1/f noise and clock jitter are included in a simulation program and their impact on the system performance is analyzed.

  20. Scales and processes in the aggregation of diatom blooms: high time resolution and wide size range records in a mesocosm study

    NASA Astrophysics Data System (ADS)

    Prieto, L.; Ruiz, J.; Echevarría, F.; García, C. M.; Bartual, A.; Gálvez, J. A.; Corzo, A.; Macías, D.

    2002-07-01

    Diatoms and the large, fast-sinking aggregates they form during blooms play an important role in downward flux of particles in the ocean. To study how the aggregation process operates on particle dynamics, diatom blooms were generated and followed under controlled conditions in nutrient-enriched laboratory mesocosm where a homogeneous mixed surface layer was emulated. The size spectrum of particles (from 12 μm to several mm) was recorded each hour during the 1 month span of the experiment by a non-intrusive image analysis system with two CCD cameras. Beam attenuation was continuously recorded as an additional estimator for particle abundance. The high time resolution and wide size range of the records obtained with this design were able to resolve the time scale for coagulation as well as to determine the lowest time resolution needed to sample any experiment aimed to study aggregation of diatoms. Our results narrow previous theoretical time scales to the order of hours to days for the process of mass transfer from small particles to marine snow. Also, daily analyses of a broad range of biological and chemical variables permitted to link phytoplankton succession to the aggregation process. Finally, the evaluated role of different copious exopolymers suggested a lower implication of Coomassie stained particles (CSP) than transparent exopolymeric particles (TEP) in the formation of marine aggregates.

  1. Aggregation in environmental systems - Part 2: Catchment mean transit times and young water fractions under hydrologic nonstationarity

    NASA Astrophysics Data System (ADS)

    Kirchner, J. W.

    2016-01-01

    Methods for estimating mean transit times from chemical or isotopic tracers (such as Cl-, δ18O, or δ2H) commonly assume that catchments are stationary (i.e., time-invariant) and homogeneous. Real catchments are neither. In a companion paper, I showed that catchment mean transit times estimated from seasonal tracer cycles are highly vulnerable to aggregation error, exhibiting strong bias and large scatter in spatially heterogeneous catchments. I proposed the young water fraction, which is virtually immune to aggregation error under spatial heterogeneity, as a better measure of transit times. Here I extend this analysis by exploring how nonstationarity affects mean transit times and young water fractions estimated from seasonal tracer cycles, using benchmark tests based on a simple two-box model. The model exhibits complex nonstationary behavior, with striking volatility in tracer concentrations, young water fractions, and mean transit times, driven by rapid shifts in the mixing ratios of fluxes from the upper and lower boxes. The transit-time distribution in streamflow becomes increasingly skewed at higher discharges, with marked increases in the young water fraction and decreases in the mean water age, reflecting the increased dominance of the upper box at higher flows. This simple two-box model exhibits strong equifinality, which can be partly resolved by simple parameter transformations. However, transit times are primarily determined by residual storage, which cannot be constrained through hydrograph calibration and must instead be estimated by tracer behavior. Seasonal tracer cycles in the two-box model are very poor predictors of mean transit times, with typical errors of several hundred percent. However, the same tracer cycles predict time-averaged young water fractions (Fyw) within a few percent, even in model catchments that are both nonstationary and spatially heterogeneous (although they may be biased by roughly 0.1-0.2 at sites where strong

  2. Virtual time and time warp on the JPL hypercube. [operating system implementation for distributed simulation

    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.

  3. 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.

  4. Simulation of Time-Reversal Processing for Electromagnetic Communication

    SciTech Connect

    Burke, G J; Poggio, A J

    2003-07-25

    Time-reversal processing was simulated for several possible electromagnetic communication channels, including random point scatterers, large plates and a conducting cavity. Communication was from a single transmitting antenna to a receiving array. The effectiveness of time-reversal processing was compared for a single receiver and the array. The aim of these simulations was to determine a communication environment that would give an interesting level of multipath interference and that can be constructed in a laboratory.

  5. Real time simulator with Ti floating point digital signal processor

    SciTech Connect

    Razazian, K.; Bobis, J.P.; Dieckman, S.L.; Raptis, A.C.

    1994-08-01

    This paper describes the design and operation of a Real Time Simulator using Texas Instruments TMS320C30 digital signal processor. This system operates with two banks of memory which provide the input data to digital signal processor chip. This feature enables the TMS320C30 to be utilized in variety of applications for which external connections to acquire input data is not needed. In addition, some practical applications of this Real Time Simulator are discussed.

  6. A Real-Time Telemetry Simulator of the IUS Spacecraft

    NASA Technical Reports Server (NTRS)

    Drews, Michael E.; Forman, Douglas A.; Baker, Damon M.; Khazoyan, Louis B.; Viazzo, Danilo

    1998-01-01

    A real-time telemetry simulator of the IUS spacecraft has recently entered operation to train Flight Control Teams for the launch of the AXAF telescope from the Shuttle. The simulator has proven to be a successful higher fidelity implementation of its predecessor, while affirming the rapid development methodology used in its design. Although composed of COTS hardware and software, the system simulates the full breadth of the mission: Launch, Pre-Deployment-Checkout, Burn Sequence, and AXAF/IUS separation. Realism is increased through patching the system into the operations facility to simulate IUS telemetry, Shuttle telemetry, and the Tracking Station link (commands and status message).

  7. Parallel-in-time molecular-dynamics simulations.

    PubMed

    Baffico, L; Bernard, S; Maday, Y; Turinici, G; Zérah, G

    2002-11-01

    While there have been many progress in the field of multiscale simulations in the space domain, in particular, due to efficient parallelization techniques, much less is known in the way to perform similar approaches in the time domain. In this paper we show on two examples that, provided we can describe in a rough but still accurate way the system under consideration, it is indeed possible to parallelize molecular dynamics simulations in time by using the recently introduced pararealalgorithm. The technique is most useful for ab initio simulations. PMID:12513644

  8. Parallel-in-time molecular-dynamics simulations

    NASA Astrophysics Data System (ADS)

    Baffico, L.; Bernard, S.; Maday, Y.; Turinici, G.; Zérah, G.

    2002-11-01

    While there have been many progress in the field of multiscale simulations in the space domain, in particular, due to efficient parallelization techniques, much less is known in the way to perform similar approaches in the time domain. In this paper we show on two examples that, provided we can describe in a rough but still accurate way the system under consideration, it is indeed possible to parallelize molecular dynamics simulations in time by using the recently introduced pararealalgorithm. The technique is most useful for ab initio simulations.

  9. Iterative Schemes for Time Parallelization with Application to Reservoir Simulation

    SciTech Connect

    Garrido, I; Fladmark, G E; Espedal, M S; Lee, B

    2005-04-18

    Parallel methods are usually not applied to the time domain because of the inherit sequentialness of time evolution. But for many evolutionary problems, computer simulation can benefit substantially from time parallelization methods. In this paper, they present several such algorithms that actually exploit the sequential nature of time evolution through a predictor-corrector procedure. This sequentialness ensures convergence of a parallel predictor-corrector scheme within a fixed number of iterations. The performance of these novel algorithms, which are derived from the classical alternating Schwarz method, are illustrated through several numerical examples using the reservoir simulator Athena.

  10. Aggregation and spatial analysis of walking activity in an urban area: results from the Halifax space-time activity survey

    NASA Astrophysics Data System (ADS)

    Neatt, K.; Millward, H.; Spinney, J.

    2016-04-01

    This study examines neighborhood characteristics affecting the incidence of walking trips in urban and suburban areas of Halifax, Canada. We employ data from the Space-Time Activity Research (STAR) survey, conducted in 2007-8. Primary respondents completed a two- day time-diary survey, and their movements were tracked using a GPS data logger. Primary respondents logged a total of 5,005 walking trips, specified by 781,205 individual GPS points. Redundant and erroneous points, such as those with zero or excessive speed, were removed. Data points were then imported into ArcGIS, converted from points to linear features, visually inspected for data quality, and cleaned appropriately. From mapped walking tracks we developed hypotheses regarding variations in walking density. To test these, walking distances were aggregated by census tracts (CTs), and expressed as walking densities (per resident, per metre of road, and per developed area). We employed multivariate regression to examine which neighborhood (CT) variables are most useful as estimators of walking densities. Contrary to much of the planning literature, built-environment measures of road connectivity and dwelling density were found to have little estimating power. Office and institutional land uses are more useful estimators, as are the income and age characteristics of the resident population.

  11. 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.

  12. Simulating a small turboshaft engine in real-time multiprocessor simulator (RTMPS) environment

    NASA Technical Reports Server (NTRS)

    Milner, E. J.; Arpasi, D. J.

    1986-01-01

    A Real-Time Multiprocessor Simulator (RTMPS) has been developed at NASA Lewis Research Center. The RTMPS uses parallel microprocessors to achieve computing speeds needed for real-time engine simulation. This report describes the use of the RTMPS system to simulate a small turboshaft engine. The process of programming the engine equations and distributing them over one, two, and four processors is discussed. Steady-state and transient results from the RTMPS simulation are compared with results from a main-frame-based simulation. Processor execution times and the associated execution time savings for the two and four processor cases are presented using actual data obtained from the RTMPS system. Included is a discussion of why the minimum achievable calculation time for the turboshaft engine model was attained using four processors. Finally, future enhancements to the RTMPS system are discussed including the development of a generalized partitioning algorithm to automatically distribute the system equations among the processors in optimum fashion.

  13. Flow-induced aggregation of colloidal particles in viscoelastic fluids.

    PubMed

    Xie, Donglin; Qiao, Greg G; Dunstan, Dave E

    2016-08-01

    The flow-induced aggregation of dilute colloidal polystyrene nanoparticles suspended in Newtonian and viscoelastic solutions is reported. A rheo-optical method has been used to detect real-time aggregation processes via measuring optical absorption or scattering in a quartz Couette cell. The observed absorbance decreases over time are attributed to the flow-induced coagulation. Numerical simulations show that the aggregation processes still follow the Smoluchowski coagulation equation in a revised version. Suspensions in a series of media are studied to evaluate the effect of the media rheological properties on the particle aggregation. The data shows that elasticity reduces the aggregation while the solution viscosity enhances the aggregation processes. PMID:27627363

  14. Laboratory Drop Towers for the Experimental Simulation of Dust-aggregate Collisions in the Early Solar System

    PubMed Central

    Blum, Jürgen; Beitz, Eike; Bukhari, Mohtashim; Gundlach, Bastian; Hagemann, Jan-Hendrik; Heißelmann, Daniel; Kothe, Stefan; Schräpler, Rainer; von Borstel, Ingo; Weidling, René

    2014-01-01

    For the purpose of investigating the evolution of dust aggregates in the early Solar System, we developed two vacuum drop towers in which fragile dust aggregates with sizes up to ~10 cm and porosities up to 70% can be collided. One of the drop towers is primarily used for very low impact speeds down to below 0.01 m/sec and makes use of a double release mechanism. Collisions are recorded in stereo-view by two high-speed cameras, which fall along the glass vacuum tube in the center-of-mass frame of the two dust aggregates. The other free-fall tower makes use of an electromagnetic accelerator that is capable of gently accelerating dust aggregates to up to 5 m/sec. In combination with the release of another dust aggregate to free fall, collision speeds up to ~10 m/sec can be achieved. Here, two fixed high-speed cameras record the collision events. In both drop towers, the dust aggregates are in free fall during the collision so that they are weightless and match the conditions in the early Solar System. PMID:24962693

  15. Laboratory drop towers for the experimental simulation of dust-aggregate collisions in the early solar system.

    PubMed

    Blum, Jürgen; Beitz, Eike; Bukhari, Mohtashim; Gundlach, Bastian; Hagemann, Jan-Hendrik; Heißelmann, Daniel; Kothe, Stefan; Schräpler, Rainer; von Borstel, Ingo; Weidling, René

    2014-06-05

    For the purpose of investigating the evolution of dust aggregates in the early Solar System, we developed two vacuum drop towers in which fragile dust aggregates with sizes up to ~10 cm and porosities up to 70% can be collided. One of the drop towers is primarily used for very low impact speeds down to below 0.01 m/sec and makes use of a double release mechanism. Collisions are recorded in stereo-view by two high-speed cameras, which fall along the glass vacuum tube in the center-of-mass frame of the two dust aggregates. The other free-fall tower makes use of an electromagnetic accelerator that is capable of gently accelerating dust aggregates to up to 5 m/sec. In combination with the release of another dust aggregate to free fall, collision speeds up to ~10 m/sec can be achieved. Here, two fixed high-speed cameras record the collision events. In both drop towers, the dust aggregates are in free fall during the collision so that they are weightless and match the conditions in the early Solar System.

  16. Laboratory Drop Towers for the Experimental Simulation of Dust-aggregate Collisions in the Early Solar System

    NASA Astrophysics Data System (ADS)

    Blum, Jürgen; Beitz, Eike; Bukhari, Mohtashim; Gundlach, Bastian; Hagemann, Jan-Hendrik; Heißelmann, Daniel; Kothe, Stefan; Schräpler, Rainer; von Borstel, Ingo; Weidling, René

    2014-06-01

    For the purpose of investigating the evolution of dust aggregates in the early Solar System, we developed two vacuum drop towers in which fragile dust aggregates with sizes up to ~10 cm and porosities up to 70% can be collided. One of the drop towers is primarily used for very low impact speeds down to below 0.01 m/sec and makes use of a double release mechanism. Collisions are recorded in stereo-view by two high-speed cameras, which fall along the glass vacuum tube in the center-of-mass frame of the two dust aggregates. The other free-fall tower makes use of an electromagnetic accelerator that is capable of gently accelerating dust aggregates to up to 5 m/sec. In combination with the release of another dust aggregate to free fall, collision speeds up to ~10 m/sec can be achieved. Here, two fixed high-speed cameras record the collision events. In both drop towers, the dust aggregates are in free fall during the collision so that they are weightless and match the conditions in the early Solar System.

  17. 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.

  18. Time-distance helioseismology of two realistic sunspot simulations

    SciTech Connect

    DeGrave, K.; Jackiewicz, J.; Rempel, M. E-mail: jasonj@nmsu.edu

    2014-10-10

    Linear time-distance helioseismic inversions are carried out using several filtering schemes to determine vector flow velocities within two ∼100{sup 2} Mm{sup 2} × 20 Mm realistic magnetohydrodynamic sunspot simulations of 25 hr. One simulation domain contains a model of a full sunspot (i.e., one with both an umbra and penumbra), while the other contains a pore (i.e., a spot without a penumbra). The goal is to test current helioseismic methods using these state-of-the-art simulations of magnetic structures. We find that horizontal flow correlations between inversion and simulation flow maps are reasonably high (∼0.5-0.8) in the upper 3 Mm at distances exceeding 25-30 Mm from spot center, but are substantially lower at smaller distances and larger depths. Inversions of forward-modeled travel times consistently outperform those of our measured travel times in terms of horizontal flow correlations, suggesting that our inability to recover flow structure near these active regions is largely due to the fact that we are unable to accurately measure travel times near strong magnetic features. In many cases the velocity amplitudes from the inversions underestimate those of the simulations by up to 50%, possibly indicating nonlinearity of the forward problem. In every case, we find that our inversions are unable to recover the vertical flow structure of the simulations at any depth.

  19. Reference Genes Selection for Quantitative Real-Time PCR Using RankAggreg Method in Different Tissues of Capra hircus

    PubMed Central

    Najafpanah, Mohammad Javad; Sadeghi, Mostafa; Bakhtiarizadeh, Mohammad Reza

    2013-01-01

    Identification of reference genes with stable levels of gene expression is an important prerequisite for obtaining reliable results in analysis of gene expression data using quantitative real time PCR (RT-qPCR). Since the underlying assumption of reference genes is that expressed at the exact same level in all sample types, in this study, we evaluated the expression stability of nine most commonly used endogenous controls (GAPDH, ACTB, 18S rRNA, RPS18, HSP-90, ALAS, HMBS, ACAC, and B2M) in four different tissues of the domestic goat, Capra hircus, including liver, visceral, subcutaneous fat and longissimus muscles, across different experimental treatments (a standard diet prepared using the NRC computer software as control and the same diet plus one mg chromium/day). We used six different software programs for ranking of reference genes and found that individual rankings of the genes differed among them. Additionally, there was a significant difference in ranking patterns of the studied genes among different tissues. A rank aggregation method was applied to combine the ranking lists of the six programs to a consensus ranking. Our results revealed that HSP-90 was nearly always among the two most stable genes in all studied tissues. Therefore, it is recommended for accurate normalization of RT-qPCR data in goats, while GAPDH, ACTB, and RPS18 showed the most varied expressions and should be avoided as reference genes. PMID:24358246

  20. Estimating the Attack Ratio of Dengue Epidemics under Time-varying Force of Infection using Aggregated Notification Data

    NASA Astrophysics Data System (ADS)

    Coelho, Flavio Codeço; Carvalho, Luiz Max De

    2015-12-01

    Quantifying the attack ratio of disease is key to epidemiological inference and public health planning. For multi-serotype pathogens, however, different levels of serotype-specific immunity make it difficult to assess the population at risk. In this paper we propose a Bayesian method for estimation of the attack ratio of an epidemic and the initial fraction of susceptibles using aggregated incidence data. We derive the probability distribution of the effective reproductive number, Rt, and use MCMC to obtain posterior distributions of the parameters of a single-strain SIR transmission model with time-varying force of infection. Our method is showcased in a data set consisting of 18 years of dengue incidence in the city of Rio de Janeiro, Brazil. We demonstrate that it is possible to learn about the initial fraction of susceptibles and the attack ratio even in the absence of serotype specific data. On the other hand, the information provided by this approach is limited, stressing the need for detailed serological surveys to characterise the distribution of serotype-specific immunity in the population.

  1. Interaction Dynamics in Inhibiting the Aggregation of Aβ Peptides by SWCNTs: A Combined Experimental and Coarse-Grained Molecular Dynamic Simulation Study.

    PubMed

    Lin, Dongdong; Qi, Ruxi; Li, Shujie; He, Ruoyu; Li, Pei; Wei, Guanghong; Yang, Xinju

    2016-09-21

    The aggregation of amyloid-β peptides (Aβ) is considered as the main possible cause of Alzheimer's disease (AD). How to suppress the formation of toxic Aβ aggregates has been an intensive concern over the past several decades. Increasing evidence shows that whether carbon nanomaterials can suppress or promote the aggregation depends on their physicochemical properties. However, their interaction dynamics remains elusive as amyloid fibrillation is a complex multistep process. In this paper, we utilized atomic force microscopy (AFM), electrostatic force microscopy (EFM), ThT/fluorescence spectroscopy, and cell viability measurements, combined with coarse-grained molecular dynamic (MD) simulations to study the dynamic interaction of full length Aβ with single-walled carbon nanotubes (SWCNT). At the single SWCNTs scale, it is found that the presence of SWCNTs would result in rapid and spontaneous adsorption of Aβ1-40 peptides on their surface and stacking into nonfibrillar aggregates with reduced toxicity, which plays an important role in inhibiting the formation of toxic oligomers and mature fibrils. Our results provide new clues for studying the interaction in amyloid/SWCNTs system as well as for seeking amyloidosis inhibitors with carbon nanomaterials. PMID:27441457

  2. A hybrid deformable model for real-time surgical simulation.

    PubMed

    Zhu, Bo; Gu, Lixu

    2012-07-01

    Modeling organ deformation in real remains a challenge in virtual minimally invasive (MIS) surgery simulation. In this paper, we propose a new hybrid deformable model to simulate deformable organs in the real-time surgical training system. Our hybrid model uses boundary element method (BEM) to compute global deformation based on a coarse surface mesh and uses a mass-spring model to simulate the dynamic behaviors of soft tissue interacting with surgical instruments. The simulation result is coupled with a high-resolution rendering mesh through a particle surface interpolation algorithm. Accurate visual and haptic feedbacks are provided in real time and temporal behaviors of biological soft tissues including viscosity and creeping are modeled as well. We prove our model to be suitable to work in complex virtual surgical environment by integrating it into a MIS training system. The hybrid model is evaluated with respect to efficiency, accuracy and robustness by a series of experiments. PMID:22483053

  3. Modelling of HVDC converters for real-time transient simulators

    NASA Astrophysics Data System (ADS)

    Acevedo, Salvador

    This thesis presents developments in the computer modelling of High Voltage Direct Current (HVDC) converters and other FACTS devices for EMTP-type simulators. The high number and frequency of switching operations in power electronic converters cause numerical difficulties that require additional computational effort. The additional computational burden requires the development of techniques that can accelerate the simulation speeds of conventional electromagnetic transient modelling and may allow real-time simulations. The main results are two models that effectively reduce the computational time required to obtain the solution of an electrical network containing HVDC converters. Both approaches have in common the principle of subdividing an electrical circuit containing a 6n-valve converter into at least n subsystems. For each 6-valve subsystem, the 64 matrix combinations are precalculated and prestored in computer memory. The interaction between subsystems to obtain the network solution is particular to each approach. With this criterion, the number of precalculated combinations for a 24-valve HVDC substation is reduced from more than 16 million to only 256. Both models present a considerable reduction in the computational time required to simulate circuits containing HVDC converters. The most efficient model has been successfully implemented in the real time power systems simulator under development by the power research group at the University of British Columbia. The exact calculation of the network solution at switching events is another important aspect required to accurately simulate power electronic converters in power systems. The thesis proposes the zero crossing detection algorithm, which eliminates the erroneous delays present in traditional EMTP simulators. The proposed algorithm resynchronizes the solution to the original simulation time increment. To solve the problem originated by the forced commutation of Gate Turn Off Thyristors, an exploratory

  4. 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.

  5. 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.

  6. Multiple time-scale methods in particle simulations of plasmas

    SciTech Connect

    Cohen, B.I.

    1985-02-14

    This paper surveys recent advances in the application of multiple time-scale methods to particle simulation of collective phenomena in plasmas. These methods dramatically improve the efficiency of simulating low-frequency kinetic behavior by allowing the use of a large timestep, while retaining accuracy. The numerical schemes surveyed provide selective damping of unwanted high-frequency waves and preserve numerical stability in a variety of physics models: electrostatic, magneto-inductive, Darwin and fully electromagnetic. The paper reviews hybrid simulation models, the implicitmoment-equation method, the direct implicit method, orbit averaging, and subcycling.

  7. Proposal for an inhibitor of Alzheimer's disease blocking aggregation of amyloid-β peptides: ab initio molecular simulations

    NASA Astrophysics Data System (ADS)

    Okamoto, A.; Nomura, K.; Yano, A.; Higai, S.; Kondo, T.; Kamba, S.; Kurita, N.

    2013-04-01

    Aggregation of amyloid-β (Aβ) peptides is believed to play a key role in the mechanism of molecular pathogenesis of Alzheimer's disease (AD). To inhibit the aggregation and prevent AD, numerous compounds have been synthesized. A previous experimental study elucidated that a triazine derivative AA3E2 has anti-amyloidogenic ability, while a triazine derivative AA3D2 having a different substituent has no inhibitory effect. However, the reason for this remarkable difference in the ability cannot be explained by the chemical structures of these derivatives. In the present study, we present stable structures of the solvated complexes with Aβ and AA3E2/AA3D2 obtained by classical molecular mechanics method. The specific interactions between Aβ and AA3E2/AA3D2 in the complexes are investigated by ab initio fragment molecular orbital calculations. Based on the results obtained, we attempt to propose new potent inhibitors for the Aβ aggregation.

  8. Simulation of Invertebrate Aggregation Shows the Importance of Stable Personality over Diversity in Consensus Decision-Making

    PubMed Central

    2016-01-01

    Aggregation of many species of invertebrate is an example of a consensus decision, the success of which is central to survival. Personality is a stable form of behavioural diversity which has been observed in the aggregation process, but neither the reasons for its stability nor its effects on consensus decisions are well understood. By using an agent-based model of invertebrate aggregation, it is found that diverse personalities have only limited benefits to the experimental consensus decision-making process, but may have a more valuable role in natural settings. Importantly, although certain personalities may ostensibly have potential drawbacks at the individual level, such as choosing to rest in unfavourable places, all individuals are likely to benefit from maintaining a constant personality, which promotes group stability. These findings help to improve understanding of consensus decision-making and the prevalence of stable personality. PMID:27755591

  9. Toward real-time regional earthquake simulation II: Real-time Online earthquake Simulation (ROS) of Taiwan earthquakes

    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.

  10. 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.

  11. 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.

  12. 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.

  13. Nonlinear time-dependent simulation of helix traveling wave tubes

    NASA Astrophysics Data System (ADS)

    Peng, Wei-Feng; Yang, Zhong-Hai; Hu, Yu-Lu; Li, Jian-Qing; Lu, Qi-Ru; Li, Bin

    2011-07-01

    A one-dimensional nonlinear time-dependent theory for helix traveling wave tubes is studied. A generalized electromagnetic field is applied to the expression of the radio frequency field. To simulate the variations of the high frequency structure, such as the pitch taper and the effect of harmonics, the spatial average over a wavelength is substituted by a time average over a wave period in the equation of the radio frequency field. Under this assumption, the space charge field of the electron beam can be treated by a space charge wave model along with the space charge coefficient. The effects of the radio frequency and the space charge fields on the electrons are presented by the equations of the electron energy and the electron phase. The time-dependent simulation is compared with the frequency-domain simulation for a helix TWT, which validates the availability of this theory.

  14. 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.

  15. ARTEMIS: Ares Real Time Environments for Modeling, Integration, and Simulation

    NASA Technical Reports Server (NTRS)

    Hughes, Ryan; Walker, David

    2009-01-01

    This slide presentation reviews the use of ARTEMIS in the development and testing of the ARES launch vehicles. Ares Real Time Environment for Modeling, Simulation and Integration (ARTEMIS) is the real time simulation supporting Ares I hardware-in-the-loop (HWIL) testing. ARTEMIS accurately models all Ares/Orion/Ground subsystems which interact with Ares avionics components from pre-launch through orbit insertion The ARTEMIS System integration Lab, and the STIF architecture is reviewed. The functional components of ARTEMIS are outlined. An overview of the models and a block diagram is presented.

  16. Aggregation and network formation in self-assembly of protein (H3.1) by a coarse-grained Monte Carlo simulation.

    PubMed

    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.

  17. Aggregation and network formation in self-assembly of protein (H3.1) by a coarse-grained Monte Carlo simulation

    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.

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

    SciTech Connect

    Gharagozloo, Patricia E.; Goodson, Kenneth E.

    2010-05-01

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

  19. The Effect of Different Mixing Methods on Working Time, Setting Time, Dimensional Changes and Film Thickness of Mineral Trioxide Aggregate and Calcium-Enriched Mixture

    PubMed Central

    Shahi, Shahriar; Ghasemi, Negin; Rahimi, Saeed; Yavari, Hamidreza; Janani, Maryam; Mokhtari, Hadi; Bahari, Mahmood; Rabbani, Parastu

    2015-01-01

    Introduction: The aim of the present study was to evaluate the effect of different mixing techniques (conventional, amalgamator and ultrasonic mixing) on the physical properties the working time (WT), setting time (ST), dimensional changes (DC) and film thickness (FT)] of calcium-enriched mixture (CEM) cement and mineral trioxide aggregate (MTA). Methods and Materials: The mentioned physical properties were determined using the ISO 6786:2001 specification. Six samples of each material were prepared for three mixing techniques (totally 36 samples). Data were analyzed using descriptive statistics, two-way ANOVA and Post Hoc Tukey’s tests. The level of significance was defined at 0.05. Results: Irrespective of mixing technique, there was no significant difference between the WT and FT of the tested materials. Except for the DC of MTA and the FT of the all materials, other properties were significantly affected with mixing techniques (P<0.05). The ultrasonic technique decreased the ST of MTA and CEM cement and increased the WT of CEM cement (P<0.05). Conclusion: The mixing technique of the materials had no significant effect on the dimensional changes of MTA and the film thickness of both materials. PMID:26523140

  20. Information diffusion, Facebook clusters, and the simplicial model of social aggregation: a computational simulation of simplicial diffusers for community health interventions.

    PubMed

    Kee, Kerk F; Sparks, Lisa; Struppa, Daniele C; Mannucci, Mirco A; Damiano, Alberto

    2016-01-01

    By integrating the simplicial model of social aggregation with existing research on opinion leadership and diffusion networks, this article introduces the constructs of simplicial diffusers (mathematically defined as nodes embedded in simplexes; a simplex is a socially bonded cluster) and simplicial diffusing sets (mathematically defined as minimal covers of a simplicial complex; a simplicial complex is a social aggregation in which socially bonded clusters are embedded) to propose a strategic approach for information diffusion of cancer screenings as a health intervention on Facebook for community cancer prevention and control. This approach is novel in its incorporation of interpersonally bonded clusters, culturally distinct subgroups, and different united social entities that coexist within a larger community into a computational simulation to select sets of simplicial diffusers with the highest degree of information diffusion for health intervention dissemination. The unique contributions of the article also include seven propositions and five algorithmic steps for computationally modeling the simplicial model with Facebook data.

  1. Construction aggregates

    USGS Publications Warehouse

    Tepordei, V.V.

    1995-01-01

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

  2. Toward real-time Monte Carlo simulation using a commercial cloud computing infrastructure.

    PubMed

    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.

  3. 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.

  4. Toward Long-Time Simulation of Ballistic Gel Penetration

    NASA Astrophysics Data System (ADS)

    Lew, Adrian

    2011-06-01

    Ballistic gelatin is used as a surrogate for tissue to study the performance of armor and ammunition. Numerical simulations of impact and penetration of ammunition into ballistic gelatin have the potential to complement experimental work. Ballistic gelatin is a nearly incompressible material with viscoelastic features, which can recover from very large strains. As a result, a bullet penetrating the gel forms a large temporary cavity behind it, which at long times collapses to a very small one. This is a marked difference with the behavior of a fluid under similar circumstances. This poses strenuous challenges to current numerical tools, since an imperfect ``memory'' of the material elasticity leads to abnormally large remaining cavities. Reaching these later times in a simulation (~10 ms) is challenging to do in a reasonable time frame of a few hours. In this presentation I will first showcase the phenomena we are trying to capture through experiments in Permagel. Among others, these show the bullet rebounding after fully stopping, the importance of the gases inside the created cavity in its long-term dynamics, and the apparent appearance of mild plastic deformations and local melting in the gel. I will then discuss about the numerical tools we are creating to simulate it. I will show a suite of variational time-integration strategies able to reach long-time simulations with reasonable accuracy. Then, I will comment on novel automatic remeshing strategies we are creating, needed to simulate the large shear deformations in the gel while retaining accurate elastic recoveries. I will illustrate these ideas with simulations in highly parallel computing environments, and discuss the challenges we face to qualitatively recover a number of the experimental observations. Department of the Army Research Grant; contract/grant number: W911NF-07-2-0027.

  5. Time and motion simulation of the WRAP Module 1 Facility

    SciTech Connect

    Van Zanten, K.D. ); Weidert, J.R. )

    1993-02-01

    A Time and Motion simulation model was developed for the Waste Receiving and Processing (WRAP) Module 1 Facility which will be located at the Hanford site. The simulation model was developed using the WITNESS computer program licensed from AT T ISTEL. The model simulates the movement of 6,825 drums per year of transuranic (TRU) and low level waste (LLW) through the WRAP 1 Facility. In the WRAP 1 Facility, four main areas were modeled: Receiving, Non-Destructive Examination/Non-Destructive Assay (NDE/NDA), Waste Process and Shipping. Movement of waste drums through the plant is accomplished with forklifts, roller conveyors, two automated guided vehicles (AGV's), lift tables, jib cranes and pallet transfer carts. In-plant drum storage is provided by an automated storage and retrieval system (ASRS) for palletized drums in the Receiving/Shipping areas, a 12- drum storage carousel in the NDE/NDA area and a 24-drum storage carousel in the Waste Process area. The process simulation models use a color graphic display of plant operations to show drum (or pallet) movement throughout the plant. Actual speeds of vehicles, conveyors and forklifts are simulated in the model as well as machine cycle times, delay times, and stop times. Vehicle load and unload times, and acceleration and deceleration are included in the model. Distributions for the arrival of trucks delivering pallets or trucks leaving with waste drums or pallets are included in the model. Random numbers for distributions are assigned to determine the effect of variability on plant performance. The simulation program generates a full range of reports that allows users to determine the plant throughput under a wide variety of conditions. Typically a warm-up period is run to allow drums to complete travel through the system until steady steady-state'' operation is achieved . The model is then run at these steady-state conditions for several days, weeks or even years, depending on the complexity of the model.

  6. Time and motion simulation of the WRAP Module 1 Facility

    SciTech Connect

    Van Zanten, K.D.; Weidert, J.R.

    1993-02-01

    A Time and Motion simulation model was developed for the Waste Receiving and Processing (WRAP) Module 1 Facility which will be located at the Hanford site. The simulation model was developed using the WITNESS computer program licensed from AT&T ISTEL. The model simulates the movement of 6,825 drums per year of transuranic (TRU) and low level waste (LLW) through the WRAP 1 Facility. In the WRAP 1 Facility, four main areas were modeled: Receiving, Non-Destructive Examination/Non-Destructive Assay (NDE/NDA), Waste Process and Shipping. Movement of waste drums through the plant is accomplished with forklifts, roller conveyors, two automated guided vehicles (AGV`s), lift tables, jib cranes and pallet transfer carts. In-plant drum storage is provided by an automated storage and retrieval system (ASRS) for palletized drums in the Receiving/Shipping areas, a 12-drum storage carousel in the NDE/NDA area and a 24-drum storage carousel in the Waste Process area. The process simulation models use a color graphic display of plant operations to show drum (or pallet) movement throughout the plant. Actual speeds of vehicles, conveyors and forklifts are simulated in the model as well as machine cycle times, delay times, and stop times. Vehicle load and unload times, and acceleration and deceleration are included in the model. Distributions for the arrival of trucks delivering pallets or trucks leaving with waste drums or pallets are included in the model. Random numbers for distributions are assigned to determine the effect of variability on plant performance. The simulation program generates a full range of reports that allows users to determine the plant throughput under a wide variety of conditions. Typically a warm-up period is run to allow drums to complete travel through the system until steady ``steady-state`` operation is achieved. The model is then run at these steady-state conditions for several days, weeks or even years, depending on the complexity of the model.

  7. Accuracy vs. computational time: translating aortic simulations to the clinic.

    PubMed

    Brown, Alistair G; Shi, Yubing; Marzo, Alberto; Staicu, Cristina; Valverde, Isra; Beerbaum, Philipp; Lawford, Patricia V; Hose, D Rodney

    2012-02-01

    State of the art simulations of aortic haemodynamics feature full fluid-structure interaction (FSI) and coupled 0D boundary conditions. Such analyses require not only significant computational resource but also weeks to months of run time, which compromises the effectiveness of their translation to a clinical workflow. This article employs three computational fluid methodologies, of varying levels of complexity with coupled 0D boundary conditions, to simulate the haemodynamics within a patient-specific aorta. The most comprehensive model is a full FSI simulation. The simplest is a rigid walled incompressible fluid simulation while an alternative middle-ground approach employs a compressible fluid, tuned to elicit a response analogous to the compliance of the aortic wall. The results demonstrate that, in the context of certain clinical questions, the simpler analysis methods may capture the important characteristics of the flow field.

  8. Using time filtering to control the long-time instability in seismic wave simulation

    NASA Astrophysics Data System (ADS)

    Gao, L.; Brossier, R.; Virieux, J.

    2016-03-01

    Long-time instabilities have been observed in various scenarios of numerical simulation for seismic wave propagation. They appear as slowly magnifying spurious oscillations in the seismograms at the late stage of the simulation. Their magnifying speed is typically much slower than the magnifying speed observed when the Courant-Friedrichs-Lewy condition is violated. The simulations can therefore continue to proceed for a relatively long period without floating-point overflow. The impact of the long-time instabilities on the simulation accuracy at the early stage can be negligible in some cases. In existing literatures, spatial-filtering techniques that, in principle, average the solution within certain spatial range at the same time level are typically utilized to control the long-time instability. In this paper, we present an alternative time-filtering approach that, in principle, averages the solution at different time levels of the same spatial location to control the long-time instability. Comparing with the spatial filtering, the advantages of this time-filtering approach lie in its flexibility, particularly when boundaries or interfaces are involved, its simplicity and low additional arithmetic operations, at the expense of extra memory cost. When application of the time filtering is localized to regions where long-time instabilities are emitted from, for example, a boundary or an interface layer, the additional cost is negligible when compared with the cost of wave simulation. For linear wave equations, this time-filtering approach can be understood as the introduction of artificial diffusion. Its application has impact on the accuracy of the solution and the restriction of the time step size. We present an indicator-based approach to adjust the filtering parameters both spatially and temporally, in order to provide the best trade-off between accuracy and stability. The indicator is calculated heuristically by monitoring the spurious oscillation as the

  9. Generating survival times to simulate Cox proportional hazards models with time-varying covariates.

    PubMed

    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.

  10. Real-Time Simulator of Black Hole Optics

    NASA Astrophysics Data System (ADS)

    Bakala, Pavel; Sramkova, Eva; Torok, Gabriel; Goluchova, Katerina

    Our electronic poster presents complex hardware and software simulator of an optical projection for an observer in strong gravitational field of axially symmetric rotating black holes described by the Kerr metric, spherically symmetric Schwarzschild black holes and compact neutron or quark stars. The real-time simulation was created by the application of advanced numerical methods for the integration of zero geodesics and massive parallel computing. The simulation software scans the surroundings and transforms them into a form of an optical projection in the local reference frame of the observers who are inside and outside the ergosphere, above and below the circular photon orbit and in the close vicinity of the black hole’s horizon or at the surface of a neutron star. The simulation contains all the characteristic effects of relativistic optics: multiple direct and indirect pictures, the gravitational and Doppler frequency shift, and the amplification of the intensity of the observed emission. The hardware part of the simulator uses two large TV monitors, four cameras for scanning the surroundings and two powerful laptops. This hardware configuration allows to process the whole surroundings around full 360 degrees and to model their relativistic optical projection in real time. The interactive computer simulation explicitly demonstrates the significant difference between the optics in the strong gravitational field background and the optics we know from our daily life. The properties of the latter, being seemingly obvious, have determined our perception, intuition and imagination from time immemorial. The simulator therefore provides the chance of an intuitive insight into the properties of the curved spacetimes in the vicinity of compact objects to the general public without specific knowledge of mathematical and physical background.

  11. Time-partitioning simulation models for calculation on parallel computers

    NASA Technical Reports Server (NTRS)

    Milner, Edward J.; Blech, Richard A.; Chima, Rodrick V.

    1987-01-01

    A technique allowing time-staggered solution of partial differential equations is presented in this report. Using this technique, called time-partitioning, simulation execution speedup is proportional to the number of processors used because all processors operate simultaneously, with each updating of the solution grid at a different time point. The technique is limited by neither the number of processors available nor by the dimension of the solution grid. Time-partitioning was used to obtain the flow pattern through a cascade of airfoils, modeled by the Euler partial differential equations. An execution speedup factor of 1.77 was achieved using a two processor Cray X-MP/24 computer.

  12. Sub-timing in fluid flow and transport simulations

    NASA Astrophysics Data System (ADS)

    Murty Bhallamudi, S.; Panday, Sorab; Huyakorn, Peter S.

    A sub-time stepping method is described for computational fluid dynamics problems that utilize implicit-type time marching procedures to resolve transients. In this method, small time-step sizes are used in portions of a domain where interest and activity is high, with larger time-step sizes being applied in other locations. The sub-time step is an integral portion of a larger time step--i.e., multiple sub-time steps over a sub-timed part of a domain add up to the time interval of the full time step used over the remainder of the domain. The technique is particularly suitable for extensive simulations where large portions of a domain are temporally over-discretized. The principles underlying implementation of the implicit sub-timing procedure, the computational effort in relation to conventional implicit time-stepping methods, and an analysis of the effects of sub-timing on the matrix structure are presented. Feasibility and applicability of the implicit sub-timing method is demonstrated through three proof-of-the-concept example problems. These examples include implementation of implicit sub-timing to one-dimensional as well as two-dimensional flow and solute transport problems.

  13. Time Advice and Learning Questions in Computer Simulations

    ERIC Educational Resources Information Center

    Rey, Gunter Daniel

    2011-01-01

    Students (N = 101) used an introductory text and a computer simulation to learn fundamental concepts about statistical analyses (e.g., analysis of variance, regression analysis and General Linear Model). Each learner was randomly assigned to one cell of a 2 (with or without time advice) x 3 (with learning questions and corrective feedback, with…

  14. 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…

  15. 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

  16. Simulation of stochastic diffusion via first exit times

    NASA Astrophysics Data System (ADS)

    Lötstedt, Per; Meinecke, Lina

    2015-11-01

    In molecular biology it is of interest to simulate diffusion stochastically. In the mesoscopic model we partition a biological cell into unstructured subvolumes. In each subvolume the number of molecules is recorded at each time step and molecules can jump between neighboring subvolumes to model diffusion. The jump rates can be computed by discretizing the diffusion equation on that unstructured mesh. If the mesh is of poor quality, due to a complicated cell geometry, standard discretization methods can generate negative jump coefficients, which no longer allows the interpretation as the probability to jump between the subvolumes. We propose a method based on the mean first exit time of a molecule from a subvolume, which guarantees positive jump coefficients. Two approaches to exit times, a global and a local one, are presented and tested in simulations on meshes of different quality in two and three dimensions.

  17. The operant reserve: a computer simulation in (accelerated) real time.

    PubMed

    Catania, A Charles

    2005-05-31

    In Skinner's Reflex Reserve theory, reinforced responses added to a reserve depleted by responding. It could not handle the finding that partial reinforcement generated more responding than continuous reinforcement, but it would have worked if its growth had depended not just on the last response but also on earlier responses preceding a reinforcer, each weighted by delay. In that case, partial reinforcement generates steady states in which reserve decrements produced by responding balance increments produced when reinforcers follow responding. A computer simulation arranged schedules for responses produced with probabilities proportional to reserve size. Each response subtracted a fixed amount from the reserve and added an amount weighted by the reciprocal of the time to the next reinforcer. Simulated cumulative records and quantitative data for extinction, random-ratio, random-interval, and other schedules were consistent with those of real performances, including some effects of history. The model also simulated rapid performance transitions with changed contingencies that did not depend on molar variables or on differential reinforcement of inter-response times. The simulation can be extended to inhomogeneous contingencies by way of continua of reserves arrayed along response and time dimensions, and to concurrent performances and stimulus control by way of different reserves created for different response classes. PMID:15845312

  18. The operant reserve: a computer simulation in (accelerated) real time.

    PubMed

    Catania, A Charles

    2005-05-31

    In Skinner's Reflex Reserve theory, reinforced responses added to a reserve depleted by responding. It could not handle the finding that partial reinforcement generated more responding than continuous reinforcement, but it would have worked if its growth had depended not just on the last response but also on earlier responses preceding a reinforcer, each weighted by delay. In that case, partial reinforcement generates steady states in which reserve decrements produced by responding balance increments produced when reinforcers follow responding. A computer simulation arranged schedules for responses produced with probabilities proportional to reserve size. Each response subtracted a fixed amount from the reserve and added an amount weighted by the reciprocal of the time to the next reinforcer. Simulated cumulative records and quantitative data for extinction, random-ratio, random-interval, and other schedules were consistent with those of real performances, including some effects of history. The model also simulated rapid performance transitions with changed contingencies that did not depend on molar variables or on differential reinforcement of inter-response times. The simulation can be extended to inhomogeneous contingencies by way of continua of reserves arrayed along response and time dimensions, and to concurrent performances and stimulus control by way of different reserves created for different response classes.

  19. 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

  20. Just-in-time Time Data Analytics and Visualization of Climate Simulations using the Bellerophon Framework

    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.

  1. Disentangling timing and amplitude errors in streamflow simulations

    NASA Astrophysics Data System (ADS)

    Seibert, Simon Paul; Ehret, Uwe; Zehe, Erwin

    2016-09-01

    This article introduces an improvement in the Series Distance (SD) approach for the improved discrimination and visualization of timing and magnitude uncertainties in streamflow simulations. SD emulates visual hydrograph comparison by distinguishing periods of low flow and periods of rise and recession in hydrological events. Within these periods, it determines the distance of two hydrographs not between points of equal time but between points that are hydrologically similar. The improvement comprises an automated procedure to emulate visual pattern matching, i.e. the determination of an optimal level of generalization when comparing two hydrographs, a scaled error model which is better applicable across large discharge ranges than its non-scaled counterpart, and "error dressing", a concept to construct uncertainty ranges around deterministic simulations or forecasts. Error dressing includes an approach to sample empirical error distributions by increasing variance contribution, which can be extended from standard one-dimensional distributions to the two-dimensional distributions of combined time and magnitude errors provided by SD. In a case study we apply both the SD concept and a benchmark model (BM) based on standard magnitude errors to a 6-year time series of observations and simulations from a small alpine catchment. Time-magnitude error characteristics for low flow and rising and falling limbs of events were substantially different. Their separate treatment within SD therefore preserves useful information which can be used for differentiated model diagnostics, and which is not contained in standard criteria like the Nash-Sutcliffe efficiency. Construction of uncertainty ranges based on the magnitude of errors of the BM approach and the combined time and magnitude errors of the SD approach revealed that the BM-derived ranges were visually narrower and statistically superior to the SD ranges. This suggests that the combined use of time and magnitude errors to

  2. Moving target, distributed, real-time simulation using Ada

    NASA Technical Reports Server (NTRS)

    Collins, W. R.; Feyock, S.; King, L. A.; Morell, L. J.

    1985-01-01

    Research on a precompiler solution is described for the moving target compiler problem encountered when trying to run parallel simulation algorithms on several microcomputers. The precompiler is under development at NASA-Lewis for simulating jet engines. Since the behavior of any component of a jet engine, e.g., the fan inlet, rear duct, forward sensor, etc., depends on the previous behaviors and not the current behaviors of other components, the behaviors can be modeled on different processors provided the outputs of the processors reach other processors in appropriate time intervals. The simulator works in compute and transfer modes. The Ada procedure sets for the behaviors of different components are divided up and routed by the precompiler, which essentially receives a multitasking program. The subroutines are synchronized after each computation cycle.

  3. Simulation-based medical education: time for a pedagogical shift.

    PubMed

    Kalaniti, Kaarthigeyan; Campbell, Douglas M

    2015-01-01

    The purpose of medical education at all levels is to prepare physicians with the knowledge and comprehensive skills, required to deliver safe and effective patient care. The traditional 'apprentice' learning model in medical education is undergoing a pedagogical shift to a 'simulation-based' learning model. Experiential learning, deliberate practice and the ability to provide immediate feedback are the primary advantages of simulation-based medical education. It is an effective way to develop new skills, identify knowledge gaps, reduce medical errors, and maintain infrequently used clinical skills even among experienced clinical teams, with the overall goal of improving patient care. Although simulation cannot replace clinical exposure as a form of experiential learning, it promotes learning without compromising patient safety. This new paradigm shift is revolutionizing medical education in the Western world. It is time that the developing countries embrace this new pedagogical shift.

  4. Simulation of MC-1 Engine on Real-Time Station

    NASA Technical Reports Server (NTRS)

    Ly, William; Roe, Fred (Technical Monitor)

    2001-01-01

    The MC-1 rocket engine is a new, 60,000-pound-thrust engine designed to boost small spacecraft carrying payloads weighing up to 500 pounds. The engine was designed in-house at NASA's Marshall Space Flight Center (MSFC) in Huntsville, Alabama, and built by SUMMA Technology, Inc. A vital part of the success of the engine development was the verification of the Propulsion System Controller (PSC) used to control the MC-1 engine during development testing at test facilities in Mississippi and California. The MC-1 engine simulation software was developed on the Applied Dynamics, Inc.'s Real-Time Station (RTS) computer system (ESL) to verify the PSC's hardware and software performance in the Marshall Avionics System Testbed's (MAST) Engine Simulation Lab at the MSFC. The engine model includes the simulation of pressure transducers, thermocouple sensors and valve-positions.

  5. Time reversal and charge conjugation in an embedding quantum simulator

    PubMed Central

    Zhang, Xiang; Shen, Yangchao; Zhang, Junhua; Casanova, Jorge; Lamata, Lucas; Solano, Enrique; Yung, Man-Hong; Zhang, Jing-Ning; Kim, Kihwan

    2015-01-01

    A quantum simulator is an important device that may soon outperform current classical computations. A basic arithmetic operation, the complex conjugate, however, is considered to be impossible to be implemented in such a quantum system due to the linear character of quantum mechanics. Here, we present the experimental quantum simulation of such an unphysical operation beyond the regime of unitary and dissipative evolutions through the embedding of a quantum dynamics in the electronic multilevels of a 171Yb+ ion. We perform time reversal and charge conjugation, which are paradigmatic examples of antiunitary symmetry operators, in the evolution of a Majorana equation without the tomographic knowledge of the evolving state. Thus, these operations can be applied regardless of the system size. Our approach offers the possibility to add unphysical operations to the toolbox of quantum simulation, and provides a route to efficiently compute otherwise intractable quantities, such as entanglement monotones. PMID:26239028

  6. Time reversal and charge conjugation in an embedding quantum simulator.

    PubMed

    Zhang, Xiang; Shen, Yangchao; Zhang, Junhua; Casanova, Jorge; Lamata, Lucas; Solano, Enrique; Yung, Man-Hong; Zhang, Jing-Ning; Kim, Kihwan

    2015-01-01

    A quantum simulator is an important device that may soon outperform current classical computations. A basic arithmetic operation, the complex conjugate, however, is considered to be impossible to be implemented in such a quantum system due to the linear character of quantum mechanics. Here, we present the experimental quantum simulation of such an unphysical operation beyond the regime of unitary and dissipative evolutions through the embedding of a quantum dynamics in the electronic multilevels of a (171)Yb(+) ion. We perform time reversal and charge conjugation, which are paradigmatic examples of antiunitary symmetry operators, in the evolution of a Majorana equation without the tomographic knowledge of the evolving state. Thus, these operations can be applied regardless of the system size. Our approach offers the possibility to add unphysical operations to the toolbox of quantum simulation, and provides a route to efficiently compute otherwise intractable quantities, such as entanglement monotones. PMID:26239028

  7. 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.

  8. Topological data analysis of biological aggregation models.

    PubMed

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

    2015-01-01

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

  9. Parareal in Time for Dynamic Simulations of Power Systems

    SciTech Connect

    Gurrala, Gurunath; Dimitrovski, Aleksandar D; Pannala, Sreekanth; Simunovic, Srdjan; Starke, Michael R

    2015-01-01

    In recent years, there have been significant developments in parallel algorithms and high performance parallel computing platforms. Parareal in time algorithm has become popular for long transient simulations (e.g., molecular dynamics, fusion, reacting flows). Parareal is a parallel algorithm which divides the time interval into sub-intervals and solves them concurrently. This paper investigates the applicability of the parareal algorithm to power system dynamic simulations. Preliminary results on the application of parareal for multi-machine power systems are reported in this paper. Two widely used test systems, WECC 3-generator 9-bus system, New England 10-generator 39- bus system, is used to explore the effectiveness of the parareal. Severe 3 phase bus faults are simulated using both the classical and detailed models of multi-machine power systems. Actual Speedup of 5-7 times is observed assuming ideal parallelization. It has been observed that the speedup factors of the order of 20 can be achieved by using fast coarse approximations of power system models. Dependency of parareal convergence on fault duration and location has been observed.

  10. Aggregation in environmental systems - Part 1: Seasonal tracer cycles quantify young water fractions, but not mean transit times, in spatially heterogeneous catchments

    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

  11. Spectral decontamination of a real-time helicopter simulation

    NASA Technical Reports Server (NTRS)

    Mcfarland, R. E.

    1983-01-01

    Nonlinear mathematical models of a rotor system, referred to as rotating blade-element models, produce steady-state, high-frequency harmonics of significant magnitude. In a discrete simulation model, certain of these harmonics may be incompatible with realistic real-time computational constraints because of their aliasing into the operational low-pass region. However, the energy is an aliased harmonic may be suppressed by increasing the computation rate of an isolated, causal nonlinearity and using an appropriate filter. This decontamination technique is applied to Sikorsky's real-time model of the Black Hawk helicopter, as supplied to NASA for handling-qualities investigations.

  12. Time-efficient numerical simulation of diatomic molecular spectra

    NASA Astrophysics Data System (ADS)

    Beuc, Robert; Movre, Mladen; Horvatić, Berislav

    2014-03-01

    We present a quantum-mechanical procedure for calculating the photoabsorption spectra of diatomic molecules, entirely based on the Fourier grid Hamiltonian method for obtaining energies and the corresponding wave functions. Discrete and continuous spectrum contributions, which are the result of transitions between bound, free, and quasibound states of diatomic molecules were treated on the same footing. Using the classical Franck-Condon principle and the stationary-phase approximation, we also developed a "semiquantum" simulation method of the spectrum which allows an extremely time-efficient numerical algorithm, reducing the computer time by up to four orders of magnitude. The proposed method was tested on the absorption spectra of potassium molecules.

  13. First Steps in the Aggregation Process of Copolymers Based on Thymine Monomers: Characterization by Molecular Dynamics Simulations and Atomic Force Microscopy.

    PubMed

    Garay, A Sergio; Rodrigues, Daniel E; Fuselli, Antonela; Martino, Debora M; Passeggi, Mario C G

    2016-04-01

    Atomistic molecular dynamic simulations were performed to study the structure of isolated VBT-VBA (vinylbenzylthymine-vinylbenzyltriethylammonium chloride) copolymer chains in water at different monomeric species ratios (1:1 and 1:4). The geometric parameters of the structure that the copolymers form in equilibrium together with the basic interactions that stabilize them were determined. Atomic force microscopy (AFM) measurements of dried diluted concentrations of the two copolymers onto highly oriented pyrolytic graphite (HOPG) substrates were carried out to study their aggregation arrangement. The experiments show that both copolymers arrange in fiber-like structures. Comparing the diameters predicted by the simulation results and those obtained by AFM, it can be concluded that individual copolymers arrange in bunches of two chains, stabilized by contra-ions-copolymer interactions for the 1:1 copolymerization ratio at the ionic strength of our samples. In contrast, for the 1:4 system the individual copolymer chains do not aggregate in bunches. These results remark the relevance of the copolymerization ratio and ionic strength of the solvent in the mesoscopic structure of these materials.

  14. Construction aggregates

    USGS Publications Warehouse

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

    2000-01-01

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

  15. Construction aggregates

    USGS Publications Warehouse

    Tepordei, V.V.

    1994-01-01

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

  16. A New Multiscale Technique for Time-Accurate Geophysics Simulations

    NASA Astrophysics Data System (ADS)

    Omelchenko, Y. A.; Karimabadi, H.

    2006-12-01

    Large-scale geophysics systems are frequently described by multiscale reactive flow models (e.g., wildfire and climate models, multiphase flows in porous rocks, etc.). Accurate and robust simulations of such systems by traditional time-stepping techniques face a formidable computational challenge. Explicit time integration suffers from global (CFL and accuracy) timestep restrictions due to inhomogeneous convective and diffusion processes, as well as closely coupled physical and chemical reactions. Application of adaptive mesh refinement (AMR) to such systems may not be always sufficient since its success critically depends on a careful choice of domain refinement strategy. On the other hand, implicit and timestep-splitting integrations may result in a considerable loss of accuracy when fast transients in the solution become important. To address this issue, we developed an alternative explicit approach to time-accurate integration of such systems: Discrete-Event Simulation (DES). DES enables asynchronous computation by automatically adjusting the CPU resources in accordance with local timescales. This is done by encapsulating flux- conservative updates of numerical variables in the form of events, whose execution and synchronization is explicitly controlled by imposing accuracy and causality constraints. As a result, at each time step DES self- adaptively updates only a fraction of the global system state, which eliminates unnecessary computation of inactive elements. DES can be naturally combined with various mesh generation techniques. The event-driven paradigm results in robust and fast simulation codes, which can be efficiently parallelized via a new preemptive event processing (PEP) technique. We discuss applications of this novel technology to time-dependent diffusion-advection-reaction and CFD models representative of various geophysics applications.

  17. Simulating transient dynamics of the time-dependent time fractional Fokker-Planck systems

    NASA Astrophysics Data System (ADS)

    Kang, Yan-Mei

    2016-09-01

    For a physically realistic type of time-dependent time fractional Fokker-Planck (FP) equation, derived as the continuous limit of the continuous time random walk with time-modulated Boltzmann jumping weight, a semi-analytic iteration scheme based on the truncated (generalized) Fourier series is presented to simulate the resultant transient dynamics when the external time modulation is a piece-wise constant signal. At first, the iteration scheme is demonstrated with a simple time-dependent time fractional FP equation on finite interval with two absorbing boundaries, and then it is generalized to the more general time-dependent Smoluchowski-type time fractional Fokker-Planck equation. The numerical examples verify the efficiency and accuracy of the iteration method, and some novel dynamical phenomena including polarized motion orientations and periodic response death are discussed.

  18. 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.

  19. Time domain simulations of preliminary breakdown pulses in natural lightning

    PubMed Central

    Carlson, B E; Liang, C; Bitzer, P; Christian, H

    2015-01-01

    Lightning discharge is a complicated process with relevant physical scales spanning many orders of magnitude. In an effort to understand the electrodynamics of lightning and connect physical properties of the channel to observed behavior, we construct a simulation of charge and current flow on a narrow conducting channel embedded in three-dimensional space with the time domain electric field integral equation, the method of moments, and the thin-wire approximation. The method includes approximate treatment of resistance evolution due to lightning channel heating and the corona sheath of charge surrounding the lightning channel. Focusing our attention on preliminary breakdown in natural lightning by simulating stepwise channel extension with a simplified geometry, our simulation reproduces the broad features observed in data collected with the Huntsville Alabama Marx Meter Array. Some deviations in pulse shape details are evident, suggesting future work focusing on the detailed properties of the stepping mechanism. Key Points Preliminary breakdown pulses can be reproduced by simulated channel extension Channel heating and corona sheath formation are crucial to proper pulse shape Extension processes and channel orientation significantly affect observations PMID:26664815

  20. Lattice simulations of real-time quantum fields

    NASA Astrophysics Data System (ADS)

    Berges, J.; Borsányi, Sz.; Sexty, D.; Stamatescu, I.-O.

    2007-02-01

    We investigate lattice simulations of scalar and non-Abelian gauge fields in Minkowski space-time. For SU(2) gauge-theory expectation values of link variables in 3+1 dimensions are constructed by a stochastic process in an additional (5th) “Langevin-time.” A sufficiently small Langevin step size and the use of a tilted real-time contour leads to converging results in general. All fixed point solutions are shown to fulfil the infinite hierarchy of Dyson-Schwinger identities, however, they are not unique without further constraints. For the non-Abelian gauge theory the thermal equilibrium fixed point is only approached at intermediate Langevin-times. It becomes more stable if the complex time path is deformed towards Euclidean space-time. We analyze this behavior further using the real-time evolution of a quantum anharmonic oscillator, which is alternatively solved by diagonalizing its Hamiltonian. Without further optimization stochastic quantization can give accurate descriptions if the real-time extent of the lattice is small on the scale of the inverse temperature.

  1. Simulation of Algorithms for Pulse Timing in FPGAs.

    PubMed

    Haselman, Michael D; Hauck, Scott; Lewellen, Thomas K; Miyaoka, Robert S

    2007-01-01

    Modern Field Programmable Gate Arrays (FPGAs) are capable of performing complex discrete signal processing algorithms with clock rates well above 100MHz. This, combined with FPGA's low expense and ease of use, make them an ideal technology for pulse timing and are a central part of our next generation of electronics for our pre-clinical PET scanner systems. To that end, our laboratory has been developing a pulse timing technique that uses pulse fitting to achieve timing resolution well below the sampling period of the analog to digital converter (ADC). While ADCs with sampling rates in excess of 400MS/s exist, we feel that using ADCs with lowing sampling rates has many advantages for positron emission tomography (PET) scanners. It is with this premise that we have started simulating timing algorithms using MATLAB in order to optimize the parameters before implementing the algorithm in Verilog. MATLAB simulations allow us to quickly investigate filter designs, ADC sampling rates and algorithms with real data before implementation in hardware. We report our results for a least squares fitting algorithm and a new version of a leading edge detector of PMT pulses.

  2. Simulations of avalanche breakdown statistics: probability and timing

    NASA Astrophysics Data System (ADS)

    Ng, Jo Shien; Tan, Chee Hing; David, John P. R.

    2010-04-01

    Important avalanche breakdown statistics for Single Photon Avalanche Diodes (SPADs), such as avalanche breakdown probability, dark count rate, and the distribution of time taken to reach breakdown (providing mean time to breakdown and jitter), were simulated. These simulations enable unambiguous studies on effects of avalanche region width, ionization coefficient ratio and carrier dead space on the avalanche statistics, which are the fundamental limits of the SPADs. The effects of quenching resistor/circuit have been ignored. Due to competing effects between dead spaces, which are significant in modern SPADs with narrow avalanche regions, and converging ionization coefficients, the breakdown probability versus overbias characteristics from different avalanche region widths are fairly close to each other. Concerning avalanche breakdown timing at given value of breakdown probability, using avalanche material with similar ionization coefficients yields fast avalanche breakdowns with small timing jitter (albeit higher operating field), compared to material with dissimilar ionization coefficients. This is the opposite requirement for abrupt breakdown probability versus overbias characteristics. In addition, by taking band-to-band tunneling current (dark carriers) into account, minimum avalanche region width for practical SPADs was found to be 0.3 and 0.2 μm, for InP and InAlAs, respectively.

  3. Time-dependent radiation dose simulations during interplanetary space flights

    NASA Astrophysics Data System (ADS)

    Dobynde, Mikhail; Shprits, Yuri; Drozdov, Alexander; Hoffman, Jeffrey; Li, Ju

    2016-07-01

    Space radiation is one of the main concerns in planning long-term interplanetary human space missions. There are two main types of hazardous radiation - Solar Energetic Particles (SEP) and Galactic Cosmic Rays (GCR). Their intensities and evolution depend on the solar activity. GCR activity is most enhanced during solar minimum, while the most intense SEPs usually occur during the solar maximum. SEPs are better shielded with thick shields, while GCR dose is less behind think shields. Time and thickness dependences of the intensity of these two components encourage looking for a time window of flight, when radiation intensity and dose of SEP and GCR would be minimized. In this study we combine state-of-the-art space environment models with GEANT4 simulations to determine the optimal shielding, geometry of the spacecraft, and launch time with respect to the phase of the solar cycle. The radiation environment was described by the time-dependent GCR model, and the SEP spectra that were measured during the period from 1990 to 2010. We included gamma rays, electrons, neutrons and 27 fully ionized elements from hydrogen to nickel. We calculated the astronaut's radiation doses during interplanetary flights using the Monte-Carlo code that accounts for the primary and the secondary radiation. We also performed sensitivity simulations for the assumed spacecraft size and thickness to find an optimal shielding. In conclusion, we present the dependences of the radiation dose as a function of launch date from 1990 to 2010, for flight durations of up to 3 years.

  4. Lab-scale simulation of the fate and transport of nano zero-valent iron in subsurface environments: aggregation, sedimentation, and contaminant desorption.

    PubMed

    Yin, Ke; Lo, Irene M C; Dong, Haoran; Rao, Pinhua; Mak, Mark S H

    2012-08-15

    Heavy metal removal using nano zero-valent iron (NZVI) has drawn growing attention due to the ease of application and high removal efficiency. However, uncertainties regarding its fate and transport in subsurface environments have raised concerns that require further exploration. In this study, aggregation, sedimentation, and Cr/As desorption of three types of NZVIs were investigated under various conditions. It was found that the aggregation behavior of the NZVIs differed from one another in regard to reaction time and ionic strength, associated with the respective critical size for sedimentation. Sedimentation of NZVIs was positively related to the concentrations and average particle sizes. The sedimentation kinetics of NZVI followed two concomitant processes, i.e., (1) direct sedimentation of larger particles, and (2) initial aggregation and then sedimentation of smaller particles. When loaded with Cr/As, NZVIs tended to deposit faster, possibly due to the precipitation of Cr/As onto the nanoparticle surfaces resulting in larger particle sizes. Moreover, desorption of Cr/As from Cr/As loaded NZVIs was detected in the presence of typical groundwater ions, as well as natural organic matter, and poses a potential risk to the subsurface environment. The desorption of Cr was linearly related to the release of iron ions, while As desorption was mitigated when the immobilization of Cr increased.

  5. Langley advanced real-time simulation (ARTS) system

    NASA Technical Reports Server (NTRS)

    Crawford, Daniel J.; Cleveland, Jeff I., II

    1988-01-01

    A system of high-speed digital data networks was developed and installed to support real-time flight simulation at the NASA Langley Research Center. This system, unlike its predecessor, employs intelligence at each network node and uses distributed 10-V signal conversion equipment rather than centralized 100-V equipment. A network switch, which replaces an elaborate system of patch panels, allows the researcher to construct a customized network from the 25 available simulation sites by invoking a computer control statement. The intent of this paper is to provide a coherent functional description of the system. This development required many significant innovations to enhance performance and functionality such as the real-time clock, the network switch, and improvements to the CAMAC network to increase both distances to sites and data rates. The system has been successfully tested at a usable data rate of 24 M. The fiber optic lines allow distances of approximately 1.5 miles from switch to site. Unlike other local networks, CAMAC does not buffer data in blocks. Therefore, time delays in the network are kept below 10 microsec total. This system underwent months of testing and was put into full service in July 1987.

  6. Time-dependent numerical simulation of vertical cavity lasers

    SciTech Connect

    Thode, L.E.; Csanak, G.; So, L.L.; Kwan, T.J.T.; Campbell, M.

    1994-12-31

    To simulate vertical cavity surface emitting lasers (VCSELs), the authors are developing a three-dimensional, time-dependent field-gain model with absorption in bulk dielectric regions and gain in quantum well regions. Since the laser linewidth is narrow, the bulk absorption coefficient is assumed to be independent of frequency with a value determined by the material and the lattice temperature. In contrast, the frequency-dependent gain regions must be solved consistently in the time domain. Treatment of frequency-dependent media in a finite-difference time-domain code is computationally intensive. However, because the volume of the quantum well regions is small relative to the volume of the multilayer dielectric (MLD) mirror regions, the computational overhead is reasonable. A key issue is the calculation of the fields in the MLD mirror regions. Although computationally intensive, good agreement has been obtained between simulation results and matrix equation solutions for the reflection coefficient, transmission coefficient, and bandwidth of MLD mirrors. The authors discuss the development and testing of the two-dimensional field-gain model. This field-gain model will be integrated with a carrier transport model to form the self-consistent laser code, VCSEL.

  7. Time-domain simulation of a guitar: model and method.

    PubMed

    Derveaux, Grégoire; Chaigne, Antoine; Joly, Patrick; Bécache, Eliane

    2003-12-01

    This paper presents a three-dimensional time-domain numerical model of the vibration and acoustic radiation from a guitar. The model involves the transverse displacement of the string excited by a force pulse, the flexural motion of the soundboard, and the sound radiation. A specific spectral method is used for solving the Kirchhoff-Love's dynamic top plate model for a damped, heterogeneous orthotropic material. The air-plate interaction is solved with a fictitious domain method, and a conservative scheme is used for the time discretization. Frequency analysis is performed on the simulated sound pressure and plate velocity waveforms in order to evaluate quantitatively the transfer of energy through the various components of the coupled system: from the string to the soundboard and from the soundboard to the air. The effects of some structural changes in soundboard thickness and cavity volume on the produced sounds are presented and discussed. Simulations of the same guitar in three different cases are also performed: "in vacuo," in air with a perfectly rigid top plate, and in air with an elastic top plate. This allows comparisons between structural, acoustic, and structural-acoustic modes of the instrument. Finally, attention is paid to the evolution with time of the spatial pressure field. This shows, in particular, the complex evolution of the directivity pattern in the near field of the instrument, especially during the attack.

  8. Measurement of time delay for a prospectively gated CT simulator.

    PubMed

    Goharian, M; Khan, R F H

    2010-04-01

    For the management of mobile tumors, respiratory gating is the ideal option, both during imaging and during therapy. The major advantage of respiratory gating during imaging is that it is possible to create a single artifact-free CT data-set during a selected phase of the patient's breathing cycle. The purpose of the present work is to present a simple technique to measure the time delay during acquisition of a prospectively gated CT. The time delay of a Philips Brilliance BigBore (Philips Medical Systems, Madison, WI) scanner attached to a Varian Real-Time Position Management (RPM) system (Varian Medical Systems, Palo Alto, CA) was measured. Two methods were used to measure the CT time delay: using a motion phantom and using a recorded data file from the RPM system. In the first technique, a rotating wheel phantom was altered by placing two plastic balls on its axis and rim, respectively. For a desired gate, the relative positions of the balls were measured from the acquired CT data and converted into corresponding phases. Phase difference was calculated between the measured phases and the desired phases. Using period of motion, the phase difference was converted into time delay. The Varian RPM system provides an external breathing signal; it also records transistor-transistor logic (TTL) 'X-Ray ON' status signal from the CT scanner in a text file. The TTL 'X-Ray ON' indicates the start of CT image acquisition. Thus, knowledge of the start time of CT acquisition, combined with the real-time phase and amplitude data from the external respiratory signal, provides time-stamping of all images in an axial CT scan. The TTL signal with time-stamp was used to calculate when (during the breathing cycle) a slice was recorded. Using the two approaches, the time delay between the prospective gating signal and CT simulator has been determined to be 367 +/- 40 ms. The delay requires corrections both at image acquisition and while setting gates for the treatment delivery

  9. The Simulation of Read-time Scalable Coherent Interface

    NASA Technical Reports Server (NTRS)

    Li, Qiang; Grant, Terry; Grover, Radhika S.

    1997-01-01

    Scalable Coherent Interface (SCI, IEEE/ANSI Std 1596-1992) (SCI1, SCI2) is a high performance interconnect for shared memory multiprocessor systems. In this project we investigate an SCI Real Time Protocols (RTSCI1) using Directed Flow Control Symbols. We studied the issues of efficient generation of control symbols, and created a simulation model of the protocol on a ring-based SCI system. This report presents the results of the study. The project has been implemented using SES/Workbench. The details that follow encompass aspects of both SCI and Flow Control Protocols, as well as the effect of realistic client/server processing delay. The report is organized as follows. Section 2 provides a description of the simulation model. Section 3 describes the protocol implementation details. The next three sections of the report elaborate on the workload, results and conclusions. Appended to the report is a description of the tool, SES/Workbench, used in our simulation, and internal details of our implementation of the protocol.

  10. On the time scale associated with Monte Carlo simulations

    SciTech Connect

    Bal, Kristof M. Neyts, Erik C.

    2014-11-28

    Uniform-acceptance force-bias Monte Carlo (fbMC) methods have been shown to be a powerful technique to access longer timescales in atomistic simulations allowing, for example, phase transitions and growth. Recently, a new fbMC method, the time-stamped force-bias Monte Carlo (tfMC) method, was derived with inclusion of an estimated effective timescale; this timescale, however, does not seem able to explain some of the successes the method. In this contribution, we therefore explicitly quantify the effective timescale tfMC is able to access for a variety of systems, namely a simple single-particle, one-dimensional model system, the Lennard-Jones liquid, an adatom on the Cu(100) surface, a silicon crystal with point defects and a highly defected graphene sheet, in order to gain new insights into the mechanisms by which tfMC operates. It is found that considerable boosts, up to three orders of magnitude compared to molecular dynamics, can be achieved for solid state systems by lowering of the apparent activation barrier of occurring processes, while not requiring any system-specific input or modifications of the method. We furthermore address the pitfalls of using the method as a replacement or complement of molecular dynamics simulations, its ability to explicitly describe correct dynamics and reaction mechanisms, and the association of timescales to MC simulations in general.

  11. On the time scale associated with Monte Carlo simulations

    NASA Astrophysics Data System (ADS)

    Bal, Kristof M.; Neyts, Erik C.

    2014-11-01

    Uniform-acceptance force-bias Monte Carlo (fbMC) methods have been shown to be a powerful technique to access longer timescales in atomistic simulations allowing, for example, phase transitions and growth. Recently, a new fbMC method, the time-stamped force-bias Monte Carlo (tfMC) method, was derived with inclusion of an estimated effective timescale; this timescale, however, does not seem able to explain some of the successes the method. In this contribution, we therefore explicitly quantify the effective timescale tfMC is able to access for a variety of systems, namely a simple single-particle, one-dimensional model system, the Lennard-Jones liquid, an adatom on the Cu(100) surface, a silicon crystal with point defects and a highly defected graphene sheet, in order to gain new insights into the mechanisms by which tfMC operates. It is found that considerable boosts, up to three orders of magnitude compared to molecular dynamics, can be achieved for solid state systems by lowering of the apparent activation barrier of occurring processes, while not requiring any system-specific input or modifications of the method. We furthermore address the pitfalls of using the method as a replacement or complement of molecular dynamics simulations, its ability to explicitly describe correct dynamics and reaction mechanisms, and the association of timescales to MC simulations in general.

  12. Initial NIF Shock Timing Experiments: Comparison with Simulation

    NASA Astrophysics Data System (ADS)

    Robey, H. F.; Celliers, P. M.; Boehly, T. R.; Datte, P. S.; Bowers, M. W.; Olson, R. E.; Munro, D. H.; Milovich, J. L.; Jones, O. S.; Nikroo, A.; Kroll, J. J.; Horner, J. B.; Hamza, A. V.; Bhandarkar, S. D.; Giraldez, E.; Castro, C.; Gibson, C. R.; Eggert, J. H.; Smith, R. F.; Park, H.-S.; Young, B. K.; Hsing, W. W.; Landen, O. L.; Meyerhofer, D. D.

    2010-11-01

    Initial experiments are underway to demonstrate the techniques required to tune the shock timing of capsule implosions on the National Ignition Facility (NIF). These experiments use a modified cryogenic hohlraum geometry designed to precisely match the performance of ignition hohlraums. The targets employ a re-entrant Au cone to provide optical access to the shocks as they propagate in the liquid deuterium-filled capsule interior. The strength and timing of the shocks is diagnosed with VISAR (Velocity Interferometer System for Any Reflector) and DANTE. The results of these measurements will be used to set the precision pulse shape for ignition capsule implosions to follow. Experimental results and comparisons with numerical simulation are presented.

  13. Detergent-mediated protein aggregation.

    PubMed

    Neale, Chris; Ghanei, Hamed; Holyoake, John; Bishop, Russell E; Privé, Gilbert G; Pomès, Régis

    2013-04-01

    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.

  14. Simulations of monomeric amyloid β-peptide (1-40) with varying solution conditions and oxidation state of Met35: implications for aggregation.

    PubMed

    Brown, Anne M; Lemkul, Justin A; Schaum, Nicholas; Bevan, David R

    2014-03-01

    The amyloid β-peptide (Aβ) is a 40-42 residue peptide that is the principal toxic species in Alzheimer's disease (AD). The oxidation of methionine-35 (Met35) to the sulfoxide form (Met35(ox)) has been identified as potential modulator of Aβ aggregation. The role Met35(ox) plays in Aβ neurotoxicity differs among experimental studies, which may be due to inconsistent solution conditions (pH, buffer, temperature). We applied atomistic molecular dynamics (MD) simulations as a means to probe the dynamics of the monomeric 40-residue alloform of Aβ (Aβ40) containing Met35 or Met35(ox) in an effort to resolve the conflicting experimental results. We found that Met35 oxidation decreases the β-strand content of the C-terminal hydrophobic region (residues 29-40), with a specific effect on the secondary structure of residues 33-35, thus potentially impeding aggregation. Further, there is an important interplay between oxidation state and solution conditions, with pH and salt concentration augmenting the effects of oxidation. The results presented here serve to rationalize the conflicting results seen in experimental studies and provide a fundamental biophysical characterization of monomeric Aβ40 dynamics in both reduced and oxidized forms, providing insight into the biochemical mechanism of Aβ40 and oxidative stress related to AD.

  15. Full-f gyrokinetic simulation over a confinement time

    SciTech Connect

    Idomura, Yasuhiro

    2014-02-15

    A long time ion temperature gradient driven turbulence simulation over a confinement time is performed using the full-f gyrokinetic Eulerian code GT5D. The convergence of steady temperature and rotation profiles is examined, and it is shown that the profile relaxation can be significantly accelerated when the simulation is initialized with linearly unstable temperature profiles. In the steady state, the temperature profile and the ion heat diffusivity are self-consistently determined by the power balance condition, while the intrinsic rotation profile is sustained by complicated momentum transport processes without momentum input. The steady turbulent momentum transport is characterized by bursty non-diffusive fluxes, and the resulting turbulent residual stress is consistent with the profile shear stress theory [Y. Camenen et al., “Consequences of profile shearing on toroidal momentum transport,” Nucl. Fusion 51, 073039 (2011)] in which the residual stress depends not only on the profile shear and the radial electric field shear but also on the radial electric field itself. Based on the toroidal angular momentum conservation, it is found that in the steady null momentum transport state, the turbulent residual stress is cancelled by the neoclassical counterpart, which is greatly enhanced in the presence of turbulent fluctuations.

  16. Multi-layer Parallel Beta-Sheet Structure of Amyloid Beta peptide (1-40) aggregate observed by discrete molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Peng, Shouyong; Urbanc, Brigita; Ding, Feng; Cruz, Luis; Buldyrev, Sergey; Dokholyan, Nikolay; Stanley, H. E.

    2003-03-01

    New evidence shows that oligomeric forms of Amyloid-Beta are potent neurotoxins that play a major role in neurodegeneration of Alzheimer's disease. Detailed knowledge of the structure and assembly dynamics of Amyloid-Beta is important for the development of new therapeutic strategies. Here we apply a two-atom model with Go interactions to model aggregation of Amyloid-Beta (1-40) peptides using the discrete molecular dynamics simulation. At temperatures above the transition temperature from an alpha-helical to random coil, we obtain two types of parallel beta-sheet structures, (a) a helical beta-sheet structure at a lower temperature and (b) a parallel beta-sheet structure at a higher temperature, both with inter-sheet distance of 10 A and with free edges which possibly enable further fibrillar elongation.

  17. Numerical Simulations of Time-dependent Herbig-Haro Jets

    NASA Astrophysics Data System (ADS)

    Biro, Susana

    1994-11-01

    Recent observations of Herbig-Haro jets (or optical jets) show evidence that these highly collimated, supersonic flows associated with young stellar objects are not steady, but rather show many types of variations. The string of shock excited nebulae that make up such jets have highly supersonic proper motions, substantial variations of radial velocity along the length of the jet and often several working surfaces. Several models (both analytic and numerical) exist which explain some of the observed properties of optical jets. However, these jets have a wide variety of shapes, sizes and velocities, so a general model for them is not possible. Three simple time-dependent effects have been simulated for this thesis using the approximate Riemann solver, Flux-Vector-Splitting. A periodic variation in the magnitude of the velocity of the flow produces a straight jet with a head (or working surface) and several regularly spaced pairs of shocks (internal working surfaces, IWS). This structure is similar to that of the HH34 and HH111 jets. Special attention is given to a single IWS. The evolution and emission properties of this structure are determined. A periodic variation in the direction of the flow produces a jet with a sinuous body and a complex working surface. Pairs of shocks appear at the bends of this sinuous beam. An adiabatic simulation of the complete jet serves to illustrate the general structure of the flow. The sinuous body and knotty working surface are similar to the HH46/47 jet. A non-adiabatic simulation of the body of the jet (excluding the head) permits the calculation of emission maps which show a structure similar to that observed in HH46/47. By combining the variations in magnitude and direction of the velocity, a jet is created which eventually breaks-up into independent knots (or ``bullets''). Maps of the emission obtained from this simulation present a structure reminiscent of the flow in L1551+IRS5. In general, groups of bow-shaped HH objects

  18. Timing Interactions in Social Simulations: The Voter Model

    NASA Astrophysics Data System (ADS)

    Fernández-Gracia, Juan; Eguíluz, Víctor M.; Miguel, Maxi San

    The recent availability of huge high resolution datasets on human activities has revealed the heavy-tailed nature of the interevent time distributions. In social simulations of interacting agents the standard approach has been to use Poisson processes to update the state of the agents, which gives rise to very homogeneous activity patterns with a well defined characteristic interevent time. As a paradigmatic opinion model we investigate the voter model and review the standard update rules and propose two new update rules which are able to account for heterogeneous activity patterns. For the new update rules each node gets updated with a probability that depends on the time since the last event of the node, where an event can be an update attempt (exogenous update) or a change of state (endogenous update). We find that both update rules can give rise to power law interevent time distributions, although the endogenous one more robustly. Apart from that for the exogenous update rule and the standard update rules the voter model does not reach consensus in the infinite size limit, while for the endogenous update there exist a coarsening process that drives the system toward consensus configurations.

  19. Satellite range delay simulator for a matrix-switched time division multiple-access network simulator

    NASA Technical Reports Server (NTRS)

    Nagy, Lawrence A.

    1989-01-01

    The Systems Integration, Test, and Evaluation (SITE) facility at NASA Lewis Research Center is presently configured as a satellite-switched time division multiple access (SS-TDMA) network simulator. The purpose of SITE is to demonstrate and evaluate advanced communication satellite technologies, presently embodied by POC components developed under NASA contracts in addition to other hardware, such as ground terminals, designed and built in-house at NASA Lewis. Each ground terminal in a satellite communications system will experience a different aspect of the satellite's motion due mainly to daily tidal effects and station keeping, hence a different duration and rate of variation in the range delay. As a result of this and other effects such as local oscillator instability, each ground terminal must constantly adjust its transmit burst timing so that data bursts from separate ground terminals arrive at the satellite in their assigned time slots, preventing overlap and keeping the system in synchronism. On the receiving end, ground terminals must synchronize their local clocks using reference transmissions received through the satellite link. A feature of the SITE facility is its capability to simulate the varying propagation delays and associated Doppler frequency shifts that the ground terminals in the network have to cope with. Delay is achieved by means of two NASA Lewis designed and built range delay simulator (RDS) systems, each independently controlled locally with front panel switches or remotely by an experiment control and monitor (EC/M) computer.

  20. a Simulated Real-Time Severe Weather Nowcasting

    NASA Astrophysics Data System (ADS)

    Liu, C.-Y.; Ackerman, S. A.

    2011-09-01

    An upper-level undergraduate course entitled "Radar and Satellite Meteorology" has offered for the past five years at the Department of Atmospheric and Oceanic Sciences, University of Wisconsin-Madison. This course has two components, one is the lectures on remote sensing theory, and the other is laboratory exercises that involve the investigation of archived radar and satellite data. One of the most popular laboratory exercises, according to the students' feedback, is the simulated real-time severe weather nowcasting in the computer-equipped classroom. The students are experienced a severe weather outbreak and placed in a real-time operational decision-making environment. Archived Level-II and Level-III Next-generation Radar (NEXRAD) data is viewed with either the freely available Integrated Data Viewer (IDV) or McIDAS software packages. The "bundling" feature of these software packages allows the instructor to pre-package radar data (e.g., reflectivity, storm-relative Doppler velocity) and feed it to the students every four to five minutes, simulating the delay between radar volume scans. Teams of students are required to monitor the evolution of the situation and issue severe weather warnings based on radar analysis skills developed in lecture and previous labs. Documented storm reports are also integrated into the lab to assist — or sometimes detract from — the students' warning decisions, and the classroom clock is even adjusted to correspond with the time of the events. This exercise provides students with a unique operational experience that is often missing from the undergraduate curriculum. Its inherent portability and flexibility allows instructors to adapt it to any historical severe weather event, making it appropriate for courses in mesoscale and synoptic meteorology in addition to remote sensing.

  1. Real-time Java simulations of multiple interference dielectric filters

    NASA Astrophysics Data System (ADS)

    Kireev, Alexandre N.; Martin, Olivier J. F.

    2008-12-01

    An interactive Java applet for real-time simulation and visualization of the transmittance properties of multiple interference dielectric filters is presented. The most commonly used interference filters as well as the state-of-the-art ones are embedded in this platform-independent applet which can serve research and education purposes. The Transmittance applet can be freely downloaded from the site http://cpc.cs.qub.ac.uk. Program summaryProgram title: Transmittance Catalogue identifier: AEBQ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBQ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 5778 No. of bytes in distributed program, including test data, etc.: 90 474 Distribution format: tar.gz Programming language: Java Computer: Developed on PC-Pentium platform Operating system: Any Java-enabled OS. Applet was tested on Windows ME, XP, Sun Solaris, Mac OS RAM: Variable Classification: 18 Nature of problem: Sophisticated wavelength selective multiple interference filters can include some tens or even hundreds of dielectric layers. The spectral response of such a stack is not obvious. On the other hand, there is a strong demand from application designers and students to get a quick insight into the properties of a given filter. Solution method: A Java applet was developed for the computation and the visualization of the transmittance of multilayer interference filters. It is simple to use and the embedded filter library can serve educational purposes. Also, its ability to handle complex structures will be appreciated as a useful research and development tool. Running time: Real-time simulations

  2. Injury Profile SIMulator, a Qualitative Aggregative Modelling Framework to Predict Crop Injury Profile as a Function of Cropping Practices, and the Abiotic and Biotic Environment. I. Conceptual Bases

    PubMed Central

    Aubertot, Jean-Noël; Robin, Marie-Hélène

    2013-01-01

    The limitation of damage caused by pests (plant pathogens, weeds, and animal pests) in any agricultural crop requires integrated management strategies. Although significant efforts have been made to i) develop, and to a lesser extent ii) combine genetic, biological, cultural, physical and chemical control methods in Integrated Pest Management (IPM) strategies (vertical integration), there is a need for tools to help manage Injury Profiles (horizontal integration). Farmers design cropping systems according to their goals, knowledge, cognition and perception of socio-economic and technological drivers as well as their physical, biological, and chemical environment. In return, a given cropping system, in a given production situation will exhibit a unique injury profile, defined as a dynamic vector of the main injuries affecting the crop. This simple description of agroecosystems has been used to develop IPSIM (Injury Profile SIMulator), a modelling framework to predict injury profiles as a function of cropping practices, abiotic and biotic environment. Due to the tremendous complexity of agroecosystems, a simple holistic aggregative approach was chosen instead of attempting to couple detailed models. This paper describes the conceptual bases of IPSIM, an aggregative hierarchical framework and a method to help specify IPSIM for a given crop. A companion paper presents a proof of concept of the proposed approach for a single disease of a major crop (eyespot on wheat). In the future, IPSIM could be used as a tool to help design ex-ante IPM strategies at the field scale if coupled with a damage sub-model, and a multicriteria sub-model that assesses the social, environmental, and economic performances of simulated agroecosystems. In addition, IPSIM could also be used to help make diagnoses on commercial fields. It is important to point out that the presented concepts are not crop- or pest-specific and that IPSIM can be used on any crop. PMID:24019908

  3. Injury Profile SIMulator, a qualitative aggregative modelling framework to predict crop injury profile as a function of cropping practices, and the abiotic and biotic environment. I. Conceptual bases.

    PubMed

    Aubertot, Jean-Noël; Robin, Marie-Hélène

    2013-01-01

    The limitation of damage caused by pests (plant pathogens, weeds, and animal pests) in any agricultural crop requires integrated management strategies. Although significant efforts have been made to i) develop, and to a lesser extent ii) combine genetic, biological, cultural, physical and chemical control methods in Integrated Pest Management (IPM) strategies (vertical integration), there is a need for tools to help manage Injury Profiles (horizontal integration). Farmers design cropping systems according to their goals, knowledge, cognition and perception of socio-economic and technological drivers as well as their physical, biological, and chemical environment. In return, a given cropping system, in a given production situation will exhibit a unique injury profile, defined as a dynamic vector of the main injuries affecting the crop. This simple description of agroecosystems has been used to develop IPSIM (Injury Profile SIMulator), a modelling framework to predict injury profiles as a function of cropping practices, abiotic and biotic environment. Due to the tremendous complexity of agroecosystems, a simple holistic aggregative approach was chosen instead of attempting to couple detailed models. This paper describes the conceptual bases of IPSIM, an aggregative hierarchical framework and a method to help specify IPSIM for a given crop. A companion paper presents a proof of concept of the proposed approach for a single disease of a major crop (eyespot on wheat). In the future, IPSIM could be used as a tool to help design ex-ante IPM strategies at the field scale if coupled with a damage sub-model, and a multicriteria sub-model that assesses the social, environmental, and economic performances of simulated agroecosystems. In addition, IPSIM could also be used to help make diagnoses on commercial fields. It is important to point out that the presented concepts are not crop- or pest-specific and that IPSIM can be used on any crop.

  4. Analytical and numerical simulation of the steady-state hydrologic effects of mining aggregate in hypothetical sand-and-gravel and fractured crystalline-rock aquifers

    USGS Publications Warehouse

    Arnold, L.R.; Langer, William H.; Paschke, Suzanne Smith

    2003-01-01

    Analytical solutions and numerical models were used to predict the extent of steady-state drawdown caused by mining of aggregate below the water table in hypothetical sand-and-gravel and fractured crystalline-rock aquifers representative of hydrogeologic settings in the Front Range area of Colorado. Analytical solutions were used to predict the extent of drawdown under a wide range of hydrologic and mining conditions that assume aquifer homogeneity, isotropy, and infinite extent. Numerical ground-water flow models were used to estimate the extent of drawdown under conditions that consider heterogeneity, anisotropy, and hydrologic boundaries and to simulate complex or unusual conditions not readily simulated using analytical solutions. Analytical simulations indicated that the drawdown radius (or distance) of influence increased as horizontal hydraulic conductivity of the aquifer, mine penetration of the water table, and mine radius increased; radius of influence decreased as aquifer recharge increased. Sensitivity analysis of analytical simulations under intermediate conditions in sand-and-gravel and fractured crystalline-rock aquifers indicated that the drawdown radius of influence was most sensitive to mine penetration of the water table and least sensitive to mine radius. Radius of influence was equally sensitive to changes in horizontal hydraulic conductivity and recharge. Numerical simulations of pits in sand-and- gravel aquifers indicated that the area of influence in a vertically anisotropic sand-and-gravel aquifer of medium size was nearly identical to that in an isotropic aquifer of the same size. Simulated area of influence increased as aquifer size increased and aquifer boundaries were farther away from the pit, and simulated drawdown was greater near the pit when aquifer boundaries were close to the pit. Pits simulated as lined with slurry walls caused mounding to occur upgradient from the pits and drawdown to occur downgradient from the pits. Pits

  5. Digital video timing analyzer for the evaluation of PC-based real-time simulation systems

    NASA Astrophysics Data System (ADS)

    Jones, Shawn R.; Crosby, Jay L.; Terry, John E., Jr.

    2009-05-01

    Due to the rapid acceleration in technology and the drop in costs, the use of commercial off-the-shelf (COTS) PC-based hardware and software components for digital and hardware-in-the-loop (HWIL) simulations has increased. However, the increase in PC-based components creates new challenges for HWIL test facilities such as cost-effective hardware and software selection, system configuration and integration, performance testing, and simulation verification/validation. This paper will discuss how the Digital Video Timing Analyzer (DiViTA) installed in the Aviation and Missile Research, Development and Engineering Center (AMRDEC) provides quantitative characterization data for PC-based real-time scene generation systems. An overview of the DiViTA is provided followed by details on measurement techniques, applications, and real-world examples of system benefits.

  6. On-farm animal welfare assessment in beef bulls: consistency over time of single measures and aggregated Welfare Quality(®) scores.

    PubMed

    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

  7. Partial least squares regression for linking aggregate pore characteristics to the detachment of undisturbed soil by simulating concentrated flow in Ultisols (subtropical China)

    NASA Astrophysics Data System (ADS)

    Ma, Renming; Cai, Chongfa; Wang, Junguang; Wang, Tianwei; Li, Zhaoxia; Xiao, Tiqiao; Peng, Guanyun

    2015-05-01

    Soil pores are known as an effective medium for water, air, and chemical movement. However, quantifying pore structures and their relationship to the detachment of undisturbed soil by concentrated flow is not fully understood. The objectives of this study were to quantify 3D aggregate microstructures using synchrotron-based high-resolution X-ray micro-computed tomography (SR-μCT) under wetting and drying cycles and to investigate the effects of pore characteristics on the detachment of undisturbed soil by simulating concentrated flow. The detachment rates (Dr) of undisturbed topsoil samples, which were subjected to a pretreatment of zero to eleven wetting and drying cycles, were measured in a 3.8-m-long, 0.2-m-wide hydraulic flume under unitary flow shear stresses (τ = 14.49 Pa); 3-5 mm aggregates were collected from the pretreatment soils, which were subjected to zero, five, and eleven wetting and drying cycles and were scanned at a 3.7 μm voxel-resolution for reconstructing three-dimensional microtomography images. The relationships among pore characteristics and Dr were analyzed using partial least squares regression (PLSR). The results indicated that Dr and the aggregate microstructure changed significantly after the wetting and drying cycles. Dr was closely associated with the pore characteristics. The pore characteristics, such as a >100 μm porosity, total porosity, fraction of regular pores, 30-75 μm porosity, fraction of elongated pores, and fraction of irregular pores, were identified as the primary parameters that control the Dr. The pore characteristics and clay content could account for as much as 68.2% of the variation in Dr. Dr was significantly and positively related to a >100 μm porosity, total porosity, and fraction of elongated pores. Thus, soil fragmentation depended on microcracks that formed during the wetting and drying cycles and on the geometrical characteristics of the pores or cracks. The results from this study provide a

  8. Transport of excitation energy in a molecular aggregate. VIII. Numerical simulation of exciton processes in thylakoid membrane

    NASA Astrophysics Data System (ADS)

    Panda, Anirban; Datta, Sambhu N.

    We investigate the exciton dynamics in a molecular crystal. The dynamics is based on the exciton Hamiltonian, the phonon Hamiltonian, and the exciton-phonon interaction linear in phonon coordinates. Using the interaction picture, expressions were previously obtained for the rate of coherent migration of the exciton clothed by phonons, and the rate of incoherent or hopping motion. In this work we derive an expression for the clothed exciton propagator, which permits an explicit calculation of the hopping rate. Thus, the rates of exciton generation, coherent transfer, and hopping are determined completely from theory. These velocity constants, along with the experimental fluorescence decay constants and reaction rate constants for the excited molecules, are used to write a generalized master equation that describes the rate of change of exciton population at each site. The master equation can be numerically solved by using a time step of the order of a few femtoseconds, while the excited-state reactions and exciton transfer occur in the picosecond scale. Exciton dynamics is numerically simulated for a simple model of thylakoid membrane in green plants. The model is based on the known characteristics of thylakoid architecture. The membrane is divided into 97 zones, each zone in the bulk containing 1,442 chlorophylls, one P700, and one P680. The latter two pigments are randomly placed in each zone, while keeping their distance between 55 and 60 Å. This accounts for the randomness in orientation. The disorder of the chlorophyll molecules within the domains of photosystems is neglected. Our findings are as follows. On average, about 6 million photons within the range of 655-681 nm pass through a membrane in 1 s. About 2.3% of incident photons are absorbed by the membrane chlorophyll molecules. For an excitation bandwidth of 70-175 cm-1, the coherent transfer rate between two adjacent molecules is 1.138 ± 0.488 ps-1. Because the Debye frequency is expected to be much

  9. Time domain simulations of arm locking in LISA

    SciTech Connect

    Thorpe, J. I.; Livas, J.; Maghami, P.

    2011-06-15

    Arm locking is a proposed laser frequency stabilization technique for the Laser Interferometer Space Antenna (LISA), a gravitational-wave observatory sensitive in the milliHertz frequency band. Arm locking takes advantage of the geometric stability of the triangular constellation of three spacecraft that compose LISA to provide a frequency reference with a stability in the LISA measurement band that exceeds that available from a standard reference such as an optical cavity or molecular absorption line. We have implemented a time-domain simulation of a Kalman-filter-based arm-locking system that includes the expected limiting noise sources as well as the effects of imperfect a priori knowledge of the constellation geometry on which the design is based. We use the simulation to study aspects of the system performance that are difficult to capture in a steady-state frequency-domain analysis such as frequency pulling of the master laser due to errors in estimates of heterodyne frequency. We find that our implementation meets requirements on both the noise and dynamic range of the laser frequency with acceptable tolerances and that the design is sufficiently insensitive to errors in the estimated constellation geometry that the required performance can be maintained for the longest continuous measurement intervals expected for the LISA mission.

  10. Using travel times to simulate multi-dimensional bioreactive transport in time-periodic flows.

    PubMed

    Sanz-Prat, Alicia; Lu, Chuanhe; Finkel, Michael; Cirpka, Olaf A

    2016-04-01

    In travel-time models, the spatially explicit description of reactive transport is replaced by associating reactive-species concentrations with the travel time or groundwater age at all locations. These models have been shown adequate for reactive transport in river-bank filtration under steady-state flow conditions. Dynamic hydrological conditions, however, can lead to fluctuations of infiltration velocities, putting the validity of travel-time models into question. In transient flow, the local travel-time distributions change with time. We show that a modified version of travel-time based reactive transport models is valid if only the magnitude of the velocity fluctuates, whereas its spatial orientation remains constant. We simulate nonlinear, one-dimensional, bioreactive transport involving oxygen, nitrate, dissolved organic carbon, aerobic and denitrifying bacteria, considering periodic fluctuations of velocity. These fluctuations make the bioreactive system pulsate: The aerobic zone decreases at times of low velocity and increases at those of high velocity. For the case of diurnal fluctuations, the biomass concentrations cannot follow the hydrological fluctuations and a transition zone containing both aerobic and obligatory denitrifying bacteria is established, whereas a clear separation of the two types of bacteria prevails in the case of seasonal velocity fluctuations. We map the 1-D results to a heterogeneous, two-dimensional domain by means of the mean groundwater age for steady-state flow in both domains. The mapped results are compared to simulation results of spatially explicit, two-dimensional, advective-dispersive-bioreactive transport subject to the same relative fluctuations of velocity as in the one-dimensional model. The agreement between the mapped 1-D and the explicit 2-D results is excellent. We conclude that travel-time models of nonlinear bioreactive transport are adequate in systems of time-periodic flow if the flow direction does not change.

  11. Using travel times to simulate multi-dimensional bioreactive transport in time-periodic flows

    NASA Astrophysics Data System (ADS)

    Sanz-Prat, Alicia; Lu, Chuanhe; Finkel, Michael; Cirpka, Olaf A.

    2016-04-01

    In travel-time models, the spatially explicit description of reactive transport is replaced by associating reactive-species concentrations with the travel time or groundwater age at all locations. These models have been shown adequate for reactive transport in river-bank filtration under steady-state flow conditions. Dynamic hydrological conditions, however, can lead to fluctuations of infiltration velocities, putting the validity of travel-time models into question. In transient flow, the local travel-time distributions change with time. We show that a modified version of travel-time based reactive transport models is valid if only the magnitude of the velocity fluctuates, whereas its spatial orientation remains constant. We simulate nonlinear, one-dimensional, bioreactive transport involving oxygen, nitrate, dissolved organic carbon, aerobic and denitrifying bacteria, considering periodic fluctuations of velocity. These fluctuations make the bioreactive system pulsate: The aerobic zone decreases at times of low velocity and increases at those of high velocity. For the case of diurnal fluctuations, the biomass concentrations cannot follow the hydrological fluctuations and a transition zone containing both aerobic and obligatory denitrifying bacteria is established, whereas a clear separation of the two types of bacteria prevails in the case of seasonal velocity fluctuations. We map the 1-D results to a heterogeneous, two-dimensional domain by means of the mean groundwater age for steady-state flow in both domains. The mapped results are compared to simulation results of spatially explicit, two-dimensional, advective-dispersive-bioreactive transport subject to the same relative fluctuations of velocity as in the one-dimensional model. The agreement between the mapped 1-D and the explicit 2-D results is excellent. We conclude that travel-time models of nonlinear bioreactive transport are adequate in systems of time-periodic flow if the flow direction does not change.

  12. Cosmic Atlas: A Real-Time Universe Simulation

    NASA Astrophysics Data System (ADS)

    Yu, K. C.; Jenkins, N. E.

    2004-05-01

    Cosmic Atlas is a software program produced at the Denver Museum of Nature & Science to generate real-time digital content for the Museum's Gates Planetarium. Created by in-house staff, Cosmic Atlas is designed to be scientifically accurate, flexible, easily updated to stay current with new discoveries, and portable to multiple platforms. It is currently developed using desktop computers running a Linux OS, and is also installed on a multi-graphics pipe SGI visualization computer running the IRIX OS in the Gates Planetarium. The software can be used in real-time presentations via traditional ``star talks'' and classes, but can also be used to devise flightpaths, perform timeline-based editing, play back flightpaths in real-time, and save out image renders for creating video files to be shown on additional playback systems. The first version of the program is meant to replicate the functionality of a traditional optical-mechanical star ball, and hence creates a replica of the night time sky, with constellations, deep sky objects, and didactic information and grids. The Solar System is a realistic, three-dimensional, navigable simulation, updated with the latest moon and minor planet discoveries, and with motions over time determined by a customized orrery. Additional modules can show traditional astronomical imagery, including an application for loading in FITS files to create three-color composites. A three-dimensional model of the Milky Way is in development, populated with HIPPARCOS stars for the local galactic neighborhood, and with molecular clouds constructed from large-scale CO survey data; more distant regions are filled with statistically generated stellar and interstellar medium distributions.

  13. Discrete-time pilot model. [human dynamics and digital simulation

    NASA Technical Reports Server (NTRS)

    Cavalli, D.

    1978-01-01

    Pilot behavior is considered as a discrete-time process where the decision making has a sequential nature. This model differs from both the quasilinear model which follows from classical control theory and from the optimal control model which considers the human operator as a Kalman estimator-predictor. An additional factor considered is that the pilot's objective may not be adequately formulated as a quadratic cost functional to be minimized, but rather as a more fuzzy measure of the closeness with which the aircraft follows a reference trajectory. All model parameters, in the digital program simulating the pilot's behavior, were successfully compared in terms of standard-deviation and performance with those of professional pilots in IFR configuration. The first practical application of the model was in the study of its performance degradation when the aircraft model static margin decreases.

  14. Time Domain Simulations of Arm Locking in LISA

    NASA Technical Reports Server (NTRS)

    Thorpe, J. I.; Maghami, P.; Livas, Jeff

    2011-01-01

    Arm locking is a technique that has been proposed for reducing laser frequency fluctuations in the Laser Interferometer Space Antenna (LISA). a gravitational-wave observatory sensitive' in the milliHertz frequency band. Arm locking takes advantage of the geometric stability of the triangular constellation of three spacecraft that comprise LISA to provide a frequency reference with a stability in the LISA measurement band that exceeds that available from a standard reference such as an optical cavity or molecular absorption line. We have implemented a time-domain simulation of arm locking including the expected limiting noise sources (shot noise, clock noise. spacecraft jitter noise. and residual laser frequency noise). The effect of imperfect a priori knowledge of the LISA heterodyne frequencies and associated "pulling" of an arm locked laser is included. We find that our implementation meets requirements both on the noise and dynamic range of the laser frequency.

  15. Travel time distribution in a hillslope: Insight from numerical simulations

    NASA Astrophysics Data System (ADS)

    Fiori, Aldo; Russo, David

    2008-12-01

    Solute transport in a three-dimensional, heterogeneous hillslope is analyzed through a series of detailed, three-dimensional numerical simulations. The investigation focuses on the transport of a pulse of a passive solute, taking into account realistic features of the relevant flow domain (i.e., the spatial heterogeneity of the soil hydraulic properties and records of the time-dependent meteorological data and evapotranspiration). The scope of the present work is to analyze a few issues regarding the travel time probability density function (pdf) f(τ) of solute, with particular reference to the following: (1) the suitability of the time invariance assumption and the circumstance under which it may represent a valid approximation, (2) the shape of the resulting travel time pdf f(τ), and (3) the difference between f(τ) and the instantaneous unit hydrograph. It is found that in many cases of practical interest the transport of contaminants in catchments can be analyzed by assuming the time-invariant approximation for f(τ), provided that the calendar time is replaced by a flow-corrected time. Here f(τ) is calculated through the analysis of the breakthrough curve represented in terms of flux-averaged concentration versus cumulate discharge. The rescaling of time with respect to the cumulated outflow takes care in an approximate way of the transient processes occurring in the porous medium. The derived f(τ) is weakly dependent on various attributes, like the level of heterogeneity, presence of evaporation or transpiration, and injection period. The main exception regards the cases in which plant transpiration is intense in the vicinity of the channel after relatively long periods of low rain. The impact of the parameters' heterogeneity on f(τ) is generally quite limited, the dispersion being ruled by the distribution of length paths within the hillslope. The derived f(τ) seems compatible with the Gamma distribution, being characterized by both fast and slow

  16. Holographic characterization of protein aggregates

    NASA Astrophysics Data System (ADS)

    Wang, Chen; Zhong, Xiao; Ruffner, David; Stutt, Alexandra; Philips, Laura; Ward, Michael; Grier, David

    Holographic characterization directly measures the size distribution of subvisible protein aggregates in suspension and offers insights into their morphology. Based on holographic video microscopy, this analytical technique records and interprets holograms of individual aggregates in protein solutions as they flow down a microfluidic channel, without requiring labeling or other exceptional sample preparation. The hologram of an individual protein aggregate is analyzed in real time with the Lorenz-Mie theory of light scattering to measure that aggregate's size and optical properties. Detecting, counting and characterizing subvisible aggregates proceeds fast enough for time-resolved studies, and lends itself to tracking trends in protein aggregation arising from changing environmental factors. No other analytical technique provides such a wealth of particle-resolved characterization data in situ. Holographic characterization promises accelerated development of therapeutic protein formulations, improved process control during manufacturing, and streamlined quality assurance during storage and at the point of use. Mrsec and MRI program of the NSF, Spheryx Inc.

  17. Construction aggregates

    USGS Publications Warehouse

    Nelson, T.I.; Bolen, W.P.

    2007-01-01

    Construction aggregates, primarily stone, sand and gravel, are recovered from widespread naturally occurring mineral deposits and processed for use primarily in the construction industry. They are mined, crushed, sorted by size and sold loose or combined with portland cement or asphaltic cement to make concrete products to build roads, houses, buildings, and other structures. Much smaller quantities are used in agriculture, cement manufacture, chemical and metallurgical processes, glass production and many other products.

  18. Construction aggregates

    USGS Publications Warehouse

    Tepordei, V.V.

    1996-01-01

    Part of the Annual Commodities Review 1995. Production of construction aggregates such as crushed stone and construction sand and gravel showed a marginal increase in 1995. Most of the 1995 increases were due to funding for highway construction work. The major areas of concern to the industry included issues relating to wetlands classification and the classification of crystalline silica as a probable human carcinogen. Despite this, an increase in demand is anticipated for 1996.

  19. Construction aggregates

    USGS Publications Warehouse

    Tepordei, V.V.

    1993-01-01

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

  20. Time-dependent simulations of disk-embedded planetary atmospheres

    NASA Astrophysics Data System (ADS)

    Stökl, A.; Dorfi, E. A.

    2014-03-01

    At the early stages of evolution of planetary systems, young Earth-like planets still embedded in the protoplanetary disk accumulate disk gas gravitationally into planetary atmospheres. The established way to study such atmospheres are hydrostatic models, even though in many cases the assumption of stationarity is unlikely to be fulfilled. Furthermore, such models rely on the specification of a planetary luminosity, attributed to a continuous, highly uncertain accretion of planetesimals onto the surface of the solid core. We present for the first time time-dependent, dynamic simulations of the accretion of nebula gas into an atmosphere around a proto-planet and the evolution of such embedded atmospheres while integrating the thermal energy budget of the solid core. The spherical symmetric models computed with the TAPIR-Code (short for The adaptive, implicit RHD-Code) range from the surface of the rocky core up to the Hill radius where the surrounding protoplanetary disk provides the boundary conditions. The TAPIR-Code includes the hydrodynamics equations, gray radiative transport and convective energy transport. The results indicate that diskembedded planetary atmospheres evolve along comparatively simple outlines and in particular settle, dependent on the mass of the solid core, at characteristic surface temperatures and planetary luminosities, quite independent on numerical parameters and initial conditions. For sufficiently massive cores, this evolution ultimately also leads to runaway accretion and the formation of a gas planet.

  1. EON: software for long time simulations of atomic scale systems

    NASA Astrophysics Data System (ADS)

    Chill, Samuel T.; Welborn, Matthew; Terrell, Rye; Zhang, Liang; Berthet, Jean-Claude; Pedersen, Andreas; Jónsson, Hannes; Henkelman, Graeme

    2014-07-01

    The EON software is designed for simulations of the state-to-state evolution of atomic scale systems over timescales greatly exceeding that of direct classical dynamics. States are defined as collections of atomic configurations from which a minimization of the potential energy gives the same inherent structure. The time evolution is assumed to be governed by rare events, where transitions between states are uncorrelated and infrequent compared with the timescale of atomic vibrations. Several methods for calculating the state-to-state evolution have been implemented in EON, including parallel replica dynamics, hyperdynamics and adaptive kinetic Monte Carlo. Global optimization methods, including simulated annealing, basin hopping and minima hopping are also implemented. The software has a client/server architecture where the computationally intensive evaluations of the interatomic interactions are calculated on the client-side and the state-to-state evolution is managed by the server. The client supports optimization for different computer architectures to maximize computational efficiency. The server is written in Python so that developers have access to the high-level functionality without delving into the computationally intensive components. Communication between the server and clients is abstracted so that calculations can be deployed on a single machine, clusters using a queuing system, large parallel computers using a message passing interface, or within a distributed computing environment. A generic interface to the evaluation of the interatomic interactions is defined so that empirical potentials, such as in LAMMPS, and density functional theory as implemented in VASP and GPAW can be used interchangeably. Examples are given to demonstrate the range of systems that can be modeled, including surface diffusion and island ripening of adsorbed atoms on metal surfaces, molecular diffusion on the surface of ice and global structural optimization of nanoparticles.

  2. Aggregation Distributions on Cells Determined by Photobleaching Image Correlation Spectroscopy

    PubMed Central

    Ciccotosto, Giuseppe D.; Kozer, Noga; Chow, Timothy T.Y.; Chon, James W.M.; Clayton, Andrew H.A.

    2013-01-01

    The organization of molecules into macromolecular (nanometer scale), supramolecular complexes (submicron-to-micron scale), and within subcellular domains, is an important architectural principle of cellular biology and biochemistry. Determining the precise nature and distribution of complexes within the cellular milieu is a challenging biophysical problem. Time-series analysis of laser scanning confocal microscopy images by image correlation spectroscopy (ICS) or fluctuation moments methods provides information on aggregation, flow, and dynamics of fluorescently tagged macromolecules. All the methods to date require a brightness standard to relate the experimental data to absolute aggregation. In this article, we show that ICS as a function of gradual photobleaching is a sensitive indicator of aggregation distribution on the submicron scale. Specifically, in photobleaching ICS, the extent of nonlinearity of the apparent cluster density as a function of bleaching is related to the size of clusters. The analysis is tested using computer simulations on model aggregate systems and then applied to an experimental determination of Aβ peptide aggregation on nerve cells. The analysis reveals time-dependent increases in Aβ1-42 peptide aggregation. Globally, the datasets could be described by a monomer-dimer-tetramer-hexamer or a monomer-dimer-trimer-pentamer model. The results demonstrate the utility of photobleaching with ICS for determining aggregation states on the supramolecular scale in intact cells without the requirement for a brightness standard. PMID:23473488

  3. MMPBSA decomposition of the binding energy throughout a molecular dynamics simulation of amyloid-beta (Abeta(10-35)) aggregation.

    PubMed

    Campanera, Josep M; Pouplana, Ramon

    2010-04-15

    Recent experiments with amyloid-beta (Abeta) peptides indicate that the formation of toxic oligomers may be an important contribution to the onset of Alzheimer's disease. The toxicity of Abeta oligomers depend on their structure, which is governed by assembly dynamics. However, a detailed knowledge of the structure of at the atomic level has not been achieved yet due to limitations of current experimental techniques. In this study, replica exchange molecular dynamics simulations are used to identify the expected diversity of dimer conformations of Abeta(10-35) monomers. The most representative dimer conformation has been used to track the dimer formation process between both monomers. The process has been characterized by means of the evolution of the decomposition of the binding free energy, which provides an energetic profile of the interaction. Dimers undergo a process of reorganization driven basically by inter-chain hydrophobic and hydrophilic interactions and also solvation/desolvation processes.

  4. Real-time simulation of jet engines with digital computer. 1: Fabrication and characteristics of the simulator

    NASA Technical Reports Server (NTRS)

    Nishio, K.; Sugiyama, N.; Koshinuma, T.; Hashimoto, T.; Ohata, T.; Ichikawa, H.

    1983-01-01

    The fabrication and performance of a real time jet engine simulator using a digital computer are discussed. The use of the simulator in developing the components and control system of a jet engine is described. Comparison of data from jet engine simulation tests with actual engine tests was conducted with good agreement.

  5. Vortex core timelines and ribbon summarizations: flow summarization over time and simulation ensembles

    NASA Astrophysics Data System (ADS)

    Chan, Alexis Y. L.; Lee, Joohwi; Taylor, Russell M.

    2013-01-01

    We present two new vortex-summarization techniques designed to portray vortex motion over an entire simulation and over an ensemble of simulations in a single image. Linear "vortex core timelines" with cone glyphs summarize flow over all time steps of a single simulation, with color varying to indicate time. Simplified "ribbon summarizations" with hue nominally encoding ensemble membership and saturation encoding time enable direct visual comparison of the distribution of vortices in time and space for a set of simulations.

  6. Construction aggregates

    USGS Publications Warehouse

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

    2001-01-01

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

  7. Multiple Time and Spatial Scale Plasma Simulation -Prospect Based on Current Status- 4.Prospect for Multiple Time and Spatial Scale Simulation Research of Laser Fusion Plasmas

    NASA Astrophysics Data System (ADS)

    Mima, Kunioki; Nagatomo, Hideo; Sakagami, Hitoshi

    Reviewed is the development of the integrated simulation code related to laser fusion plasma research. In particular, the simulation system for describing ultra-intense laser interaction with high density plasmas is discussed. In ultra-intense laser plasma interaction, the relativistic electron current reaches a few hundred mega amperes and generates strong magnetic fields which control the electron transport. Therefore, the simulation system should include particle-in-cell simulation for laser plasma interactions, Fokker-Planck simulation and hybrid simulation for transport and dense plasma heating, and radiation hydrodynamic simulation for laser implosion and fusion burning. This paper reports the present status of the research regarding those simulations and how the above 4 simulation codes are interconnected as parts of the study of multi-space-time scale laser fusion plasma phenomena.

  8. Research on fast rise time EMP radiating-wave simulator

    NASA Astrophysics Data System (ADS)

    Fan, Lisi; Liu, Haitao; Wang, Yun

    2013-03-01

    This paper presents an antenna of High altitude electromagnetic pulse (HEMP) radiating-wave simulator which expands the testing zone larger than the traditional transmission line simulator. The numerical results show that traverse electramagnetic (TEM) antenna can be used to radiate HEMP simulation radiating wave, but in low frequency band the emissive capability is poor. The experiment proves the numerical model is valid. The results of this paper show that TEM antenna can be used to HEMP radiating-wave simulator, and can prove the low frequency radiation capability through resistance loaded method.

  9. Evaluating the Human Damage of Tsunami at Each Time Frame in Aggregate Units Based on GPS data

    NASA Astrophysics Data System (ADS)

    Ogawa, Y.; Akiyama, Y.; Kanasugi, H.; Shibasaki, R.; Kaneda, H.

    2016-06-01

    Assessments of the human damage caused by the tsunami are required in order to consider disaster prevention at such a regional level. Hence, there is an increasing need for the assessments of human damage caused by earthquakes. However, damage assessments in japan currently usually rely on static population distribution data, such as statistical night time population data obtained from national census surveys. Therefore, human damage estimation that take into consideration time frames have not been assessed yet. With these backgrounds, the objectives of this study are: to develop a method for estimating the population distribution of the for each time frame, based on location positioning data observed with mass GPS loggers of mobile phones, to use a evacuation and casualties models for evaluating human damage due to the tsunami, and evaluate each time frame by using the data developed in the first objective, and 3) to discuss the factors which cause the differences in human damage for each time frame. By visualizing the results, we clarified the differences in damage depending on time frame, day and area. As this study enables us to assess damage for any time frame in and high resolution, it will be useful to consider provision for various situations when an earthquake may hit, such as during commuting hours or working hours and week day or holiday.

  10. Time-Lapse Video Microscopy for Assessment of EYFP-Parkin Aggregation as a Marker for Cellular Mitophagy.

    PubMed

    Di Sante, Gabriele; Casimiro, Mathew C; Pestell, Timothy G; Pestell, Richard G

    2016-01-01

    Time-lapse video microscopy can be defined as the real time imaging of living cells. This technique relies on the collection of images at different time points. Time intervals can be set through a computer interface that controls the microscope-integrated camera. This kind of microscopy requires both the ability to acquire very rapid events and the signal generated by the observed cellular structure during these events. After the images have been collected, a movie of the entire experiment is assembled to show the dynamic of the molecular events of interest. Time-lapse video microscopy has a broad range of applications in the biomedical research field and is a powerful and unique tool for following the dynamics of the cellular events in real time. Through this technique, we can assess cellular events such as migration, division, signal transduction, growth, and death. Moreover, using fluorescent molecular probes we are able to mark specific molecules, such as DNA, RNA or proteins and follow them through their molecular pathways and functions. Time-lapse video microscopy has multiple advantages, the major one being the ability to collect data at the single-cell level, that make it a unique technology for investigation in the field of cell biology. However, time-lapse video microscopy has limitations that can interfere with the acquisition of high quality images. Images can be compromised by both external factors; temperature fluctuations, vibrations, humidity and internal factors; pH, cell motility. Herein, we describe a protocol for the dynamic acquisition of a specific protein, Parkin, fused with the enhanced yellow fluorescent protein (EYFP) in order to track the selective removal of damaged mitochondria, using a time-lapse video microscopy approach. PMID:27168174

  11. Dynamic Simulation over Long Time Periods with 100% Solar Generation.

    SciTech Connect

    Concepcion, Ricky James; Elliott, Ryan Thomas

    2015-12-01

    This project aimed to identify the path forward for dynamic simulation tools to accommodate these needs by characterizing the properties of power systems (with high PV penetration), analyzing how these properties affect dynamic simulation software, and offering solutions for potential problems.

  12. Simulation Semantics and the Linguistics of Time. Commentary on Zwaan

    ERIC Educational Resources Information Center

    Evans, Vyvyan

    2008-01-01

    Recent work addressing the phenomenon of perceptual simulation offers new and exciting avenues of investigating how to model knowledge representation. From the perspective of language, the simulation approach has given rise to new impetus to work on models of language understanding (e.g., Zwaan, 2004, and references therein), and provides a way of…

  13. SALT: The Simulator for the Analysis of LWP Timing

    NASA Technical Reports Server (NTRS)

    Springer, Paul L.; Rodrigues, Arun; Brockman, Jay

    2006-01-01

    With the emergence of new processor architectures that are highly multithreaded, and support features such as full/empty memory semantics and split-phase memory transactions, the need for a processor simulator to handle these features becomes apparent. This paper describes such a simulator, called SALT.

  14. Energy relaxation and separation of a hot electron-hole pair in organic aggregates from a time-dependent wavepacket diffusion method

    SciTech Connect

    Han, Lu; Liang, WanZhen; Zhao, Yi; Zhong, Xinxin

    2014-06-07

    The time-dependent wavepacket diffusive method [X. Zhong and Y. Zhao, J. Chem. Phys. 138, 014111 (2013)] is extended to investigate the energy relaxation and separation of a hot electron-hole pair in organic aggregates with incorporation of Coulomb interaction and electron-phonon coupling. The pair initial condition generated by laser pulse is represented by a Gaussian wavepacket with a central momentum. The results reveal that the hot electron energy relaxation is very well described by two rate processes with the fast rate much larger than the slow one, consistent with experimental observations, and an efficient electron-hole separation is accomplished accompanying the fast energy relaxation. Furthermore, although the extra energy indeed helps the separation by overcoming the Coulomb interaction, the width of initial wavepacket is much sensitive to the separation efficiency and the narrower wavepacket generates the more separated charges. This behavior may be useful to understand the experimental controversy of the hot carrier effect on charge separation.

  15. Identification in situ and dynamics of bacteria on limnetic organic aggregates (lake snow).

    PubMed Central

    Weiss, P; Schweitzer, B; Amann, R; Simon, M

    1996-01-01

    Microbial assemblages on large organic aggregates (lake snow) of Lake Constance, Germany, were analyzed with rRNA-directed fluorescent oligonucleotide probes specific for the domain Bacteria and the alpha-, beta-, and gamma-subclasses of the class Proteobacteria. Lake snow aggregates were either collected in situ by SCUBA diving or in a sediment trap at 50 m or formed of natural lake water incubated in rolling cylinders under simulated in situ conditions. For the latter aggregates, the time course of the microbial colonization was also examined. The natural aggregates and those made in rolling cylinders were composed of the particulate organic material present in the lake and thus reflected the composition of the ambient plankton community. All types of lake snow aggregates examined were heavily colonized by microbial cells and harbored between 0.5 x 10(6) and > 2 x 10(6) cells aggregate -1. Between 55 and 100% of the microbial cells stained with 4', 6-diamidino-2-phenylindole (DAPI) could be visualized with the domain Bacteria-specific probe. In most samples, beta-subclass proteobacteria dominated the microbial community, constituting 27 to 42% of total cells as counted by DAPI staining, irrespective of the composition of the aggregates. During the time course experiments with the laboratory-made aggregates, the fraction of beta-subclass proteobacteria usually increased over time. Except for a few samples, alpha- and gamma-subclass proteobacteria were far less abundant than beta-subclass proteobacteria, constituting 11 to 25 and 9 to 33% of total cells, respectively. Therefore, we assume that a specific aggregate-adapted microbial community was established on the aggregates. Because the compositions of the microbial assemblages on natural and laboratory-made aggregates were similar, we conclude that aggregates made in rolling cylinders are good model system with which to examine the formation and microbial colonization of macroscopic organic aggregates. PMID

  16. Identification in situ and dynamics of bacteria on limnetic organic aggregates (lake snow).

    PubMed

    Weiss, P; Schweitzer, B; Amann, R; Simon, M

    1996-06-01

    Microbial assemblages on large organic aggregates (lake snow) of Lake Constance, Germany, were analyzed with rRNA-directed fluorescent oligonucleotide probes specific for the domain Bacteria and the alpha-, beta-, and gamma-subclasses of the class Proteobacteria. Lake snow aggregates were either collected in situ by SCUBA diving or in a sediment trap at 50 m or formed of natural lake water incubated in rolling cylinders under simulated in situ conditions. For the latter aggregates, the time course of the microbial colonization was also examined. The natural aggregates and those made in rolling cylinders were composed of the particulate organic material present in the lake and thus reflected the composition of the ambient plankton community. All types of lake snow aggregates examined were heavily colonized by microbial cells and harbored between 0.5 x 10(6) and > 2 x 10(6) cells aggregate -1. Between 55 and 100% of the microbial cells stained with 4', 6-diamidino-2-phenylindole (DAPI) could be visualized with the domain Bacteria-specific probe. In most samples, beta-subclass proteobacteria dominated the microbial community, constituting 27 to 42% of total cells as counted by DAPI staining, irrespective of the composition of the aggregates. During the time course experiments with the laboratory-made aggregates, the fraction of beta-subclass proteobacteria usually increased over time. Except for a few samples, alpha- and gamma-subclass proteobacteria were far less abundant than beta-subclass proteobacteria, constituting 11 to 25 and 9 to 33% of total cells, respectively. Therefore, we assume that a specific aggregate-adapted microbial community was established on the aggregates. Because the compositions of the microbial assemblages on natural and laboratory-made aggregates were similar, we conclude that aggregates made in rolling cylinders are good model system with which to examine the formation and microbial colonization of macroscopic organic aggregates.

  17. Real-time simulation of solar kiln drying of timber

    SciTech Connect

    Steinmann, D.E.

    1995-05-01

    A major problem in optimizing solar kiln design and control is that natural weather conditions cannot be repeated in consecutive drying runs. All results are, therefore, dependent on the specific weather conditions during any given drying run. The construction and testing of a simulation system to overcome this problem of non-repeatability is described. The simulation system consists of a miniature solar kiln placed inside a climatic chamber and was used to dry pieces of wood using a selected weather sequence which was repeated for consecutive drying runs. The performance of the simulation system was compared to that of the solar kiln and very good agreement was achieved. 5 refs., 8 figs.

  18. Computers for real time flight simulation: A market survey

    NASA Technical Reports Server (NTRS)

    Bekey, G. A.; Karplus, W. J.

    1977-01-01

    An extensive computer market survey was made to determine those available systems suitable for current and future flight simulation studies at Ames Research Center. The primary requirement is for the computation of relatively high frequency content (5 Hz) math models representing powered lift flight vehicles. The Rotor Systems Research Aircraft (RSRA) was used as a benchmark vehicle for computation comparison studies. The general nature of helicopter simulations and a description of the benchmark model are presented, and some of the sources of simulation difficulties are examined. A description of various applicable computer architectures is presented, along with detailed discussions of leading candidate systems and comparisons between them.

  19. Effect of pH on the Aggregation of α-syn12 Dimer in Explicit Water by Replica-Exchange Molecular Dynamics Simulation

    PubMed Central

    Cao, Zanxia; Zhang, Xiumei; Liu, Lei; Zhao, Liling; Li, Haiyan; Wang, Jihua

    2015-01-01

    The dimeric structure of the N-terminal 12 residues drives the interaction of α-synuclein protein with membranes. Moreover, experimental studies indicated that the aggregation of α-synuclein is faster at low pH than neutral pH. Nevertheless, the effects of different pH on the structural characteristics of the α-syn12 dimer remain poorly understood. We performed 500 ns temperature replica exchange molecular dynamics (T-REMD) simulations of two α-syn12 peptides in explicit solvent. The free energy surfaces contain ten highly populated regions at physiological pH, while there are only three highly populated regions contained at acidic pH. The anti-parallel β-sheet conformations were found as the lowest free energy state. Additionally, these states are nearly flat with a very small barrier which indicates that these states can easily transit between themselves. The dimer undergoes a disorder to order transition from physiological pH to acidic pH and the α-syn12 dimer at acidic pH involves a faster dimerization process. Further, the Lys6–Asp2 contact may prevent the dimerization. PMID:26114384

  20. Real-time dynamic simulation of the Cassini spacecraft using DARTS. Part 2: Parallel/vectorized real-time implementation

    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.

  1. Aggregation induced enhanced emission of 2-(2'-hydroxyphenyl)benzimidazole.

    PubMed

    Malakar, Ashim; Kumar, Manishekhar; Reddy, Anki; Biswal, Himadree T; Mandal, Biman B; Krishnamoorthy, G

    2016-07-01

    In this study, the aggregation induced emission enhancement (AIEE) of 2-(2'-hydroxyphenyl)benzimidazole (HPBI) is reported. To investigate the AIEE process of HPBI, absorption/fluorescence spectroscopy, fluorescence imaging and field emission scanning electron microscopy were employed. A comparative study with 2-phenylbenzimidazole (PBI) divulges the significance of the hydroxyl group in the AIEE process. Further, molecular dynamics simulations have been carried out with explicit solvent molecules to follow the aggregation process of HPBI with time. The obtained molecular dynamics simulation results not only predicted the formation of aggregates but also provided detailed insight and information on the molecular interactions. The cellular studies showed aggregates yield higher fluorescence in the visible region inside HeLa cells in comparison to monomeric compounds which failed to exhibit any visible fluorescence inside the cell. The obtained aggregates were further found to be biocompatible and therefore can be used for bio-imaging applications. PMID:27334264

  2. Integration of time as a factor in ergonomic simulation.

    PubMed

    Walther, Mario; Muñoz, Begoña Toledo

    2012-01-01

    The paper describes the application of a simulation based ergonomic evaluation. Within a pilot project, the algorithms of the screening method of the European Assembly Worksheet were transferred into an existing digital human model. Movement data was recorded with an especially developed hybrid Motion Capturing system. A prototype of the system was built and is currently being tested at the Volkswagen Group. First results showed the feasibility of the simulation based ergonomic evaluation with Motion Capturing. PMID:22317391

  3. Integration of time as a factor in ergonomic simulation.

    PubMed

    Walther, Mario; Muñoz, Begoña Toledo

    2012-01-01

    The paper describes the application of a simulation based ergonomic evaluation. Within a pilot project, the algorithms of the screening method of the European Assembly Worksheet were transferred into an existing digital human model. Movement data was recorded with an especially developed hybrid Motion Capturing system. A prototype of the system was built and is currently being tested at the Volkswagen Group. First results showed the feasibility of the simulation based ergonomic evaluation with Motion Capturing.

  4. Winter time orographic cloud seeding effects in WRF simulations

    NASA Astrophysics Data System (ADS)

    Tessendorf, S. A.; Xue, L.; Rasmussen, R.

    2011-12-01

    The goal of this study is to use a numerical model to investigate the feasibility of orographic cloud seeding from existing ground-based generators and aircraft seeding tracks in the Payette, Eastern Idaho, and Western Wyoming regions operated by Idaho Power. The Weather Research and Forecast (WRF) model coupled with an AgI point-source module was run at 2km horizontal resolution for 10 seeding cases including both ground-based and airborne cases from the 2010-2011 winter season. In all of the WRF simulations, a positive increase in precipitation was simulated within the entire model domain. This simulated enhancement was positive within the targeted watershed basins for about two-thirds of the cases. Some enhancements were simulated downwind of the target regions, which could be due to the wind regime and meteorological conditions, or due to model parameter specifications that could affect the location of a simulated seeding effect. The WRF simulations indicated that airborne seeding generally produces a localized seeding effect within a targeted region.

  5. Detergent-mediated protein aggregation

    PubMed Central

    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

  6. 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.

  7. Role of streams in myxobacteria aggregate formation

    NASA Astrophysics Data System (ADS)

    Kiskowski, Maria A.; Jiang, Yi; Alber, Mark S.

    2004-10-01

    Cell contact, movement and directionality are important factors in biological development (morphogenesis), and myxobacteria are a model system for studying cell-cell interaction and cell organization preceding differentiation. When starved, thousands of myxobacteria cells align, stream and form aggregates which later develop into round, non-motile spores. Canonically, cell aggregation has been attributed to attractive chemotaxis, a long range interaction, but there is growing evidence that myxobacteria organization depends on contact-mediated cell-cell communication. We present a discrete stochastic model based on contact-mediated signaling that suggests an explanation for the initialization of early aggregates, aggregation dynamics and final aggregate distribution. Our model qualitatively reproduces the unique structures of myxobacteria aggregates and detailed stages which occur during myxobacteria aggregation: first, aggregates initialize in random positions and cells join aggregates by random walk; second, cells redistribute by moving within transient streams connecting aggregates. Streams play a critical role in final aggregate size distribution by redistributing cells among fewer, larger aggregates. The mechanism by which streams redistribute cells depends on aggregate sizes and is enhanced by noise. Our model predicts that with increased internal noise, more streams would form and streams would last longer. Simulation results suggest a series of new experiments.

  8. Issues in visual support to real-time space system simulation solved in the Systems Engineering Simulator

    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.

  9. Automatic mathematical modeling for real time simulation system

    NASA Technical Reports Server (NTRS)

    Wang, Caroline; Purinton, Steve

    1988-01-01

    A methodology for automatic mathematical modeling and generating simulation models is described. The models will be verified by running in a test environment using standard profiles with the results compared against known results. The major objective is to create a user friendly environment for engineers to design, maintain, and verify their model and also automatically convert the mathematical model into conventional code for conventional computation. A demonstration program was designed for modeling the Space Shuttle Main Engine Simulation. It is written in LISP and MACSYMA and runs on a Symbolic 3670 Lisp Machine. The program provides a very friendly and well organized environment for engineers to build a knowledge base for base equations and general information. It contains an initial set of component process elements for the Space Shuttle Main Engine Simulation and a questionnaire that allows the engineer to answer a set of questions to specify a particular model. The system is then able to automatically generate the model and FORTRAN code. The future goal which is under construction is to download the FORTRAN code to VAX/VMS system for conventional computation. The SSME mathematical model will be verified in a test environment and the solution compared with the real data profile. The use of artificial intelligence techniques has shown that the process of the simulation modeling can be simplified.

  10. A Budget Simulation Model for Times of Stress.

    ERIC Educational Resources Information Center

    Miner, Alfred Norris

    The Florida Community College Inter-Institutional Research Council (IRC) has developed a computerized budget simulation model which can help administrators determine the general fiscal impact of alternate approaches to resource utilization. This model uses three basic systems and one generalized subroutine, based on the budget requirements of the…

  11. Relationship between population of the fibril-prone conformation in the monomeric state and oligomer formation times of peptides: Insights from all-atom simulations

    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.

  12. 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.

  13. VTI Driving Simulator: Mathematical Model of a Four-wheeled Vehicle for Simulation in Real Time. VTI Rapport 267A.

    ERIC Educational Resources Information Center

    Nordmark, Staffan

    1984-01-01

    This report contains a theoretical model for describing the motion of a passenger car. The simulation program based on this model is used in conjunction with an advanced driving simulator and run in real time. The mathematical model is complete in the sense that the dynamics of the engine, transmission and steering system is described in some…

  14. Efficient photoheating algorithms in time-dependent photoionization simulations

    NASA Astrophysics Data System (ADS)

    Lee, Kai-Yan; Mellema, Garrelt; Lundqvist, Peter

    2016-02-01

    We present an extension to the time-dependent photoionization code C2-RAY to calculate photoheating in an efficient and accurate way. In C2-RAY, the thermal calculation demands relatively small time-steps for accurate results. We describe two novel methods to reduce the computational cost associated with small time-steps, namely, an adaptive time-step algorithm and an asynchronous evolution approach. The adaptive time-step algorithm determines an optimal time-step for the next computational step. It uses a fast ray-tracing scheme to quickly locate the relevant cells for this determination and only use these cells for the calculation of the time-step. Asynchronous evolution allows different cells to evolve with different time-steps. The asynchronized clocks of the cells are synchronized at the times where outputs are produced. By only evolving cells which may require short time-steps with these short time-steps instead of imposing them to the whole grid, the computational cost of the calculation can be substantially reduced. We show that our methods work well for several cosmologically relevant test problems and validate our results by comparing to the results of another time-dependent photoionization code.

  15. Ground testing and simulation. II - Aerodynamic testing and simulation: Saving lives, time, and money

    NASA Technical Reports Server (NTRS)

    Dayman, B., Jr.; Fiore, A. W.

    1974-01-01

    The present work discusses in general terms the various kinds of ground facilities, in particular, wind tunnels, which support aerodynamic testing. Since not all flight parameters can be simulated simultaneously, an important problem consists in matching parameters. It is pointed out that there is a lack of wind tunnels for a complete Reynolds-number simulation. Using a computer to simulate flow fields can result in considerable reduction of wind-tunnel hours required to develop a given flight vehicle.

  16. Scaling of transverse nuclear magnetic relaxation due to magnetic nanoparticle aggregation.

    PubMed

    Brown, Keith A; Vassiliou, Christophoros C; Issadore, David; Berezovsky, Jesse; Cima, Michael J; Westervelt, R M

    2010-10-01

    The aggregation of superparamagnetic iron oxide (SPIO) nanoparticles decreases the transverse nuclear magnetic resonance (NMR) relaxation time T2CP of adjacent water molecules measured by a Carr-Purcell-Meiboom-Gill (CPMG) pulse-echo sequence. This effect is commonly used to measure the concentrations of a variety of small molecules. We perform extensive Monte Carlo simulations of water diffusing around SPIO nanoparticle aggregates to determine the relationship between T2CP and details of the aggregate. We find that in the motional averaging regime T2CP scales as a power law with the number N of nanoparticles in an aggregate. The specific scaling is dependent on the fractal dimension d of the aggregates. We find T2CP∝N-0.44 for aggregates with d = 2.2, a value typical of diffusion limited aggregation. We also find that in two-nanoparticle systems, T2CP is strongly dependent on the orientation of the two nanoparticles relative to the external magnetic field, which implies that it may be possible to sense the orientation of a two-nanoparticle aggregate. To optimize the sensitivity of SPIO nanoparticle sensors, we propose that it is best to have aggregates with few nanoparticles, close together, measured with long pulse-echo times. PMID:20689678

  17. Effects of Ocean Acidification on the Ballast of Surface Aggregates Sinking through the Twilight Zone

    PubMed Central

    de Jesus Mendes, Pedro A.; Thomsen, Laurenz

    2012-01-01

    The dissolution of CaCO3 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 pCO2 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. PMID:23272075

  18. Comparative evaluation of the calcium release from mineral trioxide aggregate and its mixture with glass ionomer cement in different proportions and time intervals – An in vitro study

    PubMed Central

    Sawhney, Surbhi; Vivekananda Pai, A.R.

    2015-01-01

    Background Addition of glass ionomer cement (GIC) has been suggested to improve the setting time and handling characteristics of mineral trioxide aggregate (MTA). This study evaluated the effect of adding GIC to MTA in terms of calcium release, an issue that has not been previously studied. Materials and methods The study comprised four groups with five samples each: a control group of MTA alone and experimental groups I (1MTA:1GIC), II (2MTA:1GIC), and III (1MTA:2GIC) based on the mixture of MTA and GIC powders in the respective proportions by volume. Calcium release from the samples was measured by atomic absorption spectrophotometry at 15 min, 6 h, 24 h, and 1 week after setting. The level of statistical significance was set at p < 0.05. Results Groups I (1MTA:1GIC) and III (1MTA:2GIC) released significantly less calcium than the control group at all time periods, except at 15 min for group I. Group II (2MTA:1GIC) showed no significant difference in calcium release compared to the control at any time period. Group II exhibited greater calcium release than group I or III at all time periods, with significant differences between groups I and II at 1 week and between groups I and III at 24 h and 1 week. There were no statistical differences in calcium release between groups I and III. Conclusions Adding GIC to improve the setting time and handling properties of the MTA powder can be detrimental to the calcium-releasing ability of the resultant mixture, depending on the proportion of GIC added. Adding MTA and GIC at a proportion of 2:1 by volume did not impact calcium release from the mixture. These findings should be verified through further clinical studies. PMID:26644757

  19. Study of the Time Response of a Simulated Hydroelectric System

    NASA Astrophysics Data System (ADS)

    Simani, S.; Alvisi, S.; Venturini, M.

    2014-12-01

    This paper addresses the design of an advanced control strategy for a typical hydroelectric dynamic process, performed in the Matlab and Simulink environments. The hydraulic system consists of a high water head and a long penstock with upstream and downstream surge tanks, and is equipped with a Francis turbine. The nonlinear characteristics of hydraulic turbine and the inelastic water hammer effects were considered to calculate and simulate the hydraulic transients. With reference to the control solution, the proposed methodology relies on an adaptive control designed by means of the on-line identification of the system model under monitoring. Extensive simulations and comparison with respect to a classic hydraulic turbine speed PID regulator show the effectiveness of the proposed modelling and control tools.

  20. Real-time simulation of the TF30-P-3 turbofan engine using a hybrid computer

    NASA Technical Reports Server (NTRS)

    Szuch, J. R.; Bruton, W. M.

    1974-01-01

    A real-time, hybrid-computer simulation of the TF30-P-3 turbofan engine was developed. The simulation was primarily analog in nature but used the digital portion of the hybrid computer to perform bivariate function generation associated with the performance of the engine's rotating components. FORTRAN listings and analog patching diagrams are provided. The hybrid simulation was controlled by a digital computer programmed to simulate the engine's standard hydromechanical control. Both steady-state and dynamic data obtained from the digitally controlled engine simulation are presented. Hybrid simulation data are compared with data obtained from a digital simulation provided by the engine manufacturer. The comparisons indicate that the real-time hybrid simulation adequately matches the baseline digital simulation.

  1. Structure of Viral Aggregates

    NASA Astrophysics Data System (ADS)

    Barr, Stephen; Luijten, Erik

    2010-03-01

    The aggregation of virus particles is a particular form of colloidal self-assembly, since viruses of a give type are monodisperse and have identical, anisotropic surface charge distributions. In small-angle X-ray scattering experiments, the Qbeta virus was found to organize in different crystal structures in the presence of divalent salt and non-adsorbing polymer. Since a simple isotropic potential cannot explain the occurrence of all observed phases, we employ computer simulations to investigate how the surface charge distribution affects the virus interactions. Using a detailed model of the virus particle, we find an asymmetric ion distribution around the virus which gives rise to the different phases observed.

  2. Aggregation of Heterogeneous Time Preferences

    ERIC Educational Resources Information Center

    Gollier, Christian; Zeckhauser, Richard

    2005-01-01

    We examine an economy whose consumers have different discount factors for utility, possibly not exponential. We characterize the properties of efficient allocations of resources and of the shadow prices that would decentralize such allocations. We show in particular that the representative agent has a decreasing discount rate when, as is usually…

  3. Simulation of Simple Controlled Processes with Dead-Time.

    ERIC Educational Resources Information Center

    Watson, Keith R.; And Others

    1985-01-01

    The determination of closed-loop response of processes containing dead-time is typically not covered in undergraduate process control, possibly because the solution by Laplace transforms requires the use of Pade approximation for dead-time, which makes the procedure lengthy and tedious. A computer-aided method is described which simplifies the…

  4. Aggregation-Induced Emission Mechanism of Dimethoxy-Tetraphenylethylene in Water Solution: Molecular Dynamics and QM/MM Investigations.

    PubMed

    Sun, Guangxu; Zhao, Yi; Liang, WanZhen

    2015-05-12

    Molecular dynamics simulations and combined quantum mechanics and molecular mechanics calculations are employed to investigate dimethoxy-tetraphenylethylene (DMO-TPE) molecules in water solution for their detailed aggregation process and the mechanism of aggregation-induced emission. The molecular dynamics simulations show that the aggregates start to appear in the nanosecond time scale, and small molecular aggregates appear at low concentration; whereas the large aggregates with a chain-type structure appear at high concentration, and the intramolecular rotation is largely restricted by a molecular aggregated environment. The average radical distribution demonstrates that the waters join the aggregation process and that two types of hydrogen bonds between DMO-TPE and water molecules are built with the peaks at about 0.5 and 0.7 nm, respectively. The spectral features further reveal that the aggregates dominantly present J-type aggregation although they fluctuate between J-type and H-type at a given temperature. The statistical absorption, emission spectra, and the aggregation-induced emission enhancement with respect to the solution concentration agree well with the experimental measurements, indicating the significant effect of molecular environments on the molecular properties. PMID:26574424

  5. Simulating total-dose and dose-rate effects on digital microelectronics timing delays using VHDL

    SciTech Connect

    Brothers, C.P. Jr.; Pugh, R.D.

    1995-12-01

    This paper describes a fast timing simulator based on Very High Speed Integrated Circuit (VHSIC) Hardware Description Language (VHDL) for simulating the timing of digital microelectronics in pre-irradiation, total dose, and dose-rate radiation environments. The goal of this research is the rapid and accurate timing simulation of radiation-hardened microelectronic circuits before, during, and after exposure to ionizing radiation. The results of this research effort were the development of VHDL compatible models capable of rapid and accurate simulation of the effect of radiation on the timing performance of microelectronic circuits. The effects of radiation for total dose at 1 Mrad(Si) and dose rates up to 2 {times} 10{sup 12} rads(Si) per second were modeled for a variety of Separation by IMplantion of OXygen (SIMOX) circuits. In all cases tested, the VHDL simulations ran at least 600 times faster than SPICE while maintaining a timing accuracy to within 15% of SPICE values.

  6. Microwave extinction characteristics of nanoparticle aggregates

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  7. 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.

  8. Math modeling and computer mechanization for real time simulation of rotary-wing aircraft

    NASA Technical Reports Server (NTRS)

    Howe, R. M.

    1979-01-01

    Mathematical modeling and computer mechanization for real time simulation of rotary wing aircraft is discussed. Error analysis in the digital simulation of dynamic systems, such as rotary wing aircraft is described. The method for digital simulation of nonlinearities with discontinuities, such as exist in typical flight control systems and rotor blade hinges, is discussed.

  9. Time-Domain Simulation of Three Dimensional Quantum Wires.

    PubMed

    Sullivan, Dennis M; Mossman, Sean; Kuzyk, Mark G

    2016-01-01

    A method is presented to calculate the eigenenergies and eigenfunctions of quantum wires. This is a true three-dimensional method based on a direct implementation of the time-dependent Schrödinger equation. It makes no approximations to the Schrödinger equation other than the finite-difference approximation of the space and time derivatives. The accuracy of our method is tested by comparing it to analytical results in a cylindrical wire. PMID:27124603

  10. Photonic-crystal time-domain simulations using Wannier functions.

    PubMed

    Blum, Christian; Wolff, Christian; Busch, Kurt

    2011-01-15

    We present a Wannier-function-based time-domain method for photonic-crystal integrated optical circuits. In contrast to other approaches, this method allows one to trade CPU time against memory consumption and therefore is particularly well suited for the treatment of large-scale systems. As an illustration, we apply the method to the design of a photonic-crystal-based sensor, which utilizes a dual Mach-Zehnder-Fano interferometer. PMID:21263535

  11. Time-Domain Simulation of Three Dimensional Quantum Wires

    PubMed Central

    Mossman, Sean; Kuzyk, Mark G.

    2016-01-01

    A method is presented to calculate the eigenenergies and eigenfunctions of quantum wires. This is a true three-dimensional method based on a direct implementation of the time-dependent Schrödinger equation. It makes no approximations to the Schrödinger equation other than the finite-difference approximation of the space and time derivatives. The accuracy of our method is tested by comparing it to analytical results in a cylindrical wire. PMID:27124603

  12. The time dependent propensity function for acceleration of spatial stochastic simulation of reaction-diffusion systems

    NASA Astrophysics Data System (ADS)

    Fu, Jin; Wu, Sheng; Li, Hong; Petzold, Linda R.

    2014-10-01

    The inhomogeneous stochastic simulation algorithm (ISSA) is a fundamental method for spatial stochastic simulation. However, when diffusion events occur more frequently than reaction events, simulating the diffusion events by ISSA is quite costly. To reduce this cost, we propose to use the time dependent propensity function in each step. In this way we can avoid simulating individual diffusion events, and use the time interval between two adjacent reaction events as the simulation stepsize. We demonstrate that the new algorithm can achieve orders of magnitude efficiency gains over widely-used exact algorithms, scales well with increasing grid resolution, and maintains a high level of accuracy.

  13. The Time Dependent Propensity Function for Acceleration of Spatial Stochastic Simulation of Reaction-Diffusion Systems

    PubMed Central

    Wu, Sheng; Li, Hong; Petzold, Linda R.

    2015-01-01

    The inhomogeneous stochastic simulation algorithm (ISSA) is a fundamental method for spatial stochastic simulation. However, when diffusion events occur more frequently than reaction events, simulating the diffusion events by ISSA is quite costly. To reduce this cost, we propose to use the time dependent propensity function in each step. In this way we can avoid simulating individual diffusion events, and use the time interval between two adjacent reaction events as the simulation stepsize. We demonstrate that the new algorithm can achieve orders of magnitude efficiency gains over widely-used exact algorithms, scales well with increasing grid resolution, and maintains a high level of accuracy. PMID:26609185

  14. The time dependent propensity function for acceleration of spatial stochastic simulation of reaction–diffusion systems

    SciTech Connect

    Fu, Jin; Wu, Sheng; Li, Hong; Petzold, Linda R.

    2014-10-01

    The inhomogeneous stochastic simulation algorithm (ISSA) is a fundamental method for spatial stochastic simulation. However, when diffusion events occur more frequently than reaction events, simulating the diffusion events by ISSA is quite costly. To reduce this cost, we propose to use the time dependent propensity function in each step. In this way we can avoid simulating individual diffusion events, and use the time interval between two adjacent reaction events as the simulation stepsize. We demonstrate that the new algorithm can achieve orders of magnitude efficiency gains over widely-used exact algorithms, scales well with increasing grid resolution, and maintains a high level of accuracy.

  15. The Space-Time Conservative Schemes for Large-Scale, Time-Accurate Flow Simulations with Tetrahedral Meshes

    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.

  16. HILS testing: the use of a PC for real-time IR reticle simulation

    NASA Astrophysics Data System (ADS)

    du Plooy, Matthys J.; Collin, Francois G.

    2001-08-01

    Hardware in the loop simulation (HILS) is used in the evaluation of various IR seeker systems. To perform IR HILS testing a number of costly peripheral systems are required. The most important of these are the motion simulation table, the IR scene generator, the IR scene projector, the dynamics simulator and the simulation controller. The cost of IR image projectors prohibits a number of scientists with access to the remaining equipment from preforming HILS testing of IR seekers. Simulating the reticle and calculating the detector signal in real-time allows the evaluator to bypass the IR scene projector and to do signal injection into the unit under test (UUT). The use of a commercial off the shelf personal computer permits the testing of single detector reticle seekers at a fraction of the cost of an IR image projector. This paper will deal with the development of the algorithms required to realize a real-time simulation of a conical scan FM reticle. The simulation makes use of image processing techniques which are computationally intensive. This paper will investigate methods to decrease the simulation time in order to generate real-time signals for the UUT. The implementation of the various techniques as well as the effect on the simulation time will be presented. The disadvantages and problems associated with these methods will also be explored. The algorithms that were developed will be presented along with the fastest simulation times achieved.

  17. A parallel algorithm for switch-level timing simulation on a hypercube multiprocessor

    NASA Technical Reports Server (NTRS)

    Rao, Hariprasad Nannapaneni

    1989-01-01

    The parallel approach to speeding up simulation is studied, specifically the simulation of digital LSI MOS circuitry on the Intel iPSC/2 hypercube. The simulation algorithm is based on RSIM, an event driven switch-level simulator that incorporates a linear transistor model for simulating digital MOS circuits. Parallel processing techniques based on the concepts of Virtual Time and rollback are utilized so that portions of the circuit may be simulated on separate processors, in parallel for as large an increase in speed as possible. A partitioning algorithm is also developed in order to subdivide the circuit for parallel processing.

  18. A real time Pegasus propulsion system model for VSTOL piloted simulation evaluation

    NASA Technical Reports Server (NTRS)

    Mihaloew, J. R.; Roth, S. P.; Creekmore, R.

    1981-01-01

    A real time propulsion system modeling technique suitable for use in man-in-the-loop simulator studies was developd. This technique provides the system accuracy, stability, and transient response required for integrated aircraft and propulsion control system studies. A Pegasus-Harrier propulsion system was selected as a baseline for developing mathematical modeling and simulation techniques for VSTOL. Initially, static and dynamic propulsion system characteristics were modeled in detail to form a nonlinear aerothermodynamic digital computer simulation of a Pegasus engine. From this high fidelity simulation, a real time propulsion model was formulated by applying a piece-wise linear state variable methodology. A hydromechanical and water injection control system was also simulated. The real time dynamic model includes the detail and flexibility required for the evaluation of critical control parameters and propulsion component limits over a limited flight envelope. The model was programmed for interfacing with a Harrier aircraft simulation. Typical propulsion system simulation results are presented.

  19. Topological Data Analysis of Biological Aggregation Models

    PubMed Central

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

    2015-01-01

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

  20. Topological data analysis of biological aggregation models.

    PubMed

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

    2015-01-01

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

  1. Diffusion Limited Aggregation: Algorithm optimization revisited

    NASA Astrophysics Data System (ADS)

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

    2011-08-01

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

  2. 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.

  3. 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.

  4. Optimal generalized multistep integration formulae for real-time digital simulation

    NASA Technical Reports Server (NTRS)

    Moerder, D. D.; Halyo, N.

    1985-01-01

    The problem of discretizing a dynamical system for real-time digital simulation is considered. Treating the system and its simulation as stochastic processes leads to a statistical characterization of simulator fidelity. A plant discretization procedure based on an efficient matrix generalization of explicit linear multistep discrete integration formulae is introduced, which minimizes a weighted sum of the mean squared steady-state and transient error between the system and simulator outputs.

  5. 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.

  6. A Group Simulation of the Development of the Geologic Time Scale.

    ERIC Educational Resources Information Center

    Bennington, J. Bret

    2000-01-01

    Explains how to demonstrate to students that the relative dating of rock layers is redundant. Uses two column diagrams to simulate stratigraphic sequences from two different geological time scales and asks students to complete the time scale. (YDS)

  7. Operational characteristic analysis of conduction cooling HTS SMES for Real Time Digital Simulator based power quality enhancement simulation

    NASA Astrophysics Data System (ADS)

    Kim, A. R.; Kim, G. H.; Kim, K. M.; Kim, D. W.; Park, M.; Yu, I. K.; Kim, S. H.; Sim, K.; Sohn, M. H.; Seong, K. C.

    2010-11-01

    This paper analyzes the operational characteristics of conduction cooling Superconducting Magnetic Energy Storage (SMES) through a real hardware based simulation. To analyze the operational characteristics, the authors manufactured a small-scale toroidal-type SMES and implemented a Real Time Digital Simulator (RTDS) based power quality enhancement simulation. The method can consider not only electrical characteristics such as inductance and current but also temperature characteristic by using the real SMES system. In order to prove the effectiveness of the proposed method, a voltage sag compensation simulation has been implemented using the RTDS connected with the High Temperature Superconducting (HTS) model coil and DC/DC converter system, and the simulation results are discussed in detail.

  8. 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.

  9. Simulations of Oligomeric Intermediates in Prion Diseases

    NASA Astrophysics Data System (ADS)

    Mobley, D.

    2003-10-01

    We extend our previous stochastic cellular automata based model for areal aggregation of prion proteins on neuronal surfaces. The new anisotropic model allow us to simulate both strong beta-sheet and weaker attachment bonds between proteins. Constraining binding directions allows us to generate aggregate structures with the hexagonal lattice symmetry found in recently observed in vitro experiments. We argue that these constraints on rules may correspond to underlying steric constraints on the aggregation process. We find that monomer dominated growth of the areal aggregate is too slow to account for some observed doubling time-to-incubation time ratios inferred from data, and so consider aggregation dominated by relatively stable but non-infectious oligomeric intermediates. We compare a kinetic theory analysis of oligomeric aggregation to spatially explicit simulations of the process. We find that with suitable rules for misfolding of oligomers, possibly due to water exclusion by the surrounding aggregate, the resulting oligomeric aggregation model maps onto our previous monomer aggregation model. Therefore it can produce some of the same attractive features for the description of prion incubation time data. We propose experiments to test the oligomeric aggregation model.

  10. Accurate Behavioral Simulator of All-Digital Time-Domain Smart Temperature Sensors by Using SIMULINK.

    PubMed

    Chen, Chun-Chi; Chen, Chao-Lieh; Lin, You-Ting

    2016-01-01

    This study proposes a new behavioral simulator that uses SIMULINK for all-digital CMOS time-domain smart temperature sensors (TDSTSs) for performing rapid and accurate simulations. Inverter-based TDSTSs offer the benefits of low cost and simple structure for temperature-to-digital conversion and have been developed. Typically, electronic design automation tools, such as HSPICE, are used to simulate TDSTSs for performance evaluations. However, such tools require extremely long simulation time and complex procedures to analyze the results and generate figures. In this paper, we organize simple but accurate equations into a temperature-dependent model (TDM) by which the TDSTSs evaluate temperature behavior. Furthermore, temperature-sensing models of a single CMOS NOT gate were devised using HSPICE simulations. Using the TDM and these temperature-sensing models, a novel simulator in SIMULINK environment was developed to substantially accelerate the simulation and simplify the evaluation procedures. Experiments demonstrated that the simulation results of the proposed simulator have favorable agreement with those obtained from HSPICE simulations, showing that the proposed simulator functions successfully. This is the first behavioral simulator addressing the rapid simulation of TDSTSs. PMID:27509507

  11. Accurate Behavioral Simulator of All-Digital Time-Domain Smart Temperature Sensors by Using SIMULINK

    PubMed Central

    Chen, Chun-Chi; Chen, Chao-Lieh; Lin, You-Ting

    2016-01-01

    This study proposes a new behavioral simulator that uses SIMULINK for all-digital CMOS time-domain smart temperature sensors (TDSTSs) for performing rapid and accurate simulations. Inverter-based TDSTSs offer the benefits of low cost and simple structure for temperature-to-digital conversion and have been developed. Typically, electronic design automation tools, such as HSPICE, are used to simulate TDSTSs for performance evaluations. However, such tools require extremely long simulation time and complex procedures to analyze the results and generate figures. In this paper, we organize simple but accurate equations into a temperature-dependent model (TDM) by which the TDSTSs evaluate temperature behavior. Furthermore, temperature-sensing models of a single CMOS NOT gate were devised using HSPICE simulations. Using the TDM and these temperature-sensing models, a novel simulator in SIMULINK environment was developed to substantially accelerate the simulation and simplify the evaluation procedures. Experiments demonstrated that the simulation results of the proposed simulator have favorable agreement with those obtained from HSPICE simulations, showing that the proposed simulator functions successfully. This is the first behavioral simulator addressing the rapid simulation of TDSTSs. PMID:27509507

  12. A real-time digital computer program for the simulation of a single rotor helicopter

    NASA Technical Reports Server (NTRS)

    Houck, J. A.; Gibson, L. H.; Steinmetz, G. G.

    1974-01-01

    A computer program was developed for the study of a single-rotor helicopter on the Langley Research Center real-time digital simulation system. Descriptions of helicopter equations and data, program subroutines (including flow charts and listings), real-time simulation system routines, and program operation are included. Program usage is illustrated by standard check cases and a representative flight case.

  13. IMPLEMENTATION OF FIRST-PASSAGE TIME APPROACH FOR OBJECT KINETIC MONTE CARLO SIMULATIONS OF IRRADIATION

    SciTech Connect

    Nandipati, Giridhar; Setyawan, Wahyu; Heinisch, Howard L.; Roche, Kenneth J.; Kurtz, Richard J.; Wirth, Brian D.

    2014-06-30

    The objective of the work is to implement a first-passage time (FPT) approach to deal with very fast 1D diffusing SIA clusters in KSOME (kinetic simulations of microstructural evolution) [1] to achieve longer time-scales during irradiation damage simulations. The goal is to develop FPT-KSOME, which has the same flexibility as KSOME.

  14. WinGraphics: An optimized windowing environment for interactive real-time simulations

    SciTech Connect

    Verboncoeur, J.P.; Vahedi, V.

    1989-01-01

    We have developed a customized windowing environment, Win Graphics, which provides particle simulation codes with an interactive user interface. The environment supports real-time animation of the simulation, displaying multiple diagnostics as they evolve in time. In addition, keyboard and printer (PostScript and dot matrix) support is provided. This paper describes this environment.

  15. Time Evolution of Galaxy Scaling Relations in Cosmological Simulations

    NASA Astrophysics Data System (ADS)

    Taylor, Philip; Kobayashi, Chiaki

    2016-08-01

    We predict the evolution of galaxy scaling relationships from cosmological, hydrodynamical simulations, that reproduce the scaling relations of present-day galaxies. Although we do not assume co-evolution between galaxies and black holes a priori, we are able to reproduce the black hole mass-velocity dispersion relation. This relation does not evolve, and black holes actually grow along the relation from significantly less massive seeds than have previously been used. AGN feedback does not very much affect the chemical evolution of our galaxies. In our predictions, the stellar mass-metallicity relation does not change its shape, but the metallicity significantly increases from z ˜ 2 to z ˜ 1, while the gas-phase mass-metallicity relation does change shape, having a steeper slope at higher redshifts (z ≲ 3). Furthermore, AGN feedback is required to reproduce observations of the most massive galaxies at z ≲ 1, specifically their positions on the star formation main sequence and galaxy mass-size relation.

  16. Real-time dynamic simulator for the Topaz II reactor power system

    SciTech Connect

    Kwok, K.S.

    1994-10-01

    A dynamic simulator of the TOPAZ II reactor system has been developed for the Nuclear Electric Propulsion Space Test Program. The simulator is a self-contained IBM-PC compatible based system that executes at a speed faster than real-time. The simulator combines first-principle modeling and empirical correlations in its algorithm to attain the modeling accuracy and computational through-put that are required for real-time execution. The overall execution time of the simulator for each time step is 15 ms when no data is written to the disk, and 18 ms when nine double precision data points are written to the disk once in every time step. The simulation program has been tested and it is able to handle a step decrease of $8 worth of reactivity. It also provides simulation of fuel, emitter, collector, stainless steel, and ZrH moderator failures. Presented in this paper are the models used in the calculations, a sample simulation session, and a discussion of the performance and limitations of the simulator. The simulator has been found to provide realistic real-time dynamic response of the TOPAZ II reactor system under both normal and causality conditions.

  17. Changes in fractal dimension during aggregation.

    PubMed

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

    2003-02-01

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

  18. 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…

  19. Formation of large micellar aggregates before equilibrium in diluted solutions

    NASA Astrophysics Data System (ADS)

    de Moraes, J. N. B.; Figueiredo, W.

    2013-06-01

    We study the formation of premicelles for different values of the concentration of amphiphile molecules in water. Our model consists of a square lattice with water molecules occupying one cell of the lattice while the amphiphilic molecules, represented by chains of five interconnected sites, occupy five cells of the lattice. We perform Monte Carlo simulations in the NVT ensemble, for a fixed temperature and different concentration of amphiphiles, ranging from below to above the critical micelle concentration. We start our simulations from a monomeric state and follow in time all the aggregates sizes until the equilibrium state is reached. We pay particular attention to two aggregate sizes, one related to the minimum and the other to the maximum of the aggregate-size distribution curve obtained at equilibrium. We show that these aggregates evolve in time exhibiting a maximum concentration well before the equilibrium state, revealing the formation of premicelles. The times to reach these maximum concentrations decrease exponentially with the total concentration of the system.

  20. Real-time simulation of F100-PW-100 turbofan engine using the hybrid computer

    NASA Technical Reports Server (NTRS)

    Szuch, J. R.; Seldner, K.

    1975-01-01

    A real-time hybrid computer simulation of the F100-PW-100 augmented turbofan is presented. The digital portion of the hybrid computer is used to perform the bivariate function generation associated with modeling the performance of the engine's rotating components. The remaining calculations are performed on the analog computer. Steady state simulation data along with sea level, static, transient data are presented to show that the real-time simulation matches baseline digital simulation results over a wide range of power settings and flight conditions. Steady state simulation data are compared with sea level, experimental data to show that the real-time hybrid and baseline digital simulations do adequately predict the performance of the actual engine. FORTRAN listings and analog patching diagrams are provided.

  1. A quantitative parameter-free prediction of simulated crystal nucleation times

    SciTech Connect

    Aga, Rachel S; Morris, James R; Hoyt, Jeffrey John; Mendelev, Mikhail I.

    2006-01-01

    We present direct comparisons between simulated crystal-nucleation times and theoretical predictions using a model of aluminum, and demonstrate that a quantitative prediction can be made. All relevant thermodynamic properties of the system are known, making the agreement of our simulation data with nucleation theories free of any adjustable parameters. The role of transient nucleation is included in the classical nucleation theory approach, and shown to be necessary to understand the observed nucleation times. The calculations provide an explanation on why nucleation is difficult to observe in simulations at moderate undercoolings. Even when the simulations are significantly larger than the critical nucleus, and when simulation times are sufficiently long, at moderate undercoolings the small concentration of critical nuclei makes the probability of the nucleation low in molecular dynamics simulations.

  2. The timing of anthropogenic emergence in simulated climate extremes

    NASA Astrophysics Data System (ADS)

    King, Andrew D.; Donat, Markus G.; Fischer, Erich M.; Hawkins, Ed; Alexander, Lisa V.; Karoly, David J.; Dittus, Andrea J.; Lewis, Sophie C.; Perkins, Sarah E.

    2015-09-01

    Determining the time of emergence of climates altered from their natural state by anthropogenic influences can help inform the development of adaptation and mitigation strategies to climate change. Previous studies have examined the time of emergence of climate averages. However, at the global scale, the emergence of changes in extreme events, which have the greatest societal impacts, has not been investigated before. Based on state-of-the-art climate models, we show that temperature extremes generally emerge slightly later from their quasi-natural climate state than seasonal means, due to greater variability in extremes. Nevertheless, according to model evidence, both hot and cold extremes have already emerged across many areas. Remarkably, even precipitation extremes that have very large variability are projected to emerge in the coming decades in Northern Hemisphere winters associated with a wettening trend. Based on our findings we expect local temperature and precipitation extremes to already differ significantly from their previous quasi-natural state at many locations or to do so in the near future. Our findings have implications for climate impacts and detection and attribution studies assessing observed changes in regional climate extremes by showing whether they will likely find a fingerprint of anthropogenic climate change.

  3. RTMPL: A structured programming and documentation utility for real-time multiprocessor simulations

    NASA Technical Reports Server (NTRS)

    Arpasi, D. J.

    1984-01-01

    The NASA Lewis Research Center is developing and evaluating experimental hardware and software systems to help meet future needs for real time simulations of air-breathing propulsion systems. The Real Time Multiprocessor Simulator (RTMPS) project is aimed at developing a prototype simulator system that uses multiple microprocessors to achieve the desired computing speed and accuracy at relatively low cost. Software utilities are being developed to provide engineering-level programming and interactive operation of the simulator. Two major software development efforts were undertaken in the RTMPS project. A real time multiprocessor operating system was developed to provide for interactive operation of the simulator. The second effort was aimed at developing a structured, high-level, engineering-oriented programming language and translator that would facilitate the programming of the simulator. The Real Time Multiprocessor Programming Language (RTMPL) allows the user to describe simulation tasks for each processor in a straight-forward, structured manner. The RTMPL utility acts as an assembly language programmer, translating the high-level simulation description into time-efficient assembly language code for the processors. The utility sets up all of the interfaces between the simulator hardware, firmware, and operating system.

  4. 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.

  5. Kinetics of cold-set diffusion-limited aggregations of denatured whey protein isolate colloids.

    PubMed

    Wu, Hua; Xie, Jianjun; Morbidelli, Massimo

    2005-01-01

    The CaCl2-induced cold-set aggregation kinetics of the denatured whey protein isolate (WPI) colloids has been investigated under dilute diffusion-limited cluster aggregation (DLCA) conditions, using small-angle light scattering. In particular, the structure factor, the scattered intensity at zero angle and the average radius of gyration have been measured for the aggregating system as a function of time. It is found that the fractal dimension of the clusters is df= 1.85, in the range typical of clusters aggregated under DLCA conditions. The aggregation kinetics in this transition region can be described by a power law relation in the initial stage of the aggregation, but the exponent of the power law is equal to 0.7, i.e., significantly larger than 1/df= 0.54, which is the typical value of the DLCA kinetics. Since it is found that the average gyration radius of the clusters has reached a value of 80 microm, leading to a cumulative volume fraction of clusters equal to 0.25, it is legitimate to expect that the process is in the region of transition from aggregation to gelation. This confirmed by the fact that, at the later stage of the aggregation, the growth of the average cluster size further accelerates with time and eventually becomes explosive, leading to gelation. The observed aggregation kinetics has been compared with that reported in the literature from DLCA Monte Carlo simulations, and a good agreement has been found with the data corresponding to the transition region from aggregation to gelation. Numerical simulations using the Smoluchowski kinetic model have also been carried out in order to support the experimental findings.

  6. 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

  7. Time series analysis for minority game simulations of financial markets

    NASA Astrophysics Data System (ADS)

    Ferreira, Fernando F.; Francisco, Gerson; Machado, Birajara S.; Muruganandam, Paulsamy

    2003-04-01

    The minority game (MG) model introduced recently provides promising insights into the understanding of the evolution of prices, indices and rates in the financial markets. In this paper we perform a time series analysis of the model employing tools from statistics, dynamical systems theory and stochastic processes. Using benchmark systems and a financial index for comparison, several conclusions are obtained about the generating mechanism for this kind of evolution. The motion is deterministic, driven by occasional random external perturbation. When the interval between two successive perturbations is sufficiently large, one can find low dimensional chaos in this regime. However, the full motion of the MG model is found to be similar to that of the first differences of the SP500 index: stochastic, nonlinear and (unit root) stationary.

  8. A real-time, dual processor simulation of the rotor system research aircraft

    NASA Technical Reports Server (NTRS)

    Mackie, D. B.; Alderete, T. S.

    1977-01-01

    A real-time, man-in-the loop, simulation of the rotor system research aircraft (RSRA) was conducted. The unique feature of this simulation was that two digital computers were used in parallel to solve the equations of the RSRA mathematical model. The design, development, and implementation of the simulation are documented. Program validation was discussed, and examples of data recordings are given. This simulation provided an important research tool for the RSRA project in terms of safe and cost-effective design analysis. In addition, valuable knowledge concerning parallel processing and a powerful simulation hardware and software system was gained.

  9. Modelling of strongly coupled particle growth and aggregation

    NASA Astrophysics Data System (ADS)

    Gruy, F.; Touboul, E.

    2013-02-01

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

  10. Time-dependent inhibitory effects of cGMP-analogues on thrombin-induced platelet-derived microparticles formation, platelet aggregation, and P-selectin expression.

    PubMed

    Nygaard, Gyrid; Herfindal, Lars; Kopperud, Reidun; Aragay, Anna M; Holmsen, Holm; Døskeland, Stein Ove; Kleppe, Rune; Selheim, Frode

    2014-07-01

    In platelets, nitric oxide (NO) activates cGMP/PKG signalling, whereas prostaglandins and adenosine signal through cAMP/PKA. Cyclic nucleotide signalling has been considered to play an inhibitory role in platelets. However, an early stimulatory effect of NO and cGMP-PKG signalling in low dose agonist-induced platelet activation have recently been suggested. Here, we investigated whether different experimental conditions could explain some of the discrepancy reported for platelet cGMP-PKG-signalling. We treated gel-filtered human platelets with cGMP and cAMP analogues, and used flow cytometric assays to detect low dose thrombin-induced formation of small platelet aggregates, single platelet disappearance (SPD), platelet-derived microparticles (PMP) and thrombin receptor agonist peptide (TRAP)-induced P-selectin expression. All four agonist-induced platelet activation phases were blocked when platelets were costimulated with the PKG activators 8-Br-PET-cGMP or 8-pCPT-cGMP and low-doses of thrombin or TRAP. However, extended incubation with 8-Br-PET-cGMP decreased its inhibition of TRAP-induced P-selectin expression in a time-dependent manner. This effect did not involve desensitisation of PKG or PKA activity, measured as site-specific VASP phosphorylation. Moreover, PKG activators in combination with the PKA activator Sp-5,6-DCL-cBIMPS revealed additive inhibitory effect on TRAP-induced P-selectin expression. Taken together, we found no evidence for a stimulatory role of cGMP/PKG in platelets activation and conclude rather that cGMP/PKG signalling has an important inhibitory function in human platelet activation.

  11. A real time Pegasus propulsion system model for VSTOL piloted simulation evaluation

    NASA Technical Reports Server (NTRS)

    Mihaloew, J. R.; Roth, S. P.; Creekmore, R.

    1981-01-01

    A Pegasus-Harrier propulsion system is selected as a baseline for developing mathematical modeling and simulation techniques for VSTOL. Initially, static and dynamic propulsion system characteristics are modeled in detail to form a nonlinear aerothermodynamic digital computer simulation of a Pegasus engine. From this high fidelity simulation, a real-time propulsion model is formulated by applying a piecewise linear state variable methodology. A hydromechanical and water injection control system is also simulated. It is noted that the real-time dynamic model includes the detail and flexibility required for evaluating critical control parameters and propulsion component limits over a limited flight envelope.

  12. Surface fractals in liposome aggregation.

    PubMed

    Roldán-Vargas, Sándalo; Barnadas-Rodríguez, Ramon; Quesada-Pérez, Manuel; Estelrich, Joan; Callejas-Fernández, José

    2009-01-01

    In this work, the aggregation of charged liposomes induced by magnesium is investigated. Static and dynamic light scattering, Fourier-transform infrared spectroscopy, and cryotransmission electron microscopy are used as experimental techniques. In particular, multiple intracluster scattering is reduced to a negligible amount using a cross-correlation light scattering scheme. The analysis of the cluster structure, probed by means of static light scattering, reveals an evolution from surface fractals to mass fractals with increasing magnesium concentration. Cryotransmission electron microscopy micrographs of the aggregates are consistent with this interpretation. In addition, a comparative analysis of these results with those previously reported in the presence of calcium suggests that the different hydration energy between lipid vesicles when these divalent cations are present plays a fundamental role in the cluster morphology. This suggestion is also supported by infrared spectroscopy data. The kinetics of the aggregation processes is also analyzed through the time evolution of the mean diffusion coefficient of the aggregates. PMID:19257067

  13. Surface fractals in liposome aggregation.

    PubMed

    Roldán-Vargas, Sándalo; Barnadas-Rodríguez, Ramon; Quesada-Pérez, Manuel; Estelrich, Joan; Callejas-Fernández, José

    2009-01-01

    In this work, the aggregation of charged liposomes induced by magnesium is investigated. Static and dynamic light scattering, Fourier-transform infrared spectroscopy, and cryotransmission electron microscopy are used as experimental techniques. In particular, multiple intracluster scattering is reduced to a negligible amount using a cross-correlation light scattering scheme. The analysis of the cluster structure, probed by means of static light scattering, reveals an evolution from surface fractals to mass fractals with increasing magnesium concentration. Cryotransmission electron microscopy micrographs of the aggregates are consistent with this interpretation. In addition, a comparative analysis of these results with those previously reported in the presence of calcium suggests that the different hydration energy between lipid vesicles when these divalent cations are present plays a fundamental role in the cluster morphology. This suggestion is also supported by infrared spectroscopy data. The kinetics of the aggregation processes is also analyzed through the time evolution of the mean diffusion coefficient of the aggregates.

  14. Model for the evolution of the time profile in optimistic parallel discrete event simulations

    NASA Astrophysics Data System (ADS)

    Ziganurova, L.; Novotny, M. A.; Shchur, L. N.

    2016-02-01

    We investigate synchronisation aspects of an optimistic algorithm for parallel discrete event simulations (PDES). We present a model for the time evolution in optimistic PDES. This model evaluates the local virtual time profile of the processing elements. We argue that the evolution of the time profile is reminiscent of the surface profile in the directed percolation problem and in unrestricted surface growth. We present results of the simulation of the model and emphasise predictive features of our approach.

  15. Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations

    NASA Astrophysics Data System (ADS)

    Bylaska, Eric J.; Weare, Jonathan Q.; Weare, John H.

    2013-08-01

    Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f (e.g., Verlet algorithm), is available to propagate the system from time ti (trajectory positions and velocities xi = (ri, vi)) to time ti + 1 (xi + 1) by xi + 1 = fi(xi), the dynamics problem spanning an interval from t0…tM can be transformed into a root finding problem, F(X) = [xi - f(x(i - 1)]i = 1, M = 0, for the trajectory variables. The root finding problem is solved using a variety of root finding techniques, including quasi-Newton and preconditioned quasi-Newton schemes that are all unconditionally convergent. The algorithms are parallelized by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed parallel in time methods is discussed, and the effectiveness of various approaches to solving the root finding problem is tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD simulations, such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The parallel in time algorithms developed are tested by applying them to MD and AIMD simulations of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD simulation using Stillinger-Weber potentials, and a HCl + 4H2O AIMD simulation at the MP2 level. The maximum speedup (serial execution time/parallel execution time) obtained by parallelizing the Stillinger-Weber MD simulation was nearly 3.0. For the AIMD MP2 simulations, the algorithms achieved speedups of up to 14.3. The parallel in time algorithms can be implemented in a distributed computing

  16. Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations

    SciTech Connect

    Bylaska, Eric J.; Weare, Jonathan Q.; Weare, John H.

    2013-08-21

    Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f (e.g., Verlet algorithm), is available to propagate the system from time t{sub i} (trajectory positions and velocities x{sub i} = (r{sub i}, v{sub i})) to time t{sub i+1} (x{sub i+1}) by x{sub i+1} = f{sub i}(x{sub i}), the dynamics problem spanning an interval from t{sub 0}…t{sub M} can be transformed into a root finding problem, F(X) = [x{sub i} − f(x{sub (i−1})]{sub i} {sub =1,M} = 0, for the trajectory variables. The root finding problem is solved using a variety of root finding techniques, including quasi-Newton and preconditioned quasi-Newton schemes that are all unconditionally convergent. The algorithms are parallelized by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed parallel in time methods is discussed, and the effectiveness of various approaches to solving the root finding problem is tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD simulations, such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The parallel in time algorithms developed are tested by applying them to MD and AIMD simulations of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD simulation using Stillinger-Weber potentials, and a HCl + 4H{sub 2}O AIMD simulation at the MP2 level. The maximum speedup ((serial execution time)/(parallel execution time) ) obtained by parallelizing the Stillinger-Weber MD simulation was nearly 3.0. For the AIMD MP2 simulations, the algorithms achieved speedups of up

  17. Taming Wild Horses: The Need for Virtual Time-based Scheduling of VMs in Network Simulations

    SciTech Connect

    Yoginath, Srikanth B; Perumalla, Kalyan S; Henz, Brian J

    2012-01-01

    The next generation of scalable network simulators employ virtual machines (VMs) to act as high-fidelity models of traffic producer/consumer nodes in simulated networks. However, network simulations could be inaccurate if VMs are not scheduled according to virtual time, especially when many VMs are hosted per simulator core in a multi-core simulator environment. Since VMs are by default free-running, on the outset, it is not clear if, and to what extent, their untamed execution affects the results in simulated scenarios. Here, we provide the first quantitative basis for establishing the need for generalized virtual time scheduling of VMs in network simulators, based on an actual prototyped implementations. To exercise breadth, our system is tested with multiple disparate applications: (a) a set of message passing parallel programs, (b) a computer worm propagation phenomenon, and (c) a mobile ad-hoc wireless network simulation. We define and use error metrics and benchmarks in scaled tests to empirically report the poor match of traditional, fairness-based VM scheduling to VM-based network simulation, and also clearly show the better performance of our simulation-specific scheduler, with up to 64 VMs hosted on a 12-core simulator node.

  18. Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations.

    PubMed

    Bylaska, Eric J; Weare, Jonathan Q; Weare, John H

    2013-08-21

    Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f (e.g., Verlet algorithm), is available to propagate the system from time ti (trajectory positions and velocities xi = (ri, vi)) to time ti + 1 (xi + 1) by xi + 1 = fi(xi), the dynamics problem spanning an interval from t0[ellipsis (horizontal)]tM can be transformed into a root finding problem, F(X) = [xi - f(x(i - 1)]i = 1, M = 0, for the trajectory variables. The root finding problem is solved using a variety of root finding techniques, including quasi-Newton and preconditioned quasi-Newton schemes that are all unconditionally convergent. The algorithms are parallelized by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed parallel in time methods is discussed, and the effectiveness of various approaches to solving the root finding problem is tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD simulations, such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The parallel in time algorithms developed are tested by applying them to MD and AIMD simulations of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD simulation using Stillinger-Weber potentials, and a HCl + 4H2O AIMD simulation at the MP2 level. The maximum speedup (serial execution/timeparallel execution time) obtained by parallelizing the Stillinger-Weber MD simulation was nearly 3.0. For the AIMD MP2 simulations, the algorithms achieved speedups of up to 14.3. The parallel in time algorithms can be implemented in a

  19. Characteristics and control response of the TOPAZ II Reactor System Real-time Dynamic Simulator

    SciTech Connect

    Kwok, K.S.

    1993-11-12

    A dynamic simulator of the TOPAZ II reactor system has been developed for the Nuclear Electric Propulsion Space Test Program. The simulator combines first-principle modeling and empirical correlations in its algorithm to attain the modeling accuracy and computational through-put that are required for real-time execution. The overall execution time of the simulator for each time step is 15 ms when no data is written to the disk, and 18 ms when nine double precision data points are written to the disk once in every time step. The simulation program has been tested and it is able to handle a step decrease of $8 worth of reactivity. It also provides simulations of fuel, emitter, collector, stainless steel, and ZrH moderator failures. Presented in this paper are the models used in the calculations, a sample simulation session, and a discussion of the performance and limitations of the simulator. The simulator has been found to provide realistic real-time dynamic response of the TOPAZ II reactor system under both normal and casualty conditions.

  20. 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.

  1. 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

  2. Real-time hybrid computer simulation of a small turboshaft engine and control system

    NASA Technical Reports Server (NTRS)

    Hart, C. E.; Wenzel, L. M.

    1984-01-01

    The development of an analytical model of a small turboshaft engine designed for helicopter propulsion systems is described. The model equations were implemented on a hybrid computer system to provide a real time nonlinear simulation of the engine performance over a wide operating range. The real time hybrid simulation of the engine was used to evaluate a microprocessor based digital control module. This digital control module was developed as part of an advanced rotorcraft control program. After tests with the hybrid engine simulation the digital control module was used to control a real engine in an experimental program. A hybrid simulation of the engine's electrical hydromechanical control system was developed. This allowed to vary the fuel flow and torque load inputs to the hybrid engine simulation for simulating transient operation. A steady-state data and the experimental tests are compared. Analytical model equations, analog computer diagrams, and a digital computer flow chart are included.

  3. Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations

    SciTech Connect

    Bylaska, Eric J.; Weare, Jonathan Q.; Weare, John H.

    2013-08-21

    Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f , (e.g. Verlet algorithm) is available to propagate the system from time ti (trajectory positions and velocities xi = (ri; vi)) to time ti+1 (xi+1) by xi+1 = fi(xi), the dynamics problem spanning an interval from t0 : : : tM can be transformed into a root finding problem, F(X) = [xi - f (x(i-1)]i=1;M = 0, for the trajectory variables. The root finding problem is solved using a variety of optimization techniques, including quasi-Newton and preconditioned quasi-Newton optimization schemes that are all unconditionally convergent. The algorithms are parallelized by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed parallel in time methods is discussed and the effectiveness of various approaches to solving the root finding problem are tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD simulations such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The parallel in time algorithms developed are tested by applying them to MD and AIMD simulations of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD simulation using Stillinger-Weber potentials, and a HCl+4H2O AIMD simulation at the MP2 level. The maximum speedup obtained by parallelizing the Stillinger-Weber MD simulation was nearly 3.0. For the AIMD MP2 simulations the algorithms achieved speedups of up to 14.3. The parallel in time algorithms can be implemented in a distributed computing environment using very slow TCP/IP networks. Scripts

  4. Electromagnetic charges in aggregation phenomena.

    NASA Astrophysics Data System (ADS)

    Rioux, Claude; Slobodrian, R. J.

    Introduction The mechanism of fine particles aggregation is of great importance in many areas of research, in particular environment sciences where the state of aggregation defines the removal speed of dust from the atmosphere. The study of this mechanism is also important to understand the first stage of planet formation from the solar nebula. The aggregates formed are generally fractals and, as mentioned in the literature [1], the fractal dimensions and the site growth probability measures of the resulting fractal structures strongly depend on the properties of the forces that cause the aggregation. Theory and experimental apparatus We began this study by the aggregation between two charged particles and we are now consid-ering the aggregation between two magnetized particles. The aggregations are produced in a gas at a pressure between 10 and 1000 mbar and by using the applicable simplifications; we find that the distance (r) between the particles as a function of time (t) is given by the following equations: r=Ce(tf -t)1/3 for the electrical attraction r=Cm(tf -t)1/5 for the magnetic dipoles aligned in an external magnetic field. The apparatus built for these measurements consists of an experimental cell from which two perpendicular views are combined via an optical system in one image recorded by a video camera. From the video, we can then measure the distance between the particles as a function of time and reconstruct the trajectories in 3-D. The horizontal and vertical resolutions are respectively 0.86 and 0.92 microns per pixel. With a depth of field of 250 microns, the usable volume for 3-D observation in then 250 microns x 250 microns x 443 microns. Results and discussion A first version of the apparatus was tested on an electrical force aggregation and the results [2] show that the corresponding equation is a good representation of the phenomenon. Preliminary results, from an experiment using iron particles, show that the magnetic force can be seen in

  5. Impact of spatial and temporal aggregation of input parameters on the assessment of irrigation scheme performance

    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

  6. 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.

  7. Optimizing off-lattice Diffusion-Limited Aggregation

    NASA Astrophysics Data System (ADS)

    Kuijpers, Kasper R.; de Martín, Lilian; van Ommen, J. Ruud

    2014-03-01

    We present a technique to improve the time scaling of Diffusion-Limited Aggregation simulations. The proposed method reduces the number of calculations by making an extensive use of the RAM memory to store information about the particles’ positions and distances. We have simulated clusters up to 5ṡ106 particles in 2D and up to 1ṡ106 particles in 3D and compared the calculation times with previous algorithms proposed in the literature. Our method scales t∝Np1.08, outperforming the current optimization techniques.

  8. The Trick Simulation Toolkit: A NASA/Opensource Framework for Running Time Based Physics Models

    NASA Technical Reports Server (NTRS)

    Penn, John M.

    2016-01-01

    The Trick Simulation Toolkit is a simulation development environment used to create high fidelity training and engineering simulations at the NASA Johnson Space Center and many other NASA facilities. Its purpose is to generate a simulation executable from a collection of user-supplied models and a simulation definition file. For each Trick-based simulation, Trick automatically provides job scheduling, numerical integration, the ability to write and restore human readable checkpoints, data recording, interactive variable manipulation, a run-time interpreter, and many other commonly needed capabilities. This allows simulation developers to concentrate on their domain expertise and the algorithms and equations of their models. Also included in Trick are tools for plotting recorded data and various other supporting utilities and libraries. Trick is written in C/C++ and Java and supports both Linux and MacOSX computer operating systems. This paper describes Trick's design and use at NASA Johnson Space Center.

  9. Satellite-matrix-switched, time-division-multiple-access network simulator

    NASA Technical Reports Server (NTRS)

    Ivancic, William D.; Andro, Monty; Nagy, Lawrence A.; Budinger, James M.; Shalkhauser, Mary JO

    1989-01-01

    A versatile experimental Ka-band network simulator has been implemented at the NASA Lewis Research Center to demonstrate and evaluate a satellite-matrix-switched, time-division-multiple-access (SMS-TDMA) network and to evaluate future digital ground terminals and radiofrequency (RF) components. The simulator was implemented by using proof-of-concept RF components developed under NASA contracts and digital ground terminal and link simulation hardware developed at Lewis. This simulator provides many unique capabilities such as satellite range delay and variation simulation and rain fade simulation. All network parameters (e.g., signal-to-noise ratio, satellite range variation rate, burst density, and rain fade) are controlled and monitored by a central computer. The simulator is presently configured as a three-ground-terminal SMS-TDMA network.

  10. Time-dependent inhibitory effects of cGMP-analogues on thrombin-induced platelet-derived microparticles formation, platelet aggregation, and P-selectin expression

    SciTech Connect

    Nygaard, Gyrid; Herfindal, Lars; Kopperud, Reidun; Aragay, Anna M.; Holmsen, Holm; Døskeland, Stein Ove; Kleppe, Rune; Selheim, Frode

    2014-07-04

    Highlights: • We investigated the impact of cyclic nucleotide analogues on platelet activation. • Different time dependence were found for inhibition of platelet activation. • Additive effect was found using PKA- and PKG-activating analogues. • Our results may explain some of the discrepancies reported for cNMP signalling. - Abstract: In platelets, nitric oxide (NO) activates cGMP/PKG signalling, whereas prostaglandins and adenosine signal through cAMP/PKA. Cyclic nucleotide signalling has been considered to play an inhibitory role in platelets. However, an early stimulatory effect of NO and cGMP-PKG signalling in low dose agonist-induced platelet activation have recently been suggested. Here, we investigated whether different experimental conditions could explain some of the discrepancy reported for platelet cGMP-PKG-signalling. We treated gel-filtered human platelets with cGMP and cAMP analogues, and used flow cytometric assays to detect low dose thrombin-induced formation of small platelet aggregates, single platelet disappearance (SPD), platelet-derived microparticles (PMP) and thrombin receptor agonist peptide (TRAP)-induced P-selectin expression. All four agonist-induced platelet activation phases were blocked when platelets were costimulated with the PKG activators 8-Br-PET-cGMP or 8-pCPT-cGMP and low-doses of thrombin or TRAP. However, extended incubation with 8-Br-PET-cGMP decreased its inhibition of TRAP-induced P-selectin expression in a time-dependent manner. This effect did not involve desensitisation of PKG or PKA activity, measured as site-specific VASP phosphorylation. Moreover, PKG activators in combination with the PKA activator Sp-5,6-DCL-cBIMPS revealed additive inhibitory effect on TRAP-induced P-selectin expression. Taken together, we found no evidence for a stimulatory role of cGMP/PKG in platelets activation and conclude rather that cGMP/PKG signalling has an important inhibitory function in human platelet activation.

  11. Some real-time simulation applications to Space Shuttle approach and landing design and test

    NASA Technical Reports Server (NTRS)

    Law, H. G., III; Stegall, H. W.

    1984-01-01

    In the present discussion of the roles played by real time, man-in-the-loop engineering simulation in the development of NASA Space Shuttle approaches and landings, attention is given to the function of the simulator as a design and verification tool. Aspects of the problem posed by Shuttle landings, and the difficulties involved in this problem's quantification, are noted. Recent results of control system studies for pitch axis control, using fixed- and motion-base simulators, are discussed.

  12. Real-time simulation of an automotive gas turbine using the hybrid computer

    NASA Technical Reports Server (NTRS)

    Costakis, W.; Merrill, W. C.

    1984-01-01

    A hybrid computer simulation of an Advanced Automotive Gas Turbine Powertrain System is reported. The system consists of a gas turbine engine, an automotive drivetrain with four speed automatic transmission, and a control system. Generally, dynamic performance is simulated on the analog portion of the hybrid computer while most of the steady state performance characteristics are calculated to run faster than real time and makes this simulation a useful tool for a variety of analytical studies.

  13. Real-time digital simulator with digital/analog conversion interface for testing power instruments

    SciTech Connect

    Taoka, Hisao; Iyoda, Isao; Noguchi, Hideo ); Sato, Nobuyuki; Nakazawa, Taro; Yamazaki, Akira )

    1994-05-01

    The need for real-time simulation stems from the fact that in many practical situations it is desirable to analyze the dynamic behavior of a large power system with advanced equipment that has complex and high-speed performance. Analog simulators are effective, however they impose serious limitations on the size of the system that is being modeled. The authors have studied and developed a real-time digital simulator using a hypercube computer, and realized a real-time performance available for the analysis of large power systems. Now as the second step of their study, they developed a digital/analog conversion interface for testing actual power instruments. The interface exchanges the variables of fundamental frequency domain in the real-time digital simulator, and the variables of exact time domain in the analog equipment connected to the simulator. In this paper, the authors describe the detail of their digital/analog conversion interface of a real-time digital simulator for testing advanced power instruments. Its conversion algorithm, system configuration of the simulator with the interface, experimental results are also presented in it.

  14. A real-time infrared imaging simulation method with physical effects modeling of infrared sensors

    NASA Astrophysics Data System (ADS)

    Li, Ni; Huai, Wenqing; Wang, Shaodan; Ren, Lei

    2016-09-01

    Infrared imaging simulation technology can provide infrared data sources for the development, improvement and evaluation of infrared imaging systems under different environment, status and weather conditions, which is reusable and more economic than physical experiments. A real-time infrared imaging simulation process is established to reproduce a complete physical imaging process. Our emphasis is put on the modeling of infrared sensors, involving physical effects of both spatial domain and frequency domain. An improved image convolution method is proposed based on GPU parallel processing to enhance the real-time simulation ability with ensuring its simulation accuracy at the same time. Finally the effectiveness of the above methods is validated by simulation analysis and result comparison.

  15. Enhancing real-time flight simulation execution by intercepting Run-Time Library calls

    NASA Technical Reports Server (NTRS)

    Reinbachs, Namejs

    1993-01-01

    Standard operating system input-output (I/O) procedures impose a large time penalty on real-time program execution. These procedures are generally invoked by way of Run-Time Library (RTL) calls. To reduce the time penalty, as well as add flexibility, a technique has been developed to dynamically intercept these calls. The design and implementation of this technique, as applied to FORTRAN WRITE statements, are described. Measured performance gains using this RTL intercept technique are on the order of 1000 percent.

  16. Land-Use Analysis and Simulated Effects of Land-Use Change and Aggregate Mining on Groundwater Flow in the South Platte River Valley, Brighton to Fort Lupton, Colorado

    USGS Publications Warehouse

    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

  17. 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.

  18. Real-time simulation of an airborne radar for overwater approaches

    NASA Technical Reports Server (NTRS)

    Karmarkar, J.; Clark, D.

    1982-01-01

    Software developed to provide a real time simulation of an airborne radar for overwater approaches to oil rig platforms is documented. The simulation is used to study advanced concepts for enhancement of airborne radar approaches (ARA) in order to reduce crew workload, improve approach tracking precision, and reduce weather minimums. ARA's are currently used for offshore helicopter operations to and from oil rigs.

  19. Stabilizing Off-pathway Oligomers by Polyphenol Nanoassemblies for IAPP Aggregation Inhibition.

    PubMed

    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. PMID:26763863

  20. Stabilizing Off-pathway Oligomers by Polyphenol Nanoassemblies for IAPP Aggregation Inhibition

    PubMed Central

    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. PMID:26763863

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

    PubMed Central

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

    2014-01-01

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

  2. Real-time infrared signature model validation for hardware-in-the-loop simulations

    NASA Astrophysics Data System (ADS)

    Sanders, Jeffrey S.; Peters, Trina S.

    1997-07-01

    Techniques and tools for validation of real-time infrared target signature models are presented. The model validation techniques presented in this paper were developed for hardware-in-the-loop (HWIL) simulations at the U.S. Army Missile Command's Research, Development, and Engineering Center. Real-time target model validation is a required deliverable to the customer of a HWIL simulation facility and is a critical part of ensuring the fidelity of a HWIL simulation. There are two levels of real-time target model validation. The first level is comparison of the target model to some baseline or measured data which answers the question `are the simulation inputs correct?'. The second level of validation is a simulation validation which answers the question `for a given target model input is the simulation hardware and software generating the correct output?'. This paper deals primarily with the first level of target model validation. IR target signature models have often been validated by subjective visual inspection or by objective, but limited, statistical comparisons. Subjective methods can be very satisfying to the simulation developer but offer little comfort to the simulation customer since subjective methods cannot be documented. Generic statistical methods offer a level of documentation, yet are often not robust enough to fully test the fidelity of an IR signature. Advances in infrared seeker and sensor technology have led to the necessity of system specific target model validation. For any HWIL simulation it must be demonstrated that the sensor responds to the real-time signature model in a manner which is functionally equivalent to the sensor's response to a baseline model. Depending on the application, a baseline method can be measured IR imagery or the output of a validated IR signature prediction code. Tools are described that generate validation data for HWIL simulations at MICOM and example real-time model validations are presented.

  3. 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.

  4. RATE-ADJUSTMENT ALGORITHM FOR AGGREGATE TCP CONGESTION CONTROL

    SciTech Connect

    P. TINNAKORNSRISUPHAP, ET AL

    2000-09-01

    The TCP congestion-control mechanism is an algorithm designed to probe the available bandwidth of the network path that TCP packets traverse. However, it is well-known that the TCP congestion-control mechanism does not perform well on networks with a large bandwidth-delay product due to the slow dynamics in adapting its congestion window, especially for short-lived flows. One promising solution to the problem is to aggregate and share the path information among TCP connections that traverse the same bottleneck path, i.e., Aggregate TCP. However, this paper shows via a queueing analysis of a generalized processor-sharing (GPS) queue with regularly-varying service time that a simple aggregation of local TCP connections together into a single aggregate TCP connection can result in a severe performance degradation. To prevent such a degradation, we introduce a rate-adjustment algorithm. Our simulation confirms that by utilizing our rate-adjustment algorithm on aggregate TCP, connections which would normally receive poor service achieve significant performance improvements without penalizing connections which already receive good service.

  5. Computational approaches to understanding protein aggregation in neurodegeneration

    PubMed Central

    Redler, Rachel L.; Shirvanyants, David; Dagliyan, Onur; Ding, Feng; Kim, Doo Nam; Kota, Pradeep; Proctor, Elizabeth A.; Ramachandran, Srinivas; Tandon, Arpit; Dokholyan, Nikolay V.

    2014-01-01

    The generation of toxic non-native protein conformers has emerged as a unifying thread among disorders such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. Atomic-level detail regarding dynamical changes that facilitate protein aggregation, as well as the structural features of large-scale ordered aggregates and soluble non-native oligomers, would contribute significantly to current understanding of these complex phenomena and offer potential strategies for inhibiting formation of cytotoxic species. However, experimental limitations often preclude the acquisition of high-resolution structural and mechanistic information for aggregating systems. Computational methods, particularly those combine both all-atom and coarse-grained simulations to cover a wide range of time and length scales, have thus emerged as crucial tools for investigating protein aggregation. Here we review the current state of computational methodology for the study of protein self-assembly, with a focus on the application of these methods toward understanding of protein aggregates in human neurodegenerative disorders. PMID:24620031

  6. The transition of a real-time single-rotor helicopter simulation program to a supercomputer

    NASA Technical Reports Server (NTRS)

    Martinez, Debbie

    1995-01-01

    This report presents the conversion effort and results of a real-time flight simulation application transition to a CONVEX supercomputer. Enclosed is a detailed description of the conversion process and a brief description of the Langley Research Center's (LaRC) flight simulation application program structure. Currently, this simulation program may be configured to represent Sikorsky S-61 helicopter (a five-blade, single-rotor, commercial passenger-type helicopter) or an Army Cobra helicopter (either the AH-1 G or AH-1 S model). This report refers to the Sikorsky S-61 simulation program since it is the most frequently used configuration.

  7. Ensemble Sampling vs. Time Sampling in Molecular Dynamics Simulations of Thermal Conductivity

    DOE PAGES

    Gordiz, Kiarash; Singh, David J.; Henry, Asegun

    2015-01-29

    In this report we compare time sampling and ensemble averaging as two different methods available for phase space sampling. For the comparison, we calculate thermal conductivities of solid argon and silicon structures, using equilibrium molecular dynamics. We introduce two different schemes for the ensemble averaging approach, and show that both can reduce the total simulation time as compared to time averaging. It is also found that velocity rescaling is an efficient mechanism for phase space exploration. Although our methodology is tested using classical molecular dynamics, the ensemble generation approaches may find their greatest utility in computationally expensive simulations such asmore » first principles molecular dynamics. For such simulations, where each time step is costly, time sampling can require long simulation times because each time step must be evaluated sequentially and therefore phase space averaging is achieved through sequential operations. On the other hand, with ensemble averaging, phase space sampling can be achieved through parallel operations, since each ensemble is independent. For this reason, particularly when using massively parallel architectures, ensemble sampling can result in much shorter simulation times and exhibits similar overall computational effort.« less

  8. Ensemble Sampling vs. Time Sampling in Molecular Dynamics Simulations of Thermal Conductivity

    SciTech Connect

    Gordiz, Kiarash; Singh, David J.; Henry, Asegun

    2015-01-29

    In this report we compare time sampling and ensemble averaging as two different methods available for phase space sampling. For the comparison, we calculate thermal conductivities of solid argon and silicon structures, using equilibrium molecular dynamics. We introduce two different schemes for the ensemble averaging approach, and show that both can reduce the total simulation time as compared to time averaging. It is also found that velocity rescaling is an efficient mechanism for phase space exploration. Although our methodology is tested using classical molecular dynamics, the ensemble generation approaches may find their greatest utility in computationally expensive simulations such as first principles molecular dynamics. For such simulations, where each time step is costly, time sampling can require long simulation times because each time step must be evaluated sequentially and therefore phase space averaging is achieved through sequential operations. On the other hand, with ensemble averaging, phase space sampling can be achieved through parallel operations, since each ensemble is independent. For this reason, particularly when using massively parallel architectures, ensemble sampling can result in much shorter simulation times and exhibits similar overall computational effort.

  9. SAR image simulation in the time domain for moving ocean surfaces.

    PubMed

    Yoshida, Takero; Rheem, Chang-Kyu

    2013-04-02

    This paper presents a fundamental simulation method to generate synthetic aperture radar (SAR) images for moving ocean surfaces. We have designed the simulation based on motion induced modulations and Bragg scattering, which are important features of ocean SAR images. The time domain simulation is able to obtain time series of microwave backscattering modulated by the orbital motions of ocean waves. Physical optics approximation is applied to calculate microwave backscattering. The computational grids are smaller than transmit microwave to demonstrate accurate interaction between electromagnetic waves and ocean surface waves. In this paper, as foundations for SAR image simulation of moving ocean surfaces, the simulation is carried out for some targets and ocean waves. The SAR images of stationary and moving targets are simulated to confirm SAR signal processing and motion induced modulation. Furthermore, the azimuth signals from the regular wave traveling to the azimuth direction also show the azimuthal shifts due to the orbital motions. In addition, incident angle dependence is simulated for irregular wind waves to compare with Bragg scattering theory. The simulation results are in good agreement with the theory. These results show that the simulation is applicable for generating numerical SAR images of moving ocean surfaces.

  10. Nonadiabatic dynamics and simulation of time resolved photoelectron spectra within time-dependent density functional theory: Ultrafast photoswitching in benzylideneaniline

    SciTech Connect

    Mitric, Roland; Werner, Ute; Bonacic-Koutecky, Vlasta

    2008-10-28

    We present a theoretical approach for the nonadiabatic dynamics 'on the fly' based on the combination of the time-dependent density functional theory (TDDFT) with Tully's stochastic surface hopping method. Our formulation is based on localized Gaussian basis sets and is suitable for the simulation of ultrafast processes in complex molecular systems including all degrees of freedom. Our approach is used for the simulation of time resolved photoelectron spectra in the framework of the Wigner distribution approach. In order to illustrate the scope of the method, we study the ultrafast photoswitching dynamics of the prototype Schiff base benzylideneaniline (BAN). The nonradiative lifetime of the S{sub 1} state of BAN is determined to be {approx}200 fs. The mechanism of the photoisomerization has been investigated and a connection between the time resolved photoelectron signal and the underlying nonadiabatic processes has been established.

  11. Wavelet-based surrogate time series for multiscale simulation of heterogeneous catalysis

    DOE PAGES

    Savara, Aditya Ashi; Daw, C. Stuart; Xiong, Qingang; Gur, Sourav; Danielson, Thomas L.; Hin, Celine N.; Pannala, Sreekanth; Frantziskonis, George N.

    2016-01-28

    We propose a wavelet-based scheme that encodes the essential dynamics of discrete microscale surface reactions in a form that can be coupled with continuum macroscale flow simulations with high computational efficiency. This makes it possible to simulate the dynamic behavior of reactor-scale heterogeneous catalysis without requiring detailed concurrent simulations at both the surface and continuum scales using different models. Our scheme is based on the application of wavelet-based surrogate time series that encodes the essential temporal and/or spatial fine-scale dynamics at the catalyst surface. The encoded dynamics are then used to generate statistically equivalent, randomized surrogate time series, which canmore » be linked to the continuum scale simulation. As a result, we illustrate an application of this approach using two different kinetic Monte Carlo simulations with different characteristic behaviors typical for heterogeneous chemical reactions.« less

  12. Continuous variable quantum optical simulation for time evolution of quantum harmonic oscillators

    PubMed Central

    Deng, Xiaowei; Hao, Shuhong; Guo, Hong; Xie, Changde; Su, Xiaolong

    2016-01-01

    Quantum simulation enables one to mimic the evolution of other quantum systems using a controllable quantum system. Quantum harmonic oscillator (QHO) is one of the most important model systems in quantum physics. To observe the transient dynamics of a QHO with high oscillation frequency directly is difficult. We experimentally simulate the transient behaviors of QHO in an open system during time evolution with an optical mode and a logical operation system of continuous variable quantum computation. The time evolution of an atomic ensemble in the collective spontaneous emission is analytically simulated by mapping the atomic ensemble onto a QHO. The measured fidelity, which is used for quantifying the quality of the simulation, is higher than its classical limit. The presented simulation scheme provides a new tool for studying the dynamic behaviors of QHO. PMID:26961962

  13. SIMSAT: An object oriented architecture for real-time satellite simulation

    NASA Technical Reports Server (NTRS)

    Williams, Adam P.

    1993-01-01

    Real-time satellite simulators are vital tools in the support of satellite missions. They are used in the testing of ground control systems, the training of operators, the validation of operational procedures, and the development of contingency plans. The simulators must provide high-fidelity modeling of the satellite, which requires detailed system information, much of which is not available until relatively near launch. The short time-scales and resulting high productivity required of such simulator developments culminates in the need for a reusable infrastructure which can be used as a basis for each simulator. This paper describes a major new simulation infrastructure package, the Software Infrastructure for Modelling Satellites (SIMSAT). It outlines the object oriented design methodology used, describes the resulting design, and discusses the advantages and disadvantages experienced in applying the methodology.

  14. Continuous variable quantum optical simulation for time evolution of quantum harmonic oscillators.

    PubMed

    Deng, Xiaowei; Hao, Shuhong; Guo, Hong; Xie, Changde; Su, Xiaolong

    2016-03-10

    Quantum simulation enables one to mimic the evolution of other quantum systems using a controllable quantum system. Quantum harmonic oscillator (QHO) is one of the most important model systems in quantum physics. To observe the transient dynamics of a QHO with high oscillation frequency directly is difficult. We experimentally simulate the transient behaviors of QHO in an open system during time evolution with an optical mode and a logical operation system of continuous variable quantum computation. The time evolution of an atomic ensemble in the collective spontaneous emission is analytically simulated by mapping the atomic ensemble onto a QHO. The measured fidelity, which is used for quantifying the quality of the simulation, is higher than its classical limit. The presented simulation scheme provides a new tool for studying the dynamic behaviors of QHO.

  15. Continuous variable quantum optical simulation for time evolution of quantum harmonic oscillators

    NASA Astrophysics Data System (ADS)

    Deng, Xiaowei; Hao, Shuhong; Guo, Hong; Xie, Changde; Su, Xiaolong

    2016-03-01

    Quantum simulation enables one to mimic the evolution of other quantum systems using a controllable quantum system. Quantum harmonic oscillator (QHO) is one of the most important model systems in quantum physics. To observe the transient dynamics of a QHO with high oscillation frequency directly is difficult. We experimentally simulate the transient behaviors of QHO in an open system during time evolution with an optical mode and a logical operation system of continuous variable quantum computation. The time evolution of an atomic ensemble in the collective spontaneous emission is analytically simulated by mapping the atomic ensemble onto a QHO. The measured fidelity, which is used for quantifying the quality of the simulation, is higher than its classical limit. The presented simulation scheme provides a new tool for studying the dynamic behaviors of QHO.

  16. Relaxation times in deformed polymer glasses: A comparison between molecular simulations and two theories

    NASA Astrophysics Data System (ADS)

    Rottler, Jörg

    2016-08-01

    Relaxation times in polymer glasses are computed with molecular dynamics simulations of a coarse-grained polymer model during creep and constant strain rate deformation. The dynamics is governed by a competition between physical aging that increases relaxation times and applied load or strain rate which accelerates dynamics. We compare the simulation results quantitatively to two recently developed theories of polymer deformation, which treat aging and rejuvenation in an additive manner. Through stress release and strain rate reversal simulations, we then show that the quantity governing mechanical rejuvenation is the rate of irreversible work performed on the polymer.

  17. Flow Partitioning in Fully Saturated Soil Aggregates

    SciTech Connect

    Yang, Xiaofan; Richmond, Marshall C.; Scheibe, Timothy D.; Perkins, William A.; Resat, Haluk

    2014-03-30

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

  18. Audibility of dispersion error in room acoustic finite-difference time-domain simulation as a function of simulation distance.

    PubMed

    Saarelma, Jukka; Botts, Jonathan; Hamilton, Brian; Savioja, Lauri

    2016-04-01

    Finite-difference time-domain (FDTD) simulation has been a popular area of research in room acoustics due to its capability to simulate wave phenomena in a wide bandwidth directly in the time-domain. A downside of the method is that it introduces a direction and frequency dependent error to the simulated sound field due to the non-linear dispersion relation of the discrete system. In this study, the perceptual threshold of the dispersion error is measured in three-dimensional FDTD schemes as a function of simulation distance. Dispersion error is evaluated for three different explicit, non-staggered FDTD schemes using the numerical wavenumber in the direction of the worst-case error of each scheme. It is found that the thresholds for the different schemes do not vary significantly when the phase velocity error level is fixed. The thresholds are found to vary significantly between the different sound samples. The measured threshold for the audibility of dispersion error at the probability level of 82% correct discrimination for three-alternative forced choice is found to be 9.1 m of propagation in a free field, that leads to a maximum group delay error of 1.8 ms at 20 kHz with the chosen phase velocity error level of 2%. PMID:27106330

  19. Audibility of dispersion error in room acoustic finite-difference time-domain simulation as a function of simulation distance.

    PubMed

    Saarelma, Jukka; Botts, Jonathan; Hamilton, Brian; Savioja, Lauri

    2016-04-01

    Finite-difference time-domain (FDTD) simulation has been a popular area of research in room acoustics due to its capability to simulate wave phenomena in a wide bandwidth directly in the time-domain. A downside of the method is that it introduces a direction and frequency dependent error to the simulated sound field due to the non-linear dispersion relation of the discrete system. In this study, the perceptual threshold of the dispersion error is measured in three-dimensional FDTD schemes as a function of simulation distance. Dispersion error is evaluated for three different explicit, non-staggered FDTD schemes using the numerical wavenumber in the direction of the worst-case error of each scheme. It is found that the thresholds for the different schemes do not vary significantly when the phase velocity error level is fixed. The thresholds are found to vary significantly between the different sound samples. The measured threshold for the audibility of dispersion error at the probability level of 82% correct discrimination for three-alternative forced choice is found to be 9.1 m of propagation in a free field, that leads to a maximum group delay error of 1.8 ms at 20 kHz with the chosen phase velocity error level of 2%.

  20. Real-Time Hardware-in-the-Loop Simulation of Ares I Launch Vehicle

    NASA Technical Reports Server (NTRS)

    Tobbe, Patrick; Matras, Alex; Walker, David; Wilson, Heath; Fulton, Chris; Alday, Nathan; 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 at the Marshall Space Flight Center. The primary purpose of the Ares System Integration Laboratory is to test the vehicle avionics hardware and software in a hardware - in-the-loop environment to certify that the integrated system is prepared for flight. ARTEMIS has been designed to be the real-time simulation backbone to stimulate all required Ares components for verification testing. ARTE_VIIS provides high -fidelity dynamics, actuator, and sensor models to simulate an accurate flight trajectory in order to ensure realistic test conditions. ARTEMIS has been designed to take advantage of the advances in underlying computational power now available to support hardware-in-the-loop testing to achieve real-time simulation with unprecedented model fidelity. A modular realtime design relying on a fully distributed computing architecture has been implemented.

  1. Third-order symplectic integration method with inverse time dispersion transform for long-term simulation

    NASA Astrophysics Data System (ADS)

    Gao, Yingjie; Zhang, Jinhai; Yao, Zhenxing

    2016-06-01

    The symplectic integration method is popular in high-accuracy numerical simulations when discretizing temporal derivatives; however, it still suffers from time-dispersion error when the temporal interval is coarse, especially for long-term simulations and large-scale models. We employ the inverse time dispersion transform (ITDT) to the third-order symplectic integration method to reduce the time-dispersion error. First, we adopt the pseudospectral algorithm for the spatial discretization and the third-order symplectic integration method for the temporal discretization. Then, we apply the ITDT to eliminate time-dispersion error from the synthetic data. As a post-processing method, the ITDT can be easily cascaded in traditional numerical simulations. We implement the ITDT in one typical exiting third-order symplectic scheme and compare its performances with the performances of the conventional second-order scheme and the rapid expansion method. Theoretical analyses and numerical experiments show that the ITDT can significantly reduce the time-dispersion error, especially for long travel times. The implementation of the ITDT requires some additional computations on correcting the time-dispersion error, but it allows us to use the maximum temporal interval under stability conditions; thus, its final computational efficiency would be higher than that of the traditional symplectic integration method for long-term simulations. With the aid of the ITDT, we can obtain much more accurate simulation results but with a lower computational cost.

  2. Real-time simulation of aeroelastic rotor loads for horizontal axis wind turbines

    NASA Astrophysics Data System (ADS)

    Marnett, M.; Wellenberg, S.; Schröder, W.

    2014-06-01

    Wind turbine drivetrain research and test facilities with hardware-in-the-loop capabilities require a robust and accurate aeroelastic real-time rotor simulation environment. Recent simulation environments do not guarantee a computational response at real-time. Which is why a novel simulation tool has been developed. It resolves the physical time domain of the turbulent wind spectra and the operational response of the turbine at real-time conditions. Therefore, there is a trade-off between accuracy of the physical models and the computational costs. However, the study shows the possibility to preserve the necessary computational accuracy while simultaneously granting dynamic interaction with the aeroelastic rotor simulation environment. The achieved computational costs allow a complete aeroelastic rotor simulation at a resolution frequency of 100 Hz on standard computer platforms. Results obtained for the 5-MW reference wind turbine by the National Renewable Energy Laboratory (NREL) are discussed and compared to NREL's fatigue, aerodynamics, structures, and turbulence (FAST)- Code. The rotor loads show a convincing match. The novel simulation tool is applied to the wind turbine drivetrain test facility at the Center for Wind Power Drives (CWD), RWTH Aachen University to show the real-time hardware-in-the-loop capabilities.

  3. A piecewise linear state variable technique for real time propulsion system simulation

    NASA Technical Reports Server (NTRS)

    Mihaloew, J. R.; Roth, S. P.

    1982-01-01

    The emphasis on increased aircraft and propulsion control system integration and piloted simulation has created a need for higher fidelity real time dynamic propulsion models. A real time propulsion system modeling technique which satisfies this need and which provides the capabilities needed to evaluate propulsion system performance and aircraft system interaction on manned flight simulators was developed and demonstrated using flight simulator facilities at NASA Ames. A piecewise linear state variable technique is used. This technique provides the system accuracy, stability and transient response required for integrated aircraft and propulsion control system studies. The real time dynamic model includes the detail and flexibility required for the evaluation of critical control parameters and propulsion component limits over a limited flight envelope. The model contains approximately 7.0 K bytes of in-line computational code and 14.7 K of block data. It has an 8.9 ms cycle time on a Xerox Sigma 9 computer. A Pegasus-Harrier propulsion system was used as a baseline for developing the mathematical modeling and simulation technique. A hydromechanical and water injection control system was also simulated. The model was programmed for interfacing with a Harrier aircraft simulation at NASA Ames. Descriptions of the real time methodology and model capabilities are presented.

  4. A Piecewise Linear State Variable Technique for Real Time Propulsion System Simulation

    NASA Technical Reports Server (NTRS)

    Mihaloew, J. R.; Roth, S. P.

    1982-01-01

    The emphasis on increased aircraft and propulsion control system integration and piloted simulation has created a need for higher fidelity real time dynamic propulsion models. A real time propulsion system modeling technique which satisfies this need and which provides the capabilities needed to evaluate propulsion system performance and aircraft system interaction on manned flight simulators was developed and demonstrated using flight simulator facilities at NASA Ames. A piecewise linear state variable technique is used. This technique provides the system accuracy, stability and transient response required for integrated aircraft and propulsion control system studies. The real time dynamic model includes the detail and flexibility required for the evaluation of critical control parameters and propulsion component limits over a limited flight envelope. The model contains approximately 7.0 K bytes of in-line computational code and 14.7 K of block data. It has an 8.9 ms cycle time on a Xerox Sigma 9 computer. A Pegasus-Harrier propulsion system was used as a baseline for developing the mathematical modeling and simulation technique. A hydromechanical and water injection control system was also simulated. The model was programmed for interfacing with a Harrier aircraft simulation at NASA Ames. Descriptions of the real time methodology and model capabilities are presented.

  5. Novel insights into amylin aggregation

    PubMed Central

    Pillay, Karen; Govender, Patrick

    2014-01-01

    Amylin is a peptide that aggregates into species that are toxic to pancreatic beta cells, leading to type II diabetes. This study has for the first time quantified amylin association and dissociation kinetics (association constant (ka) = 28.7 ± 5.1 L mol−1 s−1 and dissociation constant (kd) = 2.8 ± 0.6 ×10−4 s−1) using surface plasmon resonance (SPR). Thus far, techniques used for the sizing of amylin aggregates do not cater for the real-time monitoring of unconstrained amylin in solution. In this regard we evaluated recently innovated nanoparticle tracking analysis (NTA). In addition, both SPR and NTA were used to study the effect of previously synthesized amylin derivatives on amylin aggregation and to evaluate their potential as a cell-free system for screening potential inhibitors of amylin-mediated cytotoxicity. Results obtained from NTA highlighted a predominance of 100–300 nm amylin aggregates and correlation to previously published cytotoxicity results suggests the toxic species of amylin to be 200–300 nm in size. The results seem to indicate that NTA has potential as a new technique to monitor the aggregation potential of amyloid peptides in solution and also to screen potential inhibitors of amylin-mediated cytotoxicity. PMID:26019498

  6. Sub-Daily Runoff Simulations with Parameters Inferred at the Daily Time Scale: Impacts of the temporal distribution of rainfall in parameter inference.

    NASA Astrophysics Data System (ADS)

    Reynolds Puga, Jose Eduardo; Halldin, Sven; Xu, Chong-Yu; Seibert, Jan

    2016-04-01

    Flood forecasting at sub-daily time scales are commonly required in regions where sub-daily observational data are not available. This has led to approaches to estimate model parameters at sub-daily time scales from data with a lower time resolution. Reynolds et al. (2015) show that parameters inferred at one time scale (e.g., daily) may be used directly for runoff simulations at other time scales (e.g., 1 h) when the modelling time step is the same and sufficiently small during calibration and simulation periods. Their approach produced parameter distributions at daily and sub-daily time scales that were similar and relatively constant across the time scales. The transfer of parameter values across time scales resulted in small model-performance decrease as opposed to when the parameter sets inferred at their respective time scale were used. This decrease in performance may be attributed to the degree of information lost, in terms of the physical processes occurring at short time scales, when the rainfall-runoff data used during the parameter-inference phase become coarser. It is not yet fully understood how the aggregation (or disaggregation) of the rainfall-runoff data affects parameter inference. In this study we analyse the impacts of the temporal distribution of rainfall for inferring model parameters at a coarse time scale and their effects in model performance when they are used at finer time scales, where data may not be available for calibration. The motivation is to improve runoff predictions and model performance at sub-daily time scales when parameters inferred at the daily scale are used for simulating at these scales. First, we calibrated the HBV-light conceptual hydrological model at the daily scale, but modelled discharge internally in 1-h time steps using 3 disaggregation procedures of the rainfall data. This was done in an attempt to maximise the information content of the input data used for calibration at the daily scale. One disaggregation

  7. Comparison of molecular dynamics simulation methods for amyloid β(1-42) monomers containing D-aspartic acid residues for predicting retention times in chromatography.

    PubMed

    Oda, Akifumi; Kobayashi, Kana; Takahashi, Ohgi

    2011-11-01

    Molecular dynamics simulations of amyloid β(1-42) containing D-aspartic acid residues were performed using several continuous solvent models to investigate the usefulness of simulation methods for D-amino acid-containing proteins and peptides. Normal molecular dynamics simulations and replica exchange molecular dynamics simulations, which are one of the generalized-ensemble algorithms, were performed. Because the β-structure contents of amyloid β(1-42) peptides obtained by replica exchange molecular dynamics simulations with Onufriev-Bashford-Case generalized Born implicit solvent were qualitatively consistent with experimental data, replica exchange molecular dynamics rather than other methods appeared to be more reasonable for calculations of amyloid β(1-42) containing D-aspartic acid residues. Computational results revealed that peptides with stereoinversion of Asp23 tend to form β-sheet structures by themselves, in contrast to the wild-type peptides that form β-sheet structures only after aggregation. These results are expected to be useful for computational investigations of proteins and peptides such as prediction of retention time of peptides and proteins containing D-aspartic acid residues.

  8. Real-time simulation of ultrasound refraction phenomena using ray-trace based wavefront construction method.

    PubMed

    Szostek, Kamil; Piórkowski, Adam

    2016-10-01

    Ultrasound (US) imaging is one of the most popular techniques used in clinical diagnosis, mainly due to lack of adverse effects on patients and the simplicity of US equipment. However, the characteristics of the medium cause US imaging to imprecisely reconstruct examined tissues. The artifacts are the results of wave phenomena, i.e. diffraction or refraction, and should be recognized during examination to avoid misinterpretation of an US image. Currently, US training is based on teaching materials and simulators and ultrasound simulation has become an active research area in medical computer science. Many US simulators are limited by the complexity of the wave phenomena, leading to intensive sophisticated computation that makes it difficult for systems to operate in real time. To achieve the required frame rate, the vast majority of simulators reduce the problem of wave diffraction and refraction. The following paper proposes a solution for an ultrasound simulator based on methods known in geophysics. To improve simulation quality, a wavefront construction method was adapted which takes into account the refraction phenomena. This technique uses ray tracing and velocity averaging to construct wavefronts in the simulation. Instead of a geological medium, real CT scans are applied. This approach can produce more realistic projections of pathological findings and is also capable of providing real-time simulation. PMID:27586490

  9. Real-time simulation of ultrasound refraction phenomena using ray-trace based wavefront construction method.

    PubMed

    Szostek, Kamil; Piórkowski, Adam

    2016-10-01

    Ultrasound (US) imaging is one of the most popular techniques used in clinical diagnosis, mainly due to lack of adverse effects on patients and the simplicity of US equipment. However, the characteristics of the medium cause US imaging to imprecisely reconstruct examined tissues. The artifacts are the results of wave phenomena, i.e. diffraction or refraction, and should be recognized during examination to avoid misinterpretation of an US image. Currently, US training is based on teaching materials and simulators and ultrasound simulation has become an active research area in medical computer science. Many US simulators are limited by the complexity of the wave phenomena, leading to intensive sophisticated computation that makes it difficult for systems to operate in real time. To achieve the required frame rate, the vast majority of simulators reduce the problem of wave diffraction and refraction. The following paper proposes a solution for an ultrasound simulator based on methods known in geophysics. To improve simulation quality, a wavefront construction method was adapted which takes into account the refraction phenomena. This technique uses ray tracing and velocity averaging to construct wavefronts in the simulation. Instead of a geological medium, real CT scans are applied. This approach can produce more realistic projections of pathological findings and is also capable of providing real-time simulation.

  10. Architecture for an integrated real-time air combat and sensor network simulation

    NASA Astrophysics Data System (ADS)

    Criswell, Evans A.; Rushing, John; Lin, Hong; Graves, Sara

    2007-04-01

    An architecture for an integrated air combat and sensor network simulation is presented. The architecture integrates two components: a parallel real-time sensor fusion and target tracking simulation, and an air combat simulation. By integrating these two simulations, it becomes possible to experiment with scenarios in which one or both sides in a battle have very large numbers of primitive passive sensors, and to assess the likely effects of those sensors on the outcome of the battle. Modern Air Power is a real-time theater-level air combat simulation that is currently being used as a part of the USAF Air and Space Basic Course (ASBC). The simulation includes a variety of scenarios from the Vietnam war to the present day, and also includes several hypothetical future scenarios. Modern Air Power includes a scenario editor, an order of battle editor, and full AI customization features that make it possible to quickly construct scenarios for any conflict of interest. The scenario editor makes it possible to place a wide variety of sensors including both high fidelity sensors such as radars, and primitive passive sensors that provide only very limited information. The parallel real-time sensor network simulation is capable of handling very large numbers of sensors on a computing cluster of modest size. It can fuse information provided by disparate sensors to detect and track targets, and produce target tracks.

  11. 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.

  12. Satellite range delay simulator for a matrix-switched time division multiple-access network simulation system

    NASA Technical Reports Server (NTRS)

    Nagy, Lawrence A.

    1990-01-01

    The Systems Integration, Test, and Evaluation (SITE) facility at NASA Lewis Research Center is presently configured as a satellite-switched time division multiple access (SS-TDMA) network simulator. The purpose of SITE is to demonstrate and evaluate advanced communication satellite technologies, presently embodied by POC components developed under NASA contracts in addition to other hardware, such as ground terminals, designed and built in-house at NASA Lewis. Each ground terminal in a satellite communications system will experience a different aspect of the satellite's motion due mainly to daily tidal effects and station keeping, hence a different duration and rate of variation in the range delay. As a result of this and other effects such as local oscillator instability, each ground terminal must constantly adjust its transmit burst timing so that data bursts from separate ground terminals arrive at the satellite in their assigned time slots, preventing overlap and keeping the system in synchronism. On the receiving end, ground terminals must synchronize their local clocks using reference transmissions received through the satellite link. A feature of the SITE facility is its capability to simulate the varying propagation delays and associated Doppler frequency shifts that the ground terminals in the network have to cope with. Delay is ahcieved by means of two NASA Lewis designed and built range delay simulator (RDS) systems, each independently controlled locally with front panel switches or remotely by an experiment control and monitor (EC/M) computer.

  13. A review of volcanic ash aggregation

    NASA Astrophysics Data System (ADS)

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

    2012-01-01

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

  14. Piloted simulation of a ground-based time-control concept for air traffic control

    NASA Technical Reports Server (NTRS)

    Davis, Thomas J.; Green, Steven M.

    1989-01-01

    A concept for aiding air traffic controllers in efficiently spacing traffic and meeting scheduled arrival times at a metering fix was developed and tested in a real time simulation. The automation aid, referred to as the ground based 4-D descent advisor (DA), is based on accurate models of aircraft performance and weather conditions. The DA generates suggested clearances, including both top-of-descent-point and speed-profile data, for one or more aircraft in order to achieve specific time or distance separation objectives. The DA algorithm is used by the air traffic controller to resolve conflicts and issue advisories to arrival aircraft. A joint simulation was conducted using a piloted simulator and an advanced concept air traffic control simulation to study the acceptability and accuracy of the DA automation aid from both the pilot's and the air traffic controller's perspectives. The results of the piloted simulation are examined. In the piloted simulation, airline crews executed controller issued descent advisories along standard curved path arrival routes, and were able to achieve an arrival time precision of + or - 20 sec at the metering fix. An analysis of errors generated in turns resulted in further enhancements of the algorithm to improve the predictive accuracy. Evaluations by pilots indicate general support for the concept and provide specific recommendations for improvement.

  15. Time-Domain Simulation of Along-Track Interferometric SAR for Moving Ocean Surfaces

    PubMed Central

    Yoshida, Takero; Rheem, Chang-Kyu

    2015-01-01

    A time-domain simulation of along-track interferometric synthetic aperture radar (AT-InSAR) has been developed to support ocean observations. The simulation is in the time domain and based on Bragg scattering to be applicable for moving ocean surfaces. The time-domain simulation is suitable for examining velocities of moving objects. The simulation obtains the time series of microwave backscattering as raw signals for movements of ocean surfaces. In terms of realizing Bragg scattering, the computational grid elements for generating the numerical ocean surface are set to be smaller than the wavelength of the Bragg resonant wave. In this paper, the simulation was conducted for a Bragg resonant wave and irregular waves with currents. As a result, the phases of the received signals from two antennas differ due to the movement of the numerical ocean surfaces. The phase differences shifted by currents were in good agreement with the theoretical values. Therefore, the adaptability of the simulation to observe velocities of ocean surfaces with AT-InSAR was confirmed. PMID:26067197

  16. Time-Domain Simulation of Along-Track Interferometric SAR for Moving Ocean Surfaces.

    PubMed

    Yoshida, Takero; Rheem, Chang-Kyu

    2015-01-01

    A time-domain simulation of along-track interferometric synthetic aperture radar (AT-InSAR) has been developed to support ocean observations. The simulation is in the time domain and based on Bragg scattering to be applicable for moving ocean surfaces. The time-domain simulation is suitable for examining velocities of moving objects. The simulation obtains the time series of microwave backscattering as raw signals for movements of ocean surfaces. In terms of realizing Bragg scattering, the computational grid elements for generating the numerical ocean surface are set to be smaller than the wavelength of the Bragg resonant wave. In this paper, the simulation was conducted for a Bragg resonant wave and irregular waves with currents. As a result, the phases of the received signals from two antennas differ due to the movement of the numerical ocean surfaces. The phase differences shifted by currents were in good agreement with the theoretical values. Therefore, the adaptability of the simulation to observe velocities of ocean surfaces with AT-InSAR was confirmed. PMID:26067197

  17. Construction schedule simulation of a diversion tunnel based on the optimized ventilation time.

    PubMed

    Wang, Xiaoling; Liu, Xuepeng; Sun, Yuefeng; An, Juan; Zhang, Jing; Chen, Hongchao

    2009-06-15

    Former studies, the methods for estimating the ventilation time are all empirical in construction schedule simulation. However, in many real cases of construction schedule, the many factors have impact on the ventilation time. Therefore, in this paper the 3D unsteady quasi-single phase models are proposed to optimize the ventilation time with different tunneling lengths. The effect of buoyancy is considered in the momentum equation of the CO transport model, while the effects of inter-phase drag, lift force, and virtual mass force are taken into account in the momentum source of the dust transport model. The prediction by the present model for airflow in a diversion tunnel is confirmed by the experimental values reported by Nakayama [Nakayama, In-situ measurement and simulation by CFD of methane gas distribution at a heading faces, Shigen-to-Sozai 114 (11) (1998) 769-775]. The construction ventilation of the diversion tunnel of XinTangfang power station in China is used as a case. The distributions of airflow, CO and dust in the diversion tunnel are analyzed. A theory method for GIS-based dynamic visual simulation for the construction processes of underground structure groups is presented that combines cyclic operation network simulation, system simulation, network plan optimization, and GIS-based construction processes' 3D visualization. Based on the ventilation time the construction schedule of the diversion tunnel is simulated by the above theory method.

  18. Time-Domain Simulation of Along-Track Interferometric SAR for Moving Ocean Surfaces.

    PubMed

    Yoshida, Takero; Rheem, Chang-Kyu

    2015-06-10

    A time-domain simulation of along-track interferometric synthetic aperture radar (AT-InSAR) has been developed to support ocean observations. The simulation is in the time domain and based on Bragg scattering to be applicable for moving ocean surfaces. The time-domain simulation is suitable for examining velocities of moving objects. The simulation obtains the time series of microwave backscattering as raw signals for movements of ocean surfaces. In terms of realizing Bragg scattering, the computational grid elements for generating the numerical ocean surface are set to be smaller than the wavelength of the Bragg resonant wave. In this paper, the simulation was conducted for a Bragg resonant wave and irregular waves with currents. As a result, the phases of the received signals from two antennas differ due to the movement of the numerical ocean surfaces. The phase differences shifted by currents were in good agreement with the theoretical values. Therefore, the adaptability of the simulation to observe velocities of ocean surfaces with AT-InSAR was confirmed.

  19. Construction schedule simulation of a diversion tunnel based on the optimized ventilation time.

    PubMed

    Wang, Xiaoling; Liu, Xuepeng; Sun, Yuefeng; An, Juan; Zhang, Jing; Chen, Hongchao

    2009-06-15

    Former studies, the methods for estimating the ventilation time are all empirical in construction schedule simulation. However, in many real cases of construction schedule, the many factors have impact on the ventilation time. Therefore, in this paper the 3D unsteady quasi-single phase models are proposed to optimize the ventilation time with different tunneling lengths. The effect of buoyancy is considered in the momentum equation of the CO transport model, while the effects of inter-phase drag, lift force, and virtual mass force are taken into account in the momentum source of the dust transport model. The prediction by the present model for airflow in a diversion tunnel is confirmed by the experimental values reported by Nakayama [Nakayama, In-situ measurement and simulation by CFD of methane gas distribution at a heading faces, Shigen-to-Sozai 114 (11) (1998) 769-775]. The construction ventilation of the diversion tunnel of XinTangfang power station in China is used as a case. The distributions of airflow, CO and dust in the diversion tunnel are analyzed. A theory method for GIS-based dynamic visual simulation for the construction processes of underground structure groups is presented that combines cyclic operation network simulation, system simulation, network plan optimization, and GIS-based construction processes' 3D visualization. Based on the ventilation time the construction schedule of the diversion tunnel is simulated by the above theory method. PMID:19081188

  20. Visual analytics for finding critical structures in massive time-varying turbulent-flow simulations.

    PubMed

    Gaither, Kelly P; Childs, Hank; Schulz, Karl W; Harrison, Cyrus; Barth, William; Donzis, Diego; Yeung, Pui-Kuen

    2012-01-01

    Visualization and data analysis are crucial in analyzing and understanding a turbulent-flow simulation of size 4,096(3) cells per time slice (68 billion cells) and 17 time slices (one trillion total cells). The visualization techniques used help scientists investigate the dynamics of intense events individually and as these events form clusters.

  1. Three axis electronic flight motion simulator real time control system design and implementation

    SciTech Connect

    Gao, Zhiyuan; Miao, Zhonghua Wang, Xiaohua; Wang, Xuyong

    2014-12-15

    A three axis electronic flight motion simulator is reported in this paper including the modelling, the controller design as well as the hardware implementation. This flight motion simulator could be used for inertial navigation test and high precision inertial navigation system with good dynamic and static performances. A real time control system is designed, several control system implementation problems were solved including time unification with parallel port interrupt, high speed finding-zero method of rotary inductosyn, zero-crossing management with continuous rotary, etc. Tests were carried out to show the effectiveness of the proposed real time control system.

  2. Three axis electronic flight motion simulator real time control system design and implementation.

    PubMed

    Gao, Zhiyuan; Miao, Zhonghua; Wang, Xuyong; Wang, Xiaohua

    2014-12-01

    A three axis electronic flight motion simulator is reported in this paper including the modelling, the controller design as well as the hardware implementation. This flight motion simulator could be used for inertial navigation test and high precision inertial navigation system with good dynamic and static performances. A real time control system is designed, several control system implementation problems were solved including time unification with parallel port interrupt, high speed finding-zero method of rotary inductosyn, zero-crossing management with continuous rotary, etc. Tests were carried out to show the effectiveness of the proposed real time control system. PMID:25554333

  3. On time discretizations for the simulation of the batch settling-compression process in one dimension.

    PubMed

    Bürger, Raimund; Diehl, Stefan; Mejías, Camilo

    2016-01-01

    The main purpose of the recently introduced Bürger-Diehl simulation model for secondary settling tanks was to resolve spatial discretization problems when both hindered settling and the phenomena of compression and dispersion are included. Straightforward time integration unfortunately means long computational times. The next step in the development is to introduce and investigate time-integration methods for more efficient simulations, but where other aspects such as implementation complexity and robustness are equally considered. This is done for batch settling simulations. The key findings are partly a new time-discretization method and partly its comparison with other specially tailored and standard methods. Several advantages and disadvantages for each method are given. One conclusion is that the new linearly implicit method is easier to implement than another one (semi-implicit method), but less efficient based on two types of batch sedimentation tests.

  4. On time discretizations for the simulation of the batch settling-compression process in one dimension.

    PubMed

    Bürger, Raimund; Diehl, Stefan; Mejías, Camilo

    2016-01-01

    The main purpose of the recently introduced Bürger-Diehl simulation model for secondary settling tanks was to resolve spatial discretization problems when both hindered settling and the phenomena of compression and dispersion are included. Straightforward time integration unfortunately means long computational times. The next step in the development is to introduce and investigate time-integration methods for more efficient simulations, but where other aspects such as implementation complexity and robustness are equally considered. This is done for batch settling simulations. The key findings are partly a new time-discretization method and partly its comparison with other specially tailored and standard methods. Several advantages and disadvantages for each method are given. One conclusion is that the new linearly implicit method is easier to implement than another one (semi-implicit method), but less efficient based on two types of batch sedimentation tests. PMID:26942521

  5. From dioxin to dioxin congeners: understanding the differences in hydrophobic aggregation in water and absorption into lipid membranes by means of atomistic simulations.

    PubMed

    Casalegno, Mosé; Raos, Guido; Sello, Guido

    2016-06-29

    Translocation of small molecules through a cell membrane barrier is a fundamental step to explain the response of cells to foreign molecules. Investigating the mechanisms through which this complex process takes place is especially important in the study of the adverse effects of toxicants. In this work, we start from the results of a previous simulation study of the mechanism of dioxin (2,3,7,8-tetrachlorodibenzo-p-dioxin) absorption into a model membrane, and extend it to four structural congeners of dioxin. The new molecules have been chosen taking into consideration the structural features that characterize dioxin: aromaticity, planarity, the presence of chlorine and oxygen atoms, and hydrophobicity. Our results for the absorption mechanism confirm our expectations based on the chemical structures, but also reveal some interesting differences in single-molecules and especially in cooperative actions underlying cluster absorption. The analysis of key parameters, such as free energies of transfer and translocation times, supports the idea that dioxin, more than its congeners investigated here, likely accumulates in cell membranes. PMID:27314876

  6. Accelerating the Customer-Driven Microgrid Through Real-Time Digital Simulation

    SciTech Connect

    I. Leonard; T. Baldwin; M. Sloderbeck

    2009-07-01

    Comprehensive design and testing of realistic customer-driven microgrids requires a high performance simulation platform capable of incorporating power system and control models with external hardware systems. Traditional non real-time simulation is unable to fully capture the level of detail necessary to expose real-world implementation issues. With a real-time digital simulator as its foundation, a high-fidelity simulation environment that includes a robust electrical power system model, advanced control architecture, and a highly adaptable communication network is introduced. Hardware-in-the-loop implementation approaches for the hardware-based control and communication systems are included. An overview of the existing power system model and its suitability for investigation of autonomous island formation within the microgrid is additionally presented. Further test plans are also documented.

  7. Object oriented design (OOD) in real-time hardware-in-the-loop (HWIL) simulations

    NASA Astrophysics Data System (ADS)

    Morris, Joe; Richard, Henri; Lowman, Alan; Youngren, Rob

    2006-05-01

    Using Object Oriented Design (OOD) concepts in AMRDEC's Hardware-in-the Loop (HWIL) real-time simulations allows the user to interchange parts of the simulation to meet test requirements. A large-scale three-spectral band simulator connected via a high speed reflective memory ring for time-critical data transfers to PC controllers connected by non real-time Ethernet protocols is used to separate software objects from logical entities close to their respective controlled hardware. Each standalone object does its own dynamic initialization, real-time processing, and end of run processing; therefore it can be easily maintained and updated. A Resource Allocation Program (RAP) is also utilized along with a device table to allocate, organize, and document the communication protocol between the software and hardware components. A GUI display program lists all allocations and deallocations of HWIL memory and hardware resources. This interactive program is also used to clean up defunct allocations of dead processes. Three examples are presented using the OOD and RAP concepts. The first is the control of an ACUTRONICS built three-axis flight table using the same control for calibration and real-time functions. The second is the transportability of a six-degree-of-freedom (6-DOF) simulation from an Onyx residence to a Linux-PC. The third is the replacement of the 6-DOF simulation with a replay program to drive the facility with archived run data for demonstration or analysis purposes.

  8. A real-time, portable, microcomputer-based jet engine simulator

    NASA Technical Reports Server (NTRS)

    Blech, R. A.; Soeder, J. F.; Mihaloew, J. R.

    1984-01-01

    Modern piloted flight simulators require detailed models of many aircraft components, such as the airframe, propulsion system, flight deck controls and instrumentation, as well as motion drive and visual display systems. The amount of computing power necessary to implement these systems can exceed that offered by dedicated mainframe computers. One approach to this problem is through the use of distributed computing, where parts of the simulation are assigned to computing subsystems, such as microcomputers. One such subsystem, such as microcomputers. One such subsystem, a real-time, portable, microcomputer-based jet engine simulator, is described in this paper. The simulator will be used at the NASA Ames Vertical Motion Simulator facility to perform calculations previously done on the facility's mainframe computer. The mainframe will continue to do all other system calculations and will interface to the engine simulator through analog I/0. The engine simulator hardware includes a 16-bit microcomputer and floating-point coprocessor. There is an 8 channel analog input board and an 8 channel analog output board. A model of a small turboshaft engine/control is coded in floating-point FORTRAN. The FORTRAN code and a data monitoring program run under the control of an assembly language real-time executive. The monitoring program allows the user to isplay and/or modify simulator variables on-line through a data terminal. A dual disk drive system is used for mass storage of programs and data. The CP/M-86 operating system provides file management and overall system control. The frame time for the simulator is 30 milliseconds, which includes all analog I/0 operations.

  9. Real-time software-based end-to-end wireless visual communications simulation platform

    NASA Astrophysics Data System (ADS)

    Chen, Ting-Chung; Chang, Li-Fung; Wong, Andria H.; Sun, Ming-Ting; Hsing, T. Russell

    1995-04-01

    Wireless channel impairments pose many challenges to real-time visual communications. In this paper, we describe a real-time software based wireless visual communications simulation platform which can be used for performance evaluation in real-time. This simulation platform consists of two personal computers serving as hosts. Major components of each PC host include a real-time programmable video code, a wireless channel simulator, and a network interface for data transport between the two hosts. The three major components are interfaced in real-time to show the interaction of various wireless channels and video coding algorithms. The programmable features in the above components allow users to do performance evaluation of user-controlled wireless channel effects without physically carrying out these experiments which are limited in scope, time-consuming, and costly. Using this simulation platform as a testbed, we have experimented with several wireless channel effects including Rayleigh fading, antenna diversity, channel filtering, symbol timing, modulation, and packet loss.

  10. Advanced time integration algorithms for dislocation dynamics simulations of work hardening

    DOE PAGES

    Sills, Ryan B.; Aghaei, Amin; Cai, Wei

    2016-04-25

    Efficient time integration is a necessity for dislocation dynamics simulations of work hardening to achieve experimentally relevant strains. In this work, an efficient time integration scheme using a high order explicit method with time step subcycling and a newly-developed collision detection algorithm are evaluated. First, time integrator performance is examined for an annihilating Frank–Read source, showing the effects of dislocation line collision. The integrator with subcycling is found to significantly out-perform other integration schemes. The performance of the time integration and collision detection algorithms is then tested in a work hardening simulation. The new algorithms show a 100-fold speed-up relativemore » to traditional schemes. As a result, subcycling is shown to improve efficiency significantly while maintaining an accurate solution, and the new collision algorithm allows an arbitrarily large time step size without missing collisions.« less

  11. Advanced time integration algorithms for dislocation dynamics simulations of work hardening

    NASA Astrophysics Data System (ADS)

    Sills, Ryan B.; Aghaei, Amin; Cai, Wei

    2016-05-01

    Efficient time integration is a necessity for dislocation dynamics simulations of work hardening to achieve experimentally relevant strains. In this work, an efficient time integration scheme using a high order explicit method with time step subcycling and a newly-developed collision detection algorithm are evaluated. First, time integrator performance is examined for an annihilating Frank-Read source, showing the effects of dislocation line collision. The integrator with subcycling is found to significantly out-perform other integration schemes. The performance of the time integration and collision detection algorithms is then tested in a work hardening simulation. The new algorithms show a 100-fold speed-up relative to traditional schemes. Subcycling is shown to improve efficiency significantly while maintaining an accurate solution, and the new collision algorithm allows an arbitrarily large time step size without missing collisions.

  12. LISA simulations of time-reversed acoustic and elastic wave experiments

    NASA Astrophysics Data System (ADS)

    Delsanto, P. P.; Johnson, P. A.; Scalerandi, M.; Ten Cate, J. A.

    2002-12-01

    Several experiments in the last decade have demonstrated the enormous potential of time-reversed acoustic (TRA) and elastic (TRE) waves for applications in many fields, such as medicine, materials characterization and oceanography. In the present contribution, we demonstrate the applicability of the local interaction simulation approach (LISA) to simulate, by means of virtual experiments, both TRA and TRE and to reproduce the relevant features of both techniques.

  13. Results of two-dimensional time-evolved phase screen computer simulations

    NASA Astrophysics Data System (ADS)

    Gamble, Kevin J.; Weeks, Arthur R.; Myler, Harley R.; Rabadi, Wissam A.

    1995-06-01

    This paper presents a 2D computer simulation of observed intensity and phase behind a time evolved phase screen. Both spatial and temporal statistics of the observed intensity is compared to theoretical predictions. In particular, the intensity statistics as a function of detector position within the propagated laser beam are investigated. The computer simulation program was written using the C-programming language running on a SUN SPARC-5 workstation.

  14. Simulation of E. coli Gene Regulation including Overlapping Cell Cycles, Growth, Division, Time Delays and Noise

    PubMed Central

    Luo, Ruoyu; Ye, Lin; Tao, Chenyang; Wang, Kankan

    2013-01-01

    Due to the complexity of biological systems, simulation of biological networks is necessary but sometimes complicated. The classic stochastic simulation algorithm (SSA) by Gillespie and its modified versions are widely used to simulate the stochastic dynamics of biochemical reaction systems. However, it has remained a challenge to implement accurate and efficient simulation algorithms for general reaction schemes in growing cells. Here, we present a modeling and simulation tool, called ‘GeneCircuits’, which is specifically developed to simulate gene-regulation in exponentially growing bacterial cells (such as E. coli) with overlapping cell cycles. Our tool integrates three specific features of these cells that are not generally included in SSA tools: 1) the time delay between the regulation and synthesis of proteins that is due to transcription and translation processes; 2) cell cycle-dependent periodic changes of gene dosage; and 3) variations in the propensities of chemical reactions that have time-dependent reaction rates as a consequence of volume expansion and cell division. We give three biologically relevant examples to illustrate the use of our simulation tool in quantitative studies of systems biology and synthetic biology. PMID:23638057

  15. Wind Energy System Time-domain (WEST) analyzers using hybrid simulation techniques

    NASA Technical Reports Server (NTRS)

    Hoffman, J. A.

    1979-01-01

    Two stand-alone analyzers constructed for real time simulation of the complex dynamic characteristics of horizontal-axis wind energy systems are described. Mathematical models for an aeroelastic rotor, including nonlinear aerodynamic and elastic loads, are implemented with high speed digital and analog circuitry. Models for elastic supports, a power train, a control system, and a rotor gimbal system are also included. Limited correlation efforts show good comparisons between results produced by the analyzers and results produced by a large digital simulation. The digital simulation results correlate well with test data.

  16. Design of a real-time wind turbine simulator using a custom parallel architecture

    NASA Technical Reports Server (NTRS)

    Hoffman, John A.; Gluck, R.; Sridhar, S.

    1995-01-01

    The design of a new parallel-processing digital simulator is described. The new simulator has been developed specifically for analysis of wind energy systems in real time. The new processor has been named: the Wind Energy System Time-domain simulator, version 3 (WEST-3). Like previous WEST versions, WEST-3 performs many computations in parallel. The modules in WEST-3 are pure digital processors, however. These digital processors can be programmed individually and operated in concert to achieve real-time simulation of wind turbine systems. Because of this programmability, WEST-3 is very much more flexible and general than its two predecessors. The design features of WEST-3 are described to show how the system produces high-speed solutions of nonlinear time-domain equations. WEST-3 has two very fast Computational Units (CU's) that use minicomputer technology plus special architectural features that make them many times faster than a microcomputer. These CU's are needed to perform the complex computations associated with the wind turbine rotor system in real time. The parallel architecture of the CU causes several tasks to be done in each cycle, including an IO operation and the combination of a multiply, add, and store. The WEST-3 simulator can be expanded at any time for additional computational power. This is possible because the CU's interfaced to each other and to other portions of the simulation using special serial buses. These buses can be 'patched' together in essentially any configuration (in a manner very similar to the programming methods used in analog computation) to balance the input/ output requirements. CU's can be added in any number to share a given computational load. This flexible bus feature is very different from many other parallel processors which usually have a throughput limit because of rigid bus architecture.

  17. Dispersion curves from short-time molecular dynamics simulation. 1. Diatomic chain results

    SciTech Connect

    Noid, D.W.; Broocks, B.T.; Gray, S.K.; Marple, S.L.

    1988-06-16

    The multiple signal classification method (MUSIC) for frequency estimation is used to compute the frequency dispersion curves of a diatomic chain from the time-dependent structure factor. In this paper, the authors demonstrate that MUSIC can accurately determine the frequencies from very short time trajectories. MUSIC is also used to show how the frequencies can vary in time, i.e., along a trajectory. The method is ideally suited for analyzing molecular dynamics simulations of large systems.

  18. Wavelet-based time series bootstrap model for multidecadal streamflow simulation using climate indicators

    NASA Astrophysics Data System (ADS)

    Erkyihun, Solomon Tassew; Rajagopalan, Balaji; Zagona, Edith; Lall, Upmanu; Nowak, Kenneth

    2016-05-01

    A model to generate stochastic streamflow projections conditioned on quasi-oscillatory climate indices such as Pacific Decadal Oscillation (PDO) and Atlantic Multi-decadal Oscillation (AMO) is presented. Recognizing that each climate index has underlying band-limited components that contribute most of the energy of the signals, we first pursue a wavelet decomposition of the signals to identify and reconstruct these features from annually resolved historical data and proxy based paleoreconstructions of each climate index covering the period from 1650 to 2012. A K-Nearest Neighbor block bootstrap approach is then developed to simulate the total signal of each of these climate index series while preserving its time-frequency structure and marginal distributions. Finally, given the simulated climate signal time series, a K-Nearest Neighbor bootstrap is used to simulate annual streamflow series conditional on the joint state space defined by the simulated climate index for each year. We demonstrate this method by applying it to simulation of streamflow at Lees Ferry gauge on the Colorado River using indices of two large scale climate forcings: Pacific Decadal Oscillation (PDO) and Atlantic Multi-decadal Oscillation (AMO), which are known to modulate the Colorado River Basin (CRB) hydrology at multidecadal time scales. Skill in stochastic simulation of multidecadal projections of flow using this approach is demonstrated.

  19. 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.

  20. Temporal Gillespie Algorithm: Fast Simulation of Contagion Processes on Time-Varying Networks

    PubMed Central

    Vestergaard, Christian L.; Génois, Mathieu

    2015-01-01

    Stochastic simulations are one of the cornerstones of the analysis of dynamical processes on complex networks, and are often the only accessible way to explore their behavior. The development of fast algorithms is paramount to allow large-scale simulations. The Gillespie algorithm can be used for fast simulation of stochastic processes, and variants of it have been applied to simulate dynamical processes on static networks. However, its adaptation to temporal networks remains non-trivial. We here present a temporal Gillespie algorithm that solves this problem. Our method is applicable to general Poisson (constant-rate) processes on temporal networks, stochastically exact, and up to multiple orders of magnitude faster than traditional simulation schemes based on rejection sampling. We also show how it can be extended to simulate non-Markovian processes. The algorithm is easily applicable in practice, and as an illustration we detail how to simulate both Poissonian and non-Markovian models of epidemic spreading. Namely, we provide pseudocode and its implementation in C++ for simulating the paradigmatic Susceptible-Infected-Susceptible and Susceptible-Infected-Recovered models and a Susceptible-Infected-Recovered model with non-constant recovery rates. For empirical networks, the temporal Gillespie algorithm is here typically from 10 to 100 times faster than rejection sampling. PMID:26517860

  1. Investigation of Asymmetric Thrust Detection with Demonstration in a Real-Time Simulation Testbed

    NASA Technical Reports Server (NTRS)

    Chicatelli, Amy; Rinehart, Aidan W.; Sowers, T. Shane; Simon, Donald L.

    2015-01-01

    The purpose of this effort is to develop, demonstrate, and evaluate three asymmetric thrust detection approaches to aid in the reduction of asymmetric thrust-induced aviation accidents. This paper presents the results from that effort and their evaluation in simulation studies, including those from a real-time flight simulation testbed. Asymmetric thrust is recognized as a contributing factor in several Propulsion System Malfunction plus Inappropriate Crew Response (PSM+ICR) aviation accidents. As an improvement over the state-of-the-art, providing annunciation of asymmetric thrust to alert the crew may hold safety benefits. For this, the reliable detection and confirmation of asymmetric thrust conditions is required. For this work, three asymmetric thrust detection methods are presented along with their results obtained through simulation studies. Representative asymmetric thrust conditions are modeled in simulation based on failure scenarios similar to those reported in aviation incident and accident descriptions. These simulated asymmetric thrust scenarios, combined with actual aircraft operational flight data, are then used to conduct a sensitivity study regarding the detection capabilities of the three methods. Additional evaluation results are presented based on pilot-in-the-loop simulation studies conducted in the NASA Glenn Research Center (GRC) flight simulation testbed. Data obtained from this flight simulation facility are used to further evaluate the effectiveness and accuracy of the asymmetric thrust detection approaches. Generally, the asymmetric thrust conditions are correctly detected and confirmed.

  2. Investigation of Asymmetric Thrust Detection with Demonstration in a Real-Time Simulation Testbed

    NASA Technical Reports Server (NTRS)

    Chicatelli, Amy K.; Rinehart, Aidan W.; Sowers, T. Shane; Simon, Donald L.

    2016-01-01

    The purpose of this effort is to develop, demonstrate, and evaluate three asymmetric thrust detection approaches to aid in the reduction of asymmetric thrust-induced aviation accidents. This paper presents the results from that effort and their evaluation in simulation studies, including those from a real-time flight simulation testbed. Asymmetric thrust is recognized as a contributing factor in several Propulsion System Malfunction plus Inappropriate Crew Response (PSM+ICR) aviation accidents. As an improvement over the state-of-the-art, providing annunciation of asymmetric thrust to alert the crew may hold safety benefits. For this, the reliable detection and confirmation of asymmetric thrust conditions is required. For this work, three asymmetric thrust detection methods are presented along with their results obtained through simulation studies. Representative asymmetric thrust conditions are modeled in simulation based on failure scenarios similar to those reported in aviation incident and accident descriptions. These simulated asymmetric thrust scenarios, combined with actual aircraft operational flight data, are then used to conduct a sensitivity study regarding the detection capabilities of the three methods. Additional evaluation results are presented based on pilot-in-the-loop simulation studies conducted in the NASA Glenn Research Center (GRC) flight simulation testbed. Data obtained from this flight simulation facility are used to further evaluate the effectiveness and accuracy of the asymmetric thrust detection approaches. Generally, the asymmetric thrust conditions are correctly detected and confirmed.

  3. Periodic boundary conditions for long-time nonequilibrium molecular dynamics simulations of incompressible flows

    NASA Astrophysics Data System (ADS)

    Dobson, Matthew

    2014-11-01

    This work presents a generalization of the Kraynik-Reinelt (KR) boundary conditions for nonequilibrium molecular dynamics simulations. In the simulation of steady, homogeneous flows with periodic boundary conditions, the simulation box deforms with the flow, and it is possible for image particles to become arbitrarily close, causing a breakdown in the simulation. The KR boundary conditions avoid this problem for planar elongational flow and general planar mixed flow [T. A. Hunt, S. Bernardi, and B. D. Todd, J. Chem. Phys. 133, 154116 (2010)] through careful choice of the initial simulation box and by periodically remapping the simulation box in a way that conserves image locations. In this work, the ideas are extended to a large class of three-dimensional flows by using multiple remappings for the simulation box. The simulation box geometry is no longer time-periodic (which was shown to be impossible for uniaxial and biaxial stretching flows in the original work by Kraynik and Reinelt [Int. J. Multiphase Flow 18, 1045 (1992)]. The presented algorithm applies to all flows with nondefective flow matrices, and in particular, to uniaxial and biaxial flows.

  4. State-of-the-Art Solar Simulator Reduces Measurement Time and Uncertainty (Fact Sheet)

    SciTech Connect

    Not Available

    2012-04-01

    One-Sun Multisource Solar Simulator (OSMSS) brings accurate energy-rating predictions that account for the nonlinear behavior of multijunction photovoltaic devices. The National Renewable Energy Laboratory (NREL) is one of only a few International Organization for Standardization (ISO)-accredited calibration labs in the world for primary and secondary reference cells and modules. As such, it is critical to seek new horizons in developing simulators and measurement methods. Current solar simulators are not well suited for accurately measuring multijunction devices. To set the electrical current to each junction independently, simulators must precisely tune the spectral content with no overlap between the wavelength regions. Current simulators do not have this capability, and the overlaps lead to large measurement uncertainties of {+-}6%. In collaboration with LabSphere, NREL scientists have designed and implemented the One-Sun Multisource Solar Simulator (OSMSS), which enables automatic spectral adjustment with nine independent wavelength regions. This fiber-optic simulator allows researchers and developers to set the current to each junction independently, reducing errors relating to spectral effects. NREL also developed proprietary software that allows this fully automated simulator to rapidly 'build' a spectrum under which all junctions of a multijunction device are current matched and behave as they would under a reference spectrum. The OSMSS will reduce the measurement uncertainty for multijunction devices, while significantly reducing the current-voltage measurement time from several days to minutes. These features will enable highly accurate energy-rating predictions that take into account the nonlinear behavior of multijunction photovoltaic devices.

  5. Real-Time Building Energy Simulation Using EnergyPlus and the Building Controls Test Bed

    SciTech Connect

    Pang, Xiufeng; Bhattachayra, Prajesh; O'Neill, Zheng; Haves, Philip; Wetter, Michael; Bailey, Trevor

    2011-11-01

    Most commercial buildings do not perform as well in practice as intended by the design and their performances often deteriorate over time. Reasons include faulty construction, malfunctioning equipment, incorrectly configured control systems and inappropriate operating procedures (Haves et al., 2001, Lee et al., 2007). To address this problem, the paper presents a simulation-based whole building performance monitoring tool that allows a comparison of building actual performance and expected performance in real time. The tool continuously acquires relevant building model input variables from existing Energy Management and Control System (EMCS). It then reports expected energy consumption as simulated of EnergyPlus. The Building Control Virtual Test Bed (BCVTB) is used as the software platform to provide data linkage between the EMCS, an EnergyPlus model, and a database. This paper describes the integrated real-time simulation environment. A proof-of-concept demonstration is also presented in the paper.

  6. A study of workstation computational performance for real-time flight simulation

    NASA Technical Reports Server (NTRS)

    Maddalon, Jeffrey M.; Cleveland, Jeff I., II

    1995-01-01

    With recent advances in microprocessor technology, some have suggested that modern workstations provide enough computational power to properly operate a real-time simulation. This paper presents the results of a computational benchmark, based on actual real-time flight simulation code used at Langley Research Center, which was executed on various workstation-class machines. The benchmark was executed on different machines from several companies including: CONVEX Computer Corporation, Cray Research, Digital Equipment Corporation, Hewlett-Packard, Intel, International Business Machines, Silicon Graphics, and Sun Microsystems. The machines are compared by their execution speed, computational accuracy, and porting effort. The results of this study show that the raw computational power needed for real-time simulation is now offered by workstations.

  7. Real-time simulation model of the HL-20 lifting body

    NASA Technical Reports Server (NTRS)

    Jackson, E. Bruce; Cruz, Christopher I.; Ragsdale, W. A.

    1992-01-01

    A proposed manned spacecraft design, designated the HL-20, has been under investigation at Langley Research Center. Included in that investigation are flight control design and flying qualities studies utilizing a man-in-the-loop real-time simulator. This report documents the current real-time simulation model of the HL-20 lifting body vehicle, known as version 2.0, presently in use at NASA Langley Research Center. Included are data on vehicle aerodynamics, inertias, geometries, guidance and control laws, and cockpit displays and controllers. In addition, trim case and dynamic check case data is provided. The intent of this document is to provide the reader with sufficient information to develop and validate an equivalent simulation of the HL-20 for use in real-time or analytical studies.

  8. An MHD simulation model of time-dependent co-rotating solar wind

    NASA Astrophysics Data System (ADS)

    Hayashi, K.

    2012-08-01

    We present a treatment of observation-based time-dependent boundary conditions for the inner boundary sphere in the time-dependent three-dimensional MHD simulations of the global solar wind. With this boundary treatment, we obtain super-Alfvenic MHD solutions of time-dependent co-rotating solar wind structures. The boundary variables on the inner boundary sphere, at 50 solar radii in this study, are assumed to change linearly from one instant to the next. A new feature is that, in order to maintain the divergence-free condition of the magnetic field, the changes of the time-dependent boundary magnetic field are expressed as the potential field in a thin shell volume. The solar magnetic field data from the Wilcox Solar Observatory (WSO) and the solar wind speed data from the interplanetary scintillation (IPS) observations at Nagoya University, Japan, are used as the input boundary data. The solar wind simulated with the time-dependent boundary condition is compared with the near-Earth and Ulysses in situ measurement data and the solar wind simulated with the fixed boundary condition over a 7-month period in 1991. Reasonable agreements with the in situ measurements are obtained. The differences between the two simulations in the interplanetary field line paths are significant. The three-dimensional time-dependent MHD solution of the global solar wind will help enhance space weather models and other fields in heliophysics.

  9. Time-Accurate Unsteady Pressure Loads Simulated for the Space Launch System at Wind Tunnel Conditions

    NASA Technical Reports Server (NTRS)

    Alter, Stephen J.; Brauckmann, Gregory J.; Kleb, William L.; Glass, Christopher E.; Streett, Craig L.; Schuster, David M.

    2015-01-01

    A transonic flow field about a Space Launch System (SLS) configuration was simulated with the Fully Unstructured Three-Dimensional (FUN3D) computational fluid dynamics (CFD) code at wind tunnel conditions. Unsteady, time-accurate computations were performed using second-order Delayed Detached Eddy Simulation (DDES) for up to 1.5 physical seconds. The surface pressure time history was collected at 619 locations, 169 of which matched locations on a 2.5 percent wind tunnel model that was tested in the 11 ft. x 11 ft. test section of the NASA Ames Research Center's Unitary Plan Wind Tunnel. Comparisons between computation and experiment showed that the peak surface pressure RMS level occurs behind the forward attach hardware, and good agreement for frequency and power was obtained in this region. Computational domain, grid resolution, and time step sensitivity studies were performed. These included an investigation of pseudo-time sub-iteration convergence. Using these sensitivity studies and experimental data comparisons, a set of best practices to date have been established for FUN3D simulations for SLS launch vehicle analysis. To the author's knowledge, this is the first time DDES has been used in a systematic approach and establish simulation time needed, to analyze unsteady pressure loads on a space launch vehicle such as the NASA SLS.

  10. A comparison of thermal zone aggregation methods

    SciTech Connect

    Dobbs, Justin R.; Hencey, Brandon M.

    2012-12-10

    The impact of increasing energy prices on building operation budgets has fueled demand for more energy-efficient structures. Existing building energy simulation tools generate an immense amount of data yet comparatively little knowledge. This paper introduces a framework that allows aggregation-based model reduction to operate on geometric building information models. The resulting aggregation sequence provides designers with faster simulations and affords insight into complex multi-scale thermal interactions. A comparison of the trade-off between simulation speed and accuracy for three hierarchical cluster partitioning methods concludes the discussion.

  11. Diffusion-limited aggregation on curved surfaces

    NASA Astrophysics Data System (ADS)

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

    2010-08-01

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

  12. Multi-level Simulation of a Real Time Vibration Monitoring System Component

    NASA Technical Reports Server (NTRS)

    Robertson, Bryan A.; Wilkerson, Delisa

    2005-01-01

    This paper describes the development of a custom built Digital Signal Processing (DSP) printed circuit board designed to implement the Advanced Real Time Vibration Monitoring Subsystem proposed by Marshall Space Flight Center (MSFC) Transportation Directorate in 2000 for the Space Shuttle Main Engine Advanced Health Management System (AHMS). This Real Time Vibration Monitoring System (RTVMS) is being developed for ground use as part of the AHMS Health Management Computer-Integrated Rack Assembly (HMC-IRA). The HMC-IRA RTVMS design contains five DSPs which are highly interconnected through individual communication ports, shared memory, and a unique communication router that allows all the DSPs to receive digitized data fiom two multi-channel analog boards simultaneously. This paper will briefly cover the overall board design but will focus primarily on the state-of-the-art simulation environment within which this board was developed. This 16-layer board with over 1800 components and an additional mezzanine card has been an extremely challenging design. Utilization of a Mentor Graphics simulation environment provided the unique board and system level simulation capability to ascertain any timing or functional concerns before production. By combining VHDL, Synopsys Software and Hardware Models, and the Mentor Design Capture Environment, multiple simulations were developed to verify the RTVMS design. This multi-level simulation allowed the designers to achieve complete operability without error the first time the RTVMS printed circuit board was powered. The HMC-IRA design has completed all engineering and deliverable unit testing. P

  13. Multi-level Simulation of a Real Time Vibration Monitoring System Component

    NASA Technical Reports Server (NTRS)

    Roberston, Bryan; Wilkerson, DeLisa

    2004-01-01

    This paper describes the development of a custom built Digital Signal Processing (DSP) printed circuit board designed to implement the Advanced Real Time Vibration Monitoring Subsystem proposed by MSFC Transportation Directorate in 2000 for the Space Shuttle Main Engine Advanced Health Management System (AHMS). This Real Time Vibration Monitoring System (RTVMS) is being developed for ground use as part of the AHMS Health Management Computer-Integrated Rack Assembly (HMC-IRA). The HMC-IRA RTVMS design contains five DSPs which are highly interconnected through individual communication ports, shared memory, and a unique communication router that allows all the DSPs to receive digitized data from two multi-channel analog boards simultaneously. This paper will briefly cover the overall board design but will focus primarily on the state-of-the-art simulation environment within which this board was developed. This 16-layer board with over 1800 components and an additional mezzanine card has been an extremely challenging design. Utilization of a Mentor Graphics simulation environment provided the unique board and system level simulation capability to ascertain any timing or functional concerns before production. By combining VHDL, Synopsys Software and Hardware Models, and the Mentor Design Capture Environment, multiple simulations were developed to verify the RTVMS design. This multi-level simulation allowed the designers to achieve complete operability without error the first time the RTVMS printed circuit board was powered. The HMCIRA design has completed all engineering unit testing and the deliverable unit is currently under development.

  14. Time Accurate Unsteady Pressure Loads Simulated for the Space Launch System at a Wind Tunnel Condition

    NASA Technical Reports Server (NTRS)

    Alter, Stephen J.; Brauckmann, Gregory J.; Kleb, Bil; Streett, Craig L; Glass, Christopher E.; Schuster, David M.

    2015-01-01

    Using the Fully Unstructured Three-Dimensional (FUN3D) computational fluid dynamics code, an unsteady, time-accurate flow field about a Space Launch System configuration was simulated at a transonic wind tunnel condition (Mach = 0.9). Delayed detached eddy simulation combined with Reynolds Averaged Naiver-Stokes and a Spallart-Almaras turbulence model were employed for the simulation. Second order accurate time evolution scheme was used to simulate the flow field, with a minimum of 0.2 seconds of simulated time to as much as 1.4 seconds. Data was collected at 480 pressure taps at locations, 139 of which matched a 3% wind tunnel model, tested in the Transonic Dynamic Tunnel (TDT) facility at NASA Langley Research Center. Comparisons between computation and experiment showed agreement within 5% in terms of location for peak RMS levels, and 20% for frequency and magnitude of power spectral densities. Grid resolution and time step sensitivity studies were performed to identify methods for improved accuracy comparisons to wind tunnel data. With limited computational resources, accurate trends for reduced vibratory loads on the vehicle were observed. Exploratory methods such as determining minimized computed errors based on CFL number and sub-iterations, as well as evaluating frequency content of the unsteady pressures and evaluation of oscillatory shock structures were used in this study to enhance computational efficiency and solution accuracy. These techniques enabled development of a set of best practices, for the evaluation of future flight vehicle designs in terms of vibratory loads.

  15. Real-Time Simulation of Passage-of-Time Encoding in Cerebellum Using a Scalable FPGA-Based System.

    PubMed

    Luo, Junwen; Coapes, Graeme; Mak, Terrence; Yamazaki, Tadashi; Tin, Chung; Degenaar, Patrick

    2016-06-01

    The cerebellum plays a critical role for sensorimotor control and learning. However, dysmetria or delays in movements' onsets consequent to damages in cerebellum cannot be cured completely at the moment. Neuroprosthesis is an emerging technology that can potentially substitute such motor control module in the brain. A pre-requisite for this to become practical is the capability to simulate the cerebellum model in real-time, with low timing distortion for proper interfacing with the biological system. In this paper, we present a frame-based network-on-chip (NoC) hardware architecture for implementing a bio-realistic cerebellum model with  ∼ 100 000 neurons, which has been used for studying timing control or passage-of-time (POT) encoding mediated by the cerebellum. The simulation results verify that our implementation reproduces the POT representation by the cerebellum properly. Furthermore, our field-programmable gate array (FPGA)-based system demonstrates excellent computational speed that it can complete 1sec real world activities within 25.6 ms. It is also highly scalable such that it can maintain approximately the same computational speed even if the neuron number increases by one order of magnitude. Our design is shown to outperform three alternative approaches previously used for implementing spiking neural network model. Finally, we show a hardware electronic setup and illustrate how the silicon cerebellum can be adapted as a potential neuroprosthetic platform for future biological or clinical application. PMID:26452290

  16. Real-Time Simulation of Passage-of-Time Encoding in Cerebellum Using a Scalable FPGA-Based System.

    PubMed

    Luo, Junwen; Coapes, Graeme; Mak, Terrence; Yamazaki, Tadashi; Tin, Chung; Degenaar, Patrick

    2016-06-01

    The cerebellum plays a critical role for sensorimotor control and learning. However, dysmetria or delays in movements' onsets consequent to damages in cerebellum cannot be cured completely at the moment. Neuroprosthesis is an emerging technology that can potentially substitute such motor control module in the brain. A pre-requisite for this to become practical is the capability to simulate the cerebellum model in real-time, with low timing distortion for proper interfacing with the biological system. In this paper, we present a frame-based network-on-chip (NoC) hardware architecture for implementing a bio-realistic cerebellum model with  ∼ 100 000 neurons, which has been used for studying timing control or passage-of-time (POT) encoding mediated by the cerebellum. The simulation results verify that our implementation reproduces the POT representation by the cerebellum properly. Furthermore, our field-programmable gate array (FPGA)-based system demonstrates excellent computational speed that it can complete 1sec real world activities within 25.6 ms. It is also highly scalable such that it can maintain approximately the same computational speed even if the neuron number increases by one order of magnitude. Our design is shown to outperform three alternative approaches previously used for implementing spiking neural network model. Finally, we show a hardware electronic setup and illustrate how the silicon cerebellum can be adapted as a potential neuroprosthetic platform for future biological or clinical application.

  17. Real-Time Simulation of Three-Dimensional Shoulder Girdle and Arm Dynamics

    PubMed Central

    Chadwick, Edward K.; Blana, Dimitra; Kirsch, Robert F.; van den Bogert, Antonie J.

    2014-01-01

    Electrical stimulation is a promising technology for the restoration of arm function in paralysed individuals. Control of the paralysed arm under electrical stimulation, however, is a challenging problem that requires advanced controllers and command interfaces for the user. A real-time model describing the complex dynamics of the arm would allow user-in-the-loop type experiments where the command interface and controller could be assessed. Real-time models of the arm previously described have not included the ability to model the independently controlled scapula and clavicle, limiting their utility for clinical applications of this nature. The goal of this study therefore was to evaluate the performance and mechanical behaviour of a real-time, dynamic model of the arm and shoulder girdle. The model comprises seven segments linked by eleven degrees of freedom and actuated by 138 muscle elements. Polynomials were generated to describe the muscle lines of action to reduce computation time, and an implicit, first-order Rosenbrock formulation of the equations of motion was used to increase simulation step-size. The model simulated flexion of the arm faster than real time, simulation time being 92% of actual movement time on standard desktop hardware. Modelled maximum isometric torque values agreed well with values from the literature, showing that the model simulates the moment-generating behaviour of a real human arm. The speed of the model enables experiments where the user controls the virtual arm and receives visual feedback in real time. The ability to optimise potential solutions in simulation greatly reduces the burden on the user during development. PMID:24956613

  18. Real-time simulation of three-dimensional shoulder girdle and arm dynamics.

    PubMed

    Chadwick, Edward K; Blana, Dimitra; Kirsch, Robert F; van den Bogert, Antonie J

    2014-07-01

    Electrical stimulation is a promising technology for the restoration of arm function in paralyzed individuals. Control of the paralyzed arm under electrical stimulation, however, is a challenging problem that requires advanced controllers and command interfaces for the user. A real-time model describing the complex dynamics of the arm would allow user-in-the-loop type experiments where the command interface and controller could be assessed. Real-time models of the arm previously described have not included the ability to model the independently controlled scapula and clavicle, limiting their utility for clinical applications of this nature. The goal of this study therefore was to evaluate the performance and mechanical behavior of a real-time, dynamic model of the arm and shoulder girdle. The model comprises seven segments linked by eleven degrees of freedom and actuated by 138 muscle elements. Polynomials were generated to describe the muscle lines of action to reduce computation time, and an implicit, first-order Rosenbrock formulation of the equations of motion was used to increase simulation step-size. The model simulated flexion of the arm faster than real time, simulation time being 92% of actual movement time on standard desktop hardware. Modeled maximum isometric torque values agreed well with values from the literature, showing that the model simulates the moment-generating behavior of a real human arm. The speed of the model enables experiments where the user controls the virtual arm and receives visual feedback in real time. The ability to optimize potential solutions in simulation greatly reduces the burden on the user during development. PMID:24956613

  19. Mesoscale Simulation Data for Initializing Fast-Time Wake Transport and Decay Models

    NASA Technical Reports Server (NTRS)

    Ahmad, Nashat N.; Proctor, Fred H.; Vanvalkenburg, Randal L.; Pruis, Mathew J.; LimonDuparcmeur, Fanny M.

    2012-01-01

    The fast-time wake transport and decay models require vertical profiles of crosswinds, potential temperature and the eddy dissipation rate as initial conditions. These inputs are normally obtained from various field sensors. In case of data-denied scenarios or operational use, these initial conditions can be provided by mesoscale model simulations. In this study, the vertical profiles of potential temperature from a mesoscale model were used as initial conditions for the fast-time wake models. The mesoscale model simulations were compared against available observations and the wake model predictions were compared with the Lidar measurements from three wake vortex field experiments.

  20. Simulation of Ground Winds Time Series for the NASA Crew Launch Vehicle (CLV)

    NASA Technical Reports Server (NTRS)

    Adelfang, Stanley I.

    2008-01-01

    Simulation of wind time series based on power spectrum density (PSD) and spectral coherence models for ground wind turbulence is described. The wind models, originally developed for the Shuttle program, are based on wind measurements at the NASA 150-m meteorological tower at Cape Canaveral, FL. The current application is for the design and/or protection of the CLV from wind effects during on-pad exposure during periods from as long as days prior to launch, to seconds or minutes just prior to launch and seconds after launch. The evaluation of vehicle response to wind will influence the design and operation of constraint systems for support of the on-pad vehicle. Longitudinal and lateral wind component time series are simulated at critical vehicle locations. The PSD model for wind turbulence is a function of mean wind speed, elevation and temporal frequency. Integration of the PSD equation over a selected frequency range yields the variance of the time series to be simulated. The square root of the PSD defines a low-pass filter that is applied to adjust the components of the Fast Fourier Transform (FFT) of Gaussian white noise. The first simulated time series near the top of the launch vehicle is the inverse transform of the adjusted FFT. Simulation of the wind component time series at the nearest adjacent location (and all other succeeding next nearest locations) is based on a model for the coherence between winds at two locations as a function of frequency and separation distance, where the adjacent locations are separated vertically and/or horizontally. The coherence function is used to calculate a coherence weighted FFT of the wind at the next nearest location, given the FFT of the simulated time series at the previous location and the essentially incoherent FFT of the wind at the selected location derived a priori from the PSD model. The simulated time series at each adjacent location is the inverse Fourier transform of the coherence weighted FFT. For a selected