Science.gov

Sample records for aggregate simulation time

  1. Mesoscale Simulation of Asphaltene Aggregation.

    PubMed

    Wang, Jiang; Ferguson, Andrew L

    2016-08-18

    Asphaltenes constitute a heavy aromatic crude oil fraction with a propensity to aggregate and precipitate out of solution during petroleum processing. Aggregation is thought to proceed according to the Yen-Mullins hierarchy, but the molecular mechanisms underlying mesoscopic assembly remain poorly understood. By combining coarse-grained molecular models parametrized using all-atom data with high-performance GPU hardware, we have performed molecular dynamics simulations of the aggregation of hundreds of asphaltenes over microsecond time scales. Our simulations reveal a hierarchical self-assembly mechanism consistent with the Yen-Mullins model, but the details are sensitive and depend on asphaltene chemistry and environment. At low concentrations asphaltenes exist predominantly as dispersed monomers. Upon increasing concentration, we first observe parallel stacking into 1D rod-like nanoaggregates, followed by the formation of clusters of nanoaggregates associated by offset, T-shaped, and edge-edge stacking. Asphaltenes possessing long aliphatic side chains cannot form nanoaggregate clusters due to steric repulsions between their aliphatic coronae. At very high concentrations, we observe a porous percolating network of rod-like nanoaggregates suspended in a sea of interpenetrating aliphatic side chains with a fractal dimension of ∼2. The lifetime of the rod-like aggregates is described by an exponential distribution reflecting a dynamic equilibrium between coagulation and fragmentation. PMID:27455391

  2. Quantifying Aggregated Uncertainty in Plasmodium falciparum Malaria Prevalence and Populations at Risk via Efficient Space-Time Geostatistical Joint Simulation

    PubMed Central

    Gething, Peter W.; Patil, Anand P.; Hay, Simon I.

    2010-01-01

    Risk maps estimating the spatial distribution of infectious diseases are required to guide public health policy from local to global scales. The advent of model-based geostatistics (MBG) has allowed these maps to be generated in a formal statistical framework, providing robust metrics of map uncertainty that enhances their utility for decision-makers. In many settings, decision-makers require spatially aggregated measures over large regions such as the mean prevalence within a country or administrative region, or national populations living under different levels of risk. Existing MBG mapping approaches provide suitable metrics of local uncertainty—the fidelity of predictions at each mapped pixel—but have not been adapted for measuring uncertainty over large areas, due largely to a series of fundamental computational constraints. Here the authors present a new efficient approximating algorithm that can generate for the first time the necessary joint simulation of prevalence values across the very large prediction spaces needed for global scale mapping. This new approach is implemented in conjunction with an established model for P. falciparum allowing robust estimates of mean prevalence at any specified level of spatial aggregation. The model is used to provide estimates of national populations at risk under three policy-relevant prevalence thresholds, along with accompanying model-based measures of uncertainty. By overcoming previously unchallenged computational barriers, this study illustrates how MBG approaches, already at the forefront of infectious disease mapping, can be extended to provide large-scale aggregate measures appropriate for decision-makers. PMID:20369009

  3. 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. PMID:24020922

  4. Mesoscale simulation of asphaltene aggregation

    NASA Astrophysics Data System (ADS)

    Wang, Jiang; Ferguson, Andrew

    Asphaltenes constitute a heavy aromatic crude oil fraction that can aggregate and precipitate out of solution. Association is thought to proceed hierarchically according to the Yen-Mullins model, but the molecular mechanisms and pathways remain poorly understood. In this study, we perform molecular dynamics simulations of the aggregation of hundreds of asphaltenes over microseconds using the coarse-grained Martini force field. We identified a hierarchical self-assembly mechanism consistent with Yen-Mullins model, but the details of which are strongly dependent on asphaltene molecular structure. Monomeric asphaltenes first self-assemble into 1-D rod-like nanoaggregates, followed by the formation of clusters of nanoaggregates. At high concentrations, asphaltenes with short aliphatic side chains assemble into a percolating network with the binding of 1-D rods. Conversely, molecules with more and longer side chains cannot efficiently stack, producing a fractal network of 1-D rods suspended in a sea of interpenetrating aliphatic side chains. Our results provide the first molecularly-detailed validation of the full Yen-Mullins hierarchy, and are in good agreement with recent computational and experimental studies. ACS Petroleum Research Fund.

  5. 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.

  6. 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.

  7. 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.

  8. Melittin Aggregation in Aqueous Solutions: Insight from Molecular Dynamics Simulations.

    PubMed

    Liao, Chenyi; Esai Selvan, Myvizhi; Zhao, Jun; Slimovitch, Jonathan L; Schneebeli, Severin T; Shelley, Mee; Shelley, John C; Li, Jianing

    2015-08-20

    Melittin is a natural peptide that aggregates in aqueous solutions with paradigmatic monomer-to-tetramer and coil-to-helix transitions. Since little is known about the molecular mechanisms of melittin aggregation in solution, we simulated its self-aggregation process under various conditions. After confirming the stability of a melittin tetramer in solution, we observed—for the first time in atomistic detail—that four separated melittin monomers aggregate into a tetramer. Our simulated dependence of melittin aggregation on peptide concentration, temperature, and ionic strength is in good agreement with prior experiments. We propose that melittin mainly self-aggregates via a mechanism involving the sequential addition of monomers, which is supported by both qualitative and quantitative evidence obtained from unbiased and metadynamics simulations. Moreover, by combining computer simulations and a theory of the electrical double layer, we provide evidence to suggest why melittin aggregation in solution likely stops at the tetramer, rather than forming higher-order oligomers. Overall, our study not only explains prior experimental results at the molecular level but also provides quantitative mechanistic information that may guide the engineering of melittin for higher efficacy and safety. PMID:26208115

  9. 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

  10. 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.

  11. 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.

  12. Aggregation increases prey survival time in group chase and escape

    NASA Astrophysics Data System (ADS)

    Yang, Sicong; Jiang, Shijie; Jiang, Li; Li, Geng; Han, Zhangang

    2014-08-01

    Recently developed chase-and-escape models have addressed a fascinating pursuit-and-evasion problem that may have both theoretical significance and potential applications. We introduce three aggregation strategies for the prey in a group chase model on a lattice. Simulation results show that aggregation dramatically increases the group survival time, even allowing immortal prey. The average survival time τ and the aggregation probability P have a power-law dependence of \\tau \\sim {{(1-P)}^{-1}} for P\\in [0.9,0.997]. With increasing numbers of predators, there is still a phase transition. When the number of predators is less than the critical point value, the prey group survival time increases significantly.

  13. Simulation of Ionic Aggregation and Ion Dynamics in Model Ionomers

    NASA Astrophysics Data System (ADS)

    Frischknecht, Amalie L.

    2012-02-01

    Ionomers, polymers containing a small fraction of covalently bound ionic groups, are of interest as possible electrolytes in batteries. A single-ion conducting polymer electrolyte would be safer and have higher efficiency than the currently-used liquid electrolytes. However, to date ionomeric materials do not have sufficiently high conductivities for practical application. This is most likely because the ions tend to form aggregates, leading to slow ion transport. A key question is therefore how molecular structure affects the ionic aggregation and ion dynamics. To probe these structure-property relationships, we have performed molecular simulations of a set of recently synthesized poly(ethylene-co-acrylic acid) copolymers and ionomers, with a focus on the morphology of the ionic aggregates. The ionomers have a precise, constant spacing of charged groups, making them ideal for direct comparisons with simulations. Ab initio calculations give insight into the expected coordination of cations with fragments of the ionomers. All-atom molecular dynamics (MD) simulations of the ionomer melt show aggregation of the ionic groups into extended string-like clusters. An extensive set of coarse-grained molecular dynamics simulations extend the results to longer times and larger length scales. The structure factors calculated from the MD simulations compare favorably with x-ray scattering data. Furthermore, the simulations give a detailed picture of the sizes, shapes, and composition of the ionic aggregates, and how they depend on polymer architecture. Implications for ion transport will be discussed. [Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  14. 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.

  15. 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

  16. 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.

  17. 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

  18. Aggregation of Thermal Particles in Simulation

    NASA Astrophysics Data System (ADS)

    Chan, Iat Neng

    2011-03-01

    Based on the Schrodinger Equation, energy levels are evaluated for charged particle or atom surrounded by few atoms imitated to atomic cavity situations under multipole or Lennard-Jones interactions. To examine the states of corresponding eigenvalues, the associated wave functions from simulation are plotted in three-dimension to elucidate the space distribution of particles. In cases for testing on effect of different adjacent atomic structures, concentration region of distribution is revealed from a series of results. The range of localization shown also is affected by the type and strength of interactions between particles and atoms, besides the number and position of surrounding atoms. The thermal effect considered in the computation is modeled by average over results from random fluctuation of atom positions for a given heating grade. Moreover, analysis with fuzzy conditions is applied to reduce the complicated and time-consumption approach, also for the training in science education. Even the investigation is limited and tentative, qualitative studies on different parameters and structures can provide the influence of factors and approximate information to compare with the experience evidences. Supported by UM grant No. RG062/09-10S/CIN/FST.

  19. Cluster-cluster aggregation simulation in a concentrated suspension.

    PubMed

    Kusaka, Yasuyuki; Fukasawa, Tomonori; Adachi, Yasuhisa

    2011-11-01

    The collision radius of a floc is an indispensable parameter for the precise description of the rate of aggregation during the development of particle flocs with a wide size distribution. Herein, we report on the characteristics of the collision radius of fractal aggregates formed by off-lattice diffusion-limited cluster-cluster aggregation (DLCCA) simulations, and discuss aggregation kinetics based on the value of the estimated collision radius. The collision radius has a fractal relationship with the number of primary particles that compose the floc. Further, the obtained fractal dimensions of flocs increase from the normally accepted value of 1.6-1.8 to a value of ~2.5 when the initial volume fraction is above 8%. From an assessment of the partial radial distribution function of the particles, the increase of the fractal dimensions determined by the collision radius can be attributed to a change in the spatial distribution of neighboring particles. The DLCCA simulation also reveals an apparent increase in the rate of aggregation upon an increase in the initial volume fraction. For a relatively low initial volume fraction, the enhancement of the aggregation rate is expressed by a population balance equation taking into account additional factors, i.e., transient collision flux among particles/flocs, excluded volumes, and polydispersed features of flocs. However, for cases with high initial volume fractions, the population balance model that accounts for these three factors overestimates the aggregation rate, which supports the concept of a caging effect. PMID:21840531

  20. Temporal aggregation impacts on epidemiological simulations employing microcontact data

    PubMed Central

    2012-01-01

    Background Microcontact datasets gathered automatically by electronic devices have the potential augment the study of the spread of contagious disease by providing detailed representations of the study population’s contact dynamics. However, the impact of data collection experimental design on the subsequent simulation studies has not been adequately addressed. In particular, the impact of study duration and contact dynamics data aggregation on the ultimate outcome of epidemiological models has not been studied in detail, leaving the potential for erroneous conclusions to be made based on simulation outcomes. Methods We employ a previously published data set covering 36 participants for 92 days and a previously published agent-based H1N1 infection model to analyze the impact of contact dynamics representation on the simulated outcome of H1N1 transmission. We compared simulated attack rates resulting from the empirically recorded contact dynamics (ground truth), aggregated, typical day, and artificially generated synthetic networks. Results No aggregation or sampling policy tested was able to reliably reproduce results from the ground-truth full dynamic network. For the population under study, typical day experimental designs – which extrapolate from data collected over a brief period – exhibited too high a variance to produce consistent results. Aggregated data representations systematically overestimated disease burden, and synthetic networks only reproduced the ground truth case when fitting errors systemically underestimated the total contact, compensating for the systemic overestimation from aggregation. Conclusions The interdepedendencies of contact dynamics and disease transmission require that detailed contact dynamics data be employed to secure high fidelity in simulation outcomes of disease burden in at least some populations. This finding serves as motivation for larger, longer and more socially diverse contact dynamics tracing experiments and as a

  1. Accelerating climate simulation analytics via multilevel aggregation and synthesis

    NASA Astrophysics Data System (ADS)

    Anantharaj, Valentine; Ravindran, Krishnaraj; Gunasekaran, Raghul; Vazhkudai, Sudharshan; Butt, Ali

    2015-04-01

    A typical set of ultra high resolution (0.25 deg) climate simulation experiments produce over 50,000 files, ranging in sizes from 101 MB to 102 GB each - for a total volume of nearly 1 PB of data. The execution of the experiments will require over 100 Million CPU hours on the Titan supercomputer at the Oak Ridge Leadership Computing Facility (OLCF). The output from the simulations must then be archived, analyzed, distributed to the project partners in a timely manner. Meeting this challenge would require efficient movement of the data, staging the simulation output to a large and fast file system that provides high volume access to other computational systems used to analyze the data and synthesize results. But data movement is one of the most expensive and time consuming steps in the scientific workflow. It is be expedient to complete the diagnostics and analytics before the files are archived for long term storage. Nevertheless, it is often necessary to fetch the files from archive for further analysis. We are implementing a solution to query, extract, index and summarize key statistical information from the individual CF-compliant netCDF files that are then stored for ready-access in a database. The contents of the database can be related back to the archived files from which they were extracted. The statistical information can be quickly aggregated to provide meaningful statistical summaries that could then be related to observations and/or other simulation results for synthesis and further inference. The scientific workflow at OLCF, augmented by expedited analytics capabilities, will allow the users of our systems to shorten the time required to derive meaningful and relevant science results. We will illustrate some of the timesaving benefits via a few typical use cases, based on recent large-scale simulation experiments using the Community Earth System Model (CESM) and the DOE Accelerated Climate Model for Energy (ACME).

  2. 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.

  3. Monte Carlo simulation of the heterotypic aggregation kinetics of platelets and neutrophils.

    PubMed

    Laurenzi, I J; Diamond, S L

    1999-09-01

    The heterotypic aggregation of cell mixtures or colloidal particles such as proteins occurs in a variety of settings such as thrombosis, immunology, cell separations, and diagnostics. Using the set of population balance equations (PBEs) to predict dynamic aggregate size and composition distributions is not feasible. The stochastic algorithm of Gillespie for chemical reactions (. J. Comput. Phys. 22:403-434) was reformulated to simulate the kinetic behavior of aggregating systems. The resulting Monte Carlo (MC) algorithm permits exact calculation of the decay rates of monomers and the temporally evolving distribution of sizes and compositions of the aggregates. Moreover, it permits calculation of all moments of these distributions. Using this method, we explored the heterotypic aggregation of fully activated platelets and neutrophils in a linear shear flow of shear rate G = 335 s(-1). At plasma concentrations, the half-lives of homotypically aggregating platelet and neutrophil singlets were 8.5 and 2.4 s, respectively. However, for heterotypic aggregation, the half-lives for platelets and neutrophils decreased to 2.0 and 0.11 s, respectively, demonstrating that flowing neutrophils accelerate capture of platelets and growth of aggregates. The required number of calculations per time step of the MC algorithm was typically a small fraction of Omega(1/2), where Omega is the initial number of particles in the system, making this the fastest MC method available. The speed of the algorithm makes feasible the deconvolution of kernels for general biological heterotypic aggregation processes. PMID:10465782

  4. Simulation of aggregating particles in complex flows by the lattice kinetic Monte Carlo method

    NASA Astrophysics Data System (ADS)

    Flamm, Matthew H.; Sinno, Talid; Diamond, Scott L.

    2011-01-01

    We develop and validate an efficient lattice kinetic Monte Carlo (LKMC) method for simulating particle aggregation in laminar flows with spatially varying shear rate, such as parabolic flow or flows with standing vortices. A contact time model was developed to describe the particle-particle collision efficiency as a function of the local shear rate, G, and approach angle, θ. This model effectively accounts for the hydrodynamic interactions between approaching particles, which is not explicitly considered in the LKMC framework. For imperfect collisions, the derived collision efficiency [\\varepsilon = 1 - int_0^{{π {π /2} {sin θ exp ( { - 2\\cot θ {{Γ _{agg} }/ { Γ _{agg} } G} )} dθ] was found to depend only on Γagg/G, where Γagg is the specified aggregation rate. For aggregating platelets in tube flow, Γ _{agg} = 0.683 s-1 predicts the experimentally measured ɛ across a physiological range (G = 40-1000 s-1) and is consistent with α2bβ3-fibrinogen bond dynamics. Aggregation in parabolic flow resulted in the largest aggregates forming near the wall where shear rate and residence time were maximal, however intermediate regions between the wall and the center exhibited the highest aggregation rate due to depletion of reactants nearest the wall. Then, motivated by stenotic or valvular flows, we employed the LKMC simulation developed here for baffled geometries that exhibit regions of squeezing flow and standing recirculation zones. In these calculations, the largest aggregates were formed within the vortices (maximal residence time), while squeezing flow regions corresponded to zones of highest aggregation rate.

  5. Simulation studies on shape and growth kinetics for fractal aggregates in aerosol and colloidal systems

    NASA Astrophysics Data System (ADS)

    Heinson, William Raymond

    The aim of this work is to explore, using computational techniques that simulate the motion and subsequent aggregation of particles in aerosol and colloidal systems, many common but not well studied systems that form fractal clusters. Primarily the focus is on cluster shape and growth kinetics. The structure of clusters made under diffusion limited cluster-cluster aggregation (DLCA) is looked at. More specifically, the shape anisotropy is found to have an inverse relationship on the scaling prefactor k0 and have no effect on the fractal dimension Df . An analytical model that predicts the shape and fractal dimension of diffusion limited cluster-cluster aggregates is tested and successfully predicts cluster shape and dimensionality. Growth kinetics of cluster-cluster aggregation in the free molecular regime where the system starts with ballistic motion and then transitions to diffusive motion as the aggregates grow in size is studied. It is shown that the kinetic exponent will crossover from the ballistic to the diffusional values and the onset of this crossover is predicted by when the nearest neighbor Knudsen number reaches unity. Simulations were carried out for a system in which molten particles coalesce into spheres, then cool till coalescing stops and finally the polydispersed monomers stick at point contacts to form fractal clusters. The kinetic exponent and overall cluster structure for these aggregates was found to be in agreement with DLCA that started with monodispersed monomers. Colloidal aggregation in the presence of shear was studied in detail. Study of a colloidal system characterized a by short-range attractive potential showed that weak shear enhanced the aggregation process. Strong shear led to fragmentation and subsequent nucleation as cluster growth rebounded after an induction time.

  6. Real-Time Simulation

    NASA Technical Reports Server (NTRS)

    1997-01-01

    Coryphaeus Software, founded in 1989 by former NASA electronic engineer Steve Lakowske, creates real-time 3D software. Designer's Workbench, the company flagship product, is a modeling and simulation tool for the development of both static and dynamic 3D databases. Other products soon followed. Activation, specifically designed for game developers, allows developers to play and test the 3D games before they commit to a target platform. Game publishers can shorten development time and prove the "playability" of the title, maximizing their chances of introducing a smash hit. Another product, EasyT, lets users create massive, realistic representation of Earth terrains that can be viewed and traversed in real time. Finally, EasyScene software control the actions among interactive objects within a virtual world. Coryphaeus products are used on Silican Graphics workstation and supercomputers to simulate real-world performance in synthetic environments. Customers include aerospace, aviation, architectural and engineering firms, game developers, and the entertainment industry.

  7. 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

  8. 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

  9. The Rebound Condition of Dust Aggregates Revealed by Numerical Simulation of Their Collisions

    NASA Astrophysics Data System (ADS)

    Wada, Koji; Tanaka, Hidekazu; Suyama, Toru; Kimura, Hiroshi; Yamamoto, Tetsuo

    2011-08-01

    Collisional growth of dust aggregates is a plausible root of planetesimals forming in protoplanetary disks. However, a rebound of colliding dust aggregates prevents dust from growing into planetesimals. In fact, rebounding aggregates are observed in laboratory experiments but not in previous numerical simulations. Therefore, the condition of rebound between dust aggregates should be clarified to better understand the processes of dust growth and planetesimal formation. We have carried out numerical simulations of aggregate collisions for various types of aggregates and succeeded in reproducing a rebound of colliding aggregates under specific conditions. Our finding is that in the rebound process, the key factor of the aggregate structure is the coordination number, namely, the number of particles in contact with a particle. A rebound is governed by the energy dissipation along with restructuring of the aggregates and a large coordination number inhibits the restructuring at collisions. Results of our numerical simulation for various aggregates indicate that they stick to each other when the mean coordination number is less than 6, regardless of their materials and structures, as long as their collision velocity is less than the critical velocity for fragmentation. This criterion of the coordination number would correspond to a filling factor of ~0.3, which is somewhat larger than that reported in laboratory experiments. In protoplanetary disks, dust aggregates are expected to have low bulk densities (<0.1 g cm-3) during their growth, which would prevent dust aggregates from rebounding. This result supports the formation of planetesimals with direct dust growth in protoplanetary disks.

  10. Finite Size Effects in Simulations of Protein Aggregation

    PubMed Central

    Pawar, Amol; Favrin, Giorgio

    2008-01-01

    It is becoming increasingly clear that the soluble protofibrillar species that proceed amyloid fibril formation are associated with a range of neurodegenerative disorders such as Alzheimer's and Parkinson diseases. Computer simulations of the processes that lead to the formation of these oligomeric species are starting to make significant contributions to our understanding of the determinants of protein aggregation. We simulate different systems at constant concentration but with a different number of peptides and we study the how the finite number of proteins affects the underlying free energy of the system and therefore the relative stability of the species involved in the process. If not taken into account, this finite size effect can undermine the validity of theoretical predictions regarding the relative stability of the species involved and the rates of conversion from one to the other. We discuss the reasons that give rise to this finite size effect form both a probabilistic and energy fluctuations point of view and also how this problem can be dealt by a finite size scaling analysis. PMID:18612385

  11. Replica exchange molecular dynamics simulations of amyloid peptide aggregation

    NASA Astrophysics Data System (ADS)

    Cecchini, M.; Rao, F.; Seeber, M.; Caflisch, A.

    2004-12-01

    The replica exchange molecular dynamics (REMD) approach is applied to four oligomeric peptide systems. At physiologically relevant temperature values REMD samples conformation space and aggregation transitions more efficiently than constant temperature molecular dynamics (CTMD). During the aggregation process the energetic and structural properties are essentially the same in REMD and CTMD. A condensation stage toward disordered aggregates precedes the β-sheet formation. Two order parameters, borrowed from anisotropic fluid analysis, are used to monitor the aggregation process. The order parameters do not depend on the peptide sequence and length and therefore allow to compare the amyloidogenic propensity of different peptides.

  12. Understanding the structural properties of clusters in sheared aggregating systems using Brownian dynamics simulation

    NASA Astrophysics Data System (ADS)

    Markutsya, Sergiy; Fox, Rodney; Vigil, Dennis; Subramaniam, Shankar

    2009-11-01

    Nanoparticle synthesis in turbulent reactors subjects anoparticle aggregates to a homogeneous, time-varying shear flow. The shear flow results in anisotropic clusters and it is of interest to characterize the structural properties of these clusters and their effects on initiation and acceleration of aggregation, the restructuring of clusters, and their breakage. The anisotropic structure of a sheared cluster is characterized by the ratio of the major to minor axis length of the approximating ellipsoid oriented along the cluster moment of inertia tensor's principal axes. Brownian dynamics simulations show that shear flow dramatically changes the structure of aggregates by initiating the formation of more compact structures at smaller length scales perpendicular to the shear direction, and anisotropic, cigar--like structures along the shear direction. More compact clusters correspond to higher local volumetric potential energy density. Therefore, we classify the compactness and anisotropy of sheared clusters on a map of local volumetric potential energy density versus ratio of the principal values of the cluster's moment of inertia tensor. The effect of shear on breakage of clusters is characterized by the radius of gyration Rg^cr of the largest stable aggregate for a given value of the imposed steady shear rate (P'eclet number).

  13. 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.

  14. Monte Carlo simulations for amphiphilic aggregation near a water phase transition

    NASA Astrophysics Data System (ADS)

    Heinzelmann, G.; Figueiredo, W.; Girardi, M.

    2009-10-01

    In this study we analyze the equilibrium and dynamical properties of a lattice model for amphiphilic aggregation in a waterlike associating solvent. The amphiphiles are described as flexible chains of interconnected sites in a body-centered cubic lattice, with hydrophilic and hydrophobic portions. The solvent molecules occupy a single site and resemble the water tetrahedral molecular structure, with the possibility of hydrogen-bond formation and different densities. Following the phase diagram of the solvent model, we are able to study the effects of a phase transition of the solvent in the micellar dynamics. By carrying out Monte Carlo simulations, we analyze the micelle aggregate size distribution curve, the critical micelle concentration, the surfactant diffusion coefficient, the residence time, and the exit/entering rates of the amphiphiles from/to aggregates of different sizes. We also investigate the dipolar reorientational time correlation function for interfacial water and water molecules in the solvent bulk, as well as the number of hydrogen bonds per molecule in both cases.

  15. 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.

  16. 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

  17. 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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  19. System time-domain simulation

    NASA Technical Reports Server (NTRS)

    Dawson, C. T.; Eggleston, T. W.; Goris, A. C.; Fashano, M.; Paynter, D.; Tranter, W. H.

    1980-01-01

    Complex systems are simulated by engineers without extensive computer experience. Analyst uses free-form engineering-oriented language to input "black box" description. System Time Domain (SYSTID) Simulation Program generates appropriate algorithms and proceeds with simulation. Program is easily linked to postprocessing routines. SYSTID program is written in FORTRAN IV for batch execution and has been implemented on UNIVAC 1110 under control of EXEC 8, Level 31.

  20. 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.

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

    PubMed

    Burov, S V; Shchekin, A K

    2010-12-28

    General thermodynamic relations for the work of polydisperse micelle formation in the model of ideal solution of molecular aggregates in nonionic surfactant solution and the model of "dressed micelles" in ionic solution have been considered. In particular, the dependence of the aggregation work on the total concentration of nonionic surfactant has been analyzed. The analogous dependence for the work of formation of ionic aggregates has been examined with regard to existence of two variables of a state of an ionic aggregate, the aggregation numbers of surface active ions and counterions. To verify the thermodynamic models, the molecular dynamics simulations of micellization in nonionic and ionic surfactant solutions at two total surfactant concentrations have been performed. It was shown that for nonionic surfactants, even at relatively high total surfactant concentrations, the shape and behavior of the work of polydisperse micelle formation found within the model of the ideal solution at different total surfactant concentrations agrees fairly well with the numerical experiment. For ionic surfactant solutions, the numerical results indicate a strong screening of ionic aggregates by the bound counterions. This fact as well as independence of the coefficient in the law of mass action for ionic aggregates on total surfactant concentration and predictable behavior of the "waterfall" lines of surfaces of the aggregation work upholds the model of "dressed" ionic aggregates. PMID:21197978

  2. 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.

  3. 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.

  4. 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.

  5. Relation between Molecular Shape and the Morphology of Self-Assembling Aggregates: A Simulation Study

    PubMed Central

    Vácha, Robert; Frenkel, Daan

    2011-01-01

    Proteins can aggregate in a wide variety of structures, both compact and extended. We present simulations of a coarse-grained anisotropic model that reproduce many of the experimentally observed aggregate structures. Conversely, all structures predicted by our model have experimental counterparts (ribbons, multistranded fibrils, and vesicles). The model we use is that of a rodlike particle with an attractive (hydrophobic) stripe on its side. Our Monte Carlo simulations show that aggregate morphologies crucially depend on two parameters. The first one is the width of the attractive stripe and the second one is a presence or absence of attractive interactions at the particle ends. These results provide us with a generic insight into the relation between the shape of protein-protein interaction potential and the morphology of protein aggregates. PMID:21943424

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

    PubMed

    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. PMID:27484239

  7. 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.

  8. 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. PMID:26149857

  9. 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

  10. 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

  11. 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.

  12. Davydov Ansatz as an efficient tool for the simulation of nonlinear optical response of molecular aggregates

    NASA Astrophysics Data System (ADS)

    Sun, Ke-Wei; Gelin, Maxim F.; Chernyak, Vladimir Y.; Zhao, Yang

    2015-06-01

    We have developed a variational approach to the description of four-wave-mixing signals of molecular aggregates, in which the third-order response functions are evaluated in terms of the Davydov Ansätze. Our theory treats both singly and doubly excited excitonic states, handling the contributions due to stimulated emission, ground state bleach, and excited state absorption. As an illustration, we simulate a series of optical two-dimensional spectra of model J-aggregates. Our approach may become suitable for the computation of femtosecond optical four-wave-mixing signals of molecular aggregates with intermediate-to-strong exciton-phonon and exciton-exciton coupling strengths.

  13. Colloidal Asphaltene Deposition and Aggregation in Capillary Flow: Experiments and Mesoscopic Simulation

    NASA Astrophysics Data System (ADS)

    Boek, Edo S.; Ladva, Hemant K.; Crawshaw, John P.; Padding, Johan T.

    2008-07-01

    The aggregation and deposition of colloidal asphaltene in reservoir rock is a significant problem in the oil industry. To obtain a fundamental understanding of this phenomenon, we have studied the deposition and aggregation of colloidal asphaltene in capillary flow by experiment and simulation. For the simulation, we have used the stochastic rotation dynamics (SRD) method, in which the solvent hydrodynamic emerges from the collisions between the solvent particles, while the Brownian motion emerges naturally from the interactions between the colloidal asphaltene particles and the solvent. The asphaltene colloids interact through a screened Coulomb potential. We vary the well depth ɛ∝ and the flow rate v to obtain Peflow≫1 (hydrodynamic interactions dominate) and Re≪1 (Stokes flow). In the simulations, we impose a pressure drop over the capillary length and measure the corresponding solvent flow rate. We observe that the transient solvent flow rate decreases when the asphaltene particles become more "sticky". For a well depth ɛ∝ = 2kBT, a monolayer deposits on the capillary wall. With an increasing well depth, the capillary becomes totally blocked. The clogging is transient for ɛ∝ = 5kBT, but appears to be permanent for ɛ∝ = 10-20 kBT. We compare our simulation results with flow experiments in glass capillaries, where we use extracted asphaltenes in toluene, reprecipitated with n-heptane. In the experiments, the dynamics of asphaltene precipitation and deposition were monitored in a slot capillary using optical microscopy under flow conditions similar to those used in the simulation. Maintaining a constant flow rate of 5 μL min-1, we found that the pressure drop across the capillary first increased slowly, followed by a sharp increase, corresponding to a complete local blockage of the capillary. Doubling the flow rate to 10 μL min-1, we observe that the initial deposition occurs faster but the deposits are subsequently entrained by the flow. We

  14. 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.

  15. 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.

  16. Mobile phone usage in complex urban systems: a space-time, aggregated human activity study

    NASA Astrophysics Data System (ADS)

    Tranos, Emmanouil; Nijkamp, Peter

    2015-04-01

    The present study aims to demonstrate the importance of digital data for investigating space-time dynamics of aggregated human activity in urban systems. Such dynamics can be monitored and modelled using data from mobile phone operators regarding mobile telephone usage. Using such an extensive dataset from the city of Amsterdam, this paper introduces space-time explanatory models of aggregated human activity patterns. Various modelling experiments and results are presented, which demonstrate that mobile telephone data are a good proxy of the space-time dynamics of aggregated human activity in the city.

  17. 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.

  18. 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

  19. 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.

  20. Understanding long-time vacancy aggregation in iron: A kinetic activation-relaxation technique study

    NASA Astrophysics Data System (ADS)

    Brommer, Peter; Béland, Laurent Karim; Joly, Jean-François; Mousseau, Normand

    2014-10-01

    Vacancy diffusion and clustering processes in body-centered-cubic (bcc) Fe are studied using the kinetic activation-relaxation technique (k-ART), an off-lattice kinetic Monte Carlo method with on-the-fly catalog building capabilities. For monovacancies and divacancies, k-ART recovers previously published results while clustering in a 50-vacancy simulation box agrees with experimental estimates. Applying k-ART to the study of clustering pathways for systems containing from one to six vacancies, we find a rich set of diffusion mechanisms. In particular, we show that the path followed to reach a hexavacancy cluster influences greatly the associated mean-square displacement. Aggregation in a 50-vacancy box also shows a notable dispersion in relaxation time associated with effective barriers varying from 0.84 to 1.1 eV depending on the exact pathway selected. We isolate the effects of long-range elastic interactions between defects by comparing to simulations where those effects are deliberately suppressed. This allows us to demonstrate that in bcc Fe, suppressing long-range interactions mainly influences kinetics in the first 0.3 ms, slowing down quick energy release cascades seen more frequently in full simulations, whereas long-term behavior and final state are not significantly affected.

  1. 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.

  2. 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

  3. Segment-level evaluation of the simulated aggregation test: US corn and soybean exploratory experiment

    NASA Technical Reports Server (NTRS)

    Davidson, S. A. (Principal Investigator)

    1980-01-01

    An evaluation of the corn and soybean proportion-estimation accuracy and dot labeling accuracy of the Simulated Aggregation Test, U.S. Corn and Soybean Exploratory Experiment, is presented. These results are in turn compared with the corn and soybean proportion-estimation accuracy and dot labeling accuracy of the Classification Procedures Verification Test.

  4. 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.

  5. 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. PMID:21394178

  6. 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

  7. Multilevel space-time aggregation for bright field cell microscopy segmentation and tracking.

    PubMed

    Inglis, Tiffany; De Sterck, Hans; Sanders, Geoffrey; Djambazian, Haig; Sladek, Robert; Sundararajan, Saravanan; Hudson, Thomas J

    2010-01-01

    A multilevel aggregation method is applied to the problem of segmenting live cell bright field microscope images. The method employed is a variant of the so-called "Segmentation by Weighted Aggregation" technique, which itself is based on Algebraic Multigrid methods. The variant of the method used is described in detail, and it is explained how it is tailored to the application at hand. In particular, a new scale-invariant "saliency measure" is proposed for deciding when aggregates of pixels constitute salient segments that should not be grouped further. It is shown how segmentation based on multilevel intensity similarity alone does not lead to satisfactory results for bright field cells. However, the addition of multilevel intensity variance (as a measure of texture) to the feature vector of each aggregate leads to correct cell segmentation. Preliminary results are presented for applying the multilevel aggregation algorithm in space time to temporal sequences of microscope images, with the goal of obtaining space-time segments ("object tunnels") that track individual cells. The advantages and drawbacks of the space-time aggregation approach for segmentation and tracking of live cells in sequences of bright field microscope images are presented, along with a discussion on how this approach may be used in the future work as a building block in a complete and robust segmentation and tracking system. PMID:20467468

  8. 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.

  9. 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

  10. 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

  11. CFD simulation of shear-induced aggregation and breakage in turbulent Taylor-Couette flow.

    PubMed

    Wang, Liguang; Vigil, R Dennis; Fox, Rodney O

    2005-05-01

    An experimental and computational investigation of the effects of local fluid shear rate on the aggregation and breakage of approximately 10 microm latex spheres suspended in an aqueous solution undergoing turbulent Taylor-Couette flow was carried out. First, computational fluid dynamics (CFD) simulations were performed and the flow field predictions were validated with data from particle image velocimetry experiments. Subsequently, the quadrature method of moments (QMOM) was implemented into the CFD code to obtain predictions for mean particle size that account for the effects of local shear rate on the aggregation and breakage. These predictions were then compared with experimental data for latex sphere aggregates (using an in situ optical imaging method). Excellent agreement between the CFD-QMOM and experimental results was observed for two Reynolds numbers in the turbulent-flow regime. PMID:15797411

  12. Davydov Ansatz as an efficient tool for the simulation of nonlinear optical response of molecular aggregates.

    PubMed

    Sun, Ke-Wei; Gelin, Maxim F; Chernyak, Vladimir Y; Zhao, Yang

    2015-06-01

    We have developed a variational approach to the description of four-wave-mixing signals of molecular aggregates, in which the third-order response functions are evaluated in terms of the Davydov Ansätze. Our theory treats both singly and doubly excited excitonic states, handling the contributions due to stimulated emission, ground state bleach, and excited state absorption. As an illustration, we simulate a series of optical two-dimensional spectra of model J-aggregates. Our approach may become suitable for the computation of femtosecond optical four-wave-mixing signals of molecular aggregates with intermediate-to-strong exciton-phonon and exciton-exciton coupling strengths. PMID:26049468

  13. Study of the aggregation mechanism of polyglutamine peptides using replica exchange molecular dynamics simulations.

    PubMed

    Nakano, Miki; Ebina, Kuniyoshi; Tanaka, Shigenori

    2013-04-01

    Polyglutamine (polyQ, a peptide) with an abnormal repeat length is the causative agent of polyQ diseases, such as Huntington's disease. Although glutamine is a polar residue, polyQ peptides form insoluble aggregates in water, and the mechanism for this aggregation is still unclear. To elucidate the detailed mechanism for the nucleation and aggregation of polyQ peptides, replica exchange molecular dynamics simulations were performed for monomers and dimers of polyQ peptides with several chain lengths. Furthermore, to determine how the aggregation mechanism of polyQ differs from those of other peptides, we compared the results for polyQ with those of polyasparagine and polyleucine. The energy barrier between the monomeric and dimeric states of polyQ was found to be relatively low, and it was observed that polyQ dimers strongly favor the formation of antiparallel β-sheet structures. We also found a characteristic behavior of the monomeric polyQ peptide: a turn at the eighth residue is always present, even when the chain length is varied. We previously showed that a structure including more than two sets of β-turns is stable, so a long monomeric polyQ chain can act as an aggregation nucleus by forming several pairs of antiparallel β-sheet structures within a single chain. Since the aggregation of polyQ peptides has some features in common with an amyloid fibril, our results shed light on the mechanism for the aggregation of polyQ peptides as well as the mechanism for the formation of general amyloid fibrils, which cause the onset of amyloid diseases. PMID:23288093

  14. 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.

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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.

  20. 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.

  1. 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. PMID:25643930

  2. 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.

  3. CFD simulation of aggregation and breakage processes in laminar Taylor-Couette flow.

    PubMed

    Wang, L; Marchisio, D L; Vigil, R D; Fox, R O

    2005-02-15

    An experimental and computational investigation of the effects of local fluid shear rate on the aggregation and breakage of approximately 10 microm latex spheres suspended in an aqueous solution undergoing laminar Taylor-Couette flow was carried out according to the following program. First, computational fluid dynamics (CFD) simulations were performed and the flow field predictions were validated with data from particle image velocimetry experiments. Subsequently, the quadrature method of moments (QMOM) was implemented into the CFD code to obtain predictions for mean particle size that account for the effects of local shear rate on the aggregation and breakage. These predictions were then compared with experimental data for latex sphere aggregates (using an in situ optical imaging method) and with predictions using spatial average shear rates. The mean particle size evolution predicted by CFD and QMOM using appropriate kinetic expressions that incorporate information concerning the particle morphology (fractal dimension) and the local fluid viscous effects on aggregation collision efficiency match well with the experimental data. PMID:15589543

  4. 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.

  5. Real-time protein aggregation monitoring with a Bloch surface wave-based approach

    NASA Astrophysics Data System (ADS)

    Santi, Sara; Barakat, Elsie; Descrovi, Emiliano; Neier, Reinhard; Herzig, Hans Peter

    2014-05-01

    The misfolding and aggregation of amyloid proteins has been associated with incurable diseases such as Alzheimer's or Parkinson's disease. In the specific case of Alzheimer's disease, recent studies have shown that cell toxicity is caused by soluble oligomeric forms of aggregates appearing in the early stages of aggregation, rather than by insoluble fibrils. Research on new strategies of diagnosis is imperative to detect the disease prior to the onset of clinical symptoms. Here, we propose the use of an optical method for protein aggregation dynamic studies using a Bloch surface wave based approach. A one dimension photonic crystal made of a periodic stack of silicon oxide and silicon nitride layers is used to excite a Bloch surface wave, which is sensitive to variation of the refractive index of an aqueous solution. The aim is to detect the early dynamic events of protein aggregation and fibrillogenesis of the amyloid-beta peptide Aβ42, which plays a central role in the onset of the Alzheimer's disease. The detection principle relies on the refractive index changes caused by the depletion of the Aβ42 monomer concentration during oligomerization and fibrillization. We demonstrate the efficacy of the Bloch surface wave approach by monitoring in real-time the first crucial steps of Aβ42 oligomerization.

  6. 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

  7. Time domain analog circuit simulation

    NASA Astrophysics Data System (ADS)

    Fijnvandraat, J. G.; Houben, S. H. M. J.; Ter Maten, E. J. W.; Peters, J. M. F.

    2006-01-01

    Recent developments of new methods for simulating electric circuits are described. Emphasis is put on methods that fit existing datastructures for backward differentiation formulae methods. These methods can be modified to apply to hierarchically organized datastructures, which allows for efficient simulation of large designs of circuits in the electronics industry.

  8. Fluorescence lifetime heterogeneity in aggregates of LHCII revealed by time-resolved microscopy.

    PubMed Central

    Barzda, V; de Grauw, C J; Vroom, J; Kleima, F J; van Grondelle, R; van Amerongen, H; Gerritsen, H C

    2001-01-01

    Two-photon excitation, time-resolved fluorescence microscopy was used to investigate the fluorescence quenching mechanisms in aggregates of light-harvesting chlorophyll a/b pigment protein complexes of photosystem II from green plants (LHCII). Time-gated microscopy images show the presence of large heterogeneity in fluorescence lifetimes not only for different LHCII aggregates, but also within a single aggregate. Thus, the fluorescence decay traces obtained from macroscopic measurements reflect an average over a large distribution of local fluorescence kinetics. This opens the possibility to resolve spatially different structural/functional units in chloroplasts and other heterogeneous photosynthetic systems in vivo, and gives the opportunity to investigate individually the excited states dynamics of each unit. We show that the lifetime distribution is sensitive to the concentration of quenchers contained in the system. Triplets, which are generated at high pulse repetition rates of excitation (>1 MHz), preferentially quench domains with initially shorter fluorescence lifetimes. This proves our previous prediction from singlet-singlet annihilation investigations (Barzda, V., V. Gulbinas, R. Kananavicius, V. Cervinskas, H. van Amerongen, R. van Grondelle, and L. Valkunas. 2001. Biophys. J. 80:2409-2421) that shorter fluorescence lifetimes originate from larger domains in LHCII aggregates. We found that singlet-singlet annihilation has a strong effect in time-resolved fluorescence microscopy of connective systems and has to be taken into consideration. Despite that, clear differences in fluorescence decays can be detected that can also qualitatively be understood. PMID:11423435

  9. Simulation of infrared scattering from ice aggregates by use of a size-shape distribution of circular ice cylinders.

    PubMed

    Baran, Anthony J

    2003-05-20

    The scalar optical properties (extinction coefficient, mass extinction coefficient, single-scattering albedo, and asymmetry parameter) of a distribution of randomly oriented ice aggregates are simulated generally to well within 4% accuracy by use of a size-shape distribution of randomly oriented circular ice cylinders at wavelengths in the terrestrial window region. The single-scattering properties of the ice aggregates are calculated over the whole size distribution function by the finite-difference time-domain and improved geometric optics methods. The single-scattering properties of the size-shape distribution of circular ice cylinders are calculated by the T-matrix method supplemented by scattering solutions obtained from complex-angular-momentum theory. Moreover, radiative-transfer studies demonstrate that the maximum error in brightness temperature space when the size-shape distribution of circular ice cylinders is used to represent scattering from ice aggregates is only approximately 0.4 K The methodology presented should find wide applicability in remote sensing of ice cloud and parameterization of cirrus cloud scalar optical properties in climate models. PMID:12777019

  10. 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.

  11. Structure, Stability, and Fragmentation of Sodium bis(2-ethylhexyl)Sulfosuccinate Negatively Charged Aggregates In Vacuo by MD Simulations

    NASA Astrophysics Data System (ADS)

    Longhi, Giovanna; Abbate, Sergio; Ceselli, Alberto; Ceraulo, Leopoldo; Fornili, Sandro L.; Turco Liveri, Vincenzo

    2014-09-01

    Negatively charged supramolecular aggregates formed in vacuo by n bis(2-ethylhexyl)sulfosuccinate (AOT-) anions and n + n c sodium counterions (i.e., [AOT n Na n+nc ] nc ) have been investigated by molecular dynamics (MD) simulations for n = 1 to 20 and n c = -1 to -5. By comparing the maximum excess charge values of negatively and positively charged AOTNa aggregates, it is found that the charge storage capability is higher for the latter systems, the difference decreasing as the aggregation number increases. Statistical analysis of physical properties like gyration radii and moment of inertia tensors of aggregates provides detailed information on their structural properties. Even for n c = -5, all stable aggregates show a reverse micelle-like structure with an internal core, including sodium counterions and surfactant polar heads, surrounded by an external layer consisting of the surfactant alkyl chains. Interestingly, the reverse micelle-like structure is retained also in proximity of fragmentation. Moreover, the aggregate shapes may be approximated by elongated ellipsoids whose longer axis increases with n and | n c |. The fragmentation patterns of a number of these aggregates have also been examined and have been found to markedly depend on the aggregate charge state. The simulated fragmentation patterns of a representative aggregate show good agreement with experimental data obtained using low collision voltages.

  12. Structure, stability, and fragmentation of sodium bis(2-ethylhexyl)sulfosuccinate negatively charged aggregates in vacuo by MD simulations.

    PubMed

    Longhi, Giovanna; Abbate, Sergio; Ceselli, Alberto; Ceraulo, Leopoldo; Fornili, Sandro L; Turco Liveri, Vincenzo

    2014-09-01

    Negatively charged supramolecular aggregates formed in vacuo by n bis(2-ethylhexyl)sulfosuccinate (AOT(-)) anions and n + n(c) sodium counterions (i.e., [AOT(n) Na(n+nc)](nc)) have been investigated by molecular dynamics (MD) simulations for n = 1 to 20 and n(c) = -1 to -5. By comparing the maximum excess charge values of negatively and positively charged AOTNa aggregates, it is found that the charge storage capability is higher for the latter systems, the difference decreasing as the aggregation number increases. Statistical analysis of physical properties like gyration radii and moment of inertia tensors of aggregates provides detailed information on their structural properties. Even for n(c) = -5, all stable aggregates show a reverse micelle-like structure with an internal core, including sodium counterions and surfactant polar heads, surrounded by an external layer consisting of the surfactant alkyl chains. Interestingly, the reverse micelle-like structure is retained also in proximity of fragmentation. Moreover, the aggregate shapes may be approximated by elongated ellipsoids whose longer axis increases with n and |n(c)|. The fragmentation patterns of a number of these aggregates have also been examined and have been found to markedly depend on the aggregate charge state. The simulated fragmentation patterns of a representative aggregate show good agreement with experimental data obtained using low collision voltages. PMID:24969925

  13. Examining the aggregation behavior of polymer grafted nanoparticles using molecular simulation and theory

    NASA Astrophysics Data System (ADS)

    Haley, Jessica D.; Iacovella, Christopher R.; Cummings, Peter T.; McCabe, Clare

    2015-08-01

    Grafting polymers to nanoparticles is one approach used to control and enhance the structure and properties of nanomaterials. However, predicting the aggregation behavior of tethered nanoparticles (TNPs) is a somewhat trial and error process as a result of the large number of possible polymer tethers, nanoparticles, and solvent species that can be studied. With the main goal of understanding how to control the dispersion and aggregation of TNP systems, molecular simulations and the hetero-statistical associating fluid theory for potentials of variable range have been used to calculate the fluid phase equilibrium of TNPs in both vacuum and in simple solvents under a wide range of conditions. The role of graft length, graft density, and solvent interactions is examined and trends established. Additionally, the fluid distribution ratio (k value) is used to study the solubility of TNPs in industrially relevant solvents including carbon dioxide, nitrogen, propane, and ethylene.

  14. Sodium bis(2-ethylhexyl)sulfosuccinate self-aggregation in vacuo: molecular dynamics simulation.

    PubMed

    Longhi, Giovanna; Fornili, Sandro L; Liveri, Vincenzo Turco; Abbate, Sergio; Rebeccani, Davide; Ceraulo, Leopoldo; Gangemi, Fabrizio

    2010-05-14

    Molecular dynamics (MD) simulations were conducted for systems in vacuo consisting of n AOT(-) anions (bis(2-ethylhexyl)sulfosuccinate ions) and n+/- 1 or n Na(+) ions up to n = 20. For n = 15, positively charged systems with Li(+), K(+), and Cs(+) cations were also considered. All systems were observed to form reverse micelle-like aggregates whose centre is occupied by cations and polar heads in a very compact solid-like way, while globally the aggregate has the form of an elongated and rather flat ellipsoid. Various types of statistical analyses were carried out on the systems to enlighten structural and dynamical properties including gyration radius, atomic pair correlation functions, atomic B-factor and moment of inertia tensor. For completeness and comparison the stability of reverse micelle is tested in the case of neutral n = 20 system in CCl(4) solution. PMID:20428549

  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. Computer simulation studies of Aβ37-42 aggregation thermodynamics and kinetics in water and salt solution.

    PubMed

    Yang, Y Isaac; Gao, Yi Qin

    2015-01-22

    In vivo self-assembly of proteins into aggregates known as amyloids is related to many diseases. Although a large number of studies have been performed on the formation of amyloid, the molecular mechanism of polypeptide aggregation remains largely unclear. In this paper, we studied the aggregation of amyloid-forming peptide Aβ37-42 using all-atom molecular dynamics simulations. Using the integrated temperature sampling (ITS) simulation method, we observed the reversible formation of Aβ37-42 oligomers. The free-energy landscape for the polypeptide association was calculated, and aggregated states were then defined based on the landscape. To explore the kinetics and especially salt effects on the process of polypeptide aggregation, normal MD simulations were performed in pure water and NaCl solution, respectively. We then used the transition path theory (TPT) to analyze the transition network of polypeptide aggregation in solution. The dominant pathways of Aβ37-42 aggregation were found to differ significantly in pure water and the salt solution, indicating the change of molecular mechanism of polypeptide aggregation with the solution conditions. PMID:24861904

  17. A Simulation Study on Segmentation Methods of the Soil Aggregate Microtomographic Images

    NASA Astrophysics Data System (ADS)

    Wang, W.; Kravchenko, A.; Ananyeva, K.; Smucker, A.; Lim, C.; Rivers, M.

    2009-05-01

    Advances in X-ray microtomography open up a new way for examining the internal structures of soil aggregates in 3D space with a resolution of only several microns. However, processing of X-ray soil images in order to obtain reliable representations of pore geometries within aggregate pore remain to be established. Multiple approaches to the segmentation algorithms used to best separate gray-scale images into pores and solid material. Segmentation of soil volumes requires a combination of multiple interactive algorithms that identify specific properties of the studied features of each volume. Additionally, similar 3D objects with known pore geometries and connectivities are needed to provide specific information that identifies the most accurate segmentation of microtomographic images. The objective of this study was to compare the performance of segmentation methods on simulated soil aggregate images with various porosities as scenarios of the ground-truth standards. Simulations of the soil aggregate images were conducted on pore and solid spaces respectively. For the pore space, taking into consideration of partial volume and other pronounced artifacts, several layers of the pores at different scales were created and overlaid and random Gaussian noises were added. For the solid space, LU decomposition technique on a Gaussian random field with a specified mean and covariance structure was applied on a conditional data set of the known pore space. Several different kinds of segmentation methods, namely, entropy-based methods, indicator kriging methods and clustering methods, were examined and compared based on thresholding criterion such as non-uniformity measure and misclassification error. Majority filtering was applied to smooth the resulting images. We found that clustering methods uniformly outperformed two other methods, especially in the relatively low porosity cases. Moreover, the indicator kriging method performs better in high porosity cases, however, its

  18. 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.

  19. Photoinduced charge-transfer dynamics simulations in noncovalently bonded molecular aggregates.

    PubMed

    Medrano, Carlos R; Oviedo, M Belén; Sánchez, Cristián G

    2016-06-01

    The rational design of new materials as prototype systems for organic solar cells remains challenging. Perylene diimide has emerged as a promising material to replace fullerene derivatives because of its synthetic flexibility, leading to the manipulation of their optical properties. As a result of their fused aromatic core that favors π-π stacking interactions, the aggregation of these molecules can reach highly ordered nanostructures as one-dimensional nanofibers, with a fast photoinduced charge transfer mechanism. In this article, we present an atomistic description of the photoexcited exciton dynamics in noncovalently bonded perylene diimides by time integration of the electron density in the presence of external time varying electric fields. We show that our approach is able to capture and explain the physics that underlies the charge transport mechanism through perylene diimide aggregates. PMID:27189740

  20. 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

  1. 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

  2. Time dependent variation of human blood conductivity as a method for an estimation of RBC aggregation.

    PubMed

    Antonova, Nadia; Riha, Pavel; Ivanov, Ivan

    2008-01-01

    Time variation of whole human blood conductivity and shear stresses were investigated at rectangular and trapezium-shaped Couette viscometric flow under electric field of 2 kHz. The kinetics of conductivity signals were recorded both under transient flow and after the complete stoppage of shearing at shear rates from 0.94 to 94.5 s(-1) and temperatures T=25 degrees C and 37 degrees C. Contraves Low Shear 30 rotational viscometer as a base unit and a concurrent measuring system, including a device, developed by the conductometric method with a software for measurement of conductivity of biological fluids (data acquisition system), previously described (IFMBE Proceedings Series, Vol. 11, 2005, pp. 4247-4252; Clin. Hemorheol. Microcirc. 35(1/2) (2006), 19-29), were used for the experiments. The obtained experimental relationships show that the human blood conductivity is time, shear rate, hematocrit and temperature dependent under transient flow. It is also dependent on the regime of the applied shear rates. Non-linear curve approximation of the growth and relaxation curves is done. The results show that valuable information could be received about the kinetics of "rouleaux formation" and the time dependences of the blood conductivity follow the structural transformations of RBC aggregates during the aggregation-disaggregation processes. The results suggest that this technique may be used to clarify the mechanism of dynamics of RBC aggregates. PMID:18503112

  3. 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.

  4. 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.

  5. VERSE - Virtual Equivalent Real-time Simulation

    NASA Technical Reports Server (NTRS)

    Zheng, Yang; Martin, Bryan J.; Villaume, Nathaniel

    2005-01-01

    Distributed real-time simulations provide important timing validation and hardware in the- loop results for the spacecraft flight software development cycle. Occasionally, the need for higher fidelity modeling and more comprehensive debugging capabilities - combined with a limited amount of computational resources - calls for a non real-time simulation environment that mimics the real-time environment. By creating a non real-time environment that accommodates simulations and flight software designed for a multi-CPU real-time system, we can save development time, cut mission costs, and reduce the likelihood of errors. This paper presents such a solution: Virtual Equivalent Real-time Simulation Environment (VERSE). VERSE turns the real-time operating system RTAI (Real-time Application Interface) into an event driven simulator that runs in virtual real time. Designed to keep the original RTAI architecture as intact as possible, and therefore inheriting RTAI's many capabilities, VERSE was implemented with remarkably little change to the RTAI source code. This small footprint together with use of the same API allows users to easily run the same application in both real-time and virtual time environments. VERSE has been used to build a workstation testbed for NASA's Space Interferometry Mission (SIM PlanetQuest) instrument flight software. With its flexible simulation controls and inexpensive setup and replication costs, VERSE will become an invaluable tool in future mission development.

  6. 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

  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. 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.

  9. A particle-based model to simulate the micromechanics of single-plant parenchyma cells and aggregates

    NASA Astrophysics Data System (ADS)

    Van Liedekerke, P.; Ghysels, P.; Tijskens, E.; Samaey, G.; Smeedts, B.; Roose, D.; Ramon, H.

    2010-06-01

    This paper is concerned with addressing how plant tissue mechanics is related to the micromechanics of cells. To this end, we propose a mesh-free particle method to simulate the mechanics of both individual plant cells (parenchyma) and cell aggregates in response to external stresses. The model considers two important features in the plant cell: (1) the cell protoplasm, the interior liquid phase inducing hydrodynamic phenomena, and (2) the cell wall material, a viscoelastic solid material that contains the protoplasm. In this particle framework, the cell fluid is modeled by smoothed particle hydrodynamics (SPH), a mesh-free method typically used to address problems with gas and fluid dynamics. In the solid phase (cell wall) on the other hand, the particles are connected by pairwise interactions holding them together and preventing the fluid to penetrate the cell wall. The cell wall hydraulic conductivity (permeability) is built in as well through the SPH formulation. Although this model is also meant to be able to deal with dynamic and even violent situations (leading to cell wall rupture or cell-cell debonding), we have concentrated on quasi-static conditions. The results of single-cell compression simulations show that the conclusions found by analytical models and experiments can be reproduced at least qualitatively. Relaxation tests revealed that plant cells have short relaxation times (1 µs-10 µs) compared to mammalian cells. Simulations performed on cell aggregates indicated an influence of the cellular organization to the tissue response, as was also observed in experiments done on tissues with a similar structure.

  10. Following the aggregation of amyloid-forming peptides by computer simulations

    NASA Astrophysics Data System (ADS)

    Melquiond, Adrien; Boucher, Geneviève; Mousseau, Normand; Derreumaux, Philippe

    2005-05-01

    There is experimental evidence suggesting that the toxicity of neurodegenerative diseases such as Alzheimer's disease may result from the soluble intermediate oligomers. It is therefore important to characterize extensively the early steps of oligomer formation at atomic level. As these structures are metastable and short lived, experimental data are difficult to obtain and they must be complemented with numerical simulations. In this work, we use the activation-relaxation technique coupled with a coarse-grained energy model to study in detail the mechanisms of aggregation of four lys-phe-phe-glu (KFFE) peptides. This is the shortest peptide known to form amyloid fibrils in vitro. Our simulations indicate that four KFFE peptides adopt a variety of oligomeric states (tetramers, trimers, and dimers) with various orientations of the chains in rapid equilibrium. This conformational distribution is consistent with all-atom molecular-dynamics simulations in explicit solvent and is sequence dependent; as seen experimentally, the lys-pro-gly-glu (KPGE) peptides adopt disordered structures in solution. Our unbiased simulations also indicate that the assembly process is much more complex than previously thought and point to intermediate structures which likely are kinetic traps for longer chains.

  11. The effect of time of day and exercise on platelet functions and platelet-neutrophil aggregates in healthy male subjects.

    PubMed

    Aldemir, Hatice; Kiliç, Nedret

    2005-12-01

    Platelet activation state changes by exercise. The effect of exercise time on platelet activation state and formation of platelet-neutrophil aggregates are not known yet. In this study the effect of exercise and time of day were examined on platelet activity with platelet-neutrophil aggregates. Ten moderately active males aged 27+/- 1.63 (mean+/-S.D.) years completed sub-maximal (70% VO(2max)) exercise trials for 30 min. Blood pressure (BP) was recorded. Venous blood samples were obtained at rest, immediately post-exercise and after 30 min of recovery. Whole blood was analysed for haematocrit (Hct), haemoglobin (Hb), platelet count (PC), mean platelet count (MPV) and platelet aggregation (PA). Platelet-neutrophil aggregates and beta-thromboglobulin (beta-TG) levels were assayed. Platelet count showed significant increase after morning exercise ((236+/- 32)x10(9) l(-1) versus (202+/- 34)x10(9) l(-1) baseline, p < 0.05). Exercise resulted in significantly lower MPV after the evening exercise (9.16+/- 0.5 fl versus 9.65+/- 0.36 fl, p < 0.05). Platelet aggregation by adenosine diphosphate (ADP) decreased after morning exercise and the recovery aggregation levels were significantly different at two different times of the day (68+/- 20% a.m. versus 80+/- 12% p.m., p < 0.05). It was also showed that platelet-neutrophil aggregates increased significantly from baseline after both exercises. Exercise-induced platelet-neutrophil aggregates were higher in the evening (10.7+/- 1.3% p.m. versus 6.4+/- 1.8% a.m., p < 0.0001). It is therefore concluded that besides platelet-platelet aggregation, exercise can cause platelet- neutrophil aggregates. In addition, time of day has an effect on platelet activation related events. Circadian variations of physiological parameters may have an effect on thrombus formation by platelet activation. PMID:16311912

  12. 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

  13. Comet nuclei aggregation and thermal simulations to prepare the Rosetta mission

    NASA Astrophysics Data System (ADS)

    Lasue, Jeremie; Levasseur-Regourd, Anny-Chantal; Kofman, Wlodek; Botet, Robert; Coradini, Angioletta; de Sanctis, Maria Cristina, , Dr; Capria, Maria Teresa; Turrini, Diego; Hadamcik, Edith

    The international Rosetta mission will study in depth 67P/Churyumov-Gerasimenko's nucleus global structure and the onset of its activity during the pre-perihelion phase. Numerical simulations towards realistic models of comet nuclei will facilitate the inversion procedures and the interpretation of the data obtained during the rendez-vous of the mission. New aspects of comet nuclei formation and evolution simulations have been developed by our teams to better describe the physical processes of the origins and evolution of these small bodies. Cometesimal aggregation simulations taking into account the evolution of the cohesive energy by sintering processes during accretion in the Kuiper belt can be used to interpret the layered structure and surface features observed for previous comets [1] and quantify the tensile strengths of these objects. Simulations have been done using up to 50000 cometesimals with sizes ranging from tens to hundreds of meters. A layering of the cohesive strength of the comet nuclei material naturally occurs leading to the presence of a high cohesive core surrounded by less cohesive outer layers. Thermal evolution models of comet nuclei have been rather successful in describing the more recent evolution of these objects. A new quasi-3D approach for non-spherically shaped comet nuclei has been developed for the case of 67P/Churyumov-Gerasimenko's nucleus to analyse the effect of irregular shapes (non-spherical, mountain-like and depression-like features) on its thermal evolution, on the local dust crust formation and the onset of its activity [2]. The results of such simulations are used to derive generic cometary nuclei models to be implemented in the analyses processes of the CONSERT experiment on-board Rosetta that will study the internal dielectric properties and heterogeneities of the nucleus. Support from CNES and Europlanet is acknowledged. [1] Belton et al., Icarus 187, 332 (2007) [2] Lasue et al., PSS, submitted.

  14. Perspective: Computer simulations of long time dynamics.

    PubMed

    Elber, Ron

    2016-02-14

    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

  15. 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

  16. Simulation study of asymmetric aggregation behavior of adatoms on Si(1 1 1)7×7

    NASA Astrophysics Data System (ADS)

    Wang, Daimu; Huang, Yinsheng; Wu, Yanning

    2010-12-01

    We perform detailed simulations of the nucleation and growth of adatoms on the Si(1 1 1)7×7 reconstructed surface based on a modified cooperative diffusion model, and analyze the effect of different asymmetric diffusion and aggregation mechanisms on the growth behavior. We demonstrate that the asymmetry controlled by the difference of effective binding energies between faulted and unfaulted half cells has a strong influence on the preference of occupation of faulted half cells at higher temperatures for both irreversible and partially reversible aggregation. Using the occupation preference as a measure of cluster ordering, the simulation clearly shows growth mode transition from random nucleation at low temperatures to ordered self-organized growth at high temperatures in the case of partially reversible aggregation.

  17. Simulation on the aggregation process of spherical particle confined in a spherical shell

    NASA Astrophysics Data System (ADS)

    Wang, J.; Xu, J. J.; Zhang, L.

    2016-04-01

    The aggregation process of spherical particles confined in a spherical shell was studied by using a diffusion-limited cluster-cluster aggregation (DLCA) model. The influence of geometrical confinement and wetting-like properties of the spherical shell walls on the particle concentration profile, aggregate structure and aggregation kinetics had been explored. The results show that there will be either depletion or absorption particles near the shell walls depending on the wall properties. It is observed that there are four different types of density distribution which can be realized by modifying the property of the inner or outer spherical shell wall. In addition, the aggregate structure will become more compact in the confined spherical shell comparing to bulk system with the same particle volume fraction. The analysis on the aggregation kinetics indicates that geometrical confinement will promote the aggregation process by reducing the invalid movement of the small aggregates and by constraining the movement of those large aggregates. Due to the concave geometrical characteristic of the outer wall of the spherical shell, its effects on the aggregating kinetics and the structure of the formed aggregates are more evident than those of the inner wall. This study will provide some instructive information of controlling the density distribution of low-density porous polymer hollow spherical shells and helps to predict gel structures developed in confined geometries.

  18. 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

  19. Morphology and aggregation of RADA-16-I peptide Studied by AFM, NMR and molecular dynamics simulations.

    PubMed

    Bagrov, Dmitry; Gazizova, Yuliya; Podgorsky, Victor; Udovichenko, Igor; Danilkovich, Alexey; Prusakov, Kirill; Klinov, Dmitry

    2016-01-01

    RADA-16-I is a self-assembling peptide which forms biocompatible fibrils and hydrogels. We used molecular dynamics simulations, atomic-force microscopy, NMR spectroscopy, and thioflavin T binding assay to examine size, structure, and morphology of RADA-16-I aggregates. We used the native form of RADA-16-I (H-(ArgAlaAspAla)4 -OH) rather than the acetylated one commonly used in the previous studies. At neutral pH, RADA-16-I is mainly in the fibrillar form, the fibrils consist of an even number of stacked β-sheets. At acidic pH, RADA-16-I fibrils disassemble into monomers, which form an amorphous monolayer on graphite and monolayer lamellae on mica. RADA-16-I fibrils were compared with the fibrils of a similar peptide RLDL-16-I. Thickness of β-sheets measured by AFM was in excellent agreement with the molecular dynamics simulations. A pair of RLDL-16-I β-sheets was thicker (2.3 ± 0.4 nm) than a pair of RADA-16-I β-sheets (1.9 ± 0.1 nm) due to the volume difference between alanine and leucine residues. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 72-81, 2016. PMID:26501800

  20. 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

  1. Numerical simulations of collisional disruption of rotating gravitational aggregates: Dependence on material properties

    NASA Astrophysics Data System (ADS)

    Ballouz, R.-L.; Richardson, D. C.; Michel, P.; Schwartz, S. R.; Yu, Y.

    2015-03-01

    Our knowledge of the strengths of small bodies in the Solar System is limited by our poor understanding of their internal structures, and this, in turn, clouds our understanding of the formation and evolution of these bodies. Observations of the rotational states of asteroids whose diameters are larger than a few hundreds of meters have revealed that they are dominated by gravity and that most are unlikely to be monoliths; however, there is a wide range of plausible internal structures. Numerical and analytical studies of shape and spin limits of gravitational aggregates and their collisional evolution show a strong dependence on shear strength. In order to study this effect, we carry out a systematic exploration of the dependence of collision outcomes on dissipation and friction parameters of the material components making up the bodies. We simulate the catastrophic disruption (leading to the largest remnant retaining 50% of the original mass) of km-size asteroids modeled as gravitational aggregates using pkdgrav, a cosmology N-body code adapted to collisional problems and recently enhanced with a new soft-sphere collision algorithm that includes more realistic contact forces. We find that for a range of three different materials, higher friction and dissipation values increase the catastrophic disruption threshold by about half a magnitude. Furthermore, we find that pre-impact rotation systematically increases mass loss on average, regardless of the target's internal configuration. Our results have important implications for the efficiency of planet formation via planetesimal growth, and also more generally to estimate the impact energy threshold for catastrophic disruption, as this generally has only been evaluated for non-spinning bodies without detailed consideration of material properties.

  2. 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

  3. Simulation in pediatrics: Is it about time?

    PubMed

    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

  4. Aggregation dynamics of rigid polyelectrolytes

    NASA Astrophysics Data System (ADS)

    Tom, Anvy Moly; Rajesh, R.; Vemparala, Satyavani

    2016-01-01

    Similarly charged polyelectrolytes are known to attract each other and aggregate into bundles when the charge density of the polymers exceeds a critical value that depends on the valency of the counterions. The dynamics of aggregation of such rigid polyelectrolytes are studied using large scale molecular dynamics simulations. We find that the morphology of the aggregates depends on the value of the charge density of the polymers. For values close to the critical value, the shape of the aggregates is cylindrical with height equal to the length of a single polyelectrolyte chain. However, for larger values of charge, the linear extent of the aggregates increases as more and more polymers aggregate. In both the cases, we show that the number of aggregates decrease with time as power laws with exponents that are not numerically distinguishable from each other and are independent of charge density of the polymers, valency of the counterions, density, and length of the polyelectrolyte chain. We model the aggregation dynamics using the Smoluchowski coagulation equation with kernels determined from the molecular dynamics simulations and justify the numerically obtained value of the exponent. Our results suggest that once counterions condense, effective interactions between polyelectrolyte chains short-ranged and the aggregation of polyelectrolytes are diffusion-limited.

  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

    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.

  7. 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.

  8. Molecular simulations of micellar aggregation of polysorbate 20 ester fractions and their interaction with N-phenyl-1-naphthylamine dye.

    PubMed

    Lapelosa, Mauro; Patapoff, Thomas W; Zarraga, Isidro E

    2016-06-01

    Micellar aggregation behavior of polysorbate 20 (PS20) has generated significant interest because of the wide use of PS20 as a surfactant to minimize protein surface adsorption and mitigate protein aggregation. Thus, there is a need for better molecular understanding of what drives the biophysical behavior of PS20 in solution. We observe that a complex amphipathic PS20 molecule, which contains both hydrophobic tail and relatively large hydrophilic head, self-associates strongly within the course of a molecular dynamics simulation performed with a fully atomistic representation of the molecule and an explicit water solvent model. The in silico behavior is consistent with micellar models of PS20 in solution. The dynamics of this self-association is rather complex involving both internal reorganization of the molecule and diffusion to form stable micelle-like aggregates. The micellar aggregates of PS20 are long-lived and are formed by the balance between the large hydrophobic interactions associated with the aliphatic tail of PS20, and the steric repulsion of the hydrophilic sorbitan head structure. In the present work, molecular models of PS20 that represent naturally occurring PS20 fractions were produced and characterized in silico. The study investigated the monoester and diester fractions: PS20M, and PS20D. These fractions present differences in the strength of their hydrophobic effect, which influences the aggregation behavior. Adaptive biasing force (ABF) simulations were carried out with the PS20M and PS20D molecular constructs to calculate the free energy of their pairwise interaction. The free energy barrier for the dissociation is higher for PS20D compared with PS20M. The results show that hydrogen bonds can form when head groups are in close proximity, such as in the PS20 aggregate assembly, and the free energy of interaction can be used to predict the morphology of the micellar aggregate for the different PS20 fractions. We were also able to simulate PS20

  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. PMID:26734094

  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. 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

  13. Real Time RF Simulator (RTS) and control

    SciTech Connect

    Cancelo, G.; Armiento, C.; Treptow, K.; Vignoni, A.; Zmuda, T.; /Fermilab

    2008-10-01

    The multi-cavity RTS allows LLRF algorithm development and lab testing prior to commissioning with real cavities and cryomodules. The RTS is a valuable tool since it models the functions, errors and disturbances of real RF systems. The advantage of a RTS over an off-line simulator is that it can be implemented on the actual LLRF hardware, on the same FPGA and processor, and run at the same speed of the LLRF control loop. Additionally the RTS can be shared by collaborators who do not have access to RF systems or when the systems are not available to LLRF engineers. The RTS simulator incorporates hardware, firmware and software errors and limitations of a real implementation, which would be hard to identify and time consuming to model in off-line simulations.

  14. 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.

  15. Simulating stochastic dynamics using large time steps.

    PubMed

    Corradini, O; Faccioli, P; Orland, H

    2009-12-01

    We present an approach to investigate the long-time stochastic dynamics of multidimensional classical systems, in contact with a heat bath. When the potential energy landscape is rugged, the kinetics displays a decoupling of short- and long-time scales and both molecular dynamics or Monte Carlo (MC) simulations are generally inefficient. Using a field theoretic approach, we perform analytically the average over the short-time stochastic fluctuations. This way, we obtain an effective theory, which generates the same long-time dynamics of the original theory, but has a lower time-resolution power. Such an approach is used to develop an improved version of the MC algorithm, which is particularly suitable to investigate the dynamics of rare conformational transitions. In the specific case of molecular systems at room temperature, we show that elementary integration time steps used to simulate the effective theory can be chosen a factor approximately 100 larger than those used in the original theory. Our results are illustrated and tested on a simple system, characterized by a rugged energy landscape. PMID:20365123

  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. 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.

  19. 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.

  20. Refined structure-based simulation of plant light-harvesting complex II: linear optical spectra of trimers and aggregates.

    PubMed

    Müh, Frank; Renger, Thomas

    2012-08-01

    Linear optical spectra of solubilized trimers and small lamellar aggregates of the major light-harvesting complex II (LHCII) of higher plants are simulated employing excitonic couplings and site energies of chlorophylls (Chls) computed on the basis of the two crystal structures by a combined quantum chemical/electrostatic approach. A good agreement between simulation and experiment is achieved (except for the circular dichroism in the Chl b region), if vibronic transitions of Chls are taken into account. Site energies are further optimized by refinement fits of optical spectra. The differences between refined and directly calculated values are not significant enough to decide, whether the crystal structures are closer to trimers or aggregates. Changes in the linear dichroism spectrum upon aggregation are related to site energy shifts of Chls b601, b607, a603, a610, and a613, and are interpreted in terms of conformational changes of violaxanthin and the two luteins involving their ionone rings. Chl a610 is the energy sink at 77K in both conformations. An analysis of absorption spectra of trimers perpendicular and parallel to the C(3)-axis (van Amerongen et al. Biophys. J. 67 (1994) 837-847) shows that only Chl a604 close to neoxanthin is significantly reoriented in trimers compared to the crystal structures. Whether this pigment is orientated in aggregates as in the crystal structures, can presently not be determined faithfully. To finally decide about pigment reorientations that could be of relevance for non-photochemical quenching, further polarized absorption and fluorescence measurements of aggregates or detergent-depleted LHCII would be helpful. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial. PMID:22387396

  1. Simulating system dynamics with arbitrary time step

    NASA Astrophysics Data System (ADS)

    Kantorovich, L.

    2007-02-01

    We suggest a dynamic simulation method that allows efficient and realistic modeling of kinetic processes, such as atomic diffusion, in which time has its actual meaning. Our method is similar in spirit to widely used kinetic Monte Carlo (KMC) techniques; however, in our approach, the time step can be chosen arbitrarily. This has an advantage in some cases, e.g., when the transition rates change with time sufficiently fast over the period of the KMC time step (e.g., due to time dependence of some external factors influencing kinetics such as moving scanning probe microscopy tip or external time-dependent field) or when the clock time is set by some external conditions, and it is convenient to use equal time steps instead of the random choice of the KMC algorithm in order to build up probability distribution functions. We show that an arbitrary choice of the time step can be afforded by building up the complete list of events including the “residence site” and multihop transitions. The idea of the method is illustrated in a simple “toy” model of a finite one-dimensional lattice of potential wells with unequal jump rates to either side, which can be studied analytically. We show that for any choice of the time step, our general kinetics method reproduces exactly the solution of the corresponding master equations for any choice of the time steps. The final kinetics also matches the standard KMC, and this allows better understanding of this algorithm, in which the time step is chosen in a certain way and the system always advances by a single hop.

  2. 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

  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. Role of water repellency in aggregate stability of cultivated soils under simulated raindrop impact

    NASA Astrophysics Data System (ADS)

    Kořenková, Lucia; Matúš, Peter

    2015-07-01

    Soil aggregate stability (AS) is an important indicator of soil physical quality. For the purpose of this research it was hypothesized that particular properties such as water repellency (WR) influence soil aggregation and AS. Directly after sampling, WR was detected for three soils, after a week of air-drying two of these soils still showed some resistance to penetration by a water drop placed on the surface (WDPT test). The study examines AS of air-dried texturally different aggregates of size 0.25-0.5 mm taken from surface layers (5-15 cm depth) of six agriculturally used soils. The procedure involves exposure of soil aggregates to direct impact of water drops. Results showed that soil AS increases in order: cutanic Luvisol (siltic) < haplic Chernozem < calcic mollic Fluvisol < mollic grumic Vertisol (pellic) < mollic Fluvisol (calcaric) < gleyic Fluvisol (eutric). Gradual increase in AS can be explained by the increase in soil organic matter content and its hydrophobic properties. Although WR has been most commonly observed in soils under forests and grass cover, the results confirmed that cultivated soils may also create water-stable aggregates, especially in the case when their organic matter induces WR under particular moisture conditions.

  5. 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.

  6. 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.

  7. 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

  8. 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. PMID:27091578

  9. Aggregation-Induced Resonance Raman Optical Activity (AIRROA) and Time-Dependent Helicity Switching of Astaxanthin Supramolecular Assemblies.

    PubMed

    Dudek, Monika; Zajac, Grzegorz; Kaczor, Agnieszka; Baranska, Malgorzata

    2016-08-18

    New methods for enhancing the Raman optical activity (ROA) signal are desirable due to the low efficiency of ROA, demanding otherwise high sample concentrations, high laser powers, and/or long acquisition times. Previously, we have demonstrated a new phenomenon, aggregation-induced resonance ROA (AIRROA), that produces significant enhancement of the ROA signal provided that the excitation wavelength coincides with the absorption of the measured species and that the electronic circular dichroism (ECD) signal in the range of this absorption is nonzero. In this work, analyzing three very different supramolecular astaxanthin aggregates (H1, H2, and J), we confirm the phenomenon and demonstrate that aggregation itself is not enough to enhance the ROA signal and that the above-mentioned conditions are necessary for induction of the resonance ROA effect. Additionally, by analyzing the changes in the ECD spectra of the H1 assembly, we demonstrate that the supramolecular helicity sign switches with time, which is dependent on the prevalence of kinetic or thermodynamic stabilization of the obtained aggregates. PMID:27438433

  10. 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

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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. PMID:26028507

  16. 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.

  17. Fast Simulation of Tsunamis in Real Time

    NASA Astrophysics Data System (ADS)

    Fryer, G. J.; Wang, D.; Becker, N. C.; Weinstein, S. A.; Walsh, D.

    2011-12-01

    The U.S. Tsunami Warning Centers primarily base their wave height forecasts on precomputed tsunami scenarios, such as the SIFT model (Standby Inundation Forecasting of Tsunamis) developed by NOAA's Center for Tsunami Research. In SIFT, tsunami simulations for about 1600 individual earthquake sources, each 100x50 km, define shallow subduction worldwide. These simulations are stored in a database and combined linearly to make up the tsunami from any great earthquake. Precomputation is necessary because the nonlinear shallow-water wave equations are too time consuming to compute during an event. While such scenario-based models are valuable, they tacitly assume all energy in a tsunami comes from thrust at the décollement. The thrust assumption is often violated (e.g., 1933 Sanriku, 2007 Kurils, 2009 Samoa), while a significant number of tsunamigenic earthquakes are completely unrelated to subduction (e.g., 1812 Santa Barbara, 1939 Accra, 1975 Kalapana). Finally, parts of some subduction zones are so poorly defined that precomputations may be of little value (e.g., 1762 Arakan, 1755 Lisbon). For all such sources, a fast means of estimating tsunami size is essential. At the Pacific Tsunami Warning Center, we have been using our model RIFT (Real-time Inundation Forecasting of Tsunamis) experimentally for two years. RIFT is fast by design: it solves only the linearized form of the equations. At 4 arc-minutes resolution calculations for the entire Pacific take just a few minutes on an 8-processor Linux box. Part of the rationale for developing RIFT was earthquakes of M 7.8 or smaller, which approach the lower limit of the more complex SIFT's abilities. For such events we currently issue a fixed warning to areas within 1,000 km of the source, which typically means a lot of over-warning. With sources defined by W-phase CMTs, exhaustive comparison with runup data shows that we can reduce the warning area significantly. Even before CMTs are available, we routinely run models

  18. Time-dependent inhibition by glyceryl trinitrate of platelet aggregation caused by U46619 (a thromboxane/endoperoxide receptor agonist).

    PubMed

    Kampf, G; Ritter, J M

    1994-07-01

    Glyceryl trinitrate is a weak inhibitor of platelet aggregation in vitro. Its effect on platelet aggregation in response to U46619 (a thromboxane/endoperoxide receptor agonist) was studied turbidometrically in platelet-rich plasma from healthy volunteers. The object was to determine whether inhibition was influenced by a period of preincubation between preparation of platelet-rich plasma and addition of glyceryl trinitrate. Incubation was performed at 37 degrees C and 22 degrees C. Samples were removed at intervals and transferred to an aggregometer cuvette at 37 degrees C. Glyceryl trinitrate (100 microM) or an equal volume of distilled water was added 5 min before U46619 (2 microM), and aggregation recorded as change in light transmission. Inhibition by glyceryl trinitrate was markedly time and temperature dependent, with a progressive increase in inhibitory potency between 120 and 300 min preincubation at 37 degrees C but not at 22 degrees C. The explanation of this is unknown but the effect was not influenced by lipopolysaccharide or by cycloheximide, so it does not appear to be due to exposure to endotoxin or to enzyme induction in vitro. PMID:7946941

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

    PubMed

    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

  20. 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

  1. 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

  2. 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.

  3. 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.

  4. Time Filtering in Large Eddy Simulations

    NASA Technical Reports Server (NTRS)

    Carati, Daniele; Wray, Alan A.

    2000-01-01

    An explicit time filter is applied to the Navier-Stokes equation prior to a space filter. The time filter is supposed to be smooth, and an exact expansion depending on the time derivatives of the velocity is derived for the associated stress tensor. On the contrary, the effect of the space filter is treated as usual and an eddy viscosity model is introduced in the LES equation. The total stress is thus represented using a new class of mixed models combining time and space derivatives of the LES field.

  5. Time accurate simulations of compressible shear flows

    NASA Technical Reports Server (NTRS)

    Givi, Peyman; Steinberger, Craig J.; Vidoni, Thomas J.; Madnia, Cyrus K.

    1993-01-01

    The objectives of this research are to employ direct numerical simulation (DNS) to study the phenomenon of mixing (or lack thereof) in compressible free shear flows and to suggest new means of enhancing mixing in such flows. The shear flow configurations under investigation are those of parallel mixing layers and planar jets under both non-reacting and reacting nonpremixed conditions. During the three-years of this research program, several important issues regarding mixing and chemical reactions in compressible shear flows were investigated.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Feasibility of water seepage monitoring in concrete with embedded smart aggregates by P-wave travel time measurement

    NASA Astrophysics Data System (ADS)

    Zou, Dujian; Liu, Tiejun; Huang, Yongchao; Zhang, Fuyao; Du, Chengcheng; Li, Bo

    2014-06-01

    Water seepage in concrete threatens the safety of marine constructions and reduces the durability of concrete structures. This note presents a smart aggregate-based monitoring method to monitor the travel time evolution of a harmonic stress wave during the water infiltrating process in concrete structures. An experimental investigation, in which two plain concrete columns were examined under different water infiltration cases, verified the validity of the proposed monitoring method. The test results show that the travel time of the harmonic stress wave is sensitive to the development of water seepage in concrete and decreases with increasing water seepage depth. The proposed active monitoring method provides an innovative approach to monitor water seepage in concrete structures.

  11. Effects of hesperidin, a flavanone glycoside interaction on the conformation, stability, and aggregation of lysozyme: multispectroscopic and molecular dynamic simulation studies?

    PubMed

    Ratnaparkhi, Aditi; Muthu, Shivani A; Shiriskar, Sonali M; Pissurlenkar, Raghuvir R S; Choudhary, Sinjan; Ahmad, Basir

    2015-09-01

    Hesperidin (HESP), a flavanone glycoside, shows high antioxidant properties and possess ability to go through the blood-brain barrier. Therefore, it could be a potential drug molecule against aggregation based diseases such as Alzheimer's, Parkinson's, and systemic amyloidoses. In this work, we investigated the potential of HESP to interact with hen egg-white lysozyme (HEWL) monomer and prevent its aggregation. The HESP-HEWL binding studies were performed using a fluorescence quenching technique, molecular docking and molecular dynamics simulations. We found a strong interaction of HESP with the lysozyme monomer (Ka, ~ 5 × 10(4) M(-1)) mainly through hydrogen bonding, water bridges, and hydrophobic interactions. We showed that HESP molecule spanned the highly aggregation prone region (amino acid residues 48-101) of HEWL and prevented its fibrillar aggregation. Further, we found that HESP binding completely inhibited amorphous aggregation of the protein induced by disulfide-reducing agent tries-(2-carboxyethyl) phosphine. Conformational and stability studies as followed by various tertiary and secondary structure probes revealed that HESP binding only marginally affected the lysozyme monomer conformation and increased both stability and reversibility of the protein against thermal denaturation. Future studies should investigate detail effects of HESP on solvent dynamics, structure, and toxicity of various aggregates. The answers to these questions will not only target the basic sciences, but also have application in biomedical and biotechnological sciences. PMID:25301518

  12. 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.

  13. Real-time protein aggregation monitoring based on a simultaneous light scattering investigation and a Bloch surface wave-based approach

    NASA Astrophysics Data System (ADS)

    Santi, Sara; Barakat, Elsie; Neier, Reinhard; Herzig, Hans Peter

    2015-08-01

    We present a study of the dynamics of protein aggregation using a Bloch surface wave (BSW) label-free sensing scheme. In a previous work, we demonstrated the ability to detect the early dynamic events of fibrillogenesis of amyloid betapeptides (Aβ), linked to Alzheimer's Disease. Here, we demonstrate the efficacy of the BSW sensor by describing a simultaneous light scattering measurement, with the purpose of real-time monitoring the size change of the Aβ aggregates, throughout fibrillization.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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

  2. Research on real-time infrared simulation of ground scene

    NASA Astrophysics Data System (ADS)

    Dai, Ying; Chen, Bin; Ming, Delie

    2013-10-01

    The paper proposes a modularized infrared scene imaging simulation solution based on GPU and designs a corresponding implementation framework to contain all the key modules of infrared imaging simulation. After that, the paper presents the module of infrared radiation computation, which realizes the real-time parallel computation of infrared radiation by the technology of GPU shader and translates the simulation work from 3D graphics to 2D digital image by the technology of rendering to texture.

  3. 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.

  4. 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.

  5. 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

  6. Boosting forward-time population genetic simulators through genotype compression

    PubMed Central

    2013-01-01

    Background Forward-time population genetic simulations play a central role in deriving and testing evolutionary hypotheses. Such simulations may be data-intensive, depending on the settings to the various parameters controlling them. In particular, for certain settings, the data footprint may quickly exceed the memory of a single compute node. Results We develop a novel and general method for addressing the memory issue inherent in forward-time simulations by compressing and decompressing, in real-time, active and ancestral genotypes, while carefully accounting for the time overhead. We propose a general graph data structure for compressing the genotype space explored during a simulation run, along with efficient algorithms for constructing and updating compressed genotypes which support both mutation and recombination. We tested the performance of our method in very large-scale simulations. Results show that our method not only scales well, but that it also overcomes memory issues that would cripple existing tools. Conclusions As evolutionary analyses are being increasingly performed on genomes, pathways, and networks, particularly in the era of systems biology, scaling population genetic simulators to handle large-scale simulations is crucial. We believe our method offers a significant step in that direction. Further, the techniques we provide are generic and can be integrated with existing population genetic simulators to boost their performance in terms of memory usage. PMID:23763838

  7. 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.

  8. Numerical simulations of time-resolved quantum electronics

    NASA Astrophysics Data System (ADS)

    Gaury, Benoit; Weston, Joseph; Santin, Matthieu; Houzet, Manuel; Groth, Christoph; Waintal, Xavier

    2014-01-01

    Numerical simulation has become a major tool in quantum electronics both for fundamental and applied purposes. While for a long time those simulations focused on stationary properties (e.g. DC currents), the recent experimental trend toward GHz frequencies and beyond has triggered a new interest for handling time-dependent perturbations. As the experimental frequencies get higher, it becomes possible to conceive experiments which are both time-resolved and fast enough to probe the internal quantum dynamics of the system. This paper discusses the technical aspects-mathematical and numerical-associated with the numerical simulations of such a setup in the time domain (i.e. beyond the single-frequency AC limit). After a short review of the state of the art, we develop a theoretical framework for the calculation of time-resolved observables in a general multiterminal system subject to an arbitrary time-dependent perturbation (oscillating electrostatic gates, voltage pulses, time-varying magnetic fields, etc.) The approach is mathematically equivalent to (i) the time-dependent scattering formalism, (ii) the time-resolved non-equilibrium Green’s function (NEGF) formalism and (iii) the partition-free approach. The central object of our theory is a wave function that obeys a simple Schrödinger equation with an additional source term that accounts for the electrons injected from the electrodes. The time-resolved observables (current, density, etc.) and the (inelastic) scattering matrix are simply expressed in terms of this wave function. We use our approach to develop a numerical technique for simulating time-resolved quantum transport. We find that the use of this wave function is advantageous for numerical simulations resulting in a speed up of many orders of magnitude with respect to the direct integration of NEGF equations. Our technique allows one to simulate realistic situations beyond simple models, a subject that was until now beyond the simulation capabilities

  9. Real-Time Monitoring of Heat-Induced Aggregation of β-Lactoglobulin in Aqueous Solutions Using High-Resolution Ultrasonic Spectroscopy

    NASA Astrophysics Data System (ADS)

    Ochenduszko, Agnieszka; Buckin, Vitaly

    2010-01-01

    High-resolution ultrasonic spectroscopy was applied for real-time monitoring of the heat-induced denaturation and aggregation processes in aqueous solutions of β-lactoglobulin. The temperature profiles for the ultrasonic velocity and attenuation in the frequency range from 4MHz to 16MHz were measured during heating and cooling cycles, 35°C to 120°C to 35°C, with different heating and cooling rates. Two processes were identified in the heating profiles: transition to the molten globular state followed by formation of protein aggregates. Both processes are accompanied by a decrease in the ultrasonic velocity and an increase in compressibility. The ultrasonic attenuation did not show a significant change during the transition to the molten globule but increased significantly during aggregation. The diameter of the aggregates (calculated from ultrasonic attenuation) was of the order of 100nm and depended on the pH and the heating rate. Variation of pH from 6.0 to 7.5 had a pronounced effect on the size of protein aggregates. Some effect of pH on the intrinsic properties of aggregates was also detected.

  10. 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.

  11. 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.

  12. 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).

  13. 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.

  14. 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.

  15. Adaptive time steps in trajectory surface hopping simulations.

    PubMed

    Spörkel, Lasse; Thiel, Walter

    2016-05-21

    Trajectory surface hopping (TSH) simulations are often performed in combination with active-space multi-reference configuration interaction (MRCI) treatments. Technical problems may arise in such simulations if active and inactive orbitals strongly mix and switch in some particular regions. We propose to use adaptive time steps when such regions are encountered in TSH simulations. For this purpose, we present a computational protocol that is easy to implement and increases the computational effort only in the critical regions. We test this procedure through TSH simulations of a GFP chromophore model (OHBI) and a light-driven rotary molecular motor (F-NAIBP) on semiempirical MRCI potential 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. PMID:27208937

  16. Real-time digital simulator for protective relay testing

    SciTech Connect

    Kezunovic, M. ); McKenna, M.

    1994-07-01

    Analog power system simulators have been used for a long time in performing relay testing. A number of new transient simulator designs have been introduced in which improved performance and lower cost were the major goals. The most recent approaches are to use digital technology to implement protective relay testing simulators utilizing power system and fault modeling capabilities of electromagnetic transient programs. This approach offers modeling accuracy and user flexibility. First such designs were introduced by GEC Alshom Measurements in England in the early 1980s and by Bonneville Power Administration in the US in the mid-1980s. The use of these simulators has demonstrated some major advantages in meeting complex relay testing requirements, such as fault studies on series compensated lines. However, the main disadvantage of early digital designs was difficulty in providing any meaningful interaction between the relay and the simulation computer. The numerical techniques implemented in the existing electromagnetic transient programs did not allow for the required real-time switching of system configurations as often needed for fault simulations. This article describes a new digital simulator design which is aimed at providing the real-time operation not available in the previous designs while preserving the accuracy and the flexibility already demonstrated by the digital implementations. This is achieved by using low-cost commercial hardware and system software as well as custom-designed user interface and real-time application software.

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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

    2014-01-01

    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

  2. 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.

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

    PubMed Central

    Coelho, Flavio Codeço; Carvalho, Luiz Max de

    2015-01-01

    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. PMID:26675824

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

    PubMed

    Coelho, Flavio Codeço; de Carvalho, Luiz Max

    2015-01-01

    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. PMID:26675824

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. Self-Aggregation of Convection in Long Channel Geometry

    NASA Astrophysics Data System (ADS)

    Wing, A. A.; Cronin, T.

    2014-12-01

    Cloud cover and relative humidity in the tropics are strongly influenced by organized atmospheric convection, which occurs across a range of spatial and temporal scales. One mode of organization that is found in idealized numerical simulations is "self-aggregation", a spontaneous transition from randomly distributed convection to organized convection despite homogeneous boundary conditions. We explore the influence of domain geometry on the mechanisms and temperature-dependence of self-aggregation of tropical convection. Specifically, the System for Atmospheric Modeling is used to perform 3-d simulations of radiative-convective equilibrium in a non-rotating framework, with interactive radiation and surface fluxes and fixed sea surface temperature. The results of simulations employing a highly elongated 3-d channel domain, in which self-aggregation takes the form of multiple moist and dry bands, are compared to that of a square domain, in which self-aggregation takes the form of a single moist cluster. For both domain types, and across a range of temperatures, we characterize the fundamental physical mechanisms that lead to self-aggregation as well as its growth rate and spatial scale. The variance budget equation for the vertically integrated frozen moist static energy is used to quantify the mechanisms governing self-aggregation and characterize its time scale. We find that diabatic processes dominate the evolution of self-aggregation in the elongated channel simulations. In contrast, in the square domain simulations, similar diabatic processes dominate the initial stages of aggregation but up-gradient advection by the circulation plays a role in the later stages. Self-aggregation occurs across a much wider range of temperatures with elongated channel geometry than with square geometry. As the sea surface temperature is increased in the channel simulations, the aggregated state is characterized by smaller spatial scales and more regularity. An advantage of the

  10. Self-aggregation of convection in long channel geometry

    NASA Astrophysics Data System (ADS)

    Wing, Allison; Cronin, Timothy

    2015-04-01

    Self-aggregation is the spontaneous transition in numerical simulations from randomly distributed convection to organized convection despite homogeneous boundary conditions. We explore the influence of domain geometry on the mechanisms and temperature-dependence of self-aggregation of tropical convection. Specifically, the System for Atmospheric Modeling is used to perform 3-d simulations of radiative-convective equilibrium in a non-rotating framework, with interactive radiation and surface fluxes and fixed sea surface temperature. The results of simulations employing a highly elongated 3-d channel domain, in which self-aggregation takes the form of multiple moist and dry bands, are compared to that of a square domain, in which self-aggregation takes the form of a single moist cluster. For both domain types, and across a range of temperatures, we characterize the fundamental physical mechanisms that lead to self-aggregation as well as its growth rate and spatial scale. The variance budget equation for the vertically integrated frozen moist static energy is used to quantify the mechanisms governing self-aggregation and characterize its time scale. We find that diabatic processes dominate the evolution of self-aggregation in the elongated channel simulations. In contrast, in the square domain simulations, similar diabatic processes dominate the initial stages of aggregation but up-gradient advection by the circulation plays a role in the later stages. Self-aggregation occurs across a much wider range of temperatures with elongated channel geometry than with square geometry. As the sea surface temperature is increased in the channel simulations, the aggregated state is characterized by smaller spatial scales and more regularity. An advantage of the channel geometry is that a separation distance between convectively active regions can be defined, which is a prerequisite for developing a spatial scaling theory.

  11. 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.

  12. 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.

  13. 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.

  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. Time simulation of flutter with large stiffness changes

    NASA Technical Reports Server (NTRS)

    Karpel, M.; Wieseman, C. D.

    1992-01-01

    Time simulation of flutter, involving large local structural changes, is formulated with a state-space model that is based on a relatively small number of generalized coordinates. Free-free vibration modes are first calculated for a nominal finite-element model with relatively large fictitious masses located at the area of structural changes. A low-frequency subset of these modes is then transformed into a set of structural modal coordinates with which the entire simulation is performed. These generalized coordinates and the associated oscillatory aerodynamic force coefficient matrices are used to construct an efficient time-domain, state-space model for basic aeroelastic case. The time simulation can then be performed by simply changing the mass, stiffness and damping coupling terms when structural changes occur. It is shown that the size of the aeroelastic model required for time simulation with large structural changes at a few a priori known locations is similar to that required for direct analysis of a single structural case. The method is applied to the simulation of an aeroelastic wind-tunnel model. The diverging oscillations are followed by the activation of a tip-ballast decoupling mechanism that stabilizes the system but may cause significant transient overshoots.

  16. The Eulerian time correlation function from direct simulation data

    NASA Astrophysics Data System (ADS)

    Rubinstein, Robert; He, Guowei

    2001-11-01

    The Eulerian time correlation function in homogeneous isotropic turbulence is obtained from direct numerical simulation. We develop curvefits of this function using a producure suggested by Boon and Yip (Molecular Hydrodynamics), which develops a continued fraction expansion of the Laplace transform of the time correlation function. Results of different two-pole expressions are compared with the results of the simulations. Good agreement using one such expression is obtained. The curvefit is developed both for the DNS dataset and for the time correlation function computed from LES. The dynamic meaning of the time correlation function in turbulence is compared to the role of the time correlation function in molecular hydrodynamics, where it is associated with the hydrodynamic modes of the fluid.

  17. 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.

  18. 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

  19. 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.

  20. Toward Real-Time Monte Carlo Simulation Using a Commercial Cloud Computing Infrastructure+

    PubMed Central

    Wang, Henry; Ma, Yunzhi; Pratx, Guillem; Xing, Lei

    2011-01-01

    Purpose Monte Carlo (MC) methods are the gold standard for modeling photon and electron transport in 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. Methods 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 (MPI), 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. Results The output of the cloud-based MC simulation is identical to that produced by the single-threaded implementation. For 1 million electrons, a simulation that takes 2.58 hour on a local computer can be executed in 3.3 minutes on the cloud with 100 nodes, a 47x speed-up. Simulation time scales inversely with the number of parallel nodes. The parallelization overhead is also negligible for large simulations. Conclusion 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. PMID:21841211

  1. Real-time simulation of dynamic fluoroscopy of ERCP

    NASA Astrophysics Data System (ADS)

    Jung, Hoeryong; Lee, Doo Yong

    2010-02-01

    This paper discusses the methods for real-time rendering of time-varying dynamic fluoroscope images including fluid flow for the ERCP (Endoscopic Retrograde Cholangiopancreatography) simulation. A volume rendering technique is used to generate virtual fluoroscopy images. This paper develops an image-overlaying method which overlaps the timevarying images onto the constant background image. The full size fluoroscopy image is computed from the initial volume data set during the pre-processing stage, which is then saved as the background image. Only the time-varying images are computed from the time-varying volume data set during the actual simulation. This involves relatively small computation compared with the background image. The time-varying images are then overlaid onto the background image to obtain the complete images. This method reduces computational overhead by removing redundant computations. A simplified particle dynamics model is employed for fast simulation of the fluid flow. The fluid model, a collection of particles, interacts only with the ducts based on principles of a complete elastic collision. Hence, the velocity of the particles, when they collide with the duct, can be computed by using simple algebraic equations. The methods are implemented for fast simulation of the ERCP.

  2. 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. PMID:26362453

  3. 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.

  4. Photophoretic force on aggregate grains

    NASA Astrophysics Data System (ADS)

    Matthews, Lorin S.; Kimery, Jesse B.; Wurm, Gerhard; de Beule, Caroline; Kuepper, Markus; Hyde, Truell W.

    2016-01-01

    The photophoretic force may impact planetary formation by selectively moving solid particles based on their composition and structure. This generates collision velocities between grains of different sizes and sorts the dust in protoplanetary discs by composition. This numerical simulation studied the photophoretic force acting on fractal dust aggregates of μm-scale radii. Results show that aggregates tend to have greater photophoretic drift velocities than spheres of similar mass or radii, though with a greater spread in the velocity. While the drift velocities of compact aggregates continue to increase as the aggregates grow larger in size, fluffy aggregates have drift velocities which are relatively constant with size. Aggregates formed from an initially polydisperse size distribution of dust grains behave differently from aggregates formed from a monodisperse population, having smaller drift velocities with directions which deviate substantially from the direction of illumination. Results agree with microgravity experiments which show the difference of photophoretic forces with aggregation state.

  5. 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

  6. 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.

  7. 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…

  8. Instructional Advice, Time Advice and Learning Questions in Computer Simulations

    ERIC Educational Resources Information Center

    Rey, Gunter Daniel

    2010-01-01

    Undergraduate students (N = 97) 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 instructional advice) x 2 (with or without time advice) x 2…

  9. Vectorised simulation of the response of a time projection chamber

    NASA Astrophysics Data System (ADS)

    Georgiopoulos, C. H.; Mermikides, M. E.

    1989-12-01

    A Monte Carlo code used for the detailed simulation of the response of the ALEPH time projection chamber has been successfully restructured to exploit the vector architectures of the CDC CYBER-205, ETA10 and CRAY X-MP supercomputers. Some aspects of the vector implementation are discussed and the performance on the various processors is compared.

  10. 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…

  11. 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

  12. Weighted aggregation

    NASA Technical Reports Server (NTRS)

    Feiveson, A. H. (Principal Investigator)

    1979-01-01

    The use of a weighted aggregation technique to improve the precision of the overall LACIE estimate is considered. The manner in which a weighted aggregation technique is implemented given a set of weights is described. The problem of variance estimation is discussed and the question of how to obtain the weights in an operational environment is addressed.

  13. 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.

  14. 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

  15. Aggregate fractal dimensions and thermal conduction in nanofluids

    NASA Astrophysics Data System (ADS)

    Gharagozloo, Patricia E.; Goodson, Kenneth E.

    2010-10-01

    The mechanism producing enhanced thermal conductivities of nanofluids has been the subject of much debate. The formation of aggregates allowing for percolation paths within the fluid has shown the most promise. This work studies the aggregate formation of a nanofluid and compares the results to earlier thermal conductivity measurements and Monte Carlo simulation results. Static light scattering is employed to measure the fractal dimension of aggregates formed in the nanofluid over time at various temperatures and concentrations. As expected, 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. Predictions indicate that 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.

  16. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

    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.

  18. 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

  19. 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

  20. Quick Time-dependent Ionization Calculations Depending on MHD Simulations

    NASA Astrophysics Data System (ADS)

    Shen, Chengcai; Raymond, John C.; Murphy, Nicholas Arnold

    2014-06-01

    Time-dependent ionization is important in astrophysical environments where the thermodynamic time scale is shorter than ionization time scale. In this work, we report a FORTRAN program that performs fast non-equilibrium ionization calculations based on parallel computing. Using MHD simulation results, we trace the movements of plasma in a Lagrangian framework, and obtain evolutionary history of temperature and electron density. Then the time-dependent ionization equations are solved using the eigenvalue method. For any complex temperature and density histories, we introduce a advanced time-step strategy to improve the computational efficiency. Our tests show that this program has advantages of high numerical stability and high accuracy. In addition, it is also easy to integrate this solver with the other MHD routines.

  1. A General and Efficient Method for Incorporating Precise Spike Times in Globally Time-Driven Simulations

    PubMed Central

    Hanuschkin, Alexander; Kunkel, Susanne; Helias, Moritz; Morrison, Abigail; Diesmann, Markus

    2010-01-01

    Traditionally, event-driven simulations have been limited to the very restricted class of neuronal models for which the timing of future spikes can be expressed in closed form. Recently, the class of models that is amenable to event-driven simulation has been extended by the development of techniques to accurately calculate firing times for some integrate-and-fire neuron models that do not enable the prediction of future spikes in closed form. The motivation of this development is the general perception that time-driven simulations are imprecise. Here, we demonstrate that a globally time-driven scheme can calculate firing times that cannot be discriminated from those calculated by an event-driven implementation of the same model; moreover, the time-driven scheme incurs lower computational costs. The key insight is that time-driven methods are based on identifying a threshold crossing in the recent past, which can be implemented by a much simpler algorithm than the techniques for predicting future threshold crossings that are necessary for event-driven approaches. As run time is dominated by the cost of the operations performed at each incoming spike, which includes spike prediction in the case of event-driven simulation and retrospective detection in the case of time-driven simulation, the simple time-driven algorithm outperforms the event-driven approaches. Additionally, our method is generally applicable to all commonly used integrate-and-fire neuronal models; we show that a non-linear model employing a standard adaptive solver can reproduce a reference spike train with a high degree of precision. PMID:21031031

  2. 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.

  3. Real-time numerical simulation of the Carnot cycle

    NASA Astrophysics Data System (ADS)

    Hurkala, J.; Gall, M.; Kutner, R.; Maciejczyk, M.

    2005-09-01

    We developed a highly interactive, multi-windows Java applet which made it possible to simulate and visualize within any platform and internet the Carnot cycle (or engine) in a real-time computer experiment. We extended our previous model and algorithm (Galant et al 2003 Heat Transfer, Newton's Law of Cooling and the Law of Entropy Increase Simulated by the Real-Time Computer Experiments in Java (Lecture Notes in Computer Science vol 2657) pp 45-53, Gall and Kutner 2005 Molecular mechanisms of heat transfer: Debye relaxation versus power-law Physica A 352 347-78) to simulate not only the heat flow but also the macroscopic movement of the piston. Since in reality it is impossible to construct a reversible Carnot engine, the question arises whether it is possible to simulate it at least in a numerical experiment? The positive answer to this question which we found is related to our model and algorithm which make it possible to omit the many-body problem arising when many gas particles simultaneously interact with the mobile piston. As usual, the considerations of phenomenological thermodynamics began with a study of the basic properties of heat engines, hence our approach, besides intrinsic physical significance, is also important from the educational, technological and even environmental points of view. .

  4. Development of real-time ATC simulation facility

    NASA Technical Reports Server (NTRS)

    Pararas, J.

    1983-01-01

    The Flight Transportation Laboratory has developed a real time interactive Air Traffic Control simulation facility designed to provide a versatile and easy to use tool for research and experimentation involving air traffic control. The facility uses a VAX-11/750 as the central computer. The SANDERS GRAPHICS-7 display system is used to simulate air traffic control displays. Pseudo-pilot displays are provided on Texas Instruments TI940 video terminals. Finally, a custom designed audio system driven by a Z-80 and interfaced with the VAX provides voice communication between the air traffic controllers and the pseudo-pilots. The audio system provides computer controlled voice disguising and thus allows each aircraft to have its own audio characteristics and provides an added realism to the experiment. The facility can accommodate multiple controller stations and pseudo-pilot stations. Each station is manned by a single operator who has a large repertoire of commands with which to control his/her display and the simulated aircraft under his/her jurisdiction. An additional console and a distinct set of commands allow full controllability of the simulation environment by the experimenter in real time.

  5. Time series analysis of molecular dynamics simulation using wavelet

    NASA Astrophysics Data System (ADS)

    Toda, Mikito

    2012-08-01

    A new method is presented to extract nonstationary features of slow collective motion toward time series data of molecular dynamics simulation for proteins. The method consists of the following two steps: (1) the wavelet transformation and (2) the singular value decomposition (SVD). The wavelet transformation enables us to characterize time varying features of oscillatory motions and SVD enables us to reduce the degrees of freedom of the movement. We apply the method to molecular dynamics simulation of various proteins such as Adenylate Kinase from Escherichia coli (AKE) and Thermomyces lanuginosa lipase (TLL). Moreover, we introduce indexes to characterize collective motion of proteins. These indexes provide us with information of nonstationary deformation of protein structures. We discuss future prospects of our study involving "intrinsically disordered proteins".

  6. 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

  7. Simulations of time spreading in shallow water propagation

    NASA Astrophysics Data System (ADS)

    Thorsos, Eric I.; Elam, W. T.; Tang, Dajun; Henyey, Frank S.; Williams, Kevin L.; Reynolds, Stephen A.

    2002-11-01

    Pulse propagation in a shallow water wave guide leads to time spreading due to multipath effects. Results of PE simulations will be described for pulse propagation in shallow water with a rough sea surface and a flat sandy sea floor. The simulations illustrate that such time spreading may be significantly less at longer ranges than for the flat surface case. Pressure fields are simulated in two space dimensions and have been obtained using a wide-angle PE code developed by Rosenberg [A. D. Rosenberg, J. Acoust. Soc. Am. 105, 144-153 (1999)]. The effect of rough surface scattering is to cause acoustic energy initially propagating at relatively high angles but still below the critical angle at the sea floor to be eventually shifted to grazing angles above the critical angle. This energy is then lost into the bottom, effectively stripping higher propagating modes. The surviving energy at longer ranges is concentrated in the lowest modes and shows little effect of time spreading. Thus, the effect of rough surface scattering is found to produce a simpler temporal field structure than if the surface were treated as flat. [Work supported by ONR.

  8. 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.

  9. 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.

  10. A Computer Simulation for Teaching Quantal Time Development

    NASA Astrophysics Data System (ADS)

    Styer, Daniel F.

    1996-11-01

    The computer program QMTime (for MS-DOS machines) enables students to simulate quantal time development in one dimension. A variety of initial wave packets (Gaussian, Lorentzian, etc.) can evolve in time under the influence of a variety of potential energy functions (step, ramp, square well, harmonic oscillator, etc.) with or without an external driving force. A novel visualization technique simultaneously displays the magnitude and phase of complex-valued wavefunctions. Either position-space or momentum-space wavefunctions, or both, can be shown. The program is particularly effective in demonstrating the classical limit of quantum mechanics. This program is part of the CUPS (Consortium for Upper level Physics Software) project.

  11. 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.

  12. Time-dependent simulations of filament propagation in photoconducting switches

    SciTech Connect

    Rambo, P.W.; Lawson, W.S.; Capps, C.D.; Falk, R.A.

    1994-05-01

    The authors present a model for investigating filamentary structures observed in laser-triggered photoswitches. The model simulates electrons and holes in two-dimensional cylindrical (r-z) geometry, with realistic electron and hole mobilities and field dependent impact ionization. Because of the large range of spatial and temporal scales to be resolved, they are using an explicit approach with fast, direct solution of the field equation. A flux limiting scheme is employed to avoid the time-step constraint due to the short time for resistive relaxation in the high density filament. Self-consistent filament propagation with speeds greater than the carrier drift velocity are observed in agreement with experiments.

  13. A fast real time time-dependent density functional theory simulation method

    NASA Astrophysics Data System (ADS)

    Wang, Lin-Wang; Wang, Zhi; Li, Shu-Sheng

    2015-03-01

    We have developed an efficient real-time time-dependent density functional theory (TDDFT) method that can increase the effective time step from <1 attosecond in traditional methods to 0.1 0.5 femtosecond. Our algorithm, which carries out the non-adiabatic molecular dynamics TDDFT simulations, can have comparable speed to the Born-Oppenheimer (BO) ab initio molecular dynamics (MD). As an application, we simulated the process of an energetic Cl particle colliding onto a monolayer of MoSe2. Our simulations show a significant energy transfer from the kinetic energy of the Cl particle to the electronic energy of MoSe2, and the result of TDDFT is very different from that of BO MD simulations. This new algorithm will enable the use of real-time TD-DFT for many new simulations involving carrier dynamics and electron-phonon couplings. This work is supported by the Director, Office of Science, BES/MSED, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231, through the Material Theory program in LBNL. Zhi Wang is supported by the China Scholarship Council.

  14. 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.

  15. 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. PMID:26991880

  16. 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%.

  17. 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.

  18. 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

  19. 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.

  20. Real-time ultrasound simulation using the GPU.

    PubMed

    Gjerald, Sjur Urdson; Brekken, Reidar; Hergum, Torbjørn; D'hooge, Jan

    2012-05-01

    Ultrasound simulators can be used for training ultrasound image acquisition and interpretation. In such simulators, synthetic ultrasound images must be generated in real time. Anatomy can be modeled by computed tomography (CT). Shadows can be calculated by combining reflection coefficients and depth dependent, exponential attenuation. To include speckle, a pre-calculated texture map is typically added. Dynamic objects must be simulated separately. We propose to increase the speckle realism and allow for dynamic objects by using a physical model of the underlying scattering process. The model is based on convolution of the point spread function (PSF) of the ultrasound scanner with a scatterer distribution. The challenge is that the typical field-of-view contains millions of scatterers which must be selected by a virtual probe from an even larger body of scatterers. The main idea of this paper is to select and sample scatterers in parallel on the graphic processing unit (GPU). The method was used to image a cyst phantom and a movable needle. Speckle images were produced in real time (more than 10 frames per second) on a standard GPU. The ultrasound images were visually similar to images calculated by a reference method. PMID:22622973

  1. Simulation of between Repeat Variability in Real Time PCR Reactions

    PubMed Central

    Lievens, Antoon; Van Aelst, Stefan; Van den Bulcke, Marc; Goetghebeur, Els

    2012-01-01

    While many decisions rely on real time quantitative PCR (qPCR) analysis few attempts have hitherto been made to quantify bounds of precision accounting for the various sources of variation involved in the measurement process. Besides influences of more obvious factors such as camera noise and pipetting variation, changing efficiencies within and between reactions affect PCR results to a degree which is not fully recognized. Here, we develop a statistical framework that models measurement error and other sources of variation as they contribute to fluorescence observations during the amplification process and to derived parameter estimates. Evaluation of reproducibility is then based on simulations capable of generating realistic variation patterns. To this end, we start from a relatively simple statistical model for the evolution of efficiency in a single PCR reaction and introduce additional error components, one at a time, to arrive at stochastic data generation capable of simulating the variation patterns witnessed in repeated reactions (technical repeats). Most of the variation in values was adequately captured by the statistical model in terms of foreseen components. To recreate the dispersion of the repeats' plateau levels while keeping the other aspects of the PCR curves within realistic bounds, additional sources of reagent consumption (side reactions) enter into the model. Once an adequate data generating model is available, simulations can serve to evaluate various aspects of PCR under the assumptions of the model and beyond. PMID:23189123

  2. Real-time generation of reality scene in flight simulator

    NASA Astrophysics Data System (ADS)

    Zhang, Limin; Zhang, Linlin

    2004-03-01

    Reality scene is one of the most basic and important technologies in visual system of flight simulators. It includes real terrain, terrain object and physiognomy. Nowadays, it is usually constructed with digital elevation model (DEM) and remote sensing satellite data. In spite of the fast development of computer hardware, it is very difficult to generate large area reality scenes in real-time. Therefore, model simplification, multi-resolution rendering and level of detail (LOD) become the hotspot of recent research. Multi-resolution rendering is the development and extension of the LOD, model simplification is the key in generating a lower resolution model from a complex higher one. Based on the manufacturing practice of some flight simulators, this paper discusses ways of reality scenes' generating and simplification, and dynamic data partition and schedule based on viewpoint.

  3. 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

  4. 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.

  5. 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.

  6. Synthetic LISA: Simulating time delay interferometry in a model LISA

    SciTech Connect

    Vallisneri, Michele

    2005-01-15

    We report on three numerical experiments on the implementation of Time-Delay Interferometry (TDI) for LISA, performed with Synthetic LISA, a C++/Python package that we developed to simulate the LISA science process at the level of scientific and technical requirements. Specifically, we study the laser-noise residuals left by first-generation TDI when the LISA armlengths have a realistic time dependence; we characterize the armlength-measurement accuracies that are needed to have effective laser-noise cancellation in both first- and second-generation TDI; and we estimate the quantization and telemetry bitdepth needed for the phase measurements. Synthetic LISA generates synthetic time series of the LISA fundamental noises, as filtered through all the TDI observables; it also provides a streamlined module to compute the TDI responses to gravitational waves according to a full model of TDI, including the motion of the LISA array and the temporal and directional dependence of the armlengths. We discuss the theoretical model that underlies the simulation, its implementation, and its use in future investigations on system-characterization and data-analysis prototyping for LISA.

  7. Synthesis of rotor test data for real-time simulation

    NASA Technical Reports Server (NTRS)

    Mcveigh, M. A.

    1979-01-01

    A mathematical model of a hingeless tilting rotor is presented. The model was obtained by a systematic curve fit procedure applied to an extensive set of model scale wind tunnel data. The math model equations were used in a real time flight simulation model of a hingeless tilt rotor XV-15 to assess changes in flying qualities compared to those obtained using a previous rotor model. Extensive plots of the rotor derivatives are given. Discussions of attempts to apply multivariable linear regression technqiues to the data and the use of an analytical rotor representation are included.

  8. Real-Time Simulation Computation System. [for digital flight simulation of research aircraft

    NASA Technical Reports Server (NTRS)

    Fetter, J. L.

    1981-01-01

    The Real-Time Simulation Computation System, which will provide the flexibility necessary for operation in the research environment at the Ames Research Center is discussed. Designing the system with common subcomponents and using modular construction techniques enhances expandability and maintainability qualities. The 10-MHz series transmission scheme is the basis of the Input/Output Unit System and is the driving force providing the system flexibility. Error checking and detection performed on the transmitted data provide reliability measurements and assurances that accurate data are received at the simulators.

  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. Time to blip--stochastic simulation of single channel opening.

    PubMed

    Thul, Rüdiger

    2014-05-01

    The stochastic dynamics of the inositol-1,4,5-trisphosphate (IP3) receptor (IP3R) is key to understanding a wide range of observed calcium (Ca²⁺) signals. The stochastic nature results from the constant binding and unbinding of Ca²⁺ and IP3 to and from their respective binding sites and is especially important in the initiation of a Ca²⁺ puff (i.e., the release of Ca²⁺ through a cluster of IP3Rs). Once the first IP3R opens, the Ca²⁺ concentration rises significantly around the ion channel, increasing the open probability for neighboring IP3Rs. This opening may trigger the activation of further receptors, giving rise to a Ca²⁺ puff. In this protocol, we determine the time that it takes for a single IP3R to open from rest. We explicitly take into account the tetrameric structure of the IP3R and the fact that multiple subunits must be active before the channel opens. We develop code for a stochastic simulation of the IP3R and simulate it using the software package MATLAB. This protocol shows the basic form of a stochastic simulation algorithm and may serve as a starting point to investigate more complex gating dynamics. PMID:24786499

  11. 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.

  12. Time-dependent simulations of a Compact Ignition Tokamak

    SciTech Connect

    Stotler, D.P.; Bateman, G.

    1988-05-01

    Detailed simulations of the Compact Ignition Tokamak are carried out using a 1-1/2-D transport code. The calculations include time-varying densities, fields, and plasma shape. It is shown that ignition can be achieved in this device if somewhat better than L-mode energy confinement time scaling is possible. We also conclude that the performance of such a compact, short-pulse device can depend greatly on how the plasma is evolved to its flat-top parameters. Furthermore, in cases such as the ones discussed here, where there is not a great deal of ignition margin and the electron density is held constant, ignition ends if the helium ash is not removed. In general, control of the deuterium--tritium density is equivalent to burn control. 48 refs., 15 figs.

  13. Satellite image time series simulation for environmental monitoring

    NASA Astrophysics Data System (ADS)

    Guo, Tao

    2014-11-01

    The performance of environmental monitoring heavily depends on the availability of consecutive observation data and it turns out an increasing demand in remote sensing community for satellite image data in the sufficient resolution with respect to both spatial and temporal requirements, which appear to be conflictive and hard to tune tradeoffs. Multiple constellations could be a solution if without concerning cost, and thus it is so far interesting but very challenging to develop a method which can simultaneously improve both spatial and temporal details. There are some research efforts to deal with the problem from various aspects, a type of approaches is to enhance the spatial resolution using techniques of super resolution, pan-sharpen etc. which can produce good visual effects, but mostly cannot preserve spectral signatures and result in losing analytical value. Another type is to fill temporal frequency gaps by adopting time interpolation, which actually doesn't increase informative context at all. In this paper we presented a novel method to generate satellite images in higher spatial and temporal details, which further enables satellite image time series simulation. Our method starts with a pair of high-low resolution data set, and then a spatial registration is done by introducing LDA model to map high and low resolution pixels correspondingly. Afterwards, temporal change information is captured through a comparison of low resolution time series data, and the temporal change is then projected onto high resolution data plane and assigned to each high resolution pixel referring the predefined temporal change patterns of each type of ground objects to generate a simulated high resolution data. A preliminary experiment shows that our method can simulate a high resolution data with a good accuracy. We consider the contribution of our method is to enable timely monitoring of temporal changes through analysis of low resolution images time series only, and usage of

  14. 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.

  15. 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.

  16. Simulating continuous-time Hamiltonian dynamics by way of a discrete-time quantum walk

    NASA Astrophysics Data System (ADS)

    Schmitz, A. T.; Schwalm, W. A.

    2016-03-01

    Much effort has been made to connect the continuous-time and discrete-time quantum walks. We present a method for making that connection for a general graph Hamiltonian on a bigraph. Furthermore, such a scheme may be adapted for simulating discretized quantum models on a quantum computer. A coin operator is found for the discrete-time quantum walk which exhibits the same dynamics as the continuous-time evolution. Given the spectral decomposition of the graph Hamiltonian and certain restrictions, the discrete-time evolution is solved for explicitly and understood at or near important values of the parameters. Finally, this scheme is connected to past results for the 1D chain.

  17. 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

  18. 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.

  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. 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.

  1. 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.

  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. Lagrangian simulation of transport pathways and residence times along the western Antarctic Peninsula

    NASA Astrophysics Data System (ADS)

    Piñones, Andrea; Hofmann, Eileen E.; Dinniman, Michael S.; Klinck, John M.

    2011-07-01

    The relative contribution of ocean circulation in producing areas where marine mammals and other predators concentrate to produce biological hot spots along the continental shelf of the western Antarctic Peninsula (wAP) was investigated with numerical Lagrangian particle tracking simulations. Circulation distributions used in the Lagrangian simulations were obtained from the Regional Ocean Modeling System (ROMS) configured for the wAP region, with a horizontal resolution of 4 km and a vertical resolution of 24 sigma-layers. To determine release points for the floats, the simulated circulation fields were first analyzed to estimate scales of temporal variability. The temporal decorrelation scales of the simulated surface flow over most of the wAP shelf were 2-3 days. However, decorrelation scales of about 40 days were found for the surface flow in the southern part of Marguerite Bay. Temporal decorrelation scales for the flow below the permanent pycnocline at the depth of Circumpolar Deep Water (CDW) intrusions (below 250 m) were between 40 and 70 days along the northern flank of Marguerite Trough and extending into Marguerite Bay. Near Adelaide Island, Anvers Island and the offshore side of Alexander Island, the velocity decorrelation scales varied between 40 and 60 days. Floats were released in the wAP simulated circulation fields along the outer and mid-shelf at a range of depths in different seasons. The simulated particle trajectories showed preferred sites for across-shelf transport, with Marguerite Trough being a primary pathway for movement of floats into Marguerite Bay, Crystal Sound and the inner shelf region. The three primary biological hot spots, Crystal Sound, Laubeuf Fjord, and off Alexander Island, were sites with the longest particle residence times, being 18-27 days for Alexander Island and Crystal Sound to almost 35 days for Laubeuf Fjord. However, the source regions and circulation processes that provided the input of particles differed for each

  4. 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

  5. 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.

  6. 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

  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. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Dependence of aqua-planet simulations on time step

    NASA Astrophysics Data System (ADS)

    Williamson, David L.; Olson, Jerry G.

    2003-04-01

    Aqua-planet simulations with Eulerian and semi-Lagrangian dynamical cores coupled to the NCAR CCM3 parametrization suite produce very different zonal average precipitation patterns. The model with the Eulerian core forms a narrow single precipitation peak centred on the sea surface temperature (SST) maximum. The one with the semi-Lagrangian core forms a broad structure often with a double peak straddling the SST maximum with a precipitation minimum centred on the SST maximum. The different structure is shown to be caused primarily by the different time step adopted by each core and its effect on the parametrizations rather than by different truncation errors introduced by the dynamical cores themselves. With a longer discrete time step, the surface exchange parametrization deposits more moisture in the atmosphere in a single time step, resulting in convection being initiated farther from the equator, closer to the maximum source. Different diffusive smoothing associated with different spectral resolutions is a secondary effect influencing the strength of the double structure. When the semi-Lagrangian core is configured to match the Eulerian with the same time step, a three-time-level formulation and same spectral truncation it produces precipitation fields similar to those from the Eulerian. It is argued that the broad and double structure forms in this model with the longer time step because more water is put into the atmosphere over a longer discrete time step, the evaporation rate being the same. The additional water vapour in the region of equatorial moisture convergence results in more convective available potential energy farther from the equator which allows convection to initiate farther from the equator.The resulting heating drives upward vertical motion and low-level convergence away from the equator, resulting in much weaker upward motion at the equator. The feedback between the convective heating and dynamics reduces the instability at the equator and

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Simulation of yearly rainfall time series at microscale resolution with actual properties: Intermittency, scale invariance, and rainfall distribution

    NASA Astrophysics Data System (ADS)

    Akrour, Nawal; Chazottes, Aymeric; Verrier, Sébastien; Mallet, Cécile; Barthes, Laurent

    2015-09-01

    Rainfall is a physical phenomenon resulting from the combination of numerous physical processes involving a wide range of scales, from microphysical processes to the general circulation of the atmosphere. Moreover, unlike other geophysical variables such as water vapor concentration, rainfall is characterized by a relaxation behavior that leads to an alternation of wet and dry periods. It follows that rainfall is a complex process which is highly variable both in time and space. Precipitation is thus characterized by the following features: rain/no-rain intermittency, multiple scaling regimes, and extreme events. All these properties are difficult to model simultaneously, especially when a large time and/or space scale domain is required. The aim of this paper is to develop a simulator capable of generating high-resolution rain-rate time series (15 s), the main statistical properties of which are close to an observed rain-rate time series. We also attempt to develop a model having consistent properties even when the fine-resolution-simulated time series are aggregated to a coarser resolution. In order to break the simulation problem down into subcomponents, the authors have focused their attention on several key properties of rainfall. The simulator is based on a sequential approach in which, first, the simulation of rain/no-rain durations permits the retrieval of fractal properties of the rain support. Then, the generation of rain rates through the use of a multifractal, Fractionally Integrated Flux (FIF), model enables the restitution of the rainfall's multifractal properties. This second step includes a denormalization process that was added in order to generate realistic rain-rate distributions.

  1. 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.

  2. Potentials of mean force and escape times of surfactants from micelles and hydrophobic surfaces using molecular dynamics simulations.

    PubMed

    Yuan, Fang; Wang, Shihu; Larson, Ronald G

    2015-02-01

    We calculate potentials of mean force (PMFs) and mean first passage times for a surfactant to escape a micelle, for both ionic sodium dodecyl sulfate (SDS) and nonionic ethoxylated alcohol (C12E5) micelles using both atomistic and coarse-grained molecular dynamics (MD) simulations. The PMFs are obtained by umbrella sampling and used in a Smoluchowski first-passage-time theory to obtain the times for a surfactant to escape a micelle. The calculated mean first passage time for an SDS molecule to break away from a micelle (with an aggregation number of 60) is around 2 μs, which is consistent with previous experimental measurements of the "fast relaxation time" for exchange of surfactants between the micellar phase and the bulk solvent. The corresponding escape time calculated for a nonionic ethoxylated alcohol C12E5, with the same tail length as SDS, is 60 μs, which is significantly longer than for SDS primarily because the PMF for surfactant desorption is about 3kT smaller than for C12E5. We also show that two coarse-grained (CG) force fields, MARTINI and SDK, give predictions similar to the atomistic CHARMM force field for the nonionic C12E5 surfactant, but for the ionic SDS surfactant, the CG simulations give a PMF similar to that obtained with CHARMM only if long-range electrostatic interactions are included in the CG simulations, rather than using a shifted truncated electrostatic interaction. We also calculate that the mean first passage time for an SDS and a C12E5 to escape from a latex binder surface is of the order of milliseconds, which is more than 100 times longer than the time for escape from the micelle, indicating that in latex waterborne coatings, SDS and C12E5 surfactants likely bind preferentially to the latex polymer interface rather than form micelles, at least at low surfactant concentrations. PMID:25560633

  3. Time-Delay Interferometry Simulations and Gravitational Wave Extraction at the University of Florida Interferometric Simulator

    NASA Astrophysics Data System (ADS)

    Mitryk, Shawn; Wand, Vinzenz; Preston, Alix; Mueller, Guido; Tanner, David

    2010-02-01

    The Laser Interferometer Space Antenna (LISA) is a NASA/ESA space mission with the goal of measuring gravitational waves (GW) at frequencies of 30 uHz - 1 Hz. Going to space avoids seimic and gravity-gradient noise which limit all ground-based detectors. LISA will measure the spatial changes between drag-free proof masses separated by a distance of 5 Gm using heterodyne interferometry. The laser noise must be recorded and removed from the measurement through time-delay interferometry (TDI) to extract gravitational wave signals. The University of Florida LISA Interferometry Simulator (UFLIS) performs hardware-in-the-loop simulations of LISA by reproducing the expected pre-stabilized laser noise, delaying the laser frequency noise by the light-travel time along the LISA arms, injecting mock gravitational wave signals, and forming the required TDI combinations to extract the injected GW signals. Using the UFLIS, we present the extraction of mock GW signals buried under 9 orders of magnitude of laser frequency noise. )

  4. 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.

  5. 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

  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. 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

  8. 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.

  9. 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…

  10. Time in Language, Situation Models, and Mental Simulations

    ERIC Educational Resources Information Center

    Zwaan, Rolf A.

    2008-01-01

    The purpose of this article is to propose a view of language processing, and particularly the role of aspect therein, from a mental-simulation perspective. I argue that situation model theories can account for the flow between and interconnectedness of event representations but that mental simulation theories are needed to account for the internal…

  11. 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.

  12. 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

  13. Global kinetic analysis of seeded BSA aggregation.

    PubMed

    Sahin, Ziya; Demir, Yusuf Kemal; Kayser, Veysel

    2016-04-30

    Accelerated aggregation studies were conducted around the melting temperature (Tm) to elucidate the kinetics of seeded BSA aggregation. Aggregation was tracked by SEC-HPLC and intrinsic fluorescence spectroscopy. Time evolution of monomer, dimer and soluble aggregate concentrations were globally analysed to reliably deduce mechanistic details pertinent to the process. Results showed that BSA aggregated irreversibly through both sequential monomer addition and aggregate-aggregate interactions. Sequential monomer addition proceeded only via non-native monomers, starting to occur only by 1-2°C below the Tm. Aggregate-aggregate interactions were the dominant mechanism below the Tm due to an initial presence of small aggregates that acted as seeds. Aggregate-aggregate interactions were significant also above the Tm, particularly at later stages of aggregation when sequential monomer addition seemed to cease, leading in some cases to insoluble aggregate formation. The adherence (or non-thereof) of the mechanisms to Arrhenius kinetics were discussed alongside possible implications of seeding for biopharmaceutical shelf-life and spectroscopic data interpretation, the latter of which was found to often be overlooked in BSA aggregation studies. PMID:26970282

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. 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

  20. Effect of Rainfall Aggregation on Hydrologic Predictions

    NASA Astrophysics Data System (ADS)

    Sharif, H.; Brandes, E.

    2003-12-01

    Remotely sensed soil moisture data are becoming increasingly available, however the variability within the remotely sensed footprint is spatially averaged. The representation of spatial heterogeneity of soil moisture is essential for modeling processes that are nonlinearly related to soil moisture, such as the partitioning of sensible and latent heat fluxes. A number of studies have suggested that the spatial variability of soil moisture varies with wetness. At different locations, scales, and wetting and drying conditions, soil moisture patterns have been linked to topography, soil characteristics such as porosity and wilting point, and rainfall distribution. The objective of the proposed study is to examine the effects of rainfall temporal and spatial aggregation on spatial variability of soil moisture and runoff predictions on a 1000-km2 watershed. High-resolution radar-estimated rainfall from the IHOP2002 experiment will be used. These rain fields are aggregated in space and time. The hydrologic response of a distributed hydrologic model to the aggregated rain fields will be statistically compared with the response of the model to the original rainfall fields to quantify the impact of the spatial and temporal aggregation on hydrologic predictions. The proposed procedure will combine information from these simulations to determine what adjustments need to be made to the predicted fluxes.

  1. 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.

  2. Generic Spacecraft Model for Real-Time Simulation

    NASA Technical Reports Server (NTRS)

    Kenney, Patrick S.; Ragsdale, William; Neuhaus, Jason R.

    2008-01-01

    Generic Spacecraft is the name of an evolving library of software that provides for simulation of a generic spacecraft that can orbit the Earth and land on the Moon (and, eventually, on Mars). This library is incorporated into the Langley Standard Realtime Simulation in C++ (LaSRS++) software framework. The generic-spacecraft simulation serves as a test bed for modeling spacecraft dynamics, propulsion, control systems, guidance, and displays. The Generic Spacecraft library supplements the LaSRS++ framework with an interface that facilitates the connection of new models into the LaSRS++ simulation by eliminating what would otherwise be the necessity of writing additional C++ classes to record data from the models and code to display values on graphical user interfaces (GUIs): The library includes routines for integrating new models into the LaSRS++ framework, identifying model inputs and outputs with full descriptions and units identified, recording data, and automatically generating graphical user interfaces (GUIs). The library is designed to be used in a manner similar to that of LaSRS++ software components for simulating vehicles other than the generic spacecraft. The user specifies (1) a spacecraft and individual models to be constructed and (2) connections between individual model inputs and outputs.

  3. Forward-time simulation of realistic samples for genome-wide association studies

    PubMed Central

    2010-01-01

    Background Forward-time simulations have unique advantages in power and flexibility for the simulation of genetic samples of complex human diseases because they can closely mimic the evolution of human populations carrying these diseases. However, a number of methodological and computational constraints have prevented the power of this simulation method from being fully explored in existing forward-time simulation methods. Results Using a general-purpose forward-time population genetics simulation environment, we developed a forward-time simulation method that can be used to simulate realistic samples for genome-wide association studies. We examined the properties of this simulation method by comparing simulated samples with real data and demonstrated its wide applicability using four examples, including a simulation of case-control samples with a disease caused by multiple interacting genetic and environmental factors, a simulation of trio families affected by a disease-predisposing allele that had been subjected to either slow or rapid selective sweep, and a simulation of a structured population resulting from recent population admixture. Conclusions Our algorithm simulates populations that closely resemble the complex structure of the human genome, while allows the introduction of signals of natural selection. Because of its flexibility to generate different types of samples with arbitrary disease or quantitative trait models, this simulation method can simulate realistic samples to evaluate the performance of a wide variety of statistical gene mapping methods for genome-wide association studies. PMID:20809983

  4. Real-time graphic simulation for space telerobotics applications

    NASA Technical Reports Server (NTRS)

    Baumann, E. W.

    1987-01-01

    Designing space-based telerobotic systems presents many problems unique to telerobotics and the space environment, but it also shares many common hardware and software design problems with Earth-based industrial robot applications. Such problems include manipulator design and placement, grapple-fixture design, and of course the development of effective and reliable control algorithms. Since first being applied to industrial robotics just a few years ago, interactive graphic simulation has proven to be a powerful tool for anticipating and solving problems in the design of Earth-based robotic systems and processes. Where similar problems are encountered in the design of space-based robotic mechanisms, the same graphic simulation tools may also be of assistance. The capabilities of PLACE, a commercially available interactive graphic system for the design and simulation of robotic systems and processes is described. A space-telerobotics application of the system is presented and discussed. Potential future enhancements are described.

  5. Avoiding pitfalls in simulating real-time computer systems

    NASA Technical Reports Server (NTRS)

    Smith, R. S.

    1984-01-01

    The software simulation of a computer target system on a computer host system, known as an interpretive computer simulator (ICS), functionally models and implements the action of the target hardware. For an ICS to function as efficiently as possible and to avoid certain pitfalls in designing an ICS, it is important that the details of the hardware architectural design of both the target and the host computers be known. This paper discusses both host selection considerations and ICS design features that, without proper consideration, could make the resulting ICS too slow to use or too costly to maintain and expand.

  6. 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.

  7. 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

  8. 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

  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. 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.

  12. Growth and Destruction from Low-Velocity Dust Aggregate Collisions

    NASA Astrophysics Data System (ADS)

    Dove, Adrienne; Colwell, J.; Vamos, C.

    2012-10-01

    By exploring a variety of impactor densities and velocities, we can observe the ranges over which growth, compaction, or erosion occur for cm-sized aggregates. Evolution of proto-planetary and planetary ring systems is driven by collisions between objects that are likely to themselves be formed from aggregates of smaller particles. In these collisional systems, impacts between objects may occur at very low velocities, much less than 1 m/s. Low-velocity impacts may play a critical role in the growth of larger aggregates. In planetary ring systems and circumplanetary disks, collisions between aggregates or dust-covered objects release dust that is a more visible tracer of the underlying parent population of massive objects. We have designed and built an apparatus to simulate these low-velocity collisions in a laboratory vacuum environment. In our experiment, one aggregate is launched upward by a spring launching mechanism, while another is dropped from directly above the launcher to create the impact. Impact velocities are controlled by initial spring launch velocity, masses of the particles, and timing of the collisions. Initially, we use JSC-1 lunar regolith simulant to create the aggregates; the simulant can be packed to different densities to control the mass and porosity of the impactors. A high-speed digital video camera is used to record the impacts to observe the behavior of both impactors and the resulting ejecta material. By exploring a variety of impactor densities and velocities, we can observe the ranges over which grow, compaction, or erosion occur for cm-sized aggregates.

  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. 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

  16. 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.

  17. 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.

  18. 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

  19. Realistic soft tissue deformation strategies for real time surgery simulation.

    PubMed

    Shen, Yunhe; Zhou, Xiangmin; Zhang, Nan; Tamma, Kumar; Sweet, Robert

    2008-01-01

    A volume-preserving deformation method (VPDM) is developed in complement with the mass-spring method (MSM) to improve the deformation quality of the MSM to model soft tissue in surgical simulation. This method can also be implemented as a stand-alone model. The proposed VPDM satisfies the Newton's laws of motion by obtaining the resultant vectors form an equilibrium condition. The proposed method has been tested in virtual surgery systems with haptic rendering demands. PMID:18391343

  20. 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.

  1. Diffusion, aggregation, and the thermal conductivity of nanofluids

    NASA Astrophysics Data System (ADS)

    Gharagozloo, Patricia E.; Eaton, John K.; Goodson, Kenneth E.

    2008-09-01

    The effects of nanoparticle aggregation and diffusion are difficult to separate using most nanofluid thermal conductivity data, for which the temperature dependence is collected sequentially. The present work captures the instantaneous temperature-dependent thermal conductivity using cross-sectional infrared microscopy and tracks the effects of aggregation and diffusion over time. The resulting data are strongly influenced by spatial and temperature variations in particle size and concentration and are interpreted using a Monte Carlo simulation and rate equations for particle and heat transport. These experiments improve our understanding of nanofluid behavior in practical systems including microscale heat exchangers.

  2. 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…

  3. 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…

  4. Microwave extinction characteristics of nanoparticle aggregates

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  5. 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. Time step and shadow Hamiltonian in molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Kim, Sangrak

    2015-08-01

    We examine the time step and the shadow Hamiltonian of symplectic algorithms for a bound system of a simple harmonic oscillator as a specific example. The phase space trajectory moves on the hyperplane of a constant shadow Hamiltonian. We find a stationary condition for the time step τ n with which the motion repeats itself on the phase space with a period n. Interestingly, that the time steps satisfying the stationary condition turn out to be independent of the symplectic algorithms chosen. Furthermore, the phase volume enclosed by the phase trajectory is given by n τ n Ẽ n , where Ẽ n is the initial shadow energy of the corresponding symplectic algorithm.

  7. 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.

  8. 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

  9. 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

  10. 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

  11. IfkA, a presumptive eIF2α kinase of Dictyostelium, is required for proper timing of aggregation and regulation of mound size

    PubMed Central

    Fang, Rui; Xiong, Yanhua; Singleton, Charles K

    2003-01-01

    Background The transition from growth to development in Dictyostelium is initiated by amino acid starvation of growing amobae. In other eukaryotes, a key sensor of amino acid starvation and mediator of the resulting physiological responses is the GCN2 protein, an eIF2α kinase. GCN2 downregulates the initiation of translation of bulk mRNA and enhances translation of specific mRNAs by phosphorylating the translation initiation factor eIF2α. Two eIF2α kinases were identified in Dictyostelium and studied herein. Results Neither of the eIF2α kinases appeared to be involved in sensing amino acid starvation to initiate development. However, one of the kinases, IfkA, was shown to phosphorylate eIF2α from 1 to 7 hours after the onset of development, resulting in a shift from polysomes to free ribosomes for bulk mRNA. In the absence of the eIF2α phosphorylation, ifkA null cells aggregated earlier than normal and formed mounds and ultimately fruiting bodies that were larger than normal. The early aggregation phenotype in ifkA null cells reflected an apparent, earlier than normal establishment of the cAMP pulsing system. The large mound phenotype resulted from a reduced extracellular level of Countin, a component of the counting factor that regulates mound size. In wild type cells, phosphorylation of eIF2α by IfkA resulted in a specific stabilization and enhanced translational efficiency of countin mRNA even though reduced translation resulted for bulk mRNA. Conclusions IfkA is an eIF2α kinase of Dictyostelium that normally phosphorylates eIF2α from 1 to 7 hours after the onset of development, or during the preaggregation phase. This results in an overall reduction in the initiation of protein synthesis during this time frame and a concomitant reduction in the number of ribosomes associated with most mRNAs. For some mRNAs, however, initiation of protein synthesis is enhanced or stabilized under the conditions of increased eIF2α phosphorylation. This includes countin

  12. 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.

  13. On the concept of material strength and first simulations of asteroid disruption with explicit formation of spinning aggregates in the gravity regime

    NASA Astrophysics Data System (ADS)

    Michel, P.; Richardson, D. C.

    2007-08-01

    During their evolutions, the small bodies of our Solar System are affected by several mechanisms which can modify their properties. While dynamical mechanisms are at the origin of their orbital variations, there are other mechanisms which can change their shape, spin, and even their size when their strength threshold is reached, resulting in their disruption. Such mechanisms have been identified and studied, both by analytical and numerical tools. The main mechanisms that can result in the disruption of a small body are collisional events, tidal perturbations, and spin-ups. However, the efficiency of these mechanisms depends on the strength of the material constituing the small body, which also plays a role in its possible equilibrium shape. We will present several important aspects of material strength that are believed to be adapted to Solar System small bodies and briefly review the most recent studies of the different mechanisms that can be at the origin of the disruption of these bodies. In particular, we have recently made a major improvement in the simulations of asteroid disruption by computing explicitly the formation of aggregates during the gravitational reaccumulation of small fragments, allowing us to obtain information on their spin, the number of boulders composing them or lying on their surface, and their shape.We will present the first and preliminary results of this process taking as examples some asteroid families that we reproduced successfully with our previous simulations (Michel et al. 2001, 2002, 2003, 2004a,b), and their possible implications on the properties of asteroids generated by a disruption. Such information can for instance be compared with data provided by the Japanese space mission Hayabusa of the asteroid Itokawa, a body now understood to be a fragment of a larger parent body. It is also clear that future space missions to small bodies devoted to precise in-situ analysis and sample return will allow us to improve our

  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 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

  16. 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.

  17. 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

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. Time-Variant Simulation of Multi-Material Thermal Pultrusion

    NASA Astrophysics Data System (ADS)

    Joshi, Sunil C.; Chen, X.

    2011-08-01

    Pultrusion being the viable and economical process for producing constant cross-section composite products, many variants of it are being tried out. This paper embarks on the pultrusion with multi-materials; typically of polymer foam/glass fibre reinforced polymer (GFRP) sandwich panels. Unlike conventional composites pultrusion, this process with more than two material phases, one of them dry, poses a challenge in simulating the thermal co-curing within the die. In this paper, the formulation and development of three-dimensional, finite element/nodal control volume (FE/NCV) approach for such multi-material pultrusion is presented. The numerical features for handling the dry-wet material interfaces, material shrinkage, variations in pull speed and die heating, and foam-to-skin thickness ratio are discussed. Implementation of the FE/NCV procedure and its application in analyzing pultrusion of polymer foam/GFRP sandwich panels with multi-heater environment are presented.

  4. Relative timing of substorm features in MHD simulations

    NASA Technical Reports Server (NTRS)

    Hesse, Michael; Birn, Joachim

    1992-01-01

    An investigation of the temporal sequence of substorm phenomena based on three dimensional MHD (magnetohydrodynamic) simulations of magnetic reconnection and plasmoid formation is presented. The investigation utilizes a spatially localized resistivity model which leads to a significantly faster evolution than found in previous investigations. The analysis of the results concentrates on substorm features that have received considerable attention in the past. The formation of magnetic neutral lines, the occurrence of fast flows directed both earthward and tailward, and the magnetic field changes leading to the formation of the substorm current wedge, and to the depolarization of the magnetic field earthward of the reconnection region and its dependence on the spatial distribution of resistivity, are discussed. These phenomena are seen as an integral part of the nonlinear evolution of the three dimensional tearing instability.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. A modular method to handle multiple time-dependent quantities in Monte Carlo simulations

    NASA Astrophysics Data System (ADS)

    Shin, J.; Perl, J.; Schümann, J.; Paganetti, H.; Faddegon, B. A.

    2012-06-01

    A general method for handling time-dependent quantities in Monte Carlo simulations was developed to make such simulations more accessible to the medical community for a wide range of applications in radiotherapy, including fluence and dose calculation. To describe time-dependent changes in the most general way, we developed a grammar of functions that we call ‘Time Features’. When a simulation quantity, such as the position of a geometrical object, an angle, a magnetic field, a current, etc, takes its value from a Time Feature, that quantity varies over time. The operation of time-dependent simulation was separated into distinct parts: the Sequence samples time values either sequentially at equal increments or randomly from a uniform distribution (allowing quantities to vary continuously in time), and then each time-dependent quantity is calculated according to its Time Feature. Due to this modular structure, time-dependent simulations, even in the presence of multiple time-dependent quantities, can be efficiently performed in a single simulation with any given time resolution. This approach has been implemented in TOPAS (TOol for PArticle Simulation), designed to make Monte Carlo simulations with Geant4 more accessible to both clinical and research physicists. To demonstrate the method, three clinical situations were simulated: a variable water column used to verify constancy of the Bragg peak of the Crocker Lab eye treatment facility of the University of California, the double-scattering treatment mode of the passive beam scattering system at Massachusetts General Hospital (MGH), where a spinning range modulator wheel accompanied by beam current modulation produces a spread-out Bragg peak, and the scanning mode at MGH, where time-dependent pulse shape, energy distribution and magnetic fields control Bragg peak positions. Results confirm the clinical applicability of the method.

  11. A modular method to handle multiple time-dependent quantities in Monte Carlo simulations.

    PubMed

    Shin, J; Perl, J; Schümann, J; Paganetti, H; Faddegon, B A

    2012-06-01

    A general method for handling time-dependent quantities in Monte Carlo simulations was developed to make such simulations more accessible to the medical community for a wide range of applications in radiotherapy, including fluence and dose calculation. To describe time-dependent changes in the most general way, we developed a grammar of functions that we call 'Time Features'. When a simulation quantity, such as the position of a geometrical object, an angle, a magnetic field, a current, etc, takes its value from a Time Feature, that quantity varies over time. The operation of time-dependent simulation was separated into distinct parts: the Sequence samples time values either sequentially at equal increments or randomly from a uniform distribution (allowing quantities to vary continuously in time), and then each time-dependent quantity is calculated according to its Time Feature. Due to this modular structure, time-dependent simulations, even in the presence of multiple time-dependent quantities, can be efficiently performed in a single simulation with any given time resolution. This approach has been implemented in TOPAS (TOol for PArticle Simulation), designed to make Monte Carlo simulations with Geant4 more accessible to both clinical and research physicists. To demonstrate the method, three clinical situations were simulated: a variable water column used to verify constancy of the Bragg peak of the Crocker Lab eye treatment facility of the University of California, the double-scattering treatment mode of the passive beam scattering system at Massachusetts General Hospital (MGH), where a spinning range modulator wheel accompanied by beam current modulation produces a spread-out Bragg peak, and the scanning mode at MGH, where time-dependent pulse shape, energy distribution and magnetic fields control Bragg peak positions. Results confirm the clinical applicability of the method. PMID:22572201

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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.

  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. [Lysophosphatidic acid and human erythrocyte aggregation].

    PubMed

    Sheremet'ev, Iu A; Popovicheva, A N; Levin, G Ia

    2014-01-01

    The effects of lysophosphatidic acid on the morphology and aggregation of human erythrocytes has been studied. Morphology of erythrocytes and their aggregates were studied by light microscopy. It has been shown that lysophosphatidic acid changes the shape of red blood cells: diskocyte become echinocytes. Aggregation of red blood cells (rouleaux) was significantly reduced in autoplasma. At the same time there is a strong aggregation of echinocytes. This was accompanied by the formation of microvesicles. Adding normal plasma to echinocytes restores shape and aggregation of red blood cells consisting of "rouleaux". A possible mechanism of action of lysophosphatidic acid on erythrocytes is discussed. PMID:25509147

  1. 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…

  2. Time-domain simulation of nonlinear radiofrequency phenomena

    SciTech Connect

    Jenkins, Thomas G.; Austin, Travis M.; Smithe, David N.; Loverich, John; Hakim, Ammar H.

    2013-01-15

    Nonlinear effects associated with the physics of radiofrequency wave propagation through a plasma are investigated numerically in the time domain, using both fluid and particle-in-cell (PIC) methods. We find favorable comparisons between parametric decay instability scenarios observed on the Alcator C-MOD experiment [J. C. Rost, M. Porkolab, and R. L. Boivin, Phys. Plasmas 9, 1262 (2002)] and PIC models. The capability of fluid models to capture important nonlinear effects characteristic of wave-plasma interaction (frequency doubling, cyclotron resonant absorption) is also demonstrated.

  3. Multistep matrix integrators for real-time simulation

    NASA Technical Reports Server (NTRS)

    De Abreu-Garcia, J. A.; Hartley, T. T.

    1990-01-01

    An explicit linear multistep matrix-integration technique is presented for vector systems of ODEs which employs the stability region placement approach to permit the time-step to be chosen independently of system eigenvalues. Closed-form solutions for the general p-step method and the case where the system matrix has zero eigenvalues are given. It is shown that system mode shapes are preserved over the integration process, and that the technique remains applicable to systems with eigenvalues at their origin without need for computing a matrix inversion.

  4. Efficient simulation for fixed-receiver bistatic SAR with time and frequency synchronization errors

    NASA Astrophysics Data System (ADS)

    Yan, Feifei; Chang, Wenge; Li, Xiangyang

    2015-12-01

    Raw signal simulation is a useful tool for synthetic aperture radar (SAR) system design, mission planning, processing algorithm testing, and inversion algorithm design. Time and frequency synchronization is the key technique of bistatic SAR (BiSAR) system, and raw data simulation is an effective tool for verifying the time and frequency synchronization techniques. According to the two-dimensional (2-D) frequency spectrum of fixed-receiver BiSAR, a rapid raw data simulation approach with time and frequency synchronization errors is proposed in this paper. Through 2-D inverse Stolt transform in 2-D frequency domain and phase compensation in range-Doppler frequency domain, this method can significantly improve the efficiency of scene raw data simulation. Simulation results of point targets and extended scene are presented to validate the feasibility and efficiency of the proposed simulation approach.

  5. 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.

  6. 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.

  7. Ground target infrared signature model validation for real-time hardware-in-the-loop simulations

    NASA Astrophysics Data System (ADS)

    Sanders, Jeffrey S.; Rodgers, Jeremy B.; Siddique, Ahmed A.

    1998-07-01

    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 are the simulation hardware and software generating the correct output?' This paper deals primarily with the first level of target model validation.

  8. Dynamics across the morphological transition in two-dimensional aggregates

    NASA Astrophysics Data System (ADS)

    Bandi, Mahesh; Das, Tamoghna

    2015-03-01

    Microscopic dynamics of two-dimensional aggregates have been studied by analysing simulated particle trajectories generated by molecular dynamics. Tuning the competition between the short-range attraction and long-range repulsion in a particulate system at fixed temperature and density results in a continuous non-compact to compact morphological transition. The finite-size aggregates, obtained by very slow cooling, show long-time sub-diffusive behaviour irrespective of their morphologies. By analysing the relative displacement fluctuations of particles with respect to their nearest neighbours, non-compact aggregates can be attributed to bonding between particles while caging is found to be responsible for compact clusters. These dynamical mechanisms are further illustrated by the self-displacement fluctuation of particles which show a continuous change from power-law to exponential behaviour across the non-compact to compact transition. This work was supported by the OIST Graduate University with subsidy funding from the Cabinet Office, Government of Japan.

  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. 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.

  11. 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

  12. Time domain simulation and sound synthesis for the snare drum.

    PubMed

    Bilbao, Stefan

    2012-01-01

    The snare drum is a complex system, relying on the interaction of multiple components: the drumheads, or membranes, a set of snares, the surrounding acoustic field and an internal cavity. Because these components are multidimensional, and due to a strong distributed non-linearity (the snare interaction), many techniques used frequently in physical modeling synthesis applications, such as digital waveguides and modal methods are difficult to apply. In this article, finite difference time domain techniques are applied to a full 3D system, and various features of interest, such as the coupling between membranes, and the interaction between the membranes and the snares, are examined in detail. Also discussed are various numerical features, such as spurious splitting of degenerate modes and bandwidth limitation, and estimates of computational complexity are provided. Sound examples are presented. PMID:22280714

  13. 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.

  14. Operating system for a real-time multiprocessor propulsion system simulator

    NASA Technical Reports Server (NTRS)

    Cole, G. L.

    1984-01-01

    The success of the Real Time Multiprocessor Operating System (RTMPOS) in the development and evaluation of experimental hardware and software systems for real time interactive simulation of air breathing propulsion systems was evaluated. The Real Time Multiprocessor Operating System (RTMPOS) provides the user with a versatile, interactive means for loading, running, debugging and obtaining results from a multiprocessor based simulator. A front end processor (FEP) serves as the simulator controller and interface between the user and the simulator. These functions are facilitated by the RTMPOS which resides on the FEP. The RTMPOS acts in conjunction with the FEP's manufacturer supplied disk operating system that provides typical utilities like an assembler, linkage editor, text editor, file handling services, etc. Once a simulation is formulated, the RTMPOS provides for engineering level, run time operations such as loading, modifying and specifying computation flow of programs, simulator mode control, data handling and run time monitoring. Run time monitoring is a powerful feature of RTMPOS that allows the user to record all actions taken during a simulation session and to receive advisories from the simulator via the FEP. The RTMPOS is programmed mainly in PASCAL along with some assembly language routines. The RTMPOS software is easily modified to be applicable to hardware from different manufacturers.

  15. 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.

  16. 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

  17. 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

  18. 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.

  19. 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

  20. 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

  1. 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

  2. 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.

  3. A dimension map for molecular aggregates.

    PubMed

    Jian, Cuiying; Tang, Tian; Bhattacharjee, Subir

    2015-05-01

    A pair of gyradius ratios, defined from the principal radii of gyration, are used to generate a dimension map that describes the geometry of molecular aggregates in water and in organic solvents. Molecular dynamics simulations were performed on the aggregation of representative biomolecules and polyaromatic compounds to demonstrate application of the dimension map. It was shown that molecular aggregate data on the dimension map were bounded by two boundary curves, and that the map could be separated into three regions representing three groups of structures: one-dimensional rod-like structures; two-dimensional planar structures or short-cylinder-like structures; and three-dimensional sphere-like structures. Examining the location of the aggregates on the dimension map and how the location changes with solvent type and solute material parameter provides a simple yet effective way to infer the aggregation manner and to study solubility and mechanism of aggregation. PMID:25768393

  4. 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.

  5. 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.

  6. 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

  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. 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.

  9. 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.

  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. A Time-Dependent Simulation of the IBEX Ribbon at 1 AU

    NASA Astrophysics Data System (ADS)

    Zirnstein, E. J.; Heerikhuisen, J.; Pogorelov, N. V.

    2013-12-01

    The Interstellar Boundary Explorer (IBEX) measures fluxes of Hydrogen (H) energetic neutral atoms (ENAs) at 1 AU from every direction in space. IBEX is able to create all-sky flux maps as it spins on a Sun-pointing axis, continually producing results every 6 months since its launch in 2008. Over the course of its operation, measurements from IBEX have shown variations in flux over time. In light of these observations, we will present preliminary time-dependent simulations of H ENA fluxes measured at the IBEX spacecraft, focusing on flux from the ribbon. We use data from simulations of a time-dependent heliosphere as the "background" for our post-process flux simulations, where we include data collected from in situ measurements of the solar wind. We then simulate H ENA fluxes measured at the IBEX spacecraft by integrating backwards in time along H trajectories coinciding with IBEX lines-of-sight. We simulate the re-ionization times of pickup ions in the outer heliosheath, as well as the propagation times of ENAs as they travel back to 1 AU. We will present results simulated during various times of a solar cycle which may offer insights into time-dependent effects in past and future observations.

  12. 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.

  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. 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.

  15. 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.

  16. 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.

  17. 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

    1990-01-01

    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.

  18. 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.

  19. Operating system for a real-time multiprocessor propulsion system simulator. User's manual

    NASA Technical Reports Server (NTRS)

    Cole, G. L.

    1985-01-01

    The NASA Lewis Research Center is developing and evaluating experimental hardware and software systems to help meet future needs for real-time, high-fidelity simulations of air-breathing propulsion systems. Specifically, the real-time multiprocessor simulator project focuses on the use of multiple microprocessors to achieve the required computing speed and accuracy at relatively low cost. Operating systems for such hardware configurations are generally not available. A real time multiprocessor operating system (RTMPOS) that supports a variety of multiprocessor configurations was developed at Lewis. With some modification, RTMPOS can also support various microprocessors. RTMPOS, by means of menus and prompts, provides the user with a versatile, user-friendly environment for interactively loading, running, and obtaining results from a multiprocessor-based simulator. The menu functions are described and an example simulation session is included to demonstrate the steps required to go from the simulation loading phase to the execution phase.

  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. 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

  2. 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

  3. Stratification of colloidal aggregation coupled with sedimentation.

    PubMed

    González, Agustín E

    2006-12-01

    One of the consequences of sedimentation in colloidal aggregation is the stratification of the system in the sense that, after a sufficiently long elapsed time, the large clusters lie preferentially at the bottom zones of the confinement prism, and the structural and dynamical quantities describing the aggregates depend on the depth at which they are measured. A few years ago a computer simulation using particles for colloidal aggregation coupled with sedimentation was proposed by the author [A. E. González, Phys. Rev. Lett. 86, 1243 (2001)]. In that simulation, due to computational limitations, the mentioned quantities were averaged over all clusters in the prism, independently of the depth at which they were located, in order to have good statistics for the evaluation of the cluster fractal dimension and the cluster size distribution function. In this work we present a computer simulation using particles of colloidal aggregation coupled with sedimentation, for which the clusters in the simulation box represent those clusters inside a layer at a fixed depth and of arbitrary thickness in the prism. It would then be possible to compare the results with an eventual validation experiment, in which an aggregating sample is sipped out with a pipette at a fixed depth in the prism and subjected to further studies, or with a light scattering study in which the laser beam is focused at a fixed depth in the system. We confirm the acceleration of the aggregation rate, followed by a slowing down, compared with an aggregating system driven purely by diffusion (DLCA). In the present system, the large clusters when drifting downwards sweep smaller ones, which in turn occlude the holes and cavities of these large clusters, increasing in this way their compacticity. We also confirm that (i) in some cases of sedimentation strengths and layer depths, the mean width (perpendicular to the gravitational field direction) and the mean height of the large settling clusters scale with the

  4. 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

  5. Performance evaluation using SYSTID time domain simulation. [computer-aid design and analysis for communication systems

    NASA Technical Reports Server (NTRS)

    Tranter, W. H.; Ziemer, R. E.; Fashano, M. J.

    1975-01-01

    This paper reviews the SYSTID technique for performance evaluation of communication systems using time-domain computer simulation. An example program illustrates the language. The inclusion of both Gaussian and impulse noise models make accurate simulation possible in a wide variety of environments. A very flexible postprocessor makes possible accurate and efficient performance evaluation.

  6. 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.

  7. 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.

  8. Theoretical and Numerical Properties of a Gyrokinetic Plasma: Issues Related to Transport Time Scale Simulation

    SciTech Connect

    W.W. Lee

    2003-09-17

    Particle simulation has played an important role for the recent investigations on turbulence in magnetically confined plasmas. In this paper, theoretical and numerical properties of a gyrokinetic plasma as well as its relationship with magnetohydrodynamics (MHD) are discussed with the ultimate aim of simulating microturbulence in transport time scale using massively parallel computers.

  9. Experimental Simulation of "Future Shock" to Explore Time Perspectives Under Different Rates of Change.

    ERIC Educational Resources Information Center

    Plummer, Charles M.

    A simulated micro-society simulation/game was applied as an experimental treatment to compare the impact of high and low rate of change social environments upon individual's time perspectives. Subjects were 187 university undergraduate and graduate students who completed the covariate "Social Readjustment Rating Scale" and then were randomly…

  10. Cellular pattern formation during Dictyostelium aggregation

    NASA Astrophysics Data System (ADS)

    Höfer, Thomas; Sherratt, Jonathan A.; Maini, Philip K.

    The development of multicellularity in the life cycle of Dictyostelium discoideum provides a paradigm model system for biological pattern formation. Previously, mathematical models have shown how a collective pattern of cell communication by waves of the messenger molecule cyclic adenosine 3‧5‧-monophosphate (cAMP) arises from excitable local cAMP kinetics and cAMP diffusion. Here we derive a model of the actual cell aggregation process by considering the chemotactic cell response to cAMP and its interplay with the cAMP dynamics. Cell density, which previously has been treated as a spatially homogeneous parameter, is a crucial variable of the aggregation model. We find that the coupled dynamics of cell chemotaxis and cAMP reaction-diffusion lead to the break-up of the initially uniform cell layer and to the formation of the striking cell stream morphology which characterizes the aggregation process in situ. By a combination of stability analysis and two-dimensional simulations of the model equations, we show cell streaming to be the consequence of the growth of a small-amplitude pattern in cell density forced by the large-amplitude cAMP waves, thus representing a novel scenario of spatial patterning in a cell chemotaxis system. The instability mechanism is further analysed by means of an analytic caricature of the model, and the condition for chemotaxis-driven instability is found to be very similar to the one obtained for the standard (non-oscillatory) Keller-Segel system. The growing cell stream pattern feeds back into the cAMP dynamics, which can explain in some detail experimental observations on the time evolution of the cAMP wave pattern, and suggests the characterization of the Dictyostelium aggregation field as a self-organized excitable medium.

  11. 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.

  12. 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.

  13. Towards a Dynamical Collision Model of Highly Porous Dust Aggregates

    NASA Astrophysics Data System (ADS)

    Güttler, Carsten; Krause, Maya; Geretshauser, Ralf; Speith, Roland; Blum, Jürgen

    2009-06-01

    In the recent years we have performed various experiments on the collision dynamics of highly porous dust aggregates and although we now have a comprehensive picture of the micromechanics of those aggregates, the macroscopic understanding is still lacking. We are therefore developing a mechanical model to describe dust aggregate collisions with macroscopic parameters like tensile strength, compressive strength and shear strength. For one well defined dust sample material, the tensile and compressive strength were measured in a static experiment and implemented in a Smoothed Particle Hydrodynamics (SPH) code. A laboratory experiment was designed to compare the laboratory results with the results of the SPH simulation. In this experiment, a mm-sized glass bead is dropped into a cm-sized dust aggregate with the previously measured strength parameters. We determine the deceleration of the glass bead by high-speed imaging and the compression of the dust aggregate by x-ray micro-tomography. The measured penetration depth, stopping time and compaction under the glass bead are utilized to calibrate and test the SPH code. We find that the statically measured compressive strength curve is only applicable if we adjust it to the dynamic situation with a ``softness'' parameter. After determining this parameter, the SPH code is capable of reproducing experimental results, which have not been used for the calibration before.

  14. Validation of a real-time engineering simulation of the UH-60A helicopter

    NASA Technical Reports Server (NTRS)

    Ballin, Mark G.

    1987-01-01

    A real-time simulation of the UH-60A Black Hawk Helicopter based on the Sikorsky Gen Hel mathematical model is compared with flight test data and Sikorsky's nonreal-time computer program. An overview of the mathematical model is given, including a description of updates and expansion of the model by NASA. Also, real-time programming requirements and techniques are explained. The simulation displays very good agreement with flight test data and excellent with the nonreal-time program on which it is based. The large dedication of effort required to develop the real-time program suggests a need for development of generalized techniques for real-time simulation of high-fidelity physical models of rotorcraft.

  15. 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.

  16. Piloted simulation of an algorithm for onboard control of time-optimal intercept

    NASA Technical Reports Server (NTRS)

    Price, D. B.; Calise, A. J.; Moerder, D. D.

    1985-01-01

    A piloted simulation of algorithms for onboard computation of trajectories for time-optimal intercept of a moving target by an F-8 aircraft is described. The algorithms, use singular perturbation techniques, generate commands in the cockpit. By centering the horizontal and vertical needles, the pilot flies an approximation to a time-optimal intercept trajectory. Example simulations are shown and statistical data on the pilot's performance when presented with different display and computation modes are described.

  17. 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 joint simulation was carried out using a piloted simulator and an advanced-concept air traffic control simulation to study the acceptability and accuracy of the ground-based four-dimensional descent advisor (DA), an automation aid based on accurate models of aircraft performance and weather conditions. 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 plus or minus 20 s at the metering fix. An analysis of errors generated in turns resulted in a further enhancement of the DA algorithm.

  18. 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.

  19. Ensemble Sampling vs. Time Sampling in Molecular Dynamics Simulations of Thermal Conductivity

    DOE PAGESBeta

    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

  20. 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.

  1. Platelet aggregation test

    MedlinePlus

    ... this page: //medlineplus.gov/ency/article/003669.htm Platelet aggregation test To use the sharing features on this page, please enable JavaScript. The platelet aggregation blood test checks how well platelets , a ...

  2. Platelet aggregation test

    MedlinePlus

    The platelet aggregation blood test checks how well platelets , a part of blood, clump together and cause blood to clot. ... Decreased platelet aggregation may be due to: Autoimmune ... Fibrin degradation products Inherited platelet function defects ...

  3. SAR image simulation in the time domain for moving ocean surfaces.

    PubMed

    Yoshida, Takero; Rheem, Chang-Kyu

    2013-01-01

    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. PMID:23549367

  4. Wavelet-based surrogate time series for multiscale simulation of heterogeneous catalysis

    DOE PAGESBeta

    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

  5. 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.

  6. 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

  7. Application of special-purpose digital computers to rotorcraft real-time simulation

    NASA Technical Reports Server (NTRS)

    Mackie, D. B.; Michelson, S.

    1978-01-01

    The use of an array processor as a computational element in rotorcraft real-time simulation is studied. A multilooping scheme was considered in which the rotor would loop over its calculations a number of time while the remainder of the model cycled once on a host computer. To prove that such a method would realistically simulate rotorcraft, a FORTRAN program was constructed to emulate a typical host-array processor computing configuration. The multilooping of an expanded rotor model, which included appropriate kinematic equations, resulted in an accurate and stable simulation.

  8. 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.

  9. 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

  10. A Lagrangian scheme for time-dependent ionization in simulations of astrophysical plasmas

    NASA Astrophysics Data System (ADS)

    Shen, C.; Raymond, J. C.; Murphy, N. A.; Lin, J.

    2015-09-01

    Time-dependent ionization is important in astrophysical environments where the thermodynamical time scale is shorter than the ionization or recombination time scales. In this work, we report a FORTRAN program that performs fast non-equilibrium ionization calculations in post-processing based on hydrodynamics(HD) or magnetohydrodynamics(MHD) simulation results. Using HD or MHD simulation results, we track the movement of plasma in a Lagrangian framework, and obtain the evolutionary history of temperature and electron density. The time-dependent ionization equations are then solved by the Eigenvalue method. For any complex temperature and electron density histories, we introduce an adaptive time-step strategy to improve the computational efficiency. Our tests show that this program has advantages of high numerical stability and high accuracy. In addition, it is also easy to extend this solver to other HD and MHD simulations. This code is freely available for download from the Web.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. Towards Reconfigurable, Separable and Hard Real-Time Hybrid Simulation and Test Systems

    NASA Astrophysics Data System (ADS)

    Quartier, F.; Delatte, B.; Joubert, M.

    2009-05-01

    Formation flight needs several new technologies, new disciplines, new approaches and above all, more concurrent engineering by more players. One of the problems to be addressed are more complex simulation and test systems that are easy to re-configure to include parts of the target hardware and that can provide sufficient power to handle simulation cores that are requiring one to two orders of magnitude more processing power than the current technology provides. Critical technologies that are already addressed by CNES and Spacebel are study model reuse and simulator reconfigurability (Basiles), model portability (SMP2) and the federation of several simulators using HLA. Two more critical issues are addressed in ongoing R&D work by CNES and Spacebel and are covered by this paper and concern the time engineering and management. The first issue concerns separability (characterisation, identification and handling of separable subsystems) and the consequences on practical systems. Experiments on the Pleiades operational simulator have shown that adding precise simulation of instruments such as Doris and the Star Tracker can be added without significantly impacting overall performance. Improved time analysis leads to better system understanding and testability. The second issue concerns architectures for distributed hybrid simulators systems that provide hard real-time capabilities and can react with a relative time precision and jitter that is in the 10 to 50 µsecond range using mainstream PC's and mainstream Operating Systems. This opens a way to make smaller economic hardware test systems that can be reconfigured to make large hardware test systems without restarting development. Although such systems were considered next to impossible till now, distributed hard real-time systems are getting in reach when modern but mainstream electronics are used and when processor cores can be isolated and reserved for real-time cores. This requires a complete rethinking of the

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. Information and Complexity Measures Applied to Observed and Simulated Soil Moisture Time Series

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Time series of soil moisture-related parameters provides important insights in functioning of soil water systems. Analysis of patterns within these time series has been used in several studies. The objective of this work was to compare patterns in observed and simulated soil moisture contents to u...

  2. Predicting the timing properties of phosphor-coated scintillators using Monte Carlo light transport simulation.

    PubMed

    Roncali, Emilie; Schmall, Jeffrey P; Viswanath, Varsha; Berg, Eric; Cherry, Simon R

    2014-04-21

    Current developments in positron emission tomography focus on improving timing performance for scanners with time-of-flight (TOF) capability, and incorporating depth-of-interaction (DOI) information. Recent studies have shown that incorporating DOI correction in TOF detectors can improve timing resolution, and that DOI also becomes more important in long axial field-of-view scanners. We have previously reported the development of DOI-encoding detectors using phosphor-coated scintillation crystals; here we study the timing properties of those crystals to assess the feasibility of providing some level of DOI information without significantly degrading the timing performance. We used Monte Carlo simulations to provide a detailed understanding of light transport in phosphor-coated crystals which cannot be fully characterized experimentally. Our simulations used a custom reflectance model based on 3D crystal surface measurements. Lutetium oxyorthosilicate crystals were simulated with a phosphor coating in contact with the scintillator surfaces and an external diffuse reflector (teflon). Light output, energy resolution, and pulse shape showed excellent agreement with experimental data obtained on 3 × 3 × 10 mm³ crystals coupled to a photomultiplier tube. Scintillator intrinsic timing resolution was simulated with head-on and side-on configurations, confirming the trends observed experimentally. These results indicate that the model may be used to predict timing properties in phosphor-coated crystals and guide the coating for optimal DOI resolution/timing performance trade-off for a given crystal geometry. Simulation data suggested that a time stamp generated from early photoelectrons minimizes degradation of the timing resolution, thus making this method potentially more useful for TOF-DOI detectors than our initial experiments suggested. Finally, this approach could easily be extended to the study of timing properties in other scintillation crystals, with a range of

  3. 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.

  4. Three axis electronic flight motion simulator real time control system design and implementation

    NASA Astrophysics Data System (ADS)

    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.

  5. 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.

  6. 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

  7. Real Time Sound Field Simulator Using Field Programmable Gate Array Device

    NASA Astrophysics Data System (ADS)

    Tsuchiya, T.; Sugawara, E.; Inoguchi, Y.

    Possibility of real time simulator of three-dimensional acoustic field in the time domain is discussed. Based on the discrete Huygens' model (DHM), a digital equivalent circuit is developed. DHM elements are described by hardware description language (HDL) in the fixed-point arithmetic. It is estimated that the real time simulation of 1 m3 sound field is possible using ten-odd FPGA chips, while the CPU speed of 52 TFLOPS is required using the high performance computer. It is shown that data length of 28 bits is required for the practical accuracy. Based on FPGA-DHM, the real time simulator named "Silicon Concert Hall" may come true in the near future.

  8. 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

  9. Simulating GPS radio signal to synchronize network--a new technique for redundant timing.

    PubMed

    Shan, Qingxiao; Jun, Yang; Le Floch, Jean-Michel; Fan, Yaohui; Ivanov, Eugene N; Tobar, Michael E

    2014-07-01

    Currently, many distributed systems such as 3G mobile communications and power systems are time synchronized with a Global Positioning System (GPS) signal. If there is a GPS failure, it is difficult to realize redundant timing, and thus time-synchronized devices may fail. In this work, we develop time transfer by simulating GPS signals, which promises no extra modification to original GPS-synchronized devices. This is achieved by applying a simplified GPS simulator for synchronization purposes only. Navigation data are calculated based on a pre-assigned time at a fixed position. Pseudo-range data which describes the distance change between the space vehicle (SV) and users are calculated. Because real-time simulation requires heavy-duty computations, we use self-developed software optimized on a PC to generate data, and save the data onto memory disks while the simulator is operating. The radio signal generation is similar to the SV at an initial position, and the frequency synthesis of the simulator is locked to a pre-assigned time. A filtering group technique is used to simulate the signal transmission delay corresponding to the SV displacement. Each SV generates a digital baseband signal, where a unique identifying code is added to the signal and up-converted to generate the output radio signal at the centered frequency of 1575.42 MHz (L1 band). A prototype with a field-programmable gate array (FPGA) has been built and experiments have been conducted to prove that we can realize time transfer. The prototype has been applied to the CDMA network for a three-month long experiment. Its precision has been verified and can meet the requirements of most telecommunication systems. PMID:24960698

  10. A competitive aggregation model for flash nanoprecipitation.

    PubMed

    Cheng, Janine Chungyin; Vigil, R D; Fox, R O

    2010-11-15

    Flash NanoPrecipitation (FNP) is a novel approach for producing functional nanoparticles stabilized by amphiphilic block copolymers. FNP involves the rapid mixing of a hydrophobic active (organic) and an amphiphilic di-block copolymer with a non-solvent (water) and subsequent co-precipitation of nanoparticles composed of both the organic and copolymer. During this process, the particle size distribution (PSD) is frozen and stabilized by the hydrophilic portion of the amphiphilic di-block copolymer residing on the particle surface. That is, the particle growth is kinetically arrested and thus a narrow PSD can be attained. To model the co-precipitation process, a bivariate population balance equation (PBE) has been formulated to account for the competitive aggregation of the organic and copolymer versus pure organic-organic or copolymer-copolymer aggregation. Aggregation rate kernels have been derived to account for the major aggregation events: free coupling, unimer insertion, and aggregate fusion. The resulting PBE is solved both by direct integration and by using the conditional quadrature method of moments (CQMOM). By solving the competitive aggregation model under well-mixed conditions, it is demonstrated that the PSD is controlled primarily by the copolymer-copolymer aggregation process and that the energy barrier to aggregate fusion plays a key role in determining the PSD. It is also shown that the characteristic aggregation times are smaller than the turbulent mixing time so that the FNP process is always mixing limited. PMID:20800847

  11. A Preliminary Real-Time and Realistic Simulation Environment for Percutaneous Coronary Intervention

    PubMed Central

    Wu, Jianhuang; Wang, Haoyu; Zhang, Peng; Ma, Xin

    2015-01-01

    Percutaneous coronary intervention (PCI) is a minimally invasive surgery procedure that is widely used in the treatment of coronary artery disease. This procedure requires interventional cardiologists to have high proficiency and therefore demands an extensive training period in order to ensure successful surgical outcome. In this paper, a realistic and real-time interactive simulator for training PCI procedure is presented. A set of new approaches for core simulation components is devised and integrated into the simulator. Trainees can interact with the virtual simulation environment with real instruments and essential maneuvers encountered in real PCI procedure. Although presently targeted at PCI, our simulator could be easily extended to mimic the necessities of any vascular interventional radiology procedures by updating vascular anatomy. Preliminary validation of the proposed physical model of instruments is conducted on vascular phantom to demonstrate its performance and effectiveness. PMID:25879018

  12. A preliminary real-time and realistic simulation environment for percutaneous coronary intervention.

    PubMed

    Wu, Jianhuang; Wang, Haoyu; Zhang, Peng; Ma, Xin; Hu, Qingmao

    2015-01-01

    Percutaneous coronary intervention (PCI) is a minimally invasive surgery procedure that is widely used in the treatment of coronary artery disease. This procedure requires interventional cardiologists to have high proficiency and therefore demands an extensive training period in order to ensure successful surgical outcome. In this paper, a realistic and real-time interactive simulator for training PCI procedure is presented. A set of new approaches for core simulation components is devised and integrated into the simulator. Trainees can interact with the virtual simulation environment with real instruments and essential maneuvers encountered in real PCI procedure. Although presently targeted at PCI, our simulator could be easily extended to mimic the necessities of any vascular interventional radiology procedures by updating vascular anatomy. Preliminary validation of the proposed physical model of instruments is conducted on vascular phantom to demonstrate its performance and effectiveness. PMID:25879018

  13. 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.

  14. Empirical development of parallelization guidelines for time-driven simulation. Master's thesis

    SciTech Connect

    Huson, M.L.

    1989-12-01

    Distributed simulation is an area of research which offers great promise for speeding up simulations. Program parallelization is usually an iterative process requiring several attempts to produce an efficient parallel implementation of a sequential program. This is due to the lack of any standards or guidelines for program parallelization. In this research effort a Ballistic Missile Defense (BMD) time-driven simulation program, developed by DESE Research and Engineering, was used as a test vehicle for investigating parallelization options for distributed and shared memory architectures. Implementations were developed to address issues of functional versus data program decomposition, computation versus communications overhead, and shared versus distributed memory architectures. Performance data collected from each implementation was used to develop guidelines for implementing parallel versions of sequential time-driven simulations. These guidelines were based on the relative performance of the various implementations and on general observations made during the course of the research.

  15. Real-time TDDFT simulations of time-resolved core-level spectroscopies in solid state systems

    NASA Astrophysics Data System (ADS)

    Pemmaraju, Sri Chaitanya Das; Prendergast, David; Theory of Nanostructured Materials Facility Team

    The advent of sub-femtosecond time-resolved core-level spectroscopies based on high harmonic generated XUV pulses has enabled the study of electron dyanamics on characteristic femtosecond time-scales. Unambiguous interpretation of these powerful yet complex spectroscopies however requires the development of theoretical algorithms capable of modeling light-matter interaction across a wide energy range spanning both valence and core orbitals. In this context we present a recent implementation of the velocity-gauge formalism of real-time TDDFT within a linear combination of atomic orbital (LCAO) framework, which facilitates efficient numerical treatment of localized semi-core orbitals. Dynamics and spectra obtained from LCAO based simulations are compared to those from a real-space grid implementation. Potential applications are also illustrated by applying the method towards interpreting recent atto-second time-resolved IR-pump XUV-probe spectroscopies investigating sub-cycle excitation dynamics in bulk silicon.

  16. Finite time step and spatial grid effects in δf simulation of warm plasmas

    NASA Astrophysics Data System (ADS)

    Sturdevant, Benjamin J.; Parker, Scott E.

    2016-01-01

    This paper introduces a technique for analyzing time integration methods used with the particle weight equations in δf method particle-in-cell (PIC) schemes. The analysis applies to the simulation of warm, uniform, periodic or infinite plasmas in the linear regime and considers the collective behavior similar to the analysis performed by Langdon for full-f PIC schemes [1,2]. We perform both a time integration analysis and spatial grid analysis for a kinetic ion, adiabatic electron model of ion acoustic waves. An implicit time integration scheme is studied in detail for δf simulations using our weight equation analysis and for full-f simulations using the method of Langdon. It is found that the δf method exhibits a CFL-like stability condition for low temperature ions, which is independent of the parameter characterizing the implicitness of the scheme. The accuracy of the real frequency and damping rate due to the discrete time and spatial schemes is also derived using a perturbative method. The theoretical analysis of numerical error presented here may be useful for the verification of simulations and for providing intuition for the design of new implicit time integration schemes for the δf method, as well as understanding differences between δf and full-f approaches to plasma simulation.

  17. 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.

  18. Advanced time integration algorithms for dislocation dynamics simulations of work hardening

    DOE PAGESBeta

    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

  19. 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.

  20. Evaporation effects in elastocapillary aggregation

    NASA Astrophysics Data System (ADS)

    Vella, Dominic; Hadjittofis, Andreas; Singh, Kiran; Lister, John

    2015-11-01

    We consider the effect of evaporation on the aggregation of a number of elastic objects due to a liquid's surface tension. In particular, we consider an array of spring-block elements in which the gaps between blocks are filled by thin liquid films that evaporate during the course of an experiment. Using lubrication theory to account for the fluid flow within the gaps, we study the dynamics of aggregation. We find that a non-zero evaporation rate causes the elements to aggregate more quickly and, indeed, to contact within finite time. However, we also show that the number of elements within each cluster decreases as the evaporation rate increases. We explain these results quantitatively by comparison with the corresponding two-body problem and discuss their relevance for controlling pattern formation in carbon nanotube forests.

  1. 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

  2. A simulation model of time-dependent plasma-spacecraft interactions

    NASA Technical Reports Server (NTRS)

    Rothwell, P. L.; Rubin, A. G.; Yates, G. K.

    1977-01-01

    A plasma simulation code is presented that models the time-dependent plasma properties in the vicinity of a spherical, charged spacecraft. After showing agreement with analytic, steady-state theories and ATS-6 satellite data, the following three problems are treated: (1) transient pulses from photoemission at various emission temperatures and ambient plasma conditions, (2) spacecharge limited emission, and (3) simulated plasma oscillations in the long wavelength limit.

  3. 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

  4. On the time-dependent resonant width for Landau damping: theory and PIC simulation

    NASA Astrophysics Data System (ADS)

    Grismayer, T.; Fahlen, J. E.; Decyk, V. K.; Mori, W. B.

    2011-07-01

    We use electrostatic partice-in-cell (PIC) simulations and theory to study the damping of 1D plasma waves. We consider the linear regime where the asymptotic damping rate is much bigger than the bounce frequency. In this regime the waves are typically very small and often below the thermal noise in simulations and experiments. These waves can be studied using a subtraction technique in which two simulations with identical random number generation seeds are carried out. In the first, a small amplitude wave is excited. In the second simulation no wave is excited. The results from each simulation are subtracted providing a clean linear wave that can be studied. Since the Landau derivation does not provide a description of damping in terms of individual particle trajectories, we analyze Landau damping using a Lagrangian approach based on energy conservation and the linearized particle trajectories. This method provides a time-dependent resonance curve and the energy transfer of the particles in the damping process. The time-dependent resonant width measured in the simulations is compared with the theoretical prediction. Simulations in which particles within the resonance width are removed are also presented.

  5. Strong field ionization rates simulated with time-dependent configuration interaction and an absorbing potential

    SciTech Connect

    Krause, Pascal; Sonk, Jason A.; Schlegel, H. Bernhard

    2014-05-07

    Ionization rates of molecules have been modeled with time-dependent configuration interaction simulations using atom centered basis sets and a complex absorbing potential. The simulations agree with accurate grid-based calculations for the ionization of hydrogen atom as a function of field strength and for charge resonance enhanced ionization of H{sub 2}{sup +} as the bond is elongated. Unlike grid-based methods, the present approach can be applied to simulate electron dynamics and ionization in multi-electron polyatomic molecules. Calculations on HCl{sup +} and HCO{sup +} demonstrate that these systems also show charge resonance enhanced ionization as the bonds are stretched.

  6. 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.

  7. Real-time simulation of an F110/STOVL turbofan engine

    NASA Technical Reports Server (NTRS)

    Drummond, Colin K.; Ouzts, Peter J.

    1989-01-01

    A traditional F110-type turbofan engine model was extended to include a ventral nozzle and two thrust-augmenting ejectors for Short Take-Off Vertical Landing (STOVL) aircraft applications. Development of the real-time F110/STOVL simulation required special attention to the modeling approach to component performance maps, the low pressure turbine exit mixing region, and the tailpipe dynamic approximation. Simulation validation derives by comparing output from the ADSIM simulation with the output for a validated F110/STOVL General Electric Aircraft Engines FORTRAN deck. General Electric substantiated basic engine component characteristics through factory testing and full scale ejector data.

  8. 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.

  9. 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.

  10. SIMULINK as a development tool for real-time simulators: the ATV test facilities experience

    NASA Astrophysics Data System (ADS)

    Mauro, Marco; Bianco, Franca; Leorato, Cristiano; Segneri, Daniele; Bodemann, Christian D.; de Luca, Antonio; Guillard, Vincent

    2002-07-01

    The aim of this paper is to present the advancement of the Matlab/SIMULINK based simulator of the ATV (Automated Transfer Vehicle) project. The ATV (Automated Transfer Vehicle) program was started by ESA in 1995. The complexity of the missions and the costs involved imply the development of a complete simulator. The simulator is composed of many models, all of them running under Eurosim. It is developed on a different platform than the models and its main characteristics are that it is real time and have to support hardware in the loop. The development of each numerical model follows the same pattern: - Technical Requirement Specification - Architectural Design Phase - Implementation Phase - Model Validation - Simulator Integration and Validation. In order to fulfil these different steps, various tools have to be used: SIMULINK is used during the specification and design phases of the numerical models, the coding phase and during the models validation phases on host machine. Real Time Workshop is used for generating ANSI C code and Mosaic is used during the integration of the models into EUROSIM. EUROSIM is used for the design of the simulator, for the real time integration of the numerical models and finally for the validation of the overall simulation software. Some key points can be highlighted in the development, the testing and the integration; they will be developed further in the paper together with project management and team organization aspects.

  11. On the synthesis of sample volumes for real-time spectral Doppler ultrasound simulation.

    PubMed

    Aguilar, Luis A; Steinman, David A; Cobbold, Richard S C

    2010-12-01

    A variety of methods for simulating the ultrasound field produced by transducers are currently used in ultrasound imaging system design. However, simulations can be time-consuming, making them difficult to apply in real-time environments when the observation field changes rapidly with time. This is particularly true for interactive real-time Doppler and B-mode ultrasound simulators designed for use as training tools. In this paper, it is demonstrated that the use of a distribution of monopole sources can be used to simulate the field from a phased linear array and the accuracy should be sufficient for simulating pulsed spectral Doppler. Very good agreement can be achieved in comparison with that obtained by a more exact method and, because of the simplicity of the calculations, real-time simulations of flow in the arterial system becomes possible. Specifically, quantitative measurements were made and compared against an analytic solution for the case of a piston transducer and against Field II for the phased array. The root-mean-square error shows that it is possible to achieve 10% or less error for the latter case. For comparable conditions, the computational speed for the transmit field of phased array using the Field II method as compared with the monopole approach was found to be at least an order of magnitude faster. It is pointed out that the simplicity of the monopole approach provides the opportunity for a further order of magnitude gain. Our findings can have direct application on the simulation of spectral Doppler and other ultrasound techniques for the purpose of teaching and training. PMID:20950935

  12. Simulation of Rate-Related (Dead-Time) Losses In Passive Neutron Multiplicity Counting Systems

    SciTech Connect

    Evans, L.G.; Norman, P.I.; Leadbeater, T.W.; Croft, S.; Philips, S.

    2008-07-01

    Passive Neutron Multiplicity Counting (PNMC) based on Multiplicity Shift Register (MSR) electronics (a form of time correlation analysis) is a widely used non-destructive assay technique for quantifying spontaneously fissile materials such as Pu. At high event rates, dead-time losses perturb the count rates with the Singles, Doubles and Triples being increasingly affected. Without correction these perturbations are a major source of inaccuracy in the measured count rates and assay values derived from them. This paper presents the simulation of dead-time losses and investigates the effect of applying different dead-time models on the observed MSR data. Monte Carlo methods have been used to simulate neutron pulse trains for a variety of source intensities and with ideal detection geometry, providing an event by event record of the time distribution of neutron captures within the detection system. The action of the MSR electronics was modelled in software to analyse these pulse trains. Stored pulse trains were perturbed in software to apply the effects of dead-time according to the chosen physical process; for example, the ideal paralysable (extending) and non-paralysable models with an arbitrary dead-time parameter. Results of the simulations demonstrate the change in the observed MSR data when the system dead-time parameter is varied. In addition, the paralysable and non-paralysable models of deadtime are compared. These results form part of a larger study to evaluate existing dead-time corrections and to extend their application to correlated sources. (authors)

  13. Run-time interoperability between neuronal network simulators based on the MUSIC framework.

    PubMed

    Djurfeldt, Mikael; Hjorth, Johannes; Eppler, Jochen M; Dudani, Niraj; Helias, Moritz; Potjans, Tobias C; Bhalla, Upinder S; Diesmann, Markus; Kotaleski, Jeanette Hellgren; Ekeberg, Orjan

    2010-03-01

    MUSIC is a standard API allowing large scale neuron simulators to exchange data within a parallel computer during runtime. A pilot implementation of this API has been released as open source. We provide experiences from the implementation of MUSIC interfaces for two neuronal network simulators of different kinds, NEST and MOOSE. A multi-simulation of a cortico-striatal network model involving both simulators is performed, demonstrating how MUSIC can promote inter-operability between models written for different simulators and how these can be re-used to build a larger model system. Benchmarks show that the MUSIC pilot implementation provides efficient data transfer in a cluster computer with good scaling. We conclude that MUSIC fulfills the design goal that it should be simple to adapt existing simulators to use MUSIC. In addition, since the MUSIC API enforces independence of the applications, the multi-simulation could be built from pluggable component modules without adaptation of the components to each other in terms of simulation time-step or topology of connections between the modules. PMID:20195795

  14. 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.

  15. Investigation of Asymmetric Thrust Detection with Demonstration in a Real-Time Simulation Testbed

    NASA Technical Reports Server (NTRS)

    Rinehart, Aidan W.; Simon, Donald L.; Chicatelli, Amy; Sowers, Shane

    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.

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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.