Mechanisms of electron acceptor utilization: Implications for simulating anaerobic biodegradation

USGS Publications Warehouse

Schreiber, M.E.; Carey, G.R.; Feinstein, D.T.; Bahr, J.M.

2004-01-01

Simulation of biodegradation reactions within a reactive transport framework requires information on mechanisms of terminal electron acceptor processes (TEAPs). In initial modeling efforts, TEAPs were approximated as occurring sequentially, with the highest energy-yielding electron acceptors (e.g. oxygen) consumed before those that yield less energy (e.g., sulfate). Within this framework in a steady state plume, sequential electron acceptor utilization would theoretically produce methane at an organic-rich source and Fe(II) further downgradient, resulting in a limited zone of Fe(II) and methane overlap. However, contaminant plumes often display much more extensive zones of overlapping Fe(II) and methane. The extensive overlap could be caused by several abiotic and biotic processes including vertical mixing of byproducts in long-screened monitoring wells, adsorption of Fe(II) onto aquifer solids, or microscale heterogeneity in Fe(III) concentrations. Alternatively, the overlap could be due to simultaneous utilization of terminal electron acceptors. Because biodegradation rates are controlled by TEAPs, evaluating the mechanisms of electron acceptor utilization is critical for improving prediction of contaminant mass losses due to biodegradation. Using BioRedox-MT3DMS, a three-dimensional, multi-species reactive transport code, we simulated the current configurations of a BTEX plume and TEAP zones at a petroleum- contaminated field site in Wisconsin. Simulation results suggest that BTEX mass loss due to biodegradation is greatest under oxygen-reducing conditions, with smaller but similar contributions to mass loss from biodegradation under Fe(III)-reducing, sulfate-reducing, and methanogenic conditions. Results of sensitivity calculations document that BTEX losses due to biodegradation are most sensitive to the age of the plume, while the shape of the BTEX plume is most sensitive to effective porosity and rate constants for biodegradation under Fe(III)-reducing and methanogenic conditions. Using this transport model, we had limited success in simulating overlap of redox products using reasonable ranges of parameters within a strictly sequential electron acceptor utilization framework. Simulation results indicate that overlap of redox products cannot be accurately simulated using the constructed model, suggesting either that Fe(III) reduction and methanogenesis are occurring simultaneously in the source area, or that heterogeneities in Fe(III) concentration and/or mineral type cause the observed overlap. Additional field, experimental, and modeling studies will be needed to address these questions. ?? 2004 Elsevier B.V. All rights reserved.

Effect of Accessory Power Take-off Variation on a Turbofan Engine Performance

DTIC Science & Technology

2012-09-26

amount of energy from the low pressure spool shaft. A high bypass turbofan engine was modeled using the Numerical Propulsion System Simulation ( NPSS ...4 II.2 Power Extraction Techniques ..........................................................................8 II.3 NPSS ...Methodology and Simulation Setup ...........................................................................25 III.1 Engine NPSS Model

Storm Water Management Model Reference Manual Volume III – Water Quality

EPA Science Inventory

SWMM is a dynamic rainfall-runoff simulation model used for single event or long-term (continuous) simulation of runoff quantity and quality from primarily urban areas. The runoff component of SWMM operates on a collection of subcatchment areas that receive precipitation and gene...

Self-consistent semi-analytic models of the first stars

NASA Astrophysics Data System (ADS)

Visbal, Eli; Haiman, Zoltán; Bryan, Greg L.

2018-04-01

We have developed a semi-analytic framework to model the large-scale evolution of the first Population III (Pop III) stars and the transition to metal-enriched star formation. Our model follows dark matter haloes from cosmological N-body simulations, utilizing their individual merger histories and three-dimensional positions, and applies physically motivated prescriptions for star formation and feedback from Lyman-Werner (LW) radiation, hydrogen ionizing radiation, and external metal enrichment due to supernovae winds. This method is intended to complement analytic studies, which do not include clustering or individual merger histories, and hydrodynamical cosmological simulations, which include detailed physics, but are computationally expensive and have limited dynamic range. Utilizing this technique, we compute the cumulative Pop III and metal-enriched star formation rate density (SFRD) as a function of redshift at z ≥ 20. We find that varying the model parameters leads to significant qualitative changes in the global star formation history. The Pop III star formation efficiency and the delay time between Pop III and subsequent metal-enriched star formation are found to have the largest impact. The effect of clustering (i.e. including the three-dimensional positions of individual haloes) on various feedback mechanisms is also investigated. The impact of clustering on LW and ionization feedback is found to be relatively mild in our fiducial model, but can be larger if external metal enrichment can promote metal-enriched star formation over large distances.

3D Modeling of Forbidden Line Emission in the Binary Wind Interaction Region of Eta Carinae

NASA Technical Reports Server (NTRS)

Madura, Thomas; Gull, T. R.; Owocki, S.; Okazaki, A. T.; Russell, C. M. P.

2010-01-01

We present recent work using three-dimensional (3D) Smoothed Particle Hydrodynamics (SPH) simulations to model the high ([Fe III], [Ar III], [Ne III] and [S III]) and low ([Fe II], [Ni II]) ionization forbidden emission lines observed in Eta Carinae using the HST/STIS. These structures are interpreted as the time-averaged, outer extensions of the primary wind and the wind-wind interaction region directly excited by the FUV of the hot companion star of this massive binary system. We discuss how analyzing the results of the 3D SPH simulations and synthetic slit spectra and comparing them to the spectra obtained with the HST/STIS helps us determine the absolute orientation of the binary orbit and helps remove the degeneracy inherent to models based solely on the observed RXTE X-ray light curve. A key point of this work is that spatially resolved observations like those with HST/STIS and comparison to 3D models are necessary to determine the alignment or misalignment of the orbital angular momentum axis with the Homunculus, or correspondingly, the alignment of the orbital plane with the Homunculus skirt.

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

Bush, Brian W; Brunhart-Lupo, Nicholas J; Gruchalla, Kenny M

This brochure describes a system dynamics simulation (SD) framework that supports an end-to-end analysis workflow that is optimized for deployment on ESIF facilities(Peregrine and the Insight Center). It includes (I) parallel and distributed simulation of SD models, (ii) real-time 3D visualization of running simulations, and (iii) comprehensive database-oriented persistence of simulation metadata, inputs, and outputs.

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

Bush, Brian W; Brunhart-Lupo, Nicholas J; Gruchalla, Kenny M

This presentation describes a system dynamics simulation (SD) framework that supports an end-to-end analysis workflow that is optimized for deployment on ESIF facilities(Peregrine and the Insight Center). It includes (I) parallel and distributed simulation of SD models, (ii) real-time 3D visualization of running simulations, and (iii) comprehensive database-oriented persistence of simulation metadata, inputs, and outputs.

BIOPLUME III

EPA Science Inventory

Bioplume II is a two-dimensional finite difference and Method of Characteristics (MOC) model for simulating the natural attenuation of organic contaminants in ground water due to the processes of advection, dispersion, sorption and biodegradation. The transport simulation in Biop...

Numerical Analysis of Constrained Dynamical Systems, with Applications to Dynamic Contact of Solids, Nonlinear Elastodynamics and Fluid-Structure Interactions

DTIC Science & Technology

2000-12-01

Numerical Simulations ..... ................. .... 42 1.4.1. Impact of a rod on a rigid wall ..... ................. .... 42 1.4.2. Impact of two...dissipative properties of the proposed scheme . . . . 81 II.4. Representative Numerical Simulations ...... ................. ... 84 11.4.1. Forging of...Representative numerical simulations ...... ............. .. 123 111.3. Model Problem II: a Simplified Model of Thin Beams ... ......... ... 127 III

Workflow for Integrating Mesoscale Heterogeneities in Materials Structure with Process Simulation of Titanium Alloys (Postprint)

DTIC Science & Technology

2014-10-01

offer a practical solution to calculating the grain -scale hetero- geneity present in the deformation field. Consequently, crystal plasticity models...process/performance simulation codes (e.g., crystal plasticity finite element method). 15. SUBJECT TERMS ICME; microstructure informatics; higher...iii) protocols for direct and efficient linking of materials models/databases into process/performance simulation codes (e.g., crystal plasticity

Exploring the Origin of Differential Binding Affinities of Human Tubulin Isotypes αβII, αβIII and αβIV for DAMA-Colchicine Using Homology Modelling, Molecular Docking and Molecular Dynamics Simulations

PubMed Central

Panda, Dulal; Kunwar, Ambarish

2016-01-01

Tubulin isotypes are found to play an important role in regulating microtubule dynamics. The isotype composition is also thought to contribute in the development of drug resistance as tubulin isotypes show differential binding affinities for various anti-cancer agents. Tubulin isotypes αβII, αβIII and αβIV show differential binding affinity for colchicine. However, the origin of differential binding affinity is not well understood at the molecular level. Here, we investigate the origin of differential binding affinity of a colchicine analogue N-deacetyl-N-(2-mercaptoacetyl)-colchicine (DAMA-colchicine) for human αβII, αβIII and αβIV isotypes, employing sequence analysis, homology modeling, molecular docking, molecular dynamics simulation and MM-GBSA binding free energy calculations. The sequence analysis study shows that the residue compositions are different in the colchicine binding pocket of αβII and αβIII, whereas no such difference is present in αβIV tubulin isotypes. Further, the molecular docking and molecular dynamics simulations results show that residue differences present at the colchicine binding pocket weaken the bonding interactions and the correct binding of DAMA-colchicine at the interface of αβII and αβIII tubulin isotypes. Post molecular dynamics simulation analysis suggests that these residue variations affect the structure and dynamics of αβII and αβIII tubulin isotypes, which in turn affect the binding of DAMA-colchicine. Further, the binding free-energy calculation shows that αβIV tubulin isotype has the highest binding free-energy and αβIII has the lowest binding free-energy for DAMA-colchicine. The order of binding free-energy for DAMA-colchicine is αβIV ≃ αβII >> αβIII. Thus, our computational approaches provide an insight into the effect of residue variations on differential binding of αβII, αβIII and αβIV tubulin isotypes with DAMA-colchicine and may help to design new analogues with higher binding affinities for tubulin isotypes. PMID:27227832

Kinetics of sorption and abiotic oxidation of arsenic(III) by aquifer materials

USGS Publications Warehouse

Amirbahman, A.; Kent, D.B.; Curtis, G.P.; Davis, J.A.

2006-01-01

The fate of arsenic in groundwater depends largely on its interaction with mineral surfaces. We investigated the kinetics of As(III) oxidation by aquifer materials collected from the USGS research site at Cape Cod, MA, USA, by conducting laboratory experiments. Five different solid samples with similar specific surface areas (0.6-0.9 m2 g-1) and reductively extractable iron contents (18-26 ??mol m-2), but with varying total manganese contents (0.5-3.5 ??mol m-2) were used. Both dissolved and adsorbed As(III) and As(V) concentrations were measured with time up to 250 h. The As(III) removal rate from solution increased with increasing solid manganese content, suggesting that manganese oxide is responsible for the oxidation of As(III). Under all conditions, dissolved As(V) concentrations were very low. A quantitative model was developed to simulate the extent and kinetics of arsenic transformation by aquifer materials. The model included: (1) reversible rate-limited adsorption of As(III) onto both oxidative and non-oxidative (adsorptive) sites, (2) irreversible rate-limited oxidation of As(III), and (3) equilibrium adsorption of As(V) onto adsorptive sites. Rate constants for these processes, as well as the total oxidative site densities were used as the fitting parameters. The total adsorptive site densities were estimated based on the measured specific surface area of each material. The best fit was provided by considering one fast and one slow site for each adsorptive and oxidative site. The fitting parameters were obtained using the kinetic data for the most reactive aquifer material at different initial As(III) concentrations. Using the same parameters to simulate As(III) and As(V) surface reactions, the model predictions were compared to observations for aquifer materials with different manganese contents. The model simulated the experimental data very well for all materials at all initial As(III) concentrations. The As(V) production rate was related to the concentrations of the free oxidative surface sites and dissolved As(III), as r As(V) = k???ox [Mn(IV) OH3][AsO3] with apparent second-order rate constants of koxf??? = 6.28 ?? 10-1 and koxs??? = 1.25 ?? 10-2 M-1 s-1 for the fast and the slow oxidative sites, respectively. The As(III) removal rate decreased approximately by half for a pH increase from 4 to 7. The pH dependence was explained using the acid-base behavior of the surface oxidative sites by considering a surface pKa = 6.2 (I = 0). In the presence of excess surface adsorptive and oxidative sites, phosphate diminished the rate of As(III) removal and As(V) production only slightly due to its interaction with the oxidative sites. The observed As(III) oxidation rate here is consistent with previous observations of As(III) oxidation over short transport distances during field-scale transport experiments. The model developed here may be incorporated into groundwater transport models to predict arsenic speciation and transport in chemically heterogeneous systems. ?? 2005 Elsevier Inc. All rights reserved.

A 'first principles' potential energy surface for liquid water from VRT spectroscopy of water clusters.

PubMed

Goldman, Nir; Leforestier, Claude; Saykally, R J

2005-02-15

We present results of gas phase cluster and liquid water simulations from the recently determined VRT(ASP-W)III water dimer potential energy surface (the third fitting of the Anisotropic Site Potential with Woermer dispersion to vibration-rotation-tunnelling data). VRT(ASP-W)III is shown to not only be a model of high 'spectroscopic' accuracy for the water dimer, but also makes accurate predictions of vibrational ground-state properties for clusters up through the hexamer. Results of ambient liquid water simulations from VRT(ASP-W)III are compared with those from ab initio molecular dynamics, other potentials of 'spectroscopic' accuracy and with experiment. The results herein represent the first time to the authors' knowledge that a 'spectroscopic' potential surface is able to correctly model condensed phase properties of water.

TRAC FY15 Research Planning and Elicitation

DTIC Science & Technology

2014-09-30

Wargaming and Simulation Directorate . . . . . . . . . . . . . C-2 Table C–7. FLVN-Operations Directorate . . . . . . . . . . . . . . . . . . . . . . C...Studies and Analysis III Directorate . . . . . . . . . . . . . . C-4 Table C–14.WSMR - Modeling and Simulation Directorate...Directorate - Mr. Decker • Wargaming and Simulation Directorate - Mr. Johnson • Operations Directorate - Ms. Fratzel • Scenarios and Data Directorate - Mr

Evaluation of Simulated Marine Aerosol Production Using the WaveWatchIII Prognostic Wave Model Coupled to the Community Atmosphere Model within the Community Earth System Model

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

Long, M. S.; Keene, William C.; Zhang, J.

2016-11-08

Primary marine aerosol (PMA) is emitted into the atmosphere via breaking wind waves on the ocean surface. Most parameterizations of PMA emissions use 10-meter wind speed as a proxy for wave action. This investigation coupled the 3 rd generation prognostic WAVEWATCH-III wind-wave model within a coupled Earth system model (ESM) to drive PMA production using wave energy dissipation rate – analogous to whitecapping – in place of 10-meter wind speed. The wind speed parameterization did not capture basin-scale variability in relations between wind and wave fields. Overall, the wave parameterization did not improve comparison between simulated versus measured AOD ormore » Na +, thus highlighting large remaining uncertainties in model physics. Results confirm the efficacy of prognostic wind-wave models for air-sea exchange studies coupled with laboratory- and field-based characterizations of the primary physical drivers of PMA production. No discernible correlations were evident between simulated PMA fields and observed chlorophyll or sea surface temperature.« less

Theoretical study on ultrafast intersystem crossing of chromium(III) acetylacetonate

NASA Astrophysics Data System (ADS)

Ando, Hideo; Iuchi, Satoru; Sato, Hirofumi

2012-05-01

In the relaxation process from the 4T2g state of chromium(III) acetylacetonate, CrIII(acac)3, ultrafast intersystem crossing (ISC) competes with vibrational relaxation (VR). This contradicts the conventional cascade model, where ISC rates are slower than VR ones. We hence investigate the relaxation process with quantum chemical calculations and excited-state wavepacket simulations to obtain clues about the origins of the ultrafast ISC. It is found that a potential energy curve of the 4T2g state crosses those of the 2T1g states near the Franck-Condon region and their spin-orbit couplings are strong. Consequently, ultrafast ISC between these states is observed in the wavepacket simulation.

Regional demand forecasting and simulation model: user's manual. Task 4, final report

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

Parhizgari, A M

1978-09-25

The Department of Energy's Regional Demand Forecasting Model (RDFOR) is an econometric and simulation system designed to estimate annual fuel-sector-region specific consumption of energy for the US. Its purposes are to (1) provide the demand side of the Project Independence Evaluation System (PIES), (2) enhance our empirical insights into the structure of US energy demand, and (3) assist policymakers in their decisions on and formulations of various energy policies and/or scenarios. This report provides a self-contained user's manual for interpreting, utilizing, and implementing RDFOR simulation software packages. Chapters I and II present the theoretical structure and the simulation of RDFOR,more » respectively. Chapter III describes several potential scenarios which are (or have been) utilized in the RDFOR simulations. Chapter IV presents an overview of the complete software package utilized in simulation. Chapter V provides the detailed explanation and documentation of this package. The last chapter describes step-by-step implementation of the simulation package using the two scenarios detailed in Chapter III. The RDFOR model contains 14 fuels: gasoline, electricity, natural gas, distillate and residual fuels, liquid gases, jet fuel, coal, oil, petroleum products, asphalt, petroleum coke, metallurgical coal, and total fuels, spread over residential, commercial, industrial, and transportation sectors.« less

Geohydrology of Storage Unit III and a combined flow model of the Santa Barbara and foothill ground-water basins, Santa Barbara County, California

USGS Publications Warehouse

Freckleton, John R.; Martin, Peter; Nishikawa, Tracy

1998-01-01

The city of Santa Barbara pumps most of its ground water from the Santa Barbara and Foothill ground-water basins. The Santa Barbara basin is subdivided into two storage units: Storage Unit I and Storage Unit III. The Foothill basin and Storage Unit I of the Santa Barbara basin have been studied extensively and ground-water flow models have been developed for them. In this report, the geohydrology of the Santa Barbara ground- water basin is described with a special emphasis on Storage Unit III in the southwestern part of the basin. The purposes of this study were to summarize and evaluate the geohydrology of Storage Unit III and to develop an areawide model of the Santa Barbara and Foothill basins that includes the previously unmodeled Storage Unit III. Storage Unit III is in the southwestern part of the city of Santa Barbara. It is approximately 3.5 miles long and varies in width from about 2,000 feet in the southeast to 4,000 feet in the north-west. Storage Unit III is composed of the Santa Barbara Formation and overlying alluvium. The Santa Barbara Formation (the principal aquifer) consists of Pleistocene and Pliocene(?) unconsolidated marine sand, silt, and clay, and it has a maximum saturated thickness of about 160 feet. The alluvium that overlies the Santa Barbara Formation has a maximum saturated thickness of about 140 feet. The storage unit is bounded areally by faults and low-permeability deposits and is underlain by rocks of Tertiary age. The main sources of recharge to Storage Unit III are seepage from Arroyo Burro and infiltration of precipitation. Most of the recharge occurs in the northwest part of the storage unit, and ground water flows toward the southeast along the unit's long axis. Lesser amounts of recharge may occur as subsurface flow from the Hope Ranch subbasin and as upwelling from the underlying Tertiary rocks. Discharge from Storage Unit III occurs as pumpage, flow to underground drains, underflow through alluvium in the vicinity of Arroyo Burro across the Lavigia Fault, evapotranspiration, and underflow to the Pacific Ocean. The faults that bound Storage Unit III generally are considered to be effective barriers to the flow of ground water. Interbasin ground-water flow occurs where deposits of younger alluvium along stream channels cross faults. Ground-water quality in Storage Unit III deposits varies with location and depth. Upward leakage of poor-quality water from the underlying Tertiary rocks occurs in the storage unit, and such leakage can be influenced by poor well construction or by heavy localized pumping. The highest dissolved-solids concentration (4,710 milligrams per liter) in ground water resulting from this upward leakage is found in the coastal part of the storage unit. The ground-water system was modeled as two horizontal layers. In the Foothill basin and Storage Unit I the layers are separated by a confining bed. The upper layer represents the upper producing zone and the shallow zone near the coast. The lower layer represents the lower producing zone. In general, the faults in the study area were assumed to be no-flow boundaries, except for the offshore fault that forms the southeast boundary; the southeast boundary was simulated as a general-head boundary. The Storage Unit III model was combined with the preexisting Storage Unit I and Foothill basin models, using horizontal flow barriers, to form an areawide model. The areawide model was calibrated by simulating steady-state predevelopment conditions and transient conditions for 1978-92. The nonpumping steady- state simulation was used to verify that the calibrated model yielded physically reasonable results for predevelopment conditions. The calibrated areawide model calculates water levels in Storage Unit III that are within 10 feet of measured water levels at all sites of comparison. In addition, the model adequately simulates water levels in the Storage Unit I and Foothill basin areas. A total of 33,430 acre-feet of water was pum

Exploratory modeling and simulation to support development of motesanib in Asian patients with non-small cell lung cancer based on MONET1 study results.

PubMed

Claret, L; Bruno, R; Lu, J-F; Sun, Y-N; Hsu, C-P

2014-04-01

The motesanib phase III MONET1 study failed to show improvement in overall survival (OS) in non-small cell lung cancer, but a subpopulation of Asian patients had a favorable outcome. We performed exploratory modeling and simulations based on MONET1 data to support further development of motesanib in Asian patients. A model-based estimate of time to tumor growth was the best of tested tumor size response metrics in a multivariate OS model (P < 0.00001) to capture treatment effect (hazard ratio, HR) in Asian patients. Significant independent prognostic factors for OS were baseline tumor size (P < 0.0001), smoking history (P < 0.0001), and ethnicity (P < 0.00001). The model successfully predicted OS distributions and HR in the full population and in Asian patients. Simulations indicated that a phase III study in 500 Asian patients would exceed 80% power to confirm superior efficacy of motesanib combination therapy (expected HR: 0.74), suggesting that motesanib combination therapy may benefit Asian patients.

Development and validation of a modified Hybrid-III six-year-old dummy model for simulating submarining in motor-vehicle crashes.

PubMed

Hu, Jingwen; Klinich, Kathleen D; Reed, Matthew P; Kokkolaras, Michael; Rupp, Jonathan D

2012-06-01

In motor-vehicle crashes, young school-aged children restrained by vehicle seat belt systems often suffer from abdominal injuries due to submarining. However, the current anthropomorphic test device, so-called "crash dummy", is not adequate for proper simulation of submarining. In this study, a modified Hybrid-III six-year-old dummy model capable of simulating and predicting submarining was developed using MADYMO (TNO Automotive Safety Solutions). The model incorporated improved pelvis and abdomen geometry and properties previously tested in a modified physical dummy. The model was calibrated and validated against four sled tests under two test conditions with and without submarining using a multi-objective optimization method. A sensitivity analysis using this validated child dummy model showed that dummy knee excursion, torso rotation angle, and the difference between head and knee excursions were good predictors for submarining status. It was also shown that restraint system design variables, such as lap belt angle, D-ring height, and seat coefficient of friction (COF), may have opposite effects on head and abdomen injury risks; therefore child dummies and dummy models capable of simulating submarining are crucial for future restraint system design optimization for young school-aged children. Copyright © 2011 IPEM. Published by Elsevier Ltd. All rights reserved.

Improvement of shallow landslide prediction accuracy using soil parameterisation for a granite area in South Korea

NASA Astrophysics Data System (ADS)

Kim, M. S.; Onda, Y.; Kim, J. K.

2015-01-01

SHALSTAB model applied to shallow landslides induced by rainfall to evaluate soil properties related with the effect of soil depth for a granite area in Jinbu region, Republic of Korea. Soil depth measured by a knocking pole test and two soil parameters from direct shear test (a and b) as well as one soil parameters from a triaxial compression test (c) were collected to determine the input parameters for the model. Experimental soil data were used for the first simulation (Case I) and, soil data represented the effect of measured soil depth and average soil depth from soil data of Case I were used in the second (Case II) and third simulations (Case III), respectively. All simulations were analysed using receiver operating characteristic (ROC) analysis to determine the accuracy of prediction. ROC analysis results for first simulation showed the low ROC values under 0.75 may be due to the internal friction angle and particularly the cohesion value. Soil parameters calculated from a stochastic hydro-geomorphological model were applied to the SHALSTAB model. The accuracy of Case II and Case III using ROC analysis showed higher accuracy values rather than first simulation. Our results clearly demonstrate that the accuracy of shallow landslide prediction can be improved when soil parameters represented the effect of soil thickness.

Reconstructing the 2003/2004 H3N2 influenza epidemic in Switzerland with a spatially explicit, individual-based model

PubMed Central

2011-01-01

Background Simulation models of influenza spread play an important role for pandemic preparedness. However, as the world has not faced a severe pandemic for decades, except the rather mild H1N1 one in 2009, pandemic influenza models are inherently hypothetical and validation is, thus, difficult. We aim at reconstructing a recent seasonal influenza epidemic that occurred in Switzerland and deem this to be a promising validation strategy for models of influenza spread. Methods We present a spatially explicit, individual-based simulation model of influenza spread. The simulation model bases upon (i) simulated human travel data, (ii) data on human contact patterns and (iii) empirical knowledge on the epidemiology of influenza. For model validation we compare the simulation outcomes with empirical knowledge regarding (i) the shape of the epidemic curve, overall infection rate and reproduction number, (ii) age-dependent infection rates and time of infection, (iii) spatial patterns. Results The simulation model is capable of reproducing the shape of the 2003/2004 H3N2 epidemic curve of Switzerland and generates an overall infection rate (14.9 percent) and reproduction numbers (between 1.2 and 1.3), which are realistic for seasonal influenza epidemics. Age and spatial patterns observed in empirical data are also reflected by the model: Highest infection rates are in children between 5 and 14 and the disease spreads along the main transport axes from west to east. Conclusions We show that finding evidence for the validity of simulation models of influenza spread by challenging them with seasonal influenza outbreak data is possible and promising. Simulation models for pandemic spread gain more credibility if they are able to reproduce seasonal influenza outbreaks. For more robust modelling of seasonal influenza, serological data complementing sentinel information would be beneficial. PMID:21554680

Identifying and Quantifying Emergent Behavior Through System of Systems Modeling and Simulation

DTIC Science & Technology

2015-09-01

42 J . SUMMARY ..............................................................................................43 III. METHODOLOGY...our research. e. Ptolemy Ptolemy is a simulation and rapid prototype environment developed at the University of California Berkely in the...simulation. J . SUMMARY This chapter describes the many works used as a basis for this research. This research used the principles of Selberg’s 2008

Siderophores in Cloud Waters and Potential Impact on Atmospheric Chemistry: Photoreactivity of Iron Complexes under Sun-Simulated Conditions.

PubMed

Passananti, Monica; Vinatier, Virginie; Delort, Anne-Marie; Mailhot, Gilles; Brigante, Marcello

2016-09-06

In the present work, the photoreactivity of a mixture of iron(III)–pyoverdin (Fe(III)–Pyo) complexes was investigated under simulated cloud conditions. Pyoverdins are expected to complex ferric ions naturally present in cloudwater, thus modifying their availability and photoreactivity. The spectroscopic properties and photoreactivity of Fe(III)-Pyo were investigated, with particular attention to their fate under solar irradiation, also studied through simulations. The photolysis of the Fe(III)–Pyo complex leads to the generation of Fe(II), with rates of formation (RFe(II)f) of 6.98 and 3.96 × 10–9 M s–1 at pH 4.0 and 6.0, respectively. Interestingly, acetate formation was observed during the iron-complex photolysis, suggesting that fragmentation can occur after the ligand-to-metal charge transfer (LMCT) via a complex reaction mechanism. Moreover, photogenerated Fe(II) represent an important source of hydroxyl radical via the Fenton reaction in cloudwater. This reactivity might be relevant for the estimation of the rates of formation and steady-state concentrations of the hydroxyl radical by cloud chemistry models and for organic matter speciation in the cloud aqueous phase. In fact, the conventional models, which describe the iron photoreactivity in terms of iron–aqua and oxalate complexes, are not in accordance with our results.

Qualification of CASMO5 / SIMULATE-3K against the SPERT-III E-core cold start-up experiments

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

Grandi, G.; Moberg, L.

SIMULATE-3K is a three-dimensional kinetic code applicable to LWR Reactivity Initiated Accidents. S3K has been used to calculate several international recognized benchmarks. However, the feedback models in the benchmark exercises are different from the feedback models that SIMULATE-3K uses for LWR reactors. For this reason, it is worth comparing the SIMULATE-3K capabilities for Reactivity Initiated Accidents against kinetic experiments. The Special Power Excursion Reactor Test III was a pressurized-water, nuclear-research facility constructed to analyze the reactor kinetic behavior under initial conditions similar to those of commercial LWRs. The SPERT III E-core resembles a PWR in terms of fuel type, moderator,more » coolant flow rate, and system pressure. The initial test conditions (power, core flow, system pressure, core inlet temperature) are representative of cold start-up, hot start-up, hot standby, and hot full power. The qualification of S3K against the SPERT III E-core measurements is an ongoing work at Studsvik. In this paper, the results for the 30 cold start-up tests are presented. The results show good agreement with the experiments for the reactivity initiated accident main parameters: peak power, energy release and compensated reactivity. Predicted and measured peak powers differ at most by 13%. Measured and predicted reactivity compensations at the time of the peak power differ less than 0.01 $. Predicted and measured energy release differ at most by 13%. All differences are within the experimental uncertainty. (authors)« less

Great Lakes Simulation Studies. Volume I. NETSIM: A General Network Simulator.

DTIC Science & Technology

1972-11-01

NOV 72 DACW23-72-C-00" INCLASSZFIED TTSC-715E,1 E2nI~nhE Eh/iln/El//llEE iIII I IIll flf EEEIIIIEEEIII EEEEEIhlllEEEE EIIIIEIIIEIIEE m 111112---2...the following people and organizations: (1) Mr. M . S. Campbell, Mr. Kosky, and Mr. Ahermy of the St. Lawrence Seaway Authority, St. Catherines, Ontario...authors suggest m ;dificatlzns that, ii implemented, would develop the MCDD model Into a gene.il systems model capable of simulating, for example, the

Air quality and climate change, Topic 3 of the Model Inter-Comparison Study for Asia Phase III (MICS-Asia III) - Part 1: Overview and model evaluation

NASA Astrophysics Data System (ADS)

Gao, Meng; Han, Zhiwei; Liu, Zirui; Li, Meng; Xin, Jinyuan; Tao, Zhining; Li, Jiawei; Kang, Jeong-Eon; Huang, Kan; Dong, Xinyi; Zhuang, Bingliang; Li, Shu; Ge, Baozhu; Wu, Qizhong; Cheng, Yafang; Wang, Yuesi; Lee, Hyo-Jung; Kim, Cheol-Hee; Fu, Joshua S.; Wang, Tijian; Chin, Mian; Woo, Jung-Hun; Zhang, Qiang; Wang, Zifa; Carmichael, Gregory R.

2018-04-01

Topic 3 of the Model Inter-Comparison Study for Asia (MICS-Asia) Phase III examines how online coupled air quality models perform in simulating high aerosol pollution in the North China Plain region during wintertime haze events and evaluates the importance of aerosol radiative and microphysical feedbacks. A comprehensive overview of the MICS-Asia III Topic 3 study design, including descriptions of participating models and model inputs, the experimental designs, and results of model evaluation, are presented. Six modeling groups from China, Korea and the United States submitted results from seven applications of online coupled chemistry-meteorology models. Results are compared to meteorology and air quality measurements, including data from the Campaign on Atmospheric Aerosol Research Network of China (CARE-China) and the Acid Deposition Monitoring Network in East Asia (EANET). The correlation coefficients between the multi-model ensemble mean and the CARE-China observed near-surface air pollutants range from 0.51 to 0.94 (0.51 for ozone and 0.94 for PM2.5) for January 2010. However, large discrepancies exist between simulated aerosol chemical compositions from different models. The coefficient of variation (SD divided by the mean) can reach above 1.3 for sulfate in Beijing and above 1.6 for nitrate and organic aerosols in coastal regions, indicating that these compositions are less consistent from different models. During clean periods, simulated aerosol optical depths (AODs) from different models are similar, but peak values differ during severe haze events, which can be explained by the differences in simulated inorganic aerosol concentrations and the hygroscopic growth efficiency (affected by varied relative humidity). These differences in composition and AOD suggest that future models can be improved by including new heterogeneous or aqueous pathways for sulfate and nitrate formation under hazy conditions, a secondary organic aerosol (SOA) formation chemical mechanism with new volatile organic compound (VOCs) precursors, yield data and approaches, and a more detailed evaluation of the dependence of aerosol optical properties on size distribution and mixing state. It was also found that using the ensemble mean of the models produced the best prediction skill. While this has been shown for other conditions (for example, the prediction of high-ozone events in the US (McKeen et al., 2005)), this is to our knowledge the first time it has been shown for heavy haze events.

Simulating Univariate and Multivariate Burr Type IIII and Type XII Distributions through the Method of L-Moments

ERIC Educational Resources Information Center

Pant, Mohan Dev

2011-01-01

The Burr families (Type III and Type XII) of distributions are traditionally used in the context of statistical modeling and for simulating non-normal distributions with moment-based parameters (e.g., Skew and Kurtosis). In educational and psychological studies, the Burr families of distributions can be used to simulate extremely asymmetrical and…

Arsenic Re-Mobilization in Water Treatment Adsorbents Under Reducing Conditions: Part II, XAS and Modeling Study

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

Liu,S.; Jing, C.; Meng, X.

2008-01-01

The mechanism of arsenic re-mobilization in spent adsorbents under reducing conditions was studied using X-ray absorption spectroscopy and surface complexation model calculations. X-ray absorption near edge structure (XANES) spectroscopy demonstrated that As(V) was partially reduced to As(III) in spent granular ferric hydroxide (GFH), titanium dioxide (TiO2), activated alumina (AA) and modified activated alumina (MAA) adsorbents after 2 years of anaerobic incubation. As(V) was completely reduced to As(III) in spent granular ferric oxide (GFO) under 2-year incubation. The extended X-ray absorption fine structure (EXAFS) spectroscopy analysis showed that As(III) formed bidentate binuclear surface complexes on GFO as evidenced by an averagemore » As(III)-O bond distance of 1.78 Angstroms and As(III)-Fe distance of 3.34 Angstroms . The release of As from the spent GFO and TiO2 was simulated using the charge distribution multi-site complexation (CD-MUSIC) model. The observed redox ranges for As release and sulfate mobility were described by model calculations.« less

TETAM Model Verification Study. Volume I. Representation of Intervisibility, Initial Comparisons

DTIC Science & Technology

1976-02-01

simulation models in terms of firings, engagements, and losses between tank and antitank as compared with the field data collected during the free play battles of Field Experiment 11.8 are found in Volume III. (Author)

Data Analysis Techniques for Physical Scientists

NASA Astrophysics Data System (ADS)

Pruneau, Claude A.

2017-10-01

Preface; How to read this book; 1. The scientific method; Part I. Foundation in Probability and Statistics: 2. Probability; 3. Probability models; 4. Classical inference I: estimators; 5. Classical inference II: optimization; 6. Classical inference III: confidence intervals and statistical tests; 7. Bayesian inference; Part II. Measurement Techniques: 8. Basic measurements; 9. Event reconstruction; 10. Correlation functions; 11. The multiple facets of correlation functions; 12. Data correction methods; Part III. Simulation Techniques: 13. Monte Carlo methods; 14. Collision and detector modeling; List of references; Index.

Coupling of a finite element human head model with a lumped parameter Hybrid III dummy model: preliminary results.

PubMed

Ruan, J S; Prasad, P

1995-08-01

A skull-brain finite element model of the human head has been coupled with a multilink rigid body model of the Hybrid III dummy. The experimental coupled model is intended to represent anatomically a 50th percentile human to the extent the dummy and the skull-brain model represent a human. It has been verified by simulating several human cadaver head impact tests as well as dummy head 'impacts" during barrier crashes in an automotive environment. Skull-isostress and brain-isostrain response curves were established based on model calibration of experimental human cadaver tolerance data. The skull-isostress response curve agrees with the JARI Human Head Impact Tolerance Curve for skull fracture. The brain-isostrain response curve predicts a higher G level for concussion than does the JARI concussion curve and the Wayne State Tolerance Curve at the longer time duration range. Barrier crash simulations consist of belted dummies impacting an airbag, a hard and soft steering wheel hub, and no head contact with vehicle interior components. Head impact force, intracranial pressures and strains, skull stress, and head center-of-gravity acceleration were investigated as injury parameters. Head injury criterion (HIC) was also calculated along with these parameters. Preliminary results of the model simulations in those impact conditions are discussed.

Revisiting The First Galaxies: The effects of Population III stars on their host galaxies

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

Muratov, Alexander L.; Gnedin, Oleg Y.; Gnedin, Nickolay Y.

2013-07-12

We revisit the formation and evolution of the first galaxies using new hydrodynamic cosmological simulations with the adaptive refinement tree code. Our simulations feature a recently developed model for H 2 formation and dissociation, and a star formation recipe that is based on molecular rather than atomic gas. Here, we develop and implement a recipe for the formation of metal-free Population III (Pop III) stars in galaxy-scale simulations that resolve primordial clouds with sufficiently high density. We base our recipe on the results of prior zoom-in simulations that resolved the protostellar collapse in pre-galactic objects. We find the epoch duringmore » which Pop III stars dominated the energy and metal budget of the first galaxies to be short-lived. Galaxies that host Pop III stars do not retain dynamical signatures of their thermal and radiative feedback for more than 10 8 years after the lives of the stars end in pair-instability supernovae, even when we consider the maximum reasonable efficiency of the feedback. Though metals ejected by the supernovae can travel well beyond the virial radius of the host galaxy, they typically begin to fall back quickly, and do not enrich a large fraction of the intergalactic medium. Galaxies with a total mass in excess of 3 × 10 6 M ⊙ re-accrete most of their baryons and transition to metal-enriched Pop II star formation.« less

REVISITING THE FIRST GALAXIES: THE EFFECTS OF POPULATION III STARS ON THEIR HOST GALAXIES

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

Muratov, Alexander L.; Gnedin, Oleg Y.; Zemp, Marcel

2013-08-01

We revisit the formation and evolution of the first galaxies using new hydrodynamic cosmological simulations with the adaptive refinement tree code. Our simulations feature a recently developed model for H{sub 2} formation and dissociation, and a star formation recipe that is based on molecular rather than atomic gas. Here, we develop and implement a recipe for the formation of metal-free Population III (Pop III) stars in galaxy-scale simulations that resolve primordial clouds with sufficiently high density. We base our recipe on the results of prior zoom-in simulations that resolved the protostellar collapse in pre-galactic objects. We find the epoch duringmore » which Pop III stars dominated the energy and metal budget of the first galaxies to be short-lived. Galaxies that host Pop III stars do not retain dynamical signatures of their thermal and radiative feedback for more than 10{sup 8} years after the lives of the stars end in pair-instability supernovae, even when we consider the maximum reasonable efficiency of the feedback. Though metals ejected by the supernovae can travel well beyond the virial radius of the host galaxy, they typically begin to fall back quickly, and do not enrich a large fraction of the intergalactic medium. Galaxies with a total mass in excess of 3 Multiplication-Sign 10{sup 6} M{sub Sun} re-accrete most of their baryons and transition to metal-enriched Pop II star formation.« less

Optimal III-nitride HEMTs: from materials and device design to compact model of the 2DEG charge density

NASA Astrophysics Data System (ADS)

Li, Kexin; Rakheja, Shaloo

2017-02-01

In this paper, we develop a physically motivated compact model of the charge-voltage (Q-V) characteristics in various III-nitride high-electron mobility transistors (HEMTs) operating under highly non-equilibrium transport conditions, i.e. high drain-source current. By solving the coupled Schrödinger-Poisson equation and incorporating the two-dimensional electrostatics in the channel, we obtain the charge at the top-of-the-barrier for various applied terminal voltages. The Q-V model accounts for cutting off of the negative momenta states from the drain terminal under high drain-source bias and when the transmission in the channel is quasi-ballistic. We specifically focus on AlGaN and AlInN as barrier materials and InGaN and GaN as the channel material in the heterostructure. The Q-V model is verified and calibrated against numerical results using the commercial TCAD simulator Sentaurus from Synopsys for a 20-nm channel length III-nitride HEMT. With 10 fitting parameters, most of which have a physical origin and can easily be obtained from numerical or experimental calibration, the compact Q-V model allows us to study the limits and opportunities of III-nitride technology. We also identify optimal material and geometrical parameters of the device that maximize the carrier concentration in the HEMT channel in order to achieve superior RF performance. Additionally, the compact charge model can be easily integrated in a hierarchical circuit simulator, such as Keysight ADS and CADENCE, to facilitate circuit design and optimization of various technology parameters.

Motion Cues in Flight Simulation and Simulator Induced Sickness

DTIC Science & Technology

1988-06-01

asseusod in a driving simulator by means of a response surface methodology central-composite design . The most salient finding of the study was that visual...across treatment conditions. For an orthogonal response surface methodology (IBM) design with only tro independent variables. it can be readily shown that...J.E.Fowikes 8 SESSION III - ETIOLOGICAL FACTORS IN SIMULATOR-INDUCED AFTER EFFETS THE USE OF VE& IIBULAR MODELS FOR DESIGN AND EVALUATION OF FLIGHT

Eu(III) uptake on rectorite in the presence of humic acid: a macroscopic and spectroscopic study.

PubMed

Chen, Changlun; Yang, Xin; Wei, Juan; Tan, Xiaoli; Wang, Xiangke

2013-03-01

This work contributed to the comprehension of humic acid (HA) effect on Eu(III) uptake to Na-rectorite by batch sorption experiments, model fitting, scanning electron microscopy, powder X-ray diffraction, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and extended X-ray absorption fine structure (EXAFS) spectroscopy. At low pH, the presence of HA enhanced Eu(III) sorption on Na-rectorite, while reduced Eu(III) sorption at high pH. The experimental data of Eu(III) sorption in the absence and presence of HA were simulated by the diffuse-layer model well with the aid of FITEQL 3.2 software. The basal spacing of rectorite became large after Eu(III) and HA sorption on Na-rectorite. Some of Eu(III) ions and HA might be intercalated into the interlayer space of Na-rectorite. EXAFS analysis showed that the R(Eu-O) (the bond distance of Eu and O in the first shell of Eu) and N values (coordination number) of Eu(III)-HA-rectorite system were smaller than those of Eu(III)-rectorite system. Copyright © 2012 Elsevier Inc. All rights reserved.

Modeling and Simulation of III-Nitride-Based Solar Cells using NextnanoRTM

NASA Astrophysics Data System (ADS)

Refaei, Malak

Nextnano3 software is a well-known package for simulating semiconductor band-structures at the nanoscale and predicting the general electronic structure. In this work, it is further demonstrated as a viable tool for the simulation of III-nitride solar cells. In order to prove this feasibility, the generally accepted solar cell simulation package, PC1D, was chosen for comparison. To critique the results from both PC1D and Nextnano3, the fundamental drift-diffusion equations were used to calculate the performance of a simple p-n homojunction solar cell device analytically. Silicon was picked as the material for this comparison between the outputs of the two simulators as well as the results of the drift-diffusion equations because it is a well-known material in both software tools. After substantiating the capabilities of Nextnano3 for the simulation solar cells, an InGaN single-junction solar cell was simulated. The effects of various indium compositions and device structures on the performance of this InGaN p-n homojunction solar cell was then investigated using Nextnano 3 as a simulation tool. For single-junction devices with varying bandgap, an In0.6Ga0.4N device with a bandgap of 1.44 eV was found to be the optimum. The results of this research demonstrate that the Nextnano3 software can be used to usefully simulate solar cells in general, and III-nitride solar cells specifically, for future study of nanoscale structured devices.

Fates of the most massive primordial stars

NASA Astrophysics Data System (ADS)

Chen, Ke-Jung; Heger, Alexander; Almgren, Ann; Woosley, Stan

2012-09-01

We present our results of numerical simulations of the most massive primordial stars. For the extremely massive non-rotating Pop III stars over 300Msolar, they would simply die as black holes. But the Pop III stars with initial masses 140 - 260Msolar may have died as gigantic explosions called pair-instability supernovae (PSNe). We use a new radiation-hydrodynamics code CASTRO to study evolution of PSNe. Our models follow the entire explosive burning and the explosion until the shock breaks out from the stellar surface. In our simulations, we find that fluid instabilities occurred during the explosion. These instabilities are driven by both nuclear burning and hydrodynamical instability. In the red supergiant models, fluid instabilities can lead to significant mixing of supernova ejecta and alter the observational signature.

Ion beam nanopatterning of III-V semiconductors: Consistency of experimental and simulation trends within a chemistry-driven theory

DOE PAGES

El-Atwani, O.; Norris, S. A.; Ludwig, K.; ...

2015-12-16

In this study, several proposed mechanisms and theoretical models exist concerning nanostructure evolution on III-V semiconductors (particularly GaSb) via ion beam irradiation. However, making quantitative contact between experiment on the one hand and model-parameter dependent predictions from different theories on the other is usually difficult. In this study, we take a different approach and provide an experimental investigation with a range of targets (GaSb, GaAs, GaP) and ion species (Ne, Ar, Kr, Xe) to determine new parametric trends regarding nanostructure evolution. Concurrently, atomistic simulations using binary collision approximation over the same ion/target combinations were performed to determine parametric trends onmore » several quantities related to existing model. A comparison of experimental and numerical trends reveals that the two are broadly consistent under the assumption that instabilities are driven by chemical instability based on phase separation. Furthermore, the atomistic simulations and a survey of material thermodynamic properties suggest that a plausible microscopic mechanism for this process is an ion-enhanced mobility associated with energy deposition by collision cascades.« less

SCIENTIFIC UNCERTAINTIES IN ATMOSPHERIC MERCURY MODELS III: BOUNDARY AND INITIAL CONDITIONS, MODEL GRID RESOLUTION, AND HG(II) REDUCTION MECHANISMS

EPA Science Inventory

In this study we investigate the CMAQ model response in terms of simulated mercury concentration and deposition to boundary/initial conditions (BC/IC), model grid resolution (12- versus 36-km), and two alternative Hg(II) reduction mechanisms. The model response to the change of g...

The public health impact of malaria vaccine RTS,S in malaria endemic Africa: country-specific predictions using 18 month follow-up Phase III data and simulation models.

PubMed

Penny, Melissa A; Galactionova, Katya; Tarantino, Michael; Tanner, Marcel; Smith, Thomas A

2015-07-29

The RTS,S/AS01 malaria vaccine candidate recently completed Phase III trials in 11 African sites. Recommendations for its deployment will partly depend on predictions of public health impact in endemic countries. Previous predictions of these used only limited information on underlying vaccine properties and have not considered country-specific contextual data. Each Phase III trial cohort was simulated explicitly using an ensemble of individual-based stochastic models, and many hypothetical vaccine profiles. The true profile was estimated by Bayesian fitting of these models to the site- and time-specific incidence of clinical malaria in both trial arms over 18 months of follow-up. Health impacts of implementation via two vaccine schedules in 43 endemic sub-Saharan African countries, using country-specific prevalence, access to care, immunisation coverage and demography data, were predicted via weighted averaging over many simulations. The efficacy against infection of three doses of vaccine was initially approximately 65 % (when immunising 6-12 week old infants) and 80 % (children 5-17 months old), with a 1 year half-life (exponential decay). Either schedule will avert substantial disease, but predicted impact strongly depends on the decay rate of vaccine effects and average transmission intensity. For the first time Phase III site- and time-specific data were available to estimate both the underlying profile of RTS,S/AS01 and likely country-specific health impacts. Initial efficacy will probably be high, but decay rapidly. Adding RTS,S to existing control programs, assuming continuation of current levels of malaria exposure and of health system performance, will potentially avert 100-580 malaria deaths and 45,000 to 80,000 clinical episodes per 100,000 fully vaccinated children over an initial 10-year phase.

Unified Kinetic Approach for Simulation of Gas Flows in Rarefied and Continuum Regimes

DTIC Science & Technology

2007-06-01

potential , iii) the Lennard - Jones potential , iv) the Coulomb potential , and v) the BGK model. For 2D simulations, the BGK model was implemented in a...were performed for the Lennard - Jones interaction potential . The agreement of experimental and calculated profiles indicates the high accuracy of the...calculations by two potentials (Hard Spheres and Lennard - Jones ) demonstrated similar behavior of the main quantities. The flow field structures are quite

ALMA WILL DETERMINE THE SPECTROSCOPIC REDSHIFT z > 8 WITH FIR [O III] EMISSION LINES

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

Inoue, A. K.; Shimizu, I.; Tamura, Y.

We investigate the potential use of nebular emission lines in the rest-frame far-infrared (FIR) for determining spectroscopic redshift of z > 8 galaxies with the Atacama Large Millimeter/submillimeter Array (ALMA). After making a line emissivity model as a function of metallicity, especially for the [O III] 88 μm line which is likely to be the strongest FIR line from H II regions, we predict the line fluxes from high-z galaxies based on a cosmological hydrodynamics simulation of galaxy formation. Since the metallicity of galaxies reaches at ∼0.2 Z {sub ☉} even at z > 8 in our simulation, we expectmore » the [O III] 88 μm line as strong as 1.3 mJy for 27 AB objects, which is detectable at a high significance by <1 hr integration with ALMA. Therefore, the [O III] 88 μm line would be the best tool to confirm the spectroscopic redshifts beyond z = 8.« less

Comparison of SWAT Hydrological Model Results from TRMM 3B42, NEXRAD Stage III, and Oklahoma Mesonet Data

NASA Astrophysics Data System (ADS)

Tobin, K. J.; Bennett, M. E.

2008-05-01

The Cimarron River Basin (3110 sq km) between Dodge and Guthrie, Oklahoma is located in northern Oklahoma and was used as a test bed to compare the hydrological model performance associated with different methods of precipitation quantification. The Soil and Water Assessment Tool (SWAT) was selected for this project, which is a comprehensive model that, besides quantifying watershed hydrology, can simulate water quality as well as nutrient and sediment loading within stream reaches. An advantage of this location is the extensive monitoring of MET parameters (precipitation, temperature, relative humidity, wind speed, solar radiation) afforded by the Oklahoma Mesonet, which has been documented to improve the performance of SWAT. The utility of TRMM 3B42 and NEXRAD Stage III data in supporting the hydrologic modeling of Cimarron River Basin is demonstrated. Minor adjustments to selected model parameters were made to make parameter values more realistic based on results from previous studies and information and to more realistically simulate base flow. Significantly, no ad hoc adjustments to major parameters such as Curve Number or Available Soil Water were made and robust simulations were obtained. TRMM and NEXRAD data are aggregated into an average daily estimate of precipitation for each TRMM grid cell (0.25 degree X 0.25 degree). Preliminary simulation of stream flow (year 2004 to 2006) in the Cimarron River Basin yields acceptable monthly results with very little adjustment of model parameters using TRMM 3B42 precipitation data (mass balance error = 3 percent; Monthly Nash-Sutcliffe efficiency coefficients (NS) = 0.77). However, both Oklahoma Mesonet rain gauge (mass balance error = 13 percent; Monthly NS = 0.91; Daily NS = 0.64) and NEXRAD Stage III data (mass balance error = -5 percent; Monthly NS = 0.95; Daily NS = 0.69) produces superior simulations even at a sub-monthly time scale; daily results are time averaged over a three day period. Note that all types of precipitation data perform better than a synthetic precipitation dataset generated using a weather simulator (mass balance error = 12 percent; Monthly NS = 0.40). Our study again documents that merged precipitation satellite products, such as TRMM 3B42, can support semi-distributed hydrologic modeling at the watershed scale. However, apparently additional work is required to improve TRMM precipitation retrievals over land to generate a product that yields more robust hydrological simulations especially at finer time scales. Additionally, ongoing work in this basin will compare TRMM results with stream flow model results generated using CMORPH precipitation estimates. Finally, in the future we plan to use simulated, semi-distributed soil moisture values determined by SWAT for comparison with gridded soil moisture estimates from TRMM-TMI that should provide further validation of our modeling efforts.

Crew Exploration Vehicle (CEV) (Orion) Occupant Protection. [Appendices Part 2

NASA Technical Reports Server (NTRS)

Currie-Gregg, Nancy J.; Gernhardt, Michael L.; Lawrence, Charles; Somers, Jeffrey T.

2016-01-01

The purpose of this study was to determine the similarity between the response of the THUMS model and the Hybrid III Anthropometric Test Device (ATD) given existing Wright-Patterson (WP) sled tests. There were four tests selected for this comparison with frontal, spinal, rear, and lateral loading. The THUMS was placed in a sled configuration that replicated the WP configuration and the recorded seat acceleration for each test was applied to model seat. Once the modeling simulations were complete, they were compared to the WP results using two methods. The first was a visual inspection of the sled test videos compared to the THUMS d3plot files. This comparison resulted in an assessment of the overall kinematics of the two results. The other comparison was a comparison of the plotted data recorded for both tests. The metrics selected for comparison were seat acceleration, belt forces, head acceleration and chest acceleration. These metrics were recorded in all WP tests and were outputs of the THUMS model. Once the comparison of the THUMS to the WP tests was complete, the THUMS model output was also examined for possible injuries in these scenarios. These outputs included metrics for injury risk to the head, neck, thorax, lumbar spine and lower extremities. The metrics to evaluate head response were peak head acceleration, HIC15, and HIC36. For the neck, N (sub ij) was calculated. The thorax response was evaluated with peak chest acceleration, the Combined Thoracic Index (CTI), sternal deflection, chest deflection, and chest acceleration- 3 ms clip. The lumbar spine response was evaluated with lumbar spine force. Finally the lower extremity response was evaluated by femur and tibia force. The results of the simulation comparisons indicate the THUMS model had a similar response to the Hybrid III dummy given the same input. The primary difference seen between the two was a more flexible response of the THUMS compared to the Hybrid III. This flexibility was most pronounced in the neck flexion, shoulder deflection and chest deflection. Due to the flexibility of the THUMS, the resulting head and chest accelerations tended to lag the Hybrid III acceleration trace and have a lower peak value. The results of the injury metric comparison identified possible injury trends between simulations. Risk of head injury was highest for the lateral simulations. The risk of chest injury was highest for the rear impact. However, neck injury risk was approximately the same for all simulations. The injury metric value for lumbar spine force was highest for the spinal impact. The leg forces were highest for the rear and lateral impacts. The results of this comparison indicate the THUMS model performs in a similar manner as the Hybrid III ATD. The differences in the responses of model and the ATD are primarily due to the flexibility of the THUMS. This flexibility of the THUMS would be a more human like response. Based on the similarity between the two models, the THUMS should be used in further testing to assess risk of injury to the occupant.

Survival outcomes after radiation therapy for stage III non-small-cell lung cancer after adoption of computed tomography-based simulation.

PubMed

Chen, Aileen B; Neville, Bridget A; Sher, David J; Chen, Kun; Schrag, Deborah

2011-06-10

Technical studies suggest that computed tomography (CT) -based simulation improves the therapeutic ratio for thoracic radiation therapy (TRT), although few studies have evaluated its use or impact on outcomes. We used the Surveillance, Epidemiology and End Results (SEER) -Medicare linked data to identify CT-based simulation for TRT among Medicare beneficiaries diagnosed with stage III non-small-cell lung cancer (NSCLC) between 2000 and 2005. Demographic and clinical factors associated with use of CT simulation were identified, and the impact of CT simulation on survival was analyzed by using Cox models and propensity score analysis. The proportion of patients treated with TRT who had CT simulation increased from 2.4% in 1994 to 34.0% in 2000 to 77.6% in 2005. Of the 5,540 patients treated with TRT from 2000 to 2005, 60.1% had CT simulation. Geographic variation was seen in rates of CT simulation, with lower rates in rural areas and in the South and West compared with those in the Northeast and Midwest. Patients treated with chemotherapy were more likely to have CT simulation (65.2% v 51.2%; adjusted odds ratio, 1.67; 95% CI, 1.48 to 1.88; P < .01), although there was no significant association between use of surgery and CT simulation. Controlling for demographic and clinical characteristics, CT simulation was associated with lower risk of death (adjusted hazard ratio, 0.77; 95% CI, 0.73 to 0.82; P < .01) compared with conventional simulation. CT-based simulation has been widely, although not uniformly, adopted for the treatment of stage III NSCLC and is associated with higher survival among patients receiving TRT.

Simulating pre-galactic metal enrichment for JWST deep-field observations

NASA Astrophysics Data System (ADS)

Jaacks, Jason

2017-08-01

We propose to create a new suite of mesoscale cosmological volume simulations with custom built sub-grid physics in which we independently track the contribution from Population III and Population II star formation to the total metals in the interstellar medium (ISM) of the first galaxies, and in the diffuse IGM at an epoch prior to reionization. These simulations will fill a gap in our simulation knowledge about chemical enrichment in the pre-reionization universe, which is a crucial need given the impending observational push into this epoch with near-future ground and space-based telescopes. This project is the natural extension of our successful Cycle 24 theory proposal (HST-AR-14569.001-A; PI Jaacks) in which we developed a new Pop III star formation sub-grid model which is currently being utilized to study the baseline metal enrichment of pre-reionization systems.

Physics and performances of III-V nanowire broken-gap heterojunction TFETs using an efficient tight-binding mode-space NEGF model enabling million-atom nanowire simulations.

PubMed

Afzalian, A; Vasen, T; Ramvall, P; Shen, T-M; Wu, J; Passlack, M

2018-06-27

We report the capability to simulate in a quantum-mechanical atomistic fashion record-large nanowire devices, featuring several hundred to millions of atoms and a diameter up to 18.2 nm. We have employed a tight-binding mode-space NEGF technique demonstrating by far the fastest (up to 10 000  ×  faster) but accurate (error  <  1%) atomistic simulations to date. Such technique and capability opens new avenues to explore and understand the physics of nanoscale and mesoscopic devices dominated by quantum effects. In particular, our method addresses in an unprecedented way the technologically-relevant case of band-to-band tunneling (BTBT) in III-V nanowire broken-gap heterojunction tunnel-FETs (HTFETs). We demonstrate an accurate match of simulated BTBT currents to experimental measurements in a 12 nm diameter InAs NW and in an InAs/GaSb Esaki tunneling diode. We apply our TB MS simulations and report the first in-depth atomistic study of the scaling potential of III-V GAA nanowire HTFETs including the effect of electron-phonon scattering and discrete dopant impurity band tails, quantifying the benefits of this technology for low-power low-voltage CMOS applications.

Relations between winter precipitation and atmospheric circulation simulated by the Geophysical Fluid Dynamics Laboratory general circulation model

USGS Publications Warehouse

McCabe, G.J.; Dettinger, M.D.

1995-01-01

General circulation model (GCM) simulations of atmospheric circulation are more reliable than GCM simulations of temperature and precipitation. In this study, temporal correlations between 700 hPa height anomalies simulated winter precipitation at eight locations in the conterminous United States are compared with corresponding correlations in observations. The objectives are to 1) characterize the relations between atmospheric circulation and winter precipitation simulated by the GFDL, GCM for selected locations in the conterminous USA, ii) determine whether these relations are similar to those found in observations of the actual climate system, and iii) determine if GFDL-simulated precipitation is forced by the same circulation patterns as in the real atmosphere. -from Authors

Initial Binding of Ions to the Interhelical Loops of Divalent Ion Transporter CorA: Replica Exchange Molecular Dynamics Simulation Study

PubMed Central

Zhang, Tong; Mu, Yuguang

2012-01-01

Crystal structures of Thermotoga maritima magnesium transporter CorA, reported in 2006, revealed its homo-pentameric constructions. However, the structure of the highly conserved extracellular interhelical loops remains unsolved, due to its high flexibility. We have explored the configurations of the loops through extensive replica exchange molecular dynamics simulations in explicit solvent model with the presence of either Co(III) Hexamine ions or Mg2+ ions. We found that there are multiple binding sites available on the interhelical loops in which the negatively charged residues, E316 and E320, are located notably close to the positively charged ions during the simulations. Our simulations resolved the distinct binding patterns of the two kinds of ions: Co(III) Hexamine ions were found to bind stronger with the loop than Mg2+ ions with binding free energy −7.3 kJ/mol lower, which is nicely consistent with the previous data. Our study provides an atomic basis description of the initial binding process of Mg2+ ions on the extracellular interhelical loops of CorA and the detailed inhibition mechanism of Co(III) Hexamine ions on CorA ions transportation. PMID:22952795

Monte Carlo model for the analysis and development of III-V Tunnel-FETs and Impact Ionization-MOSFETs

NASA Astrophysics Data System (ADS)

Talbo, V.; Mateos, J.; González, T.; Lechaux, Y.; Wichmann, N.; Bollaert, S.; Vasallo, B. G.

2015-10-01

Impact-ionization metal-oxide-semiconductor FETs (I-MOSFETs) are in competition with tunnel FETs (TFETs) in order to achieve the best behaviour for low power logic circuits. Concretely, III-V I-MOSFETs are being explored as promising devices due to the proper reliability, since the impact ionization events happen away from the gate oxide, and the high cutoff frequency, due to high electron mobility. To facilitate the design process from the physical point of view, a Monte Carlo (MC) model which includes both impact ionization and band-to-band tunnel is presented. Two ungated InGaAs and InAlAs/InGaAs 100 nm PIN diodes have been simulated. In both devices, the tunnel processes are more frequent than impact ionizations, so that they are found to be appropriate for TFET structures and not for I- MOSFETs. According to our simulations, other narrow bandgap candidates for the III-V heterostructure, such as InAs or GaSb, and/or PININ structures must be considered for a correct I-MOSFET design.

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

Ortoleva, Peter J.

Illustrative embodiments of systems and methods for the deductive multiscale simulation of macromolecules are disclosed. In one illustrative embodiment, a deductive multiscale simulation method may include (i) constructing a set of order parameters that model one or more structural characteristics of a macromolecule, (ii) simulating an ensemble of atomistic configurations for the macromolecule using instantaneous values of the set of order parameters, (iii) simulating thermal-average forces and diffusivities for the ensemble of atomistic configurations, and (iv) evolving the set of order parameters via Langevin dynamics using the thermal-average forces and diffusivities.

22 CFR 124.2 - Exemptions for training and military service.

Code of Federal Regulations, 2010 CFR

2010-04-01

... methods and tools include the development and/or use of mockups, computer models and simulations, and test facilities. (iii) Manufacturing know-how, such as: Information that provides detailed manufacturing processes...

WHERE ARE THE LOW-MASS POPULATION III STARS?

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

Ishiyama, Tomoaki; Sudo, Kae; Yokoi, Shingo

2016-07-20

We study the number and the distribution of low-mass Population III (Pop III) stars in the Milky Way. In our numerical model, hierarchical formation of dark matter minihalos and Milky-Way-sized halos are followed by a high-resolution cosmological simulation. We model the Pop III formation in H{sub 2} cooling minihalos without metal under UV radiation of the Lyman–Werner bands. Assuming a Kroupa initial mass function (IMF) from 0.15 to 1.0 M {sub ⊙} for low-mass Pop III stars, as a working hypothesis, we try to constrain the theoretical models in reverse by current and future observations. We find that the survivorsmore » tend to concentrate on the center of halo and subhalos. We also evaluate the observability of Pop III survivors in the Milky Way and dwarf galaxies, and constraints on the number of Pop III survivors per minihalo. The higher latitude fields require lower sample sizes because of the high number density of stars in the galactic disk, the required sample sizes are comparable in the high- and middle-latitude fields by photometrically selecting low-metallicity stars with optimized narrow-band filters, and the required number of dwarf galaxies to find one Pop III survivor is less than 10 at <100 kpc for the tip of red giant stars. Provided that available observations have not detected any survivors, the formation models of low-mass Pop III stars with more than 10 stars per minihalo are already excluded. Furthermore, we discuss the way to constrain the IMF of Pop III stars at a high mass range of ≳10 M {sub ⊙}.« less

Finite element comparison of human and Hybrid III responses in a frontal impact.

PubMed

Danelson, Kerry A; Golman, Adam J; Kemper, Andrew R; Gayzik, F Scott; Clay Gabler, H; Duma, Stefan M; Stitzel, Joel D

2015-12-01

The improvement of finite element (FE) Human Body Models (HBMs) has made them valuable tools for investigating restraint interactions compared to anthropomorphic test devices (ATDs). The objective of this study was to evaluate the effect of various combinations of safety restraint systems on the sensitivity of thoracic injury criteria using matched ATD and Human Body Model (HBM) simulations at two crash severities. A total of seven (7) variables were investigated: 3-point belt with two (2) load limits, frontal airbag, knee bolster airbag, a buckle pretensioner, and two (2) delta-v's - 40kph and 50kph. Twenty four (24) simulations were conducted for the Hybrid III ATD FE model and repeated with a validated HBM for 48 total simulations. Metrics tested in these conditions included sternum deflection, chest acceleration, chest excursion, Viscous Criteria (V*C) criteria, pelvis acceleration, pelvis excursion, and femur forces. Additionally, chest band deflection and rib strain distribution were measured in the HBM for additional restraint condition discrimination. The addition of a frontal airbag had the largest effect on the occupant chest metrics with an increase in chest compression and acceleration but a decrease in excursion. While the THUMS and Hybrid III occupants demonstrated the same trend in the chest compression measurements, there were conflicting results in the V*C, acceleration, and displacement metrics. Similarly, the knee bolster airbag had the largest effect on the pelvis with a decrease in acceleration and excursion. With a knee bolster airbag the simulated occupants gave conflicting results, the THUMS had a decrease in femur force and the ATD had an increase. Preferential use of dummies or HBM's is not debated; however, this study highlights the ability of HBM metrics to capture additional chest response metrics. Copyright © 2015 Elsevier Ltd. All rights reserved.

Simulating Bioremediation of Chloroethenes in a Fractured Rock Aquifer.

NASA Astrophysics Data System (ADS)

Curtis, G. P.

2016-12-01

Reactive transport simulations are being conducted to synthesize the results of a field experiment on the enhanced bioremediation of chloroethenes in a heterogeneous fractured-rock aquifer near West Trenton, NJ. The aquifer consists of a sequence of dipping mudstone beds, with water-conducting bedding-plane fractures separated by low-permeability rock where transport is diffusion-limited. The enhanced bioremediation experiment was conducted by injecting emulsified vegetable oil as an electron donor (EOS™) and a microbial consortium (KB1™) that contained dehalococcoides ethenogenes into a fracture zone that had maximum trichloroethene (TCE) concentrations of 84µM. TCE was significantly biodegraded to dichloroethene, chloroethene and ethene or CO2 at the injection well and at a downgradient well. The results also show the concomitant reduction of Fe(III) and S(6) and the production of methane . The results were used to calibrate transport models for quantifying the dominant mass-removal mechanisms. A nonreactive transport model was developed to simulate advection, dispersion and matrix diffusion of bromide and deuterium tracers present in the injection solution. This calibrated model matched tracer concentrations at the injection well and a downgradient observation well and demonstrated that matrix diffusion was a dominant control on tracer transport. A reactive transport model was developed to extend the nonreactive transport model to simulate the microbially mediated sequential dechlorination reactions, reduction of Fe(III) and S(6), and methanogenesis. The reactive transport model was calibrated to concentrations of chloride, chloroethenes, pH, alkalinity, redox-sensitive species and major ions, to estimate key biogeochemical kinetic parameters. The simulation results generally match the diverse set of observations at the injection and observation wells throughout the three year experiment. In addition, the observations and model simulations indicate that a significant pool of TCE that was initially sorbed to either the fracture surfaces or in the matrix was degraded during the field experiment. The calibrated reactive transport model will be used to quantify the extent of chloroethene mass removal from a range of hypothetical aquifers.

Scavenging and recombination kinetics in a radiation spur: The successive ordered scavenging events

NASA Astrophysics Data System (ADS)

Al-Samra, Eyad H.; Green, Nicholas J. B.

2018-03-01

This study describes stochastic models to investigate the successive ordered scavenging events in a spur of four radicals, a model system based on a radiation spur. Three simulation models have been developed to obtain the probabilities of the ordered scavenging events: (i) a Monte Carlo random flight (RF) model, (ii) hybrid simulations in which the reaction rate coefficient is used to generate scavenging times for the radicals and (iii) the independent reaction times (IRT) method. The results of these simulations are found to be in agreement with one another. In addition, a detailed master equation treatment is also presented, and used to extract simulated rate coefficients of the ordered scavenging reactions from the RF simulations. These rate coefficients are transient, the rate coefficients obtained for subsequent reactions are effectively equal, and in reasonable agreement with the simple correction for competition effects that has recently been proposed.

DEVELOPMENT AND APPLICATION OF A NEW AIR POLLUTION MODELING SYSTEM. PART III: AEROSOL-PHASE SIMULATIONS (R823186)

EPA Science Inventory

Result from a new air pollution model were tested against data from the Southern California Air Quality Study (SCAQS) period of 26-29 August 1987. Gross errors for sulfate, sodium, light absorption, temperatures, surface solar radiation, sulfur dioxide gas, formaldehyde gas, and ...

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3).

PubMed

Bergmann, Frank T; Cooper, Jonathan; König, Matthias; Moraru, Ion; Nickerson, David; Le Novère, Nicolas; Olivier, Brett G; Sahle, Sven; Smith, Lucian; Waltemath, Dagmar

2018-03-19

The creation of computational simulation experiments to inform modern biological research poses challenges to reproduce, annotate, archive, and share such experiments. Efforts such as SBML or CellML standardize the formal representation of computational models in various areas of biology. The Simulation Experiment Description Markup Language (SED-ML) describes what procedures the models are subjected to, and the details of those procedures. These standards, together with further COMBINE standards, describe models sufficiently well for the reproduction of simulation studies among users and software tools. The Simulation Experiment Description Markup Language (SED-ML) is an XML-based format that encodes, for a given simulation experiment, (i) which models to use; (ii) which modifications to apply to models before simulation; (iii) which simulation procedures to run on each model; (iv) how to post-process the data; and (v) how these results should be plotted and reported. SED-ML Level 1 Version 1 (L1V1) implemented support for the encoding of basic time course simulations. SED-ML L1V2 added support for more complex types of simulations, specifically repeated tasks and chained simulation procedures. SED-ML L1V3 extends L1V2 by means to describe which datasets and subsets thereof to use within a simulation experiment.

Environmental Influences in the Simulation of a Solar Space Heating System.

DTIC Science & Technology

1980-01-01

this simulation an optimum collector size was determined from the energy requirements given by each model and a comparison made between the...Solar Collector Cross Section .. ............... 26 4. Solar System Schematic. .. .................. 31 5. Contributions to Annual Energy Cost...40 6. House Size I Annual Energy Cost. ....... ........ 46 7. House Size II Annual Energy Cost .. ..... ......... 47 8. House Size III Annual

The impact of reduced gastric acid secretion on dissolution of salts of weak bases in the fasted upper gastrointestinal lumen: Data in biorelevant media and in human aspirates.

PubMed

Litou, Chara; Vertzoni, Maria; Xu, Wei; Kesisoglou, Filippos; Reppas, Christos

2017-06-01

To propose media for simulating the intragastric environment under reduced gastric acid secretion in the fasted state at three levels of simulation of the gastric environment and evaluate their usefulness in evaluating the intragastric dissolution of salts of weak bases. To evaluate the importance of bicarbonate buffer in biorelevant in vitro dissolution testing when using Level II biorelevant media simulating the environment in the fasted upper small intestine, regardless of gastric acid secretions. Media for simulating the hypochlorhydric and achlorhydric conditions in stomach were proposed using phosphates, maleates and bicarbonates buffers. The impact of bicarbonates in Level II biorelevant media simulating the environment in upper small intestine was evaluated so that pH and bulk buffer capacity were maintained. Dissolution data were collected using two model compounds, pioglitazone hydrochloride and semifumarate cocrystal of Compound B, and the mini-paddle dissolution apparatus in biorelevant media and in human aspirates. Simulated gastric fluids proposed in this study were in line with pH, buffer capacity, pepsin content, total bile salt/lecithin content and osmolality of the fasted stomach under partial and under complete inhibition of gastric acid secretion. Fluids simulating the conditions under partial inhibition of acid secretion were useful in simulating concentrations of both model compounds in gastric aspirates. Bicarbonates in Level III biorelevant gastric media and in Level II biorelevant media simulating the composition in the upper intestinal lumen did not improve simulation of concentrations in human aspirates. Level III biorelevant media for simulating the intragastric environment under hypochlorhydric conditions were proposed and their usefulness in the evaluation of concentrations of two model salts of weak bases in gastric aspirates was shown. Level II biorelevant media for simulating the environment in upper intestinal lumen led to underestimation of concentrations in aspirates, even when bicarbonate buffer was used. Copyright © 2017 Elsevier B.V. All rights reserved.

Traffic and Driving Simulator Based on Architecture of Interactive Motion.

PubMed

Paz, Alexander; Veeramisti, Naveen; Khaddar, Romesh; de la Fuente-Mella, Hanns; Modorcea, Luiza

2015-01-01

This study proposes an architecture for an interactive motion-based traffic simulation environment. In order to enhance modeling realism involving actual human beings, the proposed architecture integrates multiple types of simulation, including: (i) motion-based driving simulation, (ii) pedestrian simulation, (iii) motorcycling and bicycling simulation, and (iv) traffic flow simulation. The architecture has been designed to enable the simulation of the entire network; as a result, the actual driver, pedestrian, and bike rider can navigate anywhere in the system. In addition, the background traffic interacts with the actual human beings. This is accomplished by using a hybrid mesomicroscopic traffic flow simulation modeling approach. The mesoscopic traffic flow simulation model loads the results of a user equilibrium traffic assignment solution and propagates the corresponding traffic through the entire system. The microscopic traffic flow simulation model provides background traffic around the vicinities where actual human beings are navigating the system. The two traffic flow simulation models interact continuously to update system conditions based on the interactions between actual humans and the fully simulated entities. Implementation efforts are currently in progress and some preliminary tests of individual components have been conducted. The implementation of the proposed architecture faces significant challenges ranging from multiplatform and multilanguage integration to multievent communication and coordination.

Traffic and Driving Simulator Based on Architecture of Interactive Motion

PubMed Central

Paz, Alexander; Veeramisti, Naveen; Khaddar, Romesh; de la Fuente-Mella, Hanns; Modorcea, Luiza

2015-01-01

This study proposes an architecture for an interactive motion-based traffic simulation environment. In order to enhance modeling realism involving actual human beings, the proposed architecture integrates multiple types of simulation, including: (i) motion-based driving simulation, (ii) pedestrian simulation, (iii) motorcycling and bicycling simulation, and (iv) traffic flow simulation. The architecture has been designed to enable the simulation of the entire network; as a result, the actual driver, pedestrian, and bike rider can navigate anywhere in the system. In addition, the background traffic interacts with the actual human beings. This is accomplished by using a hybrid mesomicroscopic traffic flow simulation modeling approach. The mesoscopic traffic flow simulation model loads the results of a user equilibrium traffic assignment solution and propagates the corresponding traffic through the entire system. The microscopic traffic flow simulation model provides background traffic around the vicinities where actual human beings are navigating the system. The two traffic flow simulation models interact continuously to update system conditions based on the interactions between actual humans and the fully simulated entities. Implementation efforts are currently in progress and some preliminary tests of individual components have been conducted. The implementation of the proposed architecture faces significant challenges ranging from multiplatform and multilanguage integration to multievent communication and coordination. PMID:26491711

Airport Landside - Volume III : ALSIM Calibration and Validation.

DOT National Transportation Integrated Search

1982-06-01

This volume discusses calibration and validation procedures applied to the Airport Landside Simulation Model (ALSIM), using data obtained at Miami, Denver and LaGuardia Airports. Criteria for the selection of a validation methodology are described. T...

DFT-based molecular modeling and vibrational study of the La(III) complex of 3,3'-(benzylidene)bis(4-hydroxycoumarin).

PubMed

Mihaylov, Tzvetan; Trendafilova, Natasha; Georgieva, Ivelina

2008-05-01

Molecular modeling of the La(III) complex of 3,3'-(benzylidene)bis(4-hydroxycoumarin) (PhDC) was performed using density functional theory (DFT) methods at B3LYP/6-31G(d) and BP86/TZP levels. Both Stuttgart-Dresden effective core potential and ZORA approximation were applied to the La(III) center. The electron density distribution and the nucleophilic centers of the deprotonated ligand PhDC(2-) in a solvent environment were estimated on the basis of Hirshfeld atomic charges, electrostatic potential values at the nuclei, and Nalewajski-Mrozek bond orders. In accordance with the empirical formula La(PhDC)(OH)(H(2)O), a chain structure of the complex was simulated by means of two types of molecular fragment: (1) two La(III) cations bound to one PhDC(2-) ligand, and (2) two PhDC(2-) ligands bound to one La(III) cation. Different orientations of PhDC(2-), OH(-) and H(2)O ligands in the La(III) complexes were investigated using 20 possible [La(PhDC(2-))(2)(OH)(H(2)O)](2-) fragments. Energy calculations predicted that the prism-like structure based on "tail-head" cis-LML2 type binding and stabilized via HO...HOH intramolecular hydrogen bonds is the most probable structure for the La(III) complex. The calculated vibrational spectrum of the lowest energy La(III) model fragment is in very good agreement with the experimental IR spectrum of the complex, supporting the suggested ligand binding mode to La(III) in a chain structure, namely, every PhDC(2-) interacts with two La(III) cations through both carbonylic and both hydroxylic oxygens, and every La(III) cation binds four oxygen atoms of two different PhDC(2-).

Synthetic nebular emission from massive galaxies - I: origin of the cosmic evolution of optical emission-line ratios

NASA Astrophysics Data System (ADS)

Hirschmann, Michaela; Charlot, Stephane; Feltre, Anna; Naab, Thorsten; Choi, Ena; Ostriker, Jeremiah P.; Somerville, Rachel S.

2017-12-01

Galaxies occupy different regions of the [O III]λ5007/H β-versus-[N II]λ6584/H α emission-line ratio diagram in the distant and local Universe. We investigate the origin of this intriguing result by modelling self-consistently, for the first time, nebular emission from young stars, accreting black holes (BHs) and older, post-asymptotic giant branch (post-AGB) stellar populations in galaxy formation simulations in a full cosmological context. In post-processing, we couple new-generation nebular-emission models with high-resolution, cosmological zoom-in simulations of massive galaxies to explore which galaxy physical properties drive the redshift evolution of the optical-line ratios [O III]λ5007/H β, [N II]λ6584/H α, [S II]λλ6717, 6731/H α and [O I]λ6300/H α. The line ratios of simulated galaxies agree well with observations of both star-forming and active local Sloan Digital Sky Survey galaxies. Towards higher redshifts, at fixed galaxy stellar mass, the average [O III]/H β is predicted to increase and [N II]/H α, [S II]/H α and [O I]/H α to decrease - widely consistent with observations. At fixed stellar mass, we identify star formation history, which controls nebular emission from young stars via the ionization parameter, as the primary driver of the cosmic evolution of [O III]/H β and [N II]/H α. For [S II]/H α and [O I]/H α, this applies only to redshifts greater than z = 1.5, the evolution at lower redshift being driven in roughly equal parts by nebular emission from active galactic nuclei and post-AGB stellar populations. Instead, changes in the hardness of ionizing radiation, ionized-gas density, the prevalence of BH accretion relative to star formation and the dust-to-metal mass ratio (whose impact on the gas-phase N/O ratio we model at fixed O/H) play at most a minor role in the cosmic evolution of simulated galaxy line ratios.

Atmospheric Dissolved Iron Depostiion to the Global Oceans: Effects of Oxalate-Promoted Fe Dissolution, Photochemical Redox Cycling, and Dust Mineralogy

NASA Technical Reports Server (NTRS)

Johnson, M. S.; Meskhidze, N.

2013-01-01

Mineral dust deposition is suggested to be a significant atmospheric supply pathway of bioavailable iron (Fe) to Fe-depleted surface oceans. In this study, mineral dust and dissolved Fe (Fed) deposition rates are predicted for March 2009 to February 2010 using the 3-D chemical transport model GEOS-Chem implemented with a comprehensive dust-Fe dissolution scheme. The model simulates Fed production during the atmospheric transport of mineral dust taking into account inorganic and organic (oxalate)-promoted Fe dissolution processes, photochemical redox cycling between ferric (Fe(III)) and ferrous (Fe(II)) forms of Fe, dissolution of three different Fe-containing minerals (hematite, goethite, and aluminosilicates), and detailed mineralogy of windblown dust from the major desert regions. Our calculations suggest that during the yearlong simulation is approximately 0.26 Tg (1 Tg = 1012 g) of Fed was deposited to global oceanic regions. Compared to simulations only taking into account proton-promoted Fe dissolution, the addition of oxalate to the dust-Fe mobilization scheme increased total annual model-predicted Fed deposition to global oceanic regions by approximately 75%. The implementation of Fe(II)/Fe(III) photochemical redox cycling in the model allows for the distinction between different oxidation states of deposited Fed. Our calculations suggest that during the daytime, large fractions of Fed deposited to the global oceans is likely to be in Fe(II) form, while nocturnal fluxes of Fed are largely in Fe(III) form. Model simulations also show that atmospheric fluxes of Fed can be strongly influenced by the mineralogy of Fe-containing compounds. This study shows that Fed deposition to the oceans is controlled by total dust-Fe mass concentrations, mineralogy, the surface area of dust particles, atmospheric chemical composition, cloud processing, and meteorological parameters and exhibits complex and spatiotemporally variable patterns. Our study suggests that the explicit model representation of individual processes leading to Fed production within mineral dust are needed to improve the understanding of the atmospheric Fe cycle, and quantify the effect of dust-Fe on ocean biological productivity, carbon cycle, and climate.

iCrowd: agent-based behavior modeling and crowd simulator

NASA Astrophysics Data System (ADS)

Kountouriotis, Vassilios I.; Paterakis, Manolis; Thomopoulos, Stelios C. A.

2016-05-01

Initially designed in the context of the TASS (Total Airport Security System) FP-7 project, the Crowd Simulation platform developed by the Integrated Systems Lab of the Institute of Informatics and Telecommunications at N.C.S.R. Demokritos, has evolved into a complete domain-independent agent-based behavior simulator with an emphasis on crowd behavior and building evacuation simulation. Under continuous development, it reflects an effort to implement a modern, multithreaded, data-oriented simulation engine employing latest state-of-the-art programming technologies and paradigms. It is based on an extensible architecture that separates core services from the individual layers of agent behavior, offering a concrete simulation kernel designed for high-performance and stability. Its primary goal is to deliver an abstract platform to facilitate implementation of several Agent-Based Simulation solutions with applicability in several domains of knowledge, such as: (i) Crowd behavior simulation during [in/out] door evacuation. (ii) Non-Player Character AI for Game-oriented applications and Gamification activities. (iii) Vessel traffic modeling and simulation for Maritime Security and Surveillance applications. (iv) Urban and Highway Traffic and Transportation Simulations. (v) Social Behavior Simulation and Modeling.

Fibronectin module FN(III)9 adsorption at contrasting solid model surfaces studied by atomistic molecular dynamics.

PubMed

Kubiak-Ossowska, Karina; Mulheran, Paul A; Nowak, Wieslaw

2014-08-21

The mechanism of human fibronectin adhesion synergy region (known as integrin binding region) in repeat 9 (FN(III)9) domain adsorption at pH 7 onto various and contrasting model surfaces has been studied using atomistic molecular dynamics simulations. We use an ionic model to mimic mica surface charge density but without a long-range electric field above the surface, a silica model with a long-range electric field similar to that found experimentally, and an Au {111} model with no partial charges or electric field. A detailed description of the adsorption processes and the contrasts between the various model surfaces is provided. In the case of our model silica surface with a long-range electrostatic field, the adsorption is rapid and primarily driven by electrostatics. Because it is negatively charged (-1e), FN(III)9 readily adsorbs to a positively charged surface. However, due to its partial charge distribution, FN(III)9 can also adsorb to the negatively charged mica model because of the absence of a long-range repulsive electric field. The protein dipole moment dictates its contrasting orientation at these surfaces, and the anchoring residues have opposite charges to the surface. Adsorption on the model Au {111} surface is possible, but less specific, and various protein regions might be involved in the interactions with the surface. Despite strongly influencing the protein mobility, adsorption at these model surfaces does not require wholesale FN(III)9 conformational changes, which suggests that the biological activity of the adsorbed protein might be preserved.

Optimization of vehicle deceleration to reduce occupant injury risks in frontal impact.

PubMed

Mizuno, Koji; Itakura, Takuya; Hirabayashi, Satoko; Tanaka, Eiichi; Ito, Daisuke

2014-01-01

In vehicle frontal impacts, vehicle acceleration has a large effect on occupant loadings and injury risks. In this research, an optimal vehicle crash pulse was determined systematically to reduce injury measures of rear seat occupants by using mathematical simulations. The vehicle crash pulse was optimized based on a vehicle deceleration-deformation diagram under the conditions that the initial velocity and the maximum vehicle deformation were constant. Initially, a spring-mass model was used to understand the fundamental parameters for optimization. In order to investigate the optimization under a more realistic situation, the vehicle crash pulse was also optimized using a multibody model of a Hybrid III dummy seated in the rear seat for the objective functions of chest acceleration and chest deflection. A sled test using a Hybrid III dummy was carried out to confirm the simulation results. Finally, the optimal crash pulses determined from the multibody simulation were applied to a human finite element (FE) model. The optimized crash pulse to minimize the occupant deceleration had a concave shape: a high deceleration in the initial phase, low in the middle phase, and high again in the final phase. This crash pulse shape depended on the occupant restraint stiffness. The optimized crash pulse determined from the multibody simulation was comparable to that from the spring-mass model. From the sled test, it was demonstrated that the optimized crash pulse was effective for the reduction of chest acceleration. The crash pulse was also optimized for the objective function of chest deflection. The optimized crash pulse in the final phase was lower than that obtained for the minimization of chest acceleration. In the FE analysis of the human FE model, the optimized pulse for the objective function of the Hybrid III chest deflection was effective in reducing rib fracture risks. The optimized crash pulse has a concave shape and is dependent on the occupant restraint stiffness and maximum vehicle deformation. The shapes of the optimized crash pulse in the final phase were different for the objective functions of chest acceleration and chest deflection due to the inertial forces of the head and upper extremities. From the human FE model analysis it was found that the optimized crash pulse for the Hybrid III chest deflection can substantially reduce the risk of rib cage fractures. Supplemental materials are available for this article. Go to the publisher's online edition of Traffic Injury Prevention to view the supplemental file.

Linearity can account for the similarity among conventional, frequency-doubling, and gabor-based perimetric tests in the glaucomatous macula.

PubMed

Sun, Hao; Dul, Mitchell W; Swanson, William H

2006-07-01

The purposes of this study are to compare macular perimetric sensitivities for conventional size III, frequency-doubling, and Gabor stimuli in terms of Weber contrast and to provide a theoretical interpretation of the results. Twenty-two patients with glaucoma performed four perimetric tests: a conventional Swedish Interactive Threshold Algorithm (SITA) 10-2 test with Goldmann size III stimuli, two frequency-doubling tests (FDT 10-2, FDT Macula) with counterphase-modulated grating stimuli, and a laboratory-designed test with Gabor stimuli. Perimetric sensitivities were converted to the reciprocal of Weber contrast and sensitivities from different tests were compared using the Bland-Altman method. Effects of ganglion cell loss on perimetric sensitivities were then simulated with a two-stage neural model. The average perimetric loss was similar for all stimuli until advanced stages of ganglion cell loss, in which perimetric loss tended to be greater for size III stimuli than for frequency-doubling and Gabor stimuli. Comparison of the experimental data and model simulation suggests that, in the macula, linear relations between ganglion cell loss and perimetric sensitivity loss hold for all three stimuli. Linear relations between perimetric loss and ganglion cell loss for all three stimuli can account for the similarity in perimetric loss until advanced stages. The results do not support the hypothesis that redundancy for frequency-doubling stimuli is lower than redundancy for size III stimuli.

Analytic drain current model for III-V cylindrical nanowire transistors

NASA Astrophysics Data System (ADS)

Marin, E. G.; Ruiz, F. G.; Schmidt, V.; Godoy, A.; Riel, H.; Gámiz, F.

2015-07-01

An analytical model is proposed to determine the drain current of III-V cylindrical nanowires (NWs). The model uses the gradual channel approximation and takes into account the complete analytical solution of the Poisson and Schrödinger equations for the Γ-valley and for an arbitrary number of subbands. Fermi-Dirac statistics are considered to describe the 1D electron gas in the NWs, being the resulting recursive Fermi-Dirac integral of order -1/2 successfully integrated under reasonable assumptions. The model has been validated against numerical simulations showing excellent agreement for different semiconductor materials, diameters up to 40 nm, gate overdrive biases up to 0.7 V, and densities of interface states up to 1013eV-1cm-2 .

Evaluating remedial alternatives for an acid mine drainage stream: Application of a reactive transport model

USGS Publications Warehouse

Runkel, R.L.; Kimball, B.A.

2002-01-01

A reactive transport model based on one-dimensional transport and equilibrium chemistry is applied to synoptic data from an acid mine drainage stream. Model inputs include streamflow estimates based on tracer dilution, inflow chemistry based on synoptic sampling, and equilibrium constants describing acid/base, complexation, precipitation/dissolution, and sorption reactions. The dominant features of observed spatial profiles in pH and metal concentration are reproduced along the 3.5-km study reach by simulating the precipitation of Fe(III) and Al solid phases and the sorption of Cu, As, and Pb onto freshly precipitated iron-(III) oxides. Given this quantitative description of existing conditions, additional simulations are conducted to estimate the streamwater quality that could result from two hypothetical remediation plans. Both remediation plans involve the addition of CaCO3 to raise the pH of a small, acidic inflow from ???2.4 to ???7.0. This pH increase results in a reduced metal load that is routed downstream by the reactive transport model, thereby providing an estimate of post-remediation water quality. The first remediation plan assumes a closed system wherein inflow Fe(II) is not oxidized by the treatment system; under the second remediation plan, an open system is assumed, and Fe(II) is oxidized within the treatment system. Both plans increase instream pH and substantially reduce total and dissolved concentrations of Al, As, Cu, and Fe(II+III) at the terminus of the study reach. Dissolved Pb concentrations are reduced by ???18% under the first remediation plan due to sorption onto iron-(III) oxides within the treatment system and stream channel. In contrast, iron(III) oxides are limiting under the second remediation plan, and removal of dissolved Pb occurs primarily within the treatment system. This limitation results in an increase in dissolved Pb concentrations over existing conditions as additional downstream sources of Pb are not attenuated by sorption.

Experimental Study of Fluid Structure Interaction Effects on Metal Plates Under Fully Developed Laminar Flow

DTIC Science & Technology

2011-12-01

UU NSN 7540–01–280–5500 Standard Form 298 (Rev. 8–98) Prescribed by ANSI Std. Z39.18 ii THIS PAGE INTENTIONALLY LEFT BLANK iii Approved for...modeled using the finite element analysis simulation code, ANSYS 13.0. The main objective of these simulations was to determine the location at which...transient response of the test plate under FSI conditions, computational studies were carried out in ANSYS 13.0 Multi-field (MFX) simulation

Adsorption of Eu(III) onto TiO2: effect of pH, concentration, ionic strength and soil fulvic acid.

PubMed

Tan, Xiaoli; Fang, Ming; Li, Jiaxing; Lu, Yi; Wang, Xiangke

2009-08-30

The effects of pH, initial Eu(III) concentration, ionic strength and fulvic acid (FA) on the adsorption of Eu(III) on TiO(2) are investigated by using batch techniques. The results indicate that the presence of FA strongly enhances the adsorption of Eu(III) on TiO(2) at low pH values. Besides, the adsorption of Eu(III) on TiO(2) is significantly dependent on pH values and independent of ionic strength. The adsorption of Eu(III) on TiO(2) is attributed to inner-sphere surface complexation. The diffuse layer model (DLM) is applied to simulate the adsorption data, and fits the experimental data well with the aid of FITEQL 3.2. X-ray photoelectron spectroscopy (XPS) is performed to study the species of Eu(III) adsorbed on the surfaces of TiO(2)/FA-TiO(2) hybrids at a molecular level, which suggest that FA act as "bridge" between Eu(III) and TiO(2) particles to enhance the ability to adsorb Eu(III) in solution.

Modeling neuropeptide transport in various types of nerve terminals containing en passant boutons.

PubMed

Kuznetsov, I A; Kuznetsov, A V

2015-03-01

We developed a mathematical model for simulating neuropeptide transport inside dense core vesicles (DCVs) in axon terminals containing en passant boutons. The motivation for this research is a recent experimental study by Levitan and colleagues (Bulgari et al., 2014) which described DCV transport in nerve terminals of type Ib and type III as well as in nerve terminals of type Ib with the transcription factor DIMM. The goal of our modeling is validating the proposition put forward by Levitan and colleagues that the dramatic difference in DCV number in type Ib and type III terminals can be explained by the difference in DCV capture in type Ib and type III boutons rather than by differences in DCV anterograde transport and half-life of resident DCVs. The developed model provides a tool for studying the dynamics of DCV transport in various types of nerve terminals. The model is also an important step in gaining a better mechanistic understanding of transport processes in axons and identifying directions for the development of new models in this area. Copyright © 2014 Elsevier Inc. All rights reserved.

Reliability and maintainability assessment factors for reliable fault-tolerant systems

NASA Technical Reports Server (NTRS)

Bavuso, S. J.

1984-01-01

A long term goal of the NASA Langley Research Center is the development of a reliability assessment methodology of sufficient power to enable the credible comparison of the stochastic attributes of one ultrareliable system design against others. This methodology, developed over a 10 year period, is a combined analytic and simulative technique. An analytic component is the Computer Aided Reliability Estimation capability, third generation, or simply CARE III. A simulative component is the Gate Logic Software Simulator capability, or GLOSS. The numerous factors that potentially have a degrading effect on system reliability and the ways in which these factors that are peculiar to highly reliable fault tolerant systems are accounted for in credible reliability assessments. Also presented are the modeling difficulties that result from their inclusion and the ways in which CARE III and GLOSS mitigate the intractability of the heretofore unworkable mathematics.

Predicting the locations of possible long-lived low-mass first stars: importance of satellite dwarf galaxies

NASA Astrophysics Data System (ADS)

Magg, Mattis; Hartwig, Tilman; Agarwal, Bhaskar; Frebel, Anna; Glover, Simon C. O.; Griffen, Brendan F.; Klessen, Ralf S.

2018-02-01

The search for metal-free stars has so far been unsuccessful, proving that if there are surviving stars from the first generation, they are rare, they have been polluted or we have been looking in the wrong place. To predict the likely location of Population III (Pop III) survivors, we semi-analytically model early star formation in progenitors of Milky Way-like galaxies and their environments. We base our model on merger trees from the high-resolution dark matter only simulation suite Caterpillar. Radiative and chemical feedback are taken into account self-consistently, based on the spatial distribution of the haloes. Our results are consistent with the non-detection of Pop III survivors in the Milky Way today. We find that possible surviving Pop III stars are more common in Milky Way satellites than in the main Galaxy. In particular, low-mass Milky Way satellites contain a much larger fraction of Pop III stars than the Milky Way. Such nearby, low-mass Milky Way satellites are promising targets for future attempts to find Pop III survivors, especially for high-resolution, high signal-to-noise spectroscopic observations. We provide the probabilities of finding a Pop III survivor in the red giant branch phase for all known Milky Way satellites to guide future observations.

Analysis and Operational Feasibility of Potable Water Production

DTIC Science & Technology

2015-09-01

III. MODELING, SIMULATION, AND TEST RESULTS ANALYSIS ..............27 A. INTRODUCTION...Regions of Study ......................57 Table 10. Drinking Water Tests ...chemicals, and coliform bacteria. Testing of the condensed water is important to ensure potability, as common tests have been conducted to ensure

Simulation of a Diode Pumped Alkali Laser; a Three Level Numerical Approach

DTIC Science & Technology

2010-03-01

The model will be developed to aid in the research and design of new DPAL systems. A DPAL is a relatively new type of laser which relies on laser...DPAL system to the fidelity required to perform testing and investigation of new systems without the creation of an experimental apparatus. Hence, to...1 26.24 * 10-9 H*Lewis Hz*L; A32@85D = 0; A32@87D = 0; III. Parameters Printed by Mathematica for Students 65 III. Parameters A. Enviromental

Integrated Nuclear and Conventional Theater Warfare Simulation (INWARS) Level III Specifications. Volume III. Air Combat Modeling.

DTIC Science & Technology

1978-07-24

will include an implicit air function that will perform the air planning and requesting associated with the various headquarters. The decision structure...air headquarters (The ATAF/TAA) will be included in the CIC to perform the implementation of the decisions /goals of the C21 elements, 1-4...realistic fashion. Once the AMPs have been formed, the operational process of launching, mission implementation etc. is no longer keyed to the decision cycle

Detectability of the first cosmic explosions

NASA Astrophysics Data System (ADS)

de Souza, R. S.; Ishida, E. E. O.; Johnson, J. L.; Whalen, D. J.; Mesinger, A.

2013-12-01

We present a fully self-consistent simulation of a synthetic survey of the furthermost cosmic explosions. The appearance of the first generation of stars (Population III) in the Universe represents a critical point during cosmic evolution, signalling the end of the dark ages, a period of absence of light sources. Despite their importance, there is no confirmed detection of Population III stars so far. A fraction of these primordial stars are expected to die as pair-instability supernovae (PISNe), and should be bright enough to be observed up to a few hundred million years after the big bang. While the quest for Population III stars continues, detailed theoretical models and computer simulations serve as a testbed for their observability. With the upcoming near-infrared missions, estimates of the feasibility of detecting PISNe are not only timely but imperative. To address this problem, we combine state-of-the-art cosmological and radiative simulations into a complete and self-consistent framework, which includes detailed features of the observational process. We show that a dedicated observational strategy using ≲ 8 per cent of the total allocation time of the James Webb Space Telescope mission can provide us with up to ˜9-15 detectable PISNe per year.

Gstat: a program for geostatistical modelling, prediction and simulation

NASA Astrophysics Data System (ADS)

Pebesma, Edzer J.; Wesseling, Cees G.

1998-01-01

Gstat is a computer program for variogram modelling, and geostatistical prediction and simulation. It provides a generic implementation of the multivariable linear model with trends modelled as a linear function of coordinate polynomials or of user-defined base functions, and independent or dependent, geostatistically modelled, residuals. Simulation in gstat comprises conditional or unconditional (multi-) Gaussian sequential simulation of point values or block averages, or (multi-) indicator sequential simulation. Besides many of the popular options found in other geostatistical software packages, gstat offers the unique combination of (i) an interactive user interface for modelling variograms and generalized covariances (residual variograms), that uses the device-independent plotting program gnuplot for graphical display, (ii) support for several ascii and binary data and map file formats for input and output, (iii) a concise, intuitive and flexible command language, (iv) user customization of program defaults, (v) no built-in limits, and (vi) free, portable ANSI-C source code. This paper describes the class of problems gstat can solve, and addresses aspects of efficiency and implementation, managing geostatistical projects, and relevant technical details.

Model-based dose selection for phase III rivaroxaban study in Japanese patients with non-valvular atrial fibrillation.

PubMed

Tanigawa, Takahiko; Kaneko, Masato; Hashizume, Kensei; Kajikawa, Mariko; Ueda, Hitoshi; Tajiri, Masahiro; Paolini, John F; Mueck, Wolfgang

2013-01-01

The global ROCKET AF phase III trial evaluated rivaroxaban 20 mg once daily (o.d.) for stroke prevention in atrial fibrillation (AF). Based on rivaroxaban pharmacokinetics in Japanese subjects and lower anticoagulation preferences in Japan, particularly in elderly patients, the optimal dose regimen for Japanese AF patients was considered. The aim of this analysis was dose selection for Japanese patients from a pharmacokinetic aspect by comparison of simulated exposure in Japanese patients with those in Caucasian patients. As a result of population pharmacokinetics-pharmacodynamics analyses, a one-compartment pharmacokinetic model with first-order absorption and direct link pharmacokinetic-pharmacodynamic models optimally described the plasma concentration and pharmacodynamic models (Factor Xa activity, prothrombin time, activated partial thromboplastin time, and HepTest), which were also consistent with previous works. Steady-state simulations indicated 15 mg rivaroxaban o.d. doses in Japanese patients with AF would yield exposures comparable to the 20 mg o.d. dose in Caucasian patients with AF. In conclusion, in the context of the lower anticoagulation targets in Japanese practice, the population pharmacokinetic and pharmacodynamic modeling supports 15 mg o.d. as the principal rivaroxaban dose in J-ROCKET AF.

INL Results for Phases I and III of the OECD/NEA MHTGR-350 Benchmark

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

Gerhard Strydom; Javier Ortensi; Sonat Sen

2013-09-01

The Idaho National Laboratory (INL) Very High Temperature Reactor (VHTR) Technology Development Office (TDO) Methods Core Simulation group led the construction of the Organization for Economic Cooperation and Development (OECD) Modular High Temperature Reactor (MHTGR) 350 MW benchmark for comparing and evaluating prismatic VHTR analysis codes. The benchmark is sponsored by the OECD's Nuclear Energy Agency (NEA), and the project will yield a set of reference steady-state, transient, and lattice depletion problems that can be used by the Department of Energy (DOE), the Nuclear Regulatory Commission (NRC), and vendors to assess their code suits. The Methods group is responsible formore » defining the benchmark specifications, leading the data collection and comparison activities, and chairing the annual technical workshops. This report summarizes the latest INL results for Phase I (steady state) and Phase III (lattice depletion) of the benchmark. The INSTANT, Pronghorn and RattleSnake codes were used for the standalone core neutronics modeling of Exercise 1, and the results obtained from these codes are compared in Section 4. Exercise 2 of Phase I requires the standalone steady-state thermal fluids modeling of the MHTGR-350 design, and the results for the systems code RELAP5-3D are discussed in Section 5. The coupled neutronics and thermal fluids steady-state solution for Exercise 3 are reported in Section 6, utilizing the newly developed Parallel and Highly Innovative Simulation for INL Code System (PHISICS)/RELAP5-3D code suit. Finally, the lattice depletion models and results obtained for Phase III are compared in Section 7. The MHTGR-350 benchmark proved to be a challenging simulation set of problems to model accurately, and even with the simplifications introduced in the benchmark specification this activity is an important step in the code-to-code verification of modern prismatic VHTR codes. A final OECD/NEA comparison report will compare the Phase I and III results of all other international participants in 2014, while the remaining Phase II transient case results will be reported in 2015.« less

HAWK MACH-III Intelligent Maintenance Tutor Design Development Report

DTIC Science & Technology

1986-12-01

objective can best be achieved by designing the MACH-IIl to provide augmented hands-on experience in troubleshooting in a setting which will emphasize...artificial intelligence supporting the development activity will focus on development of a strategy for effective and efficient hierarchical simulation of...main components of such a system are the system simulation and problem-solving expertise, the student model, and the tutorial strategies . In the MACH

FOSSIL2 energy policy model documentation: FOSSIL2 documentation

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

None

1980-10-01

This report discusses the structure, derivations, assumptions, and mathematical formulation of the FOSSIL2 model. Each major facet of the model - supply/demand interactions, industry financing, and production - has been designed to parallel closely the actual cause/effect relationships determining the behavior of the United States energy system. The data base for the FOSSIL2 program is large, as is appropriate for a system dynamics simulation model. When possible, all data were obtained from sources well known to experts in the energy field. Cost and resource estimates are based on DOE data whenever possible. This report presents the FOSSIL2 model at severalmore » levels. Volumes II and III of this report list the equations that comprise the FOSSIL2 model, along with variable definitions and a cross-reference list of the model variables. Volume III lists the model equations and a one line definition for equations, in a short, readable format.« less

Interaction Behavior between Thrust Faulting and the National Highway No. 3 - Tianliao III bridge as Determined using Numerical Simulation

NASA Astrophysics Data System (ADS)

Li, C. H.; Wu, L. C.; Chan, P. C.; Lin, M. L.

2016-12-01

The National Highway No. 3 - Tianliao III Bridge is located in the southwestern Taiwan mudstone area and crosses the Chekualin fault. Since the bridge was opened to traffic, it has been repaired 11 times. To understand the interaction behavior between thrust faulting and the bridge, a discrete element method-based software program, PFC, was applied to conduct a numerical analysis. A 3D model for simulating the thrust faulting and bridge was established, as shown in Fig. 1. In this conceptual model, the length and width were 50 and 10 m, respectively. Part of the box bottom was moveable, simulating the displacement of the thrust fault. The overburden stratum had a height of 5 m with fault dip angles of 20° (Fig. 2). The bottom-up strata were mudstone, clay, and sand, separately. The uplift was 1 m, which was 20% of the stratum thickness. In accordance with the investigation, the position of the fault tip was set, depending on the fault zone, and the bridge deformation was observed (Fig. 3). By setting "Monitoring Balls" in the numerical model to analyzes bridge displacement, we determined that the bridge deck deflection increased as the uplift distance increased. Furthermore, the force caused by the loading of the bridge deck and fault dislocation was determined to cause a down deflection of the P1 and P2 bridge piers. Finally, the fault deflection trajectory of the P4 pier displayed the maximum displacement (Fig. 4). Similar behavior has been observed through numerical simulation as well as field monitoring data. Usage of the discrete element model (PFC3D) to simulate the deformation behavior between thrust faulting and the bridge provided feedback for the design and improved planning of the bridge.

Storm Water Management Model Reference Manual Volume II ...

EPA Pesticide Factsheets

SWMM is a dynamic rainfall-runoff simulation model used for single event or long-term (continuous) simulation of runoff quantity and quality from primarily urban areas. The runoff component of SWMM operates on a collection of subcatchment areas that receive precipitation and generate runoff and pollutant loads. The routing portion of SWMM transports this runoff through a system of pipes, channels, storage/treatment devices, pumps, and regulators. SWMM tracks the quantity and quality of runoff generated within each subcatchment, and the flow rate, flow depth, and quality of water in each pipe and channel during a simulation period comprised of multiple time steps. The reference manual for this edition of SWMM is comprised of three volumes. Volume I describes SWMM’s hydrologic models, Volume II its hydraulic models, and Volume III its water quality and low impact development models. This document provides the underlying mathematics for the hydraulic calculations of the Storm Water Management Model (SWMM)

A magnetostructural study of linear NiII MnIII NiII, NiII CrIII NiII and triangular Ni(II)3 species containing (pyridine-2-aldoximato)nickel(II) unit as a building block.

PubMed

Weyhermüller, Thomas; Wagner, Rita; Khanra, Sumit; Chaudhuri, Phalguni

2005-08-07

Three trinuclear complexes, NiII MnIII NiII, NiII CrIII NiII and Ni(II)3 based on (pyridine-2-aldoximato)nickel(II) units are described. Two of them, and , contain metal-centers in linear arrangement, as is revealed by X-ray diffraction. Complex is a homonuclear complex in which the three nickel(II) centers are disposed in a triangular fashion. The compounds were characterized by various physical methods including cyclic voltammetric and variable-temperature (2-290 K) susceptibility measurements. Complexes and display antiferromagnetic exchange coupling of the neighbouring metal centers, while weak ferromagnetic spin exchange between the adjacent Ni II and Cr III ions in is observed. The experimental magnetic data were simulated by using appropriate models.

Microphysics of Clouds with the Relaxed Arakawa-Schubert Scheme (McRAS). Part I: Design and Evaluation with GATE Phase III Data.

NASA Astrophysics Data System (ADS)

Sud, Y. C.; Walker, G. K.

1999-09-01

A prognostic cloud scheme named McRAS (Microphysics of Clouds with Relaxed Arakawa-Schubert Scheme) has been designed and developed with the aim of improving moist processes, microphysics of clouds, and cloud-radiation interactions in GCMs. McRAS distinguishes three types of clouds: convective, stratiform, and boundary layer. The convective clouds transform and merge into stratiform clouds on an hourly timescale, while the boundary layer clouds merge into the stratiform clouds instantly. The cloud condensate converts into precipitation following the autoconversion equations of Sundqvist that contain a parametric adaptation for the Bergeron-Findeisen process of ice crystal growth and collection of cloud condensate by precipitation. All clouds convect, advect, as well as diffuse both horizontally and vertically with a fully interactive cloud microphysics throughout the life cycle of the cloud, while the optical properties of clouds are derived from the statistical distribution of hydrometeors and idealized cloud geometry.An evaluation of McRAS in a single-column model (SCM) with the Global Atmospheric Research Program Atlantic Tropical Experiment (GATE) Phase III data has shown that, together with the rest of the model physics, McRAS can simulate the observed temperature, humidity, and precipitation without discernible systematic errors. The time history and time mean in-cloud water and ice distribution, fractional cloudiness, cloud optical thickness, origin of precipitation in the convective anvils and towers, and the convective updraft and downdraft velocities and mass fluxes all simulate a realistic behavior. Some of these diagnostics are not verifiable with data on hand. These SCM sensitivity tests show that (i) without clouds the simulated GATE-SCM atmosphere is cooler than observed; (ii) the model's convective scheme, RAS, is an important subparameterization of McRAS; and (iii) advection of cloud water substance is helpful in simulating better cloud distribution and cloud-radiation interaction. An evaluation of the performance of McRAS in the Goddard Earth Observing System II GCM is given in a companion paper (Part II).

Main steam line break accident simulation of APR1400 using the model of ATLAS facility

NASA Astrophysics Data System (ADS)

Ekariansyah, A. S.; Deswandri; Sunaryo, Geni R.

2018-02-01

A main steam line break simulation for APR1400 as an advanced design of PWR has been performed using the RELAP5 code. The simulation was conducted in a model of thermal-hydraulic test facility called as ATLAS, which represents a scaled down facility of the APR1400 design. The main steam line break event is described in a open-access safety report document, in which initial conditions and assumptionsfor the analysis were utilized in performing the simulation and analysis of the selected parameter. The objective of this work was to conduct a benchmark activities by comparing the simulation results of the CESEC-III code as a conservative approach code with the results of RELAP5 as a best-estimate code. Based on the simulation results, a general similarity in the behavior of selected parameters was observed between the two codes. However the degree of accuracy still needs further research an analysis by comparing with the other best-estimate code. Uncertainties arising from the ATLAS model should be minimized by taking into account much more specific data in developing the APR1400 model.

Adsorption Mechanisms of Trivalent Gold onto Iron Oxy-Hydroxides: From the Molecular Scale to the Model

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

Cances, Benjamin; /Marne La Vallee U.; Benedetti, Marc

2006-12-13

Gold is a highly valuable metal that can concentrate in iron-rich exogenetic horizons such as laterites. An improved knowledge of the retention mechanisms of gold onto highly reactive soil components such as iron oxyhydroxides is therefore needed to better understand and predict the geochemical behavior of this element. In this study, we use EXAFS information and titration experiments to provide a realistic thermochemical description of the sorption of trivalent gold onto iron oxy-hydroxides. Analysis of Au L{sub III}-edge XAFS spectra shows that aqueous Au(III) adsorbs from chloride solutions onto goethite surfaces as inner-sphere square-planar complexes (Au(III)(OH,Cl){sub 4}), with dominantly OHmore » ligands at pH > 6 and mixed OH/Cl ligands at lower pH values. In combination with these spectroscopic results, Reverse Monte Carlo simulations were used to constraint the possible sorption sites on the surface of goethite. Based on this structural information, we calculated sorption isotherms of Au(III) on Fe oxy-hydroxides surfaces, using the CD-MUSIC (Charge Distribution--Multi Site Complexation) model. The various Au(III)-sorbed species were identified as a function of pH, and the results of these EXAFS+CD-MUSIC models are compared with titration experiments. The overall good agreement between the predicted and measured structural models shows the potential of this combined approach to better model sorption processes of transition elements onto highly reactive solid surfaces such as goethite and ferrihydrite.« less

How the First Stars Regulated Star Formation. II. Enrichment by Nearby Supernovae

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

Chen, Ke-Jung; Whalen, Daniel J.; Wollenberg, Katharina M. J.

Metals from Population III (Pop III) supernovae led to the formation of less massive Pop II stars in the early universe, altering the course of evolution of primeval galaxies and cosmological reionization. There are a variety of scenarios in which heavy elements from the first supernovae were taken up into second-generation stars, but cosmological simulations only model them on the largest scales. We present small-scale, high-resolution simulations of the chemical enrichment of a primordial halo by a nearby supernova after partial evaporation by the progenitor star. We find that ejecta from the explosion crash into and mix violently with ablativemore » flows driven off the halo by the star, creating dense, enriched clumps capable of collapsing into Pop II stars. Metals may mix less efficiently with the partially exposed core of the halo, so it might form either Pop III or Pop II stars. Both Pop II and III stars may thus form after the collision if the ejecta do not strip all the gas from the halo. The partial evaporation of the halo prior to the explosion is crucial to its later enrichment by the supernova.« less

How the First Stars Regulated Star Formation. II. Enrichment by Nearby Supernovae

NASA Astrophysics Data System (ADS)

Chen, Ke-Jung; Whalen, Daniel J.; Wollenberg, Katharina M. J.; Glover, Simon C. O.; Klessen, Ralf S.

2017-08-01

Metals from Population III (Pop III) supernovae led to the formation of less massive Pop II stars in the early universe, altering the course of evolution of primeval galaxies and cosmological reionization. There are a variety of scenarios in which heavy elements from the first supernovae were taken up into second-generation stars, but cosmological simulations only model them on the largest scales. We present small-scale, high-resolution simulations of the chemical enrichment of a primordial halo by a nearby supernova after partial evaporation by the progenitor star. We find that ejecta from the explosion crash into and mix violently with ablative flows driven off the halo by the star, creating dense, enriched clumps capable of collapsing into Pop II stars. Metals may mix less efficiently with the partially exposed core of the halo, so it might form either Pop III or Pop II stars. Both Pop II and III stars may thus form after the collision if the ejecta do not strip all the gas from the halo. The partial evaporation of the halo prior to the explosion is crucial to its later enrichment by the supernova.

Descriptive and sensitivity analyses of WATBALI: A dynamic soil water model

NASA Technical Reports Server (NTRS)

Hildreth, W. W. (Principal Investigator)

1981-01-01

A soil water computer model that uses the IBM Continuous System Modeling Program III to solve the dynamic equations representing the soil, plant, and atmospheric physical or physiological processes considered is presented and discussed. Using values describing the soil-plant-atmosphere characteristics, the model predicts evaporation, transpiration, drainage, and soil water profile changes from an initial soil water profile and daily meteorological data. The model characteristics and simulations that were performed to determine the nature of the response to controlled variations in the input are described the results of the simulations are included and a change that makes the response of the model more closely represent the observed characteristics of evapotranspiration and profile changes for dry soil conditions is examined.

The earth's radiation budget and its relation to atmospheric hydrology. III - Comparison of observations over the oceans with a GCM

NASA Technical Reports Server (NTRS)

Stephens, Graeme L.; Randall, David A.; Wittmeyer, Ian L.; Dazlich, Donald A.; Tjemkes, Stephen

1993-01-01

The ability of the Colorado State University general circulation model (GCM) to simulate interactions between the hydrological cycle and the radiative processes on earth was examined by comparing various sensitivity relationships established by the model with those observed on earth, and the observed and calculated seasonal cycles of the greenhouse effect and cloud radiative forcing. Results showed that, although the GCM model used was able to simulate well some aspects of the observed sensitivities, there were many serious quantitative differences, including problems in the simulation of the column vapor in the tropics and an excessively strong clear-sky greenhouse effect in the mid-latitudes. These differences led to an underestimation by the model of the sensitivity of the clear-sky greenhouse to changes in sea surface temperature.

Atmospheric Test Models and Numerical Experiments for the Simulation of the Global Distributions of Weather Data Transponders III. Horizontal Distributions

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

Molenkamp, C.R.; Grossman, A.

1999-12-20

A network of small balloon-borne transponders which gather very high resolution wind and temperature data for use by modern numerical weather predication models has been proposed to improve the reliability of long-range weather forecasts. The global distribution of an array of such transponders is simulated using LLNL's atmospheric parcel transport model (GRANTOUR) with winds supplied by two different general circulation models. An initial study used winds from CCM3 with a horizontal resolution of about 3 degrees in latitude and longitude, and a second study used winds from NOGAPS with a 0.75 degree horizontal resolution. Results from both simulations show thatmore » reasonable global coverage can be attained by releasing balloons from an appropriate set of launch sites.« less

Linearity Can Account for the Similarity Among Conventional, Frequency-Doubling, and Gabor-Based Perimetric Tests in the Glaucomatous Macula

PubMed Central

DUL, MITCHELL W.; SWANSON, WILLIAM H.

2006-01-01

Purposes The purposes of this study are to compare macular perimetric sensitivities for conventional size III, frequency-doubling, and Gabor stimuli in terms of Weber contrast and to provide a theoretical interpretation of the results. Methods Twenty-two patients with glaucoma performed four perimetric tests: a conventional Swedish Interactive Threshold Algorithm (SITA) 10-2 test with Goldmann size III stimuli, two frequency-doubling tests (FDT 10-2, FDT Macula) with counterphase-modulated grating stimuli, and a laboratory-designed test with Gabor stimuli. Perimetric sensitivities were converted to the reciprocal of Weber contrast and sensitivities from different tests were compared using the Bland-Altman method. Effects of ganglion cell loss on perimetric sensitivities were then simulated with a two-stage neural model. Results The average perimetric loss was similar for all stimuli until advanced stages of ganglion cell loss, in which perimetric loss tended to be greater for size III stimuli than for frequency-doubling and Gabor stimuli. Comparison of the experimental data and model simulation suggests that, in the macula, linear relations between ganglion cell loss and perimetric sensitivity loss hold for all three stimuli. Conclusions Linear relations between perimetric loss and ganglion cell loss for all three stimuli can account for the similarity in perimetric loss until advanced stages. The results do not support the hypothesis that redundancy for frequency-doubling stimuli is lower than redundancy for size III stimuli. PMID:16840860

Genetic Simulation Tools for Post-Genome Wide Association Studies of Complex Diseases

PubMed Central

Amos, Christopher I.; Bafna, Vineet; Hauser, Elizabeth R.; Hernandez, Ryan D.; Li, Chun; Liberles, David A.; McAllister, Kimberly; Moore, Jason H.; Paltoo, Dina N.; Papanicolaou, George J.; Peng, Bo; Ritchie, Marylyn D.; Rosenfeld, Gabriel; Witte, John S.

2014-01-01

Genetic simulation programs are used to model data under specified assumptions to facilitate the understanding and study of complex genetic systems. Standardized data sets generated using genetic simulation are essential for the development and application of novel analytical tools in genetic epidemiology studies. With continuing advances in high-throughput genomic technologies and generation and analysis of larger, more complex data sets, there is a need for updating current approaches in genetic simulation modeling. To provide a forum to address current and emerging challenges in this area, the National Cancer Institute (NCI) sponsored a workshop, entitled “Genetic Simulation Tools for Post-Genome Wide Association Studies of Complex Diseases” at the National Institutes of Health (NIH) in Bethesda, Maryland on March 11-12, 2014. The goals of the workshop were to: (i) identify opportunities, challenges and resource needs for the development and application of genetic simulation models; (ii) improve the integration of tools for modeling and analysis of simulated data; and (iii) foster collaborations to facilitate development and applications of genetic simulation. During the course of the meeting the group identified challenges and opportunities for the science of simulation, software and methods development, and collaboration. This paper summarizes key discussions at the meeting, and highlights important challenges and opportunities to advance the field of genetic simulation. PMID:25371374

Hydroclimatic Controls on the Means and Variability of Vegetation Phenology and Carbon Uptake

NASA Technical Reports Server (NTRS)

Koster, Randal Dean; Walker, Gregory K.; Collatz, George J.; Thornton, Peter E.

2013-01-01

Long-term, global offline (land-only) simulations with a dynamic vegetation phenology model are used to examine the control of hydroclimate over vegetation-related quantities. First, with a control simulation, the model is shown to capture successfully (though with some bias) key observed relationships between hydroclimate and the spatial and temporal variations of phenological expression. In subsequent simulations, the model shows that: (i) the global spatial variation of seasonal phenological maxima is controlled mostly by hydroclimate, irrespective of distributions in vegetation type, (ii) the occurrence of high interannual moisture-related phenological variability in grassland areas is determined by hydroclimate rather than by the specific properties of grassland, and (iii) hydroclimatic means and variability have a corresponding impact on the spatial and temporal distributions of gross primary productivity (GPP).

Hindcast of breaking waves and its impact at an island sheltered coast, Karwar

NASA Astrophysics Data System (ADS)

Dora, G. Udhaba; Kumar, V. Sanil

2018-01-01

Variability in the characteristics of depth-induced wave breakers along a non-uniform coastal topography and its impact on the morpho-sedimentary processes is examined at the island sheltered wave-dominated micro-tidal coast, Karwar, west coast of India. Waves are simulated using the coupled wind wave model, SWAN nested in WAVEWATCH III, forced by the reanalysis winds from different sources (NCEP/NCAR, ECMWF, and NCEP/CFSR). Impact of the wave breakers is evaluated through mean longshore current and sediment transport for various wave energy conditions across different coastal morphology. Study revealed that the NCEP/CFSR wind is comparatively reasonable in simulation of nearshore waves using the SWAN model nested by 2D wave spectra generated from WAVEWATCH III. The Galvin formula for estimating mean longshore current using the crest wave period and the Kamphuis approximation for longshore sediment transport is observed realistically at the sheltered coastal environment while the coast interacts with spilling and plunging breakers.

Validation Testing a Contaminant Transport and Natural Attenuation Simulation Model Using Field Data.

DTIC Science & Technology

1995-12-01

reactions . The following figure shows the relationship of common electron acceptors with regard to their redox potential. Redox Potential (pH = 7) in...Model 8 Fuel-Spill Plume Profile 8 Hydrocarbon Biodegradation 1° Oxygen 11 Anaerobic Electron Acceptors 12 Redox Potential *4 Contaminants of...Biodegradation Reactions 21 Oxygen Reactions 21 Nitrate 22 Manganese (IV) 22 Iron (III) 23 Sulfate 24 in Page Intrinsic Bioremediation Model

An Enriched Shell Finite Element for Progressive Damage Simulation in Composite Laminates

NASA Technical Reports Server (NTRS)

McElroy, Mark W.

2016-01-01

A formulation is presented for an enriched shell nite element capable of progressive damage simulation in composite laminates. The element uses a discrete adaptive splitting approach for damage representation that allows for a straightforward model creation procedure based on an initially low delity mesh. The enriched element is veri ed for Mode I, Mode II, and mixed Mode I/II delamination simulation using numerical benchmark data. Experimental validation is performed using test data from a delamination-migration experiment. Good correlation was found between the enriched shell element model results and the numerical and experimental data sets. The work presented in this paper is meant to serve as a rst milestone in the enriched element's development with an ultimate goal of simulating three-dimensional progressive damage processes in multidirectional laminates.

Formation of the first galaxies under Population III stellar feedback

NASA Astrophysics Data System (ADS)

Jeon, Myoungwon

2015-01-01

The first galaxies, which formed a few hundred million years after the big bang, are related to important cosmological questions. Given thatthey are thought to be the basic building blocks of large galaxies seen today, understanding their formation and properties is essentialto studying galaxy formation as a whole. In this dissertation talk, I will present the results of our highly-resolved cosmological ab-initio simulations to understand the assembly process of first galaxies under the feedback from the preceding generations of first stars, the so-called Population III (Pop III). The first stars formed at z≲30 in dark matter (DM) minihalos with M_{vir}=10^5-10^6Msun, predominately via molecular hydrogen (H_2) cooling. Radiation from Pop III stars dramatically altered the gas within their host minihalos, through photoionization, photoheating, and photoevaporation. Once a Pop III star explodes as a supernova (SN), heavy elements are dispersed, enriching the interstellar (ISM) and intergalactic medium (IGM), thus initiating the process of chemical evolution. I will begin by presenting how the SN explosion of the first stars influences early cosmic history, specifically assessing the time delay in further star formation and tracing the evolution of metal-enriched gas until the second episode star formation happens. These results will show the role of Pop III supernovae on the star formation transition from Pop III to Population II. Additionally, the more distant, diffuse IGM was heated by X-rays emitted by accreting black holes (BHs), or high-mass X-ray binaries (HMXBs), both remnants of Pop III stars. I will present results of a series of simulations where we study the impact of X-ray feedback from BHs and HMXBs on the star formation history in the early universe, and discuss the resulting implications on reionization. I will also present the role of X-rays on the early BH growth, providing constraints on models for supermassive black hole formation. Finally, I will discuss key physical quantities of the first galaxies derived from our simulations, such as their stellar population mix, star formation rates, metallicities, and resulting broad-band color and recombination spectra.

A Pharmacometric Approach to Substitute for a Conventional Dose-Finding Study in Rare Diseases: Example of Phase III Dose Selection for Emicizumab in Hemophilia A.

PubMed

Yoneyama, Koichiro; Schmitt, Christophe; Kotani, Naoki; Levy, Gallia G; Kasai, Ryu; Iida, Satofumi; Shima, Midori; Kawanishi, Takehiko

2017-12-06

Emicizumab (ACE910) is a bispecific antibody mimicking the cofactor function of activated coagulation factor VIII. In phase I-I/II studies, emicizumab reduced the bleeding frequency in patients with severe hemophilia A, regardless of the presence of factor VIII inhibitors, at once-weekly subcutaneous doses of 0.3, 1, and 3 mg/kg. Using the phase I-I/II study data, population pharmacokinetic and repeated time-to-event (RTTE) modeling were performed to quantitatively characterize the relationship between the pharmacokinetics of emicizumab and reduction in bleeding frequency. Simulations were then performed to identify the minimal exposure expected to achieve zero bleeding events for 1 year in at least 50% of patients and to select the dosing regimens to be tested in phase III studies. The RTTE model adequately predicted the bleeding onset over time as a function of plasma emicizumab concentration. Simulations suggested that plasma emicizumab concentrations of ≥  45 μg/mL should result in zero bleeding events for 1 year in at least 50% of patients. This efficacious exposure provided the basis for selecting previously untested dosing regimens of 1.5 mg/kg once weekly, 3 mg/kg every 2 weeks, and 6 mg/kg every 4 weeks for phase III studies. A pharmacometric approach guided the phase III dose selection of emicizumab in hemophilia A, without conducting a conventional dose-finding study. Phase III studies with the selected dosing regimens are currently ongoing. This case study indicates that a pharmacometric approach can substitute for a conventional dose-finding study in rare diseases and will streamline the drug development process.

Mathematical modeling and numerical simulation of unilateral dynamic rupture propagation along very-long reverse faults

NASA Astrophysics Data System (ADS)

Hirano, S.

2017-12-01

For some great earthquakes, dynamic rupture propagates unilaterally along a horizontal direction of very-long reverse faults (e.g., the Mw9.1 Sumatra earthquake in 2004, the Mw8.0 Wenchuan earthquake in 2008, and the Mw8.8 Maule earthquake in 2010, etc.). It seems that barriers or creeping sections may not lay along the opposite region of the co-seismically ruptured direction. In fact, in the case of Sumatra, the Mw8.6 earthquake occurred in the opposite region only three months after the mainshock. Mechanism of unilateral mode-II rupture along a material interface has been investigated theoretically and numerically. For mode-II rupture propagating along a material interface, an analytical solution implies that co-seismic stress perturbation depends on the rupture direction (Weertman, 1980 JGR; Hirano & Yamashita, 2016 BSSA), and numerical modeling of plastic yielding contributes to simulating the unilateral rupture (DeDonteny et al., 2011 JGR). However, mode-III rupture may dominate for the very-long reverse faults, and it can be shown that stress perturbation due to mode-III rupture does not depend on the rupture direction. Hence, an effect of the material interface is insufficient to understand the mechanism of unilateral rupture along the very-long reverse faults. In this study, I consider a two-dimensional bimaterial system with interfacial dynamic mode-III rupture under an obliquely pre-stressed configuration (i.e., the maximum shear direction of the background stress is inclined from the interfacial fault). First, I derived an analytical solution of regularized elastic stress field around a steady-state interfacial slip pulse using the method of Rice et al. (2005 BSSA). Then I found that the total stress, which is the sum of the background stress and co-seismic stress perturbation, depends on the rupture direction even in the mode-III case. Second, I executed a finite difference numerical simulation with a plastic yielding model of Andrews (1978 JGR; 2005 JGR) and succeeded in a simulation of unilateral rupture propagation in some parameter ranges (see figure). This unilateral rupture might be caused by energy dissipation due to the plastic yielding process that concentrates in the vicinity of only one rupture tip depending on the rupture direction.

JAMS - a software platform for modular hydrological modelling

NASA Astrophysics Data System (ADS)

Kralisch, Sven; Fischer, Christian

2015-04-01

Current challenges of understanding and assessing the impacts of climate and land use changes on environmental systems demand for an ever-increasing integration of data and process knowledge in corresponding simulation models. Software frameworks that allow for a seamless creation of integrated models based on less complex components (domain models, process simulation routines) have therefore gained increasing attention during the last decade. JAMS is an Open-Source software framework that has been especially designed to cope with the challenges of eco-hydrological modelling. This is reflected by (i) its flexible approach for representing time and space, (ii) a strong separation of process simulation components from the declarative description of more complex models using domain specific XML, (iii) powerful analysis and visualization functions for spatial and temporal input and output data, and (iv) parameter optimization and uncertainty analysis functions commonly used in environmental modelling. Based on JAMS, different hydrological and nutrient-transport simulation models were implemented and successfully applied during the last years. We will present the JAMS core concepts and give an overview of models, simulation components and support tools available for that framework. Sample applications will be used to underline the advantages of component-based model designs and to show how JAMS can be used to address the challenges of integrated hydrological modelling.

Modeling and Proposed Molecular Mechanism of Hydroxyurea Through Docking and Molecular Dynamic Simulation to Curtail the Action of Ribonucleotide Reductase.

PubMed

Iman, Maryam; Khansefid, Zeynab; Davood, Asghar

2016-01-01

Ribonucleotide Reductase (RNR) is an important anticancer chemotherapy target. It has main key role in DNA synthesis and cell growth. Therefore several RNR inhibitors, such as hydroxyurea, have entered the clinical trials. Based on our proposed mechanism, radical site of RNR protein reacts with hydroxyurea in which hydroxyurea is converted into its oxidized form compound III, and whereby the tyrosyl radical is converted into a normal tyrosine residue. In this study, docking and molecular dynamics simulations were used for proposed molecular mechanism of hydroxyurea in RNR inhibition as anticancer agent. The binding affinity of hydroxyurea and compound III to RNR was studied by docking method. The docking study was performed for the crystal structure of human RNR with the radical scavenger Hydroxyurea and its oxidized form to inhibit the human RNR. hydroxyurea and compound III bind at the active site with Tyr-176, which are essential for free radical formation. This helps to understand the functional aspects and also aids in the development of novel inhibitors for the human RNR2. To confirm the binding mode of inhibitors, the molecular dynamics (MD) simulations were performed using GROMACS 4.5.5, based upon the docked conformation of inhibitors. Both of the studied compounds stayed in the active site. The results of MD simulations confirmed the binding mode of ligands, accuracy of docking and the reliability of active conformations which were obtained by AutoDock. MD studies confirm our proposed mechanism in which compound III reacts with the active site residues specially Tyr-176, and inhibits the radical generation and subsequently inhibits the RNR enzyme.

Computational modeling and simulation study of electronic and thermal properties in semiconductor nanostructures

NASA Astrophysics Data System (ADS)

Paul, Abhijeet

2011-07-01

The technological progress in dimensional scaling has not only kept Silicon CMOS industry on Moore's law for the past five decades but has also benefited many other areas such as thermoelectricity, photo-voltaics, and energy storage. Extending CMOS beyond Si (More Moore, MM) and adding functional diversity to CMOS (More Than Moore, MTM) requires a thorough understanding of the basic electron and heat flow in semiconductors. Along with experiments computer modeling and simulation are playing an increasingly vital role in exploring the numerous possibilities in materials, devices and systems. With these aspects in mind the present work applies computational physics modeling and simulations to explore the, (i) electronic, (ii) thermal, and (iii) thermoelectric properties in nano-scale semiconductors. The electronic structure of zinc-blende and lead-chalcogenide nano-materials is calculated using an atomistic Tight-Binding model. The phonon dispersion in zinc-blende materials is obtained using the Modified Valence Force Field model. Electronic and thermal transport at the nano-scale is explored using Green's function method and Landauer's method. Thermoelectric properties of semiconductor nanostructures are calculated using Landauer's method. Using computer modeling and simulations the variation of the three physical properties (i-iii) are explored with varying size, transport orientation, shape, porosity, strain and alloying of nanostructures. The key findings are, (a) III-Vs and Ge with optimized strain and orientation can improve transistors' and thermoelectric performance, (b) porous Si nanowires provide a lucrative idea for enhancing the thermoelectric efficiency at room temperature, and (c) Si/Ge superlattice nanowires can be used for nano-scale tuning of lattice thermal conductivity by period control. The present work led to the development of two new interface trap density extraction methods in ultra-scaled FinFETs and correlation of the phonon shifts in Si nanowires to their shape, size and orientation benchmarked against experimental Raman spectroscopy data, thereby enabling nano-scale metrology. Contribution of two research and six educational tools on nanoHUB.org forms an integral part of the work for global dissemination of semiconductor knowledge. Atomic level manipulation holds the key to engineer material properties at the nano-scale. The findings of this work will hopefully open and guide new ways of engineering the electronic and thermal properties for better performance.

Analysis of WakeVAS Benefits Using ACES Build 3.2.1

NASA Technical Reports Server (NTRS)

Smith, Jeremy C.

2005-01-01

The FAA and NASA are currently engaged in a Wake Turbulence Research Program to revise wake turbulence separation standards, procedures, and criteria to increase airport capacity while maintaining or increasing safety. The research program is divided into three phases: Phase I near term procedural enhancements; Phase II wind dependent Wake Vortex Advisory System (WakeVAS) Concepts of Operations (ConOps); and Phase III farther term ConOps based on wake prediction and sensing. This report contains an analysis that evaluates the benefits of a closely spaced parallel runway (CSPR) Phase I ConOps, a single runway and CSPR Phase II ConOps and a single runway Phase III ConOps. A series of simulation runs were performed using the Airspace Concepts Evaluation System (ACES) Build 3.21 air traffic simulator to provide an initial assessment of the reduction in delay and cost savings obtained by the use of a WakeVAS at selected U.S. airports. The ACES simulator is being developed by NASA Ames Research Center as part of the Virtual Airspace Modelling and Simulation (VAMS) program.

Adsorption of Rh(III) complexes from chloride solutions obtained by leaching chlorinated spent automotive catalysts on ion-exchange resin Diaion WA21J.

PubMed

Shen, Shaobo; Pan, Tonglin; Liu, Xinqiang; Yuan, Lei; Wang, Jinchao; Zhang, Yongjian; Guo, Zhanchen

2010-07-15

It was found that Rh, Pd and Pt contained in the spent ceramic automotive catalysts could be effectively extracted by dry chlorination with chlorine. In order to concentrate Rh(III) ions contained in the chloride solutions obtained, thermodynamic and kinetics studies for adsorption of Rh(III) complexes from the chloride solutions on an anionic exchange resin Diaion WA21J were carried out. Rh, Pd, Pt, Al, Fe, Si, Zn and Pb from the chloride solution could be adsorbed on the resin. The distribution coefficients (K(d)) of Rh(III) decreased with the increase in initial Rh(III) concentration or in adsorption temperature. The isothermal adsorption of Rh(III) was found to fit Langmuir, Freundlich and Dubinin-Kaganer-Radushkevich models under the adsorption conditions. The maximum monolayer adsorption capacities Q(max) based on Langmuir adsorption isotherms were 6.39, 6.61 and 5.81 mg/g for temperatures 18, 28 and 40 degrees C, respectively. The apparent adsorption energy of Rh was about -7.6 kJ/mol and thus Rh(III) adsorption was a physical type. The experimental data obtained could be better simulated by pseudo-first-order kinetic model and the activation energy obtained was 6.54 J/mol. The adsorption rate of Rh(III) was controlled by intraparticle diffusion in most of time of adsorption process. 2010 Elsevier B.V. All rights reserved.

Excited-state thermionic emission in III-antimonides: Low emittance ultrafast photocathodes

NASA Astrophysics Data System (ADS)

Berger, Joel A.; Rickman, B. L.; Li, T.; Nicholls, A. W.; Andreas Schroeder, W.

2012-11-01

The normalized rms transverse emittance of an electron source is shown to be proportional to √m* , where m* is the effective mass of the state from which the electron is emitted, by direct observation of the transverse momentum distribution for excited-state thermionic emission from two III-V semiconductor photocathodes, GaSb and InSb, together with a control experiment employing two-photon emission from gold. Simulations of the experiment using an extended analytical Gaussian model of electron pulse propagation are in close agreement with the data.

Validation of the 5th and 95th Percentile Hybrid III Anthropomorphic Test Device Finite Element Model

NASA Technical Reports Server (NTRS)

Lawrence, C.; Somers, J. T.; Baldwin, M. A.; Wells, J. A.; Newby, N.; Currie, N. J.

2014-01-01

NASA spacecraft design requirements for occupant protection are a combination of the Brinkley criteria and injury metrics extracted from anthropomorphic test devices (ATD's). For the ATD injury metrics, the requirements specify the use of the 5th percentile female Hybrid III and the 95th percentile male Hybrid III. Furthermore, each of these ATD's is required to be fitted with an articulating pelvis and a straight spine. The articulating pelvis is necessary for the ATD to fit into spacecraft seats, while the straight spine is required as injury metrics for vertical accelerations are better defined for this configuration. The requirements require that physical testing be performed with both ATD's to demonstrate compliance. Before compliance testing can be conducted, extensive modeling and simulation are required to determine appropriate test conditions, simulate conditions not feasible for testing, and assess design features to better ensure compliance testing is successful. While finite element (FE) models are currently available for many of the physical ATD's, currently there are no complete models for either the 5th percentile female or the 95th percentile male Hybrid III with a straight spine and articulating pelvis. The purpose of this work is to assess the accuracy of the existing Livermore Software Technology Corporation's FE models of the 5th and 95th percentile ATD's. To perform this assessment, a series of tests will be performed at Wright Patterson Air Force Research Lab using their horizontal impact accelerator sled test facility. The ATD's will be placed in the Orion seat with a modified-advanced-crew-escape-system (MACES) pressure suit and helmet, and driven with loadings similar to what is expected for the actual Orion vehicle during landing, launch abort, and chute deployment. Test data will be compared to analytical predictions and modelling uncertainty factors will be determined for each injury metric. Additionally, the test data will be used to further improve the FE model, particularly in the areas of the ATD neck components, harness, and suit and helmet effects.

Science based integrated approach to advanced nuclear fuel development - integrated multi-scale multi-physics hierarchical modeling and simulation framework Part III: cladding

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

Tome, Carlos N; Caro, J A; Lebensohn, R A

2010-01-01

Advancing the performance of Light Water Reactors, Advanced Nuclear Fuel Cycles, and Advanced Reactors, such as the Next Generation Nuclear Power Plants, requires enhancing our fundamental understanding of fuel and materials behavior under irradiation. The capability to accurately model the nuclear fuel systems to develop predictive tools is critical. Not only are fabrication and performance models needed to understand specific aspects of the nuclear fuel, fully coupled fuel simulation codes are required to achieve licensing of specific nuclear fuel designs for operation. The backbone of these codes, models, and simulations is a fundamental understanding and predictive capability for simulating themore » phase and microstructural behavior of the nuclear fuel system materials and matrices. In this paper we review the current status of the advanced modeling and simulation of nuclear reactor cladding, with emphasis on what is available and what is to be developed in each scale of the project, how we propose to pass information from one scale to the next, and what experimental information is required for benchmarking and advancing the modeling at each scale level.« less

Bayesian Action–Perception Computational Model: Interaction of Production and Recognition of Cursive Letters

PubMed Central

Gilet, Estelle; Diard, Julien; Bessière, Pierre

2011-01-01

In this paper, we study the collaboration of perception and action representations involved in cursive letter recognition and production. We propose a mathematical formulation for the whole perception–action loop, based on probabilistic modeling and Bayesian inference, which we call the Bayesian Action–Perception (BAP) model. Being a model of both perception and action processes, the purpose of this model is to study the interaction of these processes. More precisely, the model includes a feedback loop from motor production, which implements an internal simulation of movement. Motor knowledge can therefore be involved during perception tasks. In this paper, we formally define the BAP model and show how it solves the following six varied cognitive tasks using Bayesian inference: i) letter recognition (purely sensory), ii) writer recognition, iii) letter production (with different effectors), iv) copying of trajectories, v) copying of letters, and vi) letter recognition (with internal simulation of movements). We present computer simulations of each of these cognitive tasks, and discuss experimental predictions and theoretical developments. PMID:21674043

Model interpretation of type III radio burst characteristics. I - Spatial aspects

NASA Technical Reports Server (NTRS)

Reiner, M. J.; Stone, R. G.

1988-01-01

The ways that the finite size of the source region and directivity of the emitted radiation modify the observed characteristics of type III radio bursts as they propagate through the interplanetary medium are investigated. A simple model that simulates the radio source region is developed to provide insight into the spatial behavior of the parameters that characterize radio bursts. The model is used to demonstrate that observed radio azimuths are systematically displaced from the geometric centroid of the exciter electron beam in such a way as to cause trajectories of the radio bursts to track back to the observer at low frequencies, rather than to follow expected Archimedean spiral-like paths. The source region model is used to investigate the spatial behavior of the peak intensities of radio bursts, and it is found that the model can qualitatively account for both the frequency dependence and the east-west asymmetry of the observed peak flux densities.

Utilization of rice husks modified by organomultiphosphonic acids as low-cost biosorbents for enhanced adsorption of heavy metal ions.

PubMed

Xu, Mingyu; Yin, Ping; Liu, Xiguang; Tang, Qinghua; Qu, Rongjun; Xu, Qiang

2013-12-01

Novel biosorbent materials (RH-2 and RH-3) obtained from agricultural waste materials rice husks (RH-1) were successfully developed through fast and facile esterification reactions with hydroxylethylidenediphosphonic acid and nitrilotrimethylenetriphosphonic acid, respectively. The present paper reported the feasibility of using RH-1, RH-2 and RH-3 for removal of heavy metals from simulated wastewater, the results revealed that the adsorption property of functionalized rice husks with organotriphosphonic acid RH-3 for Au(III) was very excellent, especially for gold ions. The combined effect of initial solution pH, RH-3 dosage and initial Au(III) concentration was investigated using response surface methodology (RSM), the results showed that initial Au(III) concentration exerted stronger influence on Au(III) uptake than initial pH and biomass dosage. The analysis of variance (ANOVA) of the quadratic model demonstrated that the model was highly significant, and under the optimum process conditions, the maximum adsorption capacity could reach 3.25 ± 0.07 mmol/g that is higher than other reported adsorbents. Copyright © 2013 Elsevier Ltd. All rights reserved.

Fermi-level effects in semiconductor processing: A modeling scheme for atomistic kinetic Monte Carlo simulators

NASA Astrophysics Data System (ADS)

Martin-Bragado, I.; Castrillo, P.; Jaraiz, M.; Pinacho, R.; Rubio, J. E.; Barbolla, J.; Moroz, V.

2005-09-01

Atomistic process simulation is expected to play an important role for the development of next generations of integrated circuits. This work describes an approach for modeling electric charge effects in a three-dimensional atomistic kinetic Monte Carlo process simulator. The proposed model has been applied to the diffusion of electrically active boron and arsenic atoms in silicon. Several key aspects of the underlying physical mechanisms are discussed: (i) the use of the local Debye length to smooth out the atomistic point-charge distribution, (ii) algorithms to correctly update the charge state in a physically accurate and computationally efficient way, and (iii) an efficient implementation of the drift of charged particles in an electric field. High-concentration effects such as band-gap narrowing and degenerate statistics are also taken into account. The efficiency, accuracy, and relevance of the model are discussed.

Molecular modeling of fibronectin adsorption on topographically nanostructured rutile (110) surfaces

NASA Astrophysics Data System (ADS)

Guo, Chuangqiang; Wu, Chunya; Chen, Mingjun; Zheng, Ting; Chen, Ni; Cummings, Peter T.

2016-10-01

To investigate the topographical dependency of protein adsorption, molecular dynamics simulations were employed to describe the adsorption behavior of the tenth type-III module of fibronectin (FN-III10) on nanostructured rutile (110) surfaces. The results indicated that the residence time of adsorbed FN-III10 largely relied on its binding mode (direct or indirect) with the substrate and the region for protein migration on the periphery (protrusion) or in the interior (cavity or groove) of nanostructures. In the direct binding mode, FN-III10 molecules were found to be 'trapped' at the anchoring sites of rutile surface, or even penetrate deep into the interior of nanostructures, regardless of the presented geometrical features. In the indirect binding mode, FN-III10 molecules were indirectly connected to the substrate via a hydrogen-bond network (linking FN-III10 and interfacial hydrations). The facets created by nanostructures, which exerted restraints on protein migration, were suggested to play an important role in the stability of indirect FN-III10-rutile binding. However, a doubly unfavorable situation - indirect FN-III10-rutile connections bridged by a handful of mediating waters and few constraints on movement of protein provided by nanostructures - would result in an early desorption of protein.

Simultaneous leaching of arsenite, arsenate, selenite and selenate, and their migration in tunnel-excavated sedimentary rocks: II. Kinetic and reactive transport modeling.

PubMed

Tabelin, Carlito Baltazar; Sasaki, Ryosuke; Igarashi, Toshifumi; Park, Ilhwan; Tamoto, Shuichi; Arima, Takahiko; Ito, Mayumi; Hiroyoshi, Naoki

2017-12-01

Predicting the fates of arsenic (As) and selenium (Se) in natural geologic media like rocks and soils necessitates the understanding of how their various oxyanionic species behave and migrate under dynamic conditions. In this study, geochemical factors and processes crucial in the leaching and transport of arsenite (As III ), arsenate (As V ), selenite (Se IV ) and selenate (Se VI ) in tunnel-excavated rocks of marine origin were investigated using microscopic/extraction techniques, column experiments, dissolution-precipitation kinetics and one-dimensional reactive transport modeling. The results showed that evaporite salts were important because aside from containing As and Se, they played crucial roles in the evolution of pH and concentrations of coexisting ions, both of which had strong effects on adsorption-desorption reactions of As and Se species with iron oxyhydroxide minerals/phases. The observed leaching trends of As V , As III , Se IV and Se VI were satisfactorily simulated by one-dimensional reactive transport models, which predict that preferential adsorptions of As V and Se IV were magnified by geochemical changes in the columns due to water flow. Moreover, our results showed that migrations of As III , Se IV and Se VI could be predicted adequately by 1D solute transport with simple activity-K' d approach, but surface complexation was more reliable to simulate adsorption-desorption behavior of As V . Copyright © 2017 Elsevier Ltd. All rights reserved.

Effect of accessory ostia on maxillary sinus ventilation: a computational fluid dynamics (CFD) study.

PubMed

Zhu, Jian Hua; Lee, Heow Pueh; Lim, Kian Meng; Gordon, Bruce R; Wang, De Yun

2012-08-15

We evaluated, by CFD simulation, effects of accessory ostium (AO) on maxillary sinus ventilation. A three-dimensional nasal model was constructed from an adult CT scan with two left maxillary AOs (sinus I) and one right AO (sinus II), then compared to an identical control model with all AOs sealed (sinuses III and IV). Transient simulations of quiet inspiration and expiration at 15 L/min, and nasal blow at 48 L/min, were calculated for both models using low-Reynolds-number turbulent analysis. At low flows, ventilation rates in sinuses with AOs (I ≈ 0.46 L/min, II ≈ 0.54 L/min), were both more than a magnitude higher than sinuses without AOs (II I ≈ 0.019 L/min, IV ≈ 0.020 L/min). Absence of AO almost completely prevented sinus ventilation. Increased ventilation of sinuses with AOs is complex. Under high flow conditions mimicking nose blowing, in sinuses II, III, and IV, the sinus flow rate increased. In contrast, the airflow direction through sinus I reversed between inspiration and expiration, while it remained almost constant throughout the respiration cycle in sinus II. CFD simulation demonstrated that AOs markedly increase maxillary sinus airflow rates and alter sinus air circulation patterns. Whether these airflow changes impact maxillary sinus physiology or pathophysiology is unknown. Copyright © 2012 Elsevier B.V. All rights reserved.

Examination of the nature of lattice matched III V semiconductor interfaces using computer simulated molecular beam epitaxial growth I. AC/BC interfaces

NASA Astrophysics Data System (ADS)

Thomsen, M.; Ghaisas, S. V.; Madhukar, A.

1987-07-01

A previously developed computer simulation of molecular beam epitaxial growth of III-V semiconductors based on the configuration dependent reactive incorporation (CDRI) model is extended to allow for two different cation species. Attention is focussed on examining the nature of interfaces formed in lattice matched quantum well structures of the form AC/BC/AC(100). We consider cation species with substantially different effective diffusion lengths, as is the case with Al and Ga during the growth of their respective As compounds. The degree of intermixing occuring at the interface is seen to be dependent upon, among other growth parameters, the pressure of the group V species during growth. Examination of an intraplanar order parameter at the interfaces reveals the existence of short range clustering of the cation species.

Plasma Modeling with Speed-Limited Particle-in-Cell Techniques

NASA Astrophysics Data System (ADS)

Jenkins, Thomas G.; Werner, G. R.; Cary, J. R.; Stoltz, P. H.

2017-10-01

Speed-limited particle-in-cell (SLPIC) modeling is a new particle simulation technique for modeling systems wherein numerical constraints, e.g. limitations on timestep size required for numerical stability, are significantly more restrictive than is needed to model slower kinetic processes of interest. SLPIC imposes artificial speed-limiting behavior on fast particles whose kinetics do not play meaningful roles in the system dynamics, thus enabling larger simulation timesteps and more rapid modeling of such plasma discharges. The use of SLPIC methods to model plasma sheath formation and the free expansion of plasma into vacuum will be demonstrated. Wallclock times for these simulations, relative to conventional PIC, are reduced by a factor of 2.5 for the plasma expansion problem and by over 6 for the sheath formation problem; additional speedup is likely possible. Physical quantities of interest are shown to be correct for these benchmark problems. Additional SLPIC applications will also be discussed. Supported by US DoE SBIR Phase I/II Award DE-SC0015762.

FOSSIL2 energy policy model documentation: FOSSIL2 documentation

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

None

1980-10-01

This report discusses the structure, derivations, assumptions, and mathematical formulation of the FOSSIL2 model. Each major facet of the model - supply/demand interactions, industry financing, and production - has been designed to parallel closely the actual cause/effect relationships determining the behavior of the United States energy system. The data base for the FOSSIL2 program is large, as is appropriate for a system dynamics simulation model. When possible, all data were obtained from sources well known to experts in the energy field. Cost and resource estimates are based on DOE data whenever possible. This report presents the FOSSIL2 model at severalmore » levels. Volumes II and III of this report list the equations that comprise the FOSSIL2 model, along with variable definitions and a cross-reference list of the model variables. Volume II provides the model equations with each of their variables defined, while Volume III lists the equations, and a one line definition for equations, in a shorter, more readable format.« less

Top-down NOX Emissions of European Cities Derived from Modelled and Spaceborne Tropospheric NO2 Columns

NASA Astrophysics Data System (ADS)

Verstraeten, W. W.; Boersma, K. F.; Douros, J.; Williams, J. E.; Eskes, H.; Delcloo, A. W.

2017-12-01

High nitrogen oxides (NOX = NO + NO2) concentrations near the surface impact humans and ecosystems badly and play a key role in tropospheric chemistry. NO2 is an important precursor of tropospheric ozone (O3) which in turn affects the production of the hydroxyl radical controlling the chemical lifetime of key atmospheric pollutants and reactive greenhouse gases. Combustion from industrial, traffic and household activities in large and densely populated urban areas result in high NOX emissions. Accurate mapping of these emissions is essential but hard to do since reported emissions factors may differ from real-time emissions in order of magnitude. Modelled NO2 levels and lifetimes also have large associated uncertainties and overestimation in the chemical lifetime which may mask missing NOX chemistry in current chemistry transport models (CTM's). The simultaneously estimation of both the NO2 lifetime and as well as the concentrations by applying the Exponentially Modified Gaussian (EMG) method on tropospheric NO2 columns lines densities should improve the surface NOX emission estimates. Here we evaluate if the EMG methodology applied on the tropospheric NO2 columns simulated by the LOTOS-EUROS (Long Term Ozone Simulation-European Ozone Simulation) CTM can reproduce the NOX emissions used as model input. First we process both the modelled tropospheric NO2 columns for the period April-September 2013 for 21 selected European urban areas under windy conditions (averaged vertical wind speeds between surface and 500 m from ECMWF > 2 m s-1) as well as the accompanying OMI (Ozone Monitoring Instrument) data providing us with real-time observation-based estimates of midday NO2 columns. Then we compare the top-down derived surface NOX emissions with the 2011 MACC-III emission inventory, used in the CTM as input to simulate the NO2 columns. For cities where NOX emissions can be assumed as originating from one large source good agreement is found between the top-down derived NOX emissions from CTM and OMI with the MACC-III inventory. For cities where multiple sources of NOX are observed (e.g. Brussels, London), an adapted methodology is required. For some cities such as St-Petersburg and Moscow the top-down NOX estimates from 2013 OMI data are biased low compared to the MACC-III inventory which uses a 2011 NOX emissions update.

Enhanced thermaly managed packaging for III-nitride light emitters

NASA Astrophysics Data System (ADS)

Kudsieh, Nicolas

In this Dissertation our work on `enhanced thermally managed packaging of high power semiconductor light sources for solid state lighting (SSL)' is presented. The motivation of this research and development is to design thermally high stable cost-efficient packaging of single and multi-chip arrays of III-nitrides wide bandgap semiconductor light sources through mathematical modeling and simulations. Major issues linked with this technology are device overheating which causes serious degradation in their illumination intensity and decrease in the lifetime. In the introduction the basics of III-nitrides WBG semiconductor light emitters are presented along with necessary thermal management of high power cingulated and multi-chip LEDs and laser diodes. This work starts at chip level followed by its extension to fully packaged lighting modules and devices. Different III-nitride structures of multi-quantum well InGaN/GaN and AlGaN/GaN based LEDs and LDs were analyzed using advanced modeling and simulation for different packaging designs and high thermal conductivity materials. Study started with basic surface mounted devices using conventional packaging strategies and was concluded with the latest thermal management of chip-on-plate (COP) method. Newly discovered high thermal conductivity materials have also been incorporated for this work. Our study also presents the new approach of 2D heat spreaders using such materials for SSL and micro LED array packaging. Most of the work has been presented in international conferences proceedings and peer review journals. Some of the latest work has also been submitted to well reputed international journals which are currently been reviewed for publication. .

Dust extinction in the first galaxies

NASA Astrophysics Data System (ADS)

Jaacks, Jason; Finkelstein, Steven L.; Bromm, Volker

2018-04-01

Using cosmological volume simulations and a custom built sub-grid model for Population III (Pop III) star formation, we examine the baseline dust extinction in the first galaxies due to Pop III metal enrichment in the first billion years of cosmic history. We find that although the most enriched, high-density lines of sight in primordial galaxies can experience a measurable amount of extinction from Pop III dust [E(B - V)max = 0.07, AV, max ≈ 0.28], the average extinction is very low with ≲ 10-3. We derive a power-law relationship between dark matter halo mass and extinction of E(B-V)∝ M_halo^{0.80}. Performing a Monte Carlo parameter study, we establish the baseline reddening of the ultraviolet spectra of dwarf galaxies at high redshift due to Pop III enrichment only. With this method, we find <βUV> - 2.51 ± 0.07, which is both nearly halo mass and redshift independent.

Methods for modeling non-equilibrium degenerate statistics and quantum-confined scattering in 3D ensemble Monte Carlo transport simulations

NASA Astrophysics Data System (ADS)

Crum, Dax M.; Valsaraj, Amithraj; David, John K.; Register, Leonard F.; Banerjee, Sanjay K.

2016-12-01

Particle-based ensemble semi-classical Monte Carlo (MC) methods employ quantum corrections (QCs) to address quantum confinement and degenerate carrier populations to model tomorrow's ultra-scaled metal-oxide-semiconductor-field-effect-transistors. Here, we present the most complete treatment of quantum confinement and carrier degeneracy effects in a three-dimensional (3D) MC device simulator to date, and illustrate their significance through simulation of n-channel Si and III-V FinFETs. Original contributions include our treatment of far-from-equilibrium degenerate statistics and QC-based modeling of surface-roughness scattering, as well as considering quantum-confined phonon and ionized-impurity scattering in 3D. Typical MC simulations approximate degenerate carrier populations as Fermi distributions to model the Pauli-blocking (PB) of scattering to occupied final states. To allow for increasingly far-from-equilibrium non-Fermi carrier distributions in ultra-scaled and III-V devices, we instead generate the final-state occupation probabilities used for PB by sampling the local carrier populations as function of energy and energy valley. This process is aided by the use of fractional carriers or sub-carriers, which minimizes classical carrier-carrier scattering intrinsically incompatible with degenerate statistics. Quantum-confinement effects are addressed through quantum-correction potentials (QCPs) generated from coupled Schrödinger-Poisson solvers, as commonly done. However, we use these valley- and orientation-dependent QCPs not just to redistribute carriers in real space, or even among energy valleys, but also to calculate confinement-dependent phonon, ionized-impurity, and surface-roughness scattering rates. FinFET simulations are used to illustrate the contributions of each of these QCs. Collectively, these quantum effects can substantially reduce and even eliminate otherwise expected benefits of considered In0.53Ga0.47 As FinFETs over otherwise identical Si FinFETs despite higher thermal velocities in In0.53Ga0.47 As. It also may be possible to extend these basic uses of QCPs, however calculated, to still more computationally efficient drift-diffusion and hydrodynamic simulations, and the basic concepts even to compact device modeling.

Structural analysis and modeling reveals new mechanisms governing ESCRT-III spiral filament assembly

PubMed Central

Shen, Qing-Tao; Schuh, Amber L.; Zheng, Yuqing; Quinney, Kyle; Wang, Lei; Hanna, Michael; Mitchell, Julie C.; Otegui, Marisa S.; Ahlquist, Paul; Cui, Qiang

2014-01-01

The scission of biological membranes is facilitated by a variety of protein complexes that bind and manipulate lipid bilayers. ESCRT-III (endosomal sorting complex required for transport III) filaments mediate membrane scission during the ostensibly disparate processes of multivesicular endosome biogenesis, cytokinesis, and retroviral budding. However, mechanisms by which ESCRT-III subunits assemble into a polymer remain unknown. Using cryogenic electron microscopy (cryo-EM), we found that the full-length ESCRT-III subunit Vps32/CHMP4B spontaneously forms single-stranded spiral filaments. The resolution afforded by two-dimensional cryo-EM combined with molecular dynamics simulations revealed that individual Vps32/CHMP4B monomers within a filament are flexible and able to accommodate a range of bending angles. In contrast, the interface between monomers is stable and refractory to changes in conformation. We additionally found that the carboxyl terminus of Vps32/CHMP4B plays a key role in restricting the lateral association of filaments. Our findings highlight new mechanisms by which ESCRT-III filaments assemble to generate a unique polymer capable of membrane remodeling in multiple cellular contexts. PMID:25202029

Validation of the Fully-Coupled Air-Sea-Wave COAMPS System

NASA Astrophysics Data System (ADS)

Smith, T.; Campbell, T. J.; Chen, S.; Gabersek, S.; Tsu, J.; Allard, R. A.

2017-12-01

A fully-coupled, air-sea-wave numerical model, COAMPS®, has been developed by the Naval Research Laboratory to further enhance understanding of oceanic, atmospheric, and wave interactions. The fully-coupled air-sea-wave system consists of an atmospheric component with full physics parameterizations, an ocean model, NCOM (Navy Coastal Ocean Model), and two wave components, SWAN (Simulating Waves Nearshore) and WaveWatch III. Air-sea interactions between the atmosphere and ocean components are accomplished through bulk flux formulations of wind stress and sensible and latent heat fluxes. Wave interactions with the ocean include the Stokes' drift, surface radiation stresses, and enhancement of the bottom drag coefficient in shallow water due to the wave orbital velocities at the bottom. In addition, NCOM surface currents are provided to SWAN and WaveWatch III to simulate wave-current interaction. The fully-coupled COAMPS system was executed for several regions at both regional and coastal scales for the entire year of 2015, including the U.S. East Coast, Western Pacific, and Hawaii. Validation of COAMPS® includes observational data comparisons and evaluating operational performance on the High Performance Computing (HPC) system for each of these regions.

Formation of S0 galaxies through mergers. Antitruncated stellar discs resulting from major mergers

NASA Astrophysics Data System (ADS)

Borlaff, Alejandro; Eliche-Moral, M. Carmen; Rodríguez-Pérez, Cristina; Querejeta, Miguel; Tapia, Trinidad; Pérez-González, Pablo G.; Zamorano, Jaime; Gallego, Jesús; Beckman, John

2014-10-01

Context. Lenticular galaxies (S0s) are more likely to host antitruncated (Type III) stellar discs than galaxies of later Hubble types. Major mergers are popularly considered too violent to make these breaks. Aims: We have investigated whether major mergers can result into S0-like remnants with realistic antitruncated stellar discs or not. Methods: We have analysed 67 relaxed S0 and E/S0 remnants resulting from dissipative N-body simulations of major mergers from the GalMer database. We have simulated realistic R-band surface brightness profiles of the remnants to identify those with antitruncated stellar discs. Their inner and outer discs and the breaks have been quantitatively characterized to compare with real data. Results: Nearly 70% of our S0-like remnants are antitruncated, meaning that major mergers that result in S0s have a high probability of producing Type III stellar discs. Our remnants lie on top of the extrapolations of the observational trends (towards brighter magnitudes and higher break radii) in several photometric diagrams, because of the higher luminosities and sizes of the simulations compared to observational samples. In scale-free photometric diagrams, simulations and observations overlap and the remnants reproduce the observational trends, so the physical mechanism after antitruncations is highly scalable. We have found novel photometric scaling relations between the characteristic parameters of the antitruncations in real S0s, which are also reproduced by our simulations. We show that the trends in all the photometric planes can be derived from three basic scaling relations that real and simulated Type III S0s fulfill: hi ∝ RbrkIII, ho ∝ RbrkIII, and μbrkIII ∝ RbrkIII, where hi and ho are the scalelengths of the inner and outer discs, and μbrkIII and RbrkIII are the surface brightness and radius of the breaks. Bars and antitruncations in real S0s are structurally unrelated phenomena according to the studied photometric planes. Conclusions: Major mergers provide a feasible mechanism to form realistic antitruncated S0 galaxies. Table 3 is available in electronic form at http://www.aanda.org

LATE POP III STAR FORMATION DURING THE EPOCH OF REIONIZATION: RESULTS FROM THE RENAISSANCE SIMULATIONS

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

Xu, Hao; Norman, Michael L.; O’Shea, Brian W.

2016-06-01

We present results on the formation of Population III (Pop III) stars at redshift 7.6 from the Renaissance Simulations, a suite of extremely high-resolution and physics-rich radiation transport hydrodynamics cosmological adaptive-mesh refinement simulations of high-redshift galaxy formation performed on the Blue Waters supercomputer. In a survey volume of about 220 comoving Mpc{sup 3}, we found 14 Pop III galaxies with recent star formation. The surprisingly late formation of Pop III stars is possible due to two factors: (i) the metal enrichment process is local and slow, leaving plenty of pristine gas to exist in the vast volume; and (ii) strongmore » Lyman–Werner radiation from vigorous metal-enriched star formation in early galaxies suppresses Pop III formation in (“not so”) small primordial halos with mass less than ∼3 × 10{sup 7} M {sub ⊙}. We quantify the properties of these Pop III galaxies and their Pop III star formation environments. We look for analogs to the recently discovered luminous Ly α emitter CR7, which has been interpreted as a Pop III star cluster within or near a metal-enriched star-forming galaxy. We find and discuss a system similar to this in some respects, however, the Pop III star cluster is far less massive and luminous than CR7 is inferred to be.« less

Simulation, guidance and navigation of the B-737 for rollout and turnoff using MLS measurements

NASA Technical Reports Server (NTRS)

Pines, S.; Schmidt, S. F.; Mann, F.

1975-01-01

A simulation program is described for the B-737 aircraft in landing approach, a touchdown, rollout and turnoff for normal and CAT III weather conditions. Preliminary results indicate that microwave landing systems can be used in place of instrument landing systems landing aids and that a single magnetic cable can be used for automated rollout and turnoff. Recommendations are made for further refinement of the model and additional testing to finalize a set of guidance laws for rollout and turnoff.

Langmuir turbulence driven by beams in solar wind plasmas with long wavelength density fluctuations

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

Krafft, C., E-mail: catherine.krafft@u-psud.fr; Universite´ Paris Sud, 91405 Orsay Cedex; Volokitin, A., E-mail: a.volokitin@mail.ru

2016-03-25

The self-consistent evolution of Langmuir turbulence generated by electron beams in solar wind plasmas with density inhomogeneities is calculated by numerical simulations based on a 1D Hamiltonian model. It is shown, owing to numerical simulations performed with parameters relevant to type III solar bursts’ conditions at 1 AU, that the presence of long-wavelength random density fluctuations of sufficiently large average level crucially modifies the well-known process of beam interaction with Langmuir waves in homogeneous plasmas.

An Investigation of Alternative Metamodels for the Theater Simulation of Airbase Resources Model

DTIC Science & Technology

1993-09-01

children, Lachlan and Cameron, in the hope that in their world of the future, the things that we research now are never tested. Alistair Dally iii Table...texts refer to (0,1) coding *for two level qualitative variables, but several authors including Kleijnen et al. (1979:53), Smith and Mauro (1984:254...An Introduction to Simulation using GPSS/H. New York: John Wiley and Sons, 1991. Smith , Dennis E, and Carl A. Mauro. ’"Design of Experiments in

Development and Evaluation of an Airplane Fuel Tank Ullage Composition Model. Volume 2. Experimental Determination of Airplane Fuel Tank Ullage Compositions

DTIC Science & Technology

1987-10-01

Airplane Fuel Tank Ullage Compositions ~C A. J. Roth BOEING MILITARY AIRPLANE COMPANY P. 0. Box 3707 Seattle, Washington 98124-2207 October 1987 FINAL...controlled mission simulations were made using the ModComp computer to control the Simulated Aircraft Fuel Tank Environment ( SAFTEI facility at Wright...of this report. iii PREFACE This is a final report of work conducted under F33615-84-C-2431 and submitted by the Boeing Military Airplane Company

EURODELTA-Trends, a multi-model experiment of air quality hindcast in Europe over 1990-2010

NASA Astrophysics Data System (ADS)

Colette, Augustin; Andersson, Camilla; Manders, Astrid; Mar, Kathleen; Mircea, Mihaela; Pay, Maria-Teresa; Raffort, Valentin; Tsyro, Svetlana; Cuvelier, Cornelius; Adani, Mario; Bessagnet, Bertrand; Bergström, Robert; Briganti, Gino; Butler, Tim; Cappelletti, Andrea; Couvidat, Florian; D'Isidoro, Massimo; Doumbia, Thierno; Fagerli, Hilde; Granier, Claire; Heyes, Chris; Klimont, Zig; Ojha, Narendra; Otero, Noelia; Schaap, Martijn; Sindelarova, Katarina; Stegehuis, Annemiek I.; Roustan, Yelva; Vautard, Robert; van Meijgaard, Erik; Garcia Vivanco, Marta; Wind, Peter

2017-09-01

The EURODELTA-Trends multi-model chemistry-transport experiment has been designed to facilitate a better understanding of the evolution of air pollution and its drivers for the period 1990-2010 in Europe. The main objective of the experiment is to assess the efficiency of air pollutant emissions mitigation measures in improving regional-scale air quality. The present paper formulates the main scientific questions and policy issues being addressed by the EURODELTA-Trends modelling experiment with an emphasis on how the design and technical features of the modelling experiment answer these questions. The experiment is designed in three tiers, with increasing degrees of computational demand in order to facilitate the participation of as many modelling teams as possible. The basic experiment consists of simulations for the years 1990, 2000, and 2010. Sensitivity analysis for the same three years using various combinations of (i) anthropogenic emissions, (ii) chemical boundary conditions, and (iii) meteorology complements it. The most demanding tier consists of two complete time series from 1990 to 2010, simulated using either time-varying emissions for corresponding years or constant emissions. Eight chemistry-transport models have contributed with calculation results to at least one experiment tier, and five models have - to date - completed the full set of simulations (and 21-year trend calculations have been performed by four models). The modelling results are publicly available for further use by the scientific community. The main expected outcomes are (i) an evaluation of the models' performances for the three reference years, (ii) an evaluation of the skill of the models in capturing observed air pollution trends for the 1990-2010 time period, (iii) attribution analyses of the respective role of driving factors (e.g. emissions, boundary conditions, meteorology), (iv) a dataset based on a multi-model approach, to provide more robust model results for use in impact studies related to human health, ecosystem, and radiative forcing.

Molecular simulations reveal that the long range fluctuations of human DPP III change upon ligand binding.

PubMed

Tomić, A; Berynskyy, M; Wade, R C; Tomić, S

2015-11-01

The experimentally determined structures of human dipeptidyl peptidase III (DPP III) for the wild-type protein and for the complex of its E451A mutant with the peptide substrate, tynorphin, differ significantly in their overall shape. The two domains of the enzyme are separated by a wide cleft in the structure of the ligand-free enzyme, while in the ligand-bound mutant they are very close to each other, and the protein structure is extremely compact. Here, we applied a range of molecular dynamics simulation techniques to investigate the DPP III conformational landscape and the influence of ligand binding on the protein structure and dynamics. We used conventional, accelerated and steered methods to simulate DPP III and its complexes with tynorphin and with the preferred, synthetic, substrate Arg-Arg-2-naphthylamide. We found that DPP III can adopt a number of different forms in solution. The compact forms are more stable, but the open and partially closed states, spanning a wide range of conformations, can more effectively recognize the substrate which preferentially binds to the five-stranded β-core of the lower DPP III domain. The simulations indicated the existence of a dynamic equilibrium between open and semi-closed states and revealed two ways that the protein can close, leading to two distinct compact structures. The way in which the protein closes depends on the presence of the ligand.

A field, laboratory and modeling study of reactive transport of groundwater arsenic in a coastal aquifer

PubMed Central

Jung, Hun Bok; Charette, Matthew A.; Zheng, Yan

2009-01-01

A field, laboratory, and modeling study of As in groundwater discharging to Waquoit Bay, MA, shed light on coupled control of chemistry and hydrology on reactive transport of As in a coastal aquifer. Dissolved Fe(II) and As(III) in a reducing groundwater plume bracketed by an upper and a lower redox interface are oxidized as water flows towards the bay. This results in precipitation of Fe(III) oxides, along with oxidation and adsorption of As to sediment at the redox interfaces where concentrations of sedimentary HCl-leachable Fe (80~90% Fe(III)) are 734±232 mg kg-1, sedimentary phosphate extractable As (90~100% As(V)) are 316±111 μg kg-1, and are linearly correlated. Batch adsorption of As(III) onto orange, brown and gray sediments follows Langmuir isotherms, and can be fitted by a surface complexation model (SCM) assuming a diffuse layer for ferrihydrite. The sorption capacity and distribution coefficient for As increase with decreasing sediment Fe(II)/Fe. To allow accumulation of the amount of sediment As, similar hydrogeochemical conditions would have been operating for thousands of years at Waquoit Bay. The SCM simulated the observed dissolved As concentration better than a parametric approach based on Kd. Site specific isotherms should be established for Kd or SCM based models. PMID:19708362

Modeling the clinical and economic implications of obesity using microsimulation.

PubMed

Su, W; Huang, J; Chen, F; Iacobucci, W; Mocarski, M; Dall, T M; Perreault, L

2015-01-01

The obesity epidemic has raised considerable public health concerns, but there are few validated longitudinal simulation models examining the human and economic cost of obesity. This paper describes a microsimulation model as a comprehensive tool to understand the relationship between body weight, health, and economic outcomes. Patient health and economic outcomes were simulated annually over 10 years using a Markov-based microsimulation model. The obese population examined is nationally representative of obese adults in the US from the 2005-2012 National Health and Nutrition Examination Surveys, while a matched normal weight population was constructed to have similar demographics as the obese population during the same period. Prediction equations for onset of obesity-related comorbidities, medical expenditures, economic outcomes, mortality, and quality-of-life came from published trials and studies supplemented with original research. Model validation followed International Society for Pharmacoeconomics and Outcomes Research practice guidelines. Among surviving adults, relative to a matched normal weight population, obese adults averaged $3900 higher medical expenditures in the initial year, growing to $4600 higher expenditures in year 10. Obese adults had higher initial prevalence and higher simulated onset of comorbidities as they aged. Over 10 years, excess medical expenditures attributed to obesity averaged $4280 annually-ranging from $2820 for obese category I to $5100 for obese category II, and $8710 for obese category III. Each excess kilogram of weight contributed to $140 higher annual costs, on average, ranging from $136 (obese I) to $152 (obese III). Poor health associated with obesity increased work absenteeism and mortality, and lowered employment probability, personal income, and quality-of-life. This validated model helps illustrate why obese adults have higher medical and indirect costs relative to normal weight adults, and shows that medical costs for obese adults rise more rapidly with aging relative to normal weight adults.

Process Model for Studying Regional 13C Stable Isotope Exchange between Vegetation and Atmosphere

NASA Astrophysics Data System (ADS)

Chen, J. M.; Chen, B.; Huang, L.; Tans, P.; Worthy, D.; Ishizawa, M.; Chan, D.

2007-12-01

The variation of the stable isotope 13CO2 in the air in exchange with land ecosystems results from fractionation processes in both plants and soil during photosynthesis and respiration. Its diurnal and seasonal variations therefore contain information on the carbon cycle. We developed a model (BEPS-iso) to simulate its exchange between vegetation and the atmosphere. To be useful for regional carbon cycle studies, the model has the following characteristics: (i) it considers the turbulent mixing in the vertical profile from the soil surface to the top of the planetary boundary layer (PBL); (ii) it scales individual leaf photosynthetic discrimination to the whole canopy through the separation of sunlit and shaded leaf groups; (iii) through simulating leaf-level photosynthetic processes, it has the capacity to mechanistically examine isotope discrimination resulting from meteorological forcings, such as radiation, precipitation and humidity; and (iv) through complete modeling of radiation, energy and water fluxes, it also simulates soil moisture and temperature needed for estimating ecosystem respiration and the 13C signal from the soil. After validation using flask data acquired at 20 m level on a tower near Fraserdale, Ontario, Canada, during intensive campaigns (1998-2000), the model has been used for several purposes: (i) to investigate the diurnal and seasonal variations in the disequilibrium in 13C fractionation between ecosystem respiration and photosynthesis, which is an important step in using 13C measurements to separate these carbon cycle components; (ii) to quantify the 13C rectification in the PBL, which differs significantly from CO2 rectification because of the diurnal and seasonal disequilibriums; and (iii) to model the 13C spatial and temporal variations over the global land surface for the purpose of CO2 inversion using 13C as an additional constraint.

The clustering of galaxies in the SDSS-III Baryon Oscillation Spectroscopic Survey: modelling the clustering and halo occupation distribution of BOSS CMASS galaxies in the Final Data Release

NASA Astrophysics Data System (ADS)

Rodríguez-Torres, Sergio A.; Chuang, Chia-Hsun; Prada, Francisco; Guo, Hong; Klypin, Anatoly; Behroozi, Peter; Hahn, Chang Hoon; Comparat, Johan; Yepes, Gustavo; Montero-Dorta, Antonio D.; Brownstein, Joel R.; Maraston, Claudia; McBride, Cameron K.; Tinker, Jeremy; Gottlöber, Stefan; Favole, Ginevra; Shu, Yiping; Kitaura, Francisco-Shu; Bolton, Adam; Scoccimarro, Román; Samushia, Lado; Schlegel, David; Schneider, Donald P.; Thomas, Daniel

2016-08-01

We present a study of the clustering and halo occupation distribution of Baryon Oscillation Spectroscopic Survey (BOSS) CMASS galaxies in the redshift range 0.43 < z < 0.7 drawn from the Final SDSS-III Data Release. We compare the BOSS results with the predictions of a halo abundance matching (HAM) clustering model that assigns galaxies to dark matter haloes selected from the large BigMultiDark N-body simulation of a flat Λ cold dark matter Planck cosmology. We compare the observational data with the simulated ones on a light cone constructed from 20 subsequent outputs of the simulation. Observational effects such as incompleteness, geometry, veto masks and fibre collisions are included in the model, which reproduces within 1σ errors the observed monopole of the two-point correlation function at all relevant scales: from the smallest scales, 0.5 h-1 Mpc, up to scales beyond the baryon acoustic oscillation feature. This model also agrees remarkably well with the BOSS galaxy power spectrum (up to k ˜ 1 h Mpc-1), and the three-point correlation function. The quadrupole of the correlation function presents some tensions with observations. We discuss possible causes that can explain this disagreement, including target selection effects. Overall, the standard HAM model describes remarkably well the clustering statistics of the CMASS sample. We compare the stellar-to-halo mass relation for the CMASS sample measured using weak lensing in the Canada-France-Hawaii Telescope Stripe 82 Survey with the prediction of our clustering model, and find a good agreement within 1σ. The BigMD-BOSS light cone including properties of BOSS galaxies and halo properties is made publicly available.

Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations

NASA Astrophysics Data System (ADS)

Lei, Hongxing; Wu, Chun; Wang, Zhi-Xiang; Zhou, Yaoqi; Duan, Yong

2008-06-01

Reaching the native states of small proteins, a necessary step towards a comprehensive understanding of the folding mechanisms, has remained a tremendous challenge to ab initio protein folding simulations despite the extensive effort. In this work, the folding process of the B domain of protein A (BdpA) has been simulated by both conventional and replica exchange molecular dynamics using AMBER FF03 all-atom force field. Started from an extended chain, a total of 40 conventional (each to 1.0 μs) and two sets of replica exchange (each to 200.0 ns per replica) molecular dynamics simulations were performed with different generalized-Born solvation models and temperature control schemes. The improvements in both the force field and solvent model allowed successful simulations of the folding process to the native state as demonstrated by the 0.80 A˚ Cα root mean square deviation (RMSD) of the best folded structure. The most populated conformation was the native folded structure with a high population. This was a significant improvement over the 2.8 A˚ Cα RMSD of the best nativelike structures from previous ab initio folding studies on BdpA. To the best of our knowledge, our results demonstrate, for the first time, that ab initio simulations can reach the native state of BdpA. Consistent with experimental observations, including Φ-value analyses, formation of helix II/III hairpin was a crucial step that provides a template upon which helix I could form and the folding process could complete. Early formation of helix III was observed which is consistent with the experimental results of higher residual helical content of isolated helix III among the three helices. The calculated temperature-dependent profile and the melting temperature were in close agreement with the experimental results. The simulations further revealed that phenylalanine 31 may play critical to achieve the correct packing of the three helices which is consistent with the experimental observation. In addition to the mechanistic studies, an ab initio structure prediction was also conducted based on both the physical energy and a statistical potential. Based on the lowest physical energy, the predicted structure was 2.0 A˚ Cα RMSD away from the experimentally determined structure.

The MICE Grand Challenge light-cone simulation - III. Galaxy lensing mocks from all-sky lensing maps

NASA Astrophysics Data System (ADS)

Fosalba, P.; Gaztañaga, E.; Castander, F. J.; Crocce, M.

2015-02-01

In Paper I of this series, we presented a new N-body light-cone simulation from the MICE Collaboration, the MICE Grand Challenge (MICE-GC), containing about 70 billion dark-matter particles in a (3 h-1 Gpc)3 comoving volume, from which we built halo and galaxy catalogues using a Halo Occupation Distribution and Halo Abundance Matching technique, as presented in the companion Paper II. Given its large volume and fine mass resolution, the MICE-GC simulation also allows an accurate modelling of the lensing observables from upcoming wide and deep galaxy surveys. In the last paper of this series (Paper III), we describe the construction of all-sky lensing maps, following the `Onion Universe' approach, and discuss their properties in the light-cone up to z = 1.4 with sub-arcminute spatial resolution. By comparing the convergence power spectrum in the MICE-GC to lower mass-resolution (i.e. particle mass ˜1011 h-1 M⊙) simulations, we find that resolution effects are at the 5 per cent level for multipoles ℓ ˜ 103 and 20 per cent for ℓ ˜ 104. Resolution effects have a much lower impact on our simulation, as shown by comparing the MICE-GC to recent numerical fits by Takahashi. We use the all-sky lensing maps to model galaxy lensing properties, such as the convergence, shear, and lensed magnitudes and positions, and validate them thoroughly using galaxy shear auto and cross-correlations in harmonic and configuration space. Our results show that the galaxy lensing mocks here presented can be used to accurately model lensing observables down to arcminute scales. Accompanying this series of papers, we make a first public data release of the MICE-GC galaxy mock, the MICECAT v1.0, through a dedicated web-portal for the MICE simulations, http://cosmohub.pic.es, to help developing and exploiting the new generation of astronomical surveys.

Stochastic simulation model comparing distributions of STEC O157 faecal shedding prevalence between cattle vaccinated with type III secreted protein vaccines and non-vaccinated cattle.

PubMed

Vogstad, A R; Moxley, R A; Erickson, G E; Klopfenstein, T J; Smith, D R

2014-06-01

Pens of cattle with high Escherichia coli O157:H7 (STEC O157) prevalence at harvest may present a greater risk to food safety than pens of lower prevalence. Vaccination of live cattle against STEC O157 has been proposed as an approach to reduce STEC O157 prevalence in live cattle. Our objective was to create a stochastic simulation model to evaluate the effectiveness of pre-harvest interventions. We used the model to compare STEC O157 prevalence distributions for summer- and winter-fed cattle to summer-fed cattle immunized with a type III secreted protein (TTSP) vaccine. Model inputs were an estimate of vaccine efficacy, observed frequency distributions for number of animals within a pen, and pen-level faecal shedding prevalence for summer and winter. Uncertainty about vaccine efficacy was simulated using a log-normal distribution (mean = 58%, SE = 0.14). Model outputs were distributions of STEC O157 faecal pen prevalence of summer-fed cattle unvaccinated and vaccinated, and winter-fed cattle unvaccinated. The simulation was performed 5000 times. Summer faecal prevalence ranged from 0% to 80% (average = 30%). Thirty-six per cent of summer-fed pens had STEC O157 prevalence >40%. Winter faecal prevalence ranged from 0% to 60% (average = 10%). Seven per cent of winter-fed pens had STEC O157 prevalence >40%. Faecal prevalence for summer-fed pens vaccinated with a 58% efficacious vaccine product ranged from 0% to 52% (average = 13%). Less than one per cent of vaccinated pens had STEC O157 prevalence >40%. In this simulation, vaccination mitigated the risk of STEC O157 faecal shedding to levels comparable to winter, with the major effects being reduced average shedding prevalence, reduced variability in prevalence distribution, and a reduction in the occurrence of the highest prevalence pens. Food safety decision-makers may find this modelling approach useful for evaluating the value of pre-harvest interventions. © 2013 Blackwell Verlag GmbH.

Numerical modeling of space-time wave extremes using WAVEWATCH III

NASA Astrophysics Data System (ADS)

Barbariol, Francesco; Alves, Jose-Henrique G. M.; Benetazzo, Alvise; Bergamasco, Filippo; Bertotti, Luciana; Carniel, Sandro; Cavaleri, Luigi; Y. Chao, Yung; Chawla, Arun; Ricchi, Antonio; Sclavo, Mauro; Tolman, Hendrik

2017-04-01

A novel implementation of parameters estimating the space-time wave extremes within the spectral wave model WAVEWATCH III (WW3) is presented. The new output parameters, available in WW3 version 5.16, rely on the theoretical model of Fedele (J Phys Oceanogr 42(9):1601-1615, 2012) extended by Benetazzo et al. (J Phys Oceanogr 45(9):2261-2275, 2015) to estimate the maximum second-order nonlinear crest height over a given space-time region. In order to assess the wave height associated to the maximum crest height and the maximum wave height (generally different in a broad-band stormy sea state), the linear quasi-determinism theory of Boccotti (2000) is considered. The new WW3 implementation is tested by simulating sea states and space-time extremes over the Mediterranean Sea (forced by the wind fields produced by the COSMO-ME atmospheric model). Model simulations are compared to space-time wave maxima observed on March 10th, 2014, in the northern Adriatic Sea (Italy), by a stereo camera system installed on-board the "Acqua Alta" oceanographic tower. Results show that modeled space-time extremes are in general agreement with observations. Differences are mostly ascribed to the accuracy of the wind forcing and, to a lesser extent, to the approximations introduced in the space-time extremes parameterizations. Model estimates are expected to be even more accurate over areas larger than the mean wavelength (for instance, the model grid size).

Spectral modelling of ice-induced wave decay: implementation of a new viscoelastic theory in WAVEWATCH III

NASA Astrophysics Data System (ADS)

Liu, Q.; Rogers, W. E.; Babanin, A. V.; Squire, V. A.; Mosig, J. E. M.; Li, J.; Guan, C.

2017-12-01

A new viscoelastic ice layer model is implemented in the third generation spectral wave model WAVEWATCH III to estimate the ice-induced, frequency-dependent wave attenuation rate. Two case studies are then conducted with this viscoelastic model: one is the hindcast of waves in the autumn Beaufort Sea, 2015, and the other is the modelling of wave fields in the Antarctic marginal ice zone (MIZ), 2012. It is demonstrated that the viscoelastic model is capable of reproducing the measured significant wave heights (Ηs) in these two different geophysical regions. The sensitivity of the simulated wave height on different source terms -- ice-induced decay Sice and other physical processes Sother such as wind input Sin, nonlinear four-wave interaction Snl -- is also investigated in this study. For the Antarctic MIZ experiment, Sother is found to be much less than Sice and thus contributes little to the simulated Hs. The trend of the wave height decay (dHs/dx) discovered recently -- saturating at large wave heights -- is well reproduced by the standalone linear viscoelastic model. The flattening of dHs/dx is most likely due to the only presence of longer waves, with the shorter waves having been already low-pass filtered. Nonetheless, Sother should not be disregarded within a more general modelling perspective as Sin and Snl is shown to be comparable or even much higher than Sice in the Beaufort Sea case.

Integrated optics applied to astronomical aperture synthesis III: simulation of components optimized for astronomical interferometry

NASA Astrophysics Data System (ADS)

Nabias, Laurent; Schanen, Isabelle; Berger, Jean-Philippe; Kern, Pierre; Malbet, Fabien; Benech, Pierre

2018-04-01

This paper, "Integrated optics applied to astronomical aperture synthesis III: simulation of components optimized for astronomical interferometry," was presented as part of International Conference on Space Optics—ICSO 1997, held in Toulouse, France.

Adsorption Mechanisms of Trivalent Gold onto Iron Oxy-Hydroxides: From the Molecular Scale to the Model

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

Cances, Benjamin; Benedetti, Marc; Farges, Francois

2007-02-02

Gold is a highly valuable metal that can concentrate in iron-rich exogenetic horizons such as laterites. An improved knowledge of the retention mechanisms of gold onto highly reactive soil components such as iron oxy-hydroxides is therefore needed to better understand and predict the geochemical behavior of this element. In this study, we use EXAFS information and titration experiments to provide a realistic thermochemical description of the sorption of trivalent gold onto iron oxy-hydroxides. Analysis of Au LIII-edge XAFS spectra shows that aqueous Au(III) adsorbs from chloride solutions onto goethite surfaces as inner-sphere square-planar complexes (Au(III)(OH,Cl)4), with dominantly OH ligands atmore » pH > 6 and mixed OH/Cl ligands at lower pH values. In combination with these spectroscopic results, Reverse Monte Carlo simulations were used to constraint the possible sorption sites on the surface of goethite. Based on this structural information, we calculated sorption isotherms of Au(III) on Fe oxy-hydroxides surfaces, using the CD-MUSIC (Charge Distribution - MUlti SIte Complexation) model. The various Au(III)-sorbed species were identified as a function of pH, and the results of these EXAFS+CD-MUSIC models are compared with titration experiments. The overall good agreement between the predicted and measured structural models shows the potential of this combined approach to better model sorption processes of transition elements onto highly reactive solid surfaces such as goethite and ferrihydrite.« less

Impact of tropical cyclones on modeled extreme wind-wave climate

DOE PAGES

Timmermans, Ben; Stone, Daithi; Wehner, Michael; ...

2017-02-16

Here, the effect of forcing wind resolution on the extremes of global wind-wave climate are investigated in numerical simulations. Forcing winds from the Community Atmosphere Model at horizontal resolutions of ~1.0° and ~0.25° are used to drive Wavewatch III. Differences in extreme wave height are found to manifest most strongly in tropical cyclone (TC) regions, emphasizing the need for high-resolution forcing in those areas. Comparison with observations typically show improvement in performance with increased forcing resolution, with a strong influence in the tail of the distribution, although simulated extremes can exceed observations. A simulation for the end of the 21stmore » century under a RCP 8.5 type emission scenario suggests further increases in extreme wave height in TC regions.« less

Impact of tropical cyclones on modeled extreme wind-wave climate

NASA Astrophysics Data System (ADS)

Timmermans, Ben; Stone, Dáithí; Wehner, Michael; Krishnan, Harinarayan

2017-02-01

The effect of forcing wind resolution on the extremes of global wind-wave climate are investigated in numerical simulations. Forcing winds from the Community Atmosphere Model at horizontal resolutions of ˜1.0° and ˜0.25° are used to drive Wavewatch III. Differences in extreme wave height are found to manifest most strongly in tropical cyclone (TC) regions, emphasizing the need for high-resolution forcing in those areas. Comparison with observations typically show improvement in performance with increased forcing resolution, with a strong influence in the tail of the distribution, although simulated extremes can exceed observations. A simulation for the end of the 21st century under a RCP 8.5 type emission scenario suggests further increases in extreme wave height in TC regions.

Large Eddy Simulation of a Film Cooling Technique with a Plenum

NASA Astrophysics Data System (ADS)

Dharmarathne, Suranga; Sridhar, Narendran; Araya, Guillermo; Castillo, Luciano; Parameswaran, Sivapathasund

2012-11-01

Factors that affect the film cooling performance have been categorized into three main groups: (i) coolant & mainstream conditions, (ii) hole geometry & configuration, and (iii) airfoil geometry Bogard et al. (2006). The present study focuses on the second group of factors, namely, the modeling of coolant hole and the plenum. It is required to simulate correct physics of the problem to achieve more realistic numerical results. In this regard, modeling of cooling jet hole and the plenum chamber is highly important Iourokina et al. (2006). Substitution of artificial boundary conditions instead of correct plenum design would yield unrealistic results Iourokina et al. (2006). This study attempts to model film cooling technique with a plenum using a Large Eddy Simulation.Incompressible coolant jet ejects to the surface of the plate at an angle of 30° where it meets compressible turbulent boundary layer which simulates the turbine inflow conditions. Dynamic multi-scale approach Araya (2011) is introduced to prescribe turbulent inflow conditions. Simulations are carried out for two different blowing ratios and film cooling effectiveness is calculated for both cases. Results obtained from LES will be compared with experimental results.

Relative Contributions of Regional and Sector Emissions to the Radiative Forcing of Aerosol-Radiation and Aerosol-Cloud Interactions Based on the AeroCOM Phase III/HTAP2 Experiment

NASA Astrophysics Data System (ADS)

Takemura, T.; Chin, M.

2014-12-01

It is important to understand relative contributions of each regional and sector emission of aerosols and their precursor gases to the regional and global mean radiative forcing of aerosol-radiation and aerosol-cloud interactions. This is because it is useful for international cooperation on controls of air pollution and anthropogenic climate change along most suitable reduction path of their emissions from each region and sector. The Task Force on Hemispheric Transport of Air Pollution (TF HTAP) under the United Nations researches the intercontinental transport of air pollutants including aerosols with strong support of the Aerosol Comparisons between Observations and Models (AeroCOM). The ongoing AeroCOM Phase III/HTAP2 experiment assesses relative contributions of regional and sector sources of aerosols and their precursor gases to the air quality using global aerosol transport models with latest emission inventories. In this study, the extended analyses on the relative contributions of each regional and sector emission to the radiative forcing of aerosol-radiation and aerosol-cloud interactions are done from the AeroCOM Phase III/HTAP2 experiment. Simulated results from MIROC-SPRINTARS and other some global aerosol models participating in the the AeroCOM Phase III/HTAP2 experiment are assessed. Acknowledgements: This study is based on the AeroCOM Phase III/HTAP2 experiment and partly supported by the Environment Research and Technology Development Fund (S-12-3) of the Ministry of the Environment, Japan.

Global Simulation of Bioenergy Crop Productivity: Analytical Framework and Case Study for Switchgrass

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

Kang, Shujiang; Kline, Keith L; Nair, S. Surendran

A global energy crop productivity model that provides geospatially explicit quantitative details on biomass potential and factors affecting sustainability would be useful, but does not exist now. This study describes a modeling platform capable of meeting many challenges associated with global-scale agro-ecosystem modeling. We designed an analytical framework for bioenergy crops consisting of six major components: (i) standardized natural resources datasets, (ii) global field-trial data and crop management practices, (iii) simulation units and management scenarios, (iv) model calibration and validation, (v) high-performance computing (HPC) simulation, and (vi) simulation output processing and analysis. The HPC-Environmental Policy Integrated Climate (HPC-EPIC) model simulatedmore » a perennial bioenergy crop, switchgrass (Panicum virgatum L.), estimating feedstock production potentials and effects across the globe. This modeling platform can assess soil C sequestration, net greenhouse gas (GHG) emissions, nonpoint source pollution (e.g., nutrient and pesticide loss), and energy exchange with the atmosphere. It can be expanded to include additional bioenergy crops (e.g., miscanthus, energy cane, and agave) and food crops under different management scenarios. The platform and switchgrass field-trial dataset are available to support global analysis of biomass feedstock production potential and corresponding metrics of sustainability.« less

Development of a two-dimensional zonally averaged statistical-dynamical model. III - The parameterization of the eddy fluxes of heat and moisture

NASA Technical Reports Server (NTRS)

Stone, Peter H.; Yao, Mao-Sung

1990-01-01

A number of perpetual January simulations are carried out with a two-dimensional zonally averaged model employing various parameterizations of the eddy fluxes of heat (potential temperature) and moisture. The parameterizations are evaluated by comparing these results with the eddy fluxes calculated in a parallel simulation using a three-dimensional general circulation model with zonally symmetric forcing. The three-dimensional model's performance in turn is evaluated by comparing its results using realistic (nonsymmetric) boundary conditions with observations. Branscome's parameterization of the meridional eddy flux of heat and Leovy's parameterization of the meridional eddy flux of moisture simulate the seasonal and latitudinal variations of these fluxes reasonably well, while somewhat underestimating their magnitudes. New parameterizations of the vertical eddy fluxes are developed that take into account the enhancement of the eddy mixing slope in a growing baroclinic wave due to condensation, and also the effect of eddy fluctuations in relative humidity. The new parameterizations, when tested in the two-dimensional model, simulate the seasonal, latitudinal, and vertical variations of the vertical eddy fluxes quite well, when compared with the three-dimensional model, and only underestimate the magnitude of the fluxes by 10 to 20 percent.

FRAMEWORK AND APPLICATION FOR MODELING CONTROL ROOM CREW PERFORMANCE AT NUCLEAR POWER PLANTS

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

Ronald L Boring; David I Gertman; Tuan Q Tran

2008-09-01

This paper summarizes an emerging project regarding the utilization of high-fidelity MIDAS simulations for visualizing and modeling control room crew performance at nuclear power plants. The key envisioned uses for MIDAS-based control room simulations are: (i) the estimation of human error associated with advanced control room equipment and configurations, (ii) the investigative determination of contributory cognitive factors for risk significant scenarios involving control room operating crews, and (iii) the certification of reduced staffing levels in advanced control rooms. It is proposed that MIDAS serves as a key component for the effective modeling of cognition, elements of situation awareness, and riskmore » associated with human performance in next generation control rooms.« less

Analysis of Wake VAS Benefits Using ACES Build 3.2.1: VAMS Type 1 Assessment

NASA Technical Reports Server (NTRS)

Smith, Jeremy C.

2005-01-01

The FAA and NASA are currently engaged in a Wake Turbulence Research Program to revise wake turbulence separation standards, procedures, and criteria to increase airport capacity while maintaining or increasing safety. The research program is divided into three phases: Phase I near term procedural enhancements; Phase II wind dependent Wake Vortex Advisory System (WakeVAS) Concepts of Operations (ConOps); and Phase III farther term ConOps based on wake prediction and sensing. The Phase III Wake VAS ConOps is one element of the Virtual Airspace Modelling and Simulation (VAMS) program blended concepts for enhancing the total system wide capacity of the National Airspace System (NAS). This report contains a VAMS Program Type 1 (stand-alone) assessment of the expected capacity benefits of Wake VAS at the 35 FAA Benchmark Airports and determines the consequent reduction in delay using the Airspace Concepts Evaluation System (ACES) Build 3.2.1 simulator.

Wave Information Studies of US Coastlines: Hindcast Wave Information for the Great Lakes: Lake Superior

DTIC Science & Technology

1992-01-01

to an elevation of 10 m for input into the wave model. 10 PART III: WAVE MODEL 16. The wave model used in this study, DWAVE , was developed by Dr...available from the Wave Information Study (WIS) Project Office. 17. DWAVE is a FORTRAN computer code that simulates wave growth, dissipation, and piopagation...partitioned in a directional spectrum within DWAVE . As seen there, each frequency-direction increment is envisioned as a "bin," and these "bins" are

Hindcast Wave Information for the Great Lakes. Lake Michigan

DTIC Science & Technology

1991-10-01

winds to an elevation of 10 m for input into the wave model. 9 PART III: WAVE MODEL 18. The wave model used in this study, DWAVE , was developed by Dr...available from the WIS Project Office. 19. DWAVE is a FORTRAN computer code that simulates wave growth, dissipation, and propagation in deep water. The...spectrum within DWAVE . As seen there, each frequency-direction increment is envisioned as a "bin," and these "bins" are centered on specified

Hindcast Wave Information for the Great Lakes: Lake Ontario

DTIC Science & Technology

1991-12-01

an elevation of 10 m for input into the wave model. 10 PART III: WAVE MODEL 18. The wave model used in this study, DWAVE , was developed by Dr. Donald...from the Wave Information Study (WIS) Project Office. 19. DWAVE is a FORTRAN computer code that simulates wave growth, dissipation, and propagation...partitioned in a directional spectrum within DWAVE . As seen there, each frequency-direction increment is envisioned as a "bin," and these "bins" are centered

A biomechanical study of artificial cervical discs using computer simulation.

PubMed

Ahn, Hyung Soo; DiAngelo, Denis J

2008-04-15

A virtual simulation model of the subaxial cervical spine was used to study the biomechanical effects of various disc prosthesis designs. To study the biomechanics of different design features of cervical disc arthroplasty devices. Disc arthroplasty is an alternative approach to cervical fusion surgery for restoring and maintaining motion at a diseased spinal segment. Different types of cervical disc arthroplasty devices exist and vary based on their placement and degrees of motion offered. A virtual dynamic model of the subaxial cervical spine was used to study 3 different prosthetic disc designs (PDD): (1) PDD-I: The center of rotation of a spherical joint located at the mid C5-C6 disc, (2) PDD-II: The center of rotation of a spherical joint located 6.5 mm below the mid C5-C6 disc, and (3) PDD-III: The center of rotation of a spherical joint in a plane located at the C5-C6 disc level. A constrained spherical joint placed at the disc level (PDD-I) significantly increased facet loads during extension. Lowering the rotational axis of the spherical joint towards the subjacent body (PDD-II) caused a marginal increase in facet loading during flexion, extension, and lateral bending. Lastly, unconstraining the spherical joint to move freely in a plane (PDD-III) minimized facet load build up during all loading modes. The simulation model showed the impact simple design changes may have on cervical disc dynamics. The predicted facet loads calculated from computer model have to be validated in the experimental study.

Modeling Population Exposure to Ultrafine Particles in a Major Italian Urban Area

PubMed Central

Spinazzè, Andrea; Cattaneo, Andrea; Peruzzo, Carlo; Cavallo, Domenico M.

2014-01-01

Average daily ultrafine particles (UFP) exposure of adult Milan subpopulations (defined on the basis of gender, and then for age, employment or educational status), in different exposure scenarios (typical working day in summer and winter) were simulated using a microenvironmental stochastic simulation model. The basic concept of this kind of model is that time-weighted average exposure is defined as the sum of partial microenvironmental exposures, which are determined by the product of UFP concentration and time spent in each microenvironment. In this work, environmental concentrations were derived from previous experimental studies that were based on microenvironmental measurements in the city of Milan by means of personal or individual monitoring, while time-activity patterns were derived from the EXPOLIS study. A significant difference was observed between the exposures experienced in winter (W: 28,415 pt/cm3) and summer (S: 19,558 pt/cm3). Furthermore, simulations showed a moderate difference between the total exposures experienced by women (S: 19,363 pt/cm3; W: 27,623 pt/cm3) and men (S: 18,806 pt/cm3; W: 27,897 pt/cm3). In addition, differences were found as a function of (I) age, (II) employment status and (III) educational level; accordingly, the highest total exposures resulted for (I) 55–59 years old people, (II) housewives and students and (III) people with higher educational level (more than 10 years of scholarity). Finally, significant differences were found between microenvironment-specific exposures. PMID:25321878

Fatigue crack growth and life prediction under mixed-mode loading

NASA Astrophysics Data System (ADS)

Sajith, S.; Murthy, K. S. R. K.; Robi, P. S.

2018-04-01

Fatigue crack growth life as a function of crack length is essential for the prevention of catastrophic failures from damage tolerance perspective. In damage tolerance design approach, principles of fracture mechanics are usually applied to predict the fatigue life of structural components. Numerical prediction of crack growth versus number of cycles is essential in damage tolerance design. For cracks under mixed mode I/II loading, modified Paris law (d/a d N =C (ΔKe q ) m ) along with different equivalent stress intensity factor (ΔKeq) model is used for fatigue crack growth rate prediction. There are a large number of ΔKeq models available for the mixed mode I/II loading, the selection of proper ΔKeq model has significant impact on fatigue life prediction. In the present investigation, the performance of ΔKeq models in fatigue life prediction is compared with respect to the experimental findings as there are no guidelines/suggestions available on the selection of these models for accurate and/or conservative predictions of fatigue life. Within the limitations of availability of experimental data and currently available numerical simulation techniques, the results of present study attempt to outline models that would provide accurate and conservative life predictions. Such a study aid the numerical analysts or engineers in the proper selection of the model for numerical simulation of the fatigue life. Moreover, the present investigation also suggests a procedure to enhance the accuracy of life prediction using Paris law.

The efficacy of maxillary protraction protocols with the micro-implant-assisted rapid palatal expander (MARPE) and the novel N2 mini-implant-a finite element study.

PubMed

Moon, Won; Wu, Kimberley W; MacGinnis, Matthew; Sung, Jay; Chu, Howard; Youssef, George; Machado, Andre

2015-01-01

Maxillary protraction with the novel N2 mini-implant- and micro-implant-assisted rapid palatal expander (MARPE) can potentially provide significant skeletal effects without surgery, even in older patients where conventional facemask therapy has limited skeletal effects. However, the skeletal effects of altering the location and direction of force from mini-implant-assisted maxillary protraction have not been extensively analyzed. In this study, the application of the novel N2 mini-implant as an orthopedic anchorage device is explored in its ability to treat patients with class III malocclusions. A 3D cranial mesh model with associated sutures was developed from CT images and Mimics modeling software. Utilizing ANSYS simulation software, protraction forces were applied at different locations and directions to simulate conventional facemask therapy and seven maxillary protraction protocols utilizing the novel N2 mini-implant. Stress distribution and displacement were analyzed. Video animations and superimpositions were created. By changing the vector of force and location of N2 mini-implant, the maxilla was displaced differentially. Varying degrees of forward, downward, and rotational movements were observed in each case. For brachyfacial patients, anterior micro-implant-supported protraction at -45° or intermaxillary class III elastics at -45° are recommended. For dolicofacial patients, either anterior micro-implants at -15° or an intermaxillary spring at +30° is recommended. For mesofacial patients with favorable vertical maxillary position, palatal micro-implants at -30° are recommended; anterior micro-implants at -30° are preferred for shallow bites. For patients with a severe mid-facial deficiency, intermaxillary class III elastics at -30° are most effective in promoting anterior growth of the maxilla. By varying the location of N2 mini-implants and vector of class III mechanics, clinicians can differentially alter the magnitude of forward, downward, and rotational movement of the maxilla. As a result, treatment protocol can be customized for each unique class III patient.

Nebular line emission from z > 7 galaxies in a cosmological simulation: rest-frame UV to optical lines

NASA Astrophysics Data System (ADS)

Shimizu, Ikkoh; Inoue, Akio K.; Okamoto, Takashi; Yoshida, Naoki

2016-10-01

We have performed very large and high-resolution cosmological hydrodynamic simulations in order to investigate detectability of nebular lines in the rest-frame ultraviolet (UV) to optical wavelength range from galaxies at z > 7. We find that the expected line fluxes are very well correlated with the apparent UV magnitudes. The C IV 1549 Å and C III] 1909 Å lines of galaxies brighter than 26 AB magnitudes are detectable with current facilities such as the Very Large Telescope (VLT) XShooter and the Keck Multi-Object Spectrometer for Infra-Red Exploration (MOSFIRE). Metal lines such as C IV 1549 Å, C III] 1909 Å, [O II] 3727 Å and [O III] 4959/5007 Å are good targets for spectroscopic observation with the Thirty-Metre Telescope (TMT), European Extremely Large Telescope (E-ELT), Giant Magellan Telescope (GMT) and James Webb Space Telescope (JWST). We also expect Hα and Hβ lines to be detectable with these telescopes. Additionally, we predict the detectability of nebular lines for z > 10 galaxies, which will be found with JWST, the Wide-Field Infrared Survey Telescope (WFIRST) and First Light And Reionization Explorer (FLARE) (11 ≤ z ≤ 15). We conclude that the C IV 1549 Å, C III] 1909 Å, [O III] 4959/5007 Å and Hβ lines from even z ˜15 galaxies could be strong targets for TMT, E-ELT and JWST. We also find that magnification by gravitational lensing is of great help in detecting such high-z galaxies. According to our model, the C III] 1909 Å line in z > 9 galaxy candidates is detectable even using current facilities.

Quantum chemical study of arsenic (III, V) adsorption on Mn-oxides: implications for arsenic(III) oxidation.

PubMed

Zhu, Mengqiang; Paul, Kristian W; Kubicki, James D; Sparks, Donald L

2009-09-01

Density functional theory (DFT) calculations were used to investigate As(V) and As(III) surface complex structures and reaction energies on both Mn(III) and Mn(IV) sites in an attempt to better understand As(III) oxidation bybirnessite, a layered Mn-dioxide mineral. Edge-sharing dioctahedral Mn(III) and Mn(IV) clusters with different combinations of surface functional groups (>MnOH and >MnOH2) were employed to mimic pH variability. Results show that As(V) adsorption was more thermodynamically favorable than As(III) adsorption on both Mn(III) and Mn(IV) surface sites under simulated acidic pH conditions. Therefore, we propose that As(V) adsorption inhibits As(III) oxidation by blocking adsorption sites. Under simulated acidic pH conditions, Mn(IV) sites exhibited stronger adsorption affinity than Mn(III) sites for both As(III) and As(V). Overall, we hypothesize that Mn(III) sites are less reactive in terms of As(III) oxidation due to their lower affinity for As(III) adsorption, higher potential to be blocked by As(V) complexes, and slower electron transfer rates with adsorbed As(III). Results from this study offer an explanation regarding the experimental observations of Mn(III) accumulation on birnessite and the long residence time of As(III) adsorption complexes on manganite (r-MnOOH) during As(III) oxidation.

Improving Hybrid III injury assessment in steering wheel rim to chest impacts using responses from finite element Hybrid III and human body model.

PubMed

Holmqvist, Kristian; Davidsson, Johan; Mendoza-Vazquez, Manuel; Rundberget, Peter; Svensson, Mats Y; Thorn, Stefan; Törnvall, Fredrik

2014-01-01

The main aim of this study was to improve the quality of injury risk assessments in steering wheel rim to chest impacts when using the Hybrid III crash test dummy in frontal heavy goods vehicle (HGV) collision tests. Correction factors for chest injury criteria were calculated as the model chest injury parameter ratios between finite element (FE) Hybrid III, evaluated in relevant load cases, and the Total Human Model for Safety (THUMS). This is proposed to be used to compensate Hybrid III measurements in crash tests where steering wheel rim to chest impacts occur. The study was conducted in an FE environment using an FE-Hybrid III model and the THUMS. Two impactor shapes were used, a circular hub and a long, thin horizontal bar. Chest impacts at velocities ranging from 3.0 to 6.0 m/s were simulated at 3 impact height levels. A ratio between FE-Hybrid III and THUMS chest injury parameters, maximum chest compression C max, and maximum viscous criterion VC max, were calculated for the different chest impact conditions to form a set of correction factors. The definition of the correction factor is based on the assumption that the response from a circular hub impact to the middle of the chest is well characterized and that injury risk measures are independent of impact height. The current limits for these chest injury criteria were used as a basis to develop correction factors that compensate for the limitations in biofidelity of the Hybrid III in steering wheel rim to chest impacts. The hub and bar impactors produced considerably higher C max and VC max responses in the THUMS compared to the FE-Hybrid III. The correction factor for the responses of the FE-Hybrid III showed that the criteria responses for the bar impactor were consistently overestimated. Ratios based on Hybrid III and THUMS responses provided correction factors for the Hybrid III responses ranging from 0.84 to 0.93. These factors can be used to estimate C max and VC max values when the Hybrid III is used in crash tests for which steering wheel rim to chest interaction occurs. For the FE-Hybrid III, bar impacts caused higher chest deflection compared to hub impacts, although the contrary results were obtained with the more humanlike THUMS. Correction factors were developed that can be used to correct the Hybrid III chest responses. Higher injury criteria capping limits for steering wheel impacts are acceptable. Supplemental materials are available for this article. Go to the publisher's online edition of Traffic Injury Prevention to view the supplemental file.

Evaluating the impact of fires on slope instability processes: a case study in Central Italy (Invited)

NASA Astrophysics Data System (ADS)

Rossi, M.; Torri, D.; Bacaro, G.; Mondini, A.; Reichenbach, P.; Fiorucci, F.; Marchesini, I.

2013-12-01

Fires can change significantly the characteristics of slopes. Their effect on vegetation, soil properties, and fauna can influence slope instability processes, including channeled erosion and mass movements. Even if in the literature attempts to estimate these effects were made using mostly empirical approaches, evaluating quantitatively the impact of fires on slope instability processes remain challenging. In a small basin in Central Italy, where an intense arson occurred in July 2012, we estimated the effects of fire on the hazard posed by different type of instability processes. For the purpose we modelled separately channeled erosion phenomena and rock falls, for which a significant impact of fires was expected. For the former we exploited the LANDPLANER (LANDscape, Plants, LANdslides and ERosion) model, which is able to simulate the hydrological response of a slope, and their effect on instability processes, under human-induced or natural changing scenarios, including climatic, land use, and slope morphology changes. For the latter we exploited two different modeling approaches considering directly (Rockyfor3D model) or indirectly (STONE model) the effect of the vegetation on the movement of rock masses along the slope. All the model simulations were repeated considering land use scenarios before and after the fire. Those were derived through field surveys and though the supervised classification of high resolution satellite images acquired inthe study area before and after the fire. The analysis of the effect of the fire on channeled phenomena included the estimation of (i) the overland flow on the basin, (ii) the location of the gully head, (iii) the channel eroded volume, and (iii) the change of the connectivity inside the basin. The analysis of the effect of the fire on rock fall phenomena included the estimation of (i) the increase of rock fall source areas, (ii) the increase of distances travelled by rock masses along the slopes, and (iii) the spatial distribution of the fallen rock blocks. In all models and scenarios we considered the effect of roads. Results showed a significant increase of the susceptibility to slope instability processes after the fire, mainly due to (i) the formation of hydro repellent soil horizons, (ii) the removal of the litter, (iii) the burning of vegetation.

A GIS-based modeling system for petroleum waste management. Geographical information system.

PubMed

Chen, Z; Huang, G H; Li, J B

2003-01-01

With an urgent need for effective management of petroleum-contaminated sites, a GIS-aided simulation (GISSIM) system is presented in this study. The GISSIM contains two components: an advanced 3D numerical model and a geographical information system (GIS), which are integrated within a general framework. The modeling component undertakes simulation for the fate of contaminants in subsurface unsaturated and saturated zones. The GIS component is used in three areas throughout the system development and implementation process: (i) managing spatial and non-spatial databases; (ii) linking inputs, model, and outputs; and (iii) providing an interface between the GISSIM and its users. The developed system is applied to a North American case study. Concentrations of benzene, toluene, and xylenes in groundwater under a petroleum-contaminated site are dynamically simulated. Reasonable outputs have been obtained and presented graphically. They provide quantitative and scientific bases for further assessment of site-contamination impacts and risks, as well as decisions on practical remediation actions.

The atmospheric boundary layer — advances in knowledge and application

NASA Astrophysics Data System (ADS)

Garratt, J. R.; Hess, G. D.; Physick, W. L.; Bougeault, P.

1996-02-01

We summarise major activities and advances in boundary-layer knowledge in the 25 years since 1970, with emphasis on the application of this knowledge to surface and boundary-layer parametrisation schemes in numerical models of the atmosphere. Progress in three areas is discussed: (i) the mesoscale modelling of selected phenomena; (ii) numerical weather prediction; and (iii) climate simulations. Future trends are identified, including the incorporation into models of advanced cloud schemes and interactive canopy schemes, and the nesting of high resolution boundary-layer schemes in global climate models.

Top-down NOX emissions over European cities from LOTOS-EUROS simulated and OMI observed tropospheric NO2 columns using the Exponentially Modified Gaussian approach

NASA Astrophysics Data System (ADS)

Verstraeten, Willem W.; Folkert Boersma, K.; Douros, John; Williams, Jason E.; Eskes, Henk H.; Delcloo, Andy

2017-04-01

High nitrogen oxides concentrations at the surface (NOX = NO + NO2) impact humans and ecosystem badly and play a key role in tropospheric chemistry. Surface NOX emissions drive major processes in regional and global chemistry transport models (CTM). NOX contributes to the formation of acid rain, act as aerosol precursors and is an important trace gas for the formation of tropospheric ozone (O3). Via tropospheric O3, NOX indirectly affects the production of the hydroxyl radical which controls the chemical lifetime of key atmospheric pollutants and reactive greenhouse gases. High NOX emissions are mainly observed in polluted regions produced by anthropogenic combustion from industrial, traffic and household activities typically observed in large and densely populated urban areas. Accurate NOX inventories are essential, but state-of the- art emission databases may vary substantially and uncertainties are high since reported emissions factors may differ in order of magnitude and more. To date, the modelled NO2 concentrations and lifetimes have large associated uncertainties due to the highly non-linear small-scale chemistry that occurs in urban areas and uncertainties in the reaction rate data, missing nitrogen (N) species and volatile organic compounds (VOC) emissions, and incomplete knowledge of nitrogen oxides chemistry. Any overestimation in the chemical lifetime may mask missing NOX chemistry in current CTM's. By simultaneously estimating both the NO2 lifetime and concentrations, for instance by using the Exponentially Modified Gaussian (EMG), a better surface NOX emission flux estimate can be obtained. Here we evaluate if the EMG methodology can reproduce the emissions input from the tropospheric NO2 columns simulated by the LOTOS-EUROS (Long Term Ozone Simulation-European Ozone Simulation) CTM model. We apply the EMG methodology on LOTOS-EUROS simulated tropospheric NO2 columns for the period April-September 2013 for 21 selected European urban areas under windy conditions (surface wind speeds > 3 m s-1). We then compare the top-down derived surface NOX emissions with the 2011 MACC-III emission inventory, used in the LOTOS-EUROS model as input to simulate the NO2 columns. We also apply the EMG methodology on OMI (Ozone Monitoring Instrument) tropospheric NO2 column data, providing us with real-time observation-based estimates of midday NO2 lifetime and NOX emissions over 21 European cities in 2013. Results indicate that the top-down derived NOX emissions from LOTOS-EUROS (respectively OMI) are comparable with the MACC-III inventory with a R2 of 0.99 (respectively R2 = 0.79). For St-Petersburg and Moscow the top-down NOX estimates from 2013 OMI data are biased low compared to the MACC-III inventory which uses a 2011 NOX emissions update.

SPH-DEM approach to numerically simulate the deformation of three-dimensional RBCs in non-uniform capillaries.

PubMed

Polwaththe-Gallage, Hasitha-Nayanajith; Saha, Suvash C; Sauret, Emilie; Flower, Robert; Senadeera, Wijitha; Gu, YuanTong

2016-12-28

Blood continuously flows through the blood vessels in the human body. When blood flows through the smallest blood vessels, red blood cells (RBCs) in the blood exhibit various types of motion and deformed shapes. Computational modelling techniques can be used to successfully predict the behaviour of the RBCs in capillaries. In this study, we report the application of a meshfree particle approach to model and predict the motion and deformation of three-dimensional RBCs in capillaries. An elastic spring network based on the discrete element method (DEM) is employed to model the three-dimensional RBC membrane. The haemoglobin in the RBC and the plasma in the blood are modelled as smoothed particle hydrodynamics (SPH) particles. For validation purposes, the behaviour of a single RBC in a simple shear flow is examined and compared against experimental results. Then simulations are carried out to predict the behaviour of RBCs in a capillary; (i) the motion of five identical RBCs in a uniform capillary, (ii) the motion of five identical RBCs with different bending stiffness (K b ) values in a stenosed capillary, (iii) the motion of three RBCs in a narrow capillary. Finally five identical RBCs are employed to determine the critical diameter of a stenosed capillary. Validation results showed a good agreement with less than 10% difference. From the above simulations, the following results are obtained; (i) RBCs exhibit different deformation behaviours due to the hydrodynamic interaction between them. (ii) Asymmetrical deformation behaviours of the RBCs are clearly observed when the bending stiffness (K b ) of the RBCs is changed. (iii) The model predicts the ability of the RBCs to squeeze through smaller blood vessels. Finally, from the simulations, the critical diameter of the stenosed section to stop the motion of blood flow is predicted. A three-dimensional spring network model based on DEM in combination with the SPH method is successfully used to model the motion and deformation of RBCs in capillaries. Simulation results reveal that the condition of blood flow stopping depends on the pressure gradient of the capillary and the severity of stenosis of the capillary. In addition, this model is capable of predicting the critical diameter which prevents motion of RBCs for different blood pressures.

FF12MC: A revised AMBER forcefield and new protein simulation protocol

PubMed Central

2016-01-01

ABSTRACT Specialized to simulate proteins in molecular dynamics (MD) simulations with explicit solvation, FF12MC is a combination of a new protein simulation protocol employing uniformly reduced atomic masses by tenfold and a revised AMBER forcefield FF99 with (i) shortened C—H bonds, (ii) removal of torsions involving a nonperipheral sp3 atom, and (iii) reduced 1–4 interaction scaling factors of torsions ϕ and ψ. This article reports that in multiple, distinct, independent, unrestricted, unbiased, isobaric–isothermal, and classical MD simulations FF12MC can (i) simulate the experimentally observed flipping between left‐ and right‐handed configurations for C14–C38 of BPTI in solution, (ii) autonomously fold chignolin, CLN025, and Trp‐cage with folding times that agree with the experimental values, (iii) simulate subsequent unfolding and refolding of these miniproteins, and (iv) achieve a robust Z score of 1.33 for refining protein models TMR01, TMR04, and TMR07. By comparison, the latest general‐purpose AMBER forcefield FF14SB locks the C14–C38 bond to the right‐handed configuration in solution under the same protein simulation conditions. Statistical survival analysis shows that FF12MC folds chignolin and CLN025 in isobaric–isothermal MD simulations 2–4 times faster than FF14SB under the same protein simulation conditions. These results suggest that FF12MC may be used for protein simulations to study kinetics and thermodynamics of miniprotein folding as well as protein structure and dynamics. Proteins 2016; 84:1490–1516. © 2016 The Authors Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc. PMID:27348292

Modeling and Control of State-Affine Probabilistic Systems for Atomic-Scale Dynamics

DTIC Science & Technology

2007-06-01

Analysis for Nonlinear Systems. New York: Spring -Verlag, 1987. [5] M. Itoh, "Atomic-scale homoepitaxial growth simulations of reconstructed III-V surfaces...Ridge, NJ; 1995. -- SSC function of the Node 182 [2] M. K. Weldon , K. T. Queeney, J. Eng Jr., K. Raghavachari, and Y. J. Chabal, "The surface science

Effects of water-management alternatives on streamflow in the Ipswich River basin, Massachusetts

USGS Publications Warehouse

Zarriello, Philip J.

2001-01-01

Management alternatives that could help mitigate the effects of water withdrawals on streamflow in the Ipswich River Basin were evaluated by simulation with a calibrated Hydrologic Simulation Program--Fortran (HSPF) model. The effects of management alternatives on streamflow were simulated for a 35-year period (196195). Most alternatives examined increased low flows compared to the base simulation of average 1989-93 withdrawals. Only the simulation of no septic-effluent inflow, and the simulation of a 20-percent increase in withdrawals, further lowered flows or caused the river to stop flowing for longer periods of time than the simulation of average 198993 withdrawals. Simulations of reduced seasonal withdrawals by 20 percent, and by 50 percent, resulted in a modest increase in low flow in a critical habitat reach (model reach 8 near the Reading town well field); log-Pearson Type III analysis of simulated daily-mean flow indicated that under these reduced withdrawals, model reach 8 would stop flowing for a period of seven consecutive days about every other year, whereas under average 198993 withdrawals this reach would stop flowing for a seven consecutive day period almost every year. Simulations of no seasonal withdrawals, and simulations that stopped streamflow depletion when flow in model reach 19 was below 22 cubic feet per second, indicated flow would be maintained in model reach 8 at all times. Simulations indicated wastewater-return flows would augment low flow in proportion to the rate of return flow. Simulations of a 1.5 million gallons per day return flow rate indicated model reach 8 would stop flowing for a period of seven consecutive days about once every 5 years; simulated return flow rates of 1.1 million gallons per day indicated that model reach 8 would stop flowing for a period of seven consecutive days about every other year. Simulation of reduced seasonal withdrawals, combined with no septic effluent return flow, indicated only a slight increase in low flow compared to low flows simulated under average 198993 withdrawals. Simulation of reduced seasonal withdrawal, combined with 2.6 million gallons per day wastewater-return flows, provided more flow in model reach 8 than that simulated under no withdrawals.

Constraining the Statistics of Population III Binaries

NASA Technical Reports Server (NTRS)

Stacy, Athena; Bromm, Volker

2012-01-01

We perform a cosmological simulation in order to model the growth and evolution of Population III (Pop III) stellar systems in a range of host minihalo environments. A Pop III multiple system forms in each of the ten minihaloes, and the overall mass function is top-heavy compared to the currently observed initial mass function in the Milky Way. Using a sink particle to represent each growing protostar, we examine the binary characteristics of the multiple systems, resolving orbits on scales as small as 20 AU. We find a binary fraction of approx. 36, with semi-major axes as large as 3000 AU. The distribution of orbital periods is slightly peaked at approx. < 900 yr, while the distribution of mass ratios is relatively flat. Of all sink particles formed within the ten minihaloes, approx. 50 are lost to mergers with larger sinks, and 50 of the remaining sinks are ejected from their star-forming disks. The large binary fraction may have important implications for Pop III evolution and nucleosynthesis, as well as the final fate of the first stars.

Mathematical modeling and simulation in animal health. Part I: Moving beyond pharmacokinetics.

PubMed

Riviere, J E; Gabrielsson, J; Fink, M; Mochel, J

2016-06-01

The application of mathematical modeling to problems in animal health has a rich history in the form of pharmacokinetic modeling applied to problems in veterinary medicine. Advances in modeling and simulation beyond pharmacokinetics have the potential to streamline and speed-up drug research and development programs. To foster these goals, a series of manuscripts will be published with the following goals: (i) expand the application of modeling and simulation to issues in veterinary pharmacology; (ii) bridge the gap between the level of modeling and simulation practiced in human and veterinary pharmacology; (iii) explore how modeling and simulation concepts can be used to improve our understanding of common issues not readily addressed in human pharmacology (e.g. breed differences, tissue residue depletion, vast weight ranges among adults within a single species, interspecies differences, small animal species research where data collection is limited to sparse sampling, availability of different sampling matrices); and (iv) describe how quantitative pharmacology approaches could help understanding key pharmacokinetic and pharmacodynamic characteristics of a drug candidate, with the goal of providing explicit, reproducible, and predictive evidence for optimizing drug development plans, enabling critical decision making, and eventually bringing safe and effective medicines to patients. This study introduces these concepts and introduces new approaches to modeling and simulation as well as clearly articulate basic assumptions and good practices. The driving force behind these activities is to create predictive models that are based on solid physiological and pharmacological principles as well as adhering to the limitations that are fundamental to applying mathematical and statistical models to biological systems. © 2015 John Wiley & Sons Ltd.

Simulation of radiation effects on three-dimensional computer optical memories

NASA Technical Reports Server (NTRS)

Moscovitch, M.; Emfietzoglou, D.

1997-01-01

A model was developed to simulate the effects of heavy charged-particle (HCP) radiation on the information stored in three-dimensional computer optical memories. The model is based on (i) the HCP track radial dose distribution, (ii) the spatial and temporal distribution of temperature in the track, (iii) the matrix-specific radiation-induced changes that will affect the response, and (iv) the kinetics of transition of photochromic molecules from the colored to the colorless isomeric form (bit flip). It is shown that information stored in a volume of several nanometers radius around the particle's track axis may be lost. The magnitude of the effect is dependent on the particle's track structure.

Magnetorotatioal Collapse of Supermassive Stars: Black Hole Formation and Jets

NASA Astrophysics Data System (ADS)

Sun, Lunan; Paschalidis, Vasileios; Ruiz, Milton; Shapiro, Stuart

2017-01-01

We perform magnetohydrodynamic simulations in full general relativity of the collapse of radially unstable, uniformly rotating, massive stars to black holes. The stars spin at the mass-shedding limit, account for magnetic fields and obey a Γ = 4/3 EOS. The calculations lift the restriction of axisymmetry imposed in previous simulations. Our simulations model the direct collapse of supermassive stars to supermassive BHs (>=104M⊙) at high cosmological redshifts, which may explain the appearance of supermassive BHs and quasars by z 7. They also crudely model the collapse of massive Pop III stars to massive BHs, which could power some of the long gamma-ray bursts observed by FERMI and SWIFT at z 6-8. We analyze the properties of the electromagnetic and gravitational wave signatures of these events and discuss the detectability of such multimessenger sources.

Three-Dimensional Modeling of Fracture Clusters in Geothermal Reservoirs

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

Ghassemi, Ahmad

The objective of this is to develop a 3-D numerical model for simulating mode I, II, and III (tensile, shear, and out-of-plane) propagation of multiple fractures and fracture clusters to accurately predict geothermal reservoir stimulation using the virtual multi-dimensional internal bond (VMIB). Effective development of enhanced geothermal systems can significantly benefit from improved modeling of hydraulic fracturing. In geothermal reservoirs, where the temperature can reach or exceed 350oC, thermal and poro-mechanical processes play an important role in fracture initiation and propagation. In this project hydraulic fracturing of hot subsurface rock mass will be numerically modeled by extending the virtual multiplemore » internal bond theory and implementing it in a finite element code, WARP3D, a three-dimensional finite element code for solid mechanics. The new constitutive model along with the poro-thermoelastic computational algorithms will allow modeling the initiation and propagation of clusters of fractures, and extension of pre-existing fractures. The work will enable the industry to realistically model stimulation of geothermal reservoirs. The project addresses the Geothermal Technologies Office objective of accurately predicting geothermal reservoir stimulation (GTO technology priority item). The project goal will be attained by: (i) development of the VMIB method for application to 3D analysis of fracture clusters; (ii) development of poro- and thermoelastic material sub-routines for use in 3D finite element code WARP3D; (iii) implementation of VMIB and the new material routines in WARP3D to enable simulation of clusters of fractures while accounting for the effects of the pore pressure, thermal stress and inelastic deformation; (iv) simulation of 3D fracture propagation and coalescence and formation of clusters, and comparison with laboratory compression tests; and (v) application of the model to interpretation of injection experiments (planned by our industrial partner) with reference to the impact of the variations in injection rate and temperature, rock properties, and in-situ stress.« less

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

Reedlunn, Benjamin

Room D was an in-situ, isothermal, underground experiment conducted at the Waste Isolation Pilot Plant between 1984 and 1991. The room was carefully instrumented to measure the horizontal and vertical closure immediately upon excavation and for several years thereafter. Early finite element simulations of salt creep around Room D under-predicted the vertical closure by 4.5×, causing investigators to explore a series of changes to the way Room D was modeled. Discrepancies between simulations and measurements were resolved through a series of adjustments to model parameters, which were openly acknowledged in published reports. Interest in Room D has been rekindled recentlymore » by the U.S./German Joint Project III and Project WEIMOS, which seek to improve the predictions of rock salt constitutive models. Joint Project participants calibrate their models solely against laboratory tests, and benchmark the models against underground experiments, such as room D. This report describes updating legacy Room D simulations to today’s computational standards by rectifying several numerical issues. Subsequently, the constitutive model used in previous modeling is recalibrated two different ways against a suite of new laboratory creep experiments on salt extracted from the repository horizon of the Waste Isolation Pilot Plant. Simulations with the new, laboratory-based, calibrations under-predict Room D vertical closure by 3.1×. A list of potential improvements is discussed.« less

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

Reedlunn, Benjamin

Room D was an in-situ, isothermal, underground experiment conducted at theWaste Isolation Pilot Plant between 1984 and 1991. The room was carefully instrumented to measure the horizontal and vertical closure immediately upon excavation and for several years thereafter. Early finite element simulations of salt creep around Room D under predicted the vertical closure by 4.5×, causing investigators to explore a series of changes to the way Room D was modeled. Discrepancies between simulations and measurements were resolved through a series of adjustments to model parameters, which were openly acknowledged in published reports. Interest in Room D has been rekindled recentlymore » by the U.S./German Joint Project III and Project WEIMOS, which seek to improve the predictions of rock salt constitutive models. Joint Project participants calibrate their models solely against laboratory tests, and benchmark the models against underground experiments, such as room D. This report describes updating legacy Room D simulations to today’s computational standards by rectifying several numerical issues. Subsequently, the constitutive model used in previous modeling is recalibrated two different ways against a suite of new laboratory creep experiments on salt extracted from the repository horizon of the Waste Isolation Pilot Plant. Simulations with the new, laboratory-based, calibrations under predict Room D vertical closure by 3.1×. A list of potential improvements is discussed.« less

Pore-scale characterization of biogeochemical controls on iron and uranium speciation under flow conditions.

PubMed

Pearce, Carolyn I; Wilkins, Michael J; Zhang, Changyong; Heald, Steve M; Fredrickson, Jim K; Zachara, John M

2012-08-07

Etched silicon microfluidic pore network models (micromodels) with controlled chemical and redox gradients, mineralogy, and microbiology under continuous flow conditions are used for the incremental development of complex microenvironments that simulate subsurface conditions. We demonstrate the colonization of micromodel pore spaces by an anaerobic Fe(III)-reducing bacterial species (Geobacter sulfurreducens) and the enzymatic reduction of a bioavailable Fe(III) phase within this environment. Using both X-ray microprobe and X-ray absorption spectroscopy, we investigate the combined effects of the precipitated Fe(III) phases and the microbial population on uranium biogeochemistry under flow conditions. Precipitated Fe(III) phases within the micromodel were most effectively reduced in the presence of an electron shuttle (AQDS), and Fe(II) ions adsorbed onto the precipitated mineral surface without inducing any structural change. In the absence of Fe(III), U(VI) was effectively reduced by the microbial population to insoluble U(IV), which was precipitated in discrete regions associated with biomass. In the presence of Fe(III) phases, however, both U(IV) and U(VI) could be detected associated with biomass, suggesting reoxidation of U(IV) by localized Fe(III) phases. These results demonstrate the importance of the spatial localization of biomass and redox active metals, and illustrate the key effects of pore-scale processes on contaminant fate and reactive transport.

Utilization of natural hematite as reactive barrier for immobilization of radionuclides from radioactive liquid waste.

PubMed

El Afifi, E M; Attallah, M F; Borai, E H

2016-01-01

Potential utilization of hematite as a natural material for immobilization of long-lived radionuclides from radioactive liquid waste was investigated. Hematite ore has been characterized by different analytical tools such as Fourier transformer infrared (FTIR), X-ray fluorescence (XRF), powder X-ray diffraction (XRD), thermogravimetry (TG) and differential thermal (DT) analysis, scanning electron microscopy (SEM) and BET-surface area. In this study, europium was used as REEs(III) and as a homolog of Am(III)-isotopes (such as (241)Am of 432.6 y, (242m)Am of 141 y and (243)Am of 7370 y). Micro particles of the hematite ore were used for treatment of radioactive waste containing (152+154)Eu(III). The results indicated that 96% (4.1 × 10(4) Bq) of (152+154)Eu(III) was efficiently retained onto hematite ore. Kinetic experiments indicated that the processes could be simulated by a pseudo-second-order model and suggested that the process may be chemisorption in nature. The applicability of Langmuir, Freundlich and Temkin models was investigated. It was found that Langmuir isotherm exhibited the best fit with the experimental results. It can be concluded that hematite is an economic and efficient reactive barrier for immobilization of long-lived radio isotopes of actinides and REEs(III). Copyright © 2015 Elsevier Ltd. All rights reserved.

A marketing approach to carpool demand analysis. Technical memorandum III. Tradeoff model and policy simulation. Conservation paper. [Commuter survey in 3 major urban areas

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

Not Available

1976-07-01

The memorandum discusses the theoretical basis of the trade-off model and its adaptation particularly in the simulation procedures used in evaluating specific policies. Two published articles dealing with the development and application of the trade-off model for market research are included as appendices to this memorandum. This model was the primary instrument used in connection with a research effort examining the role of individuals attitudes and perceptions in deciding whether or not to carpool. The research was based upon a survey of commuters in 3 major urban areas and has resulted in a sizeable new data base on respondents' socio-economicmore » and worktrip characteristics, travel perceptions, and travel preferences. Research is contained in the Summary Report, also available through NTIS.« less

Effets de l'humidite sur la propagation du delaminage dans un composite carbone/epoxy sollicite en mode mixte I/II

NASA Astrophysics Data System (ADS)

LeBlanc, Luc R.

Les materiaux composites sont de plus en plus utilises dans des domaines tels que l'aerospatiale, les voitures a hautes performances et les equipements sportifs, pour en nommer quelques-uns. Des etudes ont demontre qu'une exposition a l'humidite nuit a la resistance des composites en favorisant l'initiation et la propagation du delaminage. De ces etudes, tres peu traitent de l'effet de l'humidite sur l'initiation du delaminage en mode mixte I/II et aucune ne traite des effets de l'humidite sur le taux de propagation du delaminage en mode mixte I/II dans un composite. La premiere partie de cette these consiste a determiner les effets de l'humidite sur la propagation du delaminage lors d'une sollicitation en mode mixte I/II. Des eprouvettes d'un composite unidirectionnel de carbone/epoxy (G40-800/5276-1) ont ete immergees dans un bain d'eau distillee a 70°C jusqu'a leur saturation. Des essais experimentaux quasi-statiques avec des chargements d'une gamme de mixites des modes I/II (0%, 25%, 50%, 75% et 100%) ont ete executes pour determiner les effets de l'humidite sur la resistance au delaminage du composite. Des essais de fatigue ont ete realises, avec la meme gamme de mixite des modes I/II, pour determiner 1'effet de 1'humidite sur l'initiation et sur le taux de propagation du delaminage. Les resultats des essais en chargement quasi-statique ont demontre que l'humidite reduit la resistance au delaminage d'un composite carbone/epoxy pour toute la gamme des mixites des modes I/II, sauf pour le mode I ou la resistance au delaminage augmente apres une exposition a l'humidite. Pour les chargements en fatigue, l'humidite a pour effet d'accelerer l'initiation du delaminage et d'augmenter le taux de propagation pour toutes les mixites des modes I/II. Les donnees experimentales recueillies ont ete utilisees pour determiner lesquels des criteres de delaminage en statique et des modeles de taux de propagation du delaminage en fatigue en mode mixte I/II proposes dans la litterature representent le mieux le delaminage du composite etudie. Une courbe de regression a ete utilisee pour determiner le meilleur ajustement entre les donnees experimentales et les criteres de delaminage en statique etudies. Une surface de regression a ete utilisee pour determiner le meilleur ajustement entre les donnees experimentales et les modeles de taux de propagation en fatigue etudies. D'apres les ajustements, le meilleur critere de delaminage en statique est le critere B-K et le meilleur modele de propagation en fatigue est le modele de Kenane-Benzeggagh. Afin de predire le delaminage lors de la conception de pieces complexes, des modeles numeriques peuvent etre utilises. La prediction de la longueur de delaminage lors des chargements en fatigue d'une piece est tres importante pour assurer qu'une fissure interlaminaire ne va pas croitre excessivement et causer la rupture de cette piece avant la fin de sa duree de vie de conception. Selon la tendance recente, ces modeles sont souvent bases sur l'approche de zone cohesive avec une formulation par elements finis. Au cours des travaux presentes dans cette these, le modele de progression du delaminage en fatigue de Landry & LaPlante (2012) a ete ameliore en y ajoutant le traitement des chargements en mode mixte I/II et en y modifiant l'algorithme du calcul de la force d'entrainement maximale du delaminage. Une calibration des parametres de zone cohesive a ete faite a partir des essais quasi-statiques experimentaux en mode I et II. Des resultats de simulations numeriques des essais quasi-statiques en mode mixte I/II, avec des eprouvettes seches et humides, ont ete compares avec les essais experimentaux. Des simulations numeriques en fatigue ont aussi ete faites et comparees avec les resultats experimentaux du taux de propagation du delaminage. Les resultats numeriques des essais quasi-statiques et de fatigue ont montre une bonne correlation avec les resultats experimentaux pour toute la gamme des mixites des modes I/II etudiee.

Gravitational wave sources from Pop III stars are preferentially located within the cores of their host Galaxies

NASA Astrophysics Data System (ADS)

Pacucci, Fabio; Loeb, Abraham; Salvadori, Stefania

2017-10-01

The detection of gravitational waves (GWs) generated by merging black holes has recently opened up a new observational window into the Universe. The mass of the black holes in the first and third Laser Interferometer Gravitational Wave Observatory (LIGO) detections (36-29 M⊙ and 32-19 M⊙) suggests low-metallicity stars as their most likely progenitors. Based on high-resolution N-body simulations, coupled with state-of-the-art metal enrichment models, we find that the remnants of Pop III stars are preferentially located within the cores of galaxies. The probability of a GW signal to be generated by Pop III stars reaches ∼90 per cent at ∼0.5 kpc from the galaxy centre, compared to a benchmark value of ∼5 per cent outside the core. The predicted merger rates inside bulges is ∼60 × βIII Gpc-3 yr-1 (βIII is the Pop III binarity fraction). To match the 90 per cent credible range of LIGO merger rates, we obtain: 0.03 < βIII < 0.88. Future advances in GW observatories and the discovery of possible electromagnetic counterparts could allow the localization of such sources within their host galaxies. The preferential concentration of GW events within the bulge of galaxies would then provide an indirect proof for the existence of Pop III stars.

A versatile petri net based architecture for modeling and simulation of complex biological processes.

PubMed

Nagasaki, Masao; Doi, Atsushi; Matsuno, Hiroshi; Miyano, Satoru

2004-01-01

The research on modeling and simulation of complex biological systems is getting more important in Systems Biology. In this respect, we have developed Hybrid Function Petri net (HFPN) that was newly developed from existing Petri net because of their intuitive graphical representation and their capabilities for mathematical analyses. However, in the process of modeling metabolic, gene regulatory or signal transduction pathways with the architecture, we have realized three extensions of HFPN, (i) an entity should be extended to contain more than one value, (ii) an entity should be extended to handle other primitive types, e.g. boolean, string, (iii) an entity should be extended to handle more advanced type called object that consists of variables and methods, are necessary for modeling biological systems with Petri net based architecture. To deal with it, we define a new enhanced Petri net called hybrid functional Petri net with extension (HFPNe). To demonstrate the effectiveness of the enhancements, we model and simulate with HFPNe four biological processes that are diffcult to represent with the previous architecture HFPN.

Power consumption of rotary blood pumps: pulsatile versus constant-speed mode.

PubMed

Pirbodaghi, Tohid; Cotter, Chris; Bourque, Kevin

2014-12-01

We investigated the power consumption of a HeartMate III rotary blood pump based on in vitro experiments performed in a cardiovascular simulator. To create artificial-pulse mode, we modulated the pump speed by decreasing the mean speed by 2000 rpm for 200 ms and then increasing speed by 4000 rpm (mean speeds plus 2000 rpm) for another 200 ms, creating a square waveform shape. The HeartMate III was connected to a cardiovascular simulator consisting of a hydraulic pump system to simulate left ventricle pumping action, arterial and venous compliance chambers, and an adjustable valve for peripheral resistance to facilitate the desired aortic pressure. The simulator operated based on Suga's elastance model to mimic the Starling response of the heart, thereby reproducing physiological blood flow and pressure conditions. We measured the instantaneous total electrical current and voltage of the pump to evaluate its power consumption. The aim was to answer these fundamental questions: (i) How does pump speed modulation affect pump power consumption? (ii) How does the power consumption vary in relation to external pulsatile flow? The results indicate that speed modulation and external pulsatile flow both moderately increase the power consumption. Increasing the pump speed reduces the impact of external pulsatile flow. Copyright © 2014 International Center for Artificial Organs and Transplantation and Wiley Periodicals, Inc.

Simulating Blade-Strike on Fish passing through Marine Hydrokinetic Turbines

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

Romero Gomez, Pedro DJ; Richmond, Marshall C.

2014-06-16

The study reported here evaluated the occurrence, frequency, and intensity of blade strike of fish on an axial-flow marine hydrokinetic turbine by using two modeling approaches: a conventional kinematic formulation and a proposed Lagrangian particle- based scheme. The kinematic model included simplifying assumptions of fish trajectories such as distribution and velocity. The proposed method overcame the need for such simplifications by integrating the following components into a computational fluid dynamics (CFD) model: (i) advanced eddy-resolving flow simulation, (ii) generation of ambient turbulence based on field data, (iii) moving turbine blades in highly transient flows, and (iv) Lagrangian particles to mimicmore » the potential fish pathways. The test conditions to evaluate the blade-strike probability and fish survival rate were: (i) the turbulent environment, (ii) the fish size, and (iii) the approaching flow velocity. The proposed method offered the ability to produce potential fish trajectories and their interaction with the rotating turbine. Depending upon the scenario, the percentile of particles that registered a collision event ranged from 6% to 19% of the released sample size. Next, by using a set of experimental correlations of the exposure-response of living fish colliding with moving blades, the simulated collision data were used as input variables to estimate the survival rate of fish passing through the operating turbine. The resulting survival rates were greater than 96% in all scenarios, which is comparable to or better than known survival rates for conventional hydropower turbines. The figures of strike probability and mortality rate were amplified by the kinematic model. The proposed method offered the advantage of expanding the evaluation of other mechanisms of stress and injury on fish derived from hydrokinetic turbines and related devices.« less

Active transport on disordered microtubule networks: the generalized random velocity model.

PubMed

Kahana, Aviv; Kenan, Gilad; Feingold, Mario; Elbaum, Michael; Granek, Rony

2008-11-01

The motion of small cargo particles on microtubules by means of motor proteins in disordered microtubule networks is investigated theoretically using both analytical tools and computer simulations. Different network topologies in two and three dimensions are considered, one of which has been recently studied experimentally by Salman [Biophys. J. 89, 2134 (2005)]. A generalization of the random velocity model is used to derive the mean-square displacement of the cargo particle. We find that all cases belong to the class of anomalous superdiffusion, which is sensitive mainly to the dimensionality of the network and only marginally to its topology. Yet in three dimensions the motion is very close to simple diffusion, with sublogarithmic corrections that depend on the network topology. When details of the thermal diffusion in the bulk solution are included, no significant change to the asymptotic time behavior is found. However, a small asymmetry in the mean microtubule polarity affects the corresponding long-time behavior. We also study a three-dimensional model of the microtubule network in living animal cells. Three first-passage-time problems of intracellular transport are simulated and analyzed for different motor processivities: (i) cargo that originates near the nucleus and has to reach the membrane, (ii) cargo that originates from the membrane and has to reach the nucleus, and (iii) cargo that leaves the nucleus and has to reach a specific target in the cytoplasm. We conclude that while a higher motor processivity increases the transport efficiency in cases (i) and (ii), in case (iii) it has the opposite effect. We conjecture that the balance between the different network tasks, as manifested in cases (i) and (ii) versus case (iii), may be the reason for the evolutionary choice of a finite motor processivity.

Active transport on disordered microtubule networks: The generalized random velocity model

NASA Astrophysics Data System (ADS)

Kahana, Aviv; Kenan, Gilad; Feingold, Mario; Elbaum, Michael; Granek, Rony

2008-11-01

The motion of small cargo particles on microtubules by means of motor proteins in disordered microtubule networks is investigated theoretically using both analytical tools and computer simulations. Different network topologies in two and three dimensions are considered, one of which has been recently studied experimentally by Salman [Biophys. J. 89, 2134 (2005)]. A generalization of the random velocity model is used to derive the mean-square displacement of the cargo particle. We find that all cases belong to the class of anomalous superdiffusion, which is sensitive mainly to the dimensionality of the network and only marginally to its topology. Yet in three dimensions the motion is very close to simple diffusion, with sublogarithmic corrections that depend on the network topology. When details of the thermal diffusion in the bulk solution are included, no significant change to the asymptotic time behavior is found. However, a small asymmetry in the mean microtubule polarity affects the corresponding long-time behavior. We also study a three-dimensional model of the microtubule network in living animal cells. Three first-passage-time problems of intracellular transport are simulated and analyzed for different motor processivities: (i) cargo that originates near the nucleus and has to reach the membrane, (ii) cargo that originates from the membrane and has to reach the nucleus, and (iii) cargo that leaves the nucleus and has to reach a specific target in the cytoplasm. We conclude that while a higher motor processivity increases the transport efficiency in cases (i) and (ii), in case (iii) it has the opposite effect. We conjecture that the balance between the different network tasks, as manifested in cases (i) and (ii) versus case (iii), may be the reason for the evolutionary choice of a finite motor processivity.

A Comparative Analysis of Kalman Filters Using a Hypervelocity Missile Simulation.

DTIC Science & Technology

1981-12-01

2-29 2.9 Summary ......... ...................... . 2-35 III. Kalman Filter Development ..... ............... ... 3-1 3.1 Introduction...3-2 3.1.4 Assumptions ................ 3-3 3.2 Development of Line-of-Sight Filters ......... ... 3-4 3.2.1 Introduction ....... .............. . 3-4... Development of Inertial Filters ... ......... ... 3-20 3.3.1 Introduction ...... ................ ... 3-20 3.3.2 Filter Model I.I

Uncertainties in energy reconstruction of cosmic rays for ANITA III caused by differences in models of radio emission in atmospheric showers

NASA Astrophysics Data System (ADS)

Bugaev, Viatcheslav; Rauch, Brian; Schoorlemmer, Harm; Lam, Joe; Urdaneta, David; Wissel, Stephanie; Belov, Konstantin; Romero-Wolf, Andrew; Anita Collaboration

2015-04-01

The third flight of the high-altitude balloon-borne Antarctic Impulsive Transient Antenna (ANITA III) was launched on a high-altitude balloon from McMurdo, Antarctica on December 17th, 2014 and flew for 22 days. It was optimized for the measurement of impulsive radio signals from the charged component of extensive air showers initiated by ultra-high energy cosmic rays in the frequency range ~ 180 - 1200 MHz. In addition it is designed to detect radio impulses initiated by high-energy neutrinos interacting in the Antarctic ice, which was the primary objective of the first two ANITA flights. Based on an extensive set of Monte Carlo simulations of radio emissions from cosmic rays (CR) with the ZHAireS and CoREAS simulation packages, we estimate uncertainties in the electric fields at the payload due to different models used in the two packages. The uncertainties in the emission are then propagated through an algorithm for energy reconstruction of individual CR showers to assess uncertainties in the energy reconstruction. We also discuss optimization of this algorithm. This research is supported by NASA under Grant # NNX11AC49G.

Assessing and mitigating uncertainties in the Noah-MP land-model simulations over the Tibet Plateau region

NASA Astrophysics Data System (ADS)

Zhang, G.; Chen, F.; Gan, Y.

2017-12-01

Assessing and mitigating uncertainties in the Noah-MP land-model simulations over the Tibet Plateau region Guo Zhang1, Fei Chen1,2, Yanjun Gan11State Key Laboratory of Severe Weather, Chinese Academy of Meteorological Sciences, Beijing, China 2National Center for Atmospheric Research, Boulder, Colorado, USA Uncertainties in the Noah with multiparameterization (Noah-MP) land surface model were assessed through physics ensemble simulations for four sparsely-vegetated sites located in the Tibetan Plateau region. Those simulations were evaluated using observations at the four sites during the third Tibetan Plateau Experiment (TIPEX III).The impacts of uncertainties in precipitation data used as forcing conditions, parameterizations of sub-processes such as soil organic matter and rhizosphere on physics-ensemble simulations are identified using two different methods: the natural selection and Tukey's test. This study attempts to answer the following questions: 1) what is the relative contribution of precipitation-forcing uncertainty to the overall uncertainty range of Noah-MP simulations at those sites as compared to that at a more moisture and densely vegetated site; 2) what are the most sensitive physical parameterization for those sites; 3) can we identify the parameterizations that need to be improved? The investigation was conducted by evaluating simulated seasonal evolution of soil temperature, soilmoisture, surface heat fluxes through a number of Noah-MP ensemble simulations.

Effects of microphysics parameterization on simulations of summer heavy precipitation in the Yangtze-Huaihe Region, China

NASA Astrophysics Data System (ADS)

Kan, Yu; Chen, Bo; Shen, Tao; Liu, Chaoshun; Qiao, Fengxue

2017-09-01

It has been a longstanding problem for current weather/climate models to accurately predict summer heavy precipitation over the Yangtze-Huaihe Region (YHR) which is the key flood-prone area in China with intensive population and developed economy. Large uncertainty has been identified with model deficiencies in representing precipitation processes such as microphysics and cumulus parameterizations. This study focuses on examining the effects of microphysics parameterization on the simulation of different type of heavy precipitation over the YHR taking into account two different cumulus schemes. All regional persistent heavy precipitation events over the YHR during 2008-2012 are classified into three types according to their weather patterns: the type I associated with stationary front, the type II directly associated with typhoon or with its spiral rain band, and the type III associated with strong convection along the edge of the Subtropical High. Sixteen groups of experiments are conducted for three selected cases with different types and a local short-time rainstorm in Shanghai, using the WRF model with eight microphysics and two cumulus schemes. Results show that microphysics parameterization has large but different impacts on the location and intensity of regional heavy precipitation centers. The Ferrier (microphysics) -BMJ (cumulus) scheme and Thompson (microphysics) - KF (cumulus) scheme most realistically simulates the rain-bands with the center location and intensity for type I and II respectively. For type III, the Lin microphysics scheme shows advantages in regional persistent cases over YHR, while the WSM5 microphysics scheme is better in local short-term case, both with the BMJ cumulus scheme.

Numerical simulation of fiber and wire array Z-pinches with Trac-II

NASA Astrophysics Data System (ADS)

Reisman, David Barton

Trac-II is a two dimensional axisymmetric resistive MHD code. It simulates all three spatial components (r, z, φ) of the magnetic field and fluid velocity vectors, and the plasma is treated as a single fluid with two temperatures (Te,Ti). In addition, it can optionally include a self-consistent external circuit. Recent modifications to the code include the addition of the 3-T radiation model, a 4-phase (solid- liquid-vapor-plasma) equation of state model (QEOS), a 4- phase electrical/thermal conductivity model, and an implicit solution of poloidal (Bz,Br) magnetic field diffusion. These changes permit a detailed study of fiber and wire array Z-pinches. Specifically, Trac-II is used to study the wire array Z-pinch at the PBFA-Z pulse power generator at Sandia National Laboratory. First, in 1-D we examine the behavior of a single wire in the Z-pinch. Then, using these results as initial radial conditions in 2-D, we investigate the dynamics of wire array configurations in the r-z and r-θ plane. In the r- z plane we examine the growth of the m = 0 or ``sausage'' instability in single wires within the array. In the r-θ plane we examine the merging behavior between neighboring wires. Special emphasis is placed on trying to explain how instability growth affects the performance of the Z-pinch. Lastly, we introduce Trac-III, a 3-D MHD code, and illustrate the m = 1 or ``kink'' instability. We also discuss how Trac-III can be modified to simulate the wire array Z-pinch.

Experimental and Theoretical Investigation of the Anti-Ferromagnetic Coupling of CrIII Ions through Diamagnetic -O-NbV-O- Bridges.

PubMed

Jurić, Marijana; Androš Dubraja, Lidija; Pajić, Damir; Torić, Filip; Zorko, Andrej; Ozarowski, Andrew; Despoja, Vito; Lafargue-Dit-Hauret, William; Rocquefelte, Xavier

2017-06-19

The synthesis and properties of a novel hetero-tetranuclear compound [Cr 2 (bpy) 4 (μ-O) 4 Nb 2 (C 2 O 4 ) 4 ]·3H 2 O (1; bpy = 2,2'-bipyridine), investigated by single-crystal X-ray diffraction, magnetization measurements, IR, UV/visible spectroscopy, electron paramagnetic resonance (EPR; X- and Q-bands and high-field), and density functional theory (DFT) calculations, are reported. Crystal structure of 1 (orthorhombic Pcab space group) consists of a square-shaped macrocyclic {Cr 2 (μ-O) 4 Nb 2 } core in which Cr III and Nb V ions are alternately bridged by oxo ions and three uncoordinated water molecules. The intramolecular Cr III ···Cr III distances through the -O-Nb V -O- bridges are 7.410(2) and 7.419(2) Å, while diagonal separation is 5.406(2) Å. The temperature dependence of magnetization M(T) evidences an anti-ferromagnetic ground state, which originates from a magnetic interaction between two Cr III ions of spin 3/2 through two triatomic -O-Nb V -O- diamagnetic bridges. A spin Hamiltonian appropriate for polynuclear isolated magnetic units was used. The best-fitting curve for this model is obtained with the parameters g Cr = 1.992(3), J = -12.77(5) cm -1 , and |D| = 0.17(4) cm -1 . The Cr III ···Cr III dimer model is confirmed by EPR spectra, which exhibit a pronounced change of their shape around the temperature corresponding to the intradimer coupling J. The EPR spectra simulations and DFT calculations reveal the presence of a single-ion anisotropy that is close to being uniaxial, D = -0.31 cm -1 and E = 0.024 cm -1 .

SmartSIM - a virtual reality simulator for laparoscopy training using a generic physics engine.

PubMed

Khan, Zohaib Amjad; Kamal, Nabeel; Hameed, Asad; Mahmood, Amama; Zainab, Rida; Sadia, Bushra; Mansoor, Shamyl Bin; Hasan, Osman

2017-09-01

Virtual reality (VR) training simulators have started playing a vital role in enhancing surgical skills, such as hand-eye coordination in laparoscopy, and practicing surgical scenarios that cannot be easily created using physical models. We describe a new VR simulator for basic training in laparoscopy, i.e. SmartSIM, which has been developed using a generic open-source physics engine called the simulation open framework architecture (SOFA). This paper describes the systems perspective of SmartSIM including design details of both hardware and software components, while highlighting the critical design decisions. Some of the distinguishing features of SmartSIM include: (i) an easy-to-fabricate custom-built hardware interface; (ii) use of a generic physics engine to facilitate wider accessibility of our work and flexibility in terms of using various graphical modelling algorithms and their implementations; and (iii) an intelligent and smart evaluation mechanism that facilitates unsupervised and independent learning. Copyright © 2016 John Wiley & Sons, Ltd.

High-Fidelity Modeling of Computer Network Worms

DTIC Science & Technology

2004-06-22

plots the propagation of the TCP-based worm. This execution is among the largest TCP worm models simulated to date at packet-level. TCP vs . UDP Worm...the mapping of the virtual IP addresses to honeyd’s MAC address in the proxy’s ARP table. The proxy server listens for packets from both sides of...experimental setup, we used two ntium-4 ThinkPad , and an IBM Pentium-III ThinkPad ), running the proxy server and honeyd respectively. The Code Red II worm

Suited and Unsuited Hybrid III Impact Testing and Finite Element Model Characterization

NASA Technical Reports Server (NTRS)

Lawrence, C.; Somers, J. T.; Baldwin, M. A.; Wells, J. A.; Newby, N.; Currie, N. J.

2016-01-01

NASA spacecraft design requirements for occupant protection are a combination of the Brinkley Dynamic Response Criteria and injury assessment reference values (IARV) extracted from anthropomorphic test devices (ATD). For the ATD IARVs, the requirements specify the use of the 5th percentile female Hybrid III and the 95th percentile male Hybrid III. Each of these ATDs is required to be fitted with an articulating pelvis (also known as the aerospace pelvis) and a straight spine. The articulating pelvis is necessary for the ATD to fit into spacecraft seats, while the straight spine is required as injury metrics for vertical accelerations are better defined for this configuration. Sled testing of the Hybrid III 5th Percentile Female Anthropomorphic Test Device (ATD) was performed at Wright-Patterson Air Force Base (WAPFB). Two 5th Percentile ATDs were tested, the Air Force Research Lab (AFRL) and NASA owned Hybrid III ATDs with aerospace pelvises. Testing was also conducted with a NASA-owned 95th Percentile Male Hybrid III with aerospace pelvis at WPAFB. Testing was performed using an Orion seat prototype provided by Johnson Space Center (JSC). A 5-point harness comprised of 2 inch webbing was also provided by JSC. For suited runs, a small and extra-large Advanced Crew Escape System (ACES) suit and helmet were also provided by JSC. Impact vectors were combined frontal/spinal and rear/lateral. Some pure spinal and rear axis testing was also performed for model validation. Peak accelerations ranged between 15 and 20-g. This range was targeted because the ATD responses fell close to the IARV defined in the Human-Systems Integration Requirements (HSIR) document. Rise times varied between 70 and 110 ms to assess differences in ATD responses and model correlation for different impact energies. The purpose of the test series was to evaluate the Hybrid III ATD models in Orion-specific landing orientations both with and without a spacesuit. The results of these tests were used by the NASA Engineering and Safety Center (NESC) to validate the finite element model (FEM) of the Hybrid III 5th Percentile Female ATD. Physical test data was compared to analytical predictions from simulations, and modelling uncertainty factors have been determined for each injury metric. Additionally, the test data has been used to further improve the FEM, particularly in the areas of the ATD preload, harness, and suit and helmet effects.

Computing the Absorption and Emission Spectra of 5-Methylcytidine in Different Solvents: A Test-Case for Different Solvation Models.

PubMed

Martínez-Fernández, L; Pepino, A J; Segarra-Martí, J; Banyasz, A; Garavelli, M; Improta, R

2016-09-13

The optical spectra of 5-methylcytidine in three different solvents (tetrahydrofuran, acetonitrile, and water) is measured, showing that both the absorption and the emission maximum in water are significantly blue-shifted (0.08 eV). The absorption spectra are simulated based on CAM-B3LYP/TD-DFT calculations but including solvent effects with three different approaches: (i) a hybrid implicit/explicit full quantum mechanical approach, (ii) a mixed QM/MM static approach, and (iii) a QM/MM method exploiting the structures issuing from molecular dynamics classical simulations. Ab-initio Molecular dynamics simulations based on CAM-B3LYP functionals have also been performed. The adopted approaches all reproduce the main features of the experimental spectra, giving insights on the chemical-physical effects responsible for the solvent shifts in the spectra of 5-methylcytidine and providing the basis for discussing advantages and limitations of the adopted solvation models.

Pair potentials for warm dense matter and their application to x-ray Thomson scattering in aluminum and beryllium.

PubMed

Harbour, L; Dharma-Wardana, M W C; Klug, D D; Lewis, L J

2016-11-01

Ultrafast laser experiments yield increasingly reliable data on warm dense matter, but their interpretation requires theoretical models. We employ an efficient density functional neutral-pseudoatom hypernetted-chain (NPA-HNC) model with accuracy comparable to ab initio simulations and which provides first-principles pseudopotentials and pair potentials for warm-dense matter. It avoids the use of (i) ad hoc core-repulsion models and (ii) "Yukawa screening" and (iii) need not assume ion-electron thermal equilibrium. Computations of the x-ray Thomson scattering (XRTS) spectra of aluminum and beryllium are compared with recent experiments and with density-functional-theory molecular-dynamics (DFT-MD) simulations. The NPA-HNC structure factors, compressibilities, phonons, and conductivities agree closely with DFT-MD results, while Yukawa screening gives misleading results. The analysis of the XRTS data for two of the experiments, using two-temperature quasi-equilibrium models, is supported by calculations of their temperature relaxation times.

Theoretical and experimental examination of SFG polarization analysis at acetonitrile-water solution surfaces.

PubMed

Saito, Kengo; Peng, Qiling; Qiao, Lin; Wang, Lin; Joutsuka, Tatsuya; Ishiyama, Tatsuya; Ye, Shen; Morita, Akihiro

2017-03-29

Sum frequency generation (SFG) spectroscopy is widely used to observe molecular orientation at interfaces through a combination of various types of polarization. The present work thoroughly examines the relation between the polarization dependence of SFG signals and the molecular orientation, by comparing SFG measurements and molecular dynamics (MD) simulations of acetonitrile/water solutions. The present SFG experiment and MD simulations yield quite consistent results on the ratios of χ (2) elements, supporting the reliability of both means. However, the subsequent polarization analysis tends to derive more upright tilt angles of acetonitrile than the direct MD calculations. The reasons for discrepancy are examined in terms of three issues; (i) anisotropy of the Raman tensor, (ii) cross-correlation, and (iii) orientational distribution. The analysis revealed that the issues (i) and (iii) are the main causes of errors in the conventional polarization analysis of SFG spectra. In methyl CH stretching, the anisotropy of Raman tensor cannot be estimated from the simple bond polarizability model. The neglect of the orientational distribution is shown to systematically underestimate the tilt angle of acetonitrile. Further refined use of polarization analysis in collaboration with MD simulations should be proposed.

Simulation of the mobility of metal - EDTA complexes in groundwater: The influence of contaminant metals

USGS Publications Warehouse

Friedly, J.C.; Kent, D.B.; Davis, J.A.

2002-01-01

Reactive transport simulations were conducted to model chemical reactions between metal - EDTA (ethylenediaminetetraacetic acid) complexes during transport in a mildly acidic quartz - sand aquifer. Simulations were compared with the results of small-scale tracer tests wherein nickel-, zinc-, and calcium - EDTA complexes and free EDTA were injected into three distinct chemical zones of a plume of sewage-contaminated groundwater. One zone had a large mass of adsorbed, sewage-derived zinc; one zone had a large mass of adsorbed manganese resulting from mildly reducing conditions created bythe sewage plume; and one zone had significantly less adsorbed manganese and negligible zinc background. The chemical model assumed that the dissolution of iron(III) from metal - hydroxypolymer coatings on the aquifer sediments by the metal - EDTA complexes was kinetically restricted. All other reactions, including metal - EDTA complexation, zinc and manganese adsorption, and aluminum hydroxide dissolution were assumed to reach equilibrium on the time scale of transport; equilibrium constants were either taken from the literature or determined independently in the laboratory. A single iron(III) dissolution rate constant was used to fit the breakthrough curves observed in the zone with negligible zinc background. Simulation results agreed well with the experimental data in all three zones, which included temporal moments derived from breakthrough curves at different distances downgradient from the injections and spatial moments calculated from synoptic samplings conducted at different times. Results show that the tracer cloud was near equilibrium with respect to Fe in the sediment after 11 m of transport in the Zn-contaminated region but remained far from equilibrium in the other two zones. Sensitivity studies showed that the relative rate of iron(III) dissolution by the different metal - EDTA complexes was less important than the fact that these reactions are rate controlled. Results suggest that the published solubility for ferrihydrite reasonably approximates the Fe solubility of the hydroxypolymer coatings on the sediments. Aluminum may be somewhat more soluble than represented by the equilibrium constant for gibbsite, and its dissolution may be rate controlled when reacting with Ca - EDTA complexes.

Pore-Scale Characterization of Biogeochemical Controls on Iron and Uranium Speciation under Flow Conditions

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

Pearce, Carolyn I.; Wilkins, Michael J.; Zhang, Changyong

2012-09-17

Etched silicon microfluidic pore network models (micromodels) with controlled chemical and redox gradients, mineralogy, and microbiology under continuous flow conditions are used for the incremental development of complex microenvironments that simulate subsurface conditions. We demonstrate the colonization of micromodel pore spaces by an anaerobic Fe(III)-reducing bacterial species (Geobacter sulfurreducens) and the enzymatic reduction of a bioavailable Fe(III) phase within this environment. Using both X-ray Microprobe and X-ray Absorption Spectroscopy, we investigate the combined effects of the precipitated Fe(III) phases and the microbial population on uranium biogeochemistry under flow conditions. Precipitated Fe(III) phases within the micromodel were most effectively reduced inmore » the presence of an electron shuttle (AQDS), and Fe(II) ions adsorbed onto the precipitated mineral surface without inducing any structural change. In the absence of Fe(III), U(VI) was effectively reduced by the microbial population to insoluble U(IV), which was precipitated in discrete regions associated with biomass. In the presence of Fe(III) phases, however, both U(IV) and U(VI) could be detected associated with biomass, suggesting re-oxidation of U(IV) by localized Fe(III) phases. These results demonstrate the importance of the spatial localization of biomass and redox active metals, and illustrate the key effects of pore-scale processes on contaminant fate and reactive transport.« less

Modeling RF-induced Plasma-Surface Interactions with VSim

NASA Astrophysics Data System (ADS)

Jenkins, Thomas G.; Smithe, David N.; Pankin, Alexei Y.; Roark, Christine M.; Stoltz, Peter H.; Zhou, Sean C.-D.; Kruger, Scott E.

2014-10-01

An overview of ongoing enhancements to the Plasma Discharge (PD) module of Tech-X's VSim software tool is presented. A sub-grid kinetic sheath model, developed for the accurate computation of sheath potentials near metal and dielectric-coated walls, enables the physical effects of DC and RF sheath dynamics to be included in macroscopic-scale plasma simulations that need not explicitly resolve sheath scale lengths. Sheath potential evolution, together with particle behavior near the sheath (e.g. sputtering), can thus be simulated in complex, experimentally relevant geometries. Simulations of RF sheath-enhanced impurity production near surfaces of the C-Mod field-aligned ICRF antenna are presented to illustrate the model; impurity mitigation techniques are also explored. Model extensions to capture the physics of secondary electron emission and of multispecies plasmas are summarized, together with a discussion of improved tools for plasma chemistry and IEDF/EEDF visualization and modeling. The latter tools are also highly relevant for commercial plasma processing applications. Ultimately, we aim to establish VSimPD as a robust, efficient computational tool for modeling fusion and industrial plasma processes. Supported by U.S. DoE SBIR Phase I/II Award DE-SC0009501.

Applications of Displacement Transfer Functions to Deformed Shape Predictions of the G-III Swept-Wing Structure

NASA Technical Reports Server (NTRS)

Lung, Shun-Fat; Ko, William L.

2016-01-01

In support of the Adaptive Compliant Trailing Edge [ACTE] project at the NASA Armstrong Flight Research Center, displacement transfer functions were applied to the swept wing of a Gulfstream G-III airplane (Gulfstream Aerospace Corporation, Savannah, Georgia) to obtain deformed shape predictions. Four strainsensing lines (two on the lower surface, two on the upper surface) were used to calculate the deformed shape of the G III wing under bending and torsion. There being an insufficient number of surface strain sensors, the existing G III wing box finite element model was used to generate simulated surface strains for input to the displacement transfer functions. The resulting predicted deflections have good correlation with the finite-element generated deflections as well as the measured deflections from the ground load calibration test. The convergence study showed that the displacement prediction error at the G III wing tip can be reduced by increasing the number of strain stations (for each strain-sensing line) down to a minimum error of l.6 percent at 17 strain stations; using more than 17 strain stations yielded no benefit because the error slightly increased to 1.9% when 32 strain stations were used.

Modeling of sheet metal fracture via cohesive zone model and application to spot welds

NASA Astrophysics Data System (ADS)

Wu, Joseph Z.

Even though the cohesive zone model (CZM) has been widely used to analyze ductile fracture, it is not yet clearly understood how to calibrate the cohesive parameters including the specific work of separation (the work of separation per unit crack area) and the peak stress. A systematic approach is presented to first determine the cohesive values for sheet metal and then apply the calibrated model to various structure problems including the failure of spot welds. Al5754-0 was chosen for this study since it is not sensitive to heat treatment so the effect of heat-affected-zone (HAZ) can be ignored. The CZM has been applied to successfully model both mode-I and mode-III fracture for various geometries including Kahn specimens, single-notch specimens, and deep double-notch specimens for mode-I and trouser specimens for mode-III. The mode-I fracture of coach-peel spot-weld nugget and the mixed-mode fracture of nugget pull-out have also been well simulated by the CZM. Using the mode-I average specific work of separation of 13 kJ/m2 identified in a previous work and the mode-III specific work of separation of 38 kJ/m 2 found in this thesis, the cohesive peak stress has been determined to range from 285 MPa to 600 MPa for mode-I and from 165 MPa to 280 MPa for mode-III, depending on the degree of plastic deformation. The uncertainty of these cohesive values has also been examined. It is concluded that, if the specific work of separation is a material constant, the peak stress changes with the degree of plastic deformation and is therefore geometry-dependent.

Subsurface Uranium Fate and Transport: Integrated Experiments and Modeling of Coupled Biogeochemical Mechanisms of Nanocrystalline Uraninite Oxidation by Fe(III)-(hydr)oxides - Project Final Report

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

Peyton, Brent M.; Timothy, Ginn R.; Sani, Rajesh K.

2013-08-14

Subsurface bacteria including sulfate reducing bacteria (SRB) reduce soluble U(VI) to insoluble U(IV) with subsequent precipitation of UO 2. We have shown that SRB reduce U(VI) to nanometer-sized UO 2 particles (1-5 nm) which are both intra- and extracellular, with UO 2 inside the cell likely physically shielded from subsequent oxidation processes. We evaluated the UO 2 nanoparticles produced by Desulfovibrio desulfuricans G20 under growth and non-growth conditions in the presence of lactate or pyruvate and sulfate, thiosulfate, or fumarate, using ultrafiltration and HR-TEM. Results showed that a significant mass fraction of bioreduced U (35-60%) existed as a mobile phasemore » when the initial concentration of U(VI) was 160 µM. Further experiments with different initial U(VI) concentrations (25 - 900 M) in MTM with PIPES or bicarbonate buffers indicated that aggregation of uraninite depended on the initial concentrations of U(VI) and type of buffer. It is known that under some conditions SRB-mediated UO 2 nanocrystals can be reoxidized (and thus remobilized) by Fe(III)-(hydr)oxides, common constituents of soils and sediments. To elucidate the mechanism of UO 2 reoxidation by Fe(III) (hydr)oxides, we studied the impact of Fe and U chelating compounds (citrate, NTA, and EDTA) on reoxidation rates. Experiments were conducted in anaerobic batch systems in PIPES buffer. Results showed EDTA significantly accelerated UO 2 reoxidation with an initial rate of 9.5 M day-1 for ferrihydrite. In all cases, bicarbonate increased the rate and extent of UO 2 reoxidation with ferrihydrite. The highest rate of UO 2 reoxidation occurred when the chelator promoted UO 2 and Fe(III) (hydr)oxide dissolution as demonstrated with EDTA. When UO 2 dissolution did not occur, UO 2 reoxidation likely proceeded through an aqueous Fe(III) intermediate as observed for both NTA and citrate. To complement to these laboratory studies, we collected U-bearing samples from a surface seep at the Rifle field site and have measured elevated U concentrations in oxic iron-rich sediments. To translate experimental results into numerical analysis of U fate and transport, a reaction network was developed based on Sani et al. (2004) to simulate U(VI) bioreduction with concomitant UO 2 reoxidation in the presence of hematite or ferrihydrite. The reduction phase considers SRB reduction (using lactate) with the reductive dissolution of Fe(III) solids, which is set to be microbially mediated as well as abiotically driven by sulfide. Model results show the oxidation of HS– by Fe(III) directly competes with UO 2 reoxidation as Fe(III) oxidizes HS– preferentially over UO 2. The majority of Fe reduction is predicted to be abiotic, with ferrihydrite becoming fully consumed by reaction with sulfide. Predicted total dissolved carbonate concentrations from the degradation of lactate are elevated (log(pCO 2) ~ –1) and, in the hematite system, yield close to two orders-of-magnitude higher U(VI) concentrations than under initial carbonate concentrations of 3 mM. Modeling of U(VI) bioreduction with concomitant reoxidation of UO 2 in the presence of ferrihydrite was also extended to a two-dimensional field-scale groundwater flow and biogeochemically reactive transport model for the South Oyster site in eastern Virginia. This model was developed to simulate the field-scale immobilization and subsequent reoxidation of U by a biologically mediated reaction network.« less

Progress in and prospects for fluvial flood modelling.

PubMed

Wheater, H S

2002-07-15

Recent floods in the UK have raised public and political awareness of flood risk. There is an increasing recognition that flood management and land-use planning are linked, and that decision-support modelling tools are required to address issues of climate and land-use change for integrated catchment management. In this paper, the scientific context for fluvial flood modelling is discussed, current modelling capability is considered and research challenges are identified. Priorities include (i) appropriate representation of spatial precipitation, including scenarios of climate change; (ii) development of a national capability for continuous hydrological simulation of ungauged catchments; (iii) improved scientific understanding of impacts of agricultural land-use and land-management change, and the development of new modelling approaches to represent those impacts; (iv) improved representation of urban flooding, at both local and catchment scale; (v) appropriate parametrizations for hydraulic simulation of in-channel and flood-plain flows, assimilating available ground observations and remotely sensed data; and (vi) a flexible decision-support modelling framework, incorporating developments in computing, data availability, data assimilation and uncertainty analysis.

A robust two-stage design identifying the optimal biological dose for phase I/II clinical trials.

PubMed

Zang, Yong; Lee, J Jack

2017-01-15

We propose a robust two-stage design to identify the optimal biological dose for phase I/II clinical trials evaluating both toxicity and efficacy outcomes. In the first stage of dose finding, we use the Bayesian model averaging continual reassessment method to monitor the toxicity outcomes and adopt an isotonic regression method based on the efficacy outcomes to guide dose escalation. When the first stage ends, we use the Dirichlet-multinomial distribution to jointly model the toxicity and efficacy outcomes and pick the candidate doses based on a three-dimensional volume ratio. The selected candidate doses are then seamlessly advanced to the second stage for dose validation. Both toxicity and efficacy outcomes are continuously monitored so that any overly toxic and/or less efficacious dose can be dropped from the study as the trial continues. When the phase I/II trial ends, we select the optimal biological dose as the dose obtaining the minimal value of the volume ratio within the candidate set. An advantage of the proposed design is that it does not impose a monotonically increasing assumption on the shape of the dose-efficacy curve. We conduct extensive simulation studies to examine the operating characteristics of the proposed design. The simulation results show that the proposed design has desirable operating characteristics across different shapes of the underlying true dose-toxicity and dose-efficacy curves. The software to implement the proposed design is available upon request. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Mössbauer, EPR, and Modeling Study of Iron Trafficking and Regulation in Δccc1 and CCC1-up Saccharomyces cerevisiae

PubMed Central

2015-01-01

Strains lacking and overexpressing the vacuolar iron (Fe) importer CCC1 were characterized using Mössbauer and EPR spectroscopies. Vacuolar Fe import is impeded in Δccc1 cells and enhanced in CCC1-up cells, causing vacuolar Fe in these strains to decline and accumulate, respectively, relative to WT cells. Cytosolic Fe levels should behave oppositely. The Fe content of Δccc1 cells grown under low-Fe conditions was similar to that in WT cells. Most Fe was mitochondrial with some nonheme high spin (NHHS) FeII present. Δccc1 cells grown with increasing Fe concentration in the medium contained less total Fe, less vacuolar HS FeIII, and more NHHS FeII than in comparable WT cells. As the Fe concentration in the growth medium increased, the concentration of HS FeIII in Δccc1 cells increased to just 60% of WT levels, while NHHS FeII increased to twice WT levels, suggesting that the NHHS FeII was cytosolic. Δccc1 cells suffered more oxidative damage than WT cells, suggesting that the accumulated NHHS FeII promoted Fenton chemistry. The Fe concentration in CCC1-up cells was higher than in WT cells; the extra Fe was present as NHHS FeII and FeIII and as FeIII oxyhydroxide nanoparticles. These cells contained less mitochondrial Fe and exhibited less ROS damage than Δccc1 cells. CCC1-up cells were adenine-deficient on minimal medium; supplementing with adenine caused a decline of NHHS FeII suggesting that some of the NHHS FeII that accumulated in these cells was associated with adenine deficiency rather than the overexpression of CCC1. A mathematical model was developed that simulated changes in Fe distributions. Simulations suggested that only a modest proportion of the observed NHHS FeII in both strains was the cytosolic form of Fe that is sensed by the Fe import regulatory system. The remainder is probably generated by the reduction of the vacuolar NHHS FeIII species. PMID:24785783

Mössbauer, EPR, and modeling study of iron trafficking and regulation in Δccc1 and CCC1-up Saccharomyces cerevisiae.

PubMed

Cockrell, Allison; McCormick, Sean P; Moore, Michael J; Chakrabarti, Mrinmoy; Lindahl, Paul A

2014-05-13

Strains lacking and overexpressing the vacuolar iron (Fe) importer CCC1 were characterized using Mössbauer and EPR spectroscopies. Vacuolar Fe import is impeded in Δccc1 cells and enhanced in CCC1-up cells, causing vacuolar Fe in these strains to decline and accumulate, respectively, relative to WT cells. Cytosolic Fe levels should behave oppositely. The Fe content of Δccc1 cells grown under low-Fe conditions was similar to that in WT cells. Most Fe was mitochondrial with some nonheme high spin (NHHS) Fe(II) present. Δccc1 cells grown with increasing Fe concentration in the medium contained less total Fe, less vacuolar HS Fe(III), and more NHHS Fe(II) than in comparable WT cells. As the Fe concentration in the growth medium increased, the concentration of HS Fe(III) in Δccc1 cells increased to just 60% of WT levels, while NHHS Fe(II) increased to twice WT levels, suggesting that the NHHS Fe(II) was cytosolic. Δccc1 cells suffered more oxidative damage than WT cells, suggesting that the accumulated NHHS Fe(II) promoted Fenton chemistry. The Fe concentration in CCC1-up cells was higher than in WT cells; the extra Fe was present as NHHS Fe(II) and Fe(III) and as Fe(III) oxyhydroxide nanoparticles. These cells contained less mitochondrial Fe and exhibited less ROS damage than Δccc1 cells. CCC1-up cells were adenine-deficient on minimal medium; supplementing with adenine caused a decline of NHHS Fe(II) suggesting that some of the NHHS Fe(II) that accumulated in these cells was associated with adenine deficiency rather than the overexpression of CCC1. A mathematical model was developed that simulated changes in Fe distributions. Simulations suggested that only a modest proportion of the observed NHHS Fe(II) in both strains was the cytosolic form of Fe that is sensed by the Fe import regulatory system. The remainder is probably generated by the reduction of the vacuolar NHHS Fe(III) species.

Real-time simulation of contact and cutting of heterogeneous soft-tissues.

PubMed

Courtecuisse, Hadrien; Allard, Jérémie; Kerfriden, Pierre; Bordas, Stéphane P A; Cotin, Stéphane; Duriez, Christian

2014-02-01

This paper presents a numerical method for interactive (real-time) simulations, which considerably improves the accuracy of the response of heterogeneous soft-tissue models undergoing contact, cutting and other topological changes. We provide an integrated methodology able to deal both with the ill-conditioning issues associated with material heterogeneities, contact boundary conditions which are one of the main sources of inaccuracies, and cutting which is one of the most challenging issues in interactive simulations. Our approach is based on an implicit time integration of a non-linear finite element model. To enable real-time computations, we propose a new preconditioning technique, based on an asynchronous update at low frequency. The preconditioner is not only used to improve the computation of the deformation of the tissues, but also to simulate the contact response of homogeneous and heterogeneous bodies with the same accuracy. We also address the problem of cutting the heterogeneous structures and propose a method to update the preconditioner according to the topological modifications. Finally, we apply our approach to three challenging demonstrators: (i) a simulation of cataract surgery (ii) a simulation of laparoscopic hepatectomy (iii) a brain tumor surgery. Copyright © 2013 Elsevier B.V. All rights reserved.

Aircraft evacuations through type-III exits II : effects of individual subject differences.

DOT National Transportation Integrated Search

1995-08-01

Simulated emergency egress from Type III over-wing exits was studied to support regulatory action by the FAA. Passageway width from the aircraft center aisle to the Type-III exit was the major variable of interest; effects of individual subject attri...

Effects of experimental protocol on global vegetation model accuracy: a comparison of simulated and observed vegetation patterns for Asia

USGS Publications Warehouse

Tang, Guoping; Shafer, Sarah L.; Barlein, Patrick J.; Holman, Justin O.

2009-01-01

Prognostic vegetation models have been widely used to study the interactions between environmental change and biological systems. This study examines the sensitivity of vegetation model simulations to: (i) the selection of input climatologies representing different time periods and their associated atmospheric CO2 concentrations, (ii) the choice of observed vegetation data for evaluating the model results, and (iii) the methods used to compare simulated and observed vegetation. We use vegetation simulated for Asia by the equilibrium vegetation model BIOME4 as a typical example of vegetation model output. BIOME4 was run using 19 different climatologies and their associated atmospheric CO2 concentrations. The Kappa statistic, Fuzzy Kappa statistic and a newly developed map-comparison method, the Nomad index, were used to quantify the agreement between the biomes simulated under each scenario and the observed vegetation from three different global land- and tree-cover data sets: the global Potential Natural Vegetation data set (PNV), the Global Land Cover Characteristics data set (GLCC), and the Global Land Cover Facility data set (GLCF). The results indicate that the 30-year mean climatology (and its associated atmospheric CO2 concentration) for the time period immediately preceding the collection date of the observed vegetation data produce the most accurate vegetation simulations when compared with all three observed vegetation data sets. The study also indicates that the BIOME4-simulated vegetation for Asia more closely matches the PNV data than the other two observed vegetation data sets. Given the same observed data, the accuracy assessments of the BIOME4 simulations made using the Kappa, Fuzzy Kappa and Nomad index map-comparison methods agree well when the compared vegetation types consist of a large number of spatially continuous grid cells. The results of this analysis can assist model users in designing experimental protocols for simulating vegetation.

Modelling studies in aqueous solution of lanthanide (III) chelates designed for nuclear magnetic resonance biomedical applications

NASA Astrophysics Data System (ADS)

Henriques, E. S.; Geraldes, C. F. G. C.; Ramos, M. J.

Molecular dynamics simulations and complementary modelling studies have been carried out for the [Gd(DOTA)·(H2O)]- and [Tm(DOTP)]5- chelates in aqueous media, to provide a better understanding of several structural and dynamical properties of these versatile nuclear magnetic resonance (NMR) probes, including coordination shells and corresponding water exchange mechanisms, and interactions of these complexes with alkali metal ions. This knowledge is of key importance in the areas of 1H relaxation and shift reagents for NMR applications in medical diagnosis. A new refinement of our own previously developed set of parameters for these Ln(III) chelates has been used, and is reported here. Calculations of water mean residence times suggest a reassessment of the characterization of the chelates' second coordination shell, one where the simple spherical distribution model is discarded in favour of a more detailed approach. Na+ probe interaction maps are in good agreement with the available site location predictions derived from 23Na NMR shifts.

Los Angeles International Airport Runway Incursion Studies: Phase III--Center-Taxiway Simulation

NASA Technical Reports Server (NTRS)

Madson, Michael D.

2004-01-01

Phase III of the Los Angeles International Airport Runway Incursion Studies was conducted, under an agreement with HNTB Corporation, at the NASA Ames FutureFlight Central (FFC) facility in June 2003. The objective of the study was the evaluation of a new center-taxiway concept at LAX. This study is an extension of the Phase I and Phase II studies previously conducted at FFC. This report presents results from Phase III of the study, in which a center-taxiway concept between runways 25L and 25R was simulated and evaluated. Phase III data were compared objectively against the Baseline data. Subjective evaluations by participating LAX controllers were obtained with regard to workload, efficiency, and safety criteria. To facilitate a valid comparison between Baseline and Phase III data, the same scenarios were used for Phase III that were tested during Phases I and II. This required briefing participating controllers on differences in airport and airline operations between 2001 and today.

High resolution dynamical downscaling of air temperature and relative humidity: performance assessment of WRF for Portugal

NASA Astrophysics Data System (ADS)

Menezes, Isilda; Pereira, Mário; Moreira, Demerval; Carvalheiro, Luís; Bugalho, Lourdes; Corte-Real, João

2017-04-01

Air temperature and relative humidity are two of the atmospheric variables with higher impact on human and natural systems, contributing to define the stress/comfortable conditions, affecting the productivity and health of the individuals as well as diminishing the resilience to other environmental hazards. Atmospheric regional models, driven by large scale forecasts from global circulation models, are the best way to reproduce such environmental conditions in high space-time resolution. This study is focused on the performance assessment of the WRF mesoscale model to perform high resolution dynamical downscaling for Portugal with three two-way nested grids, at 60 km, 20 km and 5 km horizontal resolution. The simulations of WRF models were produced with different initial and boundary forcing conditions. The NCEP-FNL Operational Global Analysis data available on 1-degree by 1-degree grid every six hours and ERA-Interim reanalyses dataset were used to drive the models. Two alternative configurations of the WRF model, including planetary boundary, layer schemes, microphysics, land-surface models, radiation schemes, were used and tested within the 5 km spatial resolution domain. Simulations of air temperature and relative humidity were produced for January and July of 2016 and compared with the observed datasets provided by the Instituto Português do Mar e da Atmosfera (IPMA) for 83 weather stations. Different performance measures of bias, precision, and accuracy were used, namely normalized bias, standard deviation, mean absolute error, root mean square error, bias of root mean square error as well as correlation based measures (e.g., coefficient of determination) and goodness of fit measures (index of agreement). Main conclusions from the obtained results reveal: (i) great similarity between the spatial patterns of the simulated and observed fields; (ii) only small differences between simulations produced with ERA-Interim and NCEP-FNL, in spite of some differences between the input variables; (iii) the tested parametrizations do not force significantly different simulation patterns; (iv) observed and simulated hourly air temperature are very well correlated (91%), presenting similar variance and a low bias over the country. Obtained results are also in good agreement with other dynamical downscaling studies for Portugal supporting the use of WRF as a regional forecast model. Acknowledgements: This work was supported by: (i) the project Interact - Integrative Research in Environment,Agro-Chain and Technology, NORTE-01-0145-FEDER-000017, research line BEST, cofinanced by FEDER/NORTE 2020; (ii) the FIREXTR project, PTDC/ATP¬GEO/0462/2014; and, (iii) European Investment Funds by FEDER/COMPETE/POCI-Operacional Competitiveness and Internacionalization Programme, under Project POCI-01-0145-FEDER-006958 and National Funds by FCT - Portuguese Foundation for Science and Technology, under the project UID/AGR/04033.

Effect of Population III Multiplicity on Dark Star Formation

NASA Technical Reports Server (NTRS)

Stacy, Athena; Pawlik, Andreas H.; Bromm, Volker; Loeb, Abraham

2012-01-01

We numerically study the mutual interaction between dark matter (DM) and Population III (Pop III) stellar systems in order to explore the possibility of Pop III dark stars within this physical scenario. We perform a cosmological simulation, initialized at z approx. 100, which follows the evolution of gas and DM. We analyze the formation of the first mini halo at z approx. 20 and the subsequent collapse of the gas to densities of 10(exp 12)/cu cm. We then use this simulation to initialize a set of smaller-scale 'cut-out' simulations in which we further refine the DM to have spatial resolution similar to that of the gas. We test multiple DM density profiles, and we employ the sink particle method to represent the accreting star-forming region. We find that, for a range of DM configurations, the motion of the Pop III star-disk system serves to separate the positions of the protostars with respect to the DM density peak, such that there is insufficient DM to influence the formation and evolution of the protostars for more than approx. 5000 years. In addition, the star-disk system causes gravitational scattering of the central DM to lower densities, further decreasing the influence of DM over time. Any DM-powered phase of Pop III stars will thus be very short-lived for the typical multiple system, and DM will not serve to significantly prolong the life of Pop III stars.

Definition and sensitivity of the conceptual MORDOR rainfall-runoff model parameters using different multi-criteria calibration strategies

NASA Astrophysics Data System (ADS)

Garavaglia, F.; Seyve, E.; Gottardi, F.; Le Lay, M.; Gailhard, J.; Garçon, R.

2014-12-01

MORDOR is a conceptual hydrological model extensively used in Électricité de France (EDF, French electric utility company) operational applications: (i) hydrological forecasting, (ii) flood risk assessment, (iii) water balance and (iv) climate change studies. MORDOR is a lumped, reservoir, elevation based model with hourly or daily areal rainfall and air temperature as the driving input data. The principal hydrological processes represented are evapotranspiration, direct and indirect runoff, ground water, snow accumulation and melt and routing. The model has been intensively used at EDF for more than 20 years, in particular for modeling French mountainous watersheds. In the matter of parameters calibration we propose and test alternative multi-criteria techniques based on two specific approaches: automatic calibration using single-objective functions and a priori parameter calibration founded on hydrological watershed features. The automatic calibration approach uses single-objective functions, based on Kling-Gupta efficiency, to quantify the good agreement between the simulated and observed runoff focusing on four different runoff samples: (i) time-series sample, (I) annual hydrological regime, (iii) monthly cumulative distribution functions and (iv) recession sequences.The primary purpose of this study is to analyze the definition and sensitivity of MORDOR parameters testing different calibration techniques in order to: (i) simplify the model structure, (ii) increase the calibration-validation performance of the model and (iii) reduce the equifinality problem of calibration process. We propose an alternative calibration strategy that reaches these goals. The analysis is illustrated by calibrating MORDOR model to daily data for 50 watersheds located in French mountainous regions.

Analysis of long-term bacterial vs. chemical Fe(III) oxide reduction kinetics

NASA Astrophysics Data System (ADS)

Roden, Eric E.

2004-08-01

Data from studies of dissimilatory bacterial (10 8 cells mL -1 of Shewanella putrefaciens strain CN32, pH 6.8) and ascorbate (10 mM, pH 3.0) reduction of two synthetic Fe(III) oxide coated sands and three natural Fe(III) oxide-bearing subsurface materials (all at ca. 10 mmol Fe(III) L -1) were analyzed in relation to a generalized rate law for mineral dissolution (J t/m 0 = k'(m/m 0) γ, where J t is the rate of dissolution and/or reduction at time t, m 0 is the initial mass of oxide, and m/m 0 is the unreduced or undissolved mineral fraction) in order to evaluate changes in the apparent reactivity of Fe(III) oxides during long-term biological vs. chemical reduction. The natural Fe(III) oxide assemblages demonstrated larger changes in reactivity (higher γ values in the generalized rate law) compared to the synthetic oxides during long-term abiotic reductive dissolution. No such relationship was evident in the bacterial reduction experiments, in which temporal changes in the apparent reactivity of the natural and synthetic oxides were far greater (5-10 fold higher γ values) than in the abiotic reduction experiments. Kinetic and thermodynamic considerations indicated that neither the abundance of electron donor (lactate) nor the accumulation of aqueous end-products of oxide reduction (Fe(II), acetate, dissolved inorganic carbon) are likely to have posed significant limitations on the long-term kinetics of oxide reduction. Rather, accumulation of biogenic Fe(II) on residual oxide surfaces appeared to play a dominant role in governing the long-term kinetics of bacterial crystalline Fe(III) oxide reduction. The experimental findings together with numerical simulations support a conceptual model of bacterial Fe(III) oxide reduction kinetics that differs fundamentally from established models of abiotic Fe(III) oxide reductive dissolution, and indicate that information on Fe(III) oxide reactivity gained through abiotic reductive dissolution techniques cannot be used to predict long-term patterns of reactivity toward enzymatic reduction at circumneutral pH.

From DNS to RANS: A Multi-model workflow to understand the Influence of Hurricanes on Generating Turbidity Currents in the Gulf of Mexico

NASA Astrophysics Data System (ADS)

Syvitski, J. P.; Arango, H.; Harris, C. K.; Meiburg, E. H.; Jenkins, C. J.; Auad, G.; Hutton, E.; Kniskern, T. A.; Radhakrishnan, S.

2016-12-01

A loosely coupled numerical workflow is developed to address land-sea pathways for sediment routing from terrestrial and coastal sources, across the continental shelf and ultimately down the continental slope canyon system of the northern Gulf of Mexico (GOM). Model simulations represent a range of environmental conditions that might lead to the generation of turbidity-currents. The workflow comprises: 1) A simulator for the water and sediment discharged from rivers into the GOM with WMBsedv2 with calibration using USGS and USACE gauged river data; 2) Domain grids and bathymetry (ETOPO2) for the ocean models and realistic seabed sediment texture grids (dbSEABED) for the sediment transport models; 3) A spectral wave action simulator (10 km resolution) (WaveWatch III) driven by GFDL - GFS winds; 4) A simulator for ocean dynamics (ROMS) forced with ECMWF ERA winds; 5) A simulator for seafloor resuspension and transport (CSTMS); 6) Simulators (HurriSlip) of seafloor failure and flow ignition locations for boundary input to a turbidity current model; and 7) A RANS turbidity current model (TURBINS) to route sediment flows down GOM canyons, providing estimates of bottom shear stresses. TURBINS was developed first as a DNS model and then converted to an LES model wherein a dynamic turbulence closure scheme was employed. Like most DNS to LES model comparisons (these being done by the UCSB team), turbulence scaling allowed for higher Re applications but were found still not capable of simulating field scale (GOM continental canyons) environments. The LES model was next converted to a non-hydrostatic RANS model capable of field scale applications but only with a daisy-chain approach to multiple model runs along the simulated canyon floor. These model adaptations allowed the workflow to be tested for the year 1-Oct-2007 to 30-Sep-2008 that included two domain Hurricanes (Ike and Gustav). The RANS-TURBINS employed further boundary simplifications on both sediment erosion and deposition in line with the ocean model ROMS-CSTMS.

A statistical analysis of the dependency of closure assumptions in cumulus parameterization on the horizontal resolution

NASA Technical Reports Server (NTRS)

Xu, Kuan-Man

1994-01-01

Simulated data from the UCLA cumulus ensemble model are used to investigate the quasi-universal validity of closure assumptions used in existing cumulus parameterizations. A closure assumption is quasi-universally valid if it is sensitive neither to convective cloud regimes nor to horizontal resolutions of large-scale/mesoscale models. The dependency of three types of closure assumptions, as classified by Arakawa and Chen, on the horizontal resolution is addressed in this study. Type I is the constraint on the coupling of the time tendencies of large-scale temperature and water vapor mixing ratio. Type II is the constraint on the coupling of cumulus heating and cumulus drying. Type III is a direct constraint on the intensity of a cumulus ensemble. The macroscopic behavior of simulated cumulus convection is first compared with the observed behavior in view of Type I and Type II closure assumptions using 'quick-look' and canonical correlation analyses. It is found that they are statistically similar to each other. The three types of closure assumptions are further examined with simulated data averaged over selected subdomain sizes ranging from 64 to 512 km. It is found that the dependency of Type I and Type II closure assumptions on the horizontal resolution is very weak and that Type III closure assumption is somewhat dependent upon the horizontal resolution. The influences of convective and mesoscale processes on the closure assumptions are also addressed by comparing the structures of canonical components with the corresponding vertical profiles in the convective and stratiform regions of cumulus ensembles analyzed directly from simulated data. The implication of these results for cumulus parameterization is discussed.

Bifurcation Analysis and Optimal Harvesting of a Delayed Predator-Prey Model

NASA Astrophysics Data System (ADS)

Tchinda Mouofo, P.; Djidjou Demasse, R.; Tewa, J. J.; Aziz-Alaoui, M. A.

A delay predator-prey model is formulated with continuous threshold prey harvesting and Holling response function of type III. Global qualitative and bifurcation analyses are combined to determine the global dynamics of the model. The positive invariance of the non-negative orthant is proved and the uniform boundedness of the trajectories. Stability of equilibria is investigated and the existence of some local bifurcations is established: saddle-node bifurcation, Hopf bifurcation. We use optimal control theory to provide the correct approach to natural resource management. Results are also obtained for optimal harvesting. Numerical simulations are given to illustrate the results.

Particle-based membrane model for mesoscopic simulation of cellular dynamics

NASA Astrophysics Data System (ADS)

Sadeghi, Mohsen; Weikl, Thomas R.; Noé, Frank

2018-01-01

We present a simple and computationally efficient coarse-grained and solvent-free model for simulating lipid bilayer membranes. In order to be used in concert with particle-based reaction-diffusion simulations, the model is purely based on interacting and reacting particles, each representing a coarse patch of a lipid monolayer. Particle interactions include nearest-neighbor bond-stretching and angle-bending and are parameterized so as to reproduce the local membrane mechanics given by the Helfrich energy density over a range of relevant curvatures. In-plane fluidity is implemented with Monte Carlo bond-flipping moves. The physical accuracy of the model is verified by five tests: (i) Power spectrum analysis of equilibrium thermal undulations is used to verify that the particle-based representation correctly captures the dynamics predicted by the continuum model of fluid membranes. (ii) It is verified that the input bending stiffness, against which the potential parameters are optimized, is accurately recovered. (iii) Isothermal area compressibility modulus of the membrane is calculated and is shown to be tunable to reproduce available values for different lipid bilayers, independent of the bending rigidity. (iv) Simulation of two-dimensional shear flow under a gravity force is employed to measure the effective in-plane viscosity of the membrane model and show the possibility of modeling membranes with specified viscosities. (v) Interaction of the bilayer membrane with a spherical nanoparticle is modeled as a test case for large membrane deformations and budding involved in cellular processes such as endocytosis. The results are shown to coincide well with the predicted behavior of continuum models, and the membrane model successfully mimics the expected budding behavior. We expect our model to be of high practical usability for ultra coarse-grained molecular dynamics or particle-based reaction-diffusion simulations of biological systems.

Aircraft evacuations through type-III exits I : effects of seat placement at the exit.

DOT National Transportation Integrated Search

1995-07-01

Simulated emergency egress from Type III over-wing exits was studied to support regulatory action by the FAA. Passageway width and seat encroachment distance adjacent to the Type-III exit were the major variables of interest. : Methods. Two subject g...

Simulation Assisted Risk Assessment: Blast Overpressure Modeling

NASA Technical Reports Server (NTRS)

Lawrence, Scott L.; Gee, Ken; Mathias, Donovan; Olsen, Michael

2006-01-01

A probabilistic risk assessment (PRA) approach has been developed and applied to the risk analysis of capsule abort during ascent. The PRA is used to assist in the identification of modeling and simulation applications that can significantly impact the understanding of crew risk during this potentially dangerous maneuver. The PRA approach is also being used to identify the appropriate level of fidelity for the modeling of those critical failure modes. The Apollo launch escape system (LES) was chosen as a test problem for application of this approach. Failure modes that have been modeled and/or simulated to date include explosive overpressure-based failure, explosive fragment-based failure, land landing failures (range limits exceeded either near launch or Mode III trajectories ending on the African continent), capsule-booster re-contact during separation, and failure due to plume-induced instability. These failure modes have been investigated using analysis tools in a variety of technical disciplines at various levels of fidelity. The current paper focuses on the development and application of a blast overpressure model for the prediction of structural failure due to overpressure, including the application of high-fidelity analysis to predict near-field and headwinds effects.

Model for Predicting the Performance of Planetary Suit Hip Bearing Designs

NASA Technical Reports Server (NTRS)

Cowley, Matthew S.; Margerum, Sarah; Hharvill, Lauren; Rajulu, Sudhakar

2012-01-01

Designing a space suit is very complex and often requires difficult trade-offs between performance, cost, mass, and system complexity. During the development period of the suit numerous design iterations need to occur before the hardware meets human performance requirements. Using computer models early in the design phase of hardware development is advantageous, by allowing virtual prototyping to take place. A virtual design environment allows designers to think creatively, exhaust design possibilities, and study design impacts on suit and human performance. A model of the rigid components of the Mark III Technology Demonstrator Suit (planetary-type space suit) and a human manikin were created and tested in a virtual environment. The performance of the Mark III hip bearing model was first developed and evaluated virtually by comparing the differences in mobility performance between the nominal bearing configurations and modified bearing configurations. Suited human performance was then simulated with the model and compared to actual suited human performance data using the same bearing configurations. The Mark III hip bearing model was able to visually represent complex bearing rotations and the theoretical volumetric ranges of motion in three dimensions. The model was also able to predict suited human hip flexion and abduction maximums to within 10% of the actual suited human subject data, except for one modified bearing condition in hip flexion which was off by 24%. Differences between the model predictions and the human subject performance data were attributed to the lack of joint moment limits in the model, human subject fitting issues, and the limited suit experience of some of the subjects. The results demonstrate that modeling space suit rigid segments is a feasible design tool for evaluating and optimizing suited human performance. Keywords: space suit, design, modeling, performance

The clustering of galaxies in the SDSS-III Baryon Oscillation Spectroscopic Survey: measuring H(z) and DA(z) at z = 0.57 with clustering wedges

NASA Astrophysics Data System (ADS)

Kazin, Eyal A.; Sánchez, Ariel G.; Cuesta, Antonio J.; Beutler, Florian; Chuang, Chia-Hsun; Eisenstein, Daniel J.; Manera, Marc; Padmanabhan, Nikhil; Percival, Will J.; Prada, Francisco; Ross, Ashley J.; Seo, Hee-Jong; Tinker, Jeremy; Tojeiro, Rita; Xu, Xiaoying; Brinkmann, J.; Joel, Brownstein; Nichol, Robert C.; Schlegel, David J.; Schneider, Donald P.; Thomas, Daniel

2013-10-01

We analyse the 2D correlation function of the Sloan Digital Sky Survey-III Baryon Oscillation Spectroscopic Survey (BOSS) CMASS sample of massive galaxies of the ninth data release to measure cosmic expansion H and the angular diameter distance DA at a mean redshift of = 0.57. We apply, for the first time, a new correlation function technique called clustering wedges ξΔμ(s). Using a physically motivated model, the anisotropic baryonic acoustic feature in the galaxy sample is detected at a significance level of 4.7σ compared to a featureless model. The baryonic acoustic feature is used to obtain model-independent constraints cz/H/rs = 12.28 ± 0.82 (6.7 percent accuracy) and DA/rs = 9.05 ± 0.27 (3.0 per cent) with a correlation coefficient of -0.5, where rs is the sound horizon scale at the end of the baryonic drag era. We conduct thorough tests on the data and 600 simulated realizations, finding robustness of the results regardless of the details of the analysis method. Combining this with rs constraints from the cosmic microwave background, we obtain H(0.57) = 90.8 ± 6.2 km s-1 Mpc-1 and DA(0.57) = 1386 ± 45 Mpc. We use simulations to forecast results of the final BOSS CMASS data set. We apply the reconstruction technique on the simulations demonstrating that the sharpening of the anisotropic baryonic acoustic feature should improve the detection as well as tighten constraints of H and DA by ˜30 per cent on average.

Verification and Validation of COAMPS: Results from a Fully-Coupled Air/Sea/Wave Modeling System

NASA Astrophysics Data System (ADS)

Smith, T.; Allard, R. A.; Campbell, T. J.; Chu, Y. P.; Dykes, J.; Zamudio, L.; Chen, S.; Gabersek, S.

2016-02-01

The Coupled Ocean/Atmosphere Mesoscale Prediction System (COAMPS) is a state-of-the art, fully-coupled air/sea/wave modeling system that is currently being validated for operational transition to both the Naval Oceanographic Office (NAVO) and to the Fleet Numerical Meteorology and Oceanography Center (FNMOC). COAMPS is run at the Department of Defense Supercomputing Resource Center (DSRC) operated by the DoD High Performance Computing Modernization Program (HPCMP). A total of four models including the Naval Coastal Ocean Model (NCOM), Simulating Waves Nearshore (SWAN), WaveWatch III, and the COAMPS atmospheric model are coupled through both the Earth System Modeling Framework (ESMF). Results from regions of naval operational interests, including the Western Atlantic (U.S. East Coast), RIMPAC (Hawaii), and DYNAMO (Indian Ocean), will show the advantages of utilizing a coupled modeling system versus an uncoupled or stand alone model. Statistical analyses, which include model/observation comparisons, will be presented in the form of operationally approved scorecards for both the atmospheric and oceanic output. Also, computational logistics involving the HPC resources for the COAMPS simulations will be shown.

Options: A Career Development Curriculum for Rural High School Students. Unit III, Life Planning [and] Game of Life: Choice and Chance.

ERIC Educational Resources Information Center

Dunne, Faith; And Others

Designed to last approximately 12 days, Unit III of the 4-unit life planning and career development curriculum for rural high school students focuses on skills application. Through experience simulation, students apply skills learned in Unit II to the information from Unit I; they project their future lives and simulate their responses to problems…

Re-Examining of Moffitt’s Theory of Delinquency through Agent Based Modeling

PubMed Central

Leaw, Jia Ning; Ang, Rebecca P.; Huan, Vivien S.; Chan, Wei Teng; Cheong, Siew Ann

2015-01-01

Moffitt’s theory of delinquency suggests that at-risk youths can be divided into two groups, the adolescence- limited group and the life-course-persistent group, predetermined at a young age, and social interactions between these two groups become important during the adolescent years. We built an agent-based model based on the microscopic interactions Moffitt described: (i) a maturity gap that dictates (ii) the cost and reward of antisocial behavior, and (iii) agents imitating the antisocial behaviors of others more successful than themselves, to find indeed the two groups emerging in our simulations. Moreover, through an intervention simulation where we moved selected agents from one social network to another, we also found that the social network plays an important role in shaping the life course outcome. PMID:26062022

Biogeochemical modeling of CO2 and CH4 production in anoxic Arctic soil microcosms

NASA Astrophysics Data System (ADS)

Tang, Guoping; Zheng, Jianqiu; Xu, Xiaofeng; Yang, Ziming; Graham, David E.; Gu, Baohua; Painter, Scott L.; Thornton, Peter E.

2016-09-01

Soil organic carbon turnover to CO2 and CH4 is sensitive to soil redox potential and pH conditions. However, land surface models do not consider redox and pH in the aqueous phase explicitly, thereby limiting their use for making predictions in anoxic environments. Using recent data from incubations of Arctic soils, we extend the Community Land Model with coupled carbon and nitrogen (CLM-CN) decomposition cascade to include simple organic substrate turnover, fermentation, Fe(III) reduction, and methanogenesis reactions, and assess the efficacy of various temperature and pH response functions. Incorporating the Windermere Humic Aqueous Model (WHAM) enables us to approximately describe the observed pH evolution without additional parameterization. Although Fe(III) reduction is normally assumed to compete with methanogenesis, the model predicts that Fe(III) reduction raises the pH from acidic to neutral, thereby reducing environmental stress to methanogens and accelerating methane production when substrates are not limiting. The equilibrium speciation predicts a substantial increase in CO2 solubility as pH increases, and taking into account CO2 adsorption to surface sites of metal oxides further decreases the predicted headspace gas-phase fraction at low pH. Without adequate representation of these speciation reactions, as well as the impacts of pH, temperature, and pressure, the CO2 production from closed microcosms can be substantially underestimated based on headspace CO2 measurements only. Our results demonstrate the efficacy of geochemical models for simulating soil biogeochemistry and provide predictive understanding and mechanistic representations that can be incorporated into land surface models to improve climate predictions.

Numerical Modeling of Hailstorms and Hailstone Growth. Part III: Simulation of an Alberta Hailstorm--Natural and Seeded Cases.

NASA Astrophysics Data System (ADS)

Farley, Richard D.

1987-07-01

This paper reports on simulations of a multicellular hailstorm case observed during the 1983 Alberta Hail Project. The field operations on that day concentrated on two successive feeder cells which were subjected to controlled seeding experiments. The fist of these cells received the placebo treatment and the second was seeded with dry ice. The principal tool of this study is a modified version of the two-dimensional, time dependent hail category model described in Part I of this series of papers. It is with this model that hail growth processes are investigated, including the simulated effects of cloud seeding techniques as practiced in Alberta.The model simulation of the natural case produces a very good replication of the observed storm, particularly the placebo feeder cell. This is evidenced, in particular, by the high degree of fidelity of the observed and modeled radar reflectivity in terms of magnitudes, structure, and evolution. The character of the hailfall at the surface and the scale of the storm are captured nicely by the model, although cloud-top heights are generally too high, particularly for the mature storm system.Seeding experiments similar to those conducted in the field have also been simulated. These involve seeding the feeder cell early in its active development phase with dry ice (CO2) or silver iodide (AgI) introduced near cloud top. The model simulations of these seeded cases capture some of the observed seeding signatures detected by radar and aircraft. In these model experiments, CO2 seeding produced a stronger response than AgI seeding relative to inhibiting hail formation. For both seeded cases, production of precipitating ice was initially enhanced by the seeding, but retarded slightly in the later stages, the net result being modest increases in surface rainfall, with hail reduced slightly. In general, the model simulations support several subhypotheses of the operational strategy of the Alberta Research Council regarding the earlier formation of ice, snow, and graupel due to seeding.

Estimating the effect of shallow groundwater on diurnal heat transport in a vadose zone

NASA Astrophysics Data System (ADS)

Jiang, Jianmei; Zhao, Lin; Zhai, Zhe

2016-09-01

The influence of shallow groundwater on the diurnal heat transport of the soil profile was analyzed using a soil sensor automatic monitoring system that continuously measures temperature and water content of soil profiles to simulate heat transport based on the Philip and de Vries (PDV) model. Three experiments were conducted to measure soil properties at depths of 5 cm, 10 cm, 20 cm, and 30 cm when groundwater tables reached 10 cm, 30 cm, and 60 cm (Experiments I, II, and III). Results show that both the soil temperature near shallow groundwater and the soil water content were effectively simulated by the PDV model. The root mean square errors of the temperature at depths of 5 cm, 10 cm, and 20 cm were 1.018°C, 0.909°C, and 0.255°C, respectively. The total heat flux generated the convergent and divergent planes in space-time fields with valley values of-161.5W•m-2 at 7:30 and-234.6W•m-2 at 11:10 in Experiments II and III, respectively. The diurnal heat transport of the saturated soil occurred in five stages, while that of saturated-unsaturated and unsaturated soil profiles occurred in four stages because high moisture content led to high thermal conductivity, which hastened the heat transport.

The meaning of death: some simulations of a model of healthy and unhealthy consumption.

PubMed

Forster, M

2001-07-01

Simulations of a model of healthy and unhealthy consumption are used to investigate the impact of various terminal conditions on life-span, pathways of health-related consumption and health. A model in which life-span and the 'death' stock of health are fixed is compared to versions in which (i) the 'death' stock of health is freely chosen; (ii) life-span is freely chosen; (iii) both the 'death' stock of health and life-span are freely chosen. The choice of terminal conditions has a striking impact on optimal plans. Results are discussed with reference to the existing demand for health literature and illustrate the application of iterative processes to determine optimal life-span, the role played by the marginal value of health capital in determining optimal plans, and the importance of checking the second-order conditions for the optimal choice of life-span.

A novel coupled system of non-local integro-differential equations modelling Young's modulus evolution, nutrients' supply and consumption during bone fracture healing

NASA Astrophysics Data System (ADS)

Lu, Yanfei; Lekszycki, Tomasz

2016-10-01

During fracture healing, a series of complex coupled biological and mechanical phenomena occurs. They include: (i) growth and remodelling of bone, whose Young's modulus varies in space and time; (ii) nutrients' diffusion and consumption by living cells. In this paper, we newly propose to model these evolution phenomena. The considered features include: (i) a new constitutive equation for growth simulation involving the number of sensor cells; (ii) an improved equation for nutrient concentration accounting for the switch between Michaelis-Menten kinetics and linear consumption regime; (iii) a new constitutive equation for Young's modulus evolution accounting for its dependence on nutrient concentration and variable number of active cells. The effectiveness of the model and its predictive capability are qualitatively verified by numerical simulations (using COMSOL) describing the healing of bone in the presence of damaged tissue between fractured parts.

Complex patterns of abnormal heartbeats

NASA Technical Reports Server (NTRS)

Schulte-Frohlinde, Verena; Ashkenazy, Yosef; Goldberger, Ary L.; Ivanov, Plamen Ch; Costa, Madalena; Morley-Davies, Adrian; Stanley, H. Eugene; Glass, Leon

2002-01-01

Individuals having frequent abnormal heartbeats interspersed with normal heartbeats may be at an increased risk of sudden cardiac death. However, mechanistic understanding of such cardiac arrhythmias is limited. We present a visual and qualitative method to display statistical properties of abnormal heartbeats. We introduce dynamical "heartprints" which reveal characteristic patterns in long clinical records encompassing approximately 10(5) heartbeats and may provide information about underlying mechanisms. We test if these dynamics can be reproduced by model simulations in which abnormal heartbeats are generated (i) randomly, (ii) at a fixed time interval following a preceding normal heartbeat, or (iii) by an independent oscillator that may or may not interact with the normal heartbeat. We compare the results of these three models and test their limitations to comprehensively simulate the statistical features of selected clinical records. This work introduces methods that can be used to test mathematical models of arrhythmogenesis and to develop a new understanding of underlying electrophysiologic mechanisms of cardiac arrhythmia.

Statistical Inference in Hidden Markov Models Using k-Segment Constraints

PubMed Central

Titsias, Michalis K.; Holmes, Christopher C.; Yau, Christopher

2016-01-01

Hidden Markov models (HMMs) are one of the most widely used statistical methods for analyzing sequence data. However, the reporting of output from HMMs has largely been restricted to the presentation of the most-probable (MAP) hidden state sequence, found via the Viterbi algorithm, or the sequence of most probable marginals using the forward–backward algorithm. In this article, we expand the amount of information we could obtain from the posterior distribution of an HMM by introducing linear-time dynamic programming recursions that, conditional on a user-specified constraint in the number of segments, allow us to (i) find MAP sequences, (ii) compute posterior probabilities, and (iii) simulate sample paths. We collectively call these recursions k-segment algorithms and illustrate their utility using simulated and real examples. We also highlight the prospective and retrospective use of k-segment constraints for fitting HMMs or exploring existing model fits. Supplementary materials for this article are available online. PMID:27226674

Low-energy Population III supernovae and the origin of extremely metal-poor stars

NASA Astrophysics Data System (ADS)

Chen, Ke-Jung; Heger, Alexander; Whalen, Daniel J.; Moriya, Takashi J.; Bromm, Volker; Woosley, S. E.

2017-06-01

Some ancient, dim, metal-poor stars may have formed in the ashes of the first supernovae (SNe). If their chemical abundances can be reconciled with the elemental yields of specific Population III (Pop III) explosions, they could reveal the properties of primordial stars. But multidimensional simulations of such explosions are required to predict their yields because dynamical instabilities can dredge material up from deep in the ejecta that would otherwise be predicted to fall back on to the central remnant and be lost in one-dimensional (1D) models. We have performed two-dimensional (2D) numerical simulations of two low-energy Pop III SNe, a 12.4 M⊙ explosion and a 60 M⊙ explosion, and find that they produce elemental yields that are a good fit to those measured in the most iron-poor star discovered to date, SMSS J031300.36-670839.3 (J031300). Fallback on to the compact remnant in these weak explosions accounts for the lack of measurable iron in J031300 and its low iron-group abundances in general. Our 2D explosions produce higher abundances of heavy elements (atomic number Z > 20) than their 1D counterparts due to dredge-up by fluid instabilities. Since almost no 56Ni is ejected by these weak SNe, their low luminosities will prevent their detection in the near-infrared with the James Webb Space Telescope and future 30-m telescopes on the ground. The only evidence that they ever occurred will be in the fossil abundance record.

Phe71 in Type III Trypanosomal Protein Arginine Methyltransferase 7 (TbPRMT7) Restricts the Enzyme to Monomethylation.

PubMed

Cáceres, Tamar B; Thakur, Abhishek; Price, Owen M; Ippolito, Nicole; Li, Jun; Qu, Jun; Acevedo, Orlando; Hevel, Joan M

2018-02-27

Protein arginine methyltransferase 7 (PRMT7) is unique within the PRMT family as it is the only isoform known to exclusively make monomethylarginine (MMA). Given its role in epigenetics, the mechanistic basis for the strict monomethylation activity is under investigation. It is thought that PRMT7 enzymes are unable to add a second methyl group because of steric hindrance in the active site that restricts them to monomethylation. To test this, we probed the active site of trypanosomal PRMT7 (TbPRMT7) using accelerated molecular dynamics, site-directed mutagenesis, kinetic, binding, and product analyses. Both the dynamics simulations and experimental results show that the mutation of Phe71 to Ile converts the enzyme from a type III methyltransferase into a mixed type I/II, that is, an enzyme that can now perform dimethylation. In contrast, the serine and alanine mutants of Phe71 preserve the type III behavior of the native enzyme. These results are inconsistent with a sterics-only model to explain product specificity. Instead, molecular dynamics simulations of these variants bound to peptides show hydrogen bonding between would-be substrates and Glu172 of TbPRMT7. Only in the case of the Phe71 to Ile mutation is this interaction between MMA and the enzyme maintained, and the geometry for optimal S N 2 methyl transfer is obtained. The results of these studies highlight the benefit of combined computational and experimental methods in providing a better understanding for how product specificity is dictated by PRMTs.

Simulated effects of ground-water management scenarios on the Santa Fe group aquifer system, Middle Rio Grande Basin, New Mexico, 2001-40

USGS Publications Warehouse

Bexfield, Laura M.; McAda, Douglas P.

2003-01-01

Future conditions in the Santa Fe Group aquifer system through 2040 were simulated using the most recent revision of the U.S. Geological Survey groundwater- flow model for the Middle Rio Grande Basin. Three simulations were performed to investigate the likely effects of different scenarios of future groundwater pumping by the City of Albuquerque on the ground-water system. For simulation I, pumping was held constant at known year-2000 rates. For simulation II, pumping was increased to simulate the use of pumping to meet all projected city water demand through 2040. For simulation III, pumpingwas reduced in accordance with a plan by the City of Albuquerque to use surfacewater to meet most of the projectedwater demand. The simulations indicate that for each of the three pumping scenarios, substantial additional watertable declines would occur in some areas of the basin through 2040. However, the reduced pumping scenario of simulation III also results in water-table rise over a broad area of the city. All three scenarios indicate that the contributions of aquifer storage and river leakage to the ground-water system would change between 2000 and 2040. Comparisons among the results for simulations I, II, and III indicate that the various pumping scenarios have substantially different effects on water-level declines in the Albuquerque area and on the contribution of each water-budget component to the total budget for the ground-water system. Between 2000 and 2040, water-level declines for continued pumping at year-2000 rates are as much as 120 feet greater than for reduced pumping; water-level declines for increased pumping to meet all projected city demand are as much as 160 feet greater. Over the same time period, reduced pumping results in retention in aquifer storage of about 1,536,000 acre-feet of ground water as compared with continued pumping at year- 2000 rates and of about 2,257,000 acre-feet as compared with increased pumping. The quantity of water retained in the Rio Grande as a result of reduced pumping and the associated decrease in induced recharge from the river is about 731,000 acre-feet as compared with continued pumping at year-2000 rates and about 872,000 acre-feet as compared with increased pumping. Reduced pumping results in slight increases in the quantity of water lost from the groundwater system to evapotranspiration and agriculturaldrain flow compared with the other pumping scenarios.

Elucidating the 3D structures of Al(iii)-Aβ complexes: a template free strategy based on the pre-organization hypothesis.

PubMed

Mujika, Jon I; Rodríguez-Guerra Pedregal, Jaime; Lopez, Xabier; Ugalde, Jesus M; Rodríguez-Santiago, Luis; Sodupe, Mariona; Maréchal, Jean-Didier

2017-07-01

Senile plaques are extracellular deposits found in patients with Alzheimer's Disease (AD) and are mainly formed by insoluble fibrils of β-amyloid (Aβ) peptides. The mechanistic details about how AD develops are not fully understood yet, but metals such as Cu, Zn, or Fe are proposed to have a non-innocent role. Many studies have also linked the non biological metal aluminum with AD, a species whose concentration in the environment and food has been constantly increasing since the industrial revolution. Gaining a molecular picture of how Al(iii) interacts with an Aβ peptide is of fundamental interest to improve understanding of the many variables in the evolution of AD. So far, no consensus has been reached on how this metal interacts with Aβ, partially due to the experimental complexity of detecting and quantifying the resulting Al(iii)-Aβ complexes. Computational chemistry arises as a powerful alternative to investigate how Al(iii) can interact with Aβ peptides, as suitable strategies could shed light on the metal-peptide description at the molecular level. However, the absence of any reliable template that could be used for the modeling of the metallopeptide structure makes computational insight extremely difficult. Here, we present a novel strategy to generate accurate 3D models of the Al(iii)-Aβ complexes, which still circumvents first principles simulations of metal binding to peptides of Aβ. The key to this approach lies in the identification of experimental structures of the isolated peptide that are favourably pre-organized for the binding of a given metal in configurations of the first coordination sphere that were previously identified as the most stable with amino acid models. This approach solves the problem of the absence of clear structural templates for novel metallopeptide constructs. The posterior refinement of the structures via QM/MM and MD calculations allows us to provide, for the first time, physically sound models for Al(iii)-Aβ complexes with a 1 : 1 stoichiometry, where up to three carboxylic groups are involved in the metal binding, with a clear preference towards Glu3, Asp7, and Glu11.

Local Bifurcations and Optimal Theory in a Delayed Predator-Prey Model with Threshold Prey Harvesting

NASA Astrophysics Data System (ADS)

Tankam, Israel; Tchinda Mouofo, Plaire; Mendy, Abdoulaye; Lam, Mountaga; Tewa, Jean Jules; Bowong, Samuel

2015-06-01

We investigate the effects of time delay and piecewise-linear threshold policy harvesting for a delayed predator-prey model. It is the first time that Holling response function of type III and the present threshold policy harvesting are associated with time delay. The trajectories of our delayed system are bounded; the stability of each equilibrium is analyzed with and without delay; there are local bifurcations as saddle-node bifurcation and Hopf bifurcation; optimal harvesting is also investigated. Numerical simulations are provided in order to illustrate each result.

A Slam Model of the Armed Forces Courier Service CONUS Stations: A Strategic Planning Tool.

DTIC Science & Technology

1985-09-01

ii .-- - ". . ’. . i i . - , i i . "-. - -’’" . .’’ ’- -. . . . . ... .’ 12? .2.2i?.i..- .’- .- j ’. .. . . . ... i ’< - ," ’i.-l -.- ’. ,. .l...of a simulation model that provides the ARFCOS top managers with a strategic planning tool for determining ,< .- .. -F -- ....F .,I . .. , j -.... io...i ,. i .< - j ’ ’. -.- ’i’iii ,. . - - . -.- ’ < . ,] . . F . ’I 1 " vehicle weight carrying requirements, and manpower needs for their different

Structure and dynamics of the CrIII ion in aqueous solution: Ab initio QM/MM molecular dynamics simulation.

PubMed

Kritayakornupong, Chinapong; Plankensteiner, Kristof; Rode, Bernd M

2004-10-01

Structural and dynamical properties of the Cr(III) ion in aqueous solution have been investigated using a combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation. The hydration structure of Cr(III) was determined in terms of radial distribution functions, coordination numbers, and angular distributions. The QM/MM simulation gives coordination numbers of 6 and 15.4 for the first and second hydration shell, respectively. The first hydration shell is kinetically very inert but by no means rigid and variations of the first hydration shell geometry lead to distinct splitting in the vibrational spectra of Cr(H(2)O)(6) (3+). A mean residence time of 22 ps was obtained for water ligands residing in the second hydration shell, which is remarkably shorter than the experimentally estimated value. The hydration energy of -1108 +/- 7 kcal/mol, obtained from the QM/MM simulation, corresponds well to the experimental hydration enthalpy value. Copyright 2004 Wiley Periodicals, Inc.

Application of Harmony Search algorithm to the solution of groundwater management models

NASA Astrophysics Data System (ADS)

Tamer Ayvaz, M.

2009-06-01

This study proposes a groundwater resources management model in which the solution is performed through a combined simulation-optimization model. A modular three-dimensional finite difference groundwater flow model, MODFLOW is used as the simulation model. This model is then combined with a Harmony Search (HS) optimization algorithm which is based on the musical process of searching for a perfect state of harmony. The performance of the proposed HS based management model is tested on three separate groundwater management problems: (i) maximization of total pumping from an aquifer (steady-state); (ii) minimization of the total pumping cost to satisfy the given demand (steady-state); and (iii) minimization of the pumping cost to satisfy the given demand for multiple management periods (transient). The sensitivity of HS algorithm is evaluated by performing a sensitivity analysis which aims to determine the impact of related solution parameters on convergence behavior. The results show that HS yields nearly same or better solutions than the previous solution methods and may be used to solve management problems in groundwater modeling.

The Formation of Supermassive Black Holes from Population III.1 Seeds. I. Cosmic Formation Histories and Clustering Properties

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

Banik, Nilanjan; Tan, Jonathan C.; Monaco, Pierluigi

We calculate the cosmic distributions in space and time of the formation sites of the first, "Pop III.1" stars, exploring a model in which these are the progenitors of all supermassive black holes (SMBHs). Pop III.1 stars are defined to form from primordial composition gas in dark matter minihalos withmore » $$\\sim10^6\\:M_\\odot$$ that are isolated from neighboring astrophysical sources by a given isolation distance, $$d_{\\rm{iso}}$$. We assume Pop III.1 sources are seeds of SMBHs, based on protostellar support by dark matter annihilation heating that allows them to accrete a large fraction of their minihalo gas, i.e., $$\\sim 10^5\\:M_\\odot$$. Exploring $$d_{\\rm{iso}}$$ from 10--$$100\\:\\rm{kpc}$$ (proper distances), we predict the redshift evolution of Pop III.1 source and SMBH remnant number densities. The local, $z=0$ density of SMBHs constrains $$d_{\\rm{iso}}\\lesssim 100\\:\\rm{kpc}$$ (i.e., $$3\\:\\rm{Mpc}$$ comoving distance at $$z\\simeq30$$). In our simulated ($$\\sim60\\:\\rm{Mpc}$$)$^3$ comoving volume, Pop III.1 stars start forming just after $z=40$. Their formation is largely complete by $$z\\simeq25$$ to 20 for $$d_{\\rm{iso}}=100$$ to $$50\\:\\rm{kpc}$$. We follow source evolution to $z=10$, by which point most SMBHs reside in halos with $$\\gtrsim10^8\\:M_\\odot$$. Over this period, there is relatively limited merging of SMBHs for these values of $$d_{\\rm{iso}}$$. We also predict SMBH clustering properties at $z=10$$: feedback suppression of neighboring sources leads to relatively flat angular correlation functions. Finally, we consider a simple "Str\\"omgren" model for $$d_{\\rm iso}$, based on ionizing feedback from zero age main sequence supermassive Pop III.1 stars that may be the direct progenitors of SMBHs in this scenario. Such models naturally produce feedback effects on scales of $$\\sim100\\:$$kpc and thus self-consistently generate a SMBH number density similar to the observed value.« less

Application of Satellite SAR Imagery in Mapping the Active Layer of Arctic Permafrost

NASA Technical Reports Server (NTRS)

Zhang, Ting-Jun; Li, Shu-Sun

2003-01-01

The objective of this project is to map the spatial variation of the active layer over the arctic permafrost in terms of two parameters: (i) timing and duration of thaw period and (ii) differential frost heave and thaw settlement of the active layer. To achieve this goal, remote sensing, numerical modeling, and related field measurements are required. Tasks for the University of Colorado team are to: (i) determine the timing of snow disappearance in spring through changes in surface albedo (ii) simulate the freezing and thawing processes of the active layer and (iii) simulate the impact of snow cover on permafrost presence.

Three-dimensional characterisation and simulation of deformation and damage during Taylor impact in PTFE

NASA Astrophysics Data System (ADS)

Resnyansky, A. D.; McDonald, S. A.; Withers, P. J.; Bourne, N. K.; Millett, J. C. F.; Brown, E. N.; Rae, P. J.

2014-05-01

The current work presents Taylor impact experiments interrogating the effect of dynamic, high-pressure loading on polytetrafluoroethylene (PTFE). In particular, X-ray microtomography has been used to characterise the damage imparted to cylindrical samples due to impact at different velocities. Distinct regions of deformation are present and controlled by fracture within the polymer, with the extent of the deformed region and increasing propagation of fractures from the impact face showing a clear trend with increasing impact velocity. A two-phase rate sensitive strength model is implemented in the CTH hydrocode and used for simulation of the problem. The high-pressure phase transition of PTFE into Phase III within the crystalline domains from the polymer at normal conditions is managed by suitable phase transition kinetics within the model. The experimental observations are discussed with respect to the multi-phase model hydrocode predictions of the shock response from Taylor impact simulations. The damage and its progress are shown to correlate well with the onset of the phase transition and its evolution following the impact velocity increase.

Characterizing Vegetation Model Skill and Uncertainty in Simulated Ecosystem Response to Climate Change in the United States

NASA Astrophysics Data System (ADS)

Drapek, R. J.; Kim, J. B.

2013-12-01

We simulated ecosystem response to climate change in the USA and Canada at a 5 arc-minute grid resolution using the MC1 dynamic global vegetation model and nine CMIP3 future climate projections as input. The climate projections were produced by 3 GCMs simulating 3 SRES emissions scenarios. We examined MC1 outputs for the conterminous USA by summarizing them by EPA level II and III ecoregions to characterize model skill and evaluate the magnitude and uncertainties of simulated ecosystem response to climate change. First, we evaluated model skill by comparing outputs from the recent historical period with benchmark datasets. Distribution of potential natural vegetation simulated by MC1 was compared with Kuchler's map. Above ground live carbon simulated by MC1 was compared with the National Biomass and Carbon Dataset. Fire return intervals calculated by MC1 were compared with maximum and minimum values compiled for the United States. Each EPA Level III Ecoregion was scored for average agreement with corresponding benchmark data and an average score was calculated for all three types of output. Greatest agreement with benchmark data happened in the Western Cordillera, the Ozark / Ouachita-Appalachian Forests, and the Southeastern USA Plains (EPA Level II Ecoregions). The lowest agreement happened in the Everglades and the Tamaulipas-Texas Semiarid Plain. For simulated ecosystem response to future climate projections we examined MC1 output for shifts in vegetation type, vegetation carbon, runoff, and biomass consumed by fire. Each ecoregion was scored for the amount of change from historical conditions for each variable and an average score was calculated. Smallest changes were forecast for Western Cordillera and Marine West Coast Forest ecosystems. Largest changes were forecast for the Cold Deserts, the Mixed Wood Plains, and the Central USA Plains. By combining scores of model skill for the historical period for each EPA Level 3 Ecoregion with scores representing the magnitude of ecosystem changes in the future, we identified high and low uncertainty ecoregions. The largest anticipated changes and the lowest measures of model skill coincide in the Central USA Plains and the Mixed Wood Plains. The combination of low model skill and high degree of ecosystem change elevate the importance of our uncertainty in this ecoregion. The highest projected changes coincide with relatively high model skill in the Cold Deserts. Climate adaptation efforts are the most likely to pay off in these regions. Finally, highest model skill and lowest anticipated changes coincide in the Western Cordillera and the Marine West Coast Forests. These regions may be relatively low-risk for climate change impacts when compared to the other ecoregions. These results represent only the first step in this type of analysis; there exist many ways to strengthen it. One, MC1 calibrations can be optimized using a structured optimization technique. Two, a larger set of climate projections can be used to capture a fuller range of GCMs and emissions scenarios. And three, employing an ensemble of vegetation models would make the analysis more robust.

Modeling Early Galaxies Using Radiation Hydrodynamics

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

None

This simulation uses a flux-limited diffusion solver to explore the radiation hydrodynamics of early galaxies, in particular, the ionizing radiation created by Population III stars. At the time of this rendering, the simulation has evolved to a redshift of 3.5. The simulation volume is 11.2 comoving megaparsecs, and has a uniform grid of 10243 cells, with over 1 billion dark matter and star particles. This animation shows a combined view of the baryon density, dark matter density, radiation energy and emissivity from this simulation. The multi-variate rendering is particularly useful because is shows both the baryonic matter ("normal") and darkmore » matter, and the pressure and temperature variables are properties of only the baryonic matter. Visible in the gas density are "bubbles", or shells, created by the radiation feedback from young stars. Seeing the bubbles from feedback provides confirmation of the physics model implemented. Features such as these are difficult to identify algorithmically, but easily found when viewing the visualization. Simulation was performed on Kraken at the National Institute for Computational Sciences. Visualization was produced using resources of the Argonne Leadership Computing Facility at Argonne National Laboratory.« less

The possible existence of Pop III NS-BH binary and its detectability

NASA Astrophysics Data System (ADS)

Kinugawa, Tomoya; Nakamura, Takashi; Nakano, Hiroyuki

2017-02-01

In the population synthesis simulations of Pop III stars, many BH (black hole)-BH binaries with merger time less than the age of the Universe (τH) are formed, while NS (neutron star)-BH binaries are not. The reason is that Pop III stars have no metal so that no mass loss is expected. Then, in the final supernova explosion to NS, much mass is lost so that the semimajor axis becomes too large for Pop III NS-BH binaries to merge within τH . However it is almost established that the kick velocity of the order of 200 ‑500  km s‑1 exists for NS from the observation of the proper motion of the pulsar. Therefore, the semimajor axis of the half of NS-BH binaries can be smaller than that of the previous argument for Pop III NS-BH binaries to decrease the merging time. We perform population synthesis Monte Carlo simulations of Pop III NS-BH binaries including the kick of NS and find that the event rate of Pop III NS-BH merger rate is 1  Gpc‑3 yr‑1 . This suggests that there is a good chance of detecting Pop III NS-BH mergers in O2 (Observation run 2) of Advanced LIGO and Advanced Virgo from this autumn.

Influence of Earth-directed Coronal Mass Ejections on the Sun’s Shadow Observed by the Tibet-III Air Shower Array

NASA Astrophysics Data System (ADS)

Amenomori, M.; Bi, X. J.; Chen, D.; Chen, T. L.; Chen, W. Y.; Cui, S. W.; Danzengluobu; Ding, L. K.; Feng, C. F.; Feng, Zhaoyang; Feng, Z. Y.; Gou, Q. B.; Guo, Y. Q.; He, H. H.; He, Z. T.; Hibino, K.; Hotta, N.; Hu, Haibing; Hu, H. B.; Huang, J.; Jia, H. Y.; Jiang, L.; Kajino, F.; Kasahara, K.; Katayose, Y.; Kato, C.; Kawata, K.; Kozai, M.; Labaciren; Le, G. M.; Li, A. F.; Li, H. J.; Li, W. J.; Liu, C.; Liu, J. S.; Liu, M. Y.; Lu, H.; Meng, X. R.; Miyazaki, T.; Munakata, K.; Nakajima, T.; Nakamura, Y.; Nanjo, H.; Nishizawa, M.; Niwa, T.; Ohnishi, M.; Ohta, I.; Ozawa, S.; Qian, X. L.; Qu, X. B.; Saito, T.; Saito, T. Y.; Sakata, M.; Sako, T. K.; Shao, J.; Shibata, M.; Shiomi, A.; Shirai, T.; Sugimoto, H.; Takita, M.; Tan, Y. H.; Tateyama, N.; Torii, S.; Tsuchiya, H.; Udo, S.; Wang, H.; Wu, H. R.; Xue, L.; Yamamoto, Y.; Yamauchi, K.; Yang, Z.; Yuan, A. F.; Zhai, L. M.; Zhang, H. M.; Zhang, J. L.; Zhang, X. Y.; Zhang, Y.; Zhang, Yi; Zhang, Ying; Zhaxisangzhu; Zhou, X. X.; Tibet ASγ Collaboration

2018-06-01

We examine the possible influence of Earth-directed coronal mass ejections (ECMEs) on the Sun’s shadow in the 3 TeV cosmic-ray intensity observed by the Tibet-III air shower (AS) array. We confirm a clear solar-cycle variation of the intensity deficit in the Sun’s shadow during ten years between 2000 and 2009. This solar-cycle variation is overall reproduced by our Monte Carlo (MC) simulations of the Sun’s shadow based on the potential field model of the solar magnetic field averaged over each solar rotation period. We find, however, that the magnitude of the observed intensity deficit in the Sun’s shadow is significantly less than that predicted by MC simulations, particularly during the period around solar maximum when a significant number of ECMEs is recorded. The χ 2 tests of the agreement between the observations and the MC simulations show that the difference is larger during the periods when the ECMEs occur, and the difference is reduced if the periods of ECMEs are excluded from the analysis. This suggests the first experimental evidence of the ECMEs affecting the Sun’s shadow observed in the 3 TeV cosmic-ray intensity.

Fast image-based mitral valve simulation from individualized geometry.

PubMed

Villard, Pierre-Frederic; Hammer, Peter E; Perrin, Douglas P; Del Nido, Pedro J; Howe, Robert D

2018-04-01

Common surgical procedures on the mitral valve of the heart include modifications to the chordae tendineae. Such interventions are used when there is extensive leaflet prolapse caused by chordae rupture or elongation. Understanding the role of individual chordae tendineae before operating could be helpful to predict whether the mitral valve will be competent at peak systole. Biomechanical modelling and simulation can achieve this goal. We present a method to semi-automatically build a computational model of a mitral valve from micro CT (computed tomography) scans: after manually picking chordae fiducial points, the leaflets are segmented and the boundary conditions as well as the loading conditions are automatically defined. Fast finite element method (FEM) simulation is carried out using Simulation Open Framework Architecture (SOFA) to reproduce leaflet closure at peak systole. We develop three metrics to evaluate simulation results: (i) point-to-surface error with the ground truth reference extracted from the CT image, (ii) coaptation surface area of the leaflets and (iii) an indication of whether the simulated closed leaflets leak. We validate our method on three explanted porcine hearts and show that our model predicts the closed valve surface with point-to-surface error of approximately 1 mm, a reasonable coaptation surface area, and absence of any leak at peak systole (maximum closed pressure). We also evaluate the sensitivity of our model to changes in various parameters (tissue elasticity, mesh accuracy, and the transformation matrix used for CT scan registration). We also measure the influence of the positions of the chordae tendineae on simulation results and show that marginal chordae have a greater influence on the final shape than intermediate chordae. The mitral valve simulation can help the surgeon understand valve behaviour and anticipate the outcome of a procedure. Copyright © 2018 John Wiley & Sons, Ltd.

Finding the First Cosmic Explosions. II. Core-collapse Supernovae

NASA Astrophysics Data System (ADS)

Whalen, Daniel J.; Joggerst, Candace C.; Fryer, Chris L.; Stiavelli, Massimo; Heger, Alexander; Holz, Daniel E.

2013-05-01

Understanding the properties of Population III (Pop III) stars is prerequisite to elucidating the nature of primeval galaxies, the chemical enrichment and reionization of the early intergalactic medium, and the origin of supermassive black holes. While the primordial initial mass function (IMF) remains unknown, recent evidence from numerical simulations and stellar archaeology suggests that some Pop III stars may have had lower masses than previously thought, 15-50 M ⊙ in addition to 50-500 M ⊙. The detection of Pop III supernovae (SNe) by JWST, WFIRST, or the TMT could directly probe the primordial IMF for the first time. We present numerical simulations of 15-40 M ⊙ Pop III core-collapse SNe performed with the Los Alamos radiation hydrodynamics code RAGE. We find that they will be visible in the earliest galaxies out to z ~ 10-15, tracing their star formation rates and in some cases revealing their positions on the sky. Since the central engines of Pop III and solar-metallicity core-collapse SNe are quite similar, future detection of any Type II SNe by next-generation NIR instruments will in general be limited to this epoch.

Interplanetary Type III Bursts and Electron Density Fluctuations in the Solar Wind

NASA Astrophysics Data System (ADS)

Krupar, V.; Maksimovic, M.; Kontar, E. P.; Zaslavsky, A.; Santolik, O.; Soucek, J.; Kruparova, O.; Eastwood, J. P.; Szabo, A.

2018-04-01

Type III bursts are generated by fast electron beams originated from magnetic reconnection sites of solar flares. As propagation of radio waves in the interplanetary medium is strongly affected by random electron density fluctuations, type III bursts provide us with a unique diagnostic tool for solar wind remote plasma measurements. Here, we performed a statistical survey of 152 simple and isolated type III bursts observed by the twin-spacecraft Solar TErrestrial RElations Observatory mission. We investigated their time–frequency profiles in order to retrieve decay times as a function of frequency. Next, we performed Monte Carlo simulations to study the role of scattering due to random electron density fluctuations on time–frequency profiles of radio emissions generated in the interplanetary medium. For simplification, we assumed the presence of isotropic electron density fluctuations described by a power law with the Kolmogorov spectral index. Decay times obtained from observations and simulations were compared. We found that the characteristic exponential decay profile of type III bursts can be explained by the scattering of the fundamental component between the source and the observer despite restrictive assumptions included in the Monte Carlo simulation algorithm. Our results suggest that relative electron density fluctuations < δ {n}{{e}}> /{n}{{e}} in the solar wind are 0.06–0.07 over wide range of heliospheric distances.

A critical assessment of flux and source term closures in shallow water models with porosity for urban flood simulations

NASA Astrophysics Data System (ADS)

Guinot, Vincent

2017-11-01

The validity of flux and source term formulae used in shallow water models with porosity for urban flood simulations is assessed by solving the two-dimensional shallow water equations over computational domains representing periodic building layouts. The models under assessment are the Single Porosity (SP), the Integral Porosity (IP) and the Dual Integral Porosity (DIP) models. 9 different geometries are considered. 18 two-dimensional initial value problems and 6 two-dimensional boundary value problems are defined. This results in a set of 96 fine grid simulations. Analysing the simulation results leads to the following conclusions: (i) the DIP flux and source term models outperform those of the SP and IP models when the Riemann problem is aligned with the main street directions, (ii) all models give erroneous flux closures when is the Riemann problem is not aligned with one of the main street directions or when the main street directions are not orthogonal, (iii) the solution of the Riemann problem is self-similar in space-time when the street directions are orthogonal and the Riemann problem is aligned with one of them, (iv) a momentum balance confirms the existence of the transient momentum dissipation model presented in the DIP model, (v) none of the source term models presented so far in the literature allows all flow configurations to be accounted for(vi) future laboratory experiments aiming at the validation of flux and source term closures should focus on the high-resolution, two-dimensional monitoring of both water depth and flow velocity fields.

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

Tang, Guoping; Zheng, Jianqiu; Xu, Xiaofeng

Soil organic carbon turnover to CO 2 and CH 4 is sensitive to soil redox potential and pH conditions. But, land surface models do not consider redox and pH in the aqueous phase explicitly, thereby limiting their use for making predictions in anoxic environments. Using recent data from incubations of Arctic soils, we extend the Community Land Model with coupled carbon and nitrogen (CLM-CN) decomposition cascade to include simple organic substrate turnover, fermentation, Fe(III) reduction, and methanogenesis reactions, and assess the efficacy of various temperature and pH response functions. Incorporating the Windermere Humic Aqueous Model (WHAM) enables us to approximatelymore » describe the observed pH evolution without additional parameterization. Though Fe(III) reduction is normally assumed to compete with methanogenesis, the model predicts that Fe(III) reduction raises the pH from acidic to neutral, thereby reducing environmental stress to methanogens and accelerating methane production when substrates are not limiting. Furthermore, the equilibrium speciation predicts a substantial increase in CO 2 solubility as pH increases, and taking into account CO 2 adsorption to surface sites of metal oxides further decreases the predicted headspace gas-phase fraction at low pH. Without adequate representation of these speciation reactions, as well as the impacts of pH, temperature, and pressure, the CO 2 production from closed microcosms can be substantially underestimated based on headspace CO 2 measurements only. Our results demonstrate the efficacy of geochemical models for simulating soil biogeochemistry and provide predictive understanding and mechanistic representations that can be incorporated into land surface models to improve climate predictions.« less

Trade-off analysis of discharge-desiltation-turbidity and ANN analysis on sedimentation of a combined reservoir-reach system under multi-phase and multi-layer conjunctive releasing operation

NASA Astrophysics Data System (ADS)

Huang, Chien-Lin; Hsu, Nien-Sheng; Wei, Chih-Chiang; Yao, Chun-Hao

2017-10-01

Multi-objective reservoir operation considering the trade-off of discharge-desiltation-turbidity during typhoons and sediment concentration (SC) simulation modeling are the vital components for sustainable reservoir management. The purposes of this study were (1) to analyze the multi-layer release trade-offs between reservoir desiltation and intake turbidity of downstream purification plants and thus propose a superior conjunctive operation strategy and (2) to develop ANFIS-based (adaptive network-based fuzzy inference system) and RTRLNN-based (real-time recurrent learning neural networks) substitute SC simulation models. To this end, this study proposed a methodology to develop (1) a series of multi-phase and multi-layer sediment-flood conjunctive release modes and (2) a specialized SC numerical model for a combined reservoir-reach system. The conjunctive release modes involve (1) an optimization model where the decision variables are multi-phase reduction/scaling ratios and the timings to generate a superior total release hydrograph for flood control (Phase I: phase prior to flood arrival, Phase II/III: phase prior to/subsequent to peak flow) and (2) a combination method with physical limitations regarding separation of the singular hydrograph into multi-layer release hydrographs for sediment control. This study employed the featured signals obtained from statistical quartiles/sediment duration curve in mesh segmentation, and an iterative optimization model with a sediment unit response matrix and corresponding geophysical-based acceleration factors, for efficient parameter calibration. This research applied the developed methodology to the Shihmen Reservoir basin in Taiwan. The trade-off analytical results using Typhoons Sinlaku and Jangmi as case examples revealed that owing to gravity current and re-suspension effects, Phase I + II can de-silt safely without violating the intake's turbidity limitation before reservoir discharge reaches 2238 m3/s; however, Phase III can only de-silt after the release at spillway reaches 827 m3/s, and before reservoir discharge reaches 1924 m3/s, with corresponding maximum desiltation ratio being 0.221 and 0.323, respectively. Moreover, the model construction results demonstrated that the self-adaption/fuzzy inference of ANFIS can effectively simulate the SC hydrograph in an unsteady state for suspended load-dominated water bodies, and that the real-time recurrent deterministic routing of RTRLNN can accurately simulate that of a bedload-dominated flow regime.

First light - II. Emission line extinction, population III stars, and X-ray binaries

NASA Astrophysics Data System (ADS)

Barrow, Kirk S. S.; Wise, John H.; Aykutalp, Aycin; O'Shea, Brian W.; Norman, Michael L.; Xu, Hao

2018-02-01

We produce synthetic spectra and observations for metal-free stellar populations and high-mass X-ray binaries in the Renaissance Simulations at a redshift of 15. We extend our methodology from the first paper in the series by modelling the production and extinction of emission lines throughout a dusty and metal-enriched interstellar and circum-galactic media extracted from the simulation, using a Monte Carlo calculation. To capture the impact of high-energy photons, we include all frequencies from hard X-ray to far-infrared with enough frequency resolution to discern line emission and absorption profiles. The most common lines in our sample in order of their rate of occurrence are Ly α, the C IV λλ1548, 1551 doublet, H α, and the Ca II λλλ8498, 8542, 8662 triplet. The best scenario for a direct observation of a metal-free stellar population is a merger between two Population III Galaxies. In mergers between metal-enriched and metal-free stellar populations, some characteristics may be inferred indirectly. Single Population III galaxies are too dim to be observed photometrically at z = 15. Ly α emission is discernible by JWST as an increase in J200w - J277w colour off the intrinsic stellar tracks. Observations of metal-free stars will be difficult, though not impossible, with the next generation of space telescopes.

First Light II: Emission Line Extinction, Population III Stars, and X-ray Binaries

DOE PAGES

Barrow, Kirk S. S.; Wise, John H.; Aykutalp, Aycin; ...

2017-11-17

Here, we produce synthetic spectra and observations for metal-free stellar populations and high-mass X-ray binaries in the Renaissance Simulations at a redshift of 15. We extend our methodology from the first paper in the series by modelling the production and extinction of emission lines throughout a dusty and metal-enriched interstellar and circum-galactic media extracted from the simulation, using a Monte Carlo calculation. To capture the impact of high-energy photons, we include all frequencies from hard X-ray to far-infrared with enough frequency resolution to discern line emission and absorption profiles. The most common lines in our sample in order of theirmore » rate of occurrence are Ly α, the C iv λλ1548, 1551 doublet, H α, and the Ca ii λλλ8498, 8542, 8662 triplet. The best scenario for a direct observation of a metal-free stellar population is a merger between two Population III Galaxies. In mergers between metal-enriched and metal-free stellar populations, some characteristics may be inferred indirectly. Single Population III galaxies are too dim to be observed photometrically at z = 15. Ly α emission is discernible by JWST as an increase in J200w – J277w colour off the intrinsic stellar tracks. Observations of metal-free stars will be difficult, though not impossible, with the next generation of space telescopes.« less

First Light II: Emission Line Extinction, Population III Stars, and X-ray Binaries

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

Barrow, Kirk S. S.; Wise, John H.; Aykutalp, Aycin

Here, we produce synthetic spectra and observations for metal-free stellar populations and high-mass X-ray binaries in the Renaissance Simulations at a redshift of 15. We extend our methodology from the first paper in the series by modelling the production and extinction of emission lines throughout a dusty and metal-enriched interstellar and circum-galactic media extracted from the simulation, using a Monte Carlo calculation. To capture the impact of high-energy photons, we include all frequencies from hard X-ray to far-infrared with enough frequency resolution to discern line emission and absorption profiles. The most common lines in our sample in order of theirmore » rate of occurrence are Ly α, the C iv λλ1548, 1551 doublet, H α, and the Ca ii λλλ8498, 8542, 8662 triplet. The best scenario for a direct observation of a metal-free stellar population is a merger between two Population III Galaxies. In mergers between metal-enriched and metal-free stellar populations, some characteristics may be inferred indirectly. Single Population III galaxies are too dim to be observed photometrically at z = 15. Ly α emission is discernible by JWST as an increase in J200w – J277w colour off the intrinsic stellar tracks. Observations of metal-free stars will be difficult, though not impossible, with the next generation of space telescopes.« less

Three-Dimensional Computer Model of the Right Atrium Including the Sinoatrial and Atrioventricular Nodes Predicts Classical Nodal Behaviours

PubMed Central

Li, Jue; Inada, Shin; Schneider, Jurgen E.; Zhang, Henggui; Dobrzynski, Halina; Boyett, Mark R.

2014-01-01

The aim of the study was to develop a three-dimensional (3D) anatomically-detailed model of the rabbit right atrium containing the sinoatrial and atrioventricular nodes to study the electrophysiology of the nodes. A model was generated based on 3D images of a rabbit heart (atria and part of ventricles), obtained using high-resolution magnetic resonance imaging. Segmentation was carried out semi-manually. A 3D right atrium array model (∼3.16 million elements), including eighteen objects, was constructed. For description of cellular electrophysiology, the Rogers-modified FitzHugh-Nagumo model was further modified to allow control of the major characteristics of the action potential with relatively low computational resource requirements. Model parameters were chosen to simulate the action potentials in the sinoatrial node, atrial muscle, inferior nodal extension and penetrating bundle. The block zone was simulated as passive tissue. The sinoatrial node, crista terminalis, main branch and roof bundle were considered as anisotropic. We have simulated normal and abnormal electrophysiology of the two nodes. In accordance with experimental findings: (i) during sinus rhythm, conduction occurs down the interatrial septum and into the atrioventricular node via the fast pathway (conduction down the crista terminalis and into the atrioventricular node via the slow pathway is slower); (ii) during atrial fibrillation, the sinoatrial node is protected from overdrive by its long refractory period; and (iii) during atrial fibrillation, the atrioventricular node reduces the frequency of action potentials reaching the ventricles. The model is able to simulate ventricular echo beats. In summary, a 3D anatomical model of the right atrium containing the cardiac conduction system is able to simulate a wide range of classical nodal behaviours. PMID:25380074

Arsenic removal with iron(II) and iron(III) in waters with high silicate and phosphate concentrations.

PubMed

Roberts, Linda C; Hug, Stephan J; Ruettimann, Thomas; Billah, Morsaline; Khan, Abdul Wahab; Rahman, Mohammad Tariqur

2004-01-01

Arsenic removal by passive treatment, in which naturally present Fe(II) is oxidized by aeration and the forming iron(III) (hydr)oxides precipitate with adsorbed arsenic, is the simplest conceivable water treatment option. However, competing anions and low iron concentrations often require additional iron. Application of Fe(II) instead of the usually applied Fe(III) is shown to be advantageous, as oxidation of Fe(II) by dissolved oxygen causes partial oxidation of As(III) and iron(III) (hydr)oxides formed from Fe(II) have higher sorption capacities. In simulated groundwater (8.2 mM HCO3(-), 2.5 mM Ca2+, 1.6 mM Mg2+, 30 mg/L Si, 3 mg/L P, 500 ppb As(III), or As(V), pH 7.0 +/- 0.1), addition of Fe(II) clearly leads to better As removal than Fe(III). Multiple additions of Fe(II) further improved the removal of As(II). A competitive coprecipitation model that considers As(III) oxidation explains the observed results and allows the estimation of arsenic removal under different conditions. Lowering 500 microg/L As(III) to below 50 microg/L As(tot) in filtered water required > 80 mg/L Fe(III), 50-55 mg/L Fe(II) in one single addition, and 20-25 mg/L in multiple additions. With As(V), 10-12 mg/L Fe(II) and 15-18 mg/L Fe(III) was required. In the absence of Si and P, removal efficiencies for Fe(II) and Fe(III) were similar: 30-40 mg/L was required for As(II), and 2.0-2.5 mg/L was required for As(V). In a field study with 22 tubewells in Bangladesh, passive treatment efficiently removed phosphate, but iron contents were generally too low for efficient arsenic removal.

Simulated potential for enhanced performance of mechanically stacked hybrid III-V/Si tandem photovoltaic modules using DC-DC converters

NASA Astrophysics Data System (ADS)

MacAlpine, Sara; Bobela, David C.; Kurtz, Sarah; Lumb, Matthew P.; Schmieder, Kenneth J.; Moore, James E.; Walters, Robert J.; Alberi, Kirstin

2017-10-01

This work examines a tandem module design with GaInP2 mechanically stacked on top of crystalline Si, using a detailed photovoltaic (PV) system model to simulate four-terminal (4T) unconstrained and two-terminal voltage-matched (2T VM) parallel architectures. Module-level power electronics is proposed for the 2T VM module design to enhance its performance over the breadth of temperatures experienced by a typical PV installation. Annual, hourly simulations of various scenarios indicate that this design can reduce annual energy losses to ˜0.5% relative to the 4T module configuration. Consideration is given to both performance and practical design for building or ground mount installations, emphasizing compatibility with existing standard Si modules.

The importance of ligand speciation in environmental research: a case study.

PubMed

Sillanpää, M; Orama, M; Rämö, J; Oikari, A

2001-02-21

The speciations of EDTA and DTPA in process, waste and river waters are modelled and simulated, specifically to the mode of occurrence in the pulp and paper mill effluents and subsequently in receiving waters. Due to relatively short residence times in bleaching process and waste water treatment and slow exchange kinetics, it is expected that the thermodynamic equilibrium is not necessarily reached. Therefore, the initial speciation plays a key role. As such, the simulations have been extended to the process waters of the pulp and paper industry taking into account estimated average conditions. The results reveal that the main species are; Mn and Ca complexes of EDTA and DTPA in pulp mill process waters; Fe(III) and Mn complexes of EDTA and DTPA in waste waters; Fe(III) and Zn complexes of EDTA and DTPA in receiving waters. It is also shown how the increasing concentration of complexing agents effects the speciation. Alkaline earth metal chelation plays a significant role in the speciation of EDTA and DTPA when there is a noticeable molar excess of complexing agents compared with transition metals.

Exchange Interactions on the Highest-Spin Reported Molecule: the Mixed-Valence Fe42 Complex

NASA Astrophysics Data System (ADS)

Aravena, Daniel; Venegas-Yazigi, Diego; Ruiz, Eliseo

2016-04-01

The finding of high-spin molecules that could behave as conventional magnets has been one of the main challenges in Molecular Magnetism. Here, the exchange interactions, present in the highest-spin molecule published in the literature, Fe42, have been analysed using theoretical methods based on Density Functional Theory. The system with a total spin value S = 45 is formed by 42 iron centres containing 18 high-spin FeIII ferromagnetically coupled and 24 diamagnetic low-spin FeII ions. The bridging ligands between the two paramagnetic centres are two cyanide ligands coordinated to the diamagnetic FeII cations. Calculations were performed using either small Fe4 or Fe3 models or the whole Fe42 complex, showing the presence of two different ferromagnetic couplings between the paramagnetic FeIII centres. Finally, Quantum Monte Carlo simulations for the whole system were carried out in order to compare the experimental and simulated magnetic susceptibility curves from the calculated exchange coupling constants with the experimental one. This comparison allows for the evaluation of the accuracy of different exchange-correlation functionals to reproduce such magnetic properties.

Studies of a subarctic coastal marsh. III. Modelling the subsurface water fluxes and chloride distribution

NASA Astrophysics Data System (ADS)

Price, Jonathan S.; Woo, Ming-Ko

1990-12-01

A two-dimensional advection dispersion model of solute transport is used to simulate the long-term changes in the chloride distribution of the young isostatically raised beach ridge and depression sequences in a James Bay coastal marsh. The USGS-SUTRA model reproduces the hydraulic conditions in the wetland, causing recharge of freshwater to the ridges and discharge of saline water to the inter-ridge depressions, demonstrating the importance of vertical water fluxes of water and chloride. Even though water velocities are very low, molecular diffusion alone cannot explain the observed chloride distribution. Imposing the characteristics of a frozen surface during winter eliminated the vertical fluxes, and doubled the time required for the simulated chloride distribution to match the field data. The model correctly predicts the observed pattern of suppressed salinity beneath the ridges and a general decrease of salinity with distance inland. The results are useful in understanding the processes which operate in the first 100 years of marsh development.

Towards understanding of magnetization reversal in Nd-Fe-B nanocomposites: analysis by high-throughput micromagnetic simulations

NASA Astrophysics Data System (ADS)

Erokhin, Sergey; Berkov, Dmitry; Ito, Masaaki; Kato, Akira; Yano, Masao; Michels, Andreas

2018-03-01

We demonstrate how micromagnetic simulations can be employed in order to characterize and analyze the magnetic microstructure of nanocomposites. For the example of nanocrystalline Nd-Fe-B, which is a potential material for future permanent-magnet applications, we have compared three different models for the micromagnetic analysis of this material class: (i) a description of the nanocomposite microstructure in terms of Stoner-Wohlfarth particles with and without the magnetodipolar interaction; (ii) a model based on the core-shell representation of the nanograins; (iii) the latter model including a contribution of superparamagnetic clusters. The relevant parameter spaces have been systematically scanned with the aim to establish which micromagnetic approach can most adequately describe experimental data for this material. According to our results, only the last, most sophisticated model is able to provide an excellent agreement with the measured hysteresis loop. The presented methodology is generally applicable to multiphase magnetic nanocomposites and it highligths the complex interrelationship between the microstructure, magnetic interactions, and the macroscopic magnetic properties.

FATE-HD: A spatially and temporally explicit integrated model for predicting vegetation structure and diversity at regional scale

PubMed Central

Isabelle, Boulangeat; Damien, Georges; Wilfried, Thuiller

2014-01-01

During the last decade, despite strenuous efforts to develop new models and compare different approaches, few conclusions have been drawn on their ability to provide robust biodiversity projections in an environmental change context. The recurring suggestions are that models should explicitly (i) include spatiotemporal dynamics; (ii) consider multiple species in interactions; and (iii) account for the processes shaping biodiversity distribution. This paper presents a biodiversity model (FATE-HD) that meets this challenge at regional scale by combining phenomenological and process-based approaches and using well-defined plant functional groups. FATE-HD has been tested and validated in a French National Park, demonstrating its ability to simulate vegetation dynamics, structure and diversity in response to disturbances and climate change. The analysis demonstrated the importance of considering biotic interactions, spatio-temporal dynamics, and disturbances in addition to abiotic drivers to simulate vegetation dynamics. The distribution of pioneer trees was particularly improved, as were all undergrowth functional groups. PMID:24214499

Computational Toxicology of Chloroform: Reverse Dosimetry Using Bayesian Inference, Markov Chain Monte Carlo Simulation, and Human Biomonitoring Data

PubMed Central

Lyons, Michael A.; Yang, Raymond S.H.; Mayeno, Arthur N.; Reisfeld, Brad

2008-01-01

Background One problem of interpreting population-based biomonitoring data is the reconstruction of corresponding external exposure in cases where no such data are available. Objectives We demonstrate the use of a computational framework that integrates physiologically based pharmacokinetic (PBPK) modeling, Bayesian inference, and Markov chain Monte Carlo simulation to obtain a population estimate of environmental chloroform source concentrations consistent with human biomonitoring data. The biomonitoring data consist of chloroform blood concentrations measured as part of the Third National Health and Nutrition Examination Survey (NHANES III), and for which no corresponding exposure data were collected. Methods We used a combined PBPK and shower exposure model to consider several routes and sources of exposure: ingestion of tap water, inhalation of ambient household air, and inhalation and dermal absorption while showering. We determined posterior distributions for chloroform concentration in tap water and ambient household air using U.S. Environmental Protection Agency Total Exposure Assessment Methodology (TEAM) data as prior distributions for the Bayesian analysis. Results Posterior distributions for exposure indicate that 95% of the population represented by the NHANES III data had likely chloroform exposures ≤ 67 μg/L in tap water and ≤ 0.02 μg/L in ambient household air. Conclusions Our results demonstrate the application of computer simulation to aid in the interpretation of human biomonitoring data in the context of the exposure–health evaluation–risk assessment continuum. These results should be considered as a demonstration of the method and can be improved with the addition of more detailed data. PMID:18709138

Fast Particle Methods for Multiscale Phenomena Simulations

NASA Technical Reports Server (NTRS)

Koumoutsakos, P.; Wray, A.; Shariff, K.; Pohorille, Andrew

2000-01-01

We are developing particle methods oriented at improving computational modeling capabilities of multiscale physical phenomena in : (i) high Reynolds number unsteady vortical flows, (ii) particle laden and interfacial flows, (iii)molecular dynamics studies of nanoscale droplets and studies of the structure, functions, and evolution of the earliest living cell. The unifying computational approach involves particle methods implemented in parallel computer architectures. The inherent adaptivity, robustness and efficiency of particle methods makes them a multidisciplinary computational tool capable of bridging the gap of micro-scale and continuum flow simulations. Using efficient tree data structures, multipole expansion algorithms, and improved particle-grid interpolation, particle methods allow for simulations using millions of computational elements, making possible the resolution of a wide range of length and time scales of these important physical phenomena.The current challenges in these simulations are in : [i] the proper formulation of particle methods in the molecular and continuous level for the discretization of the governing equations [ii] the resolution of the wide range of time and length scales governing the phenomena under investigation. [iii] the minimization of numerical artifacts that may interfere with the physics of the systems under consideration. [iv] the parallelization of processes such as tree traversal and grid-particle interpolations We are conducting simulations using vortex methods, molecular dynamics and smooth particle hydrodynamics, exploiting their unifying concepts such as : the solution of the N-body problem in parallel computers, highly accurate particle-particle and grid-particle interpolations, parallel FFT's and the formulation of processes such as diffusion in the context of particle methods. This approach enables us to transcend among seemingly unrelated areas of research.

Pair-instability supernovae of fast rotating stars

NASA Astrophysics Data System (ADS)

Chen, Ke-Jung

2015-01-01

We present 2D simulations of pair-instability supernovae considering rapid rotation during their explosion phases. Recent studies of the Population III (Pop III) star formation suggested that these stars could be born with a mass scale about 100 M⊙ and with a strong rotation. Based on stellar evolution models, these massive Pop III stars might have died as highly energetic pair-instability supernovae. We perform 2D calculations to investigate the impact of rotation on pair-instability supernovae. Our results suggest that rotation leads to an aspherical explosion due to an anisotropic collapse. If the first stars have a 50% of keplerian rotational rate of the oxygen core before their pair-instability explosions, the overall 56Ni production can be significantly reduced by about two orders of magnitude. An extreme case of 100% keplerian rotational rate shows an interesting feature of fluid instabilities along the equatorial plane caused by non-synchronized and non-isotropic ignitions of explosions, so that the shocks run into the in-falling gas and generate the Richtmyer-Meshkov instability.

MAVIS III -- A Windows 95/NT Upgrade

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

Hardwick, M.F.

1997-12-01

MAVIS (Modeling and Analysis of Explosive Valve Interactions) is a computer program that simulates operation of explosively actuated valve. MAVIS was originally written in Fortran in the mid 1970`s and was primarily run on the Sandia Vax computers in use through the early 1990`s. During the mid to late 1980`s MAVIS was upgraded to include the effects of plastic deformation and it became MAVIS II. When the Vax computers were retired, the Gas Transfer System (GTS) Development Department ported the code to the Macintosh and PC platforms, where it ran as a simple console application. All graphical output was lostmore » during these ports. GTS code developers recently completed an upgrade that provides a Windows 95/NT MAVIS application and restores all of the original graphical output. This upgrade is called MAVIS III version 1.0. This report serves both as a user`s manual for MAVIS III v 1.0 and as a general software development reference.« less

A theoretical study on the mechanistic highlights behind the Brønsted-acid dependent mer-fac isomerization of homoleptic carbenic iridium complexes for PhOLEDs.

PubMed

Setzer, Tobias; Lennartz, Christian; Dreuw, Andreas

2017-06-06

Recently, a successful Brønsted-acid mediated geometric isomerization of the meridional homoleptic carbenic iridium(iii) complexes tris-(N-phenyl,N-methyl-benzimidazol-2-yl)iridium(iii) (1) and tris-(N-phenyl,N-benzyl-benzimidazol-2-yl)iridium(iii) (2) into their facial form has been reported. In the present work the pronounced acid-dependency of this particular isomerization procedure is revisited and additional mechanistic pathways are taken into account. Moreover, the acid-induced material decomposition is addressed. All calculations are carried out using density functional theory (DFT) while the environmental effects in solution are accounted for by the COSMO-RS model. The simulated results clearly reveal the outstanding importance of the complex interplay between acid strength, coordinating power of the corresponding base and the steric influence of the ligand system in contrast to the plain calculation of minimum energy pathways for selected complexes. Eventually, general rules to enhance the material-specific reaction yields are provided.

Performance evaluation of WAVEWATCH III model in the Persian Gulf using different wind resources

NASA Astrophysics Data System (ADS)

Kazeminezhad, Mohammad Hossein; Siadatmousavi, Seyed Mostafa

2017-07-01

The third-generation wave model, WAVEWATCH III, was employed to simulate bulk wave parameters in the Persian Gulf using three different wind sources: ERA-Interim, CCMP, and GFS-Analysis. Different formulations for whitecapping term and the energy transfer from wind to wave were used, namely the Tolman and Chalikov (J Phys Oceanogr 26:497-518, 1996), WAM cycle 4 (BJA and WAM4), and Ardhuin et al. (J Phys Oceanogr 40(9):1917-1941, 2010) (TEST405 and TEST451 parameterizations) source term packages. The obtained results from numerical simulations were compared to altimeter-derived significant wave heights and measured wave parameters at two stations in the northern part of the Persian Gulf through statistical indicators and the Taylor diagram. Comparison of the bulk wave parameters with measured values showed underestimation of wave height using all wind sources. However, the performance of the model was best when GFS-Analysis wind data were used. In general, when wind veering from southeast to northwest occurred, and wind speed was high during the rotation, the model underestimation of wave height was severe. Except for the Tolman and Chalikov (J Phys Oceanogr 26:497-518, 1996) source term package, which severely underestimated the bulk wave parameters during stormy condition, the performances of other formulations were practically similar. However, in terms of statistics, the Ardhuin et al. (J Phys Oceanogr 40(9):1917-1941, 2010) source terms with TEST405 parameterization were the most successful formulation in the Persian Gulf when compared to in situ and altimeter-derived observations.

Synaptic Plasticity and Memory Formation

DTIC Science & Technology

1994-05-31

manipulations affected the waveform of the isolated response: i) a drug ( aniracetam ) known to prolong the mean open time of the receptors, ii) LTP and iii...LTP and aniracetam combined. In agreement with our previous reports, LTP was found to produce a characteristic distortion of the waveform of the... aniracetam and LTP was readily accounted for by the computer simulation of the AMPA receptor when LTP was modelled as an increase in the rate constants

Extensions and Adjuncts to the BRL-COMGEOM Program

DTIC Science & Technology

1974-08-01

m MAGIC Code, GIFT Code, Computer Simulation, Target Description, Geometric Modeling Techniques, Vulnerability Analysis 20...Arbitrary Quadric Surf ace.. 0Oo „<>. 7 III. BRITL: A GEOMETRY PREPROCESSOR PROGRAM FOR INPUT TO THE GIFT SYSTEM „ 0 18 A. Introduction <, „. ° 18 B...the BRL- GIFT code. The tasks completed under this contract and described in the report are: Ao The addition to the list of available body types

Evaluation of fracture resistance in simulated immature teeth using Resilon and Ribbond as root reinforcements--an in vitro study.

PubMed

Hemalatha, Hiremath; Sandeep, Metgud; Kulkarni, Sadanand; Yakub, Shoeb Sheikh

2009-08-01

To compare the reinforcement and strengthening ability of resilon, gutta-percha, and ribbond in endodontically treated roots of immature teeth. Sixty five freshly extracted human maxillary anterior teeth were prepared with a Peeso no. 6 to simulate immature teeth (Cvek's stage 3 root development). After instrumentation, each root was irrigated with sodium hypochlorite and with ethylene diamino tetra acetic acid to remove the smear layer. To simulate single visit apexification technique a 4-5 mm white Pro Root mineral trioxide aggregate plug was placed apically using schilder carrier. The teeth were divided into three experimental groups and one control group. Group I--control group (root canals instrumented but not filled); Group II--backfilled with thermoplastisized gutta-percha using AH plus sealer; Group III--reinforced with Resilon using epiphany sealer; Group IV--reinforced with Ribbond fibers using Panavia F luting cement. A Universal Testing Machine was used to apply a load, at the level of the lingual cementoenamel junction with a chisel-shaped tip The peak load to fracture was recorded and statistical analysis was completed using student's t-test. Values of peak load to fracture were 1320.8, 1604.88, 1620, and 1851 newtons for Group I to Group IV respectively. The results of student's t-test, revealed no significant difference (P > 0.05,) between Group II and Group III. Comparison between Group IV and Group III and between Group IV and Group II revealed highly significant difference (P > 0.001). Teeth reinforced with Ribbond fibers using Panavia F luting cement showed the highest resistance to fracture. Resilon could not strengthen the roots and showed no statistically significant difference when compared with thermoplastisized gutta-percha in reinforcing immature tooth when tested with universal testing machine in an experimental model of immature tooth.

VBA: A Probabilistic Treatment of Nonlinear Models for Neurobiological and Behavioural Data

PubMed Central

Daunizeau, Jean; Adam, Vincent; Rigoux, Lionel

2014-01-01

This work is in line with an on-going effort tending toward a computational (quantitative and refutable) understanding of human neuro-cognitive processes. Many sophisticated models for behavioural and neurobiological data have flourished during the past decade. Most of these models are partly unspecified (i.e. they have unknown parameters) and nonlinear. This makes them difficult to peer with a formal statistical data analysis framework. In turn, this compromises the reproducibility of model-based empirical studies. This work exposes a software toolbox that provides generic, efficient and robust probabilistic solutions to the three problems of model-based analysis of empirical data: (i) data simulation, (ii) parameter estimation/model selection, and (iii) experimental design optimization. PMID:24465198

Overview of experiment design and comparison of models participating in phase 1 of the SPARC Quasi-Biennial Oscillation initiative (QBOi)

NASA Astrophysics Data System (ADS)

Butchart, Neal; Anstey, James A.; Hamilton, Kevin; Osprey, Scott; McLandress, Charles; Bushell, Andrew C.; Kawatani, Yoshio; Kim, Young-Ha; Lott, Francois; Scinocca, John; Stockdale, Timothy N.; Andrews, Martin; Bellprat, Omar; Braesicke, Peter; Cagnazzo, Chiara; Chen, Chih-Chieh; Chun, Hye-Yeong; Dobrynin, Mikhail; Garcia, Rolando R.; Garcia-Serrano, Javier; Gray, Lesley J.; Holt, Laura; Kerzenmacher, Tobias; Naoe, Hiroaki; Pohlmann, Holger; Richter, Jadwiga H.; Scaife, Adam A.; Schenzinger, Verena; Serva, Federico; Versick, Stefan; Watanabe, Shingo; Yoshida, Kohei; Yukimoto, Seiji

2018-03-01

The Stratosphere-troposphere Processes And their Role in Climate (SPARC) Quasi-Biennial Oscillation initiative (QBOi) aims to improve the fidelity of tropical stratospheric variability in general circulation and Earth system models by conducting coordinated numerical experiments and analysis. In the equatorial stratosphere, the QBO is the most conspicuous mode of variability. Five coordinated experiments have therefore been designed to (i) evaluate and compare the verisimilitude of modelled QBOs under present-day conditions, (ii) identify robustness (or alternatively the spread and uncertainty) in the simulated QBO response to commonly imposed changes in model climate forcings (e.g. a doubling of CO2 amounts), and (iii) examine model dependence of QBO predictability. This paper documents these experiments and the recommended output diagnostics. The rationale behind the experimental design and choice of diagnostics is presented. To facilitate scientific interpretation of the results in other planned QBOi studies, consistent descriptions of the models performing each experiment set are given, with those aspects particularly relevant for simulating the QBO tabulated for easy comparison.

A study of cloud microphysics and precipitation over the Tibetan Plateau by radar observations and cloud-resolving model simulations: Cloud Microphysics over Tibetan Plateau

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

Gao, Wenhua; Sui, Chung-Hsiung; Fan, Jiwen

Cloud microphysical properties and precipitation over the Tibetan Plateau (TP) are unique because of the high terrains, clean atmosphere, and sufficient water vapor. With dual-polarization precipitation radar and cloud radar measurements during the Third Tibetan Plateau Atmospheric Scientific Experiment (TIPEX-III), the simulated microphysics and precipitation by the Weather Research and Forecasting model (WRF) with the Chinese Academy of Meteorological Sciences (CAMS) microphysics and other microphysical schemes are investigated through a typical plateau rainfall event on 22 July 2014. Results show that the WRF-CAMS simulation reasonably reproduces the spatial distribution of 24-h accumulated precipitation, but has limitations in simulating time evolutionmore » of precipitation rates. The model-calculated polarimetric radar variables have biases as well, suggesting bias in modeled hydrometeor types. The raindrop sizes in convective region are larger than those in stratiform region indicated by the small intercept of raindrop size distribution in the former. The sensitivity experiments show that precipitation processes are sensitive to the changes of warm rain processes in condensation and nucleated droplet size (but less sensitive to evaporation process). Increasing droplet condensation produces the best area-averaged rain rate during weak convection period compared with the observation, suggesting a considerable bias in thermodynamics in the baseline simulation. Increasing the initial cloud droplet size causes the rain rate reduced by half, an opposite effect to that of increasing droplet condensation.« less

Solar Magnetic Carpet III: Coronal Modelling of Synthetic Magnetograms

NASA Astrophysics Data System (ADS)

Meyer, K. A.; Mackay, D. H.; van Ballegooijen, A. A.; Parnell, C. E.

2013-09-01

This article is the third in a series working towards the construction of a realistic, evolving, non-linear force-free coronal-field model for the solar magnetic carpet. Here, we present preliminary results of 3D time-dependent simulations of the small-scale coronal field of the magnetic carpet. Four simulations are considered, each with the same evolving photospheric boundary condition: a 48-hour time series of synthetic magnetograms produced from the model of Meyer et al. ( Solar Phys. 272, 29, 2011). Three simulations include a uniform, overlying coronal magnetic field of differing strength, the fourth simulation includes no overlying field. The build-up, storage, and dissipation of magnetic energy within the simulations is studied. In particular, we study their dependence upon the evolution of the photospheric magnetic field and the strength of the overlying coronal field. We also consider where energy is stored and dissipated within the coronal field. The free magnetic energy built up is found to be more than sufficient to power small-scale, transient phenomena such as nanoflares and X-ray bright points, with the bulk of the free energy found to be stored low down, between 0.5 - 0.8 Mm. The energy dissipated is currently found to be too small to account for the heating of the entire quiet-Sun corona. However, the form and location of energy-dissipation regions qualitatively agree with what is observed on small scales on the Sun. Future MHD modelling using the same synthetic magnetograms may lead to a higher energy release.

Modelling energy costs for different operational strategies of a large water resource recovery facility.

PubMed

Póvoa, P; Oehmen, A; Inocêncio, P; Matos, J S; Frazão, A

2017-05-01

The main objective of this paper is to demonstrate the importance of applying dynamic modelling and real energy prices on a full scale water resource recovery facility (WRRF) for the evaluation of control strategies in terms of energy costs with aeration. The Activated Sludge Model No. 1 (ASM1) was coupled with real energy pricing and a power consumption model and applied as a dynamic simulation case study. The model calibration is based on the STOWA protocol. The case study investigates the importance of providing real energy pricing comparing (i) real energy pricing, (ii) weighted arithmetic mean energy pricing and (iii) arithmetic mean energy pricing. The operational strategies evaluated were (i) old versus new air diffusers, (ii) different DO set-points and (iii) implementation of a carbon removal controller based on nitrate sensor readings. The application in a full scale WRRF of the ASM1 model coupled with real energy costs was successful. Dynamic modelling with real energy pricing instead of constant energy pricing enables the wastewater utility to optimize energy consumption according to the real energy price structure. Specific energy cost allows the identification of time periods with potential for linking WRRF with the electric grid to optimize the treatment costs, satisfying operational goals.

The All-Particle Spectrum of Primary Cosmic Rays in the Wide Energy Range from 10{sup 14} to 10{sup 17} eV Observed with the Tibet-III Air-Shower Array

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

Amenomori, M.; Bi, X. J.; Ding, L. K.

2008-05-10

We present an updated all-particle energy spectrum of primary cosmic rays in a wide range from 10{sup 14} to 10{sup 17} eV using 5.5 x 10{sup 7} events collected from 2000 November through 2004 October by the Tibet-III air-shower array located 4300 m above sea level (an atmospheric depth of 606 g cm{sup -2}). The size spectrum exhibits a sharp knee at a corresponding primary energy around 4 PeV. This work uses increased statistics and new simulation calculations for the analysis. We discuss our extensive Monte Carlo calculations and the model dependencies involved in the final result, assuming interaction modelsmore » QGSJET01c and SIBYLL2.1, and heavy dominant (HD) and proton dominant (PD) primary composition models. Pure proton and pure iron primary models are also examined as extreme cases. A detector simulation was also performed to improve our accuracy in determining the size of the air showers and the energy of the primary particle. We confirmed that the all-particle energy spectra obtained under various plausible model parameters are not significantly different from each other, which was the expected result given the characteristics of the experiment at high altitude, where the air showers of the primary energy around the knee reach near-maximum development, with their features dominated by electromagnetic components, leading to a weak dependence on the interaction model or the primary mass. This is the highest statistical and the best systematics-controlled measurement covering the widest energy range around the knee energy region.« less

Constraints on hydrodynamical subgrid models from quasar absorption line studies of the simulated circumgalactic medium

NASA Astrophysics Data System (ADS)

Hummels, Cameron B.; Bryan, Greg L.; Smith, Britton D.; Turk, Matthew J.

2013-04-01

Cosmological hydrodynamical simulations of galaxy evolution are increasingly able to produce realistic galaxies, but the largest hurdle remaining is in constructing subgrid models that accurately describe the behaviour of stellar feedback. As an alternate way to test and calibrate such models, we propose to focus on the circumgalactic medium (CGM). To do so, we generate a suite of adaptive mesh refinement simulations for a Milky-Way-massed galaxy run to z = 0, systematically varying the feedback implementation. We then post-process the simulation data to compute the absorbing column density for a wide range of common atomic absorbers throughout the galactic halo, including H I, Mg II, Si II, Si III, Si IV, C IV, N V, O VI and O VII. The radial profiles of these atomic column densities are compared against several quasar absorption line studies to determine if one feedback prescription is favoured. We find that although our models match some of the observations (specifically those ions with lower ionization strengths), it is particularly difficult to match O VI observations. There is some indication that the models with increased feedback intensity are better matches. We demonstrate that sufficient metals exist in these haloes to reproduce the observed column density distribution in principle, but the simulated CGM lacks significant multiphase substructure and is generally too hot. Furthermore, we demonstrate the failings of inflow-only models (without energetic feedback) at populating the CGM with adequate metals to match observations even in the presence of multiphase structure. Additionally, we briefly investigate the evolution of the CGM from z = 3 to present. Overall, we find that quasar absorption line observations of the gas around galaxies provide a new and important constraint on feedback models.

A NEW MODEL FOR MIXING BY DOUBLE-DIFFUSIVE CONVECTION (SEMI-CONVECTION). III. THERMAL AND COMPOSITIONAL TRANSPORT THROUGH NON-LAYERED ODDC

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

Moll, Ryan; Garaud, Pascale; Stellmach, Stephan, E-mail: rmoll@soe.ucsc.edu

2016-05-20

Oscillatory double-diffusive convection (ODDC; also known as semi-convection) refers to a type of double-diffusive instability that occurs in regions of planetary and stellar interiors that have a destabilizing thermal stratification and a stabilizing mean molecular weight stratification. In this series of papers, we use an extensive suite of three-dimensional (3D) numerical simulations to quantify the transport of heat and chemical species by ODDC. Rosenblum et al. first showed that ODDC can either spontaneously form layers that significantly enhance the transport of heat and chemical species compared to microscopic transport or remain in a state dominated by large-scale gravity waves, inmore » which there is a more modest enhancement of the turbulent transport rates. Subsequent studies in this series focused on identifying under what conditions layers form and quantifying transport through layered systems. Here we proceed to characterize transport through systems that are unstable to ODDC, but do not undergo spontaneous layer formation. We measure the thermal and compositional fluxes in non-layered ODDC from both two-dimensional (2D) and 3D numerical simulations, and show that 3D simulations are well approximated by similar simulations in a 2D domain. We find that the turbulent mixing rate in this regime is weak and can, to a first-level approximation, be neglected. We conclude by summarizing the findings of papers I through III into a single prescription for transport systems unstable to ODDC.« less

Trident: A Universal Tool for Generating Synthetic Absorption Spectra from Astrophysical Simulations

NASA Astrophysics Data System (ADS)

Hummels, Cameron B.; Smith, Britton D.; Silvia, Devin W.

2017-09-01

Hydrodynamical simulations are increasingly able to accurately model physical systems on stellar, galactic, and cosmological scales; however, the utility of these simulations is often limited by our ability to directly compare them with the data sets produced by observers: spectra, photometry, etc. To address this problem, we have created trident, a Python-based open-source tool for post-processing hydrodynamical simulations to produce synthetic absorption spectra and related data. trident can (I) create absorption-line spectra for any trajectory through a simulated data set mimicking both background quasar and down-the-barrel configurations; (II) reproduce the spectral characteristics of common instruments like the Cosmic Origins Spectrograph; (III) operate across the ultraviolet, optical, and infrared using customizable absorption-line lists; (IV) trace simulated physical structures directly to spectral features; (v) approximate the presence of ion species absent from the simulation outputs; (VI) generate column density maps for any ion; and (vii) provide support for all major astrophysical hydrodynamical codes. trident was originally developed to aid in the interpretation of observations of the circumgalactic medium and intergalactic medium, but it remains a general tool applicable in other contexts.

A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser

NASA Astrophysics Data System (ADS)

Yoon, Chun Hong; Yurkov, Mikhail V.; Schneidmiller, Evgeny A.; Samoylova, Liubov; Buzmakov, Alexey; Jurek, Zoltan; Ziaja, Beata; Santra, Robin; Loh, N. Duane; Tschentscher, Thomas; Mancuso, Adrian P.

2016-04-01

The advent of newer, brighter, and more coherent X-ray sources, such as X-ray Free-Electron Lasers (XFELs), represents a tremendous growth in the potential to apply coherent X-rays to determine the structure of materials from the micron-scale down to the Angstrom-scale. There is a significant need for a multi-physics simulation framework to perform source-to-detector simulations for a single particle imaging experiment, including (i) the multidimensional simulation of the X-ray source; (ii) simulation of the wave-optics propagation of the coherent XFEL beams; (iii) atomistic modelling of photon-material interactions; (iv) simulation of the time-dependent diffraction process, including incoherent scattering; (v) assembling noisy and incomplete diffraction intensities into a three-dimensional data set using the Expansion-Maximisation-Compression (EMC) algorithm and (vi) phase retrieval to obtain structural information. We demonstrate the framework by simulating a single-particle experiment for a nitrogenase iron protein using parameters of the SPB/SFX instrument of the European XFEL. This exercise demonstrably yields interpretable consequences for structure determination that are crucial yet currently unavailable for experiment design.

Elastic behavior of a red blood cell with the membrane's nonuniform natural state: equilibrium shape, motion transition under shear flow, and elongation during tank-treading motion.

PubMed

Tsubota, Ken-Ichi; Wada, Shigeo; Liu, Hao

2014-08-01

Direct numerical simulations of the mechanics of a single red blood cell (RBC) were performed by considering the nonuniform natural state of the elastic membrane. A RBC was modeled as an incompressible viscous fluid encapsulated by an elastic membrane. The in-plane shear and area dilatation deformations of the membrane were modeled by Skalak constitutive equation, while out-of-plane bending deformation was formulated by the spring model. The natural state of the membrane with respect to in-plane shear deformation was modeled as a sphere ([Formula: see text]), biconcave disk shape ([Formula: see text]) and their intermediate shapes ([Formula: see text]) with the nonuniformity parameter [Formula: see text], while the natural state with respect to out-of-plane bending deformation was modeled as a flat plane. According to the numerical simulations, at an experimentally measured in-plane shear modulus of [Formula: see text] and an out-of-plane bending rigidity of [Formula: see text] of the cell membrane, the following results were obtained. (i) The RBC shape at equilibrium was biconcave discoid for [Formula: see text] and cupped otherwise; (ii) the experimentally measured fluid shear stress at the transition between tumbling and tank-treading motions under shear flow was reproduced for [Formula: see text]; (iii) the elongation deformation of the RBC during tank-treading motion from the simulation was consistent with that from in vitro experiments, irrespective of the [Formula: see text] value. Based on our RBC modeling, the three phenomena (i), (ii), and (iii) were mechanically consistent for [Formula: see text]. The condition [Formula: see text] precludes a biconcave discoid shape at equilibrium (i); however, it gives appropriate fluid shear stress at the motion transition under shear flow (ii), suggesting that a combined effect of [Formula: see text] and the natural state with respect to out-of-plane bending deformation is necessary for understanding details of the RBC mechanics at equilibrium. Our numerical results demonstrate that moderate nonuniformity in a membrane's natural state with respect to in-plane shear deformation plays a key role in RBC mechanics.

Angular radiation temperature simulation for time-dependent capsule drive prediction in inertial confinement fusion

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

Jing, Longfei; Yang, Dong; Li, Hang

2015-02-15

The x-ray drive on a capsule in an inertial confinement fusion setup is crucial for ignition. Unfortunately, a direct measurement has not been possible so far. We propose an angular radiation temperature simulation to predict the time-dependent drive on the capsule. A simple model, based on the view-factor method for the simulation of the radiation temperature, is presented and compared with the experimental data obtained using the OMEGA laser facility and the simulation results acquired with VISRAD code. We found a good agreement between the time-dependent measurements and the simulation results obtained using this model. The validated model was thenmore » used to analyze the experimental results from the Shenguang-III prototype laser facility. More specifically, the variations of the peak radiation temperatures at different view angles with the albedo of the hohlraum, the motion of the laser spots, the closure of the laser entrance holes, and the deviation of the laser power were investigated. Furthermore, the time-dependent radiation temperature at different orientations and the drive history on the capsule were calculated. The results indicate that the radiation temperature from “U20W112” (named according to the diagnostic hole ID on the target chamber) can be used to approximately predict the drive temperature on the capsule. In addition, the influence of the capsule on the peak radiation temperature is also presented.« less

A big data approach to the development of mixed-effects models for seizure count data.

PubMed

Tharayil, Joseph J; Chiang, Sharon; Moss, Robert; Stern, John M; Theodore, William H; Goldenholz, Daniel M

2017-05-01

Our objective was to develop a generalized linear mixed model for predicting seizure count that is useful in the design and analysis of clinical trials. This model also may benefit the design and interpretation of seizure-recording paradigms. Most existing seizure count models do not include children, and there is currently no consensus regarding the most suitable model that can be applied to children and adults. Therefore, an additional objective was to develop a model that accounts for both adult and pediatric epilepsy. Using data from SeizureTracker.com, a patient-reported seizure diary tool with >1.2 million recorded seizures across 8 years, we evaluated the appropriateness of Poisson, negative binomial, zero-inflated negative binomial, and modified negative binomial models for seizure count data based on minimization of the Bayesian information criterion. Generalized linear mixed-effects models were used to account for demographic and etiologic covariates and for autocorrelation structure. Holdout cross-validation was used to evaluate predictive accuracy in simulating seizure frequencies. For both adults and children, we found that a negative binomial model with autocorrelation over 1 day was optimal. Using holdout cross-validation, the proposed model was found to provide accurate simulation of seizure counts for patients with up to four seizures per day. The optimal model can be used to generate more realistic simulated patient data with very few input parameters. The availability of a parsimonious, realistic virtual patient model can be of great utility in simulations of phase II/III clinical trials, epilepsy monitoring units, outpatient biosensors, and mobile Health (mHealth) applications. Wiley Periodicals, Inc. © 2017 International League Against Epilepsy.

Biogeochemical modeling of CO 2 and CH 4 production in anoxic Arctic soil microcosms

DOE PAGES

Tang, Guoping; Zheng, Jianqiu; Xu, Xiaofeng; ...

2016-09-12

Soil organic carbon turnover to CO 2 and CH 4 is sensitive to soil redox potential and pH conditions. But, land surface models do not consider redox and pH in the aqueous phase explicitly, thereby limiting their use for making predictions in anoxic environments. Using recent data from incubations of Arctic soils, we extend the Community Land Model with coupled carbon and nitrogen (CLM-CN) decomposition cascade to include simple organic substrate turnover, fermentation, Fe(III) reduction, and methanogenesis reactions, and assess the efficacy of various temperature and pH response functions. Incorporating the Windermere Humic Aqueous Model (WHAM) enables us to approximatelymore » describe the observed pH evolution without additional parameterization. Though Fe(III) reduction is normally assumed to compete with methanogenesis, the model predicts that Fe(III) reduction raises the pH from acidic to neutral, thereby reducing environmental stress to methanogens and accelerating methane production when substrates are not limiting. Furthermore, the equilibrium speciation predicts a substantial increase in CO 2 solubility as pH increases, and taking into account CO 2 adsorption to surface sites of metal oxides further decreases the predicted headspace gas-phase fraction at low pH. Without adequate representation of these speciation reactions, as well as the impacts of pH, temperature, and pressure, the CO 2 production from closed microcosms can be substantially underestimated based on headspace CO 2 measurements only. Our results demonstrate the efficacy of geochemical models for simulating soil biogeochemistry and provide predictive understanding and mechanistic representations that can be incorporated into land surface models to improve climate predictions.« less

CMIP5-based global wave climate projections including the entire Arctic Ocean

NASA Astrophysics Data System (ADS)

Casas-Prat, M.; Wang, X. L.; Swart, N.

2018-03-01

This study presents simulations of the global ocean wave climate corresponding to the surface winds and sea ice concentrations as simulated by five CMIP5 (Coupled Model Intercomparison Project Phase 5) climate models for the historical (1979-2005) and RCP8.5 scenario future (2081-2100) periods. To tackle the numerical complexities associated with the inclusion of the North Pole, the WAVEWATCH III (WW3) wave model was used with a customized unstructured Spherical Multi-Cell grid of ∼100 km offshore and ∼50 km along coastlines. The climate model simulated wind and sea ice data, and the corresponding WW3 simulated wave data, were evaluated against reanalysis and hindcast data. The results show that all the five sets of wave simulations projected lower waves in the North Atlantic, corresponding to decreased surface wind speeds there in the warmer climate. The selected CMIP5 models also consistently projected an increase in the surface wind speed in the Southern Hemisphere (SH) mid-high latitudes, which translates in an increase in the WW3 simulated significant wave height (Hs) there. The higher waves are accompanied with increased peak wave period and increased wave age in the East Pacific and Indian Oceans, and a significant counterclockwise rotation in the mean wave direction in the Southern Oceans. The latter is caused by more intense waves from the SH traveling equatorward and developing into swells. Future wave climate in the Arctic Ocean in summer is projected to be predominantly of mixed sea states, with the climatological mean of September maximum Hs ranging mostly 3-4 m. The new waves approaching Arctic coasts will be less fetch-limited as ice retreats since a predominantly southwards mean wave direction is projected in the surrounding seas.

Face and construct validation of a next generation virtual reality (Gen2-VR) surgical simulator.

PubMed

Sankaranarayanan, Ganesh; Li, Baichun; Manser, Kelly; Jones, Stephanie B; Jones, Daniel B; Schwaitzberg, Steven; Cao, Caroline G L; De, Suvranu

2016-03-01

Surgical performance is affected by distractors and interruptions to surgical workflow that exist in the operating room. However, traditional surgical simulators are used to train surgeons in a skills laboratory that does not recreate these conditions. To overcome this limitation, we have developed a novel, immersive virtual reality (Gen2-VR) system to train surgeons in these environments. This study was to establish face and construct validity of our system. The study was a within-subjects design, with subjects repeating a virtual peg transfer task under three different conditions: Case I: traditional VR; Case II: Gen2-VR with no distractions and Case III: Gen2-VR with distractions and interruptions. In Case III, to simulate the effects of distractions and interruptions, music was played intermittently, the camera lens was fogged for 10 s and tools malfunctioned for 15 s at random points in time during the simulation. At the completion of the study subjects filled in a 5-point Likert scale feedback questionnaire. A total of sixteen subjects participated in this study. Friedman test showed significant difference in scores between the three conditions (p < 0.0001). Post hoc analysis using Wilcoxon signed-rank tests with Bonferroni correction further showed that all the three conditions were significantly different from each other (Case I, Case II, p < 0.0001), (Case I, Case III, p < 0.0001) and (Case II, Case III, p = 0.009). Subjects rated that fog (mean 4.18) and tool malfunction (median 4.56) significantly hindered their performance. The results showed that Gen2-VR simulator has both face and construct validity and that it can accurately and realistically present distractions and interruptions in a simulated OR, in spite of limitations of the current HMD hardware technology.

Face and Construct Validation of a Next Generation Virtual Reality (Gen2-VR©) Surgical Simulator

PubMed Central

Sankaranarayanan, Ganesh; Li, Baichun; Manser, Kelly; Jones, Stephanie B.; Jones, Daniel B.; Schwaitzberg, Steven; Cao, Caroline G. L.; De, Suvranu

2015-01-01

Introduction Surgical performance is affected by distractors and interruptions to surgical workflow that exist in the operating room. However, traditional surgical simulators are used to train surgeons in a skills lab that does not recreate these conditions. To overcome this limitation, we have developed a novel, immersive virtual reality (Gen2-VR©) system to train surgeons in these environments. This study was to establish face and construct validity of our system. Methods and Procedures The study was a within-subjects design, with subjects repeating a virtual peg transfer task under three different conditions: CASE I: traditional VR; CASE II: Gen2-VR© with no distractions and CASE III: Gen2-VR© with distractions and interruptions.. In Case III, to simulate the effects of distractions and interruptions, music was played intermittently, the camera lens was fogged for 10 seconds and tools malfunctioned for 15 seconds at random points in time during the simulation. At the completion of the study subjects filled in a 5-point Likert scale feedback questionnaire. A total of sixteen subjects participated in this study. Results Friedman test showed significant difference in scores between the three conditions (p < 0.0001). Post hoc analysis using Wilcoxon Signed Rank tests with Bonferroni correction further showed that all the three conditions were significantly different from each other (Case I, Case II, p < 0.001), (Case I, Case III, p < 0.001) and (Case II, Case III, p = 0.009). Subjects rated that fog (mean= 4.18) and tool malfunction (median = 4.56) significantly hindered their performance. Conclusion The results showed that Gen2-VR© simulator has both face and construct validity and it can accurately and realistically present distractions and interruptions in a simulated OR, in spite of limitations of the current HMD hardware technology. PMID:26092010

Dose/Exposure‐Response Modeling to Support Dosing Recommendation for Phase III Development of Baricitinib in Patients with Rheumatoid Arthritis

PubMed Central

Chua, Laiyi; Ernest, Charles; Macias, William; Rooney, Terence; Tham, Lai San

2017-01-01

Baricitinib is an oral inhibitor of Janus kinases (JAKs), selective for JAK1 and 2. It demonstrated dose‐dependent efficacy in patients with moderate‐to‐severe rheumatoid arthritis (RA) in a phase IIb study up to 24 weeks. Population pharmacokinetic/pharmacodynamic (PopPK/PD) models were developed to characterize concentration‐time profiles and dose/exposure‐response (D/E‐R) relationships for the key efficacy (proportion of patients achieving American College of Rheumatology 20%, 50%, or 70% response rate) and safety endpoints (incidence of anemia) for the phase IIb study. The modeling suggested that 4 mg q.d. was likely to offer the optimum risk/benefit balance, whereas 2 mg q.d. had the potential for adequate efficacy. In addition, at the same total daily dose, a twice‐daily regimen is not expected to provide an advantage over q.d. dosing for the efficacy or safety endpoints. The model‐based simulations formed the rationale for key aspects of dosing, such as dose levels and dosing frequency for phase III development. PMID:28891251

Modifying a dynamic global vegetation model for simulating large spatial scale land surface water balances

NASA Astrophysics Data System (ADS)

Tang, G.; Bartlein, P. J.

2012-08-01

Satellite-based data, such as vegetation type and fractional vegetation cover, are widely used in hydrologic models to prescribe the vegetation state in a study region. Dynamic global vegetation models (DGVM) simulate land surface hydrology. Incorporation of satellite-based data into a DGVM may enhance a model's ability to simulate land surface hydrology by reducing the task of model parameterization and providing distributed information on land characteristics. The objectives of this study are to (i) modify a DGVM for simulating land surface water balances; (ii) evaluate the modified model in simulating actual evapotranspiration (ET), soil moisture, and surface runoff at regional or watershed scales; and (iii) gain insight into the ability of both the original and modified model to simulate large spatial scale land surface hydrology. To achieve these objectives, we introduce the "LPJ-hydrology" (LH) model which incorporates satellite-based data into the Lund-Potsdam-Jena (LPJ) DGVM. To evaluate the model we ran LH using historical (1981-2006) climate data and satellite-based land covers at 2.5 arc-min grid cells for the conterminous US and for the entire world using coarser climate and land cover data. We evaluated the simulated ET, soil moisture, and surface runoff using a set of observed or simulated data at different spatial scales. Our results demonstrate that spatial patterns of LH-simulated annual ET and surface runoff are in accordance with previously published data for the US; LH-modeled monthly stream flow for 12 major rivers in the US was consistent with observed values respectively during the years 1981-2006 (R2 > 0.46, p < 0.01; Nash-Sutcliffe Coefficient > 0.52). The modeled mean annual discharges for 10 major rivers worldwide also agreed well (differences < 15%) with observed values for these rivers. Compared to a degree-day method for snowmelt computation, the addition of the solar radiation effect on snowmelt enabled LH to better simulate monthly stream flow in winter and early spring for rivers located at mid-to-high latitudes. In addition, LH-modeled monthly soil moisture for the state of Illinois (US) agreed well (R2 = 0.79, p < 0.01) with observed data for the years 1984-2001. Overall, this study justifies both the feasibility of incorporating satellite-based land covers into a DGVM and the reliability of LH to simulate land-surface water balances. To better estimate surface/river runoff at mid-to-high latitudes, we recommended that LPJ-DGVM considers the effects of solar radiation on snowmelt.

Comparing cosmological hydrodynamic simulations with observations of high- redshift galaxy formation

NASA Astrophysics Data System (ADS)

Finlator, Kristian Markwart

We use cosmological hydrodynamic simulations to study the impact of outflows and radiative feedback on high-redshift galaxies. For outflows, we consider simulations that assume (i) no winds, (ii) a "constant-wind" model in which the mass-loading factor and outflow speed are constant, and (iii) "momentum-driven" winds in which both parameters vary smoothly with mass. In order to treat radiative feedback, we develop a moment-based radiative transfer technique that operates in both post-processing and coupled radiative hydrodynamic modes. We first ask how outflows impact the broadband spectral energy distributions (SEDs) of six observed reionization-epoch galaxies. Simulations reproduce five regardless of the outflow prescription, while the sixth suggests an unusually bursty star formation history. We conclude that (i) simulations broadly account for available constraints on reionization-epoch galaxies, (ii) individual SEDs do not constrain outflows, and (iii) SED comparisons efficiently isolate objects that challenge simulations. We next study how outflows impact the galaxy mass metallicity relation (MZR). Momentum-driven outflows uniquely reproduce observations at z = 2. In this scenario, galaxies obey two equilibria: (i) The rate at which a galaxy processes gas into stars and outflows tracks its inflow rate; and (ii) The gas enrichment rate owing to star formation balances the dilution rate owing to inflows. Combining these conditions indicates that the MZR is dominated by the (instantaneous) variation of outflows with mass, with more-massive galaxies driving less gas into outflows per unit stellar mass formed. Turning to radiative feedback, we use post-processing simulations to study the topology of reionization. Reionization begins in overdensities and then "leaks" directly into voids, with filaments reionizing last owing to their high density and low emissivity. This result conflicts with previous findings that voids ionize last. We argue that it owes to the uniqely-biased emissivity field produced by our star formation prescriptions, which have previously been shown to reproduce numerous post-reionization constraints. Finally, preliminary results from coupled radiative hydrodynamic simulations indicate that reionization suppresses the star formation rate density by at most 10-20% by z = 5. This is much less than previous estimates, which we attribute to our unique reionization topology although confirmation will have to await more detailed modeling.

Mathematical modeling of chemical composition modification and etching of polymers under the atomic oxygen influence

NASA Astrophysics Data System (ADS)

Chirskaia, Natalia; Novikov, Lev; Voronina, Ekaterina

2016-07-01

Atomic oxygen (AO) of the upper atmosphere is one of the most important space factors that can cause degradation of spacecraft surface. In our previous mathematical model the Monte Carlo method and the "large particles" approximation were used for simulating processes of polymer etching under the influence of AO [1]. The interaction of enlarged AO particles with the polymer was described in terms of probabilities of reactions such as etching of polymer and specular and diffuse scattering of the AO particles on polymer. The effects of atomic oxygen on protected polymers and microfiller containing composites were simulated. The simulation results were in quite good agreement with the results of laboratory experiments on magnetoplasmadynamic accelerator of the oxygen plasma of SINP MSU [2]. In this paper we present a new model that describes the reactions of AO interactions with polymeric materials in more detail. Reactions of formation and further emission of chemical compounds such as CO, CO _{2}, H _{2}O, etc. cause the modification of the chemical composition of the polymer and change the probabilities of its consequent interaction with the AO. The simulation results are compared with the results of previous simulation and with the results of laboratory experiments. The reasons for the differences between the results of natural experiments on spacecraft, laboratory experiments and simulations are discussed. N. Chirskaya, M. Samokhina, Computer modeling of polymer structures degradation under the atomic oxygen exposure, WDS'12 Proceedings of Contributed Papers: Part III - Physics, Matfyzpress Prague, 2012, pp. 30-35. E. Voronina, L. Novikov, V. Chernik, N. Chirskaya, K. Vernigorov, G. Bondarenko, and A. Gaidar, Mathematical and experimental simulation of impact of atomic oxygen of the earth's upper atmosphere on nanostructures and polymer composites, Inorganic Materials: Applied Research, 2012, vol. 3, no. 2, pp. 95-101.

A 3D coupled hydro-mechanical granular model for the prediction of hot tearing formation

NASA Astrophysics Data System (ADS)

Sistaninia, M.; Phillion, A. B.; Drezet, J.-M.; Rappaz, M.

2012-07-01

A new 3D coupled hydro-mechanical granular model that simulates hot tearing formation in metallic alloys is presented. The hydro-mechanical model consists of four separate 3D modules. (I) The Solidification Module (SM) is used for generating the initial solid-liquid geometry. Based on a Voronoi tessellation of randomly distributed nucleation centers, this module computes solidification within each polyhedron using a finite element based solute diffusion calculation for each element within the tessellation. (II) The Fluid Flow Module (FFM) calculates the solidification shrinkage and deformation-induced pressure drop within the intergranular liquid. (III) The Semi-solid Deformation Module (SDM) is used to simulate deformation of the granular structure via a combined finite element / discrete element method. In this module, deformation of the solid grains is modeled using an elasto-viscoplastic constitutive law. (IV) The Failure Module (FM) is used to simulate crack initiation and propagation with the fracture criterion estimated from the overpressure required to overcome the capillary forces at the liquid-gas interface. The FFM, SDM, and FM are coupled processes since solid deformation, intergranular flow, and crack initiation are deeply linked together. The granular model predictions have been validated against bulk data measured experimentally and calculated with averaging techniques.

Exposing earth surface process model simulations to a large audience

NASA Astrophysics Data System (ADS)

Overeem, I.; Kettner, A. J.; Borkowski, L.; Russell, E. L.; Peddicord, H.

2015-12-01

The Community Surface Dynamics Modeling System (CSDMS) represents a diverse group of >1300 scientists who develop and apply numerical models to better understand the Earth's surface. CSDMS has a mandate to make the public more aware of model capabilities and therefore started sharing state-of-the-art surface process modeling results with large audiences. One platform to reach audiences outside the science community is through museum displays on 'Science on a Sphere' (SOS). Developed by NOAA, SOS is a giant globe, linked with computers and multiple projectors and can display data and animations on a sphere. CSDMS has developed and contributed model simulation datasets for the SOS system since 2014, including hydrological processes, coastal processes, and human interactions with the environment. Model simulations of a hydrological and sediment transport model (WBM-SED) illustrate global river discharge patterns. WAVEWATCH III simulations have been specifically processed to show the impacts of hurricanes on ocean waves, with focus on hurricane Katrina and super storm Sandy. A large world dataset of dams built over the last two centuries gives an impression of the profound influence of humans on water management. Given the exposure of SOS, CSDMS aims to contribute at least 2 model datasets a year, and will soon provide displays of global river sediment fluxes and changes of the sea ice free season along the Arctic coast. Over 100 facilities worldwide show these numerical model displays to an estimated 33 million people every year. Datasets storyboards, and teacher follow-up materials associated with the simulations, are developed to address common core science K-12 standards. CSDMS dataset documentation aims to make people aware of the fact that they look at numerical model results, that underlying models have inherent assumptions and simplifications, and that limitations are known. CSDMS contributions aim to familiarize large audiences with the use of numerical modeling as a tool to create understanding of environmental processes.

Biogenic uraninite precipitation and its reoxidation by iron(III) (hydr)oxides: A reaction modeling approach

NASA Astrophysics Data System (ADS)

Spycher, Nicolas F.; Issarangkun, Montarat; Stewart, Brandy D.; Sevinç Şengör, S.; Belding, Eileen; Ginn, Tim R.; Peyton, Brent M.; Sani, Rajesh K.

2011-08-01

One option for immobilizing uranium present in subsurface contaminated groundwater is in situ bioremediation, whereby dissimilatory metal-reducing bacteria and/or sulfate-reducing bacteria are stimulated to catalyze the reduction of soluble U(VI) and precipitate it as uraninite (UO 2). This is typically accomplished by amending groundwater with an organic electron donor. It has been shown, however, that once the electron donor is entirely consumed, Fe(III) (hydr)oxides can reoxidize biogenically produced UO 2, thus potentially impeding cleanup efforts. On the basis of published experiments showing that such reoxidation takes place even under highly reducing conditions (e.g., sulfate-reducing conditions), thermodynamic and kinetic constraints affecting this reoxidation are examined using multicomponent biogeochemical simulations, with particular focus on the role of sulfide and Fe(II) in solution. The solubility of UO 2 and Fe(III) (hydr)oxides are presented, and the effect of nanoscale particle size on stability is discussed. Thermodynamically, sulfide is preferentially oxidized by Fe(III) (hydr)oxides, compared to biogenic UO 2, and for this reason the relative rates of sulfide and UO 2 oxidation play a key role on whether or not UO 2 reoxidizes. The amount of Fe(II) in solution is another important factor, with the precipitation of Fe(II) minerals lowering the Fe +2 activity in solution and increasing the potential for both sulfide and UO 2 reoxidation. The greater (and unintuitive) UO 2 reoxidation by hematite compared to ferrihydrite previously reported in some experiments can be explained by the exhaustion of this mineral from reaction with sulfide. Simulations also confirm previous studies suggesting that carbonate produced by the degradation of organic electron donors used for bioreduction may significantly increase the potential for UO 2 reoxidation through formation of uranyl carbonate aqueous complexes.

Novel hybrid III:V concentrator photovoltaic-thermoelectric receiver designs

NASA Astrophysics Data System (ADS)

Sweet, Tracy K. N.; Rolley, Matthew H.; Prest, Martin J.; Min, Gao

2017-09-01

This paper presents the design, manufacture and electrical characterization of novel hybrid III:V Concentrator Photovoltaic-Thermoelectric receivers. Addition of an encapsulating and spectral homogenizing single active surface secondary optic lens increased the solar cell electrical power output from 7.66mW (ALPHA no cooling) to 18.20mW (KAPPA with TE cooling). The effective optical concentration of the optics, based on short circuit current, was x2.4. A linear irradiance vs maximum power receiver output relationship was observed (R2=0.9978), confirming good optical alignment during manufacture and likewise internal current matching of the series-connected triple-junction cell. An in-depth COMSOL model for simulated evaluation of the synergistic thermally-dependent parameters inherent to hybrid devices was built and experimentally validated.

Computational multicore on two-layer 1D shallow water equations for erodible dambreak

NASA Astrophysics Data System (ADS)

Simanjuntak, C. A.; Bagustara, B. A. R. H.; Gunawan, P. H.

2018-03-01

The simulation of erodible dambreak using two-layer shallow water equations and SCHR scheme are elaborated in this paper. The results show that the two-layer SWE model in a good agreement with the data experiment which is performed by Louvain-la-Neuve Université Catholique de Louvain. Moreover, the parallel algorithm with multicore architecture are given in the results. The results show that Computer I with processor Intel(R) Core(TM) i5-2500 CPU Quad-Core has the best performance to accelerate the computational time. Moreover, Computer III with processor AMD A6-5200 APU Quad-Core is observed has higher speedup and efficiency. The speedup and efficiency of Computer III with number of grids 3200 are 3.716050530 times and 92.9% respectively.

Estimation of in-situ bioremediation system cost using a hybrid Extreme Learning Machine (ELM)-particle swarm optimization approach

NASA Astrophysics Data System (ADS)

Yadav, Basant; Ch, Sudheer; Mathur, Shashi; Adamowski, Jan

2016-12-01

In-situ bioremediation is the most common groundwater remediation procedure used for treating organically contaminated sites. A simulation-optimization approach, which incorporates a simulation model for groundwaterflow and transport processes within an optimization program, could help engineers in designing a remediation system that best satisfies management objectives as well as regulatory constraints. In-situ bioremediation is a highly complex, non-linear process and the modelling of such a complex system requires significant computational exertion. Soft computing techniques have a flexible mathematical structure which can generalize complex nonlinear processes. In in-situ bioremediation management, a physically-based model is used for the simulation and the simulated data is utilized by the optimization model to optimize the remediation cost. The recalling of simulator to satisfy the constraints is an extremely tedious and time consuming process and thus there is need for a simulator which can reduce the computational burden. This study presents a simulation-optimization approach to achieve an accurate and cost effective in-situ bioremediation system design for groundwater contaminated with BTEX (Benzene, Toluene, Ethylbenzene, and Xylenes) compounds. In this study, the Extreme Learning Machine (ELM) is used as a proxy simulator to replace BIOPLUME III for the simulation. The selection of ELM is done by a comparative analysis with Artificial Neural Network (ANN) and Support Vector Machine (SVM) as they were successfully used in previous studies of in-situ bioremediation system design. Further, a single-objective optimization problem is solved by a coupled Extreme Learning Machine (ELM)-Particle Swarm Optimization (PSO) technique to achieve the minimum cost for the in-situ bioremediation system design. The results indicate that ELM is a faster and more accurate proxy simulator than ANN and SVM. The total cost obtained by the ELM-PSO approach is held to a minimum while successfully satisfying all the regulatory constraints of the contaminated site.

An Ultrastable Heterobimetallic Uranium(IV)/Vanadium(III) Solid Compound Protected by a Redox-Active Phosphite Ligand: Crystal Structure, Oxidative Dissolution, and First-Principles Simulation.

PubMed

Gui, Daxiang; Dai, Xing; Zheng, Tao; Wang, Xiangxiang; Silver, Mark A; Chen, Lanhua; Zhang, Chao; Diwu, Juan; Zhou, Ruhong; Chai, Zhifang; Wang, Shuao

2018-02-05

The first heterobimetallic uranium(IV)/vanadium(III) phosphite compound, Na 2 UV 2 (HPO 3 ) 6 (denoted as UVP), was synthesized via an in situ redox-active hydrothermal reaction. It exhibits superior hydrolytic and antioxidant stability compared to the majority of structures containing low-valent uranium or vanadium, further elucidated by first-principles simulations, and therefore shows potential applications in nuclear waste management.

Mechanism of Ribonuclease III Catalytic Regulation by Serine Phosphorylation

NASA Astrophysics Data System (ADS)

Gone, Swapna; Alfonso-Prieto, Mercedes; Paudyal, Samridhdi; Nicholson, Allen W.

2016-05-01

Ribonuclease III (RNase III) is a conserved, gene-regulatory bacterial endonuclease that cleaves double-helical structures in diverse coding and noncoding RNAs. RNase III is subject to multiple levels of control, reflective of its global regulatory functions. Escherichia coli (Ec) RNase III catalytic activity is known to increase during bacteriophage T7 infection, reflecting the expression of the phage-encoded protein kinase, T7PK. However, the mechanism of catalytic enhancement is unknown. This study shows that Ec-RNase III is phosphorylated on serine in vitro by purified T7PK, and identifies the targets as Ser33 and Ser34 in the N-terminal catalytic domain. Kinetic experiments reveal a 5-fold increase in kcat and a 1.4-fold decrease in Km following phosphorylation, providing a 7.4-fold increase in catalytic efficiency. Phosphorylation does not change the rate of substrate cleavage under single-turnover conditions, indicating that phosphorylation enhances product release, which also is the rate-limiting step in the steady-state. Molecular dynamics simulations provide a mechanism for facilitated product release, in which the Ser33 phosphomonoester forms a salt bridge with the Arg95 guanidinium group, thereby weakening RNase III engagement of product. The simulations also show why glutamic acid substitution at either serine does not confer enhancement, thus underscoring the specific requirement for a phosphomonoester.

Towards quantifying uncertainty in predictions of Amazon 'dieback'.

PubMed

Huntingford, Chris; Fisher, Rosie A; Mercado, Lina; Booth, Ben B B; Sitch, Stephen; Harris, Phil P; Cox, Peter M; Jones, Chris D; Betts, Richard A; Malhi, Yadvinder; Harris, Glen R; Collins, Mat; Moorcroft, Paul

2008-05-27

Simulations with the Hadley Centre general circulation model (HadCM3), including carbon cycle model and forced by a 'business-as-usual' emissions scenario, predict a rapid loss of Amazonian rainforest from the middle of this century onwards. The robustness of this projection to both uncertainty in physical climate drivers and the formulation of the land surface scheme is investigated. We analyse how the modelled vegetation cover in Amazonia responds to (i) uncertainty in the parameters specified in the atmosphere component of HadCM3 and their associated influence on predicted surface climate. We then enhance the land surface description and (ii) implement a multilayer canopy light interception model and compare with the simple 'big-leaf' approach used in the original simulations. Finally, (iii) we investigate the effect of changing the method of simulating vegetation dynamics from an area-based model (TRIFFID) to a more complex size- and age-structured approximation of an individual-based model (ecosystem demography). We find that the loss of Amazonian rainforest is robust across the climate uncertainty explored by perturbed physics simulations covering a wide range of global climate sensitivity. The introduction of the refined light interception model leads to an increase in simulated gross plant carbon uptake for the present day, but, with altered respiration, the net effect is a decrease in net primary productivity. However, this does not significantly affect the carbon loss from vegetation and soil as a consequence of future simulated depletion in soil moisture; the Amazon forest is still lost. The introduction of the more sophisticated dynamic vegetation model reduces but does not halt the rate of forest dieback. The potential for human-induced climate change to trigger the loss of Amazon rainforest appears robust within the context of the uncertainties explored in this paper. Some further uncertainties should be explored, particularly with respect to the representation of rooting depth.

AQMEII3 evaluation of regional NA/EU simulations and ...

EPA Pesticide Factsheets

Through the comparison of several regional-scale chemistry transport modelling systems that simulate meteorology and air quality over the European and American continents, this study aims at i) apportioning the error to the responsible processes using time-scale analysis, ii) helping to detect causes of models error, and iii) identifying the processes and scales most urgently requiring dedicated investigations. The analysis is conducted within the framework of the third phase of the Air Quality Model Evaluation International Initiative (AQMEII) and tackles model performance gauging through measurement-to-model comparison, error decomposition and time series analysis of the models biases for several fields (ozone, CO, SO2, NO, NO2, PM10, PM2.5, wind speed, and temperature). The operational metrics (magnitude of the error, sign of the bias, associativity) provide an overall sense of model strengths and deficiencies, while apportioning the error to its constituent parts (bias, variance and covariance) can help to assess the nature and quality of the error. Each of the error components is analysed independently and apportioned to specific processes based on the corresponding timescale (long scale, synoptic, diurnal, and intra-day) using the error apportionment technique devised in the former phases of AQMEII. The application of the error apportionment method to the AQMEII Phase 3 simulations provides several key insights. In addition to reaffirming the strong impac

Modeling Contamination Migration on the Chandra X-Ray Observatory - III

NASA Technical Reports Server (NTRS)

O'Dell, Stephen L.; Swartz, Douglas A.; Tice, Neil W.; Plucinsky, Paul P.; Grant, Catherine E.; Marshall, Herman L.; Vikhlinin, Alexy A.; Tennant, Allyn F.; Dahmer, Matthew T.

2015-01-01

During its first 16 years of operation, the cold (about -60 C) optical blocking filter of the Advanced CCD Imaging Spectrometer (ACIS), aboard the Chandra X-ray Observatory, has accumulated a growing layer of molecular contamination that attenuates low-energy x rays. Over the past few years, the accumulation rate, spatial distribution, and composition have changed. This evolution has motivated further analysis of contamination migration within and near the ACIS cavity, in part to evaluate potential bake-out scenarios intended to reduce the level of contamination. Keywords: X-ray astronomy, CCDs, contamination, modeling and simulation, spacecraft operations

DNA cleavage site selection by Type III restriction enzymes provides evidence for head-on protein collisions following 1D bidirectional motion

PubMed Central

Schwarz, Friedrich W.; van Aelst, Kara; Tóth, Júlia; Seidel, Ralf; Szczelkun, Mark D.

2011-01-01

DNA cleavage by the Type III Restriction–Modification enzymes requires communication in 1D between two distant indirectly-repeated recognitions sites, yet results in non-specific dsDNA cleavage close to only one of the two sites. To test a recently proposed ATP-triggered DNA sliding model, we addressed why one site is selected over another during cleavage. We examined the relative cleavage of a pair of identical sites on DNA substrates with different distances to a free or protein blocked end, and on a DNA substrate using different relative concentrations of protein. Under these conditions a bias can be induced in the cleavage of one site over the other. Monte-Carlo simulations based on the sliding model reproduce the experimentally observed behaviour. This suggests that cleavage site selection simply reflects the dynamics of the preceding stochastic enzyme events that are consistent with bidirectional motion in 1D and DNA cleavage following head-on protein collision. PMID:21724613

An analytic current-voltage model for quasi-ballistic III-nitride high electron mobility transistors

NASA Astrophysics Data System (ADS)

Li, Kexin; Rakheja, Shaloo

2018-05-01

We present an analytic model to describe the DC current-voltage (I-V) relationship in scaled III-nitride high electron mobility transistors (HEMTs) in which transport within the channel is quasi-ballistic in nature. Following Landauer's transport theory and charge calculation based on two-dimensional electrostatics that incorporates negative momenta states from the drain terminal, an analytic expression for current as a function of terminal voltages is developed. The model interprets the non-linearity of access regions in non-self-aligned HEMTs. Effects of Joule heating with temperature-dependent thermal conductivity are incorporated in the model in a self-consistent manner. With a total of 26 input parameters, the analytic model offers reduced empiricism compared to existing GaN HEMT models. To verify the model, experimental I-V data of InAlN/GaN with InGaN back-barrier HEMTs with channel lengths of 42 and 105 nm are considered. Additionally, the model is validated against numerical I-V data obtained from DC hydrodynamic simulations of an unintentionally doped AlGaN-on-GaN HEMT with 50-nm gate length. The model is also verified against pulsed I-V measurements of a 150-nm T-gate GaN HEMT. Excellent agreement between the model and experimental and numerical results for output current, transconductance, and output conductance is demonstrated over a broad range of bias and temperature conditions.

Complexation Enhancement Drives Water-to-Oil Ion Transport: A Simulation Study

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

Qiao, Baofu; Ferru, Geoffroy; Ellis, Ross J.

We address the structures and energetics of ion solvation in aqueous and organic solutions to understand liquid-liquid ion transport. Atomistic molecular dynamics (MD) simulations with polarizable force field are performed to study the coordination transformations driving lanthanide (Ln(III)) and nitrate ion transport between aqueous and an alkylamide-oil solution. An enhancement of the coordination behavior in the organic phase is achieved in contrast with the aqueous solution. In particular, the coordination number of Ce3+ increases from 8.9 in the aqueous to 9.9 in the organic solutions (from 8 in the aqueous to 8.8 in the organic systems for Yb3+). Moreover, themore » local coordination environ ment changes dramatically. Potential of mean force calculations show that the Ln(III)-ligand coordination interaction strengths follow the order of Ln(III-)nitrate> Ln(III)-water>Ln(III)-DMDBTDMA. They increase 2-fold in the lipophilic environment in comparison to the aqueous phase, and we attribute this to the shedding of the outer solvation shell. Our findings highlight the importance of outer sphere interactions on the competitive solvation energetics that cause ions to migrate between immiscible phases; an essential ingredient for advancing important applications such as rare earth metal separations. Some open questions in simulating the coordination behavior of heavy metals are also addressed.« less

FINDING THE FIRST COSMIC EXPLOSIONS. II. CORE-COLLAPSE SUPERNOVAE

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

Whalen, Daniel J.; Joggerst, Candace C.; Fryer, Chris L.

2013-05-01

Understanding the properties of Population III (Pop III) stars is prerequisite to elucidating the nature of primeval galaxies, the chemical enrichment and reionization of the early intergalactic medium, and the origin of supermassive black holes. While the primordial initial mass function (IMF) remains unknown, recent evidence from numerical simulations and stellar archaeology suggests that some Pop III stars may have had lower masses than previously thought, 15-50 M{sub Sun} in addition to 50-500 M{sub Sun }. The detection of Pop III supernovae (SNe) by JWST, WFIRST, or the TMT could directly probe the primordial IMF for the first time. Wemore » present numerical simulations of 15-40 M{sub Sun} Pop III core-collapse SNe performed with the Los Alamos radiation hydrodynamics code RAGE. We find that they will be visible in the earliest galaxies out to z {approx} 10-15, tracing their star formation rates and in some cases revealing their positions on the sky. Since the central engines of Pop III and solar-metallicity core-collapse SNe are quite similar, future detection of any Type II SNe by next-generation NIR instruments will in general be limited to this epoch.« less

Development of Airport Noise Mapping using Matlab Software (Case Study: Adi Soemarmo Airport - Boyolali, Indonesia)

NASA Astrophysics Data System (ADS)

Andarani, Pertiwi; Setiyo Huboyo, Haryono; Setyanti, Diny; Budiawan, Wiwik

2018-02-01

Noise is considered as one of the main environmental impact of Adi Soemarmo International Airport (ASIA), the second largest airport in Central Java Province, Indonesia. In order to manage the noise of airport, airport noise mapping is necessary. However, a model that requires simple input but still reliable was not available in ASIA. Therefore, the objective of this study are to develop model using Matlab software, to verify its reliability by measuring actual noise exposure, and to analyze the area of noise levels‥ The model was developed based on interpolation or extrapolation of identified Noise-Power-Distance (NPD) data. In accordance with Indonesian Government Ordinance No.40/2012, the noise metric used is WECPNL (Weighted Equivalent Continuous Perceived Noise Level). Based on this model simulation, there are residence area in the region of noise level II (1.912 km2) and III (1.16 km2) and 18 school buildings in the area of noise levels I, II, and III. These land-uses are actually prohibited unless noise insulation is equipped. The model using Matlab in the case of Adi Soemarmo International Airport is valid based on comparison of the field measurement (6 sampling points). However, it is important to validate the model again once the case study (the airport) is changed.

Following the Cosmic Evolution of Pristine Gas. I. Implications for Milky Way Halo Stars

NASA Astrophysics Data System (ADS)

Sarmento, Richard; Scannapieco, Evan; Pan, Liubin

2017-01-01

We make use of a new subgrid model of turbulent mixing to accurately follow the cosmological evolution of the first stars, the mixing of their supernova (SN) ejecta, and the impact on the chemical composition of the Galactic Halo. Using the cosmological adaptive mesh refinement code ramses, we implement a model for the pollution of pristine gas as described in Pan et al. Tracking the metallicity of Pop III stars with metallicities below a critical value allows us to account for the fraction of Z< {Z}{crit} stars formed even in regions in which the gas’s average metallicity is well above {Z}{crit}. We demonstrate that such partially mixed regions account for 0.5 to 0.7 of all Pop III stars formed up to z = 5. Additionally, we track the creation and transport of “primordial metals” (PM) generated by Pop III SNe. These neutron-capture deficient metals are taken up by second-generation stars and likely lead to unique abundance signatures characteristic of carbon-enhanced, metal-poor (CEMP-no) stars. As an illustrative example, we associate primordial metals with abundance ratios used by Keller et al. to explain the source of metals in the star SMSS J031300.36-670839.3, finding good agreement with the observed [Fe/H], [C/H], [O/H], and [Mg/Ca] ratios in CEMP-no Milky Way halo stars. Similar future simulations will aid in further constraining the properties of Pop III stars using CEMP observations, as well as improve predictions of the spatial distribution of Pop III stars, as will be explored by the next generation of ground- and space-based telescopes.

Tracing the first stars and galaxies of the Milky Way

NASA Astrophysics Data System (ADS)

Griffen, Brendan F.; Dooley, Gregory A.; Ji, Alexander P.; O'Shea, Brian W.; Gómez, Facundo A.; Frebel, Anna

2018-02-01

We use 30 high-resolution dark matter haloes of the Caterpillar simulation suite to probe the first stars and galaxies of Milky Way-mass systems. We quantify the environment of the high-z progenitors of the Milky Way and connect them to the properties of the host and satellites today. We identify the formation sites of the first generation of Population III (Pop III) stars (z ˜ 25) and first galaxies (z ˜ 22) with several different models based on a minimum halo mass. This includes a simple model for radiative feedback, the primary limitation of the model. Through this method we find approximately 23 000 ± 5000 Pop III potentially star-forming sites per Milky Way-mass host, though this number is drastically reduced to ˜550 star-forming sites if feedback is included. The majority of these haloes identified form in isolation (96 per cent at z = 15) and are not subject to external enrichment by neighbouring haloes (median separation ˜1 kpc at z = 15), though half merge with a system larger than themselves within 1.5 Gyr. Using particle tagging, we additionally trace the Pop III remnant population to z = 0 and find an order of magnitude scatter in their number density at small (i.e. r < 5 kpc) and large (i.e. r > 50 kpc) galactocentric radii. We provide fitting functions for determining the number of progenitor minihalo and atomic cooling halo systems that present-day satellite galaxies might have accreted since their formation. We determine that observed dwarf galaxies with stellar masses below 104.6 M⊙ are unlikely to have merged with any other star-forming systems.

Structure of the CFA/III major pilin subunit CofA from human enterotoxigenic Escherichia coli determined at 0.90 Å resolution by sulfur-SAD phasing.

PubMed

Fukakusa, Shunsuke; Kawahara, Kazuki; Nakamura, Shota; Iwashita, Takaki; Baba, Seiki; Nishimura, Mitsuhiro; Kobayashi, Yuji; Honda, Takeshi; Iida, Tetsuya; Taniguchi, Tooru; Ohkubo, Tadayasu

2012-10-01

CofA, a major pilin subunit of colonization factor antigen III (CFA/III), forms pili that mediate small-intestinal colonization by enterotoxigenic Escherichia coli (ETEC). In this study, the crystal structure of an N-terminally truncated version of CofA was determined by single-wavelength anomalous diffraction (SAD) phasing using five sulfurs in the protein. Given the counterbalance between anomalous signal strength and the undesired X-ray absorption of the solvent, diffraction data were collected at 1.5 Å resolution using synchrotron radiation. These data were sufficient to elucidate the sulfur substructure at 1.38 Å resolution. The low solvent content (29%) of the crystal necessitated that density modification be performed with an additional 0.9 Å resolution data set to reduce the phase error caused by the small sulfur anomalous signal. The CofA structure showed the αβ-fold typical of type IVb pilins and showed high structural homology to that of TcpA for toxin-coregulated pili of Vibrio cholerae, including spatial distribution of key residues critical for pilin self-assembly. A pilus-filament model of CofA was built by computational docking and molecular-dynamics simulation using the previously reported filament model of TcpA as a structural template. This model revealed that the CofA filament surface was highly negatively charged and that a 23-residue-long loop between the α1 and α2 helices filled the gap between the pilin subunits. These characteristics could provide a unique binding epitope for the CFA/III pili of ETEC compared with other type IVb pili.

Sensitivity Analysis of Data Link Alternatives for LVLASO

NASA Technical Reports Server (NTRS)

Mukkamala, Ravi

1998-01-01

As part of this research, we have modeled the Mode-S system when used to enhance communications among several ground vehicles to facilitate low-visibility landing and surface operations. The model has then been simulated using Bones Designer software. The effectiveness of the model has been evaluated under several conditions: (i) different number of vehicles (100, 200, and 300), (ii) different distributions of interarrival times for squitters: uniform, exponential, and constrained exponential, and (iii) Different safe distances (for collision purpose): squitter length, 1.5*squitter length, and 2* squitter length. The model has been developed in a modular fashion to facilitate any future modifications. The results from the simulations suggest that the Mode S system is indeed capable of functioning satisfactorily even when covering up to 300 vehicles. Certainly, about 10 percent of the squitters undergo collisions and hence the interarrival times for these is much larger than the expected time of 500 msec. In fact, the delay could be as much as 2 seconds. The model could be further enhanced to incorporate more realistic scenarios.

InGaAs tunnel diodes for the calibration of semi-classical and quantum mechanical band-to-band tunneling models

NASA Astrophysics Data System (ADS)

Smets, Quentin; Verreck, Devin; Verhulst, Anne S.; Rooyackers, Rita; Merckling, Clément; Van De Put, Maarten; Simoen, Eddy; Vandervorst, Wilfried; Collaert, Nadine; Thean, Voon Y.; Sorée, Bart; Groeseneken, Guido; Heyns, Marc M.

2014-05-01

Promising predictions are made for III-V tunnel-field-effect transistor (FET), but there is still uncertainty on the parameters used in the band-to-band tunneling models. Therefore, two simulators are calibrated in this paper; the first one uses a semi-classical tunneling model based on Kane's formalism, and the second one is a quantum mechanical simulator implemented with an envelope function formalism. The calibration is done for In0.53Ga0.47As using several p+/intrinsic/n+ diodes with different intrinsic region thicknesses. The dopant profile is determined by SIMS and capacitance-voltage measurements. Error bars are used based on statistical and systematic uncertainties in the measurement techniques. The obtained parameters are in close agreement with theoretically predicted values and validate the semi-classical and quantum mechanical models. Finally, the models are applied to predict the input characteristics of In0.53Ga0.47As n- and p-lineTFET, with the n-lineTFET showing competitive performance compared to MOSFET.

Light dosimetry for focused and defocused beam irradiation in multi-layered tissue models

NASA Astrophysics Data System (ADS)

Petrova, Kremena S.; Stoykova, Elena V.

2006-09-01

Treatment of acupuncture points, trigger points, joint inflammations in low level laser therapy as well as various applications of lasers for treatment of soft tissues in dental medicine, require irradiation by a narrow converging laser beam. The aim of this study is to compare light delivery produced by focused or defocused narrow beam irradiation in a multi-layered skin tissue model at increasing depth of the target. The task is solved by 3-D Monte-Carlo simulation for matched and mismatched refractive indices at the tissue/ambient medium interface. The modeled light beams have a circular cross-section at the tissue entrance with uniform or Gaussian intensity distribution. Three are the tissue models used in simulation : i) a bloodless skin layer; ii) a bloodless skin layer with embedded scattering object; iii) a skin layer with small blood vessels of varying size, which are modeled as infinite cylinders parallel to the tissue surface located at different depths. Optical properties (absorption coefficient, scattering coefficient, anisotropy factor, g, and index of refraction) of different tissue constituents are chosen from the literature.

Modeling and simulation of maintenance treatment in first-line non-small cell lung cancer with external validation.

PubMed

Han, Kelong; Claret, Laurent; Sandler, Alan; Das, Asha; Jin, Jin; Bruno, Rene

2016-07-13

Maintenance treatment (MTx) in responders following first-line treatment has been investigated and practiced for many cancers. Modeling and simulation may support interpretation of interim data and development decisions. We aimed to develop a modeling framework to simulate overall survival (OS) for MTx in NSCLC using tumor growth inhibition (TGI) data. TGI metrics were estimated using longitudinal tumor size data from two Phase III first-line NSCLC studies evaluating bevacizumab and erlotinib as MTx in 1632 patients. Baseline prognostic factors and TGI metric estimates were assessed in multivariate parametric models to predict OS. The OS model was externally validated by simulating a third independent NSCLC study (n = 253) based on interim TGI data (up to progression-free survival database lock). The third study evaluated pemetrexed + bevacizumab vs. bevacizumab alone as MTx. Time-to-tumor-growth (TTG) was the best TGI metric to predict OS. TTG, baseline tumor size, ECOG score, Asian ethnicity, age, and gender were significant covariates in the final OS model. The OS model was qualified by simulating OS distributions and hazard ratios (HR) in the two studies used for model-building. Simulations of the third independent study based on interim TGI data showed that pemetrexed + bevacizumab MTx was unlikely to significantly prolong OS vs. bevacizumab alone given the current sample size (predicted HR: 0.81; 95 % prediction interval: 0.59-1.09). Predicted median OS was 17.3 months and 14.7 months in both arms, respectively. These simulations are consistent with the results of the final OS analysis published 2 years later (observed HR: 0.87; 95 % confidence interval: 0.63-1.21). Final observed median OS was 17.1 months and 13.2 months in both arms, respectively, consistent with our predictions. A robust TGI-OS model was developed for MTx in NSCLC. TTG captures treatment effect. The model successfully predicted the OS outcomes of an independent study based on interim TGI data and thus may facilitate trial simulation and interpretation of interim data. The model was built based on erlotinib data and externally validated using pemetrexed data, suggesting that TGI-OS models may be treatment-independent. The results supported the use of longitudinal tumor size and TTG as endpoints in early clinical oncology studies.

Dynamic evolution of Rayleigh-Taylor bubbles from sinusoidal, W-shaped, and random perturbations

NASA Astrophysics Data System (ADS)

Zhou, Zhi-Rui; Zhang, You-Sheng; Tian, Bao-Lin

2018-03-01

Implicit large eddy simulations of two-dimensional Rayleigh-Taylor instability at different density ratios (i.e., Atwood number A =0.05 , 0.5, and 0.9) are conducted to investigate the late-time dynamics of bubbles. To produce a flow field full of bounded, semibounded, and chaotic bubbles, three problems with distinct perturbations are simulated: (I) periodic sinusoidal perturbation, (II) isolated W-shaped perturbation, and (III) random short-wave perturbations. The evolution of height h , velocity v , and diameter D of the (dominant) bubble with time t are formulated and analyzed. In problem I, during the quasisteady stage, the simulations confirm Goncharov's prediction of the terminal speed v∞=Fr√{A g λ /(1 +A ) } , where Fr=1 /√{3 π } . Moreover, the diameter D at this stage is found to be proportional to the initial perturbation wavelength λ as D ≈λ . This differed from Daly's simulation result of D =λ (1 +A )/2 . In problem II, a W-shaped perturbation is designed to produce a bubble environment similar to that of chaotic bubbles in problem III. We obtain a similar terminal speed relationship as above, but Fr is replaced by Frw≈0.63 . In problem III, the simulations show that h grows quadratically with the bubble acceleration constant α ≡h /(A g t2)≈0.05 , and D expands self-similarly with a steady aspect ratio β ≡D /h ≈(1 +A )/2 , which differs from existing theories. Therefore, following the mechanism of self-similar growth, we derive a relationship of β =4 α (1 +A ) /Frw2 to relate the evolution of chaotic bubbles in problem III to that of semibounded bubbles in problem II. The validity of this relationship highlights the fact that the dynamics of chaotic bubbles in problem III are similar to the semibounded isolated bubbles in problem II, but not to that of bounded periodic bubbles in problem I.

PyRhO: A Multiscale Optogenetics Simulation Platform

PubMed Central

Evans, Benjamin D.; Jarvis, Sarah; Schultz, Simon R.; Nikolic, Konstantin

2016-01-01

Optogenetics has become a key tool for understanding the function of neural circuits and controlling their behavior. An array of directly light driven opsins have been genetically isolated from several families of organisms, with a wide range of temporal and spectral properties. In order to characterize, understand and apply these opsins, we present an integrated suite of open-source, multi-scale computational tools called PyRhO. The purpose of developing PyRhO is three-fold: (i) to characterize new (and existing) opsins by automatically fitting a minimal set of experimental data to three-, four-, or six-state kinetic models, (ii) to simulate these models at the channel, neuron and network levels, and (iii) provide functional insights through model selection and virtual experiments in silico. The module is written in Python with an additional IPython/Jupyter notebook based GUI, allowing models to be fit, simulations to be run and results to be shared through simply interacting with a webpage. The seamless integration of model fitting algorithms with simulation environments (including NEURON and Brian2) for these virtual opsins will enable neuroscientists to gain a comprehensive understanding of their behavior and rapidly identify the most suitable variant for application in a particular biological system. This process may thereby guide not only experimental design and opsin choice but also alterations of the opsin genetic code in a neuro-engineering feed-back loop. In this way, we expect PyRhO will help to significantly advance optogenetics as a tool for transforming biological sciences. PMID:27148037

PyRhO: A Multiscale Optogenetics Simulation Platform.

PubMed

Evans, Benjamin D; Jarvis, Sarah; Schultz, Simon R; Nikolic, Konstantin

2016-01-01

Optogenetics has become a key tool for understanding the function of neural circuits and controlling their behavior. An array of directly light driven opsins have been genetically isolated from several families of organisms, with a wide range of temporal and spectral properties. In order to characterize, understand and apply these opsins, we present an integrated suite of open-source, multi-scale computational tools called PyRhO. The purpose of developing PyRhO is three-fold: (i) to characterize new (and existing) opsins by automatically fitting a minimal set of experimental data to three-, four-, or six-state kinetic models, (ii) to simulate these models at the channel, neuron and network levels, and (iii) provide functional insights through model selection and virtual experiments in silico. The module is written in Python with an additional IPython/Jupyter notebook based GUI, allowing models to be fit, simulations to be run and results to be shared through simply interacting with a webpage. The seamless integration of model fitting algorithms with simulation environments (including NEURON and Brian2) for these virtual opsins will enable neuroscientists to gain a comprehensive understanding of their behavior and rapidly identify the most suitable variant for application in a particular biological system. This process may thereby guide not only experimental design and opsin choice but also alterations of the opsin genetic code in a neuro-engineering feed-back loop. In this way, we expect PyRhO will help to significantly advance optogenetics as a tool for transforming biological sciences.

A voxel-based multiscale model to simulate the radiation response of hypoxic tumors

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

Espinoza, I., E-mail: iespinoza@fis.puc.cl; Peschke, P.; Karger, C. P.

2015-01-15

Purpose: In radiotherapy, it is important to predict the response of tumors to irradiation prior to the treatment. This is especially important for hypoxic tumors, which are known to be highly radioresistant. Mathematical modeling based on the dose distribution, biological parameters, and medical images may help to improve this prediction and to optimize the treatment plan. Methods: A voxel-based multiscale tumor response model for simulating the radiation response of hypoxic tumors was developed. It considers viable and dead tumor cells, capillary and normal cells, as well as the most relevant biological processes such as (i) proliferation of tumor cells, (ii)more » hypoxia-induced angiogenesis, (iii) spatial exchange of cells leading to tumor growth, (iv) oxygen-dependent cell survival after irradiation, (v) resorption of dead cells, and (vi) spatial exchange of cells leading to tumor shrinkage. Oxygenation is described on a microscopic scale using a previously published tumor oxygenation model, which calculates the oxygen distribution for each voxel using the vascular fraction as the most important input parameter. To demonstrate the capabilities of the model, the dependence of the oxygen distribution on tumor growth and radiation-induced shrinkage is investigated. In addition, the impact of three different reoxygenation processes is compared and tumor control probability (TCP) curves for a squamous cells carcinoma of the head and neck (HNSSC) are simulated under normoxic and hypoxic conditions. Results: The model describes the spatiotemporal behavior of the tumor on three different scales: (i) on the macroscopic scale, it describes tumor growth and shrinkage during radiation treatment, (ii) on a mesoscopic scale, it provides the cell density and vascular fraction for each voxel, and (iii) on the microscopic scale, the oxygen distribution may be obtained in terms of oxygen histograms. With increasing tumor size, the simulated tumors develop a hypoxic core. Within the model, tumor shrinkage was found to be significantly more important for reoxygenation than angiogenesis or decreased oxygen consumption due to an increased fraction of dead cells. In the studied HNSSC-case, the TCD{sub 50} values (dose at 50% TCP) decreased from 71.0 Gy under hypoxic to 53.6 Gy under the oxic condition. Conclusions: The results obtained with the developed multiscale model are in accordance with expectations based on radiobiological principles and clinical experience. As the model is voxel-based, radiological imaging methods may help to provide the required 3D-characterization of the tumor prior to irradiation. For clinical application, the model has to be further validated with experimental and clinical data. If this is achieved, the model may be used to optimize fractionation schedules and dose distributions for the treatment of hypoxic tumors.« less

Influence of urban surface properties and rainfall characteristics on surface water flood outputs - insights from a physical modelling environment

NASA Astrophysics Data System (ADS)

Green, Daniel; Pattison, Ian; Yu, Dapeng

2017-04-01

Surface water (pluvial) flooding occurs when excess rainfall from intense precipitation events is unable to infiltrate into the subsurface or drain via natural or artificial drainage channels. Surface water flood events pose a major hazard to urban regions across the world, with nearly two thirds of flood damages in the UK being caused by surface water flood events. The perceived risk of surface water flooding appears to have increased in recent years due to several factors, including (i) precipitation increases associated with climatic change and variability; (ii) population growth meaning more people are occupying flood risk areas, and; (iii) land-use changes. Because urban areas are often associated with a high proportion of impermeable land-uses (e.g. tarmacked or paved surfaces and buildings) and a reduced coverage of vegetated, permeable surfaces, urban surface water flood risk during high intensity precipitation events is often exacerbated. To investigate the influence of urbanisation and terrestrial factors on surface water flood outputs, rainfall intensity, catchment slope, permeability, building density/layout scenarios were designed within a novel, 9m2 physical modelling environment. The two-tiered physical model used consists of (i) a low-cost, nozzle-type rainfall simulator component which is able to simulate consistent, uniformly distributed rainfall events of varying duration and intensity, and; (ii) a reconfigurable, modular plot surface. All experiments within the physical modelling environment were subjected to a spatiotemporally uniform 45-minute simulated rainfall event, while terrestrial factors on the physical model plot surface were altered systematically to investigate their hydrological response on modelled outflow and depth profiles. Results from the closed, controlled physical modelling experiments suggest that meteorological factors, such as the duration and intensity of simulated rainfall, and terrestrial factors, such as model slope, surface permeability and building density have a significant influence on physical model hydrological outputs. For example, changes in building density across the urban model catchment are shown to result in hydrographs having (i) a more rapid rising limb; (ii) higher peak discharges; (iii) a reduction in the total hydrograph time, and; (iv) a faster falling limb, with the dense building scenario having a 22% increase in peak discharge when compared to the no building scenario. Furthermore, the layout of buildings across the plot surface and their proximity to the outflow unit (i.e. downstream, upstream or to the side of the physical model outlet) is shown to influence outflow hydrograph response, with downstream concentrated building scenarios resulting in a delay in hydrograph onset time and a reduction in the time of the total outflow hydrograph event.

ELECTROMAGNETISM, OPTICS, ACOUSTICS, HEAT TRANSFER, CLASSICAL MECHANICS, AND FLUID DYNAMICS: Highly Efficient Lattice Boltzmann Model for Compressible Fluids: Two-Dimensional Case

NASA Astrophysics Data System (ADS)

Chen, Feng; Xu, Ai-Guo; Zhang, Guang-Cai; Gan, Yan-Biao; Cheng, Tao; Li, Ying-Jun

2009-10-01

We present a highly efficient lattice Boltzmann model for simulating compressible flows. This model is based on the combination of an appropriate finite difference scheme, a 16-discrete-velocity model [Kataoka and Tsutahara, Phys. Rev. E 69 (2004) 035701(R)] and reasonable dispersion and dissipation terms. The dispersion term effectively reduces the oscillation at the discontinuity and enhances numerical precision. The dissipation term makes the new model more easily meet with the von Neumann stability condition. This model works for both high-speed and low-speed flows with arbitrary specific-heat-ratio. With the new model simulation results for the well-known benchmark problems get a high accuracy compared with the analytic or experimental ones. The used benchmark tests include (i) Shock tubes such as the Sod, Lax, Sjogreen, Colella explosion wave, and collision of two strong shocks, (ii) Regular and Mach shock reflections, and (iii) Shock wave reaction on cylindrical bubble problems. With a more realistic equation of state or free-energy functional, the new model has the potential tostudy the complex procedure of shock wave reaction on porous materials.

Brownfield Action III - Modular use of hydrogeology instruction in the virtual classroom

NASA Astrophysics Data System (ADS)

Bower, P.; Liddicoat, J.

2009-04-01

Brownfield Action III (BA III) is a network-based, interactive, digital space and simulation developed by Barnard College and the Columbia Center for New Media Teaching and Learning in which students explore and solve problems in environmental forensics. BA III is a proven inquiry-based approach to teaching and learning that, since its inception in 1999, has been recognized as an exemplary curriculum. Indeed, in 2002 it was selected as a national model curriculum by SENCER (Science Education for New Civic Engagements and Responsibilities). BA III provides instruction in environmental site assessments and in the remediation of former industrial sites (brownfields) for secondary and higher education students. The initial full-semester, three hours of weekly laboratory instruction that complements lectures in BA II has been revised for modular use in Hydrology, Environmental Science, and Environmental Ethics undergraduate and graduate courses in the United States. The remediation of brownfields is important because they have potential as recreational, residential, and commercial real estate sites. As part of determining the value of such a site, an environmental site assessment (ESA) is required to determine the nature and extent of any contamination. To reach that objective, BA III contains a narrative that is embedded and to be discovered in simulation; it is a story of groundwater contamination complete with underground contaminant plumes in a fictitious town with buildings, roads, wells, water tower, homes, and businesses as well as a municipal government with relevant historical documents. Student companies work collaboratively in teams of two, sign a contract with a development corporation to conduct a Phase One ESA, receive a realistic budget, and compete with other teams to fulfill the contract while maximizing profit. To reach a valid conclusion in the form of a professional-level ESA and 3-D maps of the physical site, teams construct a detailed narrative from diverse forms of information, including socio-historical and a scientific dataset comprised of over 2,000,000 data points. BA III forces students to act on their perceptions of the interlocking realms of knowledge, theory and practical experience, providing an opportunity for them to gain valuable practice at tackling the complexity and ambiguity of a large-scale, interdisciplinary investigation of groundwater contamination and environmental forensics.

SPEEDES - A multiple-synchronization environment for parallel discrete-event simulation

NASA Technical Reports Server (NTRS)

Steinman, Jeff S.

1992-01-01

Synchronous Parallel Environment for Emulation and Discrete-Event Simulation (SPEEDES) is a unified parallel simulation environment. It supports multiple-synchronization protocols without requiring users to recompile their code. When a SPEEDES simulation runs on one node, all the extra parallel overhead is removed automatically at run time. When the same executable runs in parallel, the user preselects the synchronization algorithm from a list of options. SPEEDES currently runs on UNIX networks and on the California Institute of Technology/Jet Propulsion Laboratory Mark III Hypercube. SPEEDES also supports interactive simulations. Featured in the SPEEDES environment is a new parallel synchronization approach called Breathing Time Buckets. This algorithm uses some of the conservative techniques found in Time Bucket synchronization, along with the optimism that characterizes the Time Warp approach. A mathematical model derived from first principles predicts the performance of Breathing Time Buckets. Along with the Breathing Time Buckets algorithm, this paper discusses the rules for processing events in SPEEDES, describes the implementation of various other synchronization protocols supported by SPEEDES, describes some new ones for the future, discusses interactive simulations, and then gives some performance results.

Design, Evaluation and GCM-Performance of a New Parameterization for Microphysics of Clouds with Relaxed Arakawa-Schubert Scheme (McRas)

NASA Technical Reports Server (NTRS)

Sud, Y. C.; Walker, G. K.

1998-01-01

A prognostic cloud scheme named McRAS (Microphysics of clouds with Relaxed Arakawa-Schubert Scheme) was developed with the aim of improving cloud-microphysics, and cloud-radiation interactions in GCMs. McRAS distinguishes convective, stratiform, and boundary-layer clouds. The convective clouds merge into stratiform clouds on an hourly time-scale, while the boundary-layer clouds do so instantly. The cloud condensate transforms into precipitation following the auto-conversion relations of Sundqvist that contain a parametric adaptation for the Bergeron-Findeisen process of ice crystal growth and collection of cloud condensate by precipitation. All clouds convect, advect, and diffuse both horizontally and vertically with a fully active cloud-microphysics throughout its life-cycle, while the optical properties of clouds are derived from the statistical distribution of hydrometeors and idealized cloud geometry. An evaluation of McRAS in a single column model (SCM) with the GATE Phase III data has shown that McRAS can simulate the observed temperature, humidity, and precipitation without discernible systematic errors. An evaluation with the ARM-CART SCM data in a cloud model intercomparison exercise shows reasonable but not an outstanding accurate simulation. Such a discrepancy is common to almost all models and is related, in part, to the input data quality. McRAS was implemented in the GEOS II GCM. A 50 month integration that was initialized with the ECMWF analysis of observations for January 1, 1987 and forced with the observed sea-surface temperatures and sea-ice distribution and vegetation properties (biomes, and soils), with prognostic soil moisture, snow-cover, and hydrology showed a very realistic simulation of cloud process, incloud water and ice, and cloud-radiative forcing (CRF). The simulated ITCZ showed a realistic time-mean structure and seasonal cycle, while the simulated CRF showed sensitivity to vertical distribution of cloud water which can be easily altered by the choice of time constant and incloud critical cloud water amount regulators for auto-conversion. The CRF and its feedbacks also have a profound effect on the ITCZ. Even though somewhat weaker than observed, the McRAS-GCM simulation produces robust 30-60 day oscillations in the 200 hPa velocity potential. Two ensembles of 4-summer (July, August, September) simulations, one each for 1987 and 1988 show that the McRAS-GCM simulates realistic and statistically significant precipitation differences over India, Central America, and tropical Africa. Several seasonal simulations were performed with McRAS-GEOS II GCM for the summer (June-July- August) and winter (December-January-February) periods to determine how the simulated clouds and CRFs would be affected by: i) advection of clouds; ii) cloud top entrainment instability, iii) cloud water inhomogeneity correction, and (iv) cloud production and dissipation in different cloud-processes. The results show that each of these processes contributes to the simulated cloud-fraction and CRF.

R-process Enrichment in Cosmological Zoom Simulation of a Milkyway Type Halo by Neutron Star Mergers; The Origin of the MP-R and CEMP-R Stars

NASA Astrophysics Data System (ADS)

Safarzadeh, Mohammadtaher; Scannapieco, Evan

2018-06-01

The history of r-process enrichment in our galaxy is modeled through a novel set of zoom cosmo- logical simulations on a MilkyWay type galaxy. r-process sources are assumed to be neutron star mergers with a distribution of natal kicks and merge time distribution. We model turbulent mixing to estimate the pristine gas fraction in each simulation cell which we use to determine the Pop III star formation with assigned Carbon rich ejecta when going off as SNe. We follow the formation of Carbon-Enhanced Metal-Poor (CEMP) stars and the statistics of different r-process enhanced class of stars. The simulation underpredict the frequency of CEMP/MP stars by a factor of 2-4. Likewise the MP-rI/MP and MP-rII/MP and CEMP-r/CEMP cumulative ratios are all under predicted by 1-2 orders of magnitude. Our results show that NS binaries by themselves fall too short to explain the observed frequency of r-process enhanced stars and other sources of r-process enrichment at high redshifts are needed to fill the gap.

Wave energy analysis based on simulation wave data in the China Sea

NASA Astrophysics Data System (ADS)

Gao, Zhan-sheng; Qian, Yu-hao; Sui, Yu-wei; Chen, Xuan; Zhang, Da

2018-05-01

In the current world, where human beings are severely plagued by environmental problems and energy crisis, the full and reasonable utilization of marine new energy resources will contribute to alleviating the energy crisis, contributing to global energy-saving, emission reduction and environmental protection, thus to promote sustainable development. In this study, we firstly simulated a 10-year (1991-2000) 6-hourly wave data of the China Sea, by using the Simulating WAves Nearshore (SWAN) wave model nested with WAVEWATCH-III (WW3) wave model forced with Cross-Calibrated, Multi-Platform (CCMP) wind data. Considering the value size and stability of the wave energy density, we analyzed the overall characteristics of the China Sea wave energy with using the simulation wave data. Results show that: (1) The wave energy density in January and October is distinctly higher than that in April and July. The large center of annual average Wave energy density is located in the north of the South China Sea (of about 12-16 kW/m). (2) Synthetically considering the value size and stability of the wave energy density and stability, the energy-rich area is found to be located in the north region of the South China Sea.

The Radiative Forcing Model Intercomparison Project (RFMIP): Experimental protocol for CMIP6

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

Pincus, Robert; Forster, Piers M.; Stevens, Bjorn

The phrasing of the first of three questions motivating CMIP6 – “How does the Earth system respond to forcing?” – suggests that forcing is always well-known, yet the radiative forcing to which this question refers has historically been uncertain in coordinated experiments even as understanding of how best to infer radiative forcing has evolved. The Radiative Forcing Model Intercomparison Project (RFMIP) endorsed by CMIP6 seeks to provide a foundation for answering the question through three related activities: (i) accurate characterization of the effective radiative forcing relative to a near-preindustrial baseline and careful diagnosis of the components of this forcing; (ii) assessment ofmore » the absolute accuracy of clear-sky radiative transfer parameterizations against reference models on the global scales relevant for climate modeling; and (iii) identification of robust model responses to tightly specified aerosol radiative forcing from 1850 to present. Complete characterization of effective radiative forcing can be accomplished with 180 years (Tier 1) of atmosphere-only simulation using a sea-surface temperature and sea ice concentration climatology derived from the host model's preindustrial control simulation. Assessment of parameterization error requires trivial amounts of computation but the development of small amounts of infrastructure: new, spectrally detailed diagnostic output requested as two snapshots at present-day and preindustrial conditions, and results from the model's radiation code applied to specified atmospheric conditions. In conclusion, the search for robust responses to aerosol changes relies on the CMIP6 specification of anthropogenic aerosol properties; models using this specification can contribute to RFMIP with no additional simulation, while those using a full aerosol model are requested to perform at least one and up to four 165-year coupled ocean–atmosphere simulations at Tier 1.« less

The Radiative Forcing Model Intercomparison Project (RFMIP): Experimental protocol for CMIP6

DOE PAGES

Pincus, Robert; Forster, Piers M.; Stevens, Bjorn

2016-09-27

The phrasing of the first of three questions motivating CMIP6 – “How does the Earth system respond to forcing?” – suggests that forcing is always well-known, yet the radiative forcing to which this question refers has historically been uncertain in coordinated experiments even as understanding of how best to infer radiative forcing has evolved. The Radiative Forcing Model Intercomparison Project (RFMIP) endorsed by CMIP6 seeks to provide a foundation for answering the question through three related activities: (i) accurate characterization of the effective radiative forcing relative to a near-preindustrial baseline and careful diagnosis of the components of this forcing; (ii) assessment ofmore » the absolute accuracy of clear-sky radiative transfer parameterizations against reference models on the global scales relevant for climate modeling; and (iii) identification of robust model responses to tightly specified aerosol radiative forcing from 1850 to present. Complete characterization of effective radiative forcing can be accomplished with 180 years (Tier 1) of atmosphere-only simulation using a sea-surface temperature and sea ice concentration climatology derived from the host model's preindustrial control simulation. Assessment of parameterization error requires trivial amounts of computation but the development of small amounts of infrastructure: new, spectrally detailed diagnostic output requested as two snapshots at present-day and preindustrial conditions, and results from the model's radiation code applied to specified atmospheric conditions. In conclusion, the search for robust responses to aerosol changes relies on the CMIP6 specification of anthropogenic aerosol properties; models using this specification can contribute to RFMIP with no additional simulation, while those using a full aerosol model are requested to perform at least one and up to four 165-year coupled ocean–atmosphere simulations at Tier 1.« less

Model-based prediction of progression-free survival in patients with first-line renal cell carcinoma using week 8 tumor size change from baseline.

PubMed

Claret, Laurent; Zheng, Jenny; Mercier, Francois; Chanu, Pascal; Chen, Ying; Rosbrook, Brad; Yazdi, Pithavala; Milligan, Peter A; Bruno, Rene

2016-09-01

To assess the link between early tumor shrinkage (ETS) and progression-free survival (PFS) based on historical first-line metastatic renal cell carcinoma (mRCC) data. Tumor size data from 921 patients with first-line mRCC who received interferon-alpha, sunitinib, sorafenib or axitinib in two Phase III studies were modeled. The relationship between model-based estimates of ETS at week 8 as well as the baseline prognostic factors and PFS was tested in multivariate log-logistic models. Model performance was evaluated using simulations of PFS distributions and hazard ratio (HR) across treatments for the two studies. In addition, an external validation was conducted using data from an independent Phase II RCC study. The relationship between expected HR of an investigational treatment vs. sunitinib and the differences in ETS was simulated. A model with a nonlinear ETS-PFS link was qualified to predict PFS distribution by ETS quartiles as well as to predict HRs of sunitinib vs. interferon-alpha and axitinib vs. sorafenib. The model also performed well in simulations of an independent study of axitinib (external validation). The simulations suggested that if a new investigational treatment could further reduce the week 8 ETS by 30 % compared with sunitinib, an expected HR [95 % predictive interval] of the new treatment vs. sunitinib would be 0.59 [0.46, 0.79]. A model has been developed that uses early changes in tumor size to predict the HR for PFS differences between treatment arms for first-line mRCC. Such a model may have utility in predicting the outcome of ongoing studies (e.g., as part of interim futility analyses), supporting early decision making and future study design for investigational agents in development for this indication.

Simulation of water flow and nitrogen transport for a Bulgarian experimental plot using SWAP and ANIMO models.

PubMed

Marinov, Dimitar; Querner, Erik; Roelsma, Jan

2005-04-01

Unsaturated zone models are useful tools in predicting effects of measures and can be used to optimise agricultural practice aiming to minimise the impact on the environment. However, current soil models have a varying degree of abstraction level referring to simulated processes in time and space. In the framework of an EU funded project the SWAP (Soil-Water-Atmosphere-Plant) and ANIMO (Agricultural-Nutrient-Model) models were tested for an experimental arable plot in Bulgaria. SWAP was used to simulate water flow in the soil while ANIMO describes nitrogen movement and transformations. The objectives of this study are: (i) to show results of the combined application of water and nitrogen dynamics of originally Dutch models SWAP and ANIMO for specific Bulgarian soil and hydrological conditions; (ii) to calibrate and evaluate SWAP and ANIMO models by comparing numerical results with field measurements collected for an arable field in western Bulgaria and (iii) to analyse possible contamination of groundwater due to agricultural practice in the considered region. Further a short description of the experimental plot, as well as information about parameters of the investigated soil profiles, is provided. The obtained SWAP results evidenced that the model gives sufficient adaptation for soil water dynamics. The simulations of ANIMO for nitrogen cycle show greater divergence with observations but are satisfactory precise for the purposes of assessing land use impact on groundwater quality. In general, differences between model results and field measurements do not exceed 10-15%. For the experimental plot predictions indicate nitrate-N concentrations less then 5 mg/l in deeper soil compartments and low downward annual flux containing 0.133 kg N/ha. These results indicate that there is no serious pollution of the shallow groundwater table by nitrogen resulting from land use and agricultural activities.

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

El-Atwani, O.; Norris, S. A.; Ludwig, K.

In this study, several proposed mechanisms and theoretical models exist concerning nanostructure evolution on III-V semiconductors (particularly GaSb) via ion beam irradiation. However, making quantitative contact between experiment on the one hand and model-parameter dependent predictions from different theories on the other is usually difficult. In this study, we take a different approach and provide an experimental investigation with a range of targets (GaSb, GaAs, GaP) and ion species (Ne, Ar, Kr, Xe) to determine new parametric trends regarding nanostructure evolution. Concurrently, atomistic simulations using binary collision approximation over the same ion/target combinations were performed to determine parametric trends onmore » several quantities related to existing model. A comparison of experimental and numerical trends reveals that the two are broadly consistent under the assumption that instabilities are driven by chemical instability based on phase separation. Furthermore, the atomistic simulations and a survey of material thermodynamic properties suggest that a plausible microscopic mechanism for this process is an ion-enhanced mobility associated with energy deposition by collision cascades.« less

Drought Persistence Errors in Global Climate Models

NASA Astrophysics Data System (ADS)

Moon, H.; Gudmundsson, L.; Seneviratne, S. I.

2018-04-01

The persistence of drought events largely determines the severity of socioeconomic and ecological impacts, but the capability of current global climate models (GCMs) to simulate such events is subject to large uncertainties. In this study, the representation of drought persistence in GCMs is assessed by comparing state-of-the-art GCM model simulations to observation-based data sets. For doing so, we consider dry-to-dry transition probabilities at monthly and annual scales as estimates for drought persistence, where a dry status is defined as negative precipitation anomaly. Though there is a substantial spread in the drought persistence bias, most of the simulations show systematic underestimation of drought persistence at global scale. Subsequently, we analyzed to which degree (i) inaccurate observations, (ii) differences among models, (iii) internal climate variability, and (iv) uncertainty of the employed statistical methods contribute to the spread in drought persistence errors using an analysis of variance approach. The results show that at monthly scale, model uncertainty and observational uncertainty dominate, while the contribution from internal variability is small in most cases. At annual scale, the spread of the drought persistence error is dominated by the statistical estimation error of drought persistence, indicating that the partitioning of the error is impaired by the limited number of considered time steps. These findings reveal systematic errors in the representation of drought persistence in current GCMs and suggest directions for further model improvement.

The High-Excitation Planetary Nebula NCG 246: Optical and Near-Ultraviolet Observations and Two-dimensional Numerical Models

NASA Technical Reports Server (NTRS)

Szentgyorgyi, Andrew; Raymond, John; Franco, Jose; Villaver, Eva; Lopez-Martin, Luis

2003-01-01

We have imaged the planetary nebula (PN) NGC 246 in the near-ultraviolet wavelengths [Ne v] 342.6 nm, the Bowen fluorescence line of 0 111 at 344.4 nm, and a nearby line-free region centered on 338.6 nm, as well as H(alpha), [O III] 500.7 nm, and [S II] 673.0 and 671.5 nm. Imaging in the 344.4 nm line is necessary to deconvolve contamination of the [Ne v] images by O III 342.9 nm. The emission from the shell and inner parts of the nebula is detected in [Ne v]. The radial profiles of the [Ne v] brightness decrease with radius from the exciting star, indicating that the bulk of the emission from this ion is due to the hard UV stellar radiation field, with a (probably) marginal contribution from collisional ionization in a shock between the PN shell and the interstellar medium (ISM). In contrast, the radial profiles of the emission in H(alpha), [0 III] 500.7 nm, and [S II] are flatter and peak at the location of the shell. The emission of [S II] probably traces the interaction of the PN with the ambient ISM. We also present two-dimensional numerical simulations for this PN-ISM interaction. The simulations consider the stellar motion with respect to the ambient ISM, with a velocity of 85 km/s , and include the time evolution of the wind parameters and UV radiation field from the progenitor star.

Rise of the First Super-Massive Stars

NASA Astrophysics Data System (ADS)

Regan, John A.; Downes, Turlough P.

2018-05-01

We use high resolution adaptive mesh refinement simulations to model the formation of massive metal-free stars in the early Universe. By applying Lyman-Werner (LW) backgrounds of 100 J21 and 1000 J21 respectively we construct environments conducive to the formation of massive stars. We find that only in the case of the higher LW backgrounds are super-critical accretion rates realised that are necessary for super-massive star (SMS) formation. Mild fragmentation is observed for both backgrounds. Violent dynamical interactions between the stars that form in the more massive halo formed (1000 J21 background) results in the eventual expulsion of the two most massive stars from the halo. In the smaller mass halo (100 J21 background) mergers of stars occur before any multibody interactions and a single massive Pop III star is left at the centre of the halo at the end of our simulation. Feedback from the very massive Pop III stars is not effective in generating a large HII region with ionising photons absorbed within a few thousand AU of the star. In all cases a massive black hole seed is the expected final fate of the most massive objects. The seed of the massive Pop III star which remained at the centre of the less massive halo experiences steady accretion rates of almost 10-2M_{⊙}/yr and if these rates continue could potentially experience super-Eddington accretion rates in the immediate aftermath of collapsing into a black hole.

Binding energies and modelling of nuclei in semiclassical simulations

NASA Astrophysics Data System (ADS)

Pérez-García, M. Ángeles; Tsushima, K.; Valcarce, A.

2008-03-01

We study the binding energies of spin isospin saturated nuclei with nucleon number 8⩽A⩽100 in semiclassical Monte Carlo many-body simulations. The model Hamiltonian consists of (i) nucleon kinetic energy, (ii) a nucleon nucleon interaction potential, and (iii) an effective Pauli potential which depends on density. The basic ingredients of the nucleon nucleon potential are a short-range repulsion, and a medium-range attraction. Our results demonstrate that one can always expect to obtain the empirical binding energies for a set of nuclei by introducing a proper density dependent Pauli potential in terms of a single variable, the nucleon number, A. The present work shows that in the suggested procedure there is a delicate counterbalance of kinetic and potential energetic contributions allowing a good reproduction of the experimental nuclear binding energies. This type of calculations may be of interest in further reproduction of other properties of nuclei such as radii and also exotic nuclei.

Swing-leg trajectory of running guinea fowl suggests task-level priority of force regulation rather than disturbance rejection.

PubMed

Blum, Yvonne; Vejdani, Hamid R; Birn-Jeffery, Aleksandra V; Hubicki, Christian M; Hurst, Jonathan W; Daley, Monica A

2014-01-01

To achieve robust and stable legged locomotion in uneven terrain, animals must effectively coordinate limb swing and stance phases, which involve distinct yet coupled dynamics. Recent theoretical studies have highlighted the critical influence of swing-leg trajectory on stability, disturbance rejection, leg loading and economy of walking and running. Yet, simulations suggest that not all these factors can be simultaneously optimized. A potential trade-off arises between the optimal swing-leg trajectory for disturbance rejection (to maintain steady gait) versus regulation of leg loading (for injury avoidance and economy). Here we investigate how running guinea fowl manage this potential trade-off by comparing experimental data to predictions of hypothesis-based simulations of running over a terrain drop perturbation. We use a simple model to predict swing-leg trajectory and running dynamics. In simulations, we generate optimized swing-leg trajectories based upon specific hypotheses for task-level control priorities. We optimized swing trajectories to achieve i) constant peak force, ii) constant axial impulse, or iii) perfect disturbance rejection (steady gait) in the stance following a terrain drop. We compare simulation predictions to experimental data on guinea fowl running over a visible step down. Swing and stance dynamics of running guinea fowl closely match simulations optimized to regulate leg loading (priorities i and ii), and do not match the simulations optimized for disturbance rejection (priority iii). The simulations reinforce previous findings that swing-leg trajectory targeting disturbance rejection demands large increases in stance leg force following a terrain drop. Guinea fowl negotiate a downward step using unsteady dynamics with forward acceleration, and recover to steady gait in subsequent steps. Our results suggest that guinea fowl use swing-leg trajectory consistent with priority for load regulation, and not for steadiness of gait. Swing-leg trajectory optimized for load regulation may facilitate economy and injury avoidance in uneven terrain.

Swing-Leg Trajectory of Running Guinea Fowl Suggests Task-Level Priority of Force Regulation Rather than Disturbance Rejection

PubMed Central

Blum, Yvonne; Vejdani, Hamid R.; Birn-Jeffery, Aleksandra V.; Hubicki, Christian M.; Hurst, Jonathan W.; Daley, Monica A.

2014-01-01

To achieve robust and stable legged locomotion in uneven terrain, animals must effectively coordinate limb swing and stance phases, which involve distinct yet coupled dynamics. Recent theoretical studies have highlighted the critical influence of swing-leg trajectory on stability, disturbance rejection, leg loading and economy of walking and running. Yet, simulations suggest that not all these factors can be simultaneously optimized. A potential trade-off arises between the optimal swing-leg trajectory for disturbance rejection (to maintain steady gait) versus regulation of leg loading (for injury avoidance and economy). Here we investigate how running guinea fowl manage this potential trade-off by comparing experimental data to predictions of hypothesis-based simulations of running over a terrain drop perturbation. We use a simple model to predict swing-leg trajectory and running dynamics. In simulations, we generate optimized swing-leg trajectories based upon specific hypotheses for task-level control priorities. We optimized swing trajectories to achieve i) constant peak force, ii) constant axial impulse, or iii) perfect disturbance rejection (steady gait) in the stance following a terrain drop. We compare simulation predictions to experimental data on guinea fowl running over a visible step down. Swing and stance dynamics of running guinea fowl closely match simulations optimized to regulate leg loading (priorities i and ii), and do not match the simulations optimized for disturbance rejection (priority iii). The simulations reinforce previous findings that swing-leg trajectory targeting disturbance rejection demands large increases in stance leg force following a terrain drop. Guinea fowl negotiate a downward step using unsteady dynamics with forward acceleration, and recover to steady gait in subsequent steps. Our results suggest that guinea fowl use swing-leg trajectory consistent with priority for load regulation, and not for steadiness of gait. Swing-leg trajectory optimized for load regulation may facilitate economy and injury avoidance in uneven terrain. PMID:24979750

Validation of a quantitative magnetic resonance method for measuring human body composition.

PubMed

Napolitano, Antonella; Miller, Sam R; Murgatroyd, Peter R; Coward, W Andrew; Wright, Antony; Finer, Nick; De Bruin, Tjerk W; Bullmore, Edward T; Nunez, Derek J

2008-01-01

To evaluate a novel quantitative magnetic resonance (QMR) methodology (EchoMRI-AH, Echo Medical Systems) for measurement of whole-body fat and lean mass in humans. We have studied (i) the in vitro accuracy and precision by measuring 18 kg Canola oil with and without 9 kg water (ii) the accuracy and precision of measures of simulated fat mass changes in human subjects (n = 10) and (iii) QMR fat and lean mass measurements compared to those obtained using the established 4-compartment (4-C) model method (n = 30). (i) QMR represented 18 kg of oil at 40 degrees C as 17.1 kg fat and 1 kg lean while at 30 degrees C 15.8 kg fat and 4.7 kg lean were reported. The s.d. of repeated estimates was 0.13 kg for fat and 0.23 kg for lean mass. Adding 9 kg of water reduced the fat estimates, increased misrepresentation of fat as lean, and degraded the precision. (ii) the simulated change in the fat mass of human volunteers was accurately represented, independently of added water. (iii) compared to the 4-C model, QMR underestimated fat and over-estimated lean mass. The extent of difference increased with body mass. The s.d. of repeated measurements increased with adiposity, from 0.25 kg (fat) and 0.51 kg (lean) with BMI <25 kg/m(2) to 0.43 kg and 0.81 kg respectively with BMI >30 kg/m(2). EchoMRI-AH prototype showed shortcomings in absolute accuracy and specificity of fat mass measures, but detected simulated body composition change accurately and with precision roughly three times better than current best measures. This methodology should reduce the study duration and cohort number needed to evaluate anti-obesity interventions.

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 within 1% of those obtained by providing spatially specific values for about 800 parcels.

14 CFR 61.1 - Applicability and definitions.

Code of Federal Regulations, 2014 CFR

2014-01-01

....2. Aeronautical experience means pilot time obtained in an aircraft, flight simulator, or flight... from an authorized instructor in an aircraft, flight simulator, or flight training device; or (iii) Gives training as an authorized instructor in an aircraft, flight simulator, or flight training device...

Snowplow simulator training evaluation : potential fuel & drivetrain maintenance cost reduction

DOT National Transportation Integrated Search

2007-12-01

The Arizona Department of Transportation (ADOT) introduced simulator-based training in 2004, when maintenance crews in five rural districts received a third-party snowplow safety topics course on the L-3 TransSim VS III simulator. In 2005, a simulato...

Long-term soil organic carbon changes in cereal and ley rotations: model testing

NASA Astrophysics Data System (ADS)

Kynding Borgen, Signe; Dörsch, Peter; Krogstad, Tore; Azzaroli Bleken, Marina

2015-04-01

Reliable modeling of soil organic carbon (SOC) dynamics in agroecosystems is crucial to define mitigation strategies related to crop management on the farm scale as well as the regional scale. International climate agreements and national political decisions rely to a large extent on the National Greenhouse gas Inventory Reports that are submitted annually to the UNFCCC. However, lower tier methods are used to estimate SOC changes on cropland in most country reports. The application of mechanistic models in national greenhouse gas inventory estimation requires proper model testing against measurements in order to verify the estimated emissions. Few long-term field experiments measuring SOC stock changes have been conducted in Norway. We evaluate the performance of the Introductory Carbon Balance Model (ICBM) in simulating SOC changes over 60 years in a field experiment conducted in Ås from 1953-2013. The site is located in south-eastern Norway, on the boarder of the boreal and temperate climate zone, where the majority of the country's grain production occurs. The field trial consisted of four rotations: I) continuous cereal, II) cereal + row crops, III) 2 years of ley + 4 years of cereal, IV) 4 years of ley + 2 years of cereal, and four treatments per rotation: a) low NPK, b) high NPK, c) low NPK + FYM, and d) straw (on rotations I and II) or high NPK + FYM (on rotations III and IV). The annual external modifying factor of the decomposition rate was calculated based on daily minimum and maximum temperature, precipitation, relative humidity, wind speed, and net radiation, and adjusted for soil type and crop management according to default ICBM calibration. We present results of simulated C changes for the long term plots and explore options to improve parameter calibration. Finally, we provide suggestions for how problems regarding model verification can be handled with when applying the model on a national scale for inventory reporting.

Monte Carlo simulations of radioactive waste encapsulated by bisphenol-A polycarbonate and effect of bismuth-III oxide filler material

NASA Astrophysics Data System (ADS)

Özdemir, Tonguç

2017-06-01

Radioactive waste generated from the nuclear industry and non-power applications should carefully be treated, conditioned and disposed according to the regulations set by the competent authority(ies). Bisphenol-a polycarbonate (BPA-PC), a very widely used polymer, might be considered as a potential candidate material for low level radioactive waste encapsulation. In this work, the dose rate distribution in the radioactive waste drum (containing radioactive waste and the BPA-PC polymer matrix) was determined using Monte Carlo simulations. Moreover, the change of mechanical properties of BPA-PC was estimated and their variation within the waste drum was determined for the periods of 15, 30 and 300 years after disposal to the final disposal site. The change of the dose rate within the waste drum with different contents of bismuth-III oxide were also simulated. It was concluded that addition of bismuth-III oxide filler decreases the dose delivered to the polymeric matrix due to photoelectric effect.

Multiphase flow models for hydraulic fracturing technology

NASA Astrophysics Data System (ADS)

Osiptsov, Andrei A.

2017-10-01

The technology of hydraulic fracturing of a hydrocarbon-bearing formation is based on pumping a fluid with particles into a well to create fractures in porous medium. After the end of pumping, the fractures filled with closely packed proppant particles create highly conductive channels for hydrocarbon flow from far-field reservoir to the well to surface. The design of the hydraulic fracturing treatment is carried out with a simulator. Those simulators are based on mathematical models, which need to be accurate and close to physical reality. The entire process of fracture placement and flowback/cleanup can be conventionally split into the following four stages: (i) quasi-steady state effectively single-phase suspension flow down the wellbore, (ii) particle transport in an open vertical fracture, (iii) displacement of fracturing fluid by hydrocarbons from the closed fracture filled with a random close pack of proppant particles, and, finally, (iv) highly transient gas-liquid flow in a well during cleanup. The stage (i) is relatively well described by the existing hydralics models, while the models for the other three stages of the process need revisiting and considerable improvement, which was the focus of the author’s research presented in this review paper. For stage (ii), we consider the derivation of a multi-fluid model for suspension flow in a narrow vertical hydraulic fracture at moderate Re on the scale of fracture height and length and also the migration of particles across the flow on the scale of fracture width. At the stage of fracture cleanaup (iii), a novel multi-continua model for suspension filtration is developed. To provide closure relationships for permeability of proppant packings to be used in this model, a 3D direct numerical simulation of single phase flow is carried out using the lattice-Boltzmann method. For wellbore cleanup (iv), we present a combined 1D model for highly-transient gas-liquid flow based on the combination of multi-fluid and drift-flux approaches. The derivation of the drift-flux model from conservation olaws is criticall revisited in order to define the list of underlying assumptions and to mark the applicability margins of the model. All these fundamental problems share the same technological application (hydraulic fracturing) and the same method of research, namely, the multi-fluid approach to multiphase flow modeling and the consistent use of asymptotic methods. Multi-fluid models are then discussed in comparison with semi-empirical (often postulated) models widely used in the industry.

PSF modeling by spikes simulations and wings measurements for the MOONS multi fiber spectrograph

NASA Astrophysics Data System (ADS)

Li Causi, G.; Lee, D.; Vitali, F.; Royer, F.; Oliva, E.

2016-08-01

The optical design of MOONS, the next generation thousand-fiber NIR spectrograph for the VLT, involves both on-axis reflective collimators and on-axis very fast reflective cameras, which yields both beam obstruction, due to fiber slit and detector support, and image spread, due to propagation within detector substrate. The need to model and control i) the effect of the diffraction spikes produced by these obstructions, ii) the detector-induced shape variation of the Point Spread Function (PSF), and iii) the intensity profile of the PSF wings, leads us to perform both simulations and lab measurements, in order to optimize the spider design and built a reliable PSF model, useful for simulate realistic raw images for testing the data reduction. Starting from the unobstructed PSF variation, as computed with the ZEMAX software, we numerically computed the diffraction spikes for different spider shapes, to which we added the PSF wing profile, as measured on a sample of the MOONS VPH diffraction grating. Finally, we implemented the PSF defocusing due to the thick detector (for the visible channel), we convolved the PSF with the fiber core image, and we added the optical ghosts, so finally obtaining a detailed and realistic PSF model, that we use for spectral extraction testing, cross talk estimation, and sensitivity predictions.

Experimental characterization and self-consistent modeling of luminescence coupling effect in III-V multijunction solar cells

NASA Astrophysics Data System (ADS)

Sogabe, Tomah; Ogura, Akio; Hung, Chao-Yu; Evstropov, Valery; Mintairov, Mikhail; Shvarts, Maxim; Okada, Yoshitaka

2013-12-01

In this paper, we focused on developing an accurate model to describe the luminescent coupling (L-C) effect in multijunction solar cells (MJSC) under light concentration. We present here a transcend current-voltage (I-V) formula combined with a self-consistent simulation algorithm to derive the coupling yield γ dependence on light intensity by including the electrical parameters such as shunt resistance (Rsh) and series resistance (Rs), which were ignored in previous simulation models. The effects of both Rsh and Rs on γ were revealed, and the dependence of γ on the external voltage bias Vbias was investigated. Meanwhile, we have performed experiments to determine coupling yield γ by measuring the I-V curves of individual subcell of InGaP/GaAs/Ge triple junction solar cell under varied light intensity. We found that the measured results are only in good agreement with the simulated data obtained from the model where the resistance parameters were included. Based on these results, we calculated the conversion efficiency of MJSC and found that the efficiency increase due to L-C effect is 0.31% under 1 sun and 1.07% under 1000 suns. Thus the L-C analysis results presented here will work as an additional device optimization criteria for MJSC toward higher efficiency.

Hyper III on ramp with single-piece pivot wing installed & Princeton sailwing on ground, with Da

NASA Technical Reports Server (NTRS)

1969-01-01

The Hyper III's shape provided too little lift to land without some type of deployable wing. The single free flight was made using a simulated one-piece pivot wing, which was attached to the upper surface of the fuselage. This used a wing kit from an HP-11 sailplane, which was assembled by Daniel Garrabrant (shown in the photo). Another possible wing was the Flexible Princeton Sailwing. The piloted Hyper III flights were to be made using an SA-16B Albatross seaplane as the drop aircraft. The Hyper III would be carried under the SA-16B's wing on a drop-tank rack. Flight Research Center Director Paul Bikle asked NASA Headquarters for permission to exchange the Center's C-47 for the SA-16. Headquarters turned down this request, effectively ending the possibility of Hyper III flights with a pilot on board. The Flight Research Center (FRC--as Dryden was named from 1959 until 1976) already had experience with testing small-scale aircraft using model-airplane techniques, but the first true remotely piloted research vehicle was the Hyper III, which flew only once in December 1969. At that time, the Center was engaged in flight research with a variety of reentry shapes called lifting bodies, and there was a desire both to expand the flight research experience with maneuverable reentry vehicles, including a high-performance, variable-geometry craft, and to investigate a remotely piloted flight research technique that made maximum use of a research pilot's skill and experience by placing him 'in the loop' as if he were in the cockpit. (There have been, as yet, no female research pilots assigned to Dryden.) The Hyper III as originally conceived was a stiletto-shaped lifting body that had resulted from a study at NASA's Langley Research Center in Hampton, Virginia. It was one of a number of hypersonic, cross-range reentry vehicles studied at Langley. (Hypersonic means Mach 5--five times the speed of sound--or faster; cross-range means able to fly a considerable distance to the left or right of the initial reentry path.) The FRC added a small, deployable, skewed wing to compensate for the shape's extremely low glide ratio. Shop personnel built the 32-foot-long Hyper III and covered its tubular frame with dacron, aluminum, and fiberglass, for about $6,500. Hyper III employed the same '8-ball' attitude indicator developed for control-room use when flying the X-15, two model-airplane receivers to command the vehicle's hydraulic controls, and a telemetry system (surplus from the X-15 program) to transmit 12 channels of data to the ground not only for display and control but for data analysis. Dropped from a helicopter at 10,000 feet, Hyper III flew under the control of research pilot Milt Thompson to a near landing using instruments for control. When the vehicle was close to the ground, he handed the vehicle off to experienced model pilot Dick Fischer for a visual landing using standard controls. The flight demonstrated the feasibility of remotely piloting research vehicles and, among other things, that control of the vehicle in roll was much better than predicted and that the vehicle had a much lower lift-to-drag ratio than predicted (a maximum of 4.0 rather than 5.0). Pilot Milt Thompson exhibited some suprising reactions during the Hyper III flight; he behaved as if he were in the cockpit of an actual research aircraft. 'I was really stimulated emotionally and physically in exactly the same manner that I have been during actual first flights.' 'Flying the Hyper III from a ground cockpit was just as dramatic as an actual flight in any of the other vehicles....responsibility rather than fear of personal safety is the real emotional driver. I have never come out of a simulator emtionally and physically tired as is often the case after a test flight in a research aircraft. I was emotionally and physically tired after a 3-minute flight of the Hyper III.'

Radio controlled mothership, Hyper III, and M2-F2 models on lakebed with research staff

NASA Technical Reports Server (NTRS)

1968-01-01

left to right: Richard C. Eldredge, Dale Reed, James O. Newman, Bob McDonald with the mothership (top) and other models. Over the years, the Dryden Flight Research Center and its predecessors has flown various models to gather data for various purposes. The mothership has been used to launch the models. The Flight Research Center (FRC--as Dryden was named from 1959 until 1976) already had experience with testing small-scale aircraft using model-airplane techniques, but the first true remotely piloted research vehicle was the full-sized Hyper III, which flew only once in December 1969. At that time, the Center was engaged in flight research with a variety of reentry shapes called lifting bodies, and there was a desire both to expand the flight research experience with maneuverable reentry vehicles, including a high-performance, variable-geometry craft, and to investigate a remotely piloted flight research technique that made maximum use of a research pilot's skill and experience by placing him 'in the loop' as if he were in the cockpit. (There have been, as yet, no female research pilots assigned to Dryden.) The Hyper III as originally conceived was a stiletto-shaped lifting body that had resulted from a study at NASA's Langley Research Center in Hampton, Virginia. It was one of a number of hypersonic, cross-range reentry vehicles studied at Langley. (Hypersonic means Mach 5--five times the speed of sound--or faster; cross-range means able to fly a considerable distance to the left or right of the initial reentry path.) The FRC added a small, deployable, skewed wing to compensate for the shape's extremely low glide ratio. Shop personnel built the 32-foot-long Hyper III and covered its tubular frame with dacron, aluminum, and fiberglass, for about $6,500. Hyper III employed the same '8-ball' attitude indicator developed for control-room use when flying the X-15, two model-airplane receivers to command the vehicle's hydraulic controls, and a telemetry system (surplus from the X-15 program) to transmit 12 channels of data to the ground not only for display and control but for data analysis. Dropped from a helicopter at 10,000 feet, Hyper III flew under the control of research pilot Milt Thompson to a near landing using instruments for control. When the vehicle was close to the ground, he handed the vehicle off to experienced model pilot Dick Fischer for a visual landing using standard controls. The flight demonstrated the feasibility of remotely piloting research vehicles and, among other things, that control of the vehicle in roll was much better than predicted and that the vehicle had a much lower lift-to-drag ratio than predicted (a maximum of 4.0 rather than 5.0). Pilot Milt Thompson exhibited some suprising reactions during the Hyper III flight; he behaved as if he were in the cockpit of an actual research aircraft. 'I was really stimulated emotionally and physically in exactly the same manner that I have been during actual first flights.' 'Flying the Hyper III from a ground cockpit was just as dramatic as an actual flight in any of the other vehicles....responsibility rather than fear of personal safety is the real emotional driver. I have never come out of a simulator emtionally and physically tired as is often the case after a test flight in a research aircraft. I was emotionally and physically tired after a 3-minute flight of the Hyper III.'

Forecasting of global solar radiation using anfis and armax techniques

NASA Astrophysics Data System (ADS)

Muhammad, Auwal; Gaya, M. S.; Aliyu, Rakiya; Aliyu Abdulkadir, Rabi'u.; Dauda Umar, Ibrahim; Aminu Yusuf, Lukuman; Umar Ali, Mudassir; Khairi, M. T. M.

2018-01-01

Procurement of measuring device, maintenance cost coupled with calibration of the instrument contributed to the difficulty in forecasting of global solar radiation in underdeveloped countries. Most of the available regressional and mathematical models do not capture well the behavior of the global solar radiation. This paper presents the comparison of Adaptive Neuro Fuzzy Inference System (ANFIS) and Autoregressive Moving Average with eXogenous term (ARMAX) in forecasting global solar radiation. Full-Scale (experimental) data of Nigerian metrological agency, Sultan Abubakar III international airport Sokoto was used to validate the models. The simulation results demonstrated that the ANFIS model having achieved MAPE of 5.34% outperformed the ARMAX model. The ANFIS could be a valuable tool for forecasting the global solar radiation.

The Response of a Spectral General Circulation Model to Refinements in Radiative Processes.

NASA Astrophysics Data System (ADS)

Ramanathan, V.; Pitcher, Eric J.; Malone, Robert C.; Blackmon, Maurice L.

1983-03-01

We present here results and analyses of a series of numerical experiments performed with a spectral general circulation model (GCM). The purpose of the GCM experiments is to examine the role of radiation/cloud processes in the general circulation of the troposphere and stratosphere. The experiments were primarily motivated by the significant improvements in the GCM zonal mean simulation as refinements were made in the model treatment of clear-sky radiation and cloud-radiative interactions. The GCM with the improved cloud/radiation model is able to reproduce many observed features, such as: a clear separation between the wintertime tropospheric jet and the polar night jet; winter polar stratospheric temperatures of about 200 K; interhemispheric and seasonal asymmetries in the zonal winds.In a set of sensitivity experiments, we have stripped the cloud/radiation model of its improvements, the result being a significant degradation of the zonal mean simulations by the GCM. Through these experiments we have been able to identify the processes that are responsible for the improved GCM simulations: (i) careful treatment of the upper boundary condition for O3 solar heating; (ii) temperature dependence of longwave cooling by CO2 15 m bands., (iii) vertical distribution of H2O that minimizes the lower stratospheric H2O longwave cooling; (iv) dependence of cirrus emissivity on cloud liquid water content.Comparison of the GCM simulations, with and without the cloud/radiation improvements, reveals the nature and magnitude of the following radiative-dynamical interactions: (i) the temperature decrease (due to errors in radiative heating) within the winter polar stratosphere is much larger than can be accounted for by purely radiative adjustment; (ii) the role of dynamics in maintaining the winter polar stratosphere thermal structure is greatly diminished in the GCM with the degraded treatment of radiation; (iii) the radiative and radiative-dynamical response times of the atmosphere vary from periods of less than two weeks in the lower troposphere to roughly three months in the polar lower stratosphere; (iv) within the stratosphere, the radiative response times vary significantly with temperature, with the winter polar values larger than the summer polar values by as much as a factor of 2.5.Cirrus clouds, if their emissivities are arbitrarily prescribed to be black, unrealistically enhance the radiative cooling of the polar troposphere above 8 km. This results in a meridional temperature gradient much stronger than that which is observed. We employ a more realistic parameterization that accounts for the non-blackness of cirrus, and we describe the resulting improvements in the model simulation of zonal winds, temperatures, and radiation budget.

HiFiVS Modeling of Flow Diverter Deployment Enables Hemodynamic Characterization of Complex Intracranial Aneurysm Cases

PubMed Central

Xiang, Jianping; Damiano, Robert J.; Lin, Ning; Snyder, Kenneth V.; Siddiqui, Adnan H.; Levy, Elad I.; Meng, Hui

2016-01-01

Object Flow diversion via Pipeline Embolization Device (PED) represents the most recent advancement in endovascular therapy of intracranial aneurysms. This exploratory study aims at a proof of concept for an advanced device-modeling tool in conjunction with computational fluid dynamics (CFD) to evaluate flow modification effects by PED in real treatment cases. Methods We performed computational modeling of three PED-treated complex aneurysm cases. Case I had a fusiform vertebral aneurysm treated with a single PED. Case II had a giant internal carotid artery (ICA) aneurysm treated with 2 PEDs. Case III consisted of two tandem ICA aneurysms (a and b) treated by a single PED. Our recently developed high fidelity virtual stenting (HiFiVS) technique was used to recapitulate the clinical deployment process of PEDs in silico for these three cases. Pre- and post-treatment aneurysmal hemodynamics using CFD simulation was analyzed. Changes in aneurysmal flow velocity, inflow rate, and wall shear stress (WSS) (quantifying flow reduction) and turnover time (quantifying stasis) were calculated and compared with clinical outcome. Results In Case I (occluded within the first 3 months), the aneurysm experienced the most drastic aneurysmal flow reduction after PED placement, where the aneurysmal average velocity, inflow rate and average WSS was decreased by 76.3%, 82.5% and 74.0%, respectively, while the turnover time was increased to 572.1% of its pre-treatment value. In Case II (occluded at 6 months), aneurysmal average velocity, inflow rate and average WSS were decreased by 39.4%, 38.6%, and 59.1%, respectively, and turnover time increased to 163.0%. In Case III, Aneurysm III-a (occluded at 6 months) experienced decrease by 38.0%, 28.4%, and 50.9% in aneurysmal average velocity, inflow rate and average WSS, respectively and increase to 139.6% in turnover time, which was quite similar to Aneurysm II. Surprisingly, the adjacent Aneurysm III-b experienced more substantial flow reduction (decrease by 77.7%, 53.0%, and 84.4% in average velocity, inflow rate and average WSS, respectively, and increase to 213.0% in turnover time) than Aneurysm III-a, which qualitatively agreed with angiographic observation at 3-month follow-up. However, Aneurysm III-b remained patent at both 6 months and 9 months. A closer examination of the vascular anatomy of Case III revealed blood draining to the ophthalmic artery off Aneurysm III-b, which may have prevented its complete thrombosis. Conclusion This proof-of-concept study demonstrates that HiFiVE modeling of flow diverter deployment enables detailed characterization of hemodynamic alteration by PED placement. Post-treatment aneurysmal flow reduction may be correlated with aneurysm occlusion outcome. However, predicting aneurysm treatment outcome by flow diverters also requires consideration of other factors including vascular anatomy. PMID:26090829

A Morphological Analysis of Gamma-Ray Burst Early-optical Afterglows

NASA Astrophysics Data System (ADS)

Gao, He; Wang, Xiang-Gao; Mészáros, Peter; Zhang, Bing

2015-09-01

Within the framework of the external shock model of gamma-ray burst (GRB) afterglows, we perform a morphological analysis of the early-optical light curves to directly constrain model parameters. We define four morphological types, i.e., the reverse shock-dominated cases with/without the emergence of the forward shock peak (Type I/Type II), and the forward shock-dominated cases without/with νm crossing the band (Type III/IV). We systematically investigate all of the Swift GRBs that have optical detection earlier than 500 s and find 3/63 Type I bursts (4.8%), 12/63 Type II bursts (19.0%), 30/63 Type III bursts (47.6%), 8/63 Type IV bursts (12.7%), and 10/63 Type III/IV bursts (15.9%). We perform Monte Carlo simulations to constrain model parameters in order to reproduce the observations. We find that the favored value of the magnetic equipartition parameter in the forward shock ({ɛ }B{{f}}) ranges from 10-6 to 10-2, and the reverse-to-forward ratio of ɛB ({{R}}B) is about 100. The preferred electron equipartition parameter {ɛ }{{e}}{{r},{{f}}} value is 0.01, which is smaller than the commonly assumed value, e.g., 0.1. This could mitigate the so-called “efficiency problem” for the internal shock model, if ɛe during the prompt emission phase (in the internal shocks) is large (say, ˜0.1). The preferred {{R}}B value is in agreement with the results in previous works that indicate a moderately magnetized baryonic jet for GRBs.

Pop III i-process nucleosynthesis and the elemental abundances of SMSS J0313-6708 and the most iron-poor stars

NASA Astrophysics Data System (ADS)

Clarkson, O.; Herwig, F.; Pignatari, M.

2018-02-01

We have investigated a highly energetic H-ingestion event during shell He burning leading to H-burning luminosities of log (LH/L⊙) ˜ 13 in a 45 M⊙ Pop III massive stellar model. In order to track the nucleosynthesis which may occur in such an event, we run a series of single-zone nucleosynthesis models for typical conditions found in the stellar evolution model. Such nucleosynthesis conditions may lead to i-process neutron densities of up to ˜1013 cm-3. The resulting simulation abundance pattern, where Mg comes from He burning and Ca from the i process, agrees with the general observed pattern of the most iron-poor star currently known, SMSS J031300.36-670839.3. However, Na is also efficiently produced in these i-process conditions, and the prediction exceeds observations by ˜2.5 dex. While this probably rules out this model for SMSS J031300.36-670839.3, the typical i-process signature of combined He burning and i process of higher than solar [Na/Mg], [Mg/Al], and low [Ca/Mg] is reproducing abundance features of the two next most iron-poor stars HE 1017-5240 and HE 1327-2326 very well. The i process does not reach Fe which would have to come from a low level of additional enrichment. i process in hyper-metal-poor or Pop III massive stars may be able to explain certain abundance patterns observed in some of the most metal-poor CEMP-no stars.

Modeling and analysis of hybrid pixel detector deficiencies for scientific applications

NASA Astrophysics Data System (ADS)

Fahim, Farah; Deptuch, Grzegorz W.; Hoff, James R.; Mohseni, Hooman

2015-08-01

Semiconductor hybrid pixel detectors often consist of a pixellated sensor layer bump bonded to a matching pixelated readout integrated circuit (ROIC). The sensor can range from high resistivity Si to III-V materials, whereas a Si CMOS process is typically used to manufacture the ROIC. Independent, device physics and electronic design automation (EDA) tools are used to determine sensor characteristics and verify functional performance of ROICs respectively with significantly different solvers. Some physics solvers provide the capability of transferring data to the EDA tool. However, single pixel transient simulations are either not feasible due to convergence difficulties or are prohibitively long. A simplified sensor model, which includes a current pulse in parallel with detector equivalent capacitor, is often used; even then, spice type top-level (entire array) simulations range from days to weeks. In order to analyze detector deficiencies for a particular scientific application, accurately defined transient behavioral models of all the functional blocks are required. Furthermore, various simulations, such as transient, noise, Monte Carlo, inter-pixel effects, etc. of the entire array need to be performed within a reasonable time frame without trading off accuracy. The sensor and the analog front-end can be modeling using a real number modeling language, as complex mathematical functions or detailed data can be saved to text files, for further top-level digital simulations. Parasitically aware digital timing is extracted in a standard delay format (sdf) from the pixel digital back-end layout as well as the periphery of the ROIC. For any given input, detector level worst-case and best-case simulations are performed using a Verilog simulation environment to determine the output. Each top-level transient simulation takes no more than 10-15 minutes. The impact of changing key parameters such as sensor Poissonian shot noise, analog front-end bandwidth, jitter due to clock distribution etc. can be accurately analyzed to determine ROIC architectural viability and bottlenecks. Hence the impact of the detector parameters on the scientific application can be studied.

Factors that influence chest injuries in rollovers.

PubMed

Digges, Kennerly; Eigen, Ana; Tahan, Fadi; Grzebieta, Raphael

2014-01-01

The design of countermeasures to reduce serious chest injuries for belted occupants involved in rollover crashes requires an understanding of the cause of these injuries and of the test conditions to assure the effectiveness of the countermeasures. This study defines rollover environments and occupant-to-vehicle interactions that cause chest injuries for belted drivers. The NASS-CDS was examined to determine the frequency and crash severity for belted drivers with serious (Abbreviated Injury Scale [AIS] 3+) chest injuries in rollovers. Case studies of NASS crashes with serious chest injuries sustained by belted front occupants were undertaken and damage patterns were determined. Vehicle rollover tests with dummies were examined to determine occupant motion in crashes with damage similar to that observed in the NASS cases. Computer simulations were performed to further explore factors that could contribute to chest injury. Finite element model (FEM) vehicle models with both the FEM Hybrid III dummy and THUMS human model were used in the simulations. Simulation of rollovers with 6 quarter-turns or less indicated that increases in the vehicle pitch, either positive or negative, increased the severity of dummy chest loadings. This finding was consistent with vehicle damage observations from NASS cases. For the far-side occupant, the maximum chest loadings were caused by belt and side interactions during the third quarter-turn and by the center console loading during the fourth quarter-turn. The results showed that the THUMS dummy produced more realistic kinematics and improved insights into skeletal and chest organ loadings compared to the Hybrid III dummy. These results suggest that a dynamic rollover test to encourage chest injury reduction countermeasures should induce a roll of at least 4 quarter-turns and should also include initial vehicle pitch and/or yaw so that the vehicle's axis of rotation is not aligned with its inertial roll axis during the initial stage of the rollover.

40 CFR 52.73 - Approval of plans.

Code of Federal Regulations, 2014 CFR

2014-07-01

... Strategies (Section III.B.5), Modeling and Projections (Section III.B.6), Contingency Plan (Section III.B.7...), Modeling and Projections (Section III.C.6), and Air Quality Conformity Procedures (Section III.C.10); and...

Arleigh Burke Destroyers: Delaying Procurement of DDG 51 Flight III Ships Would Allow Time to Increase Design Knowledge

DTIC Science & Technology

2015-08-01

activities for DDG 51, AMDR, Aegis, and other related programs, such as the Evolved Sea Sparrow Missile. We also reviewed DOD studies and past GAO...systems—from initial SPY-6 radar detection of a target, such as an anti- ship cruise missile, through target interception by an Evolved Sea Sparrow ...required to accredit the Aegis modeling and simulation capability, (2) the Evolved Sea Sparrow Missile Block 2—a key element of Flight III’s self

Modeling Impact-induced Failure of Polysilicon MEMS: A Multi-scale Approach.

PubMed

Mariani, Stefano; Ghisi, Aldo; Corigliano, Alberto; Zerbini, Sarah

2009-01-01

Failure of packaged polysilicon micro-electro-mechanical systems (MEMS) subjected to impacts involves phenomena occurring at several length-scales. In this paper we present a multi-scale finite element approach to properly allow for: (i) the propagation of stress waves inside the package; (ii) the dynamics of the whole MEMS; (iii) the spreading of micro-cracking in the failing part(s) of the sensor. Through Monte Carlo simulations, some effects of polysilicon micro-structure on the failure mode are elucidated.

Computer Program (HEVSIM) for Heavy Duty Vehicle Fuel Economy and Performance Simulation. Volume III.

DOT National Transportation Integrated Search

1981-09-01

Volume III is the third and last volume of a three volume document describing the computer program HEVSIM. This volume includes appendices which list the HEVSIM program, sample part data, some typical outputs and updated nomenclature.

Microbial Reduction of Fe(III) and U(VI) in Aquifers: Simulations Exploring Coupled Effects of Heterogeneity and Fe(II) Sorption

NASA Astrophysics Data System (ADS)

Scheibe, T. D.; Fang, Y.; Roden, E. E.; Brooks, S. C.; Chien, Y.; Murray, C. J.

2004-05-01

Uranium is a significant groundwater contaminant at many former mining and processing sites. In its oxidized state, U(VI) is soluble and mobile, although strongly retarded by sorption to natural iron oxide surfaces. It has been demonstrated that commonly occurring subsurface microorganisms can reduce uranium and other metals when provided sufficient carbon as an electron donor. Reduced U(IV) precipitates as a solid phase; therefore biostimulation provides a potential strategy for in situ removal from contaminated groundwater. However, these biogeochemical reactions occur in the context of a complex heterogeneous environment in which flow and transport dynamics and abiotic reactions can have significant impacts. We have constructed a high-resolution numerical model of groundwater flow and multicomponent reactive transport that incorporates heterogeneity in hydraulic conductivity and initial Fe(III) distribution, microbial growth and transport dynamics, and effects of sorption or precipitation of biogenic Fe(II) on availability of Fe(III) as an electron acceptor. The biogeochemical reaction models and their parameters are based on laboratory experiments; the heterogeneous field-scale property distributions are based on interpretations of geophysical and other observations at a highly characterized field site. The model is being run in Monte Carlo mode to examine the controls that these factors exert on 1) the initial distribution of sorbed uranium in an oxic environment and 2) the reduction and immobilization of uranium upon introduction of a soluble electron donor.

Application of molecular simulation to investigate chrome(III)-crosslinked collagen problems

NASA Astrophysics Data System (ADS)

Ding, Yun-Qiao; Chen, Cheng-Lung; Gu, Qi-Rui; Liao, Jun-Min; Chuang, Po-Hsiang

2014-04-01

Molecular dynamics simulation with a modified CHARMM (Chemistry at Harvard Macromolecular Mechanics) force field was carried out to investigate the properties of chrome-tanned collagen in comparison with chrome-free collagen under hydrated and dehydrated conditions. An attempt has been made to explain the microcosmic origins of the various properties of the chromium(III)-crosslinked collagen. The present simulation describes the clear crosslinking topology of polychromiums to peptide chains, identifies the linking site and the capacity of the linkage, explains why the efficiency is not 100% in a practical tanning process and provides a new viewpoint on the crosslinking of the polychromium with the side chains of the collagen.

Exchange Interactions on the Highest-Spin Reported Molecule: the Mixed-Valence Fe42 Complex

PubMed Central

Aravena, Daniel; Venegas-Yazigi, Diego; Ruiz, Eliseo

2016-01-01

The finding of high-spin molecules that could behave as conventional magnets has been one of the main challenges in Molecular Magnetism. Here, the exchange interactions, present in the highest-spin molecule published in the literature, Fe42, have been analysed using theoretical methods based on Density Functional Theory. The system with a total spin value S = 45 is formed by 42 iron centres containing 18 high-spin FeIII ferromagnetically coupled and 24 diamagnetic low-spin FeII ions. The bridging ligands between the two paramagnetic centres are two cyanide ligands coordinated to the diamagnetic FeII cations. Calculations were performed using either small Fe4 or Fe3 models or the whole Fe42 complex, showing the presence of two different ferromagnetic couplings between the paramagnetic FeIII centres. Finally, Quantum Monte Carlo simulations for the whole system were carried out in order to compare the experimental and simulated magnetic susceptibility curves from the calculated exchange coupling constants with the experimental one. This comparison allows for the evaluation of the accuracy of different exchange-correlation functionals to reproduce such magnetic properties. PMID:27033418

[Biomechanical study of internal midface distraction after different types of maxillary osteotomy in patients with cleft lip and palate].

PubMed

Hou, Min; Shi, Guang-Yu; Pu, Li-Chen; Song, Da-Li; Zhang, Xi-Zhong; Liu, Chun-Ming

2009-09-01

To investigate the biomechanical changes of internal midface distraction after different types of maxillary osteotomy in patients with cleft lip and palate (CLP). 3-D finite element (FEM) analysis was used. 3-D models of Le Fort I, II, III osteotomy and soft tissue were established. Based on the new pattern of internal midface distractor, the distraction of maxillary complex was simulated to advance 10 mm anteriorly. The mechanical change was studied. The maxillary complex in CLP were advanced after distraction. Constriction of alveolar crest and palate occurred in Le Fort I osteotomy, but not in Le Fort II and III osteotomy. The maxillary complex was moved anteriorly en bloc after Le Fort III osteotomy, but some degree of rotation of maxillary complex was observed during the distraction after Le Fort I and II osteotomy. In vertical direction, the maxillary complex had more counterclockwise rotation after Le Fort II osteotomy. 3-D FEM analysis can be used for the study of internal distraction. It can reflect the maxillary movement and provide the theory basis for preoperative design.

Mechanical testing of bones: the positive synergy of finite-element models and in vitro experiments.

PubMed

Cristofolini, Luca; Schileo, Enrico; Juszczyk, Mateusz; Taddei, Fulvia; Martelli, Saulo; Viceconti, Marco

2010-06-13

Bone biomechanics have been extensively investigated in the past both with in vitro experiments and numerical models. In most cases either approach is chosen, without exploiting synergies. Both experiments and numerical models suffer from limitations relative to their accuracy and their respective fields of application. In vitro experiments can improve numerical models by: (i) preliminarily identifying the most relevant failure scenarios; (ii) improving the model identification with experimentally measured material properties; (iii) improving the model identification with accurately measured actual boundary conditions; and (iv) providing quantitative validation based on mechanical properties (strain, displacements) directly measured from physical specimens being tested in parallel with the modelling activity. Likewise, numerical models can improve in vitro experiments by: (i) identifying the most relevant loading configurations among a number of motor tasks that cannot be replicated in vitro; (ii) identifying acceptable simplifications for the in vitro simulation; (iii) optimizing the use of transducers to minimize errors and provide measurements at the most relevant locations; and (iv) exploring a variety of different conditions (material properties, interface, etc.) that would require enormous experimental effort. By reporting an example of successful investigation of the femur, we show how a combination of numerical modelling and controlled experiments within the same research team can be designed to create a virtuous circle where models are used to improve experiments, experiments are used to improve models and their combination synergistically provides more detailed and more reliable results than can be achieved with either approach singularly.

Autonomous Agent-Based Systems and Their Applications in Fluid Dynamics, Particle Separation, and Co-evolving Networks

NASA Astrophysics Data System (ADS)

Graeser, Oliver

This thesis comprises three parts, reporting research results in Fluid Dynamics (Part I), Particle Separation (Part II) and Co-evolving Networks (Part III). Part I deals with the simulation of fluid dynamics using the lattice-Boltzmann method. Microfluidic devices often feature two-dimensional, repetitive arrays. Flows through such devices are pressure-driven and confined by solid walls. We have defined new adaptive generalised periodic boundary conditions to represent the effects of outer solid walls, and are thus able to exploit the periodicity of the array by simulating the flow through one unit cell in lieu of the entire device. The so-calculated fully developed flow describes the flow through the entire array accurately, but with computational requirements that are reduced according to the dimensions of the array. Part II discusses the problem of separating macromolecules like proteins or DNA coils. The reliable separation of such molecules is a crucial task in molecular biology. The use of Brownian ratchets as mechanisms for the separation of such particles has been proposed and discussed during the last decade. Pressure-driven flows have so far been dismissed as possible driving forces for Brownian ratchets, as they do not generate ratchet asymmetry. We propose a microfluidic design that uses pressure-driven flows to create asymmetry and hence allows particle separation. The dependence of the asymmetry on various factors of the microfluidic geometry is discussed. We further exemplify the feasibility of our approach using Brownian dynamics simulations of particles of different sizes in such a device. The results show that ratchet-based particle separation using flows as the driving force is possible. Simulation results and ratchet theory predictions are in excellent agreement. Part III deals with the co-evolution of networks and dynamic models. A group of agents occupies the nodes of a network, which defines the relationship between these agents. The evolution of the agents is defined by the rules of the dynamic model and depends on the relationship between agents, i.e., the state of the network. In return, the evolution of the network depends on the state of the dynamic model. The concept is introduced through the adaptive SIS model. We show that the previously used criterion determining the critical infected fraction, i.e., the number of infected agents required to sustain the epidemic, is inappropriate for this model. We introduce a different criterion and show that the critical infected fraction so determined is in good agreement with results obtained by numerical simulations. We further discuss the concept of co-evolving dynamics using the Snowdrift Game as a model paradigm. Co-evolution occurs through agents cutting dissatisfied links and rewiring to other agents at random. The effect of co-evolution on the emergence of cooperation is discussed using a mean-field theory and numerical simulations. A transition between a connected and a disconnected, highly cooperative state of the system is observed, and explained using the mean-field model. Quantitative deviations regarding the level of cooperation in the disconnected regime can be fully resolved through an improved mean-field theory that includes the effect of random fluctuations into its model.

Trident: A Universal Tool for Generating Synthetic Absorption Spectra from Astrophysical Simulations

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

Hummels, Cameron B.; Smith, Britton D.; Silvia, Devin W.

Hydrodynamical simulations are increasingly able to accurately model physical systems on stellar, galactic, and cosmological scales; however, the utility of these simulations is often limited by our ability to directly compare them with the data sets produced by observers: spectra, photometry, etc. To address this problem, we have created trident, a Python-based open-source tool for post-processing hydrodynamical simulations to produce synthetic absorption spectra and related data. trident can (i) create absorption-line spectra for any trajectory through a simulated data set mimicking both background quasar and down-the-barrel configurations; (ii) reproduce the spectral characteristics of common instruments like the Cosmic Origins Spectrograph;more » (iii) operate across the ultraviolet, optical, and infrared using customizable absorption-line lists; (iv) trace simulated physical structures directly to spectral features; (v) approximate the presence of ion species absent from the simulation outputs; (vi) generate column density maps for any ion; and (vii) provide support for all major astrophysical hydrodynamical codes. trident was originally developed to aid in the interpretation of observations of the circumgalactic medium and intergalactic medium, but it remains a general tool applicable in other contexts.« less

A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser

PubMed Central

Yoon, Chun Hong; Yurkov, Mikhail V.; Schneidmiller, Evgeny A.; Samoylova, Liubov; Buzmakov, Alexey; Jurek, Zoltan; Ziaja, Beata; Santra, Robin; Loh, N. Duane; Tschentscher, Thomas; Mancuso, Adrian P.

2016-01-01

The advent of newer, brighter, and more coherent X-ray sources, such as X-ray Free-Electron Lasers (XFELs), represents a tremendous growth in the potential to apply coherent X-rays to determine the structure of materials from the micron-scale down to the Angstrom-scale. There is a significant need for a multi-physics simulation framework to perform source-to-detector simulations for a single particle imaging experiment, including (i) the multidimensional simulation of the X-ray source; (ii) simulation of the wave-optics propagation of the coherent XFEL beams; (iii) atomistic modelling of photon-material interactions; (iv) simulation of the time-dependent diffraction process, including incoherent scattering; (v) assembling noisy and incomplete diffraction intensities into a three-dimensional data set using the Expansion-Maximisation-Compression (EMC) algorithm and (vi) phase retrieval to obtain structural information. We demonstrate the framework by simulating a single-particle experiment for a nitrogenase iron protein using parameters of the SPB/SFX instrument of the European XFEL. This exercise demonstrably yields interpretable consequences for structure determination that are crucial yet currently unavailable for experiment design. PMID:27109208

A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser

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

Yoon, Chun Hong; Yurkov, Mikhail V.; Schneidmiller, Evgeny A.

The advent of newer, brighter, and more coherent X-ray sources, such as X-ray Free-Electron Lasers (XFELs), represents a tremendous growth in the potential to apply coherent X-rays to determine the structure of materials from the micron-scale down to the Angstrom-scale. There is a significant need for a multi-physics simulation framework to perform source-to-detector simulations for a single particle imaging experiment, including (i) the multidimensional simulation of the X-ray source; (ii) simulation of the wave-optics propagation of the coherent XFEL beams; (iii) atomistic modelling of photon-material interactions; (iv) simulation of the time-dependent diffraction process, including incoherent scattering; (v) assembling noisy andmore » incomplete diffraction intensities into a three-dimensional data set using the Expansion-Maximisation-Compression (EMC) algorithm and (vi) phase retrieval to obtain structural information. Furthermore, we demonstrate the framework by simulating a single-particle experiment for a nitrogenase iron protein using parameters of the SPB/SFX instrument of the European XFEL. This exercise demonstrably yields interpretable consequences for structure determination that are crucial yet currently unavailable for experiment design.« less

A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser

DOE PAGES

Yoon, Chun Hong; Yurkov, Mikhail V.; Schneidmiller, Evgeny A.; ...

2016-04-25

The advent of newer, brighter, and more coherent X-ray sources, such as X-ray Free-Electron Lasers (XFELs), represents a tremendous growth in the potential to apply coherent X-rays to determine the structure of materials from the micron-scale down to the Angstrom-scale. There is a significant need for a multi-physics simulation framework to perform source-to-detector simulations for a single particle imaging experiment, including (i) the multidimensional simulation of the X-ray source; (ii) simulation of the wave-optics propagation of the coherent XFEL beams; (iii) atomistic modelling of photon-material interactions; (iv) simulation of the time-dependent diffraction process, including incoherent scattering; (v) assembling noisy andmore » incomplete diffraction intensities into a three-dimensional data set using the Expansion-Maximisation-Compression (EMC) algorithm and (vi) phase retrieval to obtain structural information. Furthermore, we demonstrate the framework by simulating a single-particle experiment for a nitrogenase iron protein using parameters of the SPB/SFX instrument of the European XFEL. This exercise demonstrably yields interpretable consequences for structure determination that are crucial yet currently unavailable for experiment design.« less

Molecular dynamics simulations of β2-microglobulin interaction with hydrophobic surfaces.

PubMed

Dongmo Foumthuim, Cedrix J; Corazza, Alessandra; Esposito, Gennaro; Fogolari, Federico

2017-11-21

Hydrophobic surfaces are known to adsorb and unfold proteins, a process that has been studied only for a few proteins. Here we address the interaction of β2-microglobulin, a paradigmatic protein for the study of amyloidogenesis, with hydrophobic surfaces. A system with 27 copies of the protein surrounded by a model cubic hydrophobic box is studied by implicit solvent molecular dynamics simulations. Most proteins adsorb on the walls of the box without major distortions in local geometry, whereas free molecules maintain proper structures and fluctuations as observed in explicit solvent molecular dynamics simulations. The major conclusions from the simulations are as follows: (i) the adopted implicit solvent model is adequate to describe protein dynamics and thermodynamics; (ii) adsorption occurs readily and is irreversible on the simulated timescale; (iii) the regions most involved in molecular encounters and stable interactions with the walls are the same as those that are important in protein-protein and protein-nanoparticle interactions; (iv) unfolding following adsorption occurs at regions found to be flexible by both experiments and simulations; (v) thermodynamic analysis suggests a very large contribution from van der Waals interactions, whereas unfavorable electrostatic interactions are not found to contribute much to adsorption energy. Surfaces with different degrees of hydrophobicity may occur in vivo. Our simulations show that adsorption is a fast and irreversible process which is accompanied by partial unfolding. The results and the thermodynamic analysis presented here are consistent with and rationalize previous experimental work.

Surface Runoff Estimation Using SMOS Observations, Rain-gauge Measurements and Satellite Precipitation Estimations. Comparison with Model Predictions

NASA Astrophysics Data System (ADS)

Garcia Leal, Julio A.; Lopez-Baeza, Ernesto; Khodayar, Samiro; Estrela, Teodoro; Fidalgo, Arancha; Gabaldo, Onofre; Kuligowski, Robert; Herrera, Eddy

Surface runoff is defined as the amount of water that originates from precipitation, does not infiltrates due to soil saturation and therefore circulates over the surface. A good estimation of runoff is useful for the design of draining systems, structures for flood control and soil utilisation. For runoff estimation there exist different methods such as (i) rational method, (ii) isochrone method, (iii) triangular hydrograph, (iv) non-dimensional SCS hydrograph, (v) Temez hydrograph, (vi) kinematic wave model, represented by the dynamics and kinematics equations for a uniforme precipitation regime, and (vii) SCS-CN (Soil Conservation Service Curve Number) model. This work presents a way of estimating precipitation runoff through the SCS-CN model, using SMOS (Soil Moisture and Ocean Salinity) mission soil moisture observations and rain-gauge measurements, as well as satellite precipitation estimations. The area of application is the Jucar River Basin Authority area where one of the objectives is to develop the SCS-CN model in a spatial way. The results were compared to simulations performed with the 7-km COSMO-CLM (COnsortium for Small-scale MOdelling, COSMO model in CLimate Mode) model. The use of SMOS soil moisture as input to the COSMO-CLM model will certainly improve model simulations.

Speciation of the trivalent f-elements Eu(III) and Cm(III) in digestive media.

PubMed

Wilke, Claudia; Barkleit, Astrid; Stumpf, Thorsten; Ikeda-Ohno, Atsushi

2017-10-01

In case radioactive materials are released into the environment, their incorporation into our digestive system would be a significant concern. Trivalent f-elements, i.e., trivalent actinides and lanthanides, could potentially represent a serious health risk due to their chemo- and radiotoxicity, nevertheless the biochemical behavior of these elements are mostly unknown even to date. This study, therefore, focuses on the chemical speciation of trivalent f-elements in the human gastrointestinal tract. To simulate the digestive system artificial digestive juices (saliva, gastric juice, pancreatic juice and bile fluid) were prepared. The chemical speciation of lanthanides (as Eu(III)) and actinides (as Cm(III)) was determined experimentally by time-resolved laser-induced fluorescence spectroscopy (TRLFS) and the results were compared with thermodynamic modeling. The results indicate a dominant inorganic species with phosphate/carbonate in the mouth, while the aquo ion is predominantly formed with a minor contribution of the enzyme pepsin in the stomach. In the intestinal tract the most significant species are with the protein mucin. We demonstrated the first experimental results on the chemical speciation of trivalent f-elements in the digestive media by TRLFS. The results highlight a significant gap in chemical speciation between experiments and thermodynamic modeling due to the limited availability of thermodynamic stability constants particularly for organic species. Chemical speciation strongly influences the in vivo behavior of metal ions. Therefore, the results of this speciation study will help to enhance the assessment of health risks and to improve decorporation strategies after ingestion of these (radio-)toxic heavy metal ions. Copyright © 2017 Elsevier Inc. All rights reserved.

CIFOG: Cosmological Ionization Fields frOm Galaxies

NASA Astrophysics Data System (ADS)

Hutter, Anne

2018-03-01

CIFOG is a versatile MPI-parallelised semi-numerical tool to perform simulations of the Epoch of Reionization. From a set of evolving cosmological gas density and ionizing emissivity fields, it computes the time and spatially dependent ionization of neutral hydrogen (HI), neutral (HeI) and singly ionized helium (HeII) in the intergalactic medium (IGM). The code accounts for HII, HeII, HeIII recombinations, and provides different descriptions for the photoionization rate that are used to calculate the residual HI fraction in ionized regions. This tool has been designed to be coupled to semi-analytic galaxy formation models or hydrodynamical simulations. The modular fashion of the code allows the user to easily introduce new descriptions for recombinations and the photoionization rate.

Perspective: Theory and simulation of hybrid halide perovskites

PubMed Central

Jung, Young-Kwang

2017-01-01

Organic-inorganic halide perovskites present a number of challenges for first-principles atomistic materials modeling. Such “plastic crystals” feature dynamic processes across multiple length and time scales. These include the following: (i) transport of slow ions and fast electrons; (ii) highly anharmonic lattice dynamics with short phonon lifetimes; (iii) local symmetry breaking of the average crystallographic space group; (iv) strong relativistic (spin-orbit coupling) effects on the electronic band structure; and (v) thermodynamic metastability and rapid chemical breakdown. These issues, which affect the operation of solar cells, are outlined in this perspective. We also discuss general guidelines for performing quantitative and predictive simulations of these materials, which are relevant to metal-organic frameworks and other hybrid semiconducting, dielectric and ferroelectric compounds. PMID:29166078

Development of a novel ex vivo porcine laparoscopic Heller myotomy and Nissen fundoplication training model (Toronto lap-Nissen simulator).

PubMed

Ujiie, Hideki; Kato, Tatsuya; Hu, Hsin-Pei; Bauer, Patrycja; Patel, Priya; Wada, Hironobu; Lee, Daiyoon; Fujino, Kosuke; Schieman, Colin; Pierre, Andrew; Waddell, Thomas K; Keshavjee, Shaf; Darling, Gail E; Yasufuku, Kazuhiro

2017-06-01

Surgical trainees are required to develop competency in a variety of laparoscopic operations. Developing laparoscopic technical skills can be difficult as there has been a decrease in the number of procedures performed. This study aims to develop an inexpensive and anatomically relevant model for training in laparoscopic foregut procedures. An ex vivo , anatomic model of the human upper abdomen was developed using intact porcine esophagus, stomach, diaphragm and spleen. The Toronto lap-Nissen simulator was contained in a laparoscopic box-trainer and included an arch system to simulate the normal radial shape and tension of the diaphragm. We integrated the use of this training model as a part of our laparoscopic skills laboratory-training curriculum. Afterwards, we surveyed trainees to evaluate the observed benefit of the learning session. Twenty-five trainees and five faculty members completed a survey regarding the use of this model. Among the trainees, only 4 (16%) had experience with laparoscopic Heller myotomy and Nissen fundoplication. They reported that practicing with the model was a valuable use of their limited time, repeating the exercise would be of additional benefit, and that the exercise improved their ability to perform or assist in an actual case in the operating room. Significant improvements were found in the following subjective measures comparing pre- vs. post-training: (I) knowledge level (5.6 vs. 8.0, P<0.001); (II) comfort level in assisting (6.3 vs. 7.6, P<0.001); and (III) comfort level in performing as the primary surgeon (4.9 vs. 7.1, P<0.001). The trainees and faculty members agreed that this model was of adequate fidelity and was a representative simulation of actual human anatomy. We developed an easily reproducible training model for laparoscopic procedures. This simulator reproduces human anatomy and increases the trainees' comfort level in performing and assisting with myotomy and fundoplication.

Development of a novel ex vivo porcine laparoscopic Heller myotomy and Nissen fundoplication training model (Toronto lap-Nissen simulator)

PubMed Central

Ujiie, Hideki; Kato, Tatsuya; Hu, Hsin-Pei; Bauer, Patrycja; Patel, Priya; Wada, Hironobu; Lee, Daiyoon; Fujino, Kosuke; Schieman, Colin; Pierre, Andrew; Waddell, Thomas K.; Keshavjee, Shaf; Darling, Gail E.

2017-01-01

Background Surgical trainees are required to develop competency in a variety of laparoscopic operations. Developing laparoscopic technical skills can be difficult as there has been a decrease in the number of procedures performed. This study aims to develop an inexpensive and anatomically relevant model for training in laparoscopic foregut procedures. Methods An ex vivo, anatomic model of the human upper abdomen was developed using intact porcine esophagus, stomach, diaphragm and spleen. The Toronto lap-Nissen simulator was contained in a laparoscopic box-trainer and included an arch system to simulate the normal radial shape and tension of the diaphragm. We integrated the use of this training model as a part of our laparoscopic skills laboratory-training curriculum. Afterwards, we surveyed trainees to evaluate the observed benefit of the learning session. Results Twenty-five trainees and five faculty members completed a survey regarding the use of this model. Among the trainees, only 4 (16%) had experience with laparoscopic Heller myotomy and Nissen fundoplication. They reported that practicing with the model was a valuable use of their limited time, repeating the exercise would be of additional benefit, and that the exercise improved their ability to perform or assist in an actual case in the operating room. Significant improvements were found in the following subjective measures comparing pre- vs. post-training: (I) knowledge level (5.6 vs. 8.0, P<0.001); (II) comfort level in assisting (6.3 vs. 7.6, P<0.001); and (III) comfort level in performing as the primary surgeon (4.9 vs. 7.1, P<0.001). The trainees and faculty members agreed that this model was of adequate fidelity and was a representative simulation of actual human anatomy. Conclusions We developed an easily reproducible training model for laparoscopic procedures. This simulator reproduces human anatomy and increases the trainees’ comfort level in performing and assisting with myotomy and fundoplication. PMID:28740664

Postcoalescence evolution of growth stress in polycrystalline films.

PubMed

González-González, A; Polop, C; Vasco, E

2013-02-01

The growth stress generated once grains coalesce in Volmer-Weber-type thin films is investigated by time-multiscale simulations comprising complementary modules of (i) finite-element modeling to address the interactions between grains happening at atomic vibration time scales (~0.1 ps), (ii) dynamic scaling to account for the surface stress relaxation via morphology changes at surface diffusion time scales (~μs-ms), and (iii) the mesoscopic rate equation approach to simulate the bulk stress relaxation at deposition time scales (~sec-h). On the basis of addressing the main experimental evidence reported so far on the topic dealt with, the simulation results provide key findings concerning the interplay between anisotropic grain interactions at complementary space scales, deposition conditions (such as flux and mobility), and mechanisms of stress accommodation-relaxation, which underlies the origin, nature and spatial distribution, and the flux dependence of the postcoalescence growth stress.

The accuracy of seminumerical reionization models in comparison with radiative transfer simulations

NASA Astrophysics Data System (ADS)

Hutter, Anne

2018-06-01

We have developed a modular seminumerical code that computes the time and spatially dependent ionization of neutral hydrogen (H I), neutral (He I), and single-ionized helium (He II) in the intergalactic medium (IGM). The model accounts for recombinations and provides different descriptions for the photoionization rate that are used to calculate the residual H I fraction in ionized regions. We compare different seminumerical reionization schemes to a radiative transfer (RT) simulation. We use the RT simulation as a benchmark, and find that the seminumerical approaches produce similar H II and He II morphologies and power spectra of the H I 21 cm signal throughout reionization. As we do not track partial ionization of He II, the extent of the double-ionized helium (He III) regions is consistently smaller. In contrast to previous comparison projects, the ionizing emissivity in our seminumerical scheme is not adjusted to reproduce the redshift evolution of the RT simulation, but directly derived from the RT simulation spectra. Among schemes that identify the ionized regions by the ratio of the number of ionization and absorption events on different spatial smoothing scales, we find those that mark the entire sphere as ionized when the ionization criterion is fulfilled to result in significantly accelerated reionization compared to the RT simulation. Conversely, those that flag only the central cell as ionized yield very similar but slightly delayed redshift evolution of reionization, with up to 20 per cent ionizing photons lost. Despite the overall agreement with the RT simulation, our results suggest that constraining ionizing emissivity-sensitive parameters from seminumerical galaxy formation-reionization models are subject to photon nonconservation.

The accuracy of semi-numerical reionization models in comparison with radiative transfer simulations

NASA Astrophysics Data System (ADS)

Hutter, Anne

2018-03-01

We have developed a modular semi-numerical code that computes the time and spatially dependent ionization of neutral hydrogen (H I), neutral (He I) and singly ionized helium (He II) in the intergalactic medium (IGM). The model accounts for recombinations and provides different descriptions for the photoionization rate that are used to calculate the residual H I fraction in ionized regions. We compare different semi-numerical reionization schemes to a radiative transfer (RT) simulation. We use the RT simulation as a benchmark, and find that the semi-numerical approaches produce similar H II and He II morphologies and power spectra of the H I 21cm signal throughout reionization. As we do not track partial ionization of He II, the extent of the double ionized helium (He III) regions is consistently smaller. In contrast to previous comparison projects, the ionizing emissivity in our semi-numerical scheme is not adjusted to reproduce the redshift evolution of the RT simulation, but directly derived from the RT simulation spectra. Among schemes that identify the ionized regions by the ratio of the number of ionization and absorption events on different spatial smoothing scales, we find those that mark the entire sphere as ionized when the ionization criterion is fulfilled to result in significantly accelerated reionization compared to the RT simulation. Conversely, those that flag only the central cell as ionized yield very similar but slightly delayed redshift evolution of reionization, with up to 20% ionizing photons lost. Despite the overall agreement with the RT simulation, our results suggests that constraining ionizing emissivity sensitive parameters from semi-numerical galaxy formation-reionization models are subject to photon nonconservation.

Dose Titration Algorithm Tuning (DTAT) should supersede 'the' Maximum Tolerated Dose (MTD) in oncology dose-finding trials.

PubMed

Norris, David C

2017-01-01

Background . Absent adaptive, individualized dose-finding in early-phase oncology trials, subsequent 'confirmatory' Phase III trials risk suboptimal dosing, with resulting loss of statistical power and reduced probability of technical success for the investigational therapy. While progress has been made toward explicitly adaptive dose-finding and quantitative modeling of dose-response relationships, most such work continues to be organized around a concept of 'the' maximum tolerated dose (MTD). The purpose of this paper is to demonstrate concretely how the aim of early-phase trials might be conceived, not as 'dose-finding', but as dose titration algorithm (DTA) -finding. Methods. A Phase I dosing study is simulated, for a notional cytotoxic chemotherapy drug, with neutropenia constituting the critical dose-limiting toxicity. The drug's population pharmacokinetics and myelosuppression dynamics are simulated using published parameter estimates for docetaxel. The amenability of this model to linearization is explored empirically. The properties of a simple DTA targeting neutrophil nadir of 500 cells/mm 3 using a Newton-Raphson heuristic are explored through simulation in 25 simulated study subjects. Results. Individual-level myelosuppression dynamics in the simulation model approximately linearize under simple transformations of neutrophil concentration and drug dose. The simulated dose titration exhibits largely satisfactory convergence, with great variance in individualized optimal dosing. Some titration courses exhibit overshooting. Conclusions. The large inter-individual variability in simulated optimal dosing underscores the need to replace 'the' MTD with an individualized concept of MTD i . To illustrate this principle, the simplest possible DTA capable of realizing such a concept is demonstrated. Qualitative phenomena observed in this demonstration support discussion of the notion of tuning such algorithms. Although here illustrated specifically in relation to cytotoxic chemotherapy, the DTAT principle appears similarly applicable to Phase I studies of cancer immunotherapy and molecularly targeted agents.

14 CFR 61.1 - Applicability and definitions.

Code of Federal Regulations, 2013 CFR

2013-01-01

... of this part: (1) Aeronautical experience means pilot time obtained in an aircraft, flight simulator... simulator, or flight training device; or (iii) Gives training as an authorized instructor in an aircraft, flight simulator, or flight training device. (16) Practical test means a test on the areas of operations...

14 CFR 61.1 - Applicability and definitions.

Code of Federal Regulations, 2012 CFR

2012-01-01

... of this part: (1) Aeronautical experience means pilot time obtained in an aircraft, flight simulator... simulator, or flight training device; or (iii) Gives training as an authorized instructor in an aircraft, flight simulator, or flight training device. (16) Practical test means a test on the areas of operations...

Simulation of Flow and Long-Term Plutonium (Pu) Transport in the Vadose Zone at the Savannah River National Laboratory (SRNL)

NASA Astrophysics Data System (ADS)

Demirkanli, I.; Molz, F. J.; Kaplan, D. I.; Fjeld, R. A.; Serkiz, S. M.

2006-05-01

An improved understanding of flow and radionuclide transport in vadose zone sediments is fundamental to all types of future planning involving radioactive materials. One way to obtain such understanding is to perform long-term experimental studies of Pu transport in complex natural systems. With this in mind, a series of field experiments were initiated at the SRNL in the early 1980s. Lysimeters containing sources of different Pu oxidation states were placed in the shallow subsurface and left open to the natural environment for 2 to 11 years. At the end of the experiments, Pu activities were measured along vertical cores obtained from the lysimeters. Pu distributions were anomalous in nature, with transport from oxidized Pu sources being less than expected, and a small fraction of Pu from reduced sources moving more. Laboratory studies with lysimeter sediments suggested that surface-mediated, oxidation/reduction (redox) reactions could be responsible for the anomalous behavior, and this hypothesis is tested by performing both steady-state and transient Pu transport simulations that include retardation along with first-order redox reactions on mineral surfaces. Based on the simulations, we conclude that the surface-mediated, redox hypothesis is consistent with the observed downward Pu activity profiles in the experiments, and such profiles are captured well by a steady-state, net downward, flow model. (Discussion is presented as to why a steady model appears to work in a highly transient flow environment.) The redox model explains how Pu(V/VI) sources release activity that moves downward more slowly than expected based on adsorptive retardation alone, and how Pu(III/IV) sources result in a small fraction of activity that moves downward more rapidly than expected. The calibrated parameter values were robust and relatively well-defined throughout all four sets of simulations. Pu(V/VI) (i.e., oxidized Pu)retardation factors were about 15, and reduced Pu(III/IV) retardation factors were about 10,000. For these values, ko (1st order oxidation rate) averaged 2.4x10-7/hr with a standard deviation of 1.6x10-7, and kr (reduction rate)was 7.1x10-4/hr with a standard deviation of 1.6x10-4. Preliminary transient flow simulations showed a very slight increase in the fitted reaction rate constants, but otherwise reproduced the steady-state results. To date, neither approach is able to simulate the observed Pu movement above the source.

A Novel Form of Compensation in the Tg2576 Amyloid Mouse Model of Alzheimer’s Disease

PubMed Central

Somogyi, Attila; Katonai, Zoltán; Alpár, Alán; Wolf, Ervin

2016-01-01

One century after its first description, pathology of Alzheimer’s disease (AD) is still poorly understood. Amyloid-related dendritic atrophy and membrane alterations of susceptible brain neurons in AD, and in animal models of AD are widely recognized. However, little effort has been made to study the potential effects of combined morphological and membrane alterations on signal transfer and synaptic integration in neurons that build up affected neural networks in AD. In this study spatial reconstructions and electrophysiological measurements of layer II/III pyramidal neurons of the somatosensory cortex from wild-type (WT) and transgenic (TG) human amyloid precursor protein (hAPP) overexpressing Tg2576 mice were used to build faithful segmental cable models of these neurons. Local synaptic activities were simulated in various points of the dendritic arbors and properties of subthreshold dendritic impulse propagation and predictors of synaptic input pattern recognition ability were quantified and compared in modeled WT and TG neurons. Despite the widespread dendritic degeneration and membrane alterations in mutant mouse neurons, surprisingly little, or no change was detected in steady-state and 50 Hz sinusoidal voltage transfers, current transfers, and local and propagation delays of PSPs traveling along dendrites of TG neurons. Synaptic input pattern recognition ability was also predicted to be unaltered in TG neurons in two different soma-dendritic membrane models investigated. Our simulations predict the way how subthreshold dendritic signaling and pattern recognition are preserved in TG neurons: amyloid-related membrane alterations compensate for the pathological effects that dendritic atrophy has on subthreshold dendritic signal transfer and integration in layer II/III somatosensory neurons of this hAPP mouse model for AD. Since neither propagation of single PSPs nor integration of multiple PSPs (pattern recognition) changes in TG neurons, we conclude that AD-related neuronal hyperexcitability cannot be accounted for by altered subthreshold dendritic signaling in these neurons but hyperexcitability is related to changes in active membrane properties and network connectivity. PMID:27378850

A Novel Form of Compensation in the Tg2576 Amyloid Mouse Model of Alzheimer's Disease.

PubMed

Somogyi, Attila; Katonai, Zoltán; Alpár, Alán; Wolf, Ervin

2016-01-01

One century after its first description, pathology of Alzheimer's disease (AD) is still poorly understood. Amyloid-related dendritic atrophy and membrane alterations of susceptible brain neurons in AD, and in animal models of AD are widely recognized. However, little effort has been made to study the potential effects of combined morphological and membrane alterations on signal transfer and synaptic integration in neurons that build up affected neural networks in AD. In this study spatial reconstructions and electrophysiological measurements of layer II/III pyramidal neurons of the somatosensory cortex from wild-type (WT) and transgenic (TG) human amyloid precursor protein (hAPP) overexpressing Tg2576 mice were used to build faithful segmental cable models of these neurons. Local synaptic activities were simulated in various points of the dendritic arbors and properties of subthreshold dendritic impulse propagation and predictors of synaptic input pattern recognition ability were quantified and compared in modeled WT and TG neurons. Despite the widespread dendritic degeneration and membrane alterations in mutant mouse neurons, surprisingly little, or no change was detected in steady-state and 50 Hz sinusoidal voltage transfers, current transfers, and local and propagation delays of PSPs traveling along dendrites of TG neurons. Synaptic input pattern recognition ability was also predicted to be unaltered in TG neurons in two different soma-dendritic membrane models investigated. Our simulations predict the way how subthreshold dendritic signaling and pattern recognition are preserved in TG neurons: amyloid-related membrane alterations compensate for the pathological effects that dendritic atrophy has on subthreshold dendritic signal transfer and integration in layer II/III somatosensory neurons of this hAPP mouse model for AD. Since neither propagation of single PSPs nor integration of multiple PSPs (pattern recognition) changes in TG neurons, we conclude that AD-related neuronal hyperexcitability cannot be accounted for by altered subthreshold dendritic signaling in these neurons but hyperexcitability is related to changes in active membrane properties and network connectivity.

Southern Regional Center for Lightweight Innovative Design

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

Horstemeyer, Mark F.; Wang, Paul

The three major objectives of this Phase III project are: To develop experimentally validated cradle-to-grave modeling and simulation tools to optimize automotive and truck components for lightweighting materials (aluminum, steel, and Mg alloys and polymer-based composites) with consideration of uncertainty to decrease weight and cost, yet increase the performance and safety in impact scenarios; To develop multiscale computational models that quantify microstructure-property relations by evaluating various length scales, from the atomic through component levels, for each step of the manufacturing process for vehicles; and To develop an integrated K-12 educational program to educate students on lightweighting designs and impact scenarios.

‘Survival’: a simulation toolkit introducing a modular approach for radiobiological evaluations in ion beam therapy

NASA Astrophysics Data System (ADS)

Manganaro, L.; Russo, G.; Bourhaleb, F.; Fausti, F.; Giordanengo, S.; Monaco, V.; Sacchi, R.; Vignati, A.; Cirio, R.; Attili, A.

2018-04-01

One major rationale for the application of heavy ion beams in tumour therapy is their increased relative biological effectiveness (RBE). The complex dependencies of the RBE on dose, biological endpoint, position in the field etc require the use of biophysical models in treatment planning and clinical analysis. This study aims to introduce a new software, named ‘Survival’, to facilitate the radiobiological computations needed in ion therapy. The simulation toolkit was written in C++ and it was developed with a modular architecture in order to easily incorporate different radiobiological models. The following models were successfully implemented: the local effect model (LEM, version I, II and III) and variants of the microdosimetric-kinetic model (MKM). Different numerical evaluation approaches were also implemented: Monte Carlo (MC) numerical methods and a set of faster analytical approximations. Among the possible applications, the toolkit was used to reproduce the RBE versus LET for different ions (proton, He, C, O, Ne) and different cell lines (CHO, HSG). Intercomparison between different models (LEM and MKM) and computational approaches (MC and fast approximations) were performed. The developed software could represent an important tool for the evaluation of the biological effectiveness of charged particles in ion beam therapy, in particular when coupled with treatment simulations. Its modular architecture facilitates benchmarking and inter-comparison between different models and evaluation approaches. The code is open source (GPL2 license) and available at https://github.com/batuff/Survival.

Comparison of SVAT models for simulating and optimizing deficit irrigation systems in arid and semi-arid countries under climate variability

NASA Astrophysics Data System (ADS)

Kloss, Sebastian; Schuetze, Niels; Schmitz, Gerd H.

2010-05-01

The strong competition for fresh water in order to fulfill the increased demand for food worldwide has led to a renewed interest in techniques to improve water use efficiency (WUE) such as controlled deficit irrigation. Furthermore, as the implementation of crop models into complex decision support systems becomes more and more common, it is imperative to reliably predict the WUE as ratio of water consumption and yield. The objective of this paper is the assessment of the problems the crop models - such as FAO-33, DAISY, and APSIM in this study - face when maximizing the WUE. We applied these crop models for calculating the risk in yield reduction in view of different sources of uncertainty (e.g. climate) employing a stochastic framework for decision support for the planning of water supply in irrigation. The stochastic framework consists of: (i) a weather generator for simulating regional impacts of climate change; (ii) a new tailor-made evolutionary optimization algorithm for optimal irrigation scheduling with limited water supply; and (iii) the above mentioned models for simulating water transport and crop growth in a sound manner. The results present stochastic crop water production functions (SCWPF) for different crops which can be used as basic tools for assessing the impact of climate variability on the risk for the potential yield. Case studies from India, Oman, Malawi, and France are presented to assess the differences in modeling water stress and yield response for the different crop models.

An Experimentally Robust Model of Monomeric Apolipoprotein A-I Created from a Chimera of Two X-ray Structures and Molecular Dynamics Simulations

PubMed Central

2015-01-01

High-density lipoprotein (HDL) retards atherosclerosis by accepting cholesterol from the artery wall. However, the structure of the proposed acceptor, monomeric apolipoprotein A-I (apoA-I), the major protein of HDL, is poorly understood. Two published models for monomeric apoA-I used cross-linking distance constraints to derive best fit conformations. This approach has limitations. (i) Cross-linked peptides provide no information about secondary structure. (ii) A protein chain can be folded in multiple ways to create a best fit. (iii) Ad hoc folding of a secondary structure is unlikely to produce a stable orientation of hydrophobic and hydrophilic residues. To address these limitations, we used a different approach. We first noted that the dimeric apoA-I crystal structure, (Δ185–243)apoA-I, is topologically identical to a monomer in which helix 5 forms a helical hairpin, a monomer with a hydrophobic cleft running the length of the molecule. We then realized that a second crystal structure, (Δ1–43)apoA-I, contains a C-terminal structure that fits snuggly via aromatic and hydrophobic interactions into the hydrophobic cleft. Consequently, we combined these crystal structures into an initial model that was subjected to molecular dynamics simulations. We tested the initial and simulated models and the two previously published models in three ways: against two published data sets (domains predicted to be helical by H/D exchange and six spin-coupled residues) and against our own experimentally determined cross-linking distance constraints. We note that the best fit simulation model, superior by all tests to previously published models, has dynamic features of a molten globule with interesting implications for the functions of apoA-I. PMID:25423138

The effect of satellite-derived surface soil moisture and leaf area index land data assimilation on streamflow simulations over France

NASA Astrophysics Data System (ADS)

Fairbairn, David; Lavinia Barbu, Alina; Napoly, Adrien; Albergel, Clément; Mahfouf, Jean-François; Calvet, Jean-Christophe

2017-04-01

This study evaluates the impact of assimilating surface soil moisture (SSM) and leaf area index (LAI) observations into a land surface model using the SAFRAN-ISBA-MODCOU (SIM) hydrological suite. SIM consists of three stages: (1) an atmospheric reanalysis (SAFRAN) over France, which forces (2) the three-layer ISBA land surface model, which then provides drainage and runoff inputs to (3) the MODCOU hydro-geological model. The drainage and runoff outputs from ISBA are validated by comparing the simulated river discharge from MODCOU with over 500 river-gauge observations over France and with a subset of stations with low-anthropogenic influence, over several years. This study makes use of the A-gs version of ISBA that allows for physiological processes. The atmospheric forcing for the ISBA-A-gs model underestimates direct shortwave and long-wave radiation by approximately 5 % averaged over France. The ISBA-A-gs model also substantially underestimates the grassland LAI compared with satellite retrievals during winter dormancy. These differences result in an underestimation (overestimation) of evapotranspiration (drainage and runoff). The excess runoff flowing into the rivers and aquifers contributes to an overestimation of the SIM river discharge. Two experiments attempted to resolve these problems: (i) a correction of the minimum LAI model parameter for grasslands and (ii) a bias-correction of the model radiative forcing. Two data assimilation experiments were also performed, which are designed to correct random errors in the initial conditions: (iii) the assimilation of LAI observations and (iv) the assimilation of SSM and LAI observations. The data assimilation for (iii) and (iv) was done with a simplified extended Kalman filter (SEKF), which uses finite differences in the observation operator Jacobians to relate the observations to the model variables. Experiments (i) and (ii) improved the median SIM Nash scores by about 9 % and 18 % respectively. Experiment (iii) reduced the LAI phase errors in ISBA-A-gs but had little impact on the discharge Nash efficiency of SIM. In contrast, experiment (iv) resulted in spurious increases in drainage and runoff, which degraded the median discharge Nash efficiency by about 7 %. The poor performance of the SEKF originates from the observation operator Jacobians. These Jacobians are dampened when the soil is saturated and when the vegetation is dormant, which leads to positive biases in drainage and/or runoff and to insufficient corrections during winter, respectively. Possible ways to improve the model are discussed, including a new multi-layer diffusion model and a more realistic response of photosynthesis to temperature in mountainous regions. The data assimilation should be advanced by accounting for model and forcing uncertainties.

TRACING THE EVOLUTION OF HIGH-REDSHIFT GALAXIES USING STELLAR ABUNDANCES

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

Crosby, Brian D.; O’Shea, Brian W.; Beers, Timothy C.

2016-03-20

This paper presents the first results from a model for chemical evolution that can be applied to N-body cosmological simulations and quantitatively compared to measured stellar abundances from large astronomical surveys. This model convolves the chemical yield sets from a range of stellar nucleosynthesis calculations (including asymptotic giant branch stars, Type Ia and II supernovae, and stellar wind models) with a user-specified stellar initial mass function (IMF) and metallicity to calculate the time-dependent chemical evolution model for a “simple stellar population” (SSP) of uniform metallicity and formation time. These SSP models are combined with a semianalytic model for galaxy formation andmore » evolution that uses merger trees from N-body cosmological simulations to track several α- and iron-peak elements for the stellar and multiphase interstellar medium components of several thousand galaxies in the early (z ≥ 6) universe. The simulated galaxy population is then quantitatively compared to two complementary data sets of abundances in the Milky Way stellar halo and is capable of reproducing many of the observed abundance trends. The observed abundance ratio distributions are best reproduced with a Chabrier IMF, a chemically enriched star formation efficiency of 0.2, and a redshift of reionization of 7. Many abundances are qualitatively well matched by our model, but our model consistently overpredicts the carbon-enhanced fraction of stars at low metallicities, likely owing to incomplete coverage of Population III stellar yields and supernova models and the lack of dust as a component of our model.« less

The advanced receiver 2: Telemetry test results in CTA 21

NASA Technical Reports Server (NTRS)

Hinedi, S.; Bevan, R.; Marina, M.

1991-01-01

Telemetry tests with the Advanced Receiver II (ARX II) in Compatibility Test Area 21 are described. The ARX II was operated in parallel with a Block-III Receiver/baseband processor assembly combination (BLK-III/BPA) and a Block III Receiver/subcarrier demodulation assembly/symbol synchronization assembly combination (BLK-III/SDA/SSA). The telemetry simulator assembly provided the test signal for all three configurations, and the symbol signal to noise ratio as well as the symbol error rates were measured and compared. Furthermore, bit error rates were also measured by the system performance test computer for all three systems. Results indicate that the ARX-II telemetry performance is comparable and sometimes superior to the BLK-III/BPA and BLK-III/SDA/SSA combinations.

Computer Program (HEVSIM) for Heavy Duty Vehicle Fuel Economy and Performance Simulation. Volume III: Appendices A through F

DOT National Transportation Integrated Search

1981-09-01

Volume III is the third and last volume of a three volume document describing the computer program HEVSIM. This volume includes appendices which list the HEVSIM program, sample part data, some typical outputs and updated nomenclature.

The Be-WetSpa-Pest modeling approach to simulate human and environmental exposure from pesticide application

NASA Astrophysics Data System (ADS)

Binder, Claudia; Garcia-Santos, Glenda; Andreoli, Romano; Diaz, Jaime; Feola, Giuseppe; Wittensoeldner, Moritz; Yang, Jing

2016-04-01

This study presents an integrative and spatially explicit modeling approach for analyzing human and environmental exposure from pesticide application of smallholders in the potato producing Andean region in Colombia. The modeling approach fulfills the following criteria: (i) it includes environmental and human compartments; (ii) it contains a behavioral decision-making model for estimating the effect of policies on pesticide flows to humans and the environment; (iii) it is spatially explicit; and (iv) it is modular and easily expandable to include additional modules, crops or technologies. The model was calibrated and validated for the Vereda La Hoya and was used to explore the effect of different policy measures in the region. The model has moderate data requirements and can be adapted relatively easy to other regions in developing countries with similar conditions.

High resolution modelling of soil moisture patterns with TerrSysMP: A comparison with sensor network data

NASA Astrophysics Data System (ADS)

Gebler, S.; Hendricks Franssen, H.-J.; Kollet, S. J.; Qu, W.; Vereecken, H.

2017-04-01

The prediction of the spatial and temporal variability of land surface states and fluxes with land surface models at high spatial resolution is still a challenge. This study compares simulation results using TerrSysMP including a 3D variably saturated groundwater flow model (ParFlow) coupled to the Community Land Model (CLM) of a 38 ha managed grassland head-water catchment in the Eifel (Germany), with soil water content (SWC) measurements from a wireless sensor network, actual evapotranspiration recorded by lysimeters and eddy covariance stations and discharge observations. TerrSysMP was discretized with a 10 × 10 m lateral resolution, variable vertical resolution (0.025-0.575 m), and the following parameterization strategies of the subsurface soil hydraulic parameters: (i) completely homogeneous, (ii) homogeneous parameters for different soil horizons, (iii) different parameters for each soil unit and soil horizon and (iv) heterogeneous stochastic realizations. Hydraulic conductivity and Mualem-Van Genuchten parameters in these simulations were sampled from probability density functions, constructed from either (i) soil texture measurements and Rosetta pedotransfer functions (ROS), or (ii) estimated soil hydraulic parameters by 1D inverse modelling using shuffle complex evolution (SCE). The results indicate that the spatial variability of SWC at the scale of a small headwater catchment is dominated by topography and spatially heterogeneous soil hydraulic parameters. The spatial variability of the soil water content thereby increases as a function of heterogeneity of soil hydraulic parameters. For lower levels of complexity, spatial variability of the SWC was underrepresented in particular for the ROS-simulations. Whereas all model simulations were able to reproduce the seasonal evapotranspiration variability, the poor discharge simulations with high model bias are likely related to short-term ET dynamics and the lack of information about bedrock characteristics and an on-site drainage system in the uncalibrated model. In general, simulation performance was better for the SCE setups. The SCE-simulations had a higher inverse air entry parameter resulting in SWC dynamics in better correspondence with data than the ROS simulations during dry periods. This illustrates that small scale measurements of soil hydraulic parameters cannot be transferred to the larger scale and that interpolated 1D inverse parameter estimates result in an acceptable performance for the catchment.

Predicting the mixed-mode I/II spatial damage propagation along 3D-printed soft interfacial layer via a hyperelastic softening model

NASA Astrophysics Data System (ADS)

Liu, Lei; Li, Yaning

2018-07-01

A methodology was developed to use a hyperelastic softening model to predict the constitutive behavior and the spatial damage propagation of nonlinear materials with damage-induced softening under mixed-mode loading. A user subroutine (ABAQUS/VUMAT) was developed for numerical implementation of the model. 3D-printed wavy soft rubbery interfacial layer was used as a material system to verify and validate the methodology. The Arruda - Boyce hyperelastic model is incorporated with the softening model to capture the nonlinear pre-and post- damage behavior of the interfacial layer under mixed Mode I/II loads. To characterize model parameters of the 3D-printed rubbery interfacial layer, a series of scarf-joint specimens were designed, which enabled systematic variation of stress triaxiality via a single geometric parameter, the slant angle. It was found that the important model parameter m is exponentially related to the stress triaxiality. Compact tension specimens of the sinusoidal wavy interfacial layer with different waviness were designed and fabricated via multi-material 3D printing. Finite element (FE) simulations were conducted to predict the spatial damage propagation of the material within the wavy interfacial layer. Compact tension experiments were performed to verify the model prediction. The results show that the model developed is able to accurately predict the damage propagation of the 3D-printed rubbery interfacial layer under complicated stress-state without pre-defined failure criteria.

Effect of wave localization on plasma instabilities

NASA Astrophysics Data System (ADS)

Levedahl, William Kirk

1987-10-01

The Anderson model of wave localization in random media is involved to study the effect of solar wind density turbulence on plasma processes associated with the solar type III radio burst. ISEE-3 satellite data indicate that a possible model for the type III process is the parametric decay of Langmuir waves excited by solar flare electron streams into daughter electromagnetic and ion acoustic waves. The threshold for this instability, however, is much higher than observed Langmuir wave levels because of rapid wave convection of the transverse electromagnetic daughter wave in the case where the solar wind is assumed homogeneous. Langmuir and transverse waves near critical density satisfy the Ioffe-Reigel criteria for wave localization in the solar wind with observed density fluctuations -1 percent. Numerical simulations of wave propagation in random media confirm the localization length predictions of Escande and Souillard for stationary density fluctations. For mobile density fluctuations localized wave packets spread at the propagation velocity of the density fluctuations rather than the group velocity of the waves. Computer simulations using a linearized hybrid code show that an electron beam will excite localized Langmuir waves in a plasma with density turbulence. An action principle approach is used to develop a theory of non-linear wave processes when waves are localized. A theory of resonant particles diffusion by localized waves is developed to explain the saturation of the beam-plasma instability. It is argued that localization of electromagnetic waves will allow the instability threshold to be exceeded for the parametric decay discussed above.

Modelling and scale-up of chemical flooding

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

Pope, G.A.; Lake, L.W.; Sepehrnoori, K.

1990-03-01

The objective of this research is to develop, validate, and apply a comprehensive chemical flooding simulator for chemical recovery processes involving surfactants, polymers, and alkaline chemicals in various combinations. This integrated program includes components of laboratory experiments, physical property modelling, scale-up theory, and numerical analysis as necessary and integral components of the simulation activity. We have continued to develop, test, and apply our chemical flooding simulator (UTCHEM) to a wide variety of laboratory and reservoir problems involving tracers, polymers, polymer gels, surfactants, and alkaline agents. Part I is an update on the Application of Higher-Order Methods in Chemical Flooding Simulation.more » This update focuses on the comparison of grid orientation effects for four different numerical methods implemented in UTCHEM. Part II is on Simulation Design Studies and is a continuation of Saad's Big Muddy surfactant pilot simulation study reported last year. Part III reports on the Simulation of Gravity Effects under conditions similar to those of some of the oil reservoirs in the North Sea. Part IV is on Determining Oil Saturation from Interwell Tracers UTCHEM is used for large-scale interwell tracer tests. A systematic procedure for estimating oil saturation from interwell tracer data is developed and a specific example based on the actual field data provided by Sun E P Co. is given. Part V reports on the Application of Vectorization and Microtasking for Reservoir Simulation. Part VI reports on Alkaline Simulation. The alkaline/surfactant/polymer flood compositional simulator (UTCHEM) reported last year is further extended to include reactions involving chemical species containing magnesium, aluminium and silicon as constituent elements. Part VII reports on permeability and trapping of microemulsion.« less

Effect of Radiotherapy Planning Complexity on Survival of Elderly Patients With Unresected Localized Lung Cancer

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

Park, Chang H.; Bonomi, Marcelo; Cesaretti, Jamie

2011-11-01

Purpose: To evaluate whether complex radiotherapy (RT) planning was associated with improved outcomes in a cohort of elderly patients with unresected Stage I-II non-small-cell lung cancer (NSCLC). Methods and Materials: Using the Surveillance, Epidemiology, and End Results registry linked to Medicare claims, we identified 1998 patients aged >65 years with histologically confirmed, unresected stage I-II NSCLC. Patients were classified into an intermediate or complex RT planning group using Medicare physician codes. To address potential selection bias, we used propensity score modeling. Survival of patients who received intermediate and complex simulation was compared using Cox regression models adjusting for propensity scoresmore » and in a stratified and matched analysis according to propensity scores. Results: Overall, 25% of patients received complex RT planning. Complex RT planning was associated with better overall (hazard ratio 0.84; 95% confidence interval, 0.75-0.95) and lung cancer-specific (hazard ratio 0.81; 95% confidence interval, 0.71-0.93) survival after controlling for propensity scores. Similarly, stratified and matched analyses showed better overall and lung cancer-specific survival of patients treated with complex RT planning. Conclusions: The use of complex RT planning is associated with improved survival among elderly patients with unresected Stage I-II NSCLC. These findings should be validated in prospective randomized controlled trials.« less

Computational study of haemodynamic effects of entry- and exit-tear coverage in a DeBakey type III aortic dissection: technical report.

PubMed

Karmonik, C; Bismuth, J; Shah, D J; Davies, M G; Purdy, D; Lumsden, A B

2011-08-01

Outcome prediction in DeBakey Type III aortic dissections (ADs) remains challenging. Large variations in AD morphology, physiology and treatment exist. Here, we investigate if computational fluid dynamics (CFD) can provide an initial understanding of pressure changes in an AD computational model when covering entry and exit tears and removing the intra-arterial septum (IS). A computational mesh was constructed from magnetic resonance images from one patient (one entrance and one exit tear) and CFD simulations performed (scenario #1). Additional meshes were derived by virtually (1) covering the exit tear (false lumen (FL) thrombus progression) (scenario #2), (2) covering the entrance tear (thoracic endovascular treatment, TEVAR) (scenario #3) and (3) completely removing the IS (fenestration) (scenario #4). Changes in flow patterns and pressures were quantified relative to the initial mesh. Systolic pressures increased for #2 (300 Pa increase) with largest inter-luminal differences distally (2500 Pa). In #3, false lumen pressure decreased essentially to zero. In #4, systolic pressure in combined lumen reduced from 2400 to 800 Pa. CFD results from computational models of a DeBakey type III AD representing separate coverage of entrance and exit tears correlated with clinical experience. The reported results present a preliminary look at a complex clinical problem. Copyright © 2011 European Society for Vascular Surgery. Published by Elsevier Ltd. All rights reserved.

Reduction of Fe(III) colloids by Shewanella putrefaciens: A kinetic model

NASA Astrophysics Data System (ADS)

Bonneville, Steeve; Behrends, Thilo; van Cappellen, Philippe; Hyacinthe, Christelle; Röling, Wilfred F. M.

2006-12-01

A kinetic model for the microbial reduction of Fe(III) oxyhydroxide colloids in the presence of excess electron donor is presented. The model assumes a two-step mechanism: (1) attachment of Fe(III) colloids to the cell surface and (2) reduction of Fe(III) centers at the surface of attached colloids. The validity of the model is tested using Shewanella putrefaciens and nanohematite as model dissimilatory iron reducing bacteria and Fe(III) colloidal particles, respectively. Attachment of nanohematite to the bacteria is formally described by a Langmuir isotherm. Initial iron reduction rates are shown to correlate linearly with the relative coverage of the cell surface by nanohematite particles, hence supporting a direct electron transfer from membrane-bound reductases to mineral particles attached to the cells. Using internally consistent parameter values for the maximum attachment capacity of Fe(III) colloids to the cells, Mmax, the attachment constant, KP, and the first-order Fe(III) reduction rate constant, k, the model reproduces the initial reduction rates of a variety of fine-grained Fe(III) oxyhydroxides by S. putrefaciens. The model explains the observed dependency of the apparent Fe(III) half-saturation constant, Km∗, on the solid to cell ratio, and it predicts that initial iron reduction rates exhibit saturation with respect to both the cell density and the abundance of the Fe(III) oxyhydroxide substrate.

First light: exploring the spectra of high-redshift galaxies in the Renaissance Simulations

NASA Astrophysics Data System (ADS)

Barrow, Kirk S. S.; Wise, John H.; Norman, Michael L.; O'Shea, Brian W.; Xu, Hao

2017-08-01

We present synthetic observations for the first generations of galaxies in the Universe and make predictions for future deep field observations for redshifts greater than 6. Due to the strong impact of nebular emission lines and the relatively compact scale of H II regions, high-resolution cosmological simulations and a robust suite of analysis tools are required to properly simulate spectra. We created a software pipeline consisting of fsps, hyperion, cloudy and our own tools to generate synthetic IR observations from a fully three-dimensional arrangement of gas, dust, and stars. Our prescription allows us to include emission lines for a complete chemical network and tackle the effect of dust extinction and scattering in the various lines of sight. We provide spectra, 2D binned photon imagery for both HST and JWST IR filters, luminosity relationships, and emission-line strengths for a large sample of high-redshift galaxies in the Renaissance Simulations. Our resulting synthetic spectra show high variability between galactic haloes with a strong dependence on stellar mass, metallicity, gas mass fraction, and formation history. Haloes with the lowest stellar mass have the greatest variability in [O III]/Hβ, [O III], and C III], while haloes with higher masses are seen to show consistency in their spectra and [O III] equivalent widths between 1 and 10 Å. Viewing angle accounted for threefold difference in flux due to the presence of ionized gas channels in a halo. Furthermore, JWST colour plots show a discernible relationship between redshift, colour, and mean stellar age.

Short-term Climate Simulations of African Easterly Waves with a Global Mesoscale Model

NASA Astrophysics Data System (ADS)

Shen, B. W.

2015-12-01

Recent high-resolution global model simulations ( Shen et al., 2010a, 2010b, 2012; 2013), which were conducted to examine the role of multiscale processes associated with tropical waves in the predictability of mesoscale tropical cyclones (TCs), suggested that a large-scale system (e.g., tropical waves) can provide determinism on the prediction of TC genesis, making it possible to extend the lead time of genesis predictions. Selected cases include the relationship between (i) TC Nargis (2008) and an Equatorial Rossby wave; (ii) Hurricane Helene (2006) and an intensifying African Easterly Wave (AEW); (iii) Twin TCs (2002) and a mixed Rossby-gravity wave during an active phase of the Madden Julian Oscillation (MJO); (iv) Hurricane Sandy (2012) and tropical waves during an active phase of the MJO. In this talk, thirty-day simulations with different model configurations are presented to examine the model's ability to simulate AEWs and MJOs and their association with tropical cyclogenesis. I will first discuss the simulations of the initiation and propagation of 6 consecutive AEWs in late August 2006 and the mean state of the African easterly jet (AEJ) over both Africa and downstream in the tropical Atlantic. By comparing our simulations with NCEP analysis and satellite data (e.g., TRMM), it is shown that the statistical characteristics of individual AEWs are realistically simulated with larger errors in the 5th and th AEWs. Results from the sensitivity experiments suggest the following: 1) accurate representations of non-linear interactions between the atmosphere and land processes are crucial for improving the simulations of the AEWs and the AEJ; 2) improved simulations of an individual AEW and its interaction with local environments (e.g., the Guinea Highlands) could provide determinism for hurricane formation downstream. Of interest is the potential to extend the lead time for predicting hurricane formation (e.g., a lead time of up to 22 days) as the 4th AEW is realistically simulated; 3) however, the dependence of AEW simulations on accurate dynamic and surface initial conditions and boundary conditions poses a challenge in simulating their modulation on hurricane activity. In addition to the simulations of AEWs, I will also present the 30-day simulations of selected MJO cases.

Fault Diagnostics and Prognostics for Large Segmented SRMs

NASA Technical Reports Server (NTRS)

Luchinsky, Dmitry; Osipov, Viatcheslav V.; Smelyanskiy, Vadim N.; Timucin, Dogan A.; Uckun, Serdar; Hayashida, Ben; Watson, Michael; McMillin, Joshua; Shook, David; Johnson, Mont;

Effects of Pop III to PopII transition on the lowest metallicity stars in dwarf galaxies

NASA Astrophysics Data System (ADS)

Zhang, Yimiao; Keres, Dusan; FIRE Team

2018-01-01

We examine the effects of the enrichments from Population III (Pop III) stars on the formation and properties of the first generation of the Population II (Pop II) stars. Pop III stars begin to transition towards Pop II stars when the metals dispersed in Pop III supernovae pollute the nearby gas. However, details of this transition are still largely unknown. We use dwarf galaxy simulations from the Feedback In Realistic Environments (FIRE) project to identify the star-forming gas that is likely to be pre-enriched by Pop III supernovae and follow the stars that form in such gas. This pre-enrichment will leave the signature in the lowest metallicity stars that can be used to better constrain the details of the Pop III-to-Pop II transition.

The returns and risks of investment portfolio in a financial market

NASA Astrophysics Data System (ADS)

Li, Jiang-Cheng; Mei, Dong-Cheng

2014-07-01

The returns and risks of investment portfolio in a financial system was investigated by constructing a theoretical model based on the Heston model. After the theoretical model and analysis of portfolio were calculated and analyzed, we find the following: (i) The statistical properties (i.e., the probability distribution, the variance and loss rate of equity portfolio return) between simulation results of the theoretical model and the real financial data obtained from Dow Jones Industrial Average are in good agreement; (ii) The maximum dispersion of the investment portfolio is associated with the maximum stability of the equity portfolio return and minimal investment risks; (iii) An increase of the investment period and a worst investment period are associated with a decrease of stability of the equity portfolio return and a maximum investment risk, respectively.

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

NASA Astrophysics Data System (ADS)

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

2005-04-01

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

Simulation and prediction the impact of climate change into water resources in Bengawan Solo watershed based on CCAM (Conformal Cubic Atmospheric Model) data

NASA Astrophysics Data System (ADS)

Sipayung, Sinta B.; Nurlatifah, Amalia; Siswanto, Bambang

2018-05-01

Bengawan Solo Watershed is one of the largest watersheds in Indonesia. This watershed flows in many areas both in Central Java and East Java. Therefore, the water resources condition greatly affects many people. This research will be conducted on prediction of climate change effect on water resources condition in terms of rainfall conditions in Bengawan Solo River Basin. The goal of this research is to know and predict the climate change impact on water resources based on CCAM (Conformal Cubic Atmosphere Model) with downscaling baseline (historical) model data from 1949 to 2005 and RCP 4.5 from 2006 to 2069. The modeling data was validated with in-situ data (measurement data). To analyse the water availability condition in Bengawan Solo Watershed, the simulation of river flow and water balance condition were done in Bengawan Solo River. Simulation of river flow and water balance conditions were done with ArcSWAT model using climate data from CCAM, DEM SRTM 90 meter, soil type, and land use data. The results of this simulation indicate there is (i) The CCAM data itself after validation has a pretty good result when compared to the insitu data. Based on CCAM simulation results, it is predicted that in 2040-2069 rainfall in Bengawan Solo River Basin will decrease, to a maximum of only about 1 mm when compared to 1971-2000. (ii) The CCAM rainfall prediction itself shows that rainfall in Bengawan Solo River basin will decline until 2069 although the decline itself is not significant and tends to be negligible (rainfall is considered unchanged) (iii) Both in the DJF and JJA seasons, precipitation is predicted to decline as well despite the significant decline. (iv) The river flow simulation show that the water resources in Bengawan Solo River did not change significantly. This event occurred because the rainfall also did not change greatly and close to 0 mm/month.

The effect of plasma inhomogeneities on (i) radio emission generation by non-gyrotropic electron beams and (ii) particle acceleration by Langmuir waves

NASA Astrophysics Data System (ADS)

Tsiklauri, D.

2014-12-01

Extensive particle-in-cell simulations of fast electron beams injected in a background magnetised plasma with a decreasing density profile were carried out. These simulations were intended to further shed light on a newly proposed mechanism for the generation of electromagnetic waves in type III solar radio bursts [1]. Here recent progress in an alternative to the plasma emission model using Particle-In-Cell, self-consistent electromagnetic wave emission simulations of solar type III radio bursts will be presented. In particular, (i) Fourier space drift (refraction) of non-gyrotropic electron beam-generated wave packets, caused by the density gradient [1,2], (ii) parameter space investigation of numerical runs [3], (iii) concurrent generation of whistler waves [4] and a separate problem of (iv) electron acceleration by Langmuir waves in a background magnetised plasma with an increasing density profile [5] will be discussed. In all considered cases the density inhomogeneity-induced wave refraction plays a crucial role. In the case of non-gyrotropic electron beam, the wave refaction transforms the generated wave packets from standing into freely escaping EM radiation. In the case of electron acceleration by Langmuir waves, a positive density gradient in the direction of wave propagation causes a decrease in the wavenumber, and hence a higher phase velocity vph=ω/k. The k-shifted wave is then subject to absorption by a faster electron by wave-particle interaction. The overall effect is an increased number of high energy electrons in the energy spectrum. [1] D. Tsiklauri, Phys. Plasmas 18, 052903 (2011) [2] H. Schmitz, D. Tsiklauri, Phys. Plasmas 20, 062903 (2013) [3] R. Pechhacker, D. Tsiklauri, Phys. Plasmas 19, 112903 (2012) [4] M. Skender, D. Tsiklauri, Phys. Plasmas 21, 042904 (2014) [5] R. Pechhacker, D. Tsiklauri, Phys. Plasmas 21, 012903 (2014)

High-resolution stochastic generation of extreme rainfall intensity for urban drainage modelling applications

NASA Astrophysics Data System (ADS)

Peleg, Nadav; Blumensaat, Frank; Molnar, Peter; Fatichi, Simone; Burlando, Paolo

2016-04-01

Urban drainage response is highly dependent on the spatial and temporal structure of rainfall. Therefore, measuring and simulating rainfall at a high spatial and temporal resolution is a fundamental step to fully assess urban drainage system reliability and related uncertainties. This is even more relevant when considering extreme rainfall events. However, the current space-time rainfall models have limitations in capturing extreme rainfall intensity statistics for short durations. Here, we use the STREAP (Space-Time Realizations of Areal Precipitation) model, which is a novel stochastic rainfall generator for simulating high-resolution rainfall fields that preserve the spatio-temporal structure of rainfall and its statistical characteristics. The model enables a generation of rain fields at 102 m and minute scales in a fast and computer-efficient way matching the requirements for hydrological analysis of urban drainage systems. The STREAP model was applied successfully in the past to generate high-resolution extreme rainfall intensities over a small domain. A sub-catchment in the city of Luzern (Switzerland) was chosen as a case study to: (i) evaluate the ability of STREAP to disaggregate extreme rainfall intensities for urban drainage applications; (ii) assessing the role of stochastic climate variability of rainfall in flow response and (iii) evaluate the degree of non-linearity between extreme rainfall intensity and system response (i.e. flow) for a small urban catchment. The channel flow at the catchment outlet is simulated by means of a calibrated hydrodynamic sewer model.

MIZEX. A Program for Mesoscale Air-Ice-Ocean Interaction Experiments in Arctic Marginal Ice Zones. III. Modeling the Marginal Ice Zone,

DTIC Science & Technology

1984-04-01

Ii TS C]r.I2 TAB 0] Unzanro’ unoed 0 justi fica ~r: 0 April 1984 vs - ASValabilitY Codes lvyall and/or U.S. Army Cold Regions Research and Engineering...coupled model. Fig. 1. Annual average simulated velocity fields. 3 192 Aloka 190 / 902 190+ WOO S’,. o Ice OnlY Mod" D"’, 55*w F~tth Yea’ Ice Ocean Model...A more precise delinga- inflow boundary conditions. 12 4- a. [ o ll ii traspert 00 0 0- 0e a I " i i , - - I I 1161 63 15 67 69 Ti 73 75 77 1980 *= 4h

Modeling Urban Energy Savings Scenarios Using Earth System Microclimate and Urban Morphology

NASA Astrophysics Data System (ADS)

Allen, M. R.; Rose, A.; New, J. R.; Yuan, J.; Omitaomu, O.; Sylvester, L.; Branstetter, M. L.; Carvalhaes, T. M.; Seals, M.; Berres, A.

2017-12-01

We analyze and quantify the relationships among climatic conditions, urban morphology, population, land cover, and energy use so that these relationships can be used to inform energy-efficient urban development and planning. We integrate different approaches across three research areas: earth system modeling; impacts, adaptation and vulnerability; and urban planning in order to address three major gaps in the existing capability in these areas: i) neighborhood resolution modeling and simulation of urban micrometeorological processes and their effect on and from regional climate; ii) projections for future energy use under urbanization and climate change scenarios identifying best strategies for urban morphological development and energy savings; iii) analysis and visualization tools to help planners optimally use these projections.

Testing simulations of intra- and inter-annual variation in the plant production response to elevated CO(2) against measurements from an 11-year FACE experiment on grazed pasture.

PubMed

Li, Frank Yonghong; Newton, Paul C D; Lieffering, Mark

2014-01-01

Ecosystem models play a crucial role in understanding and evaluating the combined impacts of rising atmospheric CO2 concentration and changing climate on terrestrial ecosystems. However, we are not aware of any studies where the capacity of models to simulate intra- and inter-annual variation in responses to elevated CO2 has been tested against long-term experimental data. Here we tested how well the ecosystem model APSIM/AgPasture was able to simulate the results from a free air carbon dioxide enrichment (FACE) experiment on grazed pasture. At this FACE site, during 11 years of CO2 enrichment, a wide range in annual plant production response to CO2 (-6 to +28%) was observed. As well as running the full model, which includes three plant CO2 response functions (plant photosynthesis, nitrogen (N) demand and stomatal conductance), we also tested the influence of these three functions on model predictions. Model/data comparisons showed that: (i) overall the model over-predicted the mean annual plant production response to CO2 (18.5% cf 13.1%) largely because years with small or negative responses to CO2 were not well simulated; (ii) in general seasonal and inter-annual variation in plant production responses to elevated CO2 were well represented by the model; (iii) the observed CO2 enhancement in overall mean legume content was well simulated but year-to-year variation in legume content was poorly captured by the model; (iv) the best fit of the model to the data required all three CO2 response functions to be invoked; (v) using actual legume content and reduced N fixation rate under elevated CO2 in the model provided the best fit to the experimental data. We conclude that in temperate grasslands the N dynamics (particularly the legume content and N fixation activity) play a critical role in pasture production responses to elevated CO2 , and are processes for model improvement. © 2013 John Wiley & Sons Ltd.

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

Fahim, Farah; Deptuch, Grzegorz W.; Hoff, James R.

Semiconductor hybrid pixel detectors often consist of a pixellated sensor layer bump bonded to a matching pixelated readout integrated circuit (ROIC). The sensor can range from high resistivity Si to III-V materials, whereas a Si CMOS process is typically used to manufacture the ROIC. Independent, device physics and electronic design automation (EDA) tools are used to determine sensor characteristics and verify functional performance of ROICs respectively with significantly different solvers. Some physics solvers provide the capability of transferring data to the EDA tool. However, single pixel transient simulations are either not feasible due to convergence difficulties or are prohibitively long.more » A simplified sensor model, which includes a current pulse in parallel with detector equivalent capacitor, is often used; even then, spice type top-level (entire array) simulations range from days to weeks. In order to analyze detector deficiencies for a particular scientific application, accurately defined transient behavioral models of all the functional blocks are required. Furthermore, various simulations, such as transient, noise, Monte Carlo, inter-pixel effects, etc. of the entire array need to be performed within a reasonable time frame without trading off accuracy. The sensor and the analog front-end can be modeling using a real number modeling language, as complex mathematical functions or detailed data can be saved to text files, for further top-level digital simulations. Parasitically aware digital timing is extracted in a standard delay format (sdf) from the pixel digital back-end layout as well as the periphery of the ROIC. For any given input, detector level worst-case and best-case simulations are performed using a Verilog simulation environment to determine the output. Each top-level transient simulation takes no more than 10-15 minutes. The impact of changing key parameters such as sensor Poissonian shot noise, analog front-end bandwidth, jitter due to clock distribution etc. can be accurately analyzed to determine ROIC architectural viability and bottlenecks. Hence the impact of the detector parameters on the scientific application can be studied.« less

Line profile studies of hydrodynamical models of cometary compact H II regions

NASA Astrophysics Data System (ADS)

Zhu, Feng-Yao; Zhu, Qing-Feng

2015-06-01

We simulate the evolution of cometary H II regions based on several champagne flow models and bow shock models, and calculate the profiles of the [Ne II] fine-structure line at 12.81 μm, the H30α recombination line and the [Ne III] fine-structure line at 15.55 μm for these models at different inclinations of 0°, 30° and 60°. We find that the profiles in the bow shock models are generally different from those in the champagne flow models, but the profiles in the bow shock models with lower stellar velocity (≤ 5 km s-1) are similar to those in the champagne flow models. In champagne flow models, both the velocity of peak flux and the flux weighted central velocities of all three lines point outward from molecular clouds. In bow shock models, the directions of these velocities depend on the speed of stars. The central velocities of these lines are consistent with the stellar motion in the high stellar speed cases, but they are opposite directions from the stellar motion in the low speed cases. We notice that the line profiles from the slit along the symmetrical axis of the projected 2D image of these models are useful for distinguishing bow shock models from champagne flow models. It is also confirmed by the calculation that the flux weighted central velocity and the line luminosity of the [Ne III] line can be estimated from the [Ne II] line and the H30α line.

A back-fitting algorithm to improve real-time flood forecasting

NASA Astrophysics Data System (ADS)

Zhang, Xiaojing; Liu, Pan; Cheng, Lei; Liu, Zhangjun; Zhao, Yan

2018-07-01

Real-time flood forecasting is important for decision-making with regards to flood control and disaster reduction. The conventional approach involves a postprocessor calibration strategy that first calibrates the hydrological model and then estimates errors. This procedure can simulate streamflow consistent with observations, but obtained parameters are not optimal. Joint calibration strategies address this issue by refining hydrological model parameters jointly with the autoregressive (AR) model. In this study, five alternative schemes are used to forecast floods. Scheme I uses only the hydrological model, while scheme II includes an AR model for error correction. In scheme III, differencing is used to remove non-stationarity in the error series. A joint inference strategy employed in scheme IV calibrates the hydrological and AR models simultaneously. The back-fitting algorithm, a basic approach for training an additive model, is adopted in scheme V to alternately recalibrate hydrological and AR model parameters. The performance of the five schemes is compared with a case study of 15 recorded flood events from China's Baiyunshan reservoir basin. Our results show that (1) schemes IV and V outperform scheme III during the calibration and validation periods and (2) scheme V is inferior to scheme IV in the calibration period, but provides better results in the validation period. Joint calibration strategies can therefore improve the accuracy of flood forecasting. Additionally, the back-fitting recalibration strategy produces weaker overcorrection and a more robust performance compared with the joint inference strategy.

Genetic and demographic implications of aquaculture in white sturgeon (Acipenser transmontanus)conservation

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

Jager, Yetta

2005-01-01

This study uses a genetic individual-based model of white sturgeon (Acipenser transmontanus) populations in a river to examine the genetic and demographic trade-offs associated with operating a conservation hatchery. Simulation experiments evaluated three management practices: (i) setting quotas to equalize family contributions in an effort to prevent genetic swamping, (ii) an adaptive management scheme that interrupts stocking when introgression exceeds a specified threshold, and (iii) alternative broodstock selection strategies that influence domestication. The first set of simulations, designed to evaluate equalizing the genetic contribution of families, did not show the genetic benefits expected. The second set of simulations showed thatmore » simulated adaptive management was not successful in controlling introgression over the long term, especially with uncertain feedback. The third set of simulations compared the effects of three alternative broodstock selection strategies on domestication for hypothetical traits controlling early density-dependent survival. Simulated aquaculture selected for a density-tolerant phenotype when broodstock were taken from a genetically connected population. Using broodstock from an isolated population (i.e., above an upstream barrier or in a different watershed) was more effective at preventing domestication than using wild broodstock from a connected population.« less

Transmission probabilities and durations of immunity for three pathogenic group B Streptococcus serotypes

PubMed Central

Percha, Bethany; Newman, M. E. J.; Foxman, Betsy

2012-01-01

Group B Streptococcus (GBS) remains a major cause of neonatal sepsis and is an emerging cause of invasive bacterial infections. The 9 known serotypes vary in virulence, and there is little cross-immunity. Key parameters for planning an effective vaccination strategy, such as average length of immunity and transmission probabilities by serotype, are unknown. We simulated GBS spread in a population using a computational model with parameters derived from studies of GBS sexual transmission in a college dormitory. Here we provide estimates of the duration of immunity relative to the transmission probabilities for the 3 GBS serotypes most associated with invasive disease: Ia, III, and V. We also place upper limits on the durations of immunity for serotype Ia (570 days), III (1125 days) and V (260 days). Better transmission estimates are required to establish the epidemiological parameters of GBS infection and determine the best vaccination strategies to prevent GBS disease. PMID:21605704

Intermediate-mass black holes from Population III remnants in the first galactic nuclei

NASA Astrophysics Data System (ADS)

Ryu, Taeho; Tanaka, Takamitsu L.; Perna, Rosalba; Haiman, Zoltán

2016-08-01

We report the formation of intermediate-mass black holes (IMBHs) in suites of numerical N-body simulations of Population III remnant black holes (BHs) embedded in gas-rich protogalaxies at redshifts z ≳ 10. We model the effects of gas drag on the BHs' orbits, and allow BHs to grow via gas accretion, including a mode of hyper-Eddington accretion in which photon trapping and rapid gas inflow suppress any negative radiative feedback. Most initial BH configurations lead to the formation of one (but never more than one) IMBH in the centre of the protogalaxy, reaching a mass of 103-5 M⊙ through hyper-Eddington growth. Our results suggest a viable pathway to forming the earliest massive BHs in the centres of early galaxies. We also find that the nuclear IMBH typically captures a stellar-mass BH companion, making these systems observable in gravitational waves as extreme mass-ratio inspirals with eLISA.

Full-scale simulation of seawater reverse osmosis desalination processes for boron removal: Effect of membrane fouling.

PubMed

Park, Pyung-Kyu; Lee, Sangho; Cho, Jae-Seok; Kim, Jae-Hong

2012-08-01

The objective of this study is to further develop previously reported mechanistic predictive model that simulates boron removal in full-scale seawater reverse osmosis (RO) desalination processes to take into account the effect of membrane fouling. Decrease of boron removal and reduction in water production rate by membrane fouling due to enhanced concentration polarization were simulated as a decrease in solute mass transfer coefficient in boundary layer on membrane surface. Various design and operating options under fouling condition were examined including single- versus double-pass configurations, different number of RO elements per vessel, use of RO membranes with enhanced boron rejection, and pH adjustment. These options were quantitatively compared by normalizing the performance of the system in terms of E(min), the minimum energy costs per product water. Simulation results suggested that most viable options to enhance boron rejection among those tested in this study include: i) minimizing fouling, ii) exchanging the existing SWRO elements to boron-specific ones, and iii) increasing pH in the second pass. The model developed in this study is expected to help design and optimization of the RO processes to achieve the target boron removal at target water recovery under realistic conditions where membrane fouling occurs during operation. Copyright © 2012 Elsevier Ltd. All rights reserved.

Theory and simulation of electrolyte mixtures

NASA Astrophysics Data System (ADS)

Lee, B. Hribar; Vlachy, V.; Bhuiyan, L. B.; Outhwaite, C. W.; Molero, M.

Monte Carlo simulation and theoretical results on some aspects of thermodynamics of mixtures of electrolytes with a common species are presented. Both charge symmetric mixtures, where ions differ only in size, and charge asymmetric but size symmetric mixtures at ionic strength ranging generally from I = 10-4 to 1.0 M, and in a few cases up to I = M, are examined. The theoretical methods explored are: (i) the symmetric Poisson-Boltzmann theory, (ii) the modified Poisson-Boltzmann theory and (iii) the hypernetted-chain integral equation. The first two electrolyte mixing coefficients w0 and w1 of the various mixtures are calculated from an accurate determination of their osmotic pressure data. The theories are seen to be consistent among themselves, and with certain limiting laws in the literature, in predicting the trends of the mixing coefficients with respect to ionic strength. Some selected relevant experimental data have been analysed and compared with the theoretical and simulation trends. In addition the mean activity coefficients for a model mimicking the mixture of KCl and KF electrolytes are calculated and hence the Harned coefficients obtained for this system. These calculations are compared with the experimental data and Monte Carlo results available in the literature. The theoretically predicted Harned coefficients are in good agreement with the simulation results for the model KCl-KF mixture.

Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA.

PubMed

Kelly, Brendan J; Gross, Robert; Bittinger, Kyle; Sherrill-Mix, Scott; Lewis, James D; Collman, Ronald G; Bushman, Frederic D; Li, Hongzhe

2015-08-01

The variation in community composition between microbiome samples, termed beta diversity, can be measured by pairwise distance based on either presence-absence or quantitative species abundance data. PERMANOVA, a permutation-based extension of multivariate analysis of variance to a matrix of pairwise distances, partitions within-group and between-group distances to permit assessment of the effect of an exposure or intervention (grouping factor) upon the sampled microbiome. Within-group distance and exposure/intervention effect size must be accurately modeled to estimate statistical power for a microbiome study that will be analyzed with pairwise distances and PERMANOVA. We present a framework for PERMANOVA power estimation tailored to marker-gene microbiome studies that will be analyzed by pairwise distances, which includes: (i) a novel method for distance matrix simulation that permits modeling of within-group pairwise distances according to pre-specified population parameters; (ii) a method to incorporate effects of different sizes within the simulated distance matrix; (iii) a simulation-based method for estimating PERMANOVA power from simulated distance matrices; and (iv) an R statistical software package that implements the above. Matrices of pairwise distances can be efficiently simulated to satisfy the triangle inequality and incorporate group-level effects, which are quantified by the adjusted coefficient of determination, omega-squared (ω2). From simulated distance matrices, available PERMANOVA power or necessary sample size can be estimated for a planned microbiome study. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Versatile Analysis of Single-Molecule Tracking Data by Comprehensive Testing against Monte Carlo Simulations

PubMed Central

Wieser, Stefan; Axmann, Markus; Schütz, Gerhard J.

2008-01-01

We propose here an approach for the analysis of single-molecule trajectories which is based on a comprehensive comparison of an experimental data set with multiple Monte Carlo simulations of the diffusion process. It allows quantitative data analysis, particularly whenever analytical treatment of a model is infeasible. Simulations are performed on a discrete parameter space and compared with the experimental results by a nonparametric statistical test. The method provides a matrix of p-values that assess the probability for having observed the experimental data at each setting of the model parameters. We show the testing approach for three typical situations observed in the cellular plasma membrane: i), free Brownian motion of the tracer, ii), hop diffusion of the tracer in a periodic meshwork of squares, and iii), transient binding of the tracer to slowly diffusing structures. By plotting the p-value as a function of the model parameters, one can easily identify the most consistent parameter settings but also recover mutual dependencies and ambiguities which are difficult to determine by standard fitting routines. Finally, we used the test to reanalyze previous data obtained on the diffusion of the glycosylphosphatidylinositol-protein CD59 in the plasma membrane of the human T24 cell line. PMID:18805933

Population Pharmacokinetic Modeling and Dosing Simulations of Nitrogen-Scavenging Compounds: Disposition of Glycerol Phenylbutyrate and Sodium Phenylbutyrate in Adult and Pediatric Patients with Urea Cycle Disorders

PubMed Central

Monteleone, Jon P. R.; Mokhtarani, M.; Diaz, G. A.; Rhead, W.; Lichter-Konecki, U.; Berry, S. A.; LeMons, C.; Dickinson, K.; Coakley, D.; Lee, B.; Scharschmidt, B. F.

2014-01-01

Sodium phenylbutyrate and glycerol phenylbutyrate mediate waste nitrogen excretion in the form of urinary phenylacetylglutamine (PAGN) in patients with urea cycle disorders (UCDs); rare genetic disorders characterized by impaired urea synthesis and hyperammonemia. Sodium phenylbutyrate is approved for UCD treatment; the development of glycerol phenylbutyrate afforded the opportunity to characterize the pharmacokinetics (PK) of both compounds. A population PK model was developed using data from four Phase II/III trials that collectively enrolled patients ages 2 months to 72 years. Dose simulations were performed with particular attention to phenylacetic acid (PAA), which has been associated with adverse events in non-UCD populations. The final model described metabolite levels in plasma and urine for both drugs and was characterized by (a) partial presystemic metabolism of phenylbutyric acid (PBA) to PAA and/or PAGN, (b) slower PBA absorption and greater presystemic conversion with glycerol phenylbutyrate, (c) similar systemic disposition with saturable conversion of PAA to PAGN for both drugs, and (d) body surface area (BSA) as a significant covariate accounting for age-related PK differences. Dose simulations demonstrated similar PAA exposure following mole-equivalent PBA dosing of both drugs and greater PAA exposure in younger patients based on BSA. PMID:23775211

Population pharmacokinetic modeling and dosing simulations of nitrogen-scavenging compounds: disposition of glycerol phenylbutyrate and sodium phenylbutyrate in adult and pediatric patients with urea cycle disorders.

PubMed

Monteleone, Jon P R; Mokhtarani, M; Diaz, G A; Rhead, W; Lichter-Konecki, U; Berry, S A; Lemons, C; Dickinson, K; Coakley, D; Lee, B; Scharschmidt, B F

2013-07-01

Sodium phenylbutyrate and glycerol phenylbutyrate mediate waste nitrogen excretion in the form of urinary phenylacetylglutamine (PAGN) in patients with urea cycle disorders (UCDs); rare genetic disorders characterized by impaired urea synthesis and hyperammonemia. Sodium phenylbutyrate is approved for UCD treatment; the development of glycerol phenylbutyrate afforded the opportunity to characterize the pharmacokinetics (PK) of both compounds. A population PK model was developed using data from four Phase II/III trials that collectively enrolled patients ages 2 months to 72 years. Dose simulations were performed with particular attention to phenylacetic acid (PAA), which has been associated with adverse events in non-UCD populations. The final model described metabolite levels in plasma and urine for both drugs and was characterized by (a) partial presystemic metabolism of phenylbutyric acid (PBA) to PAA and/or PAGN, (b) slower PBA absorption and greater presystemic conversion with glycerol phenylbutyrate, (c) similar systemic disposition with saturable conversion of PAA to PAGN for both drugs, and (d) body surface area (BSA) as a significant covariate accounting for age-related PK differences. Dose simulations demonstrated similar PAA exposure following mole-equivalent PBA dosing of both drugs and greater PAA exposure in younger patients based on BSA. © The Author(s) 2013.

Constraining the Absolute Orientation of eta Carinae's Binary Orbit: A 3-D Dynamical Model for the Broad [Fe III] Emission

NASA Technical Reports Server (NTRS)

Madura, T. I.; Gull, T. R.; Owocki, S. P.; Groh, J. H.; Okazaki, A. T.; Russell, C. M. P.

2011-01-01

We present a three-dimensional (3-D) dynamical model for the broad [Fe III] emission observed in Eta Carinae using the Hubble Space Telescope/Space Telescope Imaging Spectrograph (HST/STIS). This model is based on full 3-D Smoothed Particle Hydrodynamics (SPH) simulations of Eta Car's binary colliding winds. Radiative transfer codes are used to generate synthetic spectro-images of [Fe III] emission line structures at various observed orbital phases and STIS slit position angles (PAs). Through a parameter study that varies the orbital inclination i, the PA(theta) that the orbital plane projection of the line-of-sight makes with the apastron side of the semi-major axis, and the PA on the sky of the orbital axis, we are able, for the first time, to tightly constrain the absolute 3-D orientation of the binary orbit. To simultaneously reproduce the blue-shifted emission arcs observed at orbital phase 0.976, STIS slit PA = +38deg, and the temporal variations in emission seen at negative slit PAs, the binary needs to have an i approx. = 130deg to 145deg, Theta approx. = -15deg to +30deg, and an orbital axis projected on the sky at a P A approx. = 302deg to 327deg east of north. This represents a system with an orbital axis that is closely aligned with the inferred polar axis of the Homunculus nebula, in 3-D. The companion star, Eta(sub B), thus orbits clockwise on the sky and is on the observer's side of the system at apastron. This orientation has important implications for theories for the formation of the Homunculus and helps lay the groundwork for orbital modeling to determine the stellar masses.

Modeling of Nonlinear Hydrodynamics of the Coastal Areas of the Black Sea by the Chain of the Proprietary and Open Source Models

NASA Astrophysics Data System (ADS)

Kantardgi, Igor; Zheleznyak, Mark; Demchenko, Raisa; Dykyi, Pavlo; Kivva, Sergei; Kolomiets, Pavlo; Sorokin, Maxim

2014-05-01

The nearshore hydrodynamic fields are produced by the nonlinear interactions of the shoaling waves of different time scales and currents. To simulate the wind wave and swells propagated to the coasts, wave generated near shore currents, nonlinear-dispersive wave transformation and wave diffraction in interaction with coastal and port structure, sediment transport and coastal erosion the chains of the models should be used. The objective of this presentation is to provide an overview of the results of the application of the model chains for the assessment of the wave impacts on new construction designed at the Black Sea coasts and the impacts of these constructions on the coastal erosion/ accretion processes to demonstrate needs for further development of the nonlinear models for the coastal engineering applications. The open source models Wave Watch III and SWAN has been used to simulate wave statistics of the dedicated areas of the Black Sea in high resolution to calculated the statistical parameters of the extreme wave approaching coastal zone construction in accordance with coastal engineering standards. As the main tool for the costal hydrodynamic simulations the modeling system COASTOX-MORPHO has been used, that includes the following models. HWAVE -code based on hyperbolic version of mild slope equations., HWAVE-S - spectral version of HWAVE., BOUSS-FNL - fully nonlinear system of Boussinesq equations for simulation wave nonlinear -dispersive wave transformation in coastal areas. COASTOX-CUR - the code provided the numerical solution of the Nonlinear Shallow Water Equations (NLSWE) by finite-volume methods on the unstructured grid describing the long wave transformation in the coastal zone with the efficient drying -wetting algorithms to simulate the inundation of the coastal areas including tsunami wave runup. Coastox -Cur equations with the radiation stress term calculated via near shore wave fields simulate the wave generated nearhore currents. COASTOX-SED - the module of the simulation of the sediment transport in which the suspended sediments are simulated on the basis of the solution of 2-D advection -diffusion equation and the bottom sediment transport calculations are provided the basis of a library of the most popular semi-empirical formulas. MORPH - the module of the simulation of the morphological transformation of coastal zone based on the mass balance equation, on the basis of the sediment fluxes, calculated in the SED module. MORPH management submodel is responsible for the execution of the model chain "waves- current- sediments - morphodynamics- waves". The open source model SWASH has been used to simulate nonlinear resonance phenomena in coastal waters. The model chain was applied to simulate the potential impact of the designed shore protection structures at the Sochi Olympic Park on coastal morphodynamics, the wave parameters and nonlinear oscillations in the new ports designed in Gelenddjik and Taman at North-East coast of the Black Sea. The modeling results are compared with the results of the physical modeling in the hydraulic flumes of Moscow University of Civil Engineering.

A biomechanical study comparing a raft of 3.5 mm cortical screws with 6.5 mm cancellous screws in depressed tibial plateau fractures.

PubMed

Patil, Sunit; Mahon, Andrew; Green, Sarah; McMurtry, Ian; Port, Andrew

2006-06-01

There has been a recent trend towards using a raft of small diameter 3.5mm cortical screws for supporting depressed tibial plateau fractures (Schatzker type III). Our aim was to compare the biomechanical properties of a raft of 3.5 mm cortical screws with that of 6.5 mm cancellous screws in a synthetic bone model. Ten rigid polyurethane foam (sawbone) blocks, with a density simulating osteoporotic bone and ten blocks with a density simulating normal density bone were obtained. A Schatzker type III fracture was created in each block. The fracture fragments were then elevated and supported using two 6.5 mm cancellous screws in ten blocks and four 3.5 mm cortical screws in the remaining. The fractures were loaded using a Lloyd testing machine. The mean force needed to produce a depression of 5 mm was 700.8 N with the four-screw construct and 512.4 N with the two-screw construct in the osteoporotic model. This difference was highly statistically significant (p = 0.009). The mean force required to produce the same depression was 1878.2 N with the two-screw construct and 1938.2 N with the four-screw construct in the non-osteoporotic model. Though the difference was not statistically significant (p = 0.42), an increased fragmentation of the synthetic bone fragments was noticed with the two-screw construct but not with the four-screw construct. A raft of four 3.5 mm cortical screws is biomechanically stronger than two 6.5 mm cancellous screws in resisting axial compression in osteoporotic bone.

New insights in the bacterial spore resistance to extreme terrestrial and extraterrestrial factors

NASA Astrophysics Data System (ADS)

Moeller, Ralf; Horneck, Gerda; Reitz, Guenther

Based on their unique resistance to various space parameters, Bacillus endospores are one of the model systems used for astrobiological studies. The extremely high resistance of bacterial endospores to environmental stress factors has intrigued researchers since long time and many characteristic spore features, especially those involved in the protection of spore DNA, have already been uncovered. The disclosure of the complete genomic sequence of Bacillus subtilis 168, one of the often used astrobiological model system, and the rapid development of tran-scriptional microarray techniques have opened new opportunities of gaining further insights in the enigma of spore resistance. Spores of B. subtilis were exposed to various extreme ter-restrial and extraterrestrial stressors to reach a better understanding of the DNA protection and repair strategies, which them to cope with the induced DNA damage. Following physical stress factors of environmental importance -either on Earth or in space -were selected for this thesis: (i) mono-and polychromatic UV radiation, (ii) ionizing radiation, (iii) exposure to ultrahigh vacuum; and (iv) high shock pressures simulating meteorite impacts. To reach a most comprehensive understanding of spore resistance to those harsh terrestrial or simulated extraterrestrial conditions, a standardized experimental protocol of the preparation and ana-lyzing methods was established including the determination of the following spore responses: (i) survival, (ii) induced mutations, (iii) DNA damage, (iv) role of different repair pathways by use of a set of repair deficient mutants, and (v) transcriptional responses during spore germi-nation by use of genome-wide transcriptome analyses and confirmation by RT-PCR. From this comprehensive set of data on spore resistance to a variety of environmental stress parameters a model of a "built-in" transcriptional program of bacterial spores in response to DNA damaging treatments to ensure DNA restoration during germination has been developed.

14 CFR 61.163 - Aeronautical experience: Powered-lift category rating.

Code of Federal Regulations, 2013 CFR

2013-01-01

... time in a flight simulator or flight training device. (ii) A maximum of 50 hours of training in a flight simulator or flight training device may be credited toward the instrument flight time requirements... training center certificated under part 142 of this chapter. (iii) Training in a flight simulator or flight...

14 CFR 61.163 - Aeronautical experience: Powered-lift category rating.

Code of Federal Regulations, 2014 CFR

2014-01-01

... time in a flight simulator or flight training device. (ii) A maximum of 50 hours of training in a flight simulator or flight training device may be credited toward the instrument flight time requirements... training center certificated under part 142 of this chapter. (iii) Training in a flight simulator or flight...

14 CFR 61.163 - Aeronautical experience: Powered-lift category rating.

Code of Federal Regulations, 2012 CFR

2012-01-01

... time in a flight simulator or flight training device. (ii) A maximum of 50 hours of training in a flight simulator or flight training device may be credited toward the instrument flight time requirements... training center certificated under part 142 of this chapter. (iii) Training in a flight simulator or flight...

Modeling SOA formation from the oxidation of intermediate volatility n-alkanes

NASA Astrophysics Data System (ADS)

Aumont, B.; Valorso, R.; Mouchel-Vallon, C.; Camredon, M.; Lee-Taylor, J.; Madronich, S.

2012-08-01

The chemical mechanism leading to SOA formation and ageing is expected to be a multigenerational process, i.e. a successive formation of organic compounds with higher oxidation degree and lower vapor pressure. This process is here investigated with the explicit oxidation model GECKO-A (Generator of Explicit Chemistry and Kinetics of Organics in the Atmosphere). Gas phase oxidation schemes are generated for the C8-C24 series of n-alkanes. Simulations are conducted to explore the time evolution of organic compounds and the behavior of secondary organic aerosol (SOA) formation for various preexisting organic aerosol concentration (COA). As expected, simulation results show that (i) SOA yield increases with the carbon chain length of the parent hydrocarbon, (ii) SOA yield decreases with decreasing COA, (iii) SOA production rates increase with increasing COA and (iv) the number of oxidation steps (i.e. generations) needed to describe SOA formation and evolution grows when COA decreases. The simulated oxidative trajectories are examined in a two dimensional space defined by the mean carbon oxidation state and the volatility. Most SOA contributors are not oxidized enough to be categorized as highly oxygenated organic aerosols (OOA) but reduced enough to be categorized as hydrocarbon like organic aerosols (HOA), suggesting that OOA may underestimate SOA. Results show that the model is unable to produce highly oxygenated aerosols (OOA) with large yields. The limitations of the model are discussed.

Modeling SOA formation from the oxidation of intermediate volatility n-alkanes

NASA Astrophysics Data System (ADS)

Aumont, B.; Valorso, R.; Mouchel-Vallon, C.; Camredon, M.; Lee-Taylor, J.; Madronich, S.

2012-06-01

The chemical mechanism leading to SOA formation and ageing is expected to be a multigenerational process, i.e. a successive formation of organic compounds with higher oxidation degree and lower vapor pressure. This process is here investigated with the explicit oxidation model GECKO-A (Generator of Explicit Chemistry and Kinetics of Organics in the Atmosphere). Gas phase oxidation schemes are generated for the C8-C24 series of n-alkanes. Simulations are conducted to explore the time evolution of organic compounds and the behavior of secondary organic aerosol (SOA) formation for various preexisting organic aerosol concentration (COA). As expected, simulation results show that (i) SOA yield increases with the carbon chain length of the parent hydrocarbon, (ii) SOA yield decreases with decreasing COA, (iii) SOA production rates increase with increasing COA and (iv) the number of oxidation steps (i.e. generations) needed to describe SOA formation and evolution grows when COA decreases. The simulated oxidative trajectories are examined in a two dimensional space defined by the mean carbon oxidation state and the volatility. Most SOA contributors are not oxidized enough to be categorized as highly oxygenated organic aerosols (OOA) but reduced enough to be categorized as hydrocarbon like organic aerosols (HOA), suggesting that OOA may underestimate SOA. Results show that the model is unable to produce highly oxygenated aerosols (OOA) with large yields. The limitations of the model are discussed.

Evaluation and error apportionment of an ensemble of ...

EPA Pesticide Factsheets

Through the comparison of several regional-scale chemistry transport modelling systems that simulate meteorology and air quality over the European and American continents, this study aims at i) apportioning the error to the responsible processes using time-scale analysis, ii) helping to detect causes of models error, and iii) identifying the processes and scales most urgently requiring dedicated investigations. The analysis is conducted within the framework of the third phase of the Air Quality Model Evaluation International Initiative (AQMEII) and tackles model performance gauging through measurement-to-model comparison, error decomposition and time series analysis of the models biases for several fields (ozone, CO, SO2, NO, NO2, PM10, PM2.5, wind speed, and temperature). The operational metrics (magnitude of the error, sign of the bias, associativity) provide an overall sense of model strengths and deficiencies, while apportioning the error to its constituent parts (bias, variance and covariance) can help to assess the nature and quality of the error. Each of the error components is analysed independently and apportioned to specific processes based on the corresponding timescale (long scale, synoptic, diurnal, and intra-day) using the error apportionment technique devised in the former phases of AQMEII.The application of the error apportionment method to the AQMEII Phase 3 simulations provides several key insights. In addition to reaffirming the strong impact

Following the Cosmic Evolution of Pristine Gas. II. The Search for Pop III–bright Galaxies

NASA Astrophysics Data System (ADS)

Sarmento, Richard; Scannapieco, Evan; Cohen, Seth

2018-02-01

Direct observational searches for Population III (Pop III) stars at high redshift are faced with the question of how to select the most promising targets for spectroscopic follow-up. To help answer this, we use a large-scale cosmological simulation, augmented with a new subgrid model that tracks the fraction of pristine gas, to follow the evolution of high-redshift galaxies and the Pop III stars they contain. We generate rest-frame ultraviolet (UV) luminosity functions for our galaxies and find that they are consistent with current z≥slant 7 observations. Throughout the redshift range 7≤slant z≤slant 15, we identify “Pop III–bright” galaxies as those with at least 75% of their flux coming from Pop III stars. While less than 1% of galaxies brighter than {m}UV,{AB}}=31.4 mag are Pop III–bright in the range 7≤slant z≤slant 8, roughly 17% of such galaxies are Pop III–bright at z = 9, immediately before reionization occurs in our simulation. Moving to z = 10, {m}UV,{AB}}=31.4 mag corresponds to larger, more luminous galaxies, and the Pop III–bright fraction falls off to 5%. Finally, at the highest redshifts, a large fraction (29% at z = 14 and 41% at z = 15) of all galaxies are Pop III–bright regardless of magnitude. While {m}UV,{AB}}=31.4 mag galaxies are extremely rare during this epoch, we find that 13% of galaxies at z = 14 are Pop III–bright with {m}UV,{AB}}≤slant 33 mag, a intrinsic magnitude within reach of the James Webb Space Telescope using lensing. Thus, we predict that the best redshift to search for luminous Pop III–bright galaxies is just before reionization, while lensing surveys for fainter galaxies should push to the highest redshifts possible.

Numerical simulation of the modulation transfer function (MTF) in infrared focal plane arrays: simulation methodology and MTF optimization

NASA Astrophysics Data System (ADS)

Schuster, J.

2018-02-01

Military requirements demand both single and dual-color infrared (IR) imaging systems with both high resolution and sharp contrast. To quantify the performance of these imaging systems, a key measure of performance, the modulation transfer function (MTF), describes how well an optical system reproduces an objects contrast in the image plane at different spatial frequencies. At the center of an IR imaging system is the focal plane array (FPA). IR FPAs are hybrid structures consisting of a semiconductor detector pixel array, typically fabricated from HgCdTe, InGaAs or III-V superlattice materials, hybridized with heat/pressure to a silicon read-out integrated circuit (ROIC) with indium bumps on each pixel providing the mechanical and electrical connection. Due to the growing sophistication of the pixel arrays in these FPAs, sophisticated modeling techniques are required to predict, understand, and benchmark the pixel array MTF that contributes to the total imaging system MTF. To model the pixel array MTF, computationally exhaustive 2D and 3D numerical simulation approaches are required to correctly account for complex architectures and effects such as lateral diffusion from the pixel corners. It is paramount to accurately model the lateral di_usion (pixel crosstalk) as it can become the dominant mechanism limiting the detector MTF if not properly mitigated. Once the detector MTF has been simulated, it is directly decomposed into its constituent contributions to reveal exactly what is limiting the total detector MTF, providing a path for optimization. An overview of the MTF will be given and the simulation approach will be discussed in detail, along with how different simulation parameters effect the MTF calculation. Finally, MTF optimization strategies (crosstalk mitigation) will be discussed.

Soil-test N recommendations augmented with PEST-optimized RZWQM simulations

USGS Publications Warehouse

Malone, R.W.; Jaynes, D.B.; Ma, Liwang; Nolan, B.T.; Meek, D.W.; Karlen, D.L.

2010-01-01

Improved understanding of year-to-year late-spring soil nitrate test (LSNT) variability could help make it more attractive to producers. We test the ability of the Root Zone Water Quality Model (RZWQM) to simulate watershed-scale variability due to the LSNT, and we use the optimized model to simulate long-term field N dynamics under related conditions. Autoregressive techniques and the automatic parameter calibration program PEST were used to show that RZWQM simulates significantly lower nitrate concentration in discharge from LSNT treatments compared with areas receiving fall N fertilizer applications within the tile-drained Walnut Creek, Iowa, watershed (>5 mg N L-1 difference for the third year of the treatment, 1999). This result is similar to field-measured data from a paired watershed experiment. A statistical model we developed using RZWQM simulations from 1970 to 2005 shows that early-season precipitation and early-season temperature account for 90% of the interannual variation in LSNT-based fertilizer N rates. Long-term simulations with similar average N application rates for corn (Zea mays L.) (151 kg N ha-1) show annual average N loss in tile flow of 20.4, 22.2, and 27.3 kg N ha -1 for LSNT, single spring, and single fall N applications. These results suggest that (i) RZWQM is a promising tool to accurately estimate the water quality effects of LSNT; (ii) the majority of N loss difference between LSNT and fall applications is because more N remains in the root zone for crop uptake; and (iii) year-to-year LSNT-based N rate differences are mainly due to variation in early-season precipitation and temperature. Copyright ?? 2010 by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America. All rights reserved.

Functional response of ungulate browsers in disturbed eastern hemlock forests

USGS Publications Warehouse

DeStefano, Stephen

2015-01-01

Ungulate browsing in predator depleted North American landscapes is believed to be causing widespread tree recruitment failures. However, canopy disturbances and variations in ungulate densities are sources of heterogeneity that can buffer ecosystems against herbivory. Relatively little is known about the functional response (the rate of consumption in relation to food availability) of ungulates in eastern temperate forests, and therefore how “top down” control of vegetation may vary with disturbance type, intensity, and timing. This knowledge gap is relevant in the Northeastern United States today with the recent arrival of hemlock woolly adelgid (HWA; Adelges tsugae) that is killing eastern hemlocks (Tsuga canadensis) and initiating salvage logging as a management response. We used an existing experiment in central New England begun in 2005, which simulated severe adelgid infestation and intensive logging of intact hemlock forest, to examine the functional response of combined moose (Alces americanus) and white-tailed deer (Odocoileus virginianus) foraging in two different time periods after disturbance (3 and 7 years). We predicted that browsing impacts would be linear or accelerating (Type I or Type III response) in year 3 when regenerating stem densities were relatively low and decelerating (Type II response) in year 7 when stem densities increased. We sampled and compared woody regeneration and browsing among logged and simulated insect attack treatments and two intact controls (hemlock and hardwood forest) in 2008 and again in 2012. We then used AIC model selection to compare the three major functional response models (Types I, II, and III) of ungulate browsing in relation to forage density. We also examined relative use of the different stand types by comparing pellet group density and remote camera images. In 2008, total and proportional browse consumption increased with stem density, and peaked in logged plots, revealing a Type I response. In 2012, stem densities were greatest in girdled plots, but proportional browse consumption was highest at intermediate stem densities in logged plots, exhibiting a Type III (rather than a Type II) functional response. Our results revealed shifting top–down control by herbivores at different stages of stand recovery after disturbance and in different understory conditions resulting from logging vs. simulated adelgid attack. If forest managers wish to promote tree regeneration in hemlock stands that is more resistant to ungulate browsers, leaving HWA-infested stands unmanaged may be a better option than preemptively logging them.

Stellar Populations and Radial Migrations in Virgo Disk Galaxies

NASA Astrophysics Data System (ADS)

Roediger, Joel C.; Courteau, Stéphane; Sánchez-Blázquez, Patricia; McDonald, Michael

2012-10-01

We present new stellar age profiles, derived from well-resolved optical and near-infrared images of 64 Virgo cluster disk galaxies, whose analysis poses a challenge for current disk galaxy formation models. Our ability to break the age-metallicity degeneracy and the significant size of our sample represent key improvements over complementary studies of field disk galaxies. Our results can be summarized as follows: first, and contrary to observations of disk galaxies in the field, these cluster galaxies are distributed almost equally amongst the three main types of disk galaxy luminosity profiles (I/II/III), indicating that the formation and/or survival of Type II breaks is suppressed within the cluster environment. Second, we find examples of statistically significant inversions ("U-shapes") in the age profiles of all three disk galaxy types, reminiscent of predictions from high-resolution simulations of classically truncated Type II disks in the field. These features characterize the age profiles for only about a third (<=36%) of each disk galaxy type in our sample. An even smaller fraction of cluster disks (~11% of the total sample) exhibit age profiles that decrease outward (i.e., negative age gradients). Instead, flat and/or positive age gradients prevail (>=50%) within our Type I, II, and III subsamples. These observations thus suggest that while stellar migrations and inside-out growth can play a significant role in the evolution of all disk galaxy types, other factors contributing to the evolution of galaxies can overwhelm the predicted signatures of these processes. We interpret our observations through a scenario whereby Virgo cluster disk galaxies formed initially like their brethren in the field but which, upon falling into the cluster, were transformed into their present state through external processes linked to the environment (e.g., ram-pressure stripping and harassment). Current disk galaxy formation models, which have largely focused on field galaxies, fail to reproduce these results, thus calling for adequate hydrodynamical simulations of dense galaxy environments if we are to understand cluster disks. The current paper highlights numerous constraints for such simulations. In the Appendix, we confirm the claim by Erwin et al. that Type II breaks are absent in Virgo cluster S0s and discuss the detection of Type III breaks in such galaxies.

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

Jaskot, A. E.; Ravindranath, S.

The increasing neutrality of the intergalactic medium at z  > 6 suppresses Ly α emission, and spectroscopic confirmation of galaxy redshifts requires the detection of alternative ultraviolet lines. The strong [C iii]  λ 1907+C iii]  λ 1909 doublet frequently observed in low-metallicity, actively star-forming galaxies is a promising emission feature. We present CLOUDY photoionization model predictions for C iii] equivalent widths (EWs) and line ratios as a function of starburst age, metallicity, and ionization parameter. Our models include a range of C/O abundances, dust content, and gas density. We also examine the effects of varying the nebular geometry and optical depth. Onlymore » the stellar models that incorporate binary interaction effects reproduce the highest observed C iii] EWs. The spectral energy distributions from the binary stellar population models also generate observable C iii] over a longer timescale relative to single-star models. We show that diagnostics using C iii] and nebular He ii  λ 1640 can separate star-forming regions from shock-ionized gas. We also find that density-bounded systems should exhibit weaker C iii] EWs at a given ionization parameter, and C iii] EWs could, therefore, select candidate Lyman continuum-leaking systems. In almost all models, C iii] is the next strongest line at <2700 Å after Ly α , and C iii] reaches detectable levels for a wide range of conditions at low metallicity. C iii] may therefore serve as an important diagnostic for characterizing galaxies at z  > 6.« less

Modeling of Stick-Slip Behavior in Sheared Granular Fault Gouge Using the Combined Finite-Discrete Element Method

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

Gao, Ke; Euser, Bryan J.; Rougier, Esteban

Sheared granular layers undergoing stick-slip behavior are broadly employed to study the physics and dynamics of earthquakes. In this paper, a two-dimensional implementation of the combined finite-discrete element method (FDEM), which merges the finite element method (FEM) and the discrete element method (DEM), is used to explicitly simulate a sheared granular fault system including both gouge and plate, and to investigate the influence of different normal loads on seismic moment, macroscopic friction coefficient, kinetic energy, gouge layer thickness, and recurrence time between slips. In the FDEM model, the deformation of plates and particles is simulated using the FEM formulation whilemore » particle-particle and particle-plate interactions are modeled using DEM-derived techniques. The simulated seismic moment distributions are generally consistent with those obtained from the laboratory experiments. In addition, the simulation results demonstrate that with increasing normal load, (i) the kinetic energy of the granular fault system increases; (ii) the gouge layer thickness shows a decreasing trend; and (iii) the macroscopic friction coefficient does not experience much change. Analyses of the slip events reveal that, as the normal load increases, more slip events with large kinetic energy release and longer recurrence time occur, and the magnitude of gouge layer thickness decrease also tends to be larger; while the macroscopic friction coefficient drop decreases. Finally, the simulations not only reveal the influence of normal loads on the dynamics of sheared granular fault gouge, but also demonstrate the capabilities of FDEM for studying stick-slip dynamic behavior of granular fault systems.« less

Modeling of Stick-Slip Behavior in Sheared Granular Fault Gouge Using the Combined Finite-Discrete Element Method

DOE PAGES

Gao, Ke; Euser, Bryan J.; Rougier, Esteban; ...

2018-06-20

Sheared granular layers undergoing stick-slip behavior are broadly employed to study the physics and dynamics of earthquakes. In this paper, a two-dimensional implementation of the combined finite-discrete element method (FDEM), which merges the finite element method (FEM) and the discrete element method (DEM), is used to explicitly simulate a sheared granular fault system including both gouge and plate, and to investigate the influence of different normal loads on seismic moment, macroscopic friction coefficient, kinetic energy, gouge layer thickness, and recurrence time between slips. In the FDEM model, the deformation of plates and particles is simulated using the FEM formulation whilemore » particle-particle and particle-plate interactions are modeled using DEM-derived techniques. The simulated seismic moment distributions are generally consistent with those obtained from the laboratory experiments. In addition, the simulation results demonstrate that with increasing normal load, (i) the kinetic energy of the granular fault system increases; (ii) the gouge layer thickness shows a decreasing trend; and (iii) the macroscopic friction coefficient does not experience much change. Analyses of the slip events reveal that, as the normal load increases, more slip events with large kinetic energy release and longer recurrence time occur, and the magnitude of gouge layer thickness decrease also tends to be larger; while the macroscopic friction coefficient drop decreases. Finally, the simulations not only reveal the influence of normal loads on the dynamics of sheared granular fault gouge, but also demonstrate the capabilities of FDEM for studying stick-slip dynamic behavior of granular fault systems.« less

Influence of Triply-Charged Ions and Ionization Cross-Sections in a Hybrid-PIC Model of a Hall Thruster Discharge

NASA Technical Reports Server (NTRS)

Smith, Brandon D.; Boyd, Iain D.; Kamhawi, Hani

2014-01-01

The sensitivity of xenon ionization rates to collision cross-sections is studied within the framework of a hybrid-PIC model of a Hall thruster discharge. A revised curve fit based on the Drawin form is proposed and is shown to better reproduce the measured crosssections at high electron energies, with differences in the integrated rate coefficients being on the order of 10% for electron temperatures between 20 eV and 30 eV. The revised fit is implemented into HPHall and the updated model is used to simulate NASA's HiVHAc EDU2 Hall thruster at discharge voltages of 300, 400, and 500 V. For all three operating points, the revised cross-sections result in an increase in the predicted thrust and anode efficiency, reducing the error relative to experimental performance measurements. Electron temperature and ionization reaction rates are shown to follow the trends expected based on the integrated rate coefficients. The effects of triply-charged xenon are also assessed. The predicted thruster performance is found to have little or no dependence on the presence of triply-charged ions. The fraction of ion current carried by triply-charged ions is found to be on the order of 1% and increases slightly with increasing discharge voltage. The reaction rates for the 0?III, I?III, and II?III ionization reactions are found to be of similar order of magnitude and are about one order of magnitude smaller than the rate of 0?II ionization in the discharge channel.

An eleven-year validation of a physically-based distributed dynamic ecohydorological model tRIBS+VEGGIE: Walnut Gulch Experimental Watershed

NASA Astrophysics Data System (ADS)

Sivandran, G.; Bisht, G.; Ivanov, V. Y.; Bras, R. L.

2008-12-01

A coupled, dynamic vegetation and hydrologic model, tRIBS+VEGGIE, was applied to the semiarid Walnut Gulch Experimental Watershed in Arizona. The physically-based, distributed nature of the coupled model allows for parameterization and simulation of watershed vegetation-water-energy dynamics on timescales varying from hourly to interannual. The model also allows for explicit spatial representation of processes that vary due to complex topography, such as lateral redistribution of moisture and partitioning of radiation with respect to aspect and slope. Model parameterization and forcing was conducted using readily available databases for topography, soil types, and land use cover as well as the data from network of meteorological stations located within the Walnut Gulch watershed. In order to test the performance of the model, three sets of simulations were conducted over an 11 year period from 1997 to 2007. Two simulations focus on heavily instrumented nested watersheds within the Walnut Gulch basin; (i) Kendall watershed, which is dominated by annual grasses; and (ii) Lucky Hills watershed, which is dominated by a mixture of deciduous and evergreen shrubs. The third set of simulations cover the entire Walnut Gulch Watershed. Model validation and performance were evaluated in relation to three broad categories; (i) energy balance components: the network of meteorological stations were used to validate the key energy fluxes; (ii) water balance components: the network of flumes, rain gauges and soil moisture stations installed within the watershed were utilized to validate the manner in which the model partitions moisture; and (iii) vegetation dynamics: remote sensing products from MODIS were used to validate spatial and temporal vegetation dynamics. Model results demonstrate satisfactory spatial and temporal agreement with observed data, giving confidence that key ecohydrological processes can be adequately represented for future applications of tRIBS+VEGGIE in regional modeling of land-atmosphere interactions.

Air quality modelling over the Eastern Mediterranean using the WRF/Chem model: Comparison of gas-phase chemistry and aerosol mechanisms

NASA Astrophysics Data System (ADS)

Georgiou, George K.; Christoudias, Theodoros; Proestos, Yiannis; Kushta, Jonilda; Hadjinicolaou, Panos; Lelieveld, Jos

2017-04-01

A comprehensive analysis of the performance of three coupled gas-phase chemistry and aerosol mechanisms included in the WRF/Chem model has been performed over the Eastern Mediterranean focusing on Cyprus during the CYPHEX campaign in 2014, using high temporal and spatial resolution. The model performance was evaluated by comparing calculations to measurements of gas phase species (O3, CO, NOx, SO2) and aerosols (PM10, PM2.5) from 13 ground stations. Initial results indicate that the calculated day-to-day and diurnal variations of the aforementioned species show good agreement with observations. The model was set up with three nested grids, downscaling to 4km over Cyprus. The meteorological boundary conditions were updated every 3 hours throughout the simulation using the Global Forecast System (GFS), while chemical boundary conditions were updated every 6 hours using the MOZART global chemical transport model. Biogenic emissions were calculated online by the the Model of Emissions of Gases and Aerosols from Nature version 2.1 (MEGAN2.1). Anthropogenic emissions were based on the EDGAR HTAP v2 global emission inventory, provided on a horizontal grid resolution of 0.1o × 0.1o. Three simulations were performed employing different chemistry and aerosol mechanisms; i) RADM2 chemical mechanism and MADE/SORGAM aerosols, ii) CBMZ chemical mechanism and MOSAIC aerosols, iii) MOZART chemical mechanism and MOSAIC aerosols. Results show that the WRF/Chem model satisfactorily estimates the trace gases relative concentrations at the background sites but not at the urban and traffic sites, while some differences appear between the simulated concentrations by the three mechanisms. The resulting discrepancies between the model outcome and measurements, especially at the urban and traffic sites, suggest that a higher resolution anthropogenic emission inventory might help improve fine resolution, regional air quality modelling. Differences in the simulated concentrations by the three chemical mechanisms are attributed to the different chemical species and reaction rate constants used.

Do maize models capture the impacts of heat and drought stresses on yield? Using algorithm ensembles to identify successful approaches.

PubMed

Jin, Zhenong; Zhuang, Qianlai; Tan, Zeli; Dukes, Jeffrey S; Zheng, Bangyou; Melillo, Jerry M

2016-09-01

Stresses from heat and drought are expected to increasingly suppress crop yields, but the degree to which current models can represent these effects is uncertain. Here we evaluate the algorithms that determine impacts of heat and drought stress on maize in 16 major maize models by incorporating these algorithms into a standard model, the Agricultural Production Systems sIMulator (APSIM), and running an ensemble of simulations. Although both daily mean temperature and daylight temperature are common choice of forcing heat stress algorithms, current parameterizations in most models favor the use of daylight temperature even though the algorithm was designed for daily mean temperature. Different drought algorithms (i.e., a function of soil water content, of soil water supply to demand ratio, and of actual to potential transpiration ratio) simulated considerably different patterns of water shortage over the growing season, but nonetheless predicted similar decreases in annual yield. Using the selected combination of algorithms, our simulations show that maize yield reduction was more sensitive to drought stress than to heat stress for the US Midwest since the 1980s, and this pattern will continue under future scenarios; the influence of excessive heat will become increasingly prominent by the late 21st century. Our review of algorithms in 16 crop models suggests that the impacts of heat and drought stress on plant yield can be best described by crop models that: (i) incorporate event-based descriptions of heat and drought stress, (ii) consider the effects of nighttime warming, and (iii) coordinate the interactions among multiple stresses. Our study identifies the proficiency with which different model formulations capture the impacts of heat and drought stress on maize biomass and yield production. The framework presented here can be applied to other modeled processes and used to improve yield predictions of other crops with a wide variety of crop models. © 2016 John Wiley & Sons Ltd.

Interfacial properties in a discrete model for tumor growth

NASA Astrophysics Data System (ADS)

Moglia, Belén; Guisoni, Nara; Albano, Ezequiel V.

2013-03-01

We propose and study, by means of Monte Carlo numerical simulations, a minimal discrete model for avascular tumor growth, which can also be applied for the description of cell cultures in vitro. The interface of the tumor is self-affine and its width can be characterized by the following exponents: (i) the growth exponent β=0.32(2) that governs the early time regime, (ii) the roughness exponent α=0.49(2) related to the fluctuations in the stationary regime, and (iii) the dynamic exponent z=α/β≃1.49(2), which measures the propagation of correlations in the direction parallel to the interface, e.g., ξ∝t1/z, where ξ is the parallel correlation length. Therefore, the interface belongs to the Kardar-Parisi-Zhang universality class, in agreement with recent experiments of cell cultures in vitro. Furthermore, density profiles of the growing cells are rationalized in terms of traveling waves that are solutions of the Fisher-Kolmogorov equation. In this way, we achieved excellent agreement between the simulation results of the discrete model and the continuous description of the growth front of the culture or tumor.

Final Technical Report

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

Alexander Pigarov

2012-06-05

This is the final report for the Research Grant DE-FG02-08ER54989 'Edge Plasma Simulations in NSTX and CTF: Synergy of Lithium Coating, Non-Diffusive Anomalous Transport and Drifts'. The UCSD group including: A.Yu. Pigarov (PI), S.I. Krasheninnikov and R.D. Smirnov, was working on modeling of the impact of lithium coatings on edge plasma parameters in NSTX with the multi-species multi-fluid code UEDGE. The work was conducted in the following main areas: (i) improvements of UEDGE model for plasma-lithium interactions, (ii) understanding the physics of low-recycling divertor regime in NSTX caused by lithium pumping, (iii) study of synergistic effects with lithium coatings andmore » non-diffusive ballooning-like cross-field transport, (iv) simulation of experimental multi-diagnostic data on edge plasma with lithium pumping in NSTX via self-consistent modeling of D-Li-C plasma with UEDGE, and (v) working-gas balance analysis. The accomplishments in these areas are given in the corresponding subsections in Section 2. Publications and presentations made under the Grant are listed in Section 3.« less

Deformation of periodic nanovoid structures in Mg single crystals

NASA Astrophysics Data System (ADS)

Xu, Shuozhi; Su, Yanqing; Zare Chavoshi, Saeed

2018-01-01

Large scale molecular dynamics (MD) simulations in Mg single crystal containing periodic cylindrical voids subject to uniaxial tension along the z direction are carried out. Models with different initial void sizes and crystallographic orientations are explored using two interatomic potentials. It is found that (i) a larger initial void always leads to a lower yield stress, in agreement with an analytic prediction; (ii) in the model with x[\\bar{1}100]-y[0001]-z[11\\bar{2}0] orientations, the two potentials predict different types of tension twins and phase transformation; (iii) in the model with x[0001]-y[11\\bar{2}0]-z[\\bar{1}100] orientations, the two potentials identically predict the nucleation of edge dislocations on the prismatic plane, which then glide away from the void, resulting in extrusions at the void surface; in the case of the smallest initial void, these surface extrusions pinch the void into two voids. Besides bringing new physical understanding of the nanovoid structures, our work highlights the variability and uncertainty in MD simulations arising from the interatomic potential, an issue relatively lightly addressed in the literature to date.

Thermomechanical Fatigue of Ductile Cast Iron and Its Life Prediction

NASA Astrophysics Data System (ADS)

Wu, Xijia; Quan, Guangchun; MacNeil, Ryan; Zhang, Zhong; Liu, Xiaoyang; Sloss, Clayton

2015-06-01

Thermomechanical fatigue (TMF) behaviors of ductile cast iron (DCI) were investigated under out-of-phase (OP), in-phase (IP), and constrained strain-control conditions with temperature hold in various temperature ranges: 573 K to 1073 K, 723 K to 1073 K, and 433 K to 873 K (300 °C to 800 °C, 450 °C to 800 °C, and 160 °C to 600 °C). The integrated creep-fatigue theory (ICFT) model was incorporated into the finite element method to simulate the hysteresis behavior and predict the TMF life of DCI under those test conditions. With the consideration of four deformation/damage mechanisms: (i) plasticity-induced fatigue, (ii) intergranular embrittlement, (iii) creep, and (iv) oxidation, as revealed from the previous study on low cycle fatigue of the material, the model delineates the contributions of these physical mechanisms in the asymmetrical hysteresis behavior and the damage accumulation process leading to final TMF failure. This study shows that the ICFT model can simulate the stress-strain response and life of DCI under complex TMF loading profiles (OP and IP, and constrained with temperature hold).

Data Centric Sensor Stream Reduction for Real-Time Applications in Wireless Sensor Networks

PubMed Central

Aquino, Andre Luiz Lins; Nakamura, Eduardo Freire

2009-01-01

This work presents a data-centric strategy to meet deadlines in soft real-time applications in wireless sensor networks. This strategy considers three main aspects: (i) The design of real-time application to obtain the minimum deadlines; (ii) An analytic model to estimate the ideal sample size used by data-reduction algorithms; and (iii) Two data-centric stream-based sampling algorithms to perform data reduction whenever necessary. Simulation results show that our data-centric strategies meet deadlines without loosing data representativeness. PMID:22303145

RIME: The Recoverable Item Management Evaluator. Volume II. Section III. RIME Simulation Model Programs.

DTIC Science & Technology

1980-05-01

ve3 573U~5V * 3commovfirol?1@3ollpo 5 COROIIfTglzT@ RH T~ 41 CONNONAIDTZTAT 1 CORR601Z Io*nZ’PQ 2 CONN onkl!Z.lanal 2 COKKOIJZINIAYT RIME3T .3...16CRO/ ~8Z!55ri53S 27 C0OolzU./!L.rse/z2( isy 23CQII503fl3VoIfl30R( 103M 24I CoRKoflnevesUI/Z3CIUAISO *:25 C0KROWIX3b /xIsociigesoll 26 COMMON)lIOZ

Tracking Expected Improvements of Decadal Prediction in Climate Services

NASA Astrophysics Data System (ADS)

Suckling, E.; Thompson, E.; Smith, L. A.

2013-12-01

Physics-based simulation models are ultimately expected to provide the best available (decision-relevant) probabilistic climate predictions, as they can capture the dynamics of the Earth System across a range of situations, situations for which observations for the construction of empirical models are scant if not nonexistent. This fact in itself provides neither evidence that predictions from today's Earth Systems Models will outperform today's empirical models, nor a guide to the space and time scales on which today's model predictions are adequate for a given purpose. Empirical (data-based) models are employed to make probability forecasts on decadal timescales. The skill of these forecasts is contrasted with that of state-of-the-art climate models, and the challenges faced by each approach are discussed. The focus is on providing decision-relevant probability forecasts for decision support. An empirical model, known as Dynamic Climatology is shown to be competitive with CMIP5 climate models on decadal scale probability forecasts. Contrasting the skill of simulation models not only with each other but also with empirical models can reveal the space and time scales on which a generation of simulation models exploits their physical basis effectively. It can also quantify their ability to add information in the formation of operational forecasts. Difficulties (i) of information contamination (ii) of the interpretation of probabilistic skill and (iii) of artificial skill complicate each modelling approach, and are discussed. "Physics free" empirical models provide fixed, quantitative benchmarks for the evaluation of ever more complex climate models, that is not available from (inter)comparisons restricted to only complex models. At present, empirical models can also provide a background term for blending in the formation of probability forecasts from ensembles of simulation models. In weather forecasting this role is filled by the climatological distribution, and can significantly enhance the value of longer lead-time weather forecasts to those who use them. It is suggested that the direct comparison of simulation models with empirical models become a regular component of large model forecast intercomparison and evaluation. This would clarify the extent to which a given generation of state-of-the-art simulation models provide information beyond that available from simpler empirical models. It would also clarify current limitations in using simulation forecasting for decision support. No model-based probability forecast is complete without a quantitative estimate if its own irrelevance; this estimate is likely to increase as a function of lead time. A lack of decision-relevant quantitative skill would not bring the science-based foundation of anthropogenic warming into doubt. Similar levels of skill with empirical models does suggest a clear quantification of limits, as a function of lead time, for spatial and temporal scales on which decisions based on such model output are expected to prove maladaptive. Failing to clearly state such weaknesses of a given generation of simulation models, while clearly stating their strength and their foundation, risks the credibility of science in support of policy in the long term.

Object Orientated Simulation on Transputer Arrays Using Time Warp

DTIC Science & Technology

1989-12-01

Transputer based Machines, Grenoble, Sept 14-16 1987, Ed. Traian Muntean. [ 3 ] Muntean T., "PARX operating system kernal; application to Minix ", Esprit P1085...Simulation 3 Time Warp Simulation 8 3.1 Rollback Mechanism ........ ............................. 8 3.2 Simulation Outp,,t...23 4.3.* Importan Noc .......... ............................ 23 5 Low Level Operations 24 • 3 IIiI 5.1 Global Virtual Timne Estimiation

Hard Sphere Simulation by Event-Driven Molecular Dynamics: Breakthrough, Numerical Difficulty, and Overcoming the issues

NASA Astrophysics Data System (ADS)

Isobe, Masaharu

Hard sphere/disk systems are among the simplest models and have been used to address numerous fundamental problems in the field of statistical physics. The pioneering numerical works on the solid-fluid phase transition based on Monte Carlo (MC) and molecular dynamics (MD) methods published in 1957 represent historical milestones, which have had a significant influence on the development of computer algorithms and novel tools to obtain physical insights. This chapter addresses the works of Alder's breakthrough regarding hard sphere/disk simulation: (i) event-driven molecular dynamics, (ii) long-time tail, (iii) molasses tail, and (iv) two-dimensional melting/crystallization. From a numerical viewpoint, there are serious issues that must be overcome for further breakthrough. Here, we present a brief review of recent progress in this area.

Thermodynamic model for solution behavior and solid-liquid equilibrium in Na-Al(III)-Fe(III)-Cr(III)-Cl-H2O system at 25°C

NASA Astrophysics Data System (ADS)

André, Laurent; Christov, Christomir; Lassin, Arnault; Azaroual, Mohamed

2018-03-01

The knowledge of the thermodynamic behavior of multicomponent aqueous electrolyte systems is of main interest in geo-, and environmental-sciences. The main objective of this study is the development of a high accuracy thermodynamic model for solution behavior, and highly soluble M(III)Cl3(s) (M= Al, Fe, Cr) minerals solubility in Na-Al(III)-Cr(III)-Fe(III)-Cl-H2O system at 25°C. Comprehensive thermodynamic models that accurately predict aluminium, chromium and iron aqueous chemistry and M(III) mineral solubilities as a function of pH, solution composition and concentration are critical for understanding many important geochemical and environmental processes involving these metals (e.g., mineral dissolution/alteration, rock formation, changes in rock permeability and fluid flow, soil formation, mass transport, toxic M(III) remediation). Such a model would also have many industrial applications (e.g., aluminium, chromium and iron production, and their corrosion, solve scaling problems in geothermal energy and oil production). Comparisons of solubility and activity calculations with the experimental data in binary and ternary systems indicate that model predictions are within the uncertainty of the data. Limitations of the model due to data insufficiencies are discussed. The solubility modeling approach, implemented to the Pitzer specific interaction equations is employed. The resulting parameterization was developed for the geochemical Pitzer formalism based PHREEQC database.

The effects of wearing Passenger Protective Breathing Equipment on evacuation times through type III and type IV emergency aircraft exits in clear air and smoke.

DOT National Transportation Integrated Search

1989-11-01

The effects of Passenger Protective Breathing Equipment (PPBE) on the time required for simulated emergency evacuations through Type III and Type IV overwing aircraft exits were studied in two quasi-independent experiments, one in clear air and anoth...

A High-resolution Simulation of the Transport of Gazeous Pollutants from a Severe Effusive Volcanic Eruption

NASA Astrophysics Data System (ADS)

Durand, J.; Tulet, P.; Filippi, J. B.; Leriche, M.

2014-12-01

The Reunion Island experienced its biggest eruption of Piton de la Fournaise volcano during April 2007. Known as "the eruption of the century", this event degassed more than 230 KT of SO2. Theses emissions led to important health issues, accompanied by environmental and infrastructure degradations. We want to show a modeling study uses the mesoscale chemical model MesoNH to simulate the transport of gazeous SO2 between April 2nd and 7th, with a focus on the influence of heat fluxes from lava. Three domains are nested from 2km to 100m horizontal spacing grid, allow us to better represent the phenomenology of its eruption. This modelling study have coupled on-line (i) the MesoNH mesoscale dynamics, (ii) a gas and aqueous chemical scheme, and (iii) a surface scheme that integrates a new sheme for the lava heat flux and its surface propagation. Thus, all flows (heat sensible and latent, vapor, SO2, CO2, CO) are triggered depending on its dynamic. Our simulations reproduce quite faithfully the surface field observation of SO2. Various sensitivity analyzes exhibit that volcano sulfur distribution was mainly controlled by the lava heat flow.Without heat flow parameterization, the surface concentrations are multiplied by a factor 30 compared to the reference simulation.Numerical modeling allows us to distinguish acid rain produced by the emission of water vapor and chloride when the lava flows into the seawater of those formed by the mixing of the volcanic SO2 into the raindrops of convective clouds.

Metabolic flexibility of mitochondrial respiratory chain disorders predicted by computer modelling.

PubMed

Zieliński, Łukasz P; Smith, Anthony C; Smith, Alexander G; Robinson, Alan J

2016-11-01

Mitochondrial respiratory chain dysfunction causes a variety of life-threatening diseases affecting about 1 in 4300 adults. These diseases are genetically heterogeneous, but have the same outcome; reduced activity of mitochondrial respiratory chain complexes causing decreased ATP production and potentially toxic accumulation of metabolites. Severity and tissue specificity of these effects varies between patients by unknown mechanisms and treatment options are limited. So far most research has focused on the complexes themselves, and the impact on overall cellular metabolism is largely unclear. To illustrate how computer modelling can be used to better understand the potential impact of these disorders and inspire new research directions and treatments, we simulated them using a computer model of human cardiomyocyte mitochondrial metabolism containing over 300 characterised reactions and transport steps with experimental parameters taken from the literature. Overall, simulations were consistent with patient symptoms, supporting their biological and medical significance. These simulations predicted: complex I deficiencies could be compensated using multiple pathways; complex II deficiencies had less metabolic flexibility due to impacting both the TCA cycle and the respiratory chain; and complex III and IV deficiencies caused greatest decreases in ATP production with metabolic consequences that parallel hypoxia. Our study demonstrates how results from computer models can be compared to a clinical phenotype and used as a tool for hypothesis generation for subsequent experimental testing. These simulations can enhance understanding of dysfunctional mitochondrial metabolism and suggest new avenues for research into treatment of mitochondrial disease and other areas of mitochondrial dysfunction. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Early Design Choices: Capture, Model, Integrate, Analyze, Simulate

NASA Technical Reports Server (NTRS)

Malin, Jane T.

2004-01-01

I. Designs are constructed incrementally to meet requirements and solve problems: a) Requirements types: objectives, scenarios, constraints, ilities. etc. b) Problem/issue types: risk/safety, cost/difficulty, interaction, conflict, etc. II. Capture requirements, problems and solutions: a) Collect design and analysis products and make them accessible for integration and analysis; b) Link changes in design requirements, problems and solutions; and c) Harvest design data for design models and choice structures. III. System designs are constructed by multiple groups designing interacting subsystems a) Diverse problems, choice criteria, analysis methods and point solutions. IV. Support integration and global analysis of repercussions: a) System implications of point solutions; b) Broad analysis of interactions beyond totals of mass, cost, etc.

Evaluation of the Interplanetary Magnetic Field Strength Using the Cosmic-Ray Shadow of the Sun

NASA Astrophysics Data System (ADS)

Amenomori, M.; Bi, X. J.; Chen, D.; Chen, T. L.; Chen, W. Y.; Cui, S. W.; Danzengluobu, Ding, L. K.; Feng, C. F.; Feng, Zhaoyang; Feng, Z. Y.; Gou, Q. B.; Guo, Y. Q.; He, H. H.; He, Z. T.; Hibino, K.; Hotta, N.; Hu, Haibing; Hu, H. B.; Huang, J.; Jia, H. Y.; Jiang, L.; Kajino, F.; Kasahara, K.; Katayose, Y.; Kato, C.; Kawata, K.; Kozai, M.; Labaciren, Le, G. M.; Li, A. F.; Li, H. J.; Li, W. J.; Liu, C.; Liu, J. S.; Liu, M. Y.; Lu, H.; Meng, X. R.; Miyazaki, T.; Mizutani, K.; Munakata, K.; Nakajima, T.; Nakamura, Y.; Nanjo, H.; Nishizawa, M.; Niwa, T.; Ohnishi, M.; Ohta, I.; Ozawa, S.; Qian, X. L.; Qu, X. B.; Saito, T.; Saito, T. Y.; Sakata, M.; Sako, T. K.; Shao, J.; Shibata, M.; Shiomi, A.; Shirai, T.; Sugimoto, H.; Takita, M.; Tan, Y. H.; Tateyama, N.; Torii, S.; Tsuchiya, H.; Udo, S.; Wang, H.; Wu, H. R.; Xue, L.; Yamamoto, Y.; Yamauchi, K.; Yang, Z.; Yuan, A. F.; Yuda, T.; Zhai, L. M.; Zhang, H. M.; Zhang, J. L.; Zhang, X. Y.; Zhang, Y.; Zhang, Yi; Zhang, Ying; Zhaxisangzhu, Zhou, X. X.; Tibet AS γ Collaboration

2018-01-01

We analyze the Sun's shadow observed with the Tibet-III air shower array and find that the shadow's center deviates northward (southward) from the optical solar disk center in the "away" ("toward") interplanetary magnetic field (IMF) sector. By comparing with numerical simulations based on the solar magnetic field model, we find that the average IMF strength in the away (toward) sector is 1.54 ±0.21stat±0.20syst (1.62 ±0.15stat±0.22syst ) times larger than the model prediction. These demonstrate that the observed Sun's shadow is a useful tool for the quantitative evaluation of the average solar magnetic field.

Evaluation of the Interplanetary Magnetic Field Strength Using the Cosmic-Ray Shadow of the Sun.

PubMed

Amenomori, M; Bi, X J; Chen, D; Chen, T L; Chen, W Y; Cui, S W; Danzengluobu; Ding, L K; Feng, C F; Feng, Zhaoyang; Feng, Z Y; Gou, Q B; Guo, Y Q; He, H H; He, Z T; Hibino, K; Hotta, N; Hu, Haibing; Hu, H B; Huang, J; Jia, H Y; Jiang, L; Kajino, F; Kasahara, K; Katayose, Y; Kato, C; Kawata, K; Kozai, M; Labaciren; Le, G M; Li, A F; Li, H J; Li, W J; Liu, C; Liu, J S; Liu, M Y; Lu, H; Meng, X R; Miyazaki, T; Mizutani, K; Munakata, K; Nakajima, T; Nakamura, Y; Nanjo, H; Nishizawa, M; Niwa, T; Ohnishi, M; Ohta, I; Ozawa, S; Qian, X L; Qu, X B; Saito, T; Saito, T Y; Sakata, M; Sako, T K; Shao, J; Shibata, M; Shiomi, A; Shirai, T; Sugimoto, H; Takita, M; Tan, Y H; Tateyama, N; Torii, S; Tsuchiya, H; Udo, S; Wang, H; Wu, H R; Xue, L; Yamamoto, Y; Yamauchi, K; Yang, Z; Yuan, A F; Yuda, T; Zhai, L M; Zhang, H M; Zhang, J L; Zhang, X Y; Zhang, Y; Zhang, Yi; Zhang, Ying; Zhaxisangzhu; Zhou, X X

2018-01-19

We analyze the Sun's shadow observed with the Tibet-III air shower array and find that the shadow's center deviates northward (southward) from the optical solar disk center in the "away" ("toward") interplanetary magnetic field (IMF) sector. By comparing with numerical simulations based on the solar magnetic field model, we find that the average IMF strength in the away (toward) sector is 1.54±0.21_{stat}±0.20_{syst} (1.62±0.15_{stat}±0.22_{syst}) times larger than the model prediction. These demonstrate that the observed Sun's shadow is a useful tool for the quantitative evaluation of the average solar magnetic field.

On improving the performance of nonphotochemical quenching in CP29 light-harvesting antenna complex

NASA Astrophysics Data System (ADS)

Berman, Gennady P.; Nesterov, Alexander I.; Sayre, Richard T.; Still, Susanne

2016-03-01

We model and simulate the performance of charge-transfer in nonphotochemical quenching (NPQ) in the CP29 light-harvesting antenna-complex associated with photosystem II (PSII). The model consists of five discrete excitonic energy states and two sinks, responsible for the potentially damaging processes and charge-transfer channels, respectively. We demonstrate that by varying (i) the parameters of the chlorophyll-based dimer, (ii) the resonant properties of the protein-solvent environment interaction, and (iii) the energy transfer rates to the sinks, one can significantly improve the performance of the NPQ. Our analysis suggests strategies for improving the performance of the NPQ in response to environmental changes, and may stimulate experimental verification.

Refinement of the probability density function model for preferential concentration of aerosol particles in isotropic turbulence

NASA Astrophysics Data System (ADS)

Zaichik, Leonid I.; Alipchenkov, Vladimir M.

2007-11-01

The purposes of the paper are threefold: (i) to refine the statistical model of preferential particle concentration in isotropic turbulence that was previously proposed by Zaichik and Alipchenkov [Phys. Fluids 15, 1776 (2003)], (ii) to investigate the effect of clustering of low-inertia particles using the refined model, and (iii) to advance a simple model for predicting the collision rate of aerosol particles. The model developed is based on a kinetic equation for the two-point probability density function of the relative velocity distribution of particle pairs. Improvements in predicting the preferential concentration of low-inertia particles are attained due to refining the description of the turbulent velocity field of the carrier fluid by including a difference between the time scales of the of strain and rotation rate correlations. The refined model results in a better agreement with direct numerical simulations for aerosol particles.

Design and modeling of an SJ infrared solar cell approaching upper limit of theoretical efficiency

NASA Astrophysics Data System (ADS)

Sahoo, G. S.; Mishra, G. P.

2018-01-01

Recent trends of photovoltaics account for the conversion efficiency limit making them more cost effective. To achieve this we have to leave the golden era of silicon cell and make a path towards III-V compound semiconductor groups to take advantages like bandgap engineering by alloying these compounds. In this work we have used a low bandgap GaSb material and designed a single junction (SJ) cell with a conversion efficiency of 32.98%. SILVACO ATLAS TCAD simulator has been used to simulate the proposed model using both Ray Tracing and Transfer Matrix Method (under 1 sun and 1000 sun of AM1.5G spectrum). A detailed analyses of photogeneration rate, spectral response, potential developed, external quantum efficiency (EQE), internal quantum efficiency (IQE), short-circuit current density (JSC), open-circuit voltage (VOC), fill factor (FF) and conversion efficiency (η) are discussed. The obtained results are compared with previously reported SJ solar cell reports.

Extreme Scale Plasma Turbulence Simulations on Top Supercomputers Worldwide

DOE PAGES

Tang, William; Wang, Bei; Ethier, Stephane; ...

2016-11-01

The goal of the extreme scale plasma turbulence studies described in this paper is to expedite the delivery of reliable predictions on confinement physics in large magnetic fusion systems by using world-class supercomputers to carry out simulations with unprecedented resolution and temporal duration. This has involved architecture-dependent optimizations of performance scaling and addressing code portability and energy issues, with the metrics for multi-platform comparisons being 'time-to-solution' and 'energy-to-solution'. Realistic results addressing how confinement losses caused by plasma turbulence scale from present-day devices to the much larger $25 billion international ITER fusion facility have been enabled by innovative advances in themore » GTC-P code including (i) implementation of one-sided communication from MPI 3.0 standard; (ii) creative optimization techniques on Xeon Phi processors; and (iii) development of a novel performance model for the key kernels of the PIC code. Our results show that modeling data movement is sufficient to predict performance on modern supercomputer platforms.« less