: “Developing Regional Modeling Techniques Applicable for Simulating Future Climate Conditions in the Carolinas”

EPA Science Inventory

Global climate models (GCMs) are currently used to obtain information about future changes in the large-scale climate. However, such simulations are typically done at coarse spatial resolutions, with model grid boxes on the order of 100 km on a horizontal side. Therefore, techniq...

Evolving Waves and Turbulence in the Outer Corona and Inner Heliosphere: The Accelerating Expanding Box

NASA Astrophysics Data System (ADS)

Tenerani, Anna; Velli, Marco

2017-07-01

Alfvénic fluctuations in the solar wind display many properties reflecting an ongoing nonlinear cascade, e.g., a well-defined spectrum in frequency, together with some characteristics more commonly associated with the linear propagation of waves from the Sun, such as the variation of fluctuation amplitude with distance, dominated by solar wind expansion effects. Therefore, both nonlinearities and expansion must be included simultaneously in any successful model of solar wind turbulence evolution. Because of the disparate spatial scales involved, direct numerical simulations of turbulence in the solar wind represent an arduous task, especially if one wants to go beyond the incompressible approximation. Indeed, most simulations neglect solar wind expansion effects entirely. Here we develop a numerical model to simulate turbulent fluctuations from the outer corona to 1 au and beyond, including the sub-Alfvénic corona. The accelerating expanding box (AEB) extends the validity of previous expanding box models by taking into account both the acceleration of the solar wind and the inhomogeneity of background density and magnetic field. Our method incorporates a background accelerating wind within a magnetic field that naturally follows the Parker spiral evolution using a two-scale analysis in which the macroscopic spatial effect coupling fluctuations with background gradients becomes a time-dependent coupling term in a homogeneous box. In this paper we describe the AEB model in detail and discuss its main properties, illustrating its validity by studying Alfvén wave propagation across the Alfvén critical point.

Box Model of a Series of Salt Ponds, as Applied to the Alviso Salt Pond Complex, South San Francisco Bay, California

USGS Publications Warehouse

Lionberger, Megan A.; Schoellhamer, David H.; Shellenbarger, Gregory; Orlando, James L.; Ganju, Neil K.

2007-01-01

This report documents the development and application of a box model to simulate water level, salinity, and temperature of the Alviso Salt Pond Complex in South San Francisco Bay. These ponds were purchased for restoration in 2003 and currently are managed by the U.S. Fish and Wildlife Service to maintain existing wildlife habitat and prevent a build up of salt during the development of a long-term restoration plan. The model was developed for the purpose of aiding pond managers during the current interim management period to achieve these goals. A previously developed box model of a salt pond, SPOOM, which calculates daily pond volume and salinity, was reconfigured to simulate multiple connected ponds and a temperature subroutine was added. The updated model simulates rainfall, evaporation, water flowing between the ponds and the adjacent tidal slough network, and water flowing from one pond to the next by gravity and pumps. Theoretical and measured relations between discharge and corresponding differences in water level are used to simulate most flows between ponds and between ponds and sloughs. The principle of conservation of mass is used to calculate daily pond volume and salinity. The model configuration includes management actions specified in the Interim Stewardship Plan for the ponds. The temperature subroutine calculates hourly net heat transfer to or from a pond resulting in a rise or drop in pond temperature and daily average, minimum, and maximum pond temperatures are recorded. Simulated temperature was compared with hourly measured data from pond 3 of the Napa?Sonoma Salt Pond Complex and monthly measured data from pond A14 of the Alviso Salt-Pond Complex. Comparison showed good agreement of measured and simulated pond temperature on the daily and monthly time scales.

A fast ellipse extended target PHD filter using box-particle implementation

NASA Astrophysics Data System (ADS)

Zhang, Yongquan; Ji, Hongbing; Hu, Qi

2018-01-01

This paper presents a box-particle implementation of the ellipse extended target probability hypothesis density (ET-PHD) filter, called the ellipse extended target box particle PHD (EET-BP-PHD) filter, where the extended targets are described as a Poisson model developed by Gilholm et al. and the term "box" is here equivalent to the term "interval" used in interval analysis. The proposed EET-BP-PHD filter is capable of dynamically tracking multiple ellipse extended targets and estimating the target states and the number of targets, in the presence of clutter measurements, false alarms and missed detections. To derive the PHD recursion of the EET-BP-PHD filter, a suitable measurement likelihood is defined for a given partitioning cell, and the main implementation steps are presented along with the necessary box approximations and manipulations. The limitations and capabilities of the proposed EET-BP-PHD filter are illustrated by simulation examples. The simulation results show that a box-particle implementation of the ET-PHD filter can avoid the high number of particles and reduce computational burden, compared to a particle implementation of that for extended target tracking.

Simulation-based training for thoracoscopic lobectomy: a randomized controlled trial: virtual-reality versus black-box simulation.

PubMed

Jensen, Katrine; Ringsted, Charlotte; Hansen, Henrik Jessen; Petersen, René Horsleben; Konge, Lars

2014-06-01

Video-assisted thoracic surgery is gradually replacing conventional open thoracotomy as the method of choice for the treatment of early-stage non-small cell lung cancers, and thoracic surgical trainees must learn and master this technique. Simulation-based training could help trainees overcome the first part of the learning curve, but no virtual-reality simulators for thoracoscopy are commercially available. This study aimed to investigate whether training on a laparoscopic simulator enables trainees to perform a thoracoscopic lobectomy. Twenty-eight surgical residents were randomized to either virtual-reality training on a nephrectomy module or traditional black-box simulator training. After a retention period they performed a thoracoscopic lobectomy on a porcine model and their performance was scored using a previously validated assessment tool. The groups did not differ in age or gender. All participants were able to complete the lobectomy. The performance of the black-box group was significantly faster during the test scenario than the virtual-reality group: 26.6 min (SD 6.7 min) versus 32.7 min (SD 7.5 min). No difference existed between the two groups when comparing bleeding and anatomical and non-anatomical errors. Simulation-based training and targeted instructions enabled the trainees to perform a simulated thoracoscopic lobectomy. Traditional black-box training was more effective than virtual-reality laparoscopy training. Thus, a dedicated simulator for thoracoscopy should be available before establishing systematic virtual-reality training programs for trainees in thoracic surgery.

BEATBOX v1.0: Background Error Analysis Testbed with Box Models

NASA Astrophysics Data System (ADS)

Knote, Christoph; Barré, Jérôme; Eckl, Max

2018-02-01

The Background Error Analysis Testbed (BEATBOX) is a new data assimilation framework for box models. Based on the BOX Model eXtension (BOXMOX) to the Kinetic Pre-Processor (KPP), this framework allows users to conduct performance evaluations of data assimilation experiments, sensitivity analyses, and detailed chemical scheme diagnostics from an observation simulation system experiment (OSSE) point of view. The BEATBOX framework incorporates an observation simulator and a data assimilation system with the possibility of choosing ensemble, adjoint, or combined sensitivities. A user-friendly, Python-based interface allows for the tuning of many parameters for atmospheric chemistry and data assimilation research as well as for educational purposes, for example observation error, model covariances, ensemble size, perturbation distribution in the initial conditions, and so on. In this work, the testbed is described and two case studies are presented to illustrate the design of a typical OSSE experiment, data assimilation experiments, a sensitivity analysis, and a method for diagnosing model errors. BEATBOX is released as an open source tool for the atmospheric chemistry and data assimilation communities.

Uncertainty propagation of p-boxes using sparse polynomial chaos expansions

NASA Astrophysics Data System (ADS)

Schöbi, Roland; Sudret, Bruno

2017-06-01

In modern engineering, physical processes are modelled and analysed using advanced computer simulations, such as finite element models. Furthermore, concepts of reliability analysis and robust design are becoming popular, hence, making efficient quantification and propagation of uncertainties an important aspect. In this context, a typical workflow includes the characterization of the uncertainty in the input variables. In this paper, input variables are modelled by probability-boxes (p-boxes), accounting for both aleatory and epistemic uncertainty. The propagation of p-boxes leads to p-boxes of the output of the computational model. A two-level meta-modelling approach is proposed using non-intrusive sparse polynomial chaos expansions to surrogate the exact computational model and, hence, to facilitate the uncertainty quantification analysis. The capabilities of the proposed approach are illustrated through applications using a benchmark analytical function and two realistic engineering problem settings. They show that the proposed two-level approach allows for an accurate estimation of the statistics of the response quantity of interest using a small number of evaluations of the exact computational model. This is crucial in cases where the computational costs are dominated by the runs of high-fidelity computational models.

Uncertainty propagation of p-boxes using sparse polynomial chaos expansions

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

Schöbi, Roland, E-mail: schoebi@ibk.baug.ethz.ch; Sudret, Bruno, E-mail: sudret@ibk.baug.ethz.ch

2017-06-15

In modern engineering, physical processes are modelled and analysed using advanced computer simulations, such as finite element models. Furthermore, concepts of reliability analysis and robust design are becoming popular, hence, making efficient quantification and propagation of uncertainties an important aspect. In this context, a typical workflow includes the characterization of the uncertainty in the input variables. In this paper, input variables are modelled by probability-boxes (p-boxes), accounting for both aleatory and epistemic uncertainty. The propagation of p-boxes leads to p-boxes of the output of the computational model. A two-level meta-modelling approach is proposed using non-intrusive sparse polynomial chaos expansions tomore » surrogate the exact computational model and, hence, to facilitate the uncertainty quantification analysis. The capabilities of the proposed approach are illustrated through applications using a benchmark analytical function and two realistic engineering problem settings. They show that the proposed two-level approach allows for an accurate estimation of the statistics of the response quantity of interest using a small number of evaluations of the exact computational model. This is crucial in cases where the computational costs are dominated by the runs of high-fidelity computational models.« less

Quantifying parameter uncertainty in stochastic models using the Box Cox transformation

NASA Astrophysics Data System (ADS)

Thyer, Mark; Kuczera, George; Wang, Q. J.

2002-08-01

The Box-Cox transformation is widely used to transform hydrological data to make it approximately Gaussian. Bayesian evaluation of parameter uncertainty in stochastic models using the Box-Cox transformation is hindered by the fact that there is no analytical solution for the posterior distribution. However, the Markov chain Monte Carlo method known as the Metropolis algorithm can be used to simulate the posterior distribution. This method properly accounts for the nonnegativity constraint implicit in the Box-Cox transformation. Nonetheless, a case study using the AR(1) model uncovered a practical problem with the implementation of the Metropolis algorithm. The use of a multivariate Gaussian jump distribution resulted in unacceptable convergence behaviour. This was rectified by developing suitable parameter transformations for the mean and variance of the AR(1) process to remove the strong nonlinear dependencies with the Box-Cox transformation parameter. Applying this methodology to the Sydney annual rainfall data and the Burdekin River annual runoff data illustrates the efficacy of these parameter transformations and demonstrate the value of quantifying parameter uncertainty.

Evolving Waves and Turbulence in the Outer Corona and Inner Heliosphere: The Accelerating Expanding Box

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

Tenerani, Anna; Velli, Marco

Alfvénic fluctuations in the solar wind display many properties reflecting an ongoing nonlinear cascade, e.g., a well-defined spectrum in frequency, together with some characteristics more commonly associated with the linear propagation of waves from the Sun, such as the variation of fluctuation amplitude with distance, dominated by solar wind expansion effects. Therefore, both nonlinearities and expansion must be included simultaneously in any successful model of solar wind turbulence evolution. Because of the disparate spatial scales involved, direct numerical simulations of turbulence in the solar wind represent an arduous task, especially if one wants to go beyond the incompressible approximation. Indeed,more » most simulations neglect solar wind expansion effects entirely. Here we develop a numerical model to simulate turbulent fluctuations from the outer corona to 1 au and beyond, including the sub-Alfvénic corona. The accelerating expanding box (AEB) extends the validity of previous expanding box models by taking into account both the acceleration of the solar wind and the inhomogeneity of background density and magnetic field. Our method incorporates a background accelerating wind within a magnetic field that naturally follows the Parker spiral evolution using a two-scale analysis in which the macroscopic spatial effect coupling fluctuations with background gradients becomes a time-dependent coupling term in a homogeneous box. In this paper we describe the AEB model in detail and discuss its main properties, illustrating its validity by studying Alfvén wave propagation across the Alfvén critical point.« less

A Box-Cox normal model for response times.

PubMed

Klein Entink, R H; van der Linden, W J; Fox, J-P

2009-11-01

The log-transform has been a convenient choice in response time modelling on test items. However, motivated by a dataset of the Medical College Admission Test where the lognormal model violated the normality assumption, the possibilities of the broader class of Box-Cox transformations for response time modelling are investigated. After an introduction and an outline of a broader framework for analysing responses and response times simultaneously, the performance of a Box-Cox normal model for describing response times is investigated using simulation studies and a real data example. A transformation-invariant implementation of the deviance information criterium (DIC) is developed that allows for comparing model fit between models with different transformation parameters. Showing an enhanced description of the shape of the response time distributions, its application in an educational measurement context is discussed at length.

On the biomechanical analysis of the calories expended in a straight boxing jab

PubMed Central

2017-01-01

Boxing and related sports activities have become a standard workout regime at many fitness studios worldwide. Oftentimes, people are interested in the calories expended during these workouts. This note focuses on determining the calories in a boxer's jab, using kinematic vector-loop relations and basic work–energy principles. Numerical simulations are undertaken to illustrate the basic model. Multi-limb extensions of the model are also discussed. PMID:28404871

The influence of temperature on ozone production under varying NOx conditions - a modelling study

NASA Astrophysics Data System (ADS)

Coates, Jane; Mar, Kathleen A.; Ojha, Narendra; Butler, Tim M.

2016-09-01

Surface ozone is a secondary air pollutant produced during the atmospheric photochemical degradation of emitted volatile organic compounds (VOCs) in the presence of sunlight and nitrogen oxides (NOx). Temperature directly influences ozone production through speeding up the rates of chemical reactions and increasing the emissions of VOCs, such as isoprene, from vegetation. In this study, we used an idealised box model with different chemical mechanisms (Master Chemical Mechanism, MCMv3.2; Common Representative Intermediates, CRIv2; Model for OZone and Related Chemical Tracers, MOZART-4; Regional Acid Deposition Model, RADM2; Carbon Bond Mechanism, CB05) to examine the non-linear relationship between ozone, NOx and temperature, and we compared this to previous observational studies. Under high-NOx conditions, an increase in ozone from 20 to 40 °C of up to 20 ppbv was due to faster reaction rates, while increased isoprene emissions added up to a further 11 ppbv of ozone. The largest inter-mechanism differences were obtained at high temperatures and high-NOx emissions. CB05 and RADM2 simulated more NOx-sensitive chemistry than MCMv3.2, CRIv2 and MOZART-4, which could lead to different mitigation strategies being proposed depending on the chemical mechanism. The increased oxidation rate of emitted VOC with temperature controlled the rate of Ox production; the net influence of peroxy nitrates increased net Ox production per molecule of emitted VOC oxidised. The rate of increase in ozone mixing ratios with temperature from our box model simulations was about half the rate of increase in ozone with temperature observed over central Europe or simulated by a regional chemistry transport model. Modifying the box model set-up to approximate stagnant meteorological conditions increased the rate of increase of ozone with temperature as the accumulation of oxidants enhanced ozone production through the increased production of peroxy radicals from the secondary degradation of emitted VOCs. The box model simulations approximating stagnant conditions and the maximal ozone production chemical regime reproduced the 2 ppbv increase in ozone per degree Celsius from the observational and regional model data over central Europe. The simulated ozone-temperature relationship was more sensitive to mixing than the choice of chemical mechanism. Our analysis suggests that reductions in NOx emissions would be required to offset the additional ozone production due to an increase in temperature in the future.

Modeling and simulation of Li-ion conduction in poly(ethylene oxide)

NASA Astrophysics Data System (ADS)

Gitelman, L.; Israeli, M.; Averbuch, A.; Nathan, M.; Schuss, Z.; Golodnitsky, D.

2007-12-01

Polyethylene oxide (PEO) containing a lithium salt (e.g., LiI) serves as a solid polymer electrolyte (SPE) in thin-film batteries and its ionic conductivity is a key parameter of their performance. We model and simulate Li + ion conduction in a single PEO molecule. Our simplified stochastic model of ionic motion is based on an analogy between protein channels of biological membranes that conduct Na +, K +, and other ions, and the PEO helical chain that conducts Li + ions. In contrast with protein channels and salt solutions, the PEO is both the channel and the solvent for the lithium salt (e.g., LiI). The mobile ions are treated as charged spherical Brownian particles. We simulate Smoluchowski dynamics in channels with a radius of ca. 0.1 nm and study the effect of stretching and temperature on ion conductivity. We assume that each helix (molecule) forms a random angle with the axis between these electrodes and the polymeric film is composed of many uniformly distributed oriented boxes that include molecules with the same direction. We further assume that mechanical stretching aligns the molecular structures in each box along the axis of stretching (intra-box alignment). Our model thus predicts the PEO conductivity as a function of the stretching, the salt concentration and the temperature. The computed enhancement of the ionic conductivity in the stretch direction is in good agreement with experimental results. The simulation results are also in qualitative agreement with recent theoretical and experimental results.

Possible Changes in the Characteristics of the Rainy Season over Northern South America: Results from a Regional Climate Simulation

NASA Astrophysics Data System (ADS)

Vasconcelos, Francisco; Costa, Alexandre; Gandu, Adilson; Sales, Domingo; Araújo, Luiz

2013-04-01

Regional Climate Simulations were performed with RAMS6.0 to evaluate possible changes in the behaviour of the rainy season over the Amazon region, within the CORDEX domain of the Inter-tropical Americas. We forced the regional model using data from one of the CMIP5 participants (HadGEM2-ES), both for the Historical Experiment (1980-2005) and along the XXI century under RCP 8.5 (heavy-emission scenario). Regarding projections, we analyzed results for three time slices, short (2014-2035), middle (2044-2065) and long term (2078-2099), according to the following steps. First, the spatially averaged precipitation in non-overlapping pentads over 7 sub-regions over northern South America was calculated ("boxes" 1 to 7). Then, we calculated the climatological annual cycle for each one of them. Finally, dates of the onset and demise of the rainy season are found, validating the model results against GPCP observations and checking for projected changes. In general, in the Historical Experiment, the model delays the onset of the rainy season over the northern areas and anticipates it over most inland sub-regions. Over eastern Amazon, the regional model represents it properly, besides a delay in the demise of about one month. In short-term projections, there is a slight increase in precipitation and a modest anticipation of the rainy season onset in the coastal areas. Projected changes in the annual cycle of most sub-regions are relatively modest for the short-term and mid-term periods, but may become very significant by the end of the century. Over Colombia (Box 1), which has a bimodal precipitation annual cycle, the model projects a late century increase in the first precipitation peak. Little change is projected for the two boxes roughly covering Venezuela, the Guianas and the northernmost portion of northern Brazilian states (Boxes 2 and 3). The box covering northern Peru and Ecuador (Box 4) shows increased March-April precipitation, but with no significant changes in the phase of the annual cycle. The most important changes are expected over the three boxes corresponding to Brazilian Amazon. Over the westernmost box of them (Box 5), enhanced precipitation is projected towards the end of the century with a marked development of a bimodal annual distribution in the simulation, with well-defined rainfall peaks in November-January and March-May. Over Box 6 (Eastern Amazon) the most dramatic change is expected, with very large reduction of the springtime precipitation and a shift of about a 5-7 pentads in the onset of the rainy season over that area (in contrast, the later portion and the demise of the rainy season remain essentially unchanged). Finally, over Box 7, which covers the transition between the Amazon rainforest and the semiarid Northeast Brazil, the major projected features are a general increase in the wet season precipitation accompanied by a reduction of the dry season rainfall. Onset and demise dates of the rainy season are expected to remain unchanged over that area.

On the biomechanical analysis of the calories expended in a straight boxing jab.

PubMed

Zohdi, T I

2017-04-01

Boxing and related sports activities have become a standard workout regime at many fitness studios worldwide. Oftentimes, people are interested in the calories expended during these workouts. This note focuses on determining the calories in a boxer's jab, using kinematic vector-loop relations and basic work-energy principles. Numerical simulations are undertaken to illustrate the basic model. Multi-limb extensions of the model are also discussed. © 2017 The Author(s).

Global dynamic modeling of a transmission system

NASA Technical Reports Server (NTRS)

Choy, F. K.; Qian, W.

1993-01-01

The work performed on global dynamic simulation and noise correlation of gear transmission systems at the University of Akron is outlined. The objective is to develop a comprehensive procedure to simulate the dynamics of the gear transmission system coupled with the effects of gear box vibrations. The developed numerical model is benchmarked with results from experimental tests at NASA Lewis Research Center. The modal synthesis approach is used to develop the global transient vibration analysis procedure used in the model. Modal dynamic characteristics of the rotor-gear-bearing system are calculated by the matrix transfer method while those of the gear box are evaluated by the finite element method (NASTRAN). A three-dimensional, axial-lateral coupled bearing model is used to couple the rotor vibrations with the gear box motion. The vibrations between the individual rotor systems are coupled through the nonlinear gear mesh interactions. The global equations of motion are solved in modal coordinates and the transient vibration of the system is evaluated by a variable time-stepping integration scheme. The relationship between housing vibration and resulting noise of the gear transmission system is generated by linear transfer functions using experimental data. A nonlinear relationship of the noise components to the fundamental mesh frequency is developed using the hypercoherence function. The numerically simulated vibrations and predicted noise of the gear transmission system are compared with the experimental results from the gear noise test rig at NASA Lewis Research Center. Results of the comparison indicate that the global dynamic model developed can accurately simulate the dynamics of a gear transmission system.

Simulations of the north sea circulation, its variability, and its implementation as hydrodynamical forcing in ERSEM

NASA Astrophysics Data System (ADS)

Lenhart, Hermann J.; Radach, Günther; Backhaus, Jan O.; Pohlmann, Thomas

The rationale is given of how the gross physical features of the circulation and the stratification of the North Sea have been aggregated for inclusion in the ecosystem box model ERSEM. As the ecosystem dynamics are to a large extent determined by small-scale physical events, the ecosystem model is forced with the circulation of a specific year rather than using the long-term mean circulation field. Especially the vertical exchange processes have been explicitly included, because the primary production strongly depends on them. Simulations with a general circulation model (GCM), forced by three-hourly meteorological fields, have been utilized to derive daily horizontal transport values driving ERSEM on boxes of sizes of a few 100 km. The daily vertical transports across a fixed 30-m interface provide the necessary short-term event character of the vertical exchange. For the years 1988 and 1989 the properties of the hydrodynamic flow fields are presented in terms of trajectories of the flow, thermocline depths, of water budgets, flushing times and diffusion rates. The results of the standard simulation with ERSEM show that the daily variability of the circulation, being smoothed by the box integration procedure, is transferred to the chemical and biological state variables to a very limited degree only.

Implementing the DC Mode in Cosmological Simulations with Supercomoving Variables

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

Gnedin, Nickolay Y; Kravtsov, Andrey V; Rudd, Douglas H

2011-06-02

As emphasized by previous studies, proper treatment of the density fluctuation on the fundamental scale of a cosmological simulation volume - the 'DC mode' - is critical for accurate modeling of spatial correlations on scales ~> 10% of simulation box size. We provide further illustration of the effects of the DC mode on the abundance of halos in small boxes and show that it is straightforward to incorporate this mode in cosmological codes that use the 'supercomoving' variables. The equations governing evolution of dark matter and baryons recast with these variables are particularly simple and include the expansion factor, andmore » hence the effect of the DC mode, explicitly only in the Poisson equation.« less

A fast, calibrated model for pyroclastic density currents kinematics and hazard

NASA Astrophysics Data System (ADS)

Esposti Ongaro, Tomaso; Orsucci, Simone; Cornolti, Fulvio

2016-11-01

Multiphase flow models represent valuable tools for the study of the complex, non-equilibrium dynamics of pyroclastic density currents. Particle sedimentation, flow stratification and rheological changes, depending on the flow regime, interaction with topographic obstacles, turbulent air entrainment, buoyancy reversal, and other complex features of pyroclastic currents can be simulated in two and three dimensions, by exploiting efficient numerical solvers and the improved computational capability of modern supercomputers. However, numerical simulations of polydisperse gas-particle mixtures are quite computationally expensive, so that their use in hazard assessment studies (where there is the need of evaluating the probability of hazardous actions over hundreds of possible scenarios) is still challenging. To this aim, a simplified integral (box) model can be used, under the appropriate hypotheses, to describe the kinematics of pyroclastic density currents over a flat topography, their scaling properties and their depositional features. In this work, multiphase flow simulations are used to evaluate integral model approximations, to calibrate its free parameters and to assess the influence of the input data on the results. Two-dimensional numerical simulations describe the generation and decoupling of a dense, basal layer (formed by progressive particle sedimentation) from the dilute transport system. In the Boussinesq regime (i.e., for solid mass fractions below about 0.1), the current Froude number (i.e., the ratio between the current inertia and buoyancy) does not strongly depend on initial conditions and it is consistent to that measured in laboratory experiments (i.e., between 1.05 and 1.2). For higher density ratios (solid mass fraction in the range 0.1-0.9) but still in a relatively dilute regime (particle volume fraction lower than 0.01), numerical simulations demonstrate that the box model is still applicable, but the Froude number depends on the reduced gravity. When the box model is opportunely calibrated with the numerical simulation results, the prediction of the flow runout is fairly accurate and the model predicts a rapid, non-linear decay of the flow kinetic energy (or dynamic pressure) with the distance from the source. The capability of PDC to overcome topographic obstacles can thus be analysed in the framework of the energy-conoid approach, in which the predicted kinetic energy of the flow front is compared with the potential energy jump associated with the elevated topography to derive a condition for blocking. Model results show that, although preferable to the energy-cone, the energy-conoid approach still has some serious limitations, mostly associated with the behaviour of the flow head. Implications of these outcomes are discussed in the context of probabilistic hazard assessment studies, in which a calibrated box model can be used as a fast pyroclastic density current emulator for Monte Carlo simulations.

Dynamics of movie competition and popularity spreading in recommender systems.

PubMed

Yeung, C H; Cimini, G; Jin, C-H

2011-01-01

We introduce a simple model to study movie competition in recommender systems. Movies of heterogeneous quality compete against each other through viewers' reviews and generate interesting dynamics at the box office. By assuming mean-field interactions between the competing movies, we show that the runaway effect of popularity spreading is triggered by defeating the average review score, leading to box-office hits: Popularity rises and peaks before fade-out. The average review score thus characterizes the critical movie quality necessary for transition from box-office bombs to blockbusters. The major factors affecting the critical review score are examined. By iterating the mean-field dynamical equations, we obtain qualitative agreements with simulations and real systems in the dynamical box-office forms, revealing the significant role of competition in understanding box-office dynamics.

Dynamics of movie competition and popularity spreading in recommender systems

NASA Astrophysics Data System (ADS)

Yeung, C. H.; Cimini, G.; Jin, C.-H.

2011-01-01

We introduce a simple model to study movie competition in recommender systems. Movies of heterogeneous quality compete against each other through viewers’ reviews and generate interesting dynamics at the box office. By assuming mean-field interactions between the competing movies, we show that the runaway effect of popularity spreading is triggered by defeating the average review score, leading to box-office hits: Popularity rises and peaks before fade-out. The average review score thus characterizes the critical movie quality necessary for transition from box-office bombs to blockbusters. The major factors affecting the critical review score are examined. By iterating the mean-field dynamical equations, we obtain qualitative agreements with simulations and real systems in the dynamical box-office forms, revealing the significant role of competition in understanding box-office dynamics.

A THREE-DIMENSIONAL MODEL ASSESSMENT OF THE GLOBAL DISTRIBUTION OF HEXACHLOROBENZENE

EPA Science Inventory

The distributions of persistent organic pollutants (POPs) in the global environment have been studied typically with box/fugacity models with simplified treatments of atmospheric transport processes1. Such models are incapable of simulating the complex three-dimensional mechanis...

The role of simulation in the development of technical competence during surgical training: a literature review

PubMed Central

2013-01-01

Objectives To establish the current state of knowledge on the effect of surgical simulation on the development of technical competence during surgical training. Methods Using a defined search strategy, the medical and educational literature was searched to identify empirical research that uses simulation as an educational intervention with surgical trainees. Included studies were analysed according to guidelines adapted from a Best Evidence in Medical Education review. Results A total of 32 studies were analysed, across 5 main categories of surgical simulation technique - use of bench models and box trainers (9 studies); Virtual Reality (14 studies); human cadavers (4 studies); animal models (2 studies) and robotics (3 studies). An improvement in technical skill was seen within the simulated environment across all five categories. This improvement was seen to transfer to the real patient in the operating room in all categories except the use of animals. Conclusions Based on current evidence, surgical trainees should be confident in the effects of using simulation, and should have access to formal, structured simulation as part of their training. Surgical simulation should incorporate the use of bench models and box trainers, with the use of Virtual Reality where resources allow. Alternatives to cadaveric and animal models should be considered due to the ethical and moral issues surrounding their use, and due to their equivalency with other simulation techniques. However, any use of surgical simulation must be tailored to the individual needs of trainees, and should be accompanied by feedback from expert tutors.

Surface reflectance drives nest box temperature profiles and thermal suitability for target wildlife.

PubMed

Griffiths, Stephen R; Rowland, Jessica A; Briscoe, Natalie J; Lentini, Pia E; Handasyde, Kathrine A; Lumsden, Linda F; Robert, Kylie A

2017-01-01

Thermal properties of tree hollows play a major role in survival and reproduction of hollow-dependent fauna. Artificial hollows (nest boxes) are increasingly being used to supplement the loss of natural hollows; however, the factors that drive nest box thermal profiles have received surprisingly little attention. We investigated how differences in surface reflectance influenced temperature profiles of nest boxes painted three different colors (dark-green, light-green, and white: total solar reflectance 5.9%, 64.4%, and 90.3% respectively) using boxes designed for three groups of mammals: insectivorous bats, marsupial gliders and brushtail possums. Across the three different box designs, dark-green (low reflectance) boxes experienced the highest average and maximum daytime temperatures, had the greatest magnitude of variation in daytime temperatures within the box, and were consistently substantially warmer than light-green boxes (medium reflectance), white boxes (high reflectance), and ambient air temperatures. Results from biophysical model simulations demonstrated that variation in diurnal temperature profiles generated by painting boxes either high or low reflectance colors could have significant ecophysiological consequences for animals occupying boxes, with animals in dark-green boxes at high risk of acute heat-stress and dehydration during extreme heat events. Conversely in cold weather, our modelling indicated that there are higher cumulative energy costs for mammals, particularly smaller animals, occupying light-green boxes. Given their widespread use as a conservation tool, we suggest that before boxes are installed, consideration should be given to the effect of color on nest box temperature profiles, and the resultant thermal suitability of boxes for wildlife, particularly during extremes in weather. Managers of nest box programs should consider using several different colors and installing boxes across a range of both orientations and shade profiles (i.e., levels of canopy cover), to ensure target animals have access to artificial hollows with a broad range of thermal profiles, and can therefore choose boxes with optimal thermal conditions across different seasons.

Surface reflectance drives nest box temperature profiles and thermal suitability for target wildlife

PubMed Central

Rowland, Jessica A.; Briscoe, Natalie J.; Lentini, Pia E.; Handasyde, Kathrine A.; Lumsden, Linda F.; Robert, Kylie A.

2017-01-01

Thermal properties of tree hollows play a major role in survival and reproduction of hollow-dependent fauna. Artificial hollows (nest boxes) are increasingly being used to supplement the loss of natural hollows; however, the factors that drive nest box thermal profiles have received surprisingly little attention. We investigated how differences in surface reflectance influenced temperature profiles of nest boxes painted three different colors (dark-green, light-green, and white: total solar reflectance 5.9%, 64.4%, and 90.3% respectively) using boxes designed for three groups of mammals: insectivorous bats, marsupial gliders and brushtail possums. Across the three different box designs, dark-green (low reflectance) boxes experienced the highest average and maximum daytime temperatures, had the greatest magnitude of variation in daytime temperatures within the box, and were consistently substantially warmer than light-green boxes (medium reflectance), white boxes (high reflectance), and ambient air temperatures. Results from biophysical model simulations demonstrated that variation in diurnal temperature profiles generated by painting boxes either high or low reflectance colors could have significant ecophysiological consequences for animals occupying boxes, with animals in dark-green boxes at high risk of acute heat-stress and dehydration during extreme heat events. Conversely in cold weather, our modelling indicated that there are higher cumulative energy costs for mammals, particularly smaller animals, occupying light-green boxes. Given their widespread use as a conservation tool, we suggest that before boxes are installed, consideration should be given to the effect of color on nest box temperature profiles, and the resultant thermal suitability of boxes for wildlife, particularly during extremes in weather. Managers of nest box programs should consider using several different colors and installing boxes across a range of both orientations and shade profiles (i.e., levels of canopy cover), to ensure target animals have access to artificial hollows with a broad range of thermal profiles, and can therefore choose boxes with optimal thermal conditions across different seasons. PMID:28472147

Can Condensing Organic Aerosols Lead to Less Cloud Particles?

NASA Astrophysics Data System (ADS)

Gao, C. Y.; Tsigaridis, K.; Bauer, S.

2017-12-01

We examined the impact of condensing organic aerosols on activated cloud number concentration in a new aerosol microphysics box model, MATRIX-VBS. The model includes the volatility-basis set (VBS) framework in an aerosol microphysical scheme MATRIX (Multiconfiguration Aerosol TRacker of mIXing state) that resolves aerosol mass and number concentrations and aerosol mixing state. Preliminary results show that by including the condensation of organic aerosols, the new model (MATRIX-VBS) has less activated particles compared to the original model (MATRIX), which treats organic aerosols as non-volatile. Parameters such as aerosol chemical composition, mass and number concentrations, and particle sizes which affect activated cloud number concentration are thoroughly evaluated via a suite of Monte-Carlo simulations. The Monte-Carlo simulations also provide information on which climate-relevant parameters play a critical role in the aerosol evolution in the atmosphere. This study also helps simplifying the newly developed box model which will soon be implemented in the global model GISS ModelE as a module.

Inferring mass in complex scenes by mental simulation.

PubMed

Hamrick, Jessica B; Battaglia, Peter W; Griffiths, Thomas L; Tenenbaum, Joshua B

2016-12-01

After observing a collision between two boxes, you can immediately tell which is empty and which is full of books based on how the boxes moved. People form rich perceptions about the physical properties of objects from their interactions, an ability that plays a crucial role in learning about the physical world through our experiences. Here, we present three experiments that demonstrate people's capacity to reason about the relative masses of objects in naturalistic 3D scenes. We find that people make accurate inferences, and that they continue to fine-tune their beliefs over time. To explain our results, we propose a cognitive model that combines Bayesian inference with approximate knowledge of Newtonian physics by estimating probabilities from noisy physical simulations. We find that this model accurately predicts judgments from our experiments, suggesting that the same simulation mechanism underlies both peoples' predictions and inferences about the physical world around them. Copyright © 2016 Elsevier B.V. All rights reserved.

Assessing image quality of low-cost laparoscopic box trainers: options for residents training at home.

PubMed

Kiely, Daniel J; Stephanson, Kirk; Ross, Sue

2011-10-01

Low-cost laparoscopic box trainers built using home computers and webcams may provide residents with a useful tool for practice at home. This study set out to evaluate the image quality of low-cost laparoscopic box trainers compared with a commercially available model. Five low-cost laparoscopic box trainers including the components listed were compared in random order to one commercially available box trainer: A (high-definition USB 2.0 webcam, PC laptop), B (Firewire webcam, Mac laptop), C (high-definition USB 2.0 webcam, Mac laptop), D (standard USB webcam, PC desktop), E (Firewire webcam, PC desktop), and F (the TRLCD03 3-DMEd Standard Minimally Invasive Training System). Participants observed still image quality and performed a peg transfer task using each box trainer. Participants rated still image quality, image quality with motion, and whether the box trainer had sufficient image quality to be useful for training. Sixteen residents in obstetrics and gynecology took part in the study. The box trainers showing no statistically significant difference from the commercially available model were A, B, C, D, and E for still image quality; A for image quality with motion; and A and B for usefulness of the simulator based on image quality. The cost of the box trainers A-E is approximately $100 to $160 each, not including a computer or laparoscopic instruments. Laparoscopic box trainers built from a high-definition USB 2.0 webcam with a PC (box trainer A) or from a Firewire webcam with a Mac (box trainer B) provide image quality comparable with a commercial standard.

Structure prediction and molecular simulation of gases diffusion pathways in hydrogenase.

PubMed

Sundaram, Shanthy; Tripathi, Ashutosh; Gupta, Vipul

2010-10-06

Although hydrogen is considered to be one of the most promising future energy sources and the technical aspects involved in using it have advanced considerably, the future supply of hydrogen from renewable sources is still unsolved. The [Fe]- hydrogenase enzymes are highly efficient H(2) catalysts found in ecologically and phylogenetically diverse microorganisms, including the photosynthetic green alga, Chlamydomonas reinhardtii. While these enzymes can occur in several forms, H(2) catalysis takes place at a unique [FeS] prosthetic group or H-cluster, located at the active site. 3D structure of the protein hydA1 hydrogenase from Chlamydomonas reinhardtti was predicted using the MODELER 8v2 software. Conserved region was depicted from the NCBI CDD Search. Template selection was done on the basis NCBI BLAST results. For single template 1FEH was used and for multiple templates 1FEH and 1HFE were used. The result of the Homology modeling was verified by uploading the file to SAVS server. On the basis of the SAVS result 3D structure predicted using single template was chosen for performing molecular simulation. For performing molecular simulation three strategies were used. First the molecular simulation of the protein was performed in solvated box containing bulk water. Then 100 H(2) molecules were randomly inserted in the solvated box and two simulations of 50 and 100 ps were performed. Similarly 100 O(2) molecules were randomly placed in the solvated box and again 50 and 100 ps simulation were performed. Energy minimization was performed before each simulation was performed. Conformations were saved after each simulation. Analysis of the gas diffusion was done on the basis of RMSD, Radius of Gyration and no. of gas molecule/ps plot.

An improved portmanteau test for autocorrelated errors in interrupted time-series regression models.

PubMed

Huitema, Bradley E; McKean, Joseph W

2007-08-01

A new portmanteau test for autocorrelation among the errors of interrupted time-series regression models is proposed. Simulation results demonstrate that the inferential properties of the proposed Q(H-M) test statistic are considerably more satisfactory than those of the well known Ljung-Box test and moderately better than those of the Box-Pierce test. These conclusions generally hold for a wide variety of autoregressive (AR), moving averages (MA), and ARMA error processes that are associated with time-series regression models of the form described in Huitema and McKean (2000a, 2000b).

Graphene: A partially ordered non-periodic solid

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

Wei, Dongshan; Wang, Feng, E-mail: fengwang@uark.edu

2014-10-14

Molecular dynamics simulations were performed to study the structural features of graphene over a wide range of temperatures from 50 to 4000 K using the PPBE-G potential [D. Wei, Y. Song, and F. Wang, J. Chem. Phys. 134, 184704 (2011)]. This potential was developed by force matching the Perdew-Burke-Ernzerhof (PBE) exchange correlation functional and has been validated previously to provide accurate potential energy surface for graphene at temperatures as high as 3000 K. Simulations with the PPBE‑G potential are the best available approximation to a direct Car-Parrinello Molecular Dynamics study of graphene. One advantage of the PBE-G potential is to allowmore » large simulation boxes to be modeled efficiently so that properties showing strong finite size effects can be studied. Our simulation box contains more than 600 000 C atoms and is one of the largest graphene boxes ever modeled. With the PPBE-G potential, the thermal-expansion coefficient is negative up to 4000 K. With a large box and an accurate potential, the critical exponent for the scaling properties associated with the normal-normal and height-height correlation functions was confirmed to be 0.85. This exponent remains constant up to 4000 K suggesting graphene to be in the deeply cooled regime even close to the experimental melting temperature. The reduced peak heights in the radial distribution function of graphene show an inverse power law dependence to distance, which indicates that a macroscopic graphene sheet will lose long-range crystalline order as predicted by the Mermin-Wagner instability. Although graphene loses long-range translational order, it retains long range orientational order as indicated by its orientational correlation function; graphene is thus partially ordered but not periodic.« less

Advanced solar box and flat plate collector cookers

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

Grupp, M.; Bergler, H.

Several new solar cooker systems have been developed at Synopsis during the last years: advanced box type cookers, featuring an optimized heat transfer from the absorber into the cooking vessel; flat plate cookers, based on a particular two-way collector with air as transfer fluid; flat plate cookers with heat-pipe transfer; specialized cookers for the baking of bread and flat bread. The working principle of these cookers is described, the structure of a thermal simulation model and results of thermal tests are presented. The results of the first year of local production and use of advanced boxes in India are reported.

Testing density-dependent groundwater models: Two-dimensional steady state unstable convection in infinite, finite and inclined porous layers

USGS Publications Warehouse

Weatherill, D.; Simmons, C.T.; Voss, C.I.; Robinson, N.I.

2004-01-01

This study proposes the use of several problems of unstable steady state convection with variable fluid density in a porous layer of infinite horizontal extent as two-dimensional (2-D) test cases for density-dependent groundwater flow and solute transport simulators. Unlike existing density-dependent model benchmarks, these problems have well-defined stability criteria that are determined analytically. These analytical stability indicators can be compared with numerical model results to test the ability of a code to accurately simulate buoyancy driven flow and diffusion. The basic analytical solution is for a horizontally infinite fluid-filled porous layer in which fluid density decreases with depth. The proposed test problems include unstable convection in an infinite horizontal box, in a finite horizontal box, and in an infinite inclined box. A dimensionless Rayleigh number incorporating properties of the fluid and the porous media determines the stability of the layer in each case. Testing the ability of numerical codes to match both the critical Rayleigh number at which convection occurs and the wavelength of convection cells is an addition to the benchmark problems currently in use. The proposed test problems are modelled in 2-D using the SUTRA [SUTRA-A model for saturated-unsaturated variable-density ground-water flow with solute or energy transport. US Geological Survey Water-Resources Investigations Report, 02-4231, 2002. 250 p] density-dependent groundwater flow and solute transport code. For the case of an infinite horizontal box, SUTRA results show a distinct change from stable to unstable behaviour around the theoretical critical Rayleigh number of 4??2 and the simulated wavelength of unstable convection agrees with that predicted by the analytical solution. The effects of finite layer aspect ratio and inclination on stability indicators are also tested and numerical results are in excellent agreement with theoretical stability criteria and with numerical results previously reported in traditional fluid mechanics literature. ?? 2004 Elsevier Ltd. All rights reserved.

Predicting a future lifetime through Box-Cox transformation.

PubMed

Yang, Z

1999-09-01

In predicting a future lifetime based on a sample of past lifetimes, the Box-Cox transformation method provides a simple and unified procedure that is shown in this article to meet or often outperform the corresponding frequentist solution in terms of coverage probability and average length of prediction intervals. Kullback-Leibler information and second-order asymptotic expansion are used to justify the Box-Cox procedure. Extensive Monte Carlo simulations are also performed to evaluate the small sample behavior of the procedure. Certain popular lifetime distributions, such as Weibull, inverse Gaussian and Birnbaum-Saunders are served as illustrative examples. One important advantage of the Box-Cox procedure lies in its easy extension to linear model predictions where the exact frequentist solutions are often not available.

Laboratory Simulation of Urban Runoff and Estimation of Runoff Hydrographs with Experimental Curve Numbers Implemented in USEPA SWMM

EPA Science Inventory

The prognostic capabilities of a lumped hydrologic modeling approach may be complicated by routing and connectivity among infiltrative and impervious surfaces. We used artificial rainfall to generate runoff from impervious and bare soil boxes arranged in series to simulate differ...

The Framework for 0-D Atmospheric Modeling (F0AM) v3.1

NASA Technical Reports Server (NTRS)

Wolfe, Glenn M.; Marvin, Margaret R.; Roberts, Sandra J.; Travis, Katherine R.; Liao, Jin

2016-01-01

The Framework for 0-D Atmospheric Modeling(F0AM) is a flexible and user-friendly MATLAB-based platform for simulation of atmospheric chemistry systems. The F0AM interface incorporates front-end configuration of observational constraints and model setups, making it readily adaptable to simulation of photochemical chambers, Lagrangian plumes, and steady-state or time-evolving solar cycles. Six different chemical mechanisms and three options for calculation of photolysis frequencies are currently available. Example simulations are presented to illustrate model capabilities and, more generally, highlight some of the advantages and challenges of 0-D box modeling.

DSMC simulations of vapor transport toward development of the lithium vapor box divertor concept

NASA Astrophysics Data System (ADS)

Jagoe, Christopher; Schwartz, Jacob; Goldston, Robert

2016-10-01

The lithium vapor divertor box concept attempts to achieve volumetric dissipation of the high heat efflux from a fusion power system. The vapor extracts the heat of the incoming plasma by ionization and radiation, while remaining localized in the vapor box due to differential pumping based on rapid condensation. Preliminary calculations with lithium vapor at densities appropriate for an NSTX-U-scale machine give Knudsen numbers between 0.01 and 1, outside both the range of continuum fluid dynamics and of collisionless Monte Carlo. The direct-simulation Monte Carlo (DSMC) method, however, can simulate rarefied gas flows in this regime. Using the solver contained in the OpenFOAM package, pressure-driven flows of water vapor will be analyzed. The use of water vapor in the relevant range of Knudsen number allows for a flexible similarity experiment to verify the reliability of the code before moving to tests with lithium. The simulation geometry consists of chains of boxes on a temperature gradient, connected by slots with widths that are a representative fraction of the dimensions of the box. We expect choked flow, sonic shocks, and order-of-magnitude pressure and density drops from box to box, but this expectation will be tested in the simulation and then experiment. This work is supported by the Princeton Environmental Institute.

Explicit modeling of groundwater-surface water interactions using a simple bucket-type model

NASA Astrophysics Data System (ADS)

Staudinger, Maria; Carlier, Claire; Brunner, Philip; Seibert, Jan

2017-04-01

Longer dry spells can become critical for water supply and groundwater dependent ecosystems. During these dry spells groundwater is often the most relevant source for streams. Hence, the hydrological behavior of a catchment is often dominated by groundwater surface water interactions, which can vary considerably in space and time. While classical hydrological approaches hardly consider this spatial dependence, quantitative, hydrogeological modeling approaches can couple surface runoff processes and groundwater processes. Hydrogeological modeling can help to gain an improved understanding of catchment processes during low flow. However, due to their complex parametrization and large computational requirements, such hydrogeological models are difficult to employ at catchment scale, particularly for a larger set of catchments. Then bucket-type hydrological models remain a practical alternative. In this study we combine the strengths of both the hydrogeological and bucket-type hydrological models to better understand low flow processes and ultimately to use this knowledge for low flow projections. Bucket-type hydrological models have traditionally not been developed with focus on the simulation of low flow. One consequence is that interactions between surface and groundwater are not explicitly considered. Water fluxes in bucket-type hydrological models are commonly simulated only in one direction, namely from the groundwater to the stream but not from the stream to the groundwater. This latter flux, however, can become more important during low flow situations. We therefore further developed the bucket-type hydrological model HBV to simulate low flow situations by allowing for exchange in both directions i.e. also from the stream to the groundwater. The additional HBV exchange box is developed by using a variety of synthetic hydrogeological models as training set that were generated using a fully coupled, physically based hydrogeological model. In this way processes that occur in different spatial settings within the catchment are translated to functional relationships and effective parameter values for the conceptual exchange box can be extracted. Here, we show the development and evaluation of the HBV exchange box. We further show a first application in real catchments and evaluate the model performance by comparing the simulations to benchmark models that do not consider groundwater surface water interaction.

Black-hole universe: time evolution.

PubMed

Yoo, Chul-Moon; Okawa, Hirotada; Nakao, Ken-ichi

2013-10-18

Time evolution of a black hole lattice toy model universe is simulated. The vacuum Einstein equations in a cubic box with a black hole at the origin are numerically solved with periodic boundary conditions on all pairs of faces opposite to each other. Defining effective scale factors by using the area of a surface and the length of an edge of the cubic box, we compare them with that in the Einstein-de Sitter universe. It is found that the behavior of the effective scale factors is well approximated by that in the Einstein-de Sitter universe. In our model, if the box size is sufficiently larger than the horizon radius, local inhomogeneities do not significantly affect the global expansion law of the Universe even though the inhomogeneity is extremely nonlinear.

Electron and ion heating by whistler turbulence: Three-dimensional particle-in-cell simulations

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

Hughes, R. Scott; Gary, S. Peter; Wang, Joseph

2014-12-17

Three-dimensional particle-in-cell simulations of decaying whistler turbulence are carried out on a collisionless, homogeneous, magnetized, electron-ion plasma model. In addition, the simulations use an initial ensemble of relatively long wavelength whistler modes with a broad range of initial propagation directions with an initial electron beta β e = 0.05. The computations follow the temporal evolution of the fluctuations as they cascade into broadband turbulent spectra at shorter wavelengths. Three simulations correspond to successively larger simulation boxes and successively longer wavelengths of the initial fluctuations. The computations confirm previous results showing electron heating is preferentially parallel to the background magnetic fieldmore » B o, and ion heating is preferentially perpendicular to B o. The new results here are that larger simulation boxes and longer initial whistler wavelengths yield weaker overall dissipation, consistent with linear dispersion theory predictions of decreased damping, stronger ion heating, consistent with a stronger ion Landau resonance, and weaker electron heating.« less

Influence of the choice of gas-phase mechanism on predictions of key gaseous pollutants during the AQMEII phase-2 intercomparison

EPA Science Inventory

The formulations of tropospheric gas-phase chemistry (“mechanisms”)used in the regional-scale chemistry-transport models participating in theAir Quality Modelling Evaluation International Initiative (AQMEII) Phase2 are intercompared by the means of box model studies. Simulations ...

Large-scale Density Structures in Magneto-rotational Disk Turbulence

NASA Astrophysics Data System (ADS)

Youdin, Andrew; Johansen, A.; Klahr, H.

2009-01-01

Turbulence generated by the magneto-rotational instability (MRI) is a strong candidate to drive accretion flows in disks, including sufficiently ionized regions of protoplanetary disks. The MRI is often studied in local shearing boxes, which model a small section of the disk at high resolution. I will present simulations of large, stratified shearing boxes which extend up to 10 gas scale-heights across. These simulations are a useful bridge to fully global disk simulations. We find that MRI turbulence produces large-scale, axisymmetric density perturbations . These structures are part of a zonal flow --- analogous to the banded flow in Jupiter's atmosphere --- which survives in near geostrophic balance for tens of orbits. The launching mechanism is large-scale magnetic tension generated by an inverse cascade. We demonstrate the robustness of these results by careful study of various box sizes, grid resolutions, and microscopic diffusion parameterizations. These gas structures can trap solid material (in the form of large dust or ice particles) with important implications for planet formation. Resolved disk images at mm-wavelengths (e.g. from ALMA) will verify or constrain the existence of these structures.

Laparoscopic surgical box model training for surgical trainees with limited prior laparoscopic experience.

PubMed

Gurusamy, Kurinchi Selvan; Nagendran, Myura; Toon, Clare D; Davidson, Brian R

2014-03-01

Surgical training has traditionally been one of apprenticeship, where the surgical trainee learns to perform surgery under the supervision of a trained surgeon. This is time consuming, costly, and of variable effectiveness. Training using a box model physical simulator is an option to supplement standard training. However, the value of this modality on trainees with limited prior laparoscopic experience is unknown. To compare the benefits and harms of box model training for surgical trainees with limited prior laparoscopic experience versus standard surgical training or supplementary animal model training. We searched the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, EMBASE, and Science Citation Index Expanded to May 2013. We planned to include all randomised clinical trials comparing box model trainers versus other forms of training including standard laparoscopic training and supplementary animal model training in surgical trainees with limited prior laparoscopic experience. We also planned to include trials comparing different methods of box model training. Two authors independently identified trials and collected data. We analysed the data with both the fixed-effect and the random-effects models using Review Manager 5. For each outcome, we calculated the risk ratio (RR), mean difference (MD), or standardised mean difference (SMD) with 95% confidence intervals (CI) based on intention-to-treat analysis whenever possible. We identified eight trials that met the inclusion criteria. One trial including 17 surgical trainees did not contribute to the meta-analysis. We included seven trials (249 surgical trainees belonging to various postgraduate years ranging from year one to four) in which the participants were randomised to supplementary box model training (122 trainees) versus standard training (127 trainees). Only one trial (50 trainees) was at low risk of bias. The box trainers used in all the seven trials were video trainers. Six trials were conducted in USA and one trial in Canada. The surgeries in which the final assessments were made included laparoscopic total extraperitoneal hernia repairs, laparoscopic cholecystectomy, laparoscopic tubal ligation, laparoscopic partial salpingectomy, and laparoscopic bilateral mid-segment salpingectomy. The final assessments were made on a single operative procedure.There were no deaths in three trials (0/82 (0%) supplementary box model training versus 0/86 (0%) standard training; RR not estimable; very low quality evidence). The other trials did not report mortality. The estimated effect on serious adverse events was compatible with benefit and harm (three trials; 168 patients; 0/82 (0%) supplementary box model training versus 1/86 (1.1%) standard training; RR 0.36; 95% CI 0.02 to 8.43; very low quality evidence). None of the trials reported patient quality of life. The operating time was significantly shorter in the supplementary box model training group versus the standard training group (1 trial; 50 patients; MD -6.50 minutes; 95% CI -10.85 to -2.15). The proportion of patients who were discharged as day-surgery was significantly higher in the supplementary box model training group versus the standard training group (1 trial; 50 patients; 24/24 (100%) supplementary box model training versus 15/26 (57.7%) standard training; RR 1.71; 95% CI 1.23 to 2.37). None of the trials reported trainee satisfaction. The operating performance was significantly better in the supplementary box model training group versus the standard training group (seven trials; 249 trainees; SMD 0.84; 95% CI 0.57 to 1.10).None of the trials compared box model training versus animal model training or versus different methods of box model training. There is insufficient evidence to determine whether laparoscopic box model training reduces mortality or morbidity. There is very low quality evidence that it improves technical skills compared with standard surgical training in trainees with limited previous laparoscopic experience. It may also decrease operating time and increase the proportion of patients who were discharged as day-surgery in the first total extraperitoneal hernia repair after box model training. However, the duration of the benefit of box model training is unknown. Further well-designed trials of low risk of bias and random errors are necessary. Such trials should assess the long-term impact of box model training on clinical outcomes and compare box training with other forms of training.

MASER: A Tool Box for Solar System Low Frequency Radio Astronomy

NASA Astrophysics Data System (ADS)

Cecconi, B.; Le Sidaner, P.; Savalle, R.; Bonnin, X.; Zarka, P.; Louis, C.; Coffre, A.; Lamy, L.; Denis, L.; Griessmeier, J.-M.; Faden, J.; Piker, C.; André, N.; Génot, V.; Erard, S.; King, T. A.; Mafi, J. N.; Sharlow, M.; Sky, J.; Demleitner, M.

2018-04-01

MASER (Measuring, Analysing, and Simulating Radio Emissions) is a toolbox for solar system radio astronomy. It provides tools for reading, displaying, finding, and modeling low frequency radio datasets.

The Box-Cox power transformation on nursing sensitive indicators: Does it matter if structural effects are omitted during the estimation of the transformation parameter?

PubMed Central

2011-01-01

Background Many nursing and health related research studies have continuous outcome measures that are inherently non-normal in distribution. The Box-Cox transformation provides a powerful tool for developing a parsimonious model for data representation and interpretation when the distribution of the dependent variable, or outcome measure, of interest deviates from the normal distribution. The objectives of this study was to contrast the effect of obtaining the Box-Cox power transformation parameter and subsequent analysis of variance with or without a priori knowledge of predictor variables under the classic linear or linear mixed model settings. Methods Simulation data from a 3 × 4 factorial treatments design, along with the Patient Falls and Patient Injury Falls from the National Database of Nursing Quality Indicators (NDNQI®) for the 3rd quarter of 2007 from a convenience sample of over one thousand US hospitals were analyzed. The effect of the nonlinear monotonic transformation was contrasted in two ways: a) estimating the transformation parameter along with factors with potential structural effects, and b) estimating the transformation parameter first and then conducting analysis of variance for the structural effect. Results Linear model ANOVA with Monte Carlo simulation and mixed models with correlated error terms with NDNQI examples showed no substantial differences on statistical tests for structural effects if the factors with structural effects were omitted during the estimation of the transformation parameter. Conclusions The Box-Cox power transformation can still be an effective tool for validating statistical inferences with large observational, cross-sectional, and hierarchical or repeated measure studies under the linear or the mixed model settings without prior knowledge of all the factors with potential structural effects. PMID:21854614

The Box-Cox power transformation on nursing sensitive indicators: does it matter if structural effects are omitted during the estimation of the transformation parameter?

PubMed

Hou, Qingjiang; Mahnken, Jonathan D; Gajewski, Byron J; Dunton, Nancy

2011-08-19

Many nursing and health related research studies have continuous outcome measures that are inherently non-normal in distribution. The Box-Cox transformation provides a powerful tool for developing a parsimonious model for data representation and interpretation when the distribution of the dependent variable, or outcome measure, of interest deviates from the normal distribution. The objectives of this study was to contrast the effect of obtaining the Box-Cox power transformation parameter and subsequent analysis of variance with or without a priori knowledge of predictor variables under the classic linear or linear mixed model settings. Simulation data from a 3 × 4 factorial treatments design, along with the Patient Falls and Patient Injury Falls from the National Database of Nursing Quality Indicators (NDNQI® for the 3rd quarter of 2007 from a convenience sample of over one thousand US hospitals were analyzed. The effect of the nonlinear monotonic transformation was contrasted in two ways: a) estimating the transformation parameter along with factors with potential structural effects, and b) estimating the transformation parameter first and then conducting analysis of variance for the structural effect. Linear model ANOVA with Monte Carlo simulation and mixed models with correlated error terms with NDNQI examples showed no substantial differences on statistical tests for structural effects if the factors with structural effects were omitted during the estimation of the transformation parameter. The Box-Cox power transformation can still be an effective tool for validating statistical inferences with large observational, cross-sectional, and hierarchical or repeated measure studies under the linear or the mixed model settings without prior knowledge of all the factors with potential structural effects.

Analysis of Soft Error Rates in 65- and 28-nm FD-SOI Processes Depending on BOX Region Thickness and Body Bias by Monte-Carlo Based Simulations

NASA Astrophysics Data System (ADS)

Zhang, Kuiyuan; Umehara, Shigehiro; Yamaguchi, Junki; Furuta, Jun; Kobayashi, Kazutoshi

2016-08-01

This paper analyzes how body bias and BOX region thickness affect soft error rates in 65-nm SOTB (Silicon on Thin BOX) and 28-nm UTBB (Ultra Thin Body and BOX) FD-SOI processes. Soft errors are induced by alpha-particle and neutron irradiation and the results are then analyzed by Monte Carlo based simulation using PHITS-TCAD. The alpha-particle-induced single event upset (SEU) cross-section and neutron-induced soft error rate (SER) obtained by simulation are consistent with measurement results. We clarify that SERs decreased in response to an increase in the BOX thickness for SOTB while SERs in UTBB are independent of BOX thickness. We also discover SOTB develops a higher tolerance to soft errors when reverse body bias is applied while UTBB become more susceptible.

Using High-Resolution Forward Model Simulations of Ideal Atmospheric Tracers to Assess the Spatial Information Content of Inverse CO2 Flux Estimates

NASA Technical Reports Server (NTRS)

Pawson, Steven; Nielsen, J. Eric

2011-01-01

Attribution of observed atmospheric carbon concentrations to emissions on the country, state or city level is often inferred using "inversion" techniques. Such computations are often performed using advanced mathematical techniques, such as synthesis inversion or four-dimensional variational analysis, that invoke tracing observed atmospheric concentrations backwards through a transport model to a source region. It is, to date, not well understood how well such techniques can represent fine spatial (and temporal) structure in the inverted flux fields. This question is addressed using forward-model computations with idealized tracers emitted at the surface in a large number of grid boxes over selected regions and examining how distinctly these emitted tracers can be detected downstream. Initial results show that tracers emitted in half-degree grid boxes over a large region of the Eastern USA cannot be distinguished from each other, even at short distances over the Atlantic Ocean, when they are emitted in grid boxes separated by less than five degrees of latitude - especially when only total-column observations are available. A large number of forward model simulations, with varying meteorological conditions, are used to assess how distinctly three types observations (total column, upper tropospheric column, and surface mixing ratio) can separate emissions from different sources. Inferences inverse modeling and source attribution will be drawn.

Laparoscopic surgical box model training for surgical trainees with no prior laparoscopic experience.

PubMed

Nagendran, Myura; Toon, Clare D; Davidson, Brian R; Gurusamy, Kurinchi Selvan

2014-01-17

Surgical training has traditionally been one of apprenticeship, where the surgical trainee learns to perform surgery under the supervision of a trained surgeon. This is time consuming, costly, and of variable effectiveness. Training using a box model physical simulator - either a video box or a mirrored box - is an option to supplement standard training. However, the impact of this modality on trainees with no prior laparoscopic experience is unknown. To compare the benefits and harms of box model training versus no training, another box model, animal model, or cadaveric model training for surgical trainees with no prior laparoscopic experience. We searched the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, EMBASE, and Science Citation Index Expanded to May 2013. We included all randomised clinical trials comparing box model trainers versus no training in surgical trainees with no prior laparoscopic experience. We also included trials comparing different methods of box model training. Two authors independently identified trials and collected data. We analysed the data with both the fixed-effect and the random-effects models using Review Manager for analysis. For each outcome, we calculated the standardised mean difference (SMD) with 95% confidence intervals (CI) based on intention-to-treat analysis whenever possible. Twenty-five trials contributed data to the quantitative synthesis in this review. All but one trial were at high risk of bias. Overall, 16 trials (464 participants) provided data for meta-analysis of box training (248 participants) versus no supplementary training (216 participants). All the 16 trials in this comparison used video trainers. Overall, 14 trials (382 participants) provided data for quantitative comparison of different methods of box training. There were no trials comparing box model training versus animal model or cadaveric model training. Box model training versus no training: The meta-analysis showed that the time taken for task completion was significantly shorter in the box trainer group than the control group (8 trials; 249 participants; SMD -0.48 seconds; 95% CI -0.74 to -0.22). Compared with the control group, the box trainer group also had lower error score (3 trials; 69 participants; SMD -0.69; 95% CI -1.21 to -0.17), better accuracy score (3 trials; 73 participants; SMD 0.67; 95% CI 0.18 to 1.17), and better composite performance scores (SMD 0.65; 95% CI 0.42 to 0.88). Three trials reported movement distance but could not be meta-analysed as they were not in a format for meta-analysis. There was significantly lower movement distance in the box model training compared with no training in one trial, and there were no significant differences in the movement distance between the two groups in the other two trials. None of the remaining secondary outcomes such as mortality and morbidity were reported in the trials when animal models were used for assessment of training, error in movements, and trainee satisfaction. Different methods of box training: One trial (36 participants) found significantly shorter time taken to complete the task when box training was performed using a simple cardboard box trainer compared with the standard pelvic trainer (SMD -3.79 seconds; 95% CI -4.92 to -2.65). There was no significant difference in the time taken to complete the task in the remaining three comparisons (reverse alignment versus forward alignment box training; box trainer suturing versus box trainer drills; and single incision versus multiport box model training). There were no significant differences in the error score between the two groups in any of the comparisons (box trainer suturing versus box trainer drills; single incision versus multiport box model training; Z-maze box training versus U-maze box training). The only trial that reported accuracy score found significantly higher accuracy score with Z-maze box training than U-maze box training (1 trial; 16 participants; SMD 1.55; 95% CI 0.39 to 2.71). One trial (36 participants) found significantly higher composite score with simple cardboard box trainer compared with conventional pelvic trainer (SMD 0.87; 95% CI 0.19 to 1.56). Another trial (22 participants) found significantly higher composite score with reverse alignment compared with forward alignment box training (SMD 1.82; 95% CI 0.79 to 2.84). There were no significant differences in the composite score between the intervention and control groups in any of the remaining comparisons. None of the secondary outcomes were adequately reported in the trials. The results of this review are threatened by both risks of systematic errors (bias) and risks of random errors (play of chance). Laparoscopic box model training appears to improve technical skills compared with no training in trainees with no previous laparoscopic experience. The impacts of this decreased time on patients and healthcare funders in terms of improved outcomes or decreased costs are unknown. There appears to be no significant differences in the improvement of technical skills between different methods of box model training. Further well-designed trials of low risk of bias and random errors are necessary. Such trials should assess the impacts of box model training on surgical skills in both the short and long term, as well as clinical outcomes when the trainee becomes competent to operate on patients.

Gray-box reservoir routing to compute flow propagation in operational forecasting and decision support systems

NASA Astrophysics Data System (ADS)

Russano, Euan; Schwanenberg, Dirk; Alvarado Montero, Rodolfo

2017-04-01

Operational forecasting and decision support systems for flood mitigation and the daily management of water resources require computationally efficient flow routing models. If backwater effects do not play an important role, a hydrological routing approach is often a pragmatic choice. It offers a reasonable accuracy at low computational costs in comparison to a more detailed hydraulic model. This work presents a nonlinear reservoir routing scheme as well as its implementation for the flow propagation between the hydro reservoir Três Marias and a downstream inundation-affected city Pirapora in Brazil. We refer to the model as a gray-box approach due to the identification of the parameter k by a data-driven approach for each reservoir of the cascade, instead of using estimates based on physical characteristics. The model reproduces the discharge at the gauge Pirapora, using 15 reservoirs in the cascade. The obtained results are compared with the ones obtained from the full-hydrodynamic model SOBEK. Results show a relatively good performance for the validation period, with a RMSE of 139.48 for the gray-box model, while the full-hydrodynamic model shows a RMSE of 136.67. The simulation time for a period of several years for the full-hydrodynamic took approximately 64s, while the gray-box model only required about 0.50s. This provides a significant speedup of the computation by only a little trade-off in accuracy, pointing at the potential of the simple approach in the context of time-critical, operational applications. Key-words: flow routing, reservoir routing, gray-box model

Non-Black-Box Simulation from One-Way Functions and Applications to Resettable Security

DTIC Science & Technology

2012-11-05

from 2001, Barak (FOCS’01) introduced a novel non-black-box simulation technique. This technique enabled the construc- tion of new cryptographic...primitives, such as resettably-sound zero-knowledge arguments, that cannot be proven secure using just black-box simulation techniques. The work of Barak ... Barak requires the existence of collision-resistant hash functions, and a very recent result by Bitansky and Paneth (FOCS’12) instead requires the

Gyrokinetic δ f simulation of collisionless and semi-collisional tearing mode instabilities

NASA Astrophysics Data System (ADS)

Wan, Weigang; Chen, Yang; Parker, Scott

2004-11-01

The evolution of collisionless and semi-collisional tearing mode instabilities is studied using a three-dimensional particle-in-cell simulation model that utilizes the δ f-method with the split-weight scheme to enhance the time step, and a novel algorithm(Y. Chen and S.E. Parker, J. Comput. Phys. 198), 463 (2003) to accurately solve the Ampere's equation for experimentally relevant β values, βfracm_im_e≫ 1. We use the model of drift-kinetic electrons and gyrokinetic ions. Linear simulation results are benchmarked with eigenmode analysis for the case of fixed ions. In small box simulations the ions response can be neglected but for large box simulations the ions response is important because the width of perturbed current is larger than ρ_i.The nonlinear dynamics of magnetic islands will be studied and the results will be compared with previous theoretical studiesfootnote J.F. Drake and Y. C. Lee, Phys. Rev. Lett. 39, 453 (1977) on the saturation level and the electron bounce frequency. A collision operator is included in the electron drift kinetic equation to study the simulation in the semi-collisional regime. The algebraical growth stage has been observed and compared quantitatively with theory. Our progress on three-dimensional simulations of tearing mode instabilities will be reported.

Flexible mixture modeling via the multivariate t distribution with the Box-Cox transformation: an alternative to the skew-t distribution

PubMed Central

Lo, Kenneth

2011-01-01

Cluster analysis is the automated search for groups of homogeneous observations in a data set. A popular modeling approach for clustering is based on finite normal mixture models, which assume that each cluster is modeled as a multivariate normal distribution. However, the normality assumption that each component is symmetric is often unrealistic. Furthermore, normal mixture models are not robust against outliers; they often require extra components for modeling outliers and/or give a poor representation of the data. To address these issues, we propose a new class of distributions, multivariate t distributions with the Box-Cox transformation, for mixture modeling. This class of distributions generalizes the normal distribution with the more heavy-tailed t distribution, and introduces skewness via the Box-Cox transformation. As a result, this provides a unified framework to simultaneously handle outlier identification and data transformation, two interrelated issues. We describe an Expectation-Maximization algorithm for parameter estimation along with transformation selection. We demonstrate the proposed methodology with three real data sets and simulation studies. Compared with a wealth of approaches including the skew-t mixture model, the proposed t mixture model with the Box-Cox transformation performs favorably in terms of accuracy in the assignment of observations, robustness against model misspecification, and selection of the number of components. PMID:22125375

Flexible mixture modeling via the multivariate t distribution with the Box-Cox transformation: an alternative to the skew-t distribution.

PubMed

Lo, Kenneth; Gottardo, Raphael

2012-01-01

Cluster analysis is the automated search for groups of homogeneous observations in a data set. A popular modeling approach for clustering is based on finite normal mixture models, which assume that each cluster is modeled as a multivariate normal distribution. However, the normality assumption that each component is symmetric is often unrealistic. Furthermore, normal mixture models are not robust against outliers; they often require extra components for modeling outliers and/or give a poor representation of the data. To address these issues, we propose a new class of distributions, multivariate t distributions with the Box-Cox transformation, for mixture modeling. This class of distributions generalizes the normal distribution with the more heavy-tailed t distribution, and introduces skewness via the Box-Cox transformation. As a result, this provides a unified framework to simultaneously handle outlier identification and data transformation, two interrelated issues. We describe an Expectation-Maximization algorithm for parameter estimation along with transformation selection. We demonstrate the proposed methodology with three real data sets and simulation studies. Compared with a wealth of approaches including the skew-t mixture model, the proposed t mixture model with the Box-Cox transformation performs favorably in terms of accuracy in the assignment of observations, robustness against model misspecification, and selection of the number of components.

Topology-Aware Performance Optimization and Modeling of Adaptive Mesh Refinement Codes for Exascale

DOE PAGES

Chan, Cy P.; Bachan, John D.; Kenny, Joseph P.; ...

2017-01-26

Here, we introduce a topology-aware performance optimization and modeling workflow for AMR simulation that includes two new modeling tools, ProgrAMR and Mota Mapper, which interface with the BoxLib AMR framework and the SSTmacro network simulator. ProgrAMR allows us to generate and model the execution of task dependency graphs from high-level specifications of AMR-based applications, which we demonstrate by analyzing two example AMR-based multigrid solvers with varying degrees of asynchrony. Mota Mapper generates multiobjective, network topology-aware box mappings, which we apply to optimize the data layout for the example multigrid solvers. While the sensitivity of these solvers to layout and executionmore » strategy appears to be modest for balanced scenarios, the impact of better mapping algorithms can be significant when performance is highly constrained by network hop latency. Furthermore, we show that network latency in the multigrid bottom solve is the main contributing factor preventing good scaling on exascale-class machines.« less

Topology-Aware Performance Optimization and Modeling of Adaptive Mesh Refinement Codes for Exascale

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

Chan, Cy P.; Bachan, John D.; Kenny, Joseph P.

Here, we introduce a topology-aware performance optimization and modeling workflow for AMR simulation that includes two new modeling tools, ProgrAMR and Mota Mapper, which interface with the BoxLib AMR framework and the SSTmacro network simulator. ProgrAMR allows us to generate and model the execution of task dependency graphs from high-level specifications of AMR-based applications, which we demonstrate by analyzing two example AMR-based multigrid solvers with varying degrees of asynchrony. Mota Mapper generates multiobjective, network topology-aware box mappings, which we apply to optimize the data layout for the example multigrid solvers. While the sensitivity of these solvers to layout and executionmore » strategy appears to be modest for balanced scenarios, the impact of better mapping algorithms can be significant when performance is highly constrained by network hop latency. Furthermore, we show that network latency in the multigrid bottom solve is the main contributing factor preventing good scaling on exascale-class machines.« less

Flow model for open-channel reach or network

USGS Publications Warehouse

Schaffranek, R.W.

1987-01-01

Formulation of a one-dimensional model for simulating unsteady flow in a single open-channel reach or in a network of interconnected channels is presented. The model is both general and flexible in that it can be used to simulate a wide range of flow conditions for various channel configurations. It is based on a four-point (box), implicit, finite-difference approximation of the governing nonlinear flow equations with user-definable weighting coefficients to permit varying the solution scheme from box-centered to fully forward. Unique transformation equations are formulated that permit correlation of the unknowns at the extremities of the channels, thereby reducing coefficient matrix and execution time requirements. Discharges and water-surface elevations computed at intermediate locations within a channel are determined following solution of the transformation equations. The matrix of transformation and boundary-condition equations is solved by Gauss elimination using maximum pivot strategy. Two diverse applications of the model are presented to illustrate its broad utility. (USGS)

Box-Cox Mixed Logit Model for Travel Behavior Analysis

NASA Astrophysics Data System (ADS)

Orro, Alfonso; Novales, Margarita; Benitez, Francisco G.

2010-09-01

To represent the behavior of travelers when they are deciding how they are going to get to their destination, discrete choice models, based on the random utility theory, have become one of the most widely used tools. The field in which these models were developed was halfway between econometrics and transport engineering, although the latter now constitutes one of their principal areas of application. In the transport field, they have mainly been applied to mode choice, but also to the selection of destination, route, and other important decisions such as the vehicle ownership. In usual practice, the most frequently employed discrete choice models implement a fixed coefficient utility function that is linear in the parameters. The principal aim of this paper is to present the viability of specifying utility functions with random coefficients that are nonlinear in the parameters, in applications of discrete choice models to transport. Nonlinear specifications in the parameters were present in discrete choice theory at its outset, although they have seldom been used in practice until recently. The specification of random coefficients, however, began with the probit and the hedonic models in the 1970s, and, after a period of apparent little practical interest, has burgeoned into a field of intense activity in recent years with the new generation of mixed logit models. In this communication, we present a Box-Cox mixed logit model, original of the authors. It includes the estimation of the Box-Cox exponents in addition to the parameters of the random coefficients distribution. Probability of choose an alternative is an integral that will be calculated by simulation. The estimation of the model is carried out by maximizing the simulated log-likelihood of a sample of observed individual choices between alternatives. The differences between the predictions yielded by models that are inconsistent with real behavior have been studied with simulation experiments.

A class of Box-Cox transformation models for recurrent event data.

PubMed

Sun, Liuquan; Tong, Xingwei; Zhou, Xian

2011-04-01

In this article, we propose a class of Box-Cox transformation models for recurrent event data, which includes the proportional means models as special cases. The new model offers great flexibility in formulating the effects of covariates on the mean functions of counting processes while leaving the stochastic structure completely unspecified. For the inference on the proposed models, we apply a profile pseudo-partial likelihood method to estimate the model parameters via estimating equation approaches and establish large sample properties of the estimators and examine its performance in moderate-sized samples through simulation studies. In addition, some graphical and numerical procedures are presented for model checking. An example of application on a set of multiple-infection data taken from a clinic study on chronic granulomatous disease (CGD) is also illustrated.

Vibration signature analysis of multistage gear transmission

NASA Technical Reports Server (NTRS)

Choy, F. K.; Tu, Y. K.; Savage, M.; Townsend, D. P.

1989-01-01

An analysis is presented for multistage multimesh gear transmission systems. The analysis predicts the overall system dynamics and the transmissibility to the gear box or the enclosed structure. The modal synthesis approach of the analysis treats the uncoupled lateral/torsional model characteristics of each stage or component independently. The vibration signature analysis evaluates the global dynamics coupling in the system. The method synthesizes the interaction of each modal component or stage with the nonlinear gear mesh dynamics and the modal support geometry characteristics. The analysis simulates transient and steady state vibration events to determine the resulting torque variations, speeds, changes, rotor imbalances, and support gear box motion excitations. A vibration signature analysis examines the overall dynamic characteristics of the system, and the individual model component responses. The gear box vibration analysis also examines the spectral characteristics of the support system.

Spatial Pattern of Cell Damage in Tissue from Heavy Ions

NASA Technical Reports Server (NTRS)

Ponomarev, Artem L.; Huff, Janice L.; Cucinotta, Francis A.

2007-01-01

A new Monte Carlo algorithm was developed that can model passage of heavy ions in a tissue, and their action on the cellular matrix for 2- or 3-dimensional cases. The build-up of secondaries such as projectile fragments, target fragments, other light fragments, and delta-rays was simulated. Cells were modeled as a cell culture monolayer in one example, where the data were taken directly from microscopy (2-d cell matrix). A simple model of tissue was given as abstract spheres with close approximation to real cell geometries (3-d cell matrix), as well as a realistic model of tissue was proposed based on microscopy images. Image segmentation was used to identify cells in an irradiated cell culture monolayer, or slices of tissue. The cells were then inserted into the model box pixel by pixel. In the case of cell monolayers (2-d), the image size may exceed the modeled box size. Such image was is moved with respect to the box in order to sample as many cells as possible. In the case of the simple tissue (3-d), the tissue box is modeled with periodic boundary conditions, which extrapolate the technique to macroscopic volumes of tissue. For real tissue, specific spatial patterns for cell apoptosis and necrosis are expected. The cell patterns were modeled based on action cross sections for apoptosis and necrosis estimated based on BNL data, and other experimental data.

Estimating ICU bed capacity using discrete event simulation.

PubMed

Zhu, Zhecheng; Hen, Bee Hoon; Teow, Kiok Liang

2012-01-01

The intensive care unit (ICU) in a hospital caters for critically ill patients. The number of the ICU beds has a direct impact on many aspects of hospital performance. Lack of the ICU beds may cause ambulance diversion and surgery cancellation, while an excess of ICU beds may cause a waste of resources. This paper aims to develop a discrete event simulation (DES) model to help the healthcare service providers determine the proper ICU bed capacity which strikes the balance between service level and cost effectiveness. The DES model is developed to reflect the complex patient flow of the ICU system. Actual operational data, including emergency arrivals, elective arrivals and length of stay, are directly fed into the DES model to capture the variations in the system. The DES model is validated by open box test and black box test. The validated model is used to test two what-if scenarios which the healthcare service providers are interested in: the proper number of the ICU beds in service to meet the target rejection rate and the extra ICU beds in service needed to meet the demand growth. A 12-month period of actual operational data was collected from an ICU department with 13 ICU beds in service. Comparison between the simulation results and the actual situation shows that the DES model accurately captures the variations in the system, and the DES model is flexible to simulate various what-if scenarios. DES helps the healthcare service providers describe the current situation, and simulate the what-if scenarios for future planning.

Blast Load Simulator Experiments for Computational Model Validation Report 3

DTIC Science & Technology

2017-07-01

establish confidence in the results produced by the simulations. This report describes a set of replicate experiments in which a small, non - responding steel...designed to simulate blast waveforms for explosive yields up to 20,000 lb of TNT equivalent at a peak reflected pressure up to 80 psi and a peak...the pressure loading on a non - responding box-type structure at varying obliquities located in the flow of the BLS simulated blast environment for

Modeling and Simulation of Fleet Air Defense Systems Using EADSIM

DTIC Science & Technology

1993-06-01

LT DAVID VAN VELDHUIZEN PHILLIPS LABORATORY/WST 3550ABERDEEN AVE SE KIRTLAND AFB NM 87117-5776 85 PLESSEY POC: Paul Markwardt Addr: PLESSEY ELECTRONICS...LAIL, JR. Addr: PEO, GPALS ATTN SFAE-GPL-TMD-SI-B (LAIL) PO BOX 1500 HUNTSVILLE AL 35807-301 84 PHILLIPS LABORATORY POC: L. David Van Velclhuizen Addr...SHURE PO BOX 92957 EL SEGUNDO CA 90009-2957 107 TRW-HUNTSVILLE POC: Don Owens Addr: TRW 213 WYNN DRIVE ATTN DON OWENS HUNTSVILLE AL 35805 108 TRW

3D modelling of the flow of self-compacting concrete with or without steel fibres. Part II: L-box test and the assessment of fibre reorientation during the flow

NASA Astrophysics Data System (ADS)

Deeb, R.; Kulasegaram, S.; Karihaloo, B. L.

2014-12-01

The three-dimensional Lagrangian particle-based smooth particle hydrodynamics method described in Part I of this two-part paper is used to simulate the flow of self-compacting concrete (SCC) with and without steel fibres in the L-box configuration. As in Part I, the simulation of the SCC mixes without fibres emphasises the distribution of large aggregate particles of different sizes throughout the flow, whereas the simulation of high strength SCC mixes which contain steel fibres is focused on the distribution of fibres and their orientation during the flow. The capabilities of this methodology are validated by comparing the simulation results with the L-box test carried out in the laboratory. A simple method is developed to assess the reorientation and distribution of short steel fibres in self-compacting concrete mixes during the flow. The reorientation of the fibres during the flow is used to estimate the fibre orientation factor (FOF) in a cross section perpendicular to the principal direction of flow. This estimation procedure involves the number of fibres cut by the section and their inclination to the cutting plane. This is useful to determine the FOF in practical image analysis on cut sections.

Experimental and numerical study on thermal conductivity of partially saturated unconsolidated sands

NASA Astrophysics Data System (ADS)

Lee, Youngmin; Keehm, Youngseuk; Kim, Seong-Kyun; Shin, Sang Ho

2016-04-01

A class of problems in heat flow applications requires an understanding of how water saturation affects thermal conductivity in the shallow subsurface. We conducted a series of experiments using a sand box to evaluate thermal conductivity (TC) of partially saturated unconsolidated sands under varying water saturation (Sw). We first saturated sands fully with water and varied water saturation by drainage through the bottom of the sand box. Five water-content sensors were integrated vertically into the sand box to monitor water saturation changes and a needle probe was embedded to measure thermal conductivity of partially saturated sands. The experimental result showed that thermal conductivity decreases from 2.5 W/mK for fully saturated sands to 0.7 W/mK when water saturation is 5%. We found that the decreasing trend is quite non-linear: highly sensitive at very high and low water saturations. However, the boundary effects on the top and the bottom of the sand box seemed to be responsible for this high nonlinearity. We also found that the determination of water saturation is quite important: the saturation by averaging values from all five sensors and that from the sensor at the center position, showed quite different trends in the TC-Sw domain. In parallel, we conducted a pore-scale numerical modeling, which consists of the steady-state two-phase Lattice-Boltzmann simulator and FEM thermal conduction simulator on digital pore geometry of sand aggregation. The simulation results showed a monotonous decreasing trend, and are reasonably well matched with experimental data when using average water saturations. We concluded that thermal conductivity would decrease smoothly as water saturation decreases if we can exclude boundary effects. However, in dynamic conditions, i.e. imbibition or drainage, the thermal conductivity might show hysteresis, which can be investigated with pore-scale numerical modeling with unsteady-state two-phase flow simulators in our future work.

Rocks in a Box: A Three-Point Problem.

ERIC Educational Resources Information Center

Leyden, Michael B.

1981-01-01

Describes a simulation drilling core activity involving the use of a physical model from which students gather data and solve a three-point problem to determine the strike and dip of a buried stratum. Includes descriptions of model making, data plots, and additional problems involving strike and dip. (DS)

Polar Ozone Loss Rates: Comparison Of Match Observations With Simulations Of 3-D Chemical Transport Model And Box Model

NASA Astrophysics Data System (ADS)

Tripathi, O. P.; Godin-Beekmann, S.; Lefevre, F.; Marchand, M.; Pazmino, A.; Hauchecorne, A.

2005-12-01

Model simulations of ozone loss rates during recent arctic and Antarctic winters are compared with the observed ozone loss rates from the match technique. Arctic winters 1994/1995, 1999/2000, 2002/2003 and the Antarctic winter 2003 were considered for the analysis. We use a high resolution chemical transport model MIMOSA-CHIM and REPROBUS box model for the calculation of ozone loss rates. Trajectory model calculations show that the ozone loss rates are dependent on the initialization fields. On the one hand when chemical fields are initialized by UCAM (University of Cambridge SLIMCAT model simulated fields) the loss rates were underestimated by a factor of two whereas on the other hand when it is initialized by UL (University of Leeds) fields the model loss rates are in a very good agreement with match loss rates at lower levels. The study shows a very good agreement between MIMOSA-CHIM simulation and match observation in 1999/2000 winter at both levels, 450 and 500 K, except slight underestimation in March at 500 K. But in January we have a very good agreement. This is also true for 1994/1995 when we consider simulated ozone loss rate in view of the ECMWF wind deficiency assuming that match observations were not made on isolated trajectories. Sensitivity tests, by changing JCl2O2 value, particle number density and heating rates, performed for the arctic winter 1999/2000 shows that we need to improve our understanding of particle number density and heating rate calculation mechanism. Burkholder JCl2O2 has improved the comparison of MIMOSA-CHIM model results with observations (Tripathi et al., 2005). In the same study the comparison results were shown to improved by changing heating rates and number density through NAT particle sedimentation.

Comparison of 3D dynamic virtual model to link segment model for estimation of net L4/L5 reaction moments during lifting.

PubMed

Abdoli-Eramaki, Mohammad; Stevenson, Joan M; Agnew, Michael J; Kamalzadeh, Amin

2009-04-01

The purpose of this study was to validate a 3D dynamic virtual model for lifting tasks against a validated link segment model (LSM). A face validation study was conducted by collecting x, y, z coordinate data and using them in both virtual and LSM models. An upper body virtual model was needed to calculate the 3D torques about human joints for use in simulated lifting styles and to estimate the effect of external mechanical devices on human body. Firstly, the model had to be validated to be sure it provided accurate estimates of 3D moments in comparison to a previously validated LSM. Three synchronised Fastrak units with nine sensors were used to record data from one male subject who completed dynamic box lifting under 27 different load conditions (box weights (3), lifting techniques (3) and rotations (3)). The external moments about three axes of L4/L5 were compared for both models. A pressure switch on the box was used to denote the start and end of the lift. An excellent agreement [image omitted] was found between the two models for dynamic lifting tasks, especially for larger moments in flexion and extension. This virtual model was considered valid for use in a complete simulation of the upper body skeletal system. This biomechanical virtual model of the musculoskeletal system can be used by researchers and practitioners to give a better tool to study the causes of LBP and the effect of intervention strategies, by permitting the researcher to see and control a virtual subject's motions.

POD Model Reconstruction for Gray-Box Fault Detection

NASA Technical Reports Server (NTRS)

Park, Han; Zak, Michail

2007-01-01

Proper orthogonal decomposition (POD) is the mathematical basis of a method of constructing low-order mathematical models for the "gray-box" fault-detection algorithm that is a component of a diagnostic system known as beacon-based exception analysis for multi-missions (BEAM). POD has been successfully applied in reducing computational complexity by generating simple models that can be used for control and simulation for complex systems such as fluid flows. In the present application to BEAM, POD brings the same benefits to automated diagnosis. BEAM is a method of real-time or offline, automated diagnosis of a complex dynamic system.The gray-box approach makes it possible to utilize incomplete or approximate knowledge of the dynamics of the system that one seeks to diagnose. In the gray-box approach, a deterministic model of the system is used to filter a time series of system sensor data to remove the deterministic components of the time series from further examination. What is left after the filtering operation is a time series of residual quantities that represent the unknown (or at least unmodeled) aspects of the behavior of the system. Stochastic modeling techniques are then applied to the residual time series. The procedure for detecting abnormal behavior of the system then becomes one of looking for statistical differences between the residual time series and the predictions of the stochastic model.

[Virtual reality simulation training in gynecology: review and perspectives].

PubMed

Ricard-Gauthier, Dominique; Popescu, Silvia; Benmohamed, Naida; Petignat, Patrick; Dubuisson, Jean

2016-10-26

Laparoscopic simulation has rapidly become an important tool for learning and acquiring technical skills in surgery. It is based on two different complementary pedagogic tools : the box model trainer and the virtual reality simulator. The virtual reality simulator has shown its efficiency by improving surgical skills, decreasing operating time, improving economy of movements and improving self-confidence. The main objective of this tool is the opportunity to easily organize a regular, structured and uniformed training program enabling an automated individualized feedback.

Application of a Three-Layer Photochemical Box Model in an Athens Street Canyon.

PubMed

Proyou, Athena G; Ziomas, Loannis C; Stathopoulos, Antony

1998-05-01

The aim of this paper is to show that a photochemical box model could describe the air pollution diurnal profiles within a typical street canyon in the city of Athens. As sophisticated three-dimensional dispersion models are computationally expensive and they cannot serve to simulate pollution levels in the scale of an urban street canyon, a suitably modified three-layer photochemical box model was applied. A street canyon of Athens with heavy traffic was chosen to apply the aforementioned model. The model was used to calculate pollutant concentrations during two days with meteorological conditions favoring pollutant accumulation. Road traffic emissions were calculated based on existing traffic load measurements. Meteorological data, as well as various pollutant concentrations, in order to compare with the model results, were provided by available measurements. The calculated concentrations were found to be in good agreement with measured concentration levels and show that, when traffic load and traffic composition data are available, this model can be used to predict pollution episodes. It is noteworthy that high concentrations persisted, even after additional traffic restriction measures were taken on the second day because of the high pollution levels.

Simulation of Thin Film Equations on an Eye-Shaped Domain with Moving Boundary

NASA Astrophysics Data System (ADS)

Brosch, Joseph; Driscoll, Tobin; Braun, Richard

During a normal eye blink, the upper lid moves, and during the upstroke the lid paints a thin tear film over the exposed corneal and conjunctival surfaces. This thin tear film may be modeled by a nonlinear fourth-order PDE derived from lubrication theory. A major stumbling block in the numerical simulation of this model is to include both the geometry of the eye and the movement of the eyelid. Using a pair of orthogonal and conformal maps, we transform a computational box into a rough representation of a human eye where we proceed to simulate the thin tear film equations. Although we give up some realism, we gain spectrally accurate numerical methods on the computational box. We have applied this method to the heat equation on the blinking domain with both Dirichlet and no-flux boundary conditions, in each case demonstrating at least 10 digits of accuracy.. We are able to perform these simulations very quickly (generally in under a minute) using a desktop version of MATLAB. This project was supported by Grant 1022706 (R.J.B., T.A.D., J.K.B.) from the NSF.

Analysis Of Dynamic Interactions Between Solar Array Simulators And Spacecraft Power Conditioning And Distribution Units

NASA Astrophysics Data System (ADS)

Valdivia, V.; Barrado, A.; Lazaro, A.; Rueda, P.; Tonicello, F.; Fernandez, A.; Mourra, O.

2011-10-01

Solar array simulators (SASs) are hardware devices, commonly applied instead of actual solar arrays (SAs) during the design process of spacecrafts power conditioning and distribution units (PCDUs), and during spacecrafts assembly integration and tests. However, the dynamic responses between SASs and actual SAs are usually different. This fact plays an important role, since the dynamic response of the SAS may influence significantly the dynamic behaviour of the PCDU under certain conditions, even leading to instability. This paper deals with the dynamic interactions between SASs and PCDUs. Several methods for dynamic characterization of the SASs are discussed, and the response of commercial SASs widely applied in the space industry is compared to that of actual SAs. After that, the interactions are experimentally analyzed by using a boost converter connected to the aforementioned SASs, thus demonstrating their critical importance. The interactions are first tackled analytically by means of small-signal models, and finally a black-box modelling method of SASs is proposed as a useful tool to analyze the interactions by means of simulation. The capabilities of both the analytical method and the black- box model to predict the interactions are demonstrated.

Fault detection method for railway wheel flat using an adaptive multiscale morphological filter

NASA Astrophysics Data System (ADS)

Li, Yifan; Zuo, Ming J.; Lin, Jianhui; Liu, Jianxin

2017-02-01

This study explores the capacity of the morphology analysis for railway wheel flat fault detection. A dynamic model of vehicle systems with 56 degrees of freedom was set up along with a wheel flat model to calculate the dynamic responses of axle box. The vehicle axle box vibration signal is complicated because it not only contains the information of wheel defect, but also includes track condition information. Thus, how to extract the influential features of wheels from strong background noise effectively is a typical key issue for railway wheel fault detection. In this paper, an algorithm for adaptive multiscale morphological filtering (AMMF) was proposed, and its effect was evaluated by a simulated signal. And then this algorithm was employed to study the axle box vibration caused by wheel flats, as well as the influence of track irregularity and vehicle running speed on diagnosis results. Finally, the effectiveness of the proposed method was verified by bench testing. Research results demonstrate that the AMMF extracts the influential characteristic of axle box vibration signals effectively and can diagnose wheel flat faults in real time.

Evaluating indoor exposure modeling alternatives for LCA: A case study in the vehicle repair industry

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

Demou, Evangelia; Hellweg, Stefanie; Wilson, Michael P.

2009-05-01

We evaluated three exposure models with data obtained from measurements among workers who use"aerosol" solvent products in the vehicle repair industry and with field experiments using these products to simulate the same exposure conditions. The three exposure models were the: 1) homogeneously-mixed-one-box model, 2) multi-zone model, and 3) eddy-diffusion model. Temporally differentiated real-time breathing zone volatile organic compound (VOC) concentration measurements, integrated far-field area samples, and simulated experiments were used in estimating parameters, such as emission rates, diffusivity, and near-field dimensions. We assessed differences in model input requirements and their efficacy for predictive modeling. The One-box model was not ablemore » to resemble the temporal profile of exposure concentrations, but it performed well concerning time-weighted exposure over extended time periods. However, this model required an adjustment for spatial concentration gradients. Multi-zone models and diffusion-models may solve this problem. However, we found that the reliable use of both these models requires extensive field data to appropriately define pivotal parameters such as diffusivity or near-field dimensions. We conclude that it is difficult to apply these models for predicting VOC exposures in the workplace. However, for comparative exposure scenarios in life-cycle assessment they may be useful.« less

FVS out of the box - assembly required

Treesearch

Don Vandendriesche

2010-01-01

The Forest Vegetation Simulator (FVS) is a prominent growth and yield model used for forecasting stand dynamics. However, users need to be aware of model behavior regarding stocking density, tree senescence, and understory recruitment; otherwise over long projections, FVS tends to concentrate substantial growth on few survivor trees. If the intent is to forecast...

Stochastic modelling of temperatures affecting the in situ performance of a solar-assisted heat pump: The multivariate approach and physical interpretation

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

Loveday, D.L.; Craggs, C.

Box-Jenkins-based multivariate stochastic modeling is carried out using data recorded from a domestic heating system. The system comprises an air-source heat pump sited in the roof space of a house, solar assistance being provided by the conventional tile roof acting as a radiation absorber. Multivariate models are presented which illustrate the time-dependent relationships between three air temperatures - at external ambient, at entry to, and at exit from, the heat pump evaporator. Using a deterministic modeling approach, physical interpretations are placed on the results of the multivariate technique. It is concluded that the multivariate Box-Jenkins approach is a suitable techniquemore » for building thermal analysis. Application to multivariate Box-Jenkins approach is a suitable technique for building thermal analysis. Application to multivariate model-based control is discussed, with particular reference to building energy management systems. It is further concluded that stochastic modeling of data drawn from a short monitoring period offers a means of retrofitting an advanced model-based control system in existing buildings, which could be used to optimize energy savings. An approach to system simulation is suggested.« less

An asymptotically exact reduced PDE model for the magnetorotational instability: derivation and numerical simulations

NASA Astrophysics Data System (ADS)

Jamroz, Ben; Julien, Keith; Knobloch, Edgar

2008-12-01

Taking advantage of disparate spatio-temporal scales relevant to astrophysics and laboratory experiments, we derive asymptotically exact reduced partial differential equation models for the magnetorotational instability. These models extend recent single-mode formulations leading to saturation in the presence of weak dissipation, and are characterized by a back-reaction on the imposed shear. Numerical simulations performed for a broad class of initial conditions indicate an initial phase of growth dominated by the optimal (fastest growing) magnetorotational instability fingering mode, followed by a vertical coarsening to a box-filling mode.

Simulation of Satellite, Airborne and Terrestrial LiDAR with DART (I):Waveform Simulation with Quasi-Monte Carlo Ray Tracing

NASA Technical Reports Server (NTRS)

Gastellu-Etchegorry, Jean-Philippe; Yin, Tiangang; Lauret, Nicolas; Grau, Eloi; Rubio, Jeremy; Cook, Bruce D.; Morton, Douglas C.; Sun, Guoqing

2016-01-01

Light Detection And Ranging (LiDAR) provides unique data on the 3-D structure of atmosphere constituents and the Earth's surface. Simulating LiDAR returns for different laser technologies and Earth scenes is fundamental for evaluating and interpreting signal and noise in LiDAR data. Different types of models are capable of simulating LiDAR waveforms of Earth surfaces. Semi-empirical and geometric models can be imprecise because they rely on simplified simulations of Earth surfaces and light interaction mechanisms. On the other hand, Monte Carlo ray tracing (MCRT) models are potentially accurate but require long computational time. Here, we present a new LiDAR waveform simulation tool that is based on the introduction of a quasi-Monte Carlo ray tracing approach in the Discrete Anisotropic Radiative Transfer (DART) model. Two new approaches, the so-called "box method" and "Ray Carlo method", are implemented to provide robust and accurate simulations of LiDAR waveforms for any landscape, atmosphere and LiDAR sensor configuration (view direction, footprint size, pulse characteristics, etc.). The box method accelerates the selection of the scattering direction of a photon in the presence of scatterers with non-invertible phase function. The Ray Carlo method brings traditional ray-tracking into MCRT simulation, which makes computational time independent of LiDAR field of view (FOV) and reception solid angle. Both methods are fast enough for simulating multi-pulse acquisition. Sensitivity studies with various landscapes and atmosphere constituents are presented, and the simulated LiDAR signals compare favorably with their associated reflectance images and Laser Vegetation Imaging Sensor (LVIS) waveforms. The LiDAR module is fully integrated into DART, enabling more detailed simulations of LiDAR sensitivity to specific scene elements (e.g., atmospheric aerosols, leaf area, branches, or topography) and sensor configuration for airborne or satellite LiDAR sensors.

A size-composition resolved aerosol model for simulating the dynamics of externally mixed particles: SCRAM (v 1.0)

NASA Astrophysics Data System (ADS)

Zhu, S.; Sartelet, K. N.; Seigneur, C.

2015-06-01

The Size-Composition Resolved Aerosol Model (SCRAM) for simulating the dynamics of externally mixed atmospheric particles is presented. This new model classifies aerosols by both composition and size, based on a comprehensive combination of all chemical species and their mass-fraction sections. All three main processes involved in aerosol dynamics (coagulation, condensation/evaporation and nucleation) are included. The model is first validated by comparison with a reference solution and with results of simulations using internally mixed particles. The degree of mixing of particles is investigated in a box model simulation using data representative of air pollution in Greater Paris. The relative influence on the mixing state of the different aerosol processes (condensation/evaporation, coagulation) and of the algorithm used to model condensation/evaporation (bulk equilibrium, dynamic) is studied.

Stochastic optimization of GeantV code by use of genetic algorithms

DOE PAGES

Amadio, G.; Apostolakis, J.; Bandieramonte, M.; ...

2017-10-01

GeantV is a complex system based on the interaction of different modules needed for detector simulation, which include transport of particles in fields, physics models simulating their interactions with matter and a geometrical modeler library for describing the detector and locating the particles and computing the path length to the current volume boundary. The GeantV project is recasting the classical simulation approach to get maximum benefit from SIMD/MIMD computational architectures and highly massive parallel systems. This involves finding the appropriate balance between several aspects influencing computational performance (floating-point performance, usage of off-chip memory bandwidth, specification of cache hierarchy, etc.) andmore » handling a large number of program parameters that have to be optimized to achieve the best simulation throughput. This optimization task can be treated as a black-box optimization problem, which requires searching the optimum set of parameters using only point-wise function evaluations. Here, the goal of this study is to provide a mechanism for optimizing complex systems (high energy physics particle transport simulations) with the help of genetic algorithms and evolution strategies as tuning procedures for massive parallel simulations. One of the described approaches is based on introducing a specific multivariate analysis operator that could be used in case of resource expensive or time consuming evaluations of fitness functions, in order to speed-up the convergence of the black-box optimization problem.« less

Stochastic optimization of GeantV code by use of genetic algorithms

NASA Astrophysics Data System (ADS)

Amadio, G.; Apostolakis, J.; Bandieramonte, M.; Behera, S. P.; Brun, R.; Canal, P.; Carminati, F.; Cosmo, G.; Duhem, L.; Elvira, D.; Folger, G.; Gheata, A.; Gheata, M.; Goulas, I.; Hariri, F.; Jun, S. Y.; Konstantinov, D.; Kumawat, H.; Ivantchenko, V.; Lima, G.; Nikitina, T.; Novak, M.; Pokorski, W.; Ribon, A.; Seghal, R.; Shadura, O.; Vallecorsa, S.; Wenzel, S.

2017-10-01

GeantV is a complex system based on the interaction of different modules needed for detector simulation, which include transport of particles in fields, physics models simulating their interactions with matter and a geometrical modeler library for describing the detector and locating the particles and computing the path length to the current volume boundary. The GeantV project is recasting the classical simulation approach to get maximum benefit from SIMD/MIMD computational architectures and highly massive parallel systems. This involves finding the appropriate balance between several aspects influencing computational performance (floating-point performance, usage of off-chip memory bandwidth, specification of cache hierarchy, etc.) and handling a large number of program parameters that have to be optimized to achieve the best simulation throughput. This optimization task can be treated as a black-box optimization problem, which requires searching the optimum set of parameters using only point-wise function evaluations. The goal of this study is to provide a mechanism for optimizing complex systems (high energy physics particle transport simulations) with the help of genetic algorithms and evolution strategies as tuning procedures for massive parallel simulations. One of the described approaches is based on introducing a specific multivariate analysis operator that could be used in case of resource expensive or time consuming evaluations of fitness functions, in order to speed-up the convergence of the black-box optimization problem.

Stochastic optimization of GeantV code by use of genetic algorithms

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

Amadio, G.; Apostolakis, J.; Bandieramonte, M.

GeantV is a complex system based on the interaction of different modules needed for detector simulation, which include transport of particles in fields, physics models simulating their interactions with matter and a geometrical modeler library for describing the detector and locating the particles and computing the path length to the current volume boundary. The GeantV project is recasting the classical simulation approach to get maximum benefit from SIMD/MIMD computational architectures and highly massive parallel systems. This involves finding the appropriate balance between several aspects influencing computational performance (floating-point performance, usage of off-chip memory bandwidth, specification of cache hierarchy, etc.) andmore » handling a large number of program parameters that have to be optimized to achieve the best simulation throughput. This optimization task can be treated as a black-box optimization problem, which requires searching the optimum set of parameters using only point-wise function evaluations. Here, the goal of this study is to provide a mechanism for optimizing complex systems (high energy physics particle transport simulations) with the help of genetic algorithms and evolution strategies as tuning procedures for massive parallel simulations. One of the described approaches is based on introducing a specific multivariate analysis operator that could be used in case of resource expensive or time consuming evaluations of fitness functions, in order to speed-up the convergence of the black-box optimization problem.« less

[Value of laparoscopic virtual reality simulator in laparoscopic suture ability training of catechumen].

PubMed

Cai, Jian-liang; Zhang, Yi; Sun, Guo-feng; Li, Ning-chen; Zhang, Xiang-hua; Na, Yan-qun

2012-12-01

To investigate the value of laparoscopic virtual reality simulator in laparoscopic suture ability training of catechumen. After finishing the virtual reality training of basic laparoscopic skills, 26 catechumen were divided randomly into 2 groups, one group undertook advanced laparoscopic skill (suture technique) training with laparoscopic virtual reality simulator (virtual group), another used laparoscopic box trainer (box group). Using our homemade simulations, before grouping and after training, every trainee performed nephropyeloureterostomy under laparoscopy, the running time, anastomosis quality and proficiency were recorded and assessed. For virtual group, the running time, anastomosis quality and proficiency scores before grouping were (98 ± 11) minutes, 3.20 ± 0.41, 3.47 ± 0.64, respectively, after training were (53 ± 8) minutes, 6.87 ± 0.74, 6.33 ± 0.82, respectively, all the differences were statistically significant (all P < 0.01). In box group, before grouping were (98 ± 10) minutes, 3.17 ± 0.39, 3.42 ± 0.67, respectively, after training were (52 ± 9) minutes, 6.08 ± 0.90, 6.33 ± 0.78, respectively, all the differences also were statistically significant (all P < 0.01). After training, the running time and proficiency scores of virtual group were similar to box group (all P > 0.05), however, anstomosis quality scores in virtual group were higher than in box group (P = 0.02). The laparoscopic virtual reality simulator is better than traditional box trainer in advanced laparoscopic suture ability training of catechumen.

Laparoscopic virtual reality simulator and box trainer in gynecology.

PubMed

Akdemir, Ali; Sendağ, Fatih; Oztekin, Mehmet K

2014-05-01

To investigate whether a virtual reality simulator (LapSim) and traditional box trainer are effective tools for the acquisition of basic laparoscopic skills, and whether the LapSim is superior to the box trainer in surgical education. In a study at Ege University School of Medicine, Izmir, Turkey, between September 2008 and March 2013, 40 first- and second-year residents were randomized to train via the LapSim or box trainer for 4 weeks, and 20 senior residents were allocated to a control group. All 3 groups performed laparoscopic bilateral tubal ligation. Video records of each operation were assessed via the general rating scale of the Objective Structured Assessment of Laparoscopic Salpingectomy and by operation time in seconds. Compared with the control group, the LapSim and box trainer groups performed significantly better in total score (P<0.01 and P<0.01, respectively) and time (P=0.03 and P=0.01, respectively). There were no differences between the LapSim and box trainer groups. Novice residents who trained on a LapSim or box trainer performed better live laparoscopies than residents who trained via standard clinical surgical education. Training with a virtual reality simulator or box trainer should be considered before actual laparoscopic procedures are carried out. Copyright © 2014 International Federation of Gynecology and Obstetrics. Published by Elsevier Ireland Ltd. All rights reserved.

Initial mass function of planetesimals formed by the streaming instability

NASA Astrophysics Data System (ADS)

Schäfer, Urs; Yang, Chao-Chin; Johansen, Anders

2017-01-01

The streaming instability is a mechanism to concentrate solid particles into overdense filaments that undergo gravitational collapse and form planetesimals. However, it remains unclear how the initial mass function of these planetesimals depends on the box dimensions of numerical simulations. To resolve this, we perform simulations of planetesimal formation with the largest box dimensions to date, allowing planetesimals to form simultaneously in multiple filaments that can only emerge within such large simulation boxes. In our simulations, planetesimals with sizes between 80 km and several hundred kilometers form. We find that a power law with a rather shallow exponential cutoff at the high-mass end represents the cumulative birth mass function better than an integrated power law. The steepness of the exponential cutoff is largely independent of box dimensions and resolution, while the exponent of the power law is not constrained at the resolutions we employ. Moreover, we find that the characteristic mass scale of the exponential cutoff correlates with the mass budget in each filament. Together with previous studies of high-resolution simulations with small box domains, our results therefore imply that the cumulative birth mass function of planetesimals is consistent with an exponentially tapered power law with a power-law exponent of approximately -1.6 and a steepness of the exponential cutoff in the range of 0.3-0.4.

Scales of variability of black carbon plumes and their dependence on resolution of ECHAM6-HAM

NASA Astrophysics Data System (ADS)

Weigum, Natalie; Stier, Philip; Schutgens, Nick; Kipling, Zak

2015-04-01

Prediction of the aerosol effect on climate depends on the ability of three-dimensional numerical models to accurately estimate aerosol properties. However, a limitation of traditional grid-based models is their inability to resolve variability on scales smaller than a grid box. Past research has shown that significant aerosol variability exists on scales smaller than these grid-boxes, which can lead to discrepancies between observations and aerosol models. The aim of this study is to understand how a global climate model's (GCM) inability to resolve sub-grid scale variability affects simulations of important aerosol features. This problem is addressed by comparing observed black carbon (BC) plume scales from the HIPPO aircraft campaign to those simulated by ECHAM-HAM GCM, and testing how model resolution affects these scales. This study additionally investigates how model resolution affects BC variability in remote and near-source regions. These issues are examined using three different approaches: comparison of observed and simulated along-flight-track plume scales, two-dimensional autocorrelation analysis, and 3-dimensional plume analysis. We find that the degree to which GCMs resolve variability can have a significant impact on the scales of BC plumes, and it is important for models to capture the scales of aerosol plume structures, which account for a large degree of aerosol variability. In this presentation, we will provide further results from the three analysis techniques along with a summary of the implication of these results on future aerosol model development.

Scattering and Emission from Inhomogeneous Vegetation Canopy and Alien Target by Using Three-Dimensional Vector Radiative Transfer (3D-VRT) Equation

NASA Astrophysics Data System (ADS)

Jin, Ya-Qiu; Liang, Zichang

2005-01-01

To solve 3D-VRT equation for the model of spatially inhomogeneous scatter media, the finite enclosure of the scatter media is geometrically divided, in both the vertical z and horizontal (x,y) directions, to form very thin multi-boxes. The zero-th order emission, first-order Mueller matrix of each thin box and an iterative approach of high-order radiative transfer are applied to deriving high-order scattering and emission of whole inhomogeneous scatter media. Numerical results of polarized brightness temperature at microwave frequency and under different radiometer's resolutions from inhomogeneous scatter model such as vegetation canopy and embedded alien target are simulated and discussed.

Buckling and Post-Buckling Behaviors of a Variable Stiffness Composite Laminated Wing Box Structure

NASA Astrophysics Data System (ADS)

Wang, Peiyan; Huang, Xinting; Wang, Zhongnan; Geng, Xiaoliang; Wang, Yuansheng

2018-04-01

The buckling and post-buckling behaviors of variable stiffness composite laminates (VSCL) with curvilinear fibers were investigated and compared with constant stiffness composite laminates (CSCL) with straight fibers. A VSCL box structure was evaluated under a pure bending moment. The results of the comparative test showed that the critical buckling load of the VSCL box was approximately 3% higher than that of the CSCL box. However, the post-buckling load-bearing capacity was similar due to the layup angle and the immature status of the material processing technology. The properties of the VSCL and CSCL boxes under a pure bending moment were simulated using the Hashin criterion and cohesive interface elements. The simulation results are consistent with the experimental results in stiffness, critical buckling load and failure modes but not in post-buckling load capacity. The results of the experiment, the simulation and laminated plate theory show that VSCL greatly improves the critical buckling load but has little influence on the post-buckling load-bearing capacity.

Modelling the Krebs cycle and oxidative phosphorylation.

PubMed

Korla, Kalyani; Mitra, Chanchal K

2014-01-01

The Krebs cycle and oxidative phosphorylation are the two most important sets of reactions in a eukaryotic cell that meet the major part of the total energy demands of a cell. In this paper, we present a computer simulation of the coupled reactions using open source tools for simulation. We also show that it is possible to model the Krebs cycle with a simple black box with a few inputs and outputs. However, the kinetics of the internal processes has been modelled using numerical tools. We also show that the Krebs cycle and oxidative phosphorylation together can be combined in a similar fashion - a black box with a few inputs and outputs. The Octave script is flexible and customisable for any chosen set-up for this model. In several cases, we had no explicit idea of the underlying reaction mechanism and the rate determining steps involved, and we have used the stoichiometric equations that can be easily changed as and when more detailed information is obtained. The script includes the feedback regulation of the various enzymes of the Krebs cycle. For the electron transport chain, the pH gradient across the membrane is an essential regulator of the kinetics and this has been modelled empirically but fully consistent with experimental results. The initial conditions can be very easily changed and the simulation is potentially very useful in a number of cases of clinical importance.

The Multi-SAG project: filling the MultiDark simulations with semi-analytic galaxies

NASA Astrophysics Data System (ADS)

Vega-Martínez, C. A.; Cora, S. A.; Padilla, N. D.; Muñoz Arancibia, A. M.; Orsi, A. A.; Ruiz, A. N.

2016-08-01

The semi-analytical model sag is a code of galaxy formation and evolution which is applied to halo catalogs and merger trees extracted from cosmological -body simulations of dark matter. This contribution describes the project of constructing a catalog of simulated galaxies by adapting and applying the model sag over two dark matter simulations of the spanish MultiDark Project publicly available. Those simulations have particles, each, in boxes with sizes of 1000 Mpc and 400 Mpc respectively with Planck cosmological parameters. They cover a large range of masses and have halo mass resolutions of , therefore each simulation is able to produce more than 150 millions of simulated galaxies. A detailed description of the method is explained, and the first statistical results are shown.

A laparoscopic simulator – maybe it is worth making it yourself

PubMed Central

Piotrowski, Piotr; Jędrzejczyk, Adam; Pawełczak, Dariusz; Pasieka, Zbigniew

2014-01-01

Introduction Laparoscopic trainers have gained recognition for improving laparoscopic surgery skills and preparing for operations on humans. Unfortunately, due to their high price, commercial simulators are hard to obtain, especially for young surgeons in small medical centers. The solution might be for them to construct a device by themselves. Aim To make a relatively cheap and easy to construct laparoscopic trainer for residents who wish to develop their skills at home. Material and methods Two laparoscopic simulators were designed and constructed: 1) a box model with an optical system based on two parallel mirrors, 2) a box model with an HD webcam, a light source consisting of LED diodes placed on a camera casing, and a modeling servo between the webcam and aluminum pipe to allow electronic adjustment of the optical axis. Results The two self-constructed simulators were found to be effective training devices, the total cost of parts for each not exceeding $100. Advice is also given for future constructors. Conclusions Home made trainers are accessible to any personal budget and can be constructed with a minimum of practical skill. They allow more frequent practice at home, outside the venue and hours of surgical departments. What is more, home made trainers have been shown to be comparable to commercial trainers in facilitating the acquisition of basic laparoscopic skills. PMID:25337161

Migration of DEHP from plastic to food simulants under microwave heating

NASA Astrophysics Data System (ADS)

Zhu, X.; Li, F.; Qiu, Z. Z.; Huang, J. W.

2017-05-01

The migration of plasticizer DEHP from the plastic products (4 kinds of commonly used plastic food containers under microwave heating: plastic wrap, food bags, ordinary plastic boxes, microwave special plastic boxes) through food contact materials to food simulants (isooctane, 10% ethanol-water solution (v/v), 3% acetic acid-water solution (w/w) and distilled water) was studied under microwave heating (power levels of 400 W). The results shows that the DEHP mobility increases with the increase of microwave heating time, DEHP mobility in isooctane and 3% acetic acid-water solution (w/w) is significantly greater than in 10% ethanol-water solution (v/v) and distilled water; the order of DEHP mobility in isooctane is plastic wrap>food bag>common plastic box>microwave-safe plastic box, while in 3% acetic acid (w/w), the order is food bag>common plastic box>microwave-safe plastic box>plastic wrap.

Evaluation of Containment Boxes as a Fire Mitigation Method in Elevated Oxygen Conditions

NASA Technical Reports Server (NTRS)

Juarez, Alfredo; Harper, Susana; Perez, Horacio

2016-01-01

NASA performed testing to evaluate the efficacy of fire containment boxes without forced ventilation. Configurational flammability testing was performed on a simulation avionics box replicating critical design features and filled with materials possessing representative flammability characteristics. This paper discusses the box's ability, under simulated end-use conditions, to inhibit the propagation of combustion to surrounding materials. Analysis was also performed to evaluate the potential for the fire containment box to serve as an overheat/ignition source to temperature sensitive equipment (such as items with lithium-ion batteries). Unrealistically severe combustion scenarios were used as a means to better understand the fire containment mechanism. These scenarios were achieved by utilizing materials/fuels not typically used in space vehicles due to flammability concerns. Oxygen depletion, during combustion within the fire containment boxes, drove self-extinguishment and proved an effective method of fire containment

[The design of heat dissipation of the field low temperature box for storage and transportation].

PubMed

Wei, Jiancang; Suin, Jianjun; Wu, Jian

2013-02-01

Because of the compact structure of the field low temperature box for storage and transportation, which is due to the same small space where the compressor, the condenser, the control circuit, the battery and the power supply device are all placed in, the design for heat dissipation and ventilation is of critical importance for the stability and reliability of the box. Several design schemes of the heat dissipation design of the box were simulated using the FLOEFD hot fluid analysis software in this study. Different distributions of the temperature field in every design scheme were constructed intimately in the present study. It is well concluded that according to the result of the simulation analysis, the optimal heat dissipation design is decent for the field low temperature box for storage and transportation, and the box can operate smoothly for a long time using the results of the design.

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.

Machine learning of atmospheric chemistry. Applications to a global chemistry transport model.

NASA Astrophysics Data System (ADS)

Evans, M. J.; Keller, C. A.

2017-12-01

Atmospheric chemistry is central to many environmental issues such as air pollution, climate change, and stratospheric ozone loss. Chemistry Transport Models (CTM) are a central tool for understanding these issues, whether for research or for forecasting. These models split the atmosphere in a large number of grid-boxes and consider the emission of compounds into these boxes and their subsequent transport, deposition, and chemical processing. The chemistry is represented through a series of simultaneous ordinary differential equations, one for each compound. Given the difference in life-times between the chemical compounds (mili-seconds for O(1D) to years for CH4) these equations are numerically stiff and solving them consists of a significant fraction of the computational burden of a CTM.We have investigated a machine learning approach to solving the differential equations instead of solving them numerically. From an annual simulation of the GEOS-Chem model we have produced a training dataset consisting of the concentration of compounds before and after the differential equations are solved, together with some key physical parameters for every grid-box and time-step. From this dataset we have trained a machine learning algorithm (random regression forest) to be able to predict the concentration of the compounds after the integration step based on the concentrations and physical state at the beginning of the time step. We have then included this algorithm back into the GEOS-Chem model, bypassing the need to integrate the chemistry.This machine learning approach shows many of the characteristics of the full simulation and has the potential to be substantially faster. There are a wide range of application for such an approach - generating boundary conditions, for use in air quality forecasts, chemical data assimilation systems, centennial scale climate simulations etc. We discuss our approches' speed and accuracy, and highlight some potential future directions for improving this approach.

Minimal Access Surgery Educational Needs of Trainees from Africa: Perspectives from an Asian Training Institution.

PubMed

Ahmad, J I; Mishra, R K

2015-01-01

The establishment of minimal access surgery (MAS) in the last three decades brought new dimensions to surgical training. The sole role of traditional apprenticeship training model was challenged and adjunctive surgical simulation models were introduced. Knowledge of the trainees' educational needs is important in designing MAS training curriculum. To study the MAS educational needs of trainees from Africa, review MAS training models and offer recommendations for MAS training. Data was obtained from questionnaires filled by trainees from Africa who attended the monthly MAS training at the World Laparoscopy Hospital, India from October 2013 to May 2014 about their MAS educational needs. There were 38 trainees from different parts of Africa (Central, East, North, South and West Africa) with average age of 41.92 ± 8.67 years (minimum-28 years and maximum 63 years) and majority were males (92%). General surgeons constituted 57% while Gynaecologists were 41%. Only a quarter have MAS training integrated in their training curriculum. Box trainers, Animal models, live human surgeries and virtual reality simulation were the commonest models used in previous trainings and favoured in the educational needs for MAS training. Using cadaveric models and self sponsorship were deemphasised. Widespread application of MAS, globalisation and trainees educational needs call for establishing training programmes. Box trainers, animal models, live human surgeries and virtual reality simulators should be adopted and a synergy between Postgraduate surgical programmes, biomedical industry, universities and trainees will facilitate the setting of MAS skills laboratories and programmes.

Finite Element Simulations of Two Vertical Drop Tests of F-28 Fuselage Sections

NASA Technical Reports Server (NTRS)

Jackson, Karen E.; Littell, Justin D.; Annett, Martin S.; Haskin, Ian M.

2018-01-01

In March 2017, a vertical drop test of a forward fuselage section of a Fokker F-28 MK4000 aircraft was conducted as part of a joint NASA/FAA project to investigate the performance of transport aircraft under realistic crash conditions. In June 2017, a vertical drop test was conducted of a wing-box fuselage section of the same aircraft. Both sections were configured with two rows of aircraft seats, in a triple-double configuration. A total of ten Anthropomorphic Test Devices (ATDs) were secured in seats using standard lap belt restraints. The forward fuselage section was also configured with luggage in the cargo hold. Both sections were outfitted with two hat racks, each with added ballast mass. The drop tests were performed at the Landing and Impact Research facility located at NASA Langley Research Center in Hampton, Virginia. The measured impact velocity for the forward fuselage section was 346.8-in/s onto soil. The wing-box section was dropped with a downward facing pitch angle onto a sloping soil surface in order to create an induced forward acceleration in the airframe. The vertical impact velocity of the wing-box section was 349.2-in/s. A second objective of this project was to assess the capabilities of finite element simulations to predict the test responses. Finite element models of both fuselage sections were developed for execution in LS-DYNA(Registered Trademark), a commercial explicit nonlinear transient dynamic code. The models contained accurate representations of the airframe structure, the hat racks and hat rack masses, the floor and seat tracks, the luggage in the cargo hold for the forward section, and the detailed under-floor structure in the wing-box section. Initially, concentrated masses were used to represent the inertial properties of the seats, restraints, and ATD occupants. However, later simulations were performed that included finite element representations of the seats, restraints, and ATD occupants. These models were developed to more accurately replicate the seat loading of the floor and to enable prediction of occupant impact responses. Models were executed to generate analytical predictions of airframe responses, which were compared with test data to validate the model. Comparisons of predicted and experimental structural deformation and failures were made. Finally, predicted and experimental soil deformation and crater depths were also compared for both drop test configurations.

Modelling Pollutant Dispersion in a Street Network

NASA Astrophysics Data System (ADS)

Salem, N. Ben; Garbero, V.; Salizzoni, P.; Lamaison, G.; Soulhac, L.

2015-04-01

This study constitutes a further step in the analysis of the performances of a street network model to simulate atmospheric pollutant dispersion in urban areas. The model, named SIRANE, is based on the decomposition of the urban atmosphere into two sub-domains: the urban boundary layer, whose dynamics is assumed to be well established, and the urban canopy, represented as a series of interconnected boxes. Parametric laws govern the mass exchanges between the boxes under the assumption that the pollutant dispersion within the canopy can be fully simulated by modelling three main bulk transfer phenomena: channelling along street axes, transfers at street intersections, and vertical exchange between street canyons and the overlying atmosphere. Here, we aim to evaluate the reliability of the parametrizations adopted to simulate these phenomena, by focusing on their possible dependence on the external wind direction. To this end, we test the model against concentration measurements within an idealized urban district whose geometrical layout closely matches the street network represented in SIRANE. The analysis is performed for an urban array with a fixed geometry and a varying wind incidence angle. The results show that the model provides generally good results with the reference parametrizations adopted in SIRANE and that its performances are quite robust for a wide range of the model parameters. This proves the reliability of the street network approach in simulating pollutant dispersion in densely built city districts. The results also show that the model performances may be improved by considering a dependence of the wind fluctuations at street intersections and of the vertical exchange velocity on the direction of the incident wind. This opens the way for further investigations to clarify the dependence of these parameters on wind direction and street aspect ratios.

A Reduced Model for the Magnetorotational Instability

NASA Astrophysics Data System (ADS)

Jamroz, Ben; Julien, Keith; Knobloch, Edgar

2008-11-01

The magnetorotational instability is investigated within the shearing box approximation in the large Elsasser number regime. In this regime, which is of fundamental importance to astrophysical accretion disk theory, shear is the dominant source of energy, but the instability itself requires the presence of a weaker vertical magnetic field. Dissipative effects are weaker still. However, they are sufficiently large to permit a nonlinear feedback mechanism whereby the turbulent stresses generated by the MRI act on and modify the local background shear in the angular velocity profile. To date this response has been omitted in shearing box simulations and is captured by a reduced pde model derived here from the global MHD fluid equations using multiscale asymptotic perturbation theory. Results from numerical simulations of the reduced pde model indicate a linear phase of exponential growth followed by a nonlinear adjustment to algebraic growth and decay in the fluctuating quantities. Remarkably, the velocity and magnetic field correlations associated with these algebraic growth and decay laws conspire to achieve saturation of the angular momentum transport. The inclusion of subdominant ohmic dissipation arrests the algebraic growth of the fluctuations on a longer, dissipative time scale.

Nuclear spin noise in the central spin model

NASA Astrophysics Data System (ADS)

Fröhling, Nina; Anders, Frithjof B.; Glazov, Mikhail

2018-05-01

We study theoretically the fluctuations of the nuclear spins in quantum dots employing the central spin model which accounts for the hyperfine interaction of the nuclei with the electron spin. These fluctuations are calculated both with an analytical approach using homogeneous hyperfine couplings (box model) and with a numerical simulation using a distribution of hyperfine coupling constants. The approaches are in good agreement. The box model serves as a benchmark with low computational cost that explains the basic features of the nuclear spin noise well. We also demonstrate that the nuclear spin noise spectra comprise a two-peak structure centered at the nuclear Zeeman frequency in high magnetic fields with the shape of the spectrum controlled by the distribution of the hyperfine constants. This allows for direct access to this distribution function through nuclear spin noise spectroscopy.

Root architecture simulation improves the inference from seedling root phenotyping towards mature root systems

PubMed Central

Zhao, Jiangsan; Rewald, Boris; Leitner, Daniel; Nagel, Kerstin A.; Nakhforoosh, Alireza

2017-01-01

Abstract Root phenotyping provides trait information for plant breeding. A shortcoming of high-throughput root phenotyping is the limitation to seedling plants and failure to make inferences on mature root systems. We suggest root system architecture (RSA) models to predict mature root traits and overcome the inference problem. Sixteen pea genotypes were phenotyped in (i) seedling (Petri dishes) and (ii) mature (sand-filled columns) root phenotyping platforms. The RSA model RootBox was parameterized with seedling traits to simulate the fully developed root systems. Measured and modelled root length, first-order lateral number, and root distribution were compared to determine key traits for model-based prediction. No direct relationship in root traits (tap, lateral length, interbranch distance) was evident between phenotyping systems. RootBox significantly improved the inference over phenotyping platforms. Seedling plant tap and lateral root elongation rates and interbranch distance were sufficient model parameters to predict genotype ranking in total root length with an RSpearman of 0.83. Parameterization including uneven lateral spacing via a scaling function substantially improved the prediction of architectures underlying the differently sized root systems. We conclude that RSA models can solve the inference problem of seedling root phenotyping. RSA models should be included in the phenotyping pipeline to provide reliable information on mature root systems to breeding research. PMID:28168270

Numerical Modeling of the Hydrothermal System at East Pacific Rise 9°50'N Including Anhydrite Precipitation

NASA Astrophysics Data System (ADS)

Kolandaivelu, K. P.; Lowell, R. P.

2015-12-01

To better understand the effects of anhydrite precipitation on mid-ocean ridge hydrothermal systems, we conducted 2-D numerical simulations of two-phase hydrothermal circulation in a NaCl-H2O fluid at the East Pacific Rise 9°50'N. The simulations were constrained by key observational thermal data and seismicity that suggests the fluid flow is primarily along axis with recharge focused into a small zone near a 4th order discontinuity. The simulations considered an open-top square box with a fixed seafloor pressure of 25 MPa, and nominal seafloor temperature of 10 °C. The sides of the box were assumed to be impermeable and insulated. We considered two models: a homogeneous model with a permeability of 10-13 m2 and a heterogeneous model in which layer 2A extrusives were given a higher permeability. Both models had a fixed bottom temperature distribution and initial porosity of 0.1. Assuming that anhydrite precipitation resulted from the decrease in solubility with increasing temperature as downwelling fluid gets heated, we calculated the rate of porosity decrease and sealing times in each cell at certain time snapshots in the simulations. The results showed that sealing would occur most rapidly in limited regions near the base of the high-temperature plumes, where complete sealing could occur on decadal time scales. Though more detailed analysis is needed, it appeared that the areas of rapid sealing would likely have negligible impact on the overall circulation pattern and hydrothermal vent temperatures. The simulations also indicated that sealing due to anhydrite precipitation would occur more slowly at the margins of the ascending plumes. The sealing times in the deep recharge zone determined in these simulations were considerably greater than estimated from 1D analytical calculations, suggesting that with a 2D model, focused recharge at the EPR 9°50'N site may occur, at least on a decadal time scale.

Methane and Environmental Change during the Paleocene-Eocene Thermal Maximum (PETM): Modeling the PETM Onset as a Two-stage Event

NASA Technical Reports Server (NTRS)

Carozza, David A.; Mysak, Lawrence A.; Schmidt, Gavin A.

2011-01-01

An atmospheric CH4 box model coupled to a global carbon cycle box model is used to constrain the carbon emission associated with the PETM and assess the role of CH4 during this event. A range of atmospheric and oceanic emission scenarios representing different amounts, rates, and isotopic signatures of emitted carbon are used to model the PETM onset. The first 3 kyr of the onset, a pre-isotope excursion stage, is simulated by the atmospheric release of 900 to 1100 Pg C CH4 with a delta C-13 of -22 to - 30 %. For a global average warming of 3 deg C, a release of CO2 to the ocean and CH4 to the atmosphere totalling 900 to 1400 Pg C, with a delta C-13 of -50 to -60%, simulates the subsequent 1 -kyr isotope excursion stage. To explain the observations, the carbon must have been released over at most 500 years. The first stage results cannot be associated with any known PETM hypothesis. However, the second stage results are consistent with a methane hydrate source. More than a single source of carbon is required to explain the PETM onset.

The Abacus Cosmos: A Suite of Cosmological N-body Simulations

NASA Astrophysics Data System (ADS)

Garrison, Lehman H.; Eisenstein, Daniel J.; Ferrer, Douglas; Tinker, Jeremy L.; Pinto, Philip A.; Weinberg, David H.

2018-06-01

We present a public data release of halo catalogs from a suite of 125 cosmological N-body simulations from the ABACUS project. The simulations span 40 wCDM cosmologies centered on the Planck 2015 cosmology at two mass resolutions, 4 × 1010 h ‑1 M ⊙ and 1 × 1010 h ‑1 M ⊙, in 1.1 h ‑1 Gpc and 720 h ‑1 Mpc boxes, respectively. The boxes are phase-matched to suppress sample variance and isolate cosmology dependence. Additional volume is available via 16 boxes of fixed cosmology and varied phase; a few boxes of single-parameter excursions from Planck 2015 are also provided. Catalogs spanning z = 1.5 to 0.1 are available for friends-of-friends and ROCKSTAR halo finders and include particle subsamples. All data products are available at https://lgarrison.github.io/AbacusCosmos.

Electric Power Distribution System Model Simplification Using Segment Substitution

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

Reiman, Andrew P.; McDermott, Thomas E.; Akcakaya, Murat

Quasi-static time-series (QSTS) simulation is used to simulate the behavior of distribution systems over long periods of time (typically hours to years). The technique involves repeatedly solving the load-flow problem for a distribution system model and is useful for distributed energy resource (DER) planning. When a QSTS simulation has a small time step and a long duration, the computational burden of the simulation can be a barrier to integration into utility workflows. One way to relieve the computational burden is to simplify the system model. The segment substitution method of simplifying distribution system models introduced in this paper offers modelmore » bus reduction of up to 98% with a simplification error as low as 0.2% (0.002 pu voltage). In contrast to existing methods of distribution system model simplification, which rely on topological inspection and linearization, the segment substitution method uses black-box segment data and an assumed simplified topology.« less

Scattering and emission from inhomogeneous vegetation canopy and alien target beneath by using three-dimensional vector radiative transfer (3D-VRT) equation

NASA Astrophysics Data System (ADS)

Jin, Ya-Qiu; Liang, Zichang

2005-05-01

To solve the 3D-VRT equation for the model of spatially inhomogeneous scatter media, the finite enclosure of the scatter media is geometrically divided, in both vertical z and transversal (x,y) directions, to form very thin multi-boxes. The zeroth order emission, first-order Mueller matrix of each thin box and an iterative approach of high-order radiative transfer are applied to derive high-order scattering and emission of whole inhomogeneous scatter media. Numerical results of polarized brightness temperature at microwave frequency and under different radiometer resolutions from inhomogeneous scatter model such as vegetation canopy and alien target beneath canopy are simulated and discussed.

Peanuts, brezels and bananas: food for thought on the orbital structure of the Galactic bulge

NASA Astrophysics Data System (ADS)

Portail, Matthieu; Wegg, Christopher; Gerhard, Ortwin

2015-06-01

Recent observations have discovered the presence of a box/peanut or X-shape structure in the Galactic bulge. Such box/peanut structures are common in external disc galaxies, and are well known in N-body simulations where they form following the buckling instability of a bar. From studies of analytical potentials and N-body models, it has been claimed in the past that box/peanut bulges are supported by `bananas', or x1v1 orbits. We present here a set of N-body models where instead the peanut bulge is mainly supported by brezel-like orbits, allowing strong peanuts to form with short extent relative to the bar length. This shows that stars in the X-shape do not necessarily stream along banana orbits which follow the arms of the X-shape. The brezel orbits are also found to be the main orbital component supporting the peanut shape in our recent made-to-measure dynamical models of the Galactic bulge. We also show that in these models the fraction of stellar orbits that contribute to the X-structure account for 40-45 per cent of the stellar mass.

Use of advanced modeling techniques to optimize thermal packaging designs.

PubMed

Formato, Richard M; Potami, Raffaele; Ahmed, Iftekhar

2010-01-01

Through a detailed case study the authors demonstrate, for the first time, the capability of using advanced modeling techniques to correctly simulate the transient temperature response of a convective flow-based thermal shipper design. The objective of this case study was to demonstrate that simulation could be utilized to design a 2-inch-wall polyurethane (PUR) shipper to hold its product box temperature between 2 and 8 °C over the prescribed 96-h summer profile (product box is the portion of the shipper that is occupied by the payload). Results obtained from numerical simulation are in excellent agreement with empirical chamber data (within ±1 °C at all times), and geometrical locations of simulation maximum and minimum temperature match well with the corresponding chamber temperature measurements. Furthermore, a control simulation test case was run (results taken from identical product box locations) to compare the coupled conduction-convection model with a conduction-only model, which to date has been the state-of-the-art method. For the conduction-only simulation, all fluid elements were replaced with "solid" elements of identical size and assigned thermal properties of air. While results from the coupled thermal/fluid model closely correlated with the empirical data (±1 °C), the conduction-only model was unable to correctly capture the payload temperature trends, showing a sizeable error compared to empirical values (ΔT > 6 °C). A modeling technique capable of correctly capturing the thermal behavior of passively refrigerated shippers can be used to quickly evaluate and optimize new packaging designs. Such a capability provides a means to reduce the cost and required design time of shippers while simultaneously improving their performance. Another advantage comes from using thermal modeling (assuming a validated model is available) to predict the temperature distribution in a shipper that is exposed to ambient temperatures which were not bracketed during its validation. Thermal packaging is routinely used by the pharmaceutical industry to provide passive and active temperature control of their thermally sensitive products from manufacture through end use (termed the cold chain). In this study, the authors focus on passive temperature control (passive control does not require any external energy source and is entirely based on specific and/or latent heat of shipper components). As temperature-sensitive pharmaceuticals are being transported over longer distances, cold chain reliability is essential. To achieve reliability, a significant amount of time and resources must be invested in design, test, and production of optimized temperature-controlled packaging solutions. To shorten the cumbersome trial and error approach (design/test/design/test …), computer simulation (virtual prototyping and testing of thermal shippers) is a promising method. Although several companies have attempted to develop such a tool, there has been limited success to date. Through a detailed case study the authors demonstrate, for the first time, the capability of using advanced modeling techniques to correctly simulate the transient temperature response of a coupled conductive/convective-based thermal shipper. A modeling technique capable of correctly capturing shipper thermal behavior can be used to develop packaging designs more quickly, reducing up-front costs while also improving shipper performance.

Lipid Adjustment for Chemical Exposures: Accounting for Concomitant Variables

PubMed Central

Li, Daniel; Longnecker, Matthew P.; Dunson, David B.

2013-01-01

Background Some environmental chemical exposures are lipophilic and need to be adjusted by serum lipid levels before data analyses. There are currently various strategies that attempt to account for this problem, but all have their drawbacks. To address such concerns, we propose a new method that uses Box-Cox transformations and a simple Bayesian hierarchical model to adjust for lipophilic chemical exposures. Methods We compared our Box-Cox method to existing methods. We ran simulation studies in which increasing levels of lipid-adjusted chemical exposure did and did not increase the odds of having a disease, and we looked at both single-exposure and multiple-exposures cases. We also analyzed an epidemiology dataset that examined the effects of various chemical exposures on the risk of birth defects. Results Compared with existing methods, our Box-Cox method produced unbiased estimates, good coverage, similar power, and lower type-I error rates. This was the case in both single- and multiple-exposure simulation studies. Results from analysis of the birth-defect data differed from results using existing methods. Conclusion Our Box-Cox method is a novel and intuitive way to account for the lipophilic nature of certain chemical exposures. It addresses some of the problems with existing methods, is easily extendable to multiple exposures, and can be used in any analyses that involve concomitant variables. PMID:24051893

Modeling radiation forces acting on TOPEX/Poseidon for precision orbit determination

NASA Technical Reports Server (NTRS)

Marshall, J. A.; Luthcke, S. B.; Antreasian, P. G.; Rosborough, G. W.

1992-01-01

Geodetic satellites such as GEOSAT, SPOT, ERS-1, and TOPEX/Poseidon require accurate orbital computations to support the scientific data they collect. Until recently, gravity field mismodeling was the major source of error in precise orbit definition. However, albedo and infrared re-radiation, and spacecraft thermal imbalances produce in combination no more than a 6-cm radial root-mean-square (RMS) error over a 10-day period. This requires the development of nonconservative force models that take the satellite's complex geometry, attitude, and surface properties into account. For TOPEX/Poseidon, a 'box-wing' satellite form was investigated that models the satellite as a combination of flat plates arranged in a box shape with a connected solar array. The nonconservative forces acting on each of the eight surfaces are computed independently, yielding vector accelerations which are summed to compute the total aggregate effect on the satellite center-of-mass. In order to test the validity of this concept, 'micro-models' based on finite element analysis of TOPEX/Poseidon were used to generate acceleration histories in a wide variety of orbit orientations. These profiles are then compared to the box-wing model. The results of these simulations and their implication on the ability to precisely model the TOPEX/Poseidon orbit are discussed.

Seismic wave propagation in granular media

NASA Astrophysics Data System (ADS)

Tancredi, Gonzalo; López, Francisco; Gallot, Thomas; Ginares, Alejandro; Ortega, Henry; Sanchís, Johnny; Agriela, Adrián; Weatherley, Dion

2016-10-01

Asteroids and small bodies of the Solar System are thought to be agglomerates of irregular boulders, therefore cataloged as granular media. It is a consensus that many asteroids might be considered as rubble or gravel piles.Impacts on their surface could produce seismic waves which propagate in the interior of these bodies, thus causing modifications in the internal distribution of rocks and ejections of particles and dust, resulting in a cometary-type comma.We present experimental and numerical results on the study of propagation of impact-induced seismic waves in granular media, with special focus on behavior changes by increasing compression.For the experiment, we use an acrylic box filled with granular materials such as sand, gravel and glass spheres. Pressure inside the box is controlled by a movable side wall and measured with sensors. Impacts are created on the upper face of the box through a hole, ranging from free-falling spheres to gunshots. We put high-speed cameras outside the box to record the impact as well as piezoelectic sensors and accelerometers placed at several depths in the granular material to detect the seismic wave.Numerical simulations are performed with ESyS-Particle, a software that implements the Discrete Element Method. The experimental setting is reproduced in the numerical simulations using both individual spherical particles and agglomerates of spherical particles shaped as irregular boulders, according to rock models obtained with a 3D scanner. The numerical experiments also reproduces the force loading on one of the wall to vary the pressure inside the box.We are interested in the velocity, attenuation and energy transmission of the waves. These quantities are measured in the experiments and in the simulations. We study the dependance of these three parameters with characteristics like: impact speed, properties of the target material and the pressure in the media.These results are relevant to understand the outcomes of impacts in rubble/gravel pile asteroids.

Constraining a hybrid volatility basis-set model for aging of wood-burning emissions using smog chamber experiments: a box-model study based on the VBS scheme of the CAMx model (v5.40)

NASA Astrophysics Data System (ADS)

Ciarelli, Giancarlo; El Haddad, Imad; Bruns, Emily; Aksoyoglu, Sebnem; Möhler, Ottmar; Baltensperger, Urs; Prévôt, André S. H.

2017-06-01

In this study, novel wood combustion aging experiments performed at different temperatures (263 and 288 K) in a ˜ 7 m3 smog chamber were modelled using a hybrid volatility basis set (VBS) box model, representing the emission partitioning and their oxidation against OH. We combine aerosol-chemistry box-model simulations with unprecedented measurements of non-traditional volatile organic compounds (NTVOCs) from a high-resolution proton transfer reaction mass spectrometer (PTR-MS) and with organic aerosol measurements from an aerosol mass spectrometer (AMS). Due to this, we are able to observationally constrain the amounts of different NTVOC aerosol precursors (in the model) relative to low volatility and semi-volatile primary organic material (OMsv), which is partitioned based on current published volatility distribution data. By comparing the NTVOC / OMsv ratios at different temperatures, we determine the enthalpies of vaporization of primary biomass-burning organic aerosols. Further, the developed model allows for evaluating the evolution of oxidation products of the semi-volatile and volatile precursors with aging. More than 30 000 box-model simulations were performed to retrieve the combination of parameters that best fit the observed organic aerosol mass and O : C ratios. The parameters investigated include the NTVOC reaction rates and yields as well as enthalpies of vaporization and the O : C of secondary organic aerosol surrogates. Our results suggest an average ratio of NTVOCs to the sum of non-volatile and semi-volatile organic compounds of ˜ 4.75. The mass yields of these compounds determined for a wide range of atmospherically relevant temperatures and organic aerosol (OA) concentrations were predicted to vary between 8 and 30 % after 5 h of continuous aging. Based on the reaction scheme used, reaction rates of the NTVOC mixture range from 3.0 × 10-11 to 4. 0 × 10-11 cm3 molec-1 s-1. The average enthalpy of vaporization of secondary organic aerosol (SOA) surrogates was determined to be between 55 000 and 35 000 J mol-1, which implies a yield increase of 0.03-0.06 % K-1 with decreasing temperature. The improved VBS scheme is suitable for implementation into chemical transport models to predict the burden and oxidation state of primary and secondary biomass-burning aerosols.

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

Kumar, Dinesh; Thapliyal, Himanshu; Mohammad, Azhar

Differential Power Analysis (DPA) attack is considered to be a main threat while designing cryptographic processors. In cryptographic algorithms like DES and AES, S-Box is used to indeterminate the relationship between the keys and the cipher texts. However, S-box is prone to DPA attack due to its high power consumption. In this paper, we are implementing an energy-efficient 8-bit S-Box circuit using our proposed Symmetric Pass Gate Adiabatic Logic (SPGAL). SPGAL is energy-efficient as compared to the existing DPAresistant adiabatic and non-adiabatic logic families. SPGAL is energy-efficient due to reduction of non-adiabatic loss during the evaluate phase of the outputs.more » Further, the S-Box circuit implemented using SPGAL is resistant to DPA attacks. The results are verified through SPICE simulations in 180nm technology. SPICE simulations show that the SPGAL based S-Box circuit saves upto 92% and 67% of energy as compared to the conventional CMOS and Secured Quasi-Adiabatic Logic (SQAL) based S-Box circuit. From the simulation results, it is evident that the SPGAL based circuits are energy-efficient as compared to the existing DPAresistant adiabatic and non-adiabatic logic families. In nutshell, SPGAL based gates can be used to build secure hardware for lowpower portable electronic devices and Internet-of-Things (IoT) based electronic devices.« less

Simulation of Cavern Formation and Karst Development Using Salt

ERIC Educational Resources Information Center

Kent, Douglas C.; Ross, Alex R.

1975-01-01

A salt model was developed as a teaching tool to demonstrate the development of caverns and karst topography. Salt slabs are placed in a watertight box to represent fractured limestone. Erosion resulting from water flow can be photographed in time-lapse sequence or demonstrated in the laboratory. (Author/CP)

SURVIAC Bulletin: AFRL Research Audit Trail Viewer (ATV). Volume 19, Issue 1, 2003

DTIC Science & Technology

2003-01-01

Trail Viewer, the analyst obtained a close up view of the detailed aircraft model using the Orbit View, enabled the SkyBox , enabled fictional ter...trails and element projections, several simulated terrain types and Skybox environments to help the user maintain perspective, file based

Zonal Flows and Long-lived Axisymmetric Pressure Bumps in Magnetorotational Turbulence

NASA Astrophysics Data System (ADS)

Johansen, A.; Youdin, A.; Klahr, H.

2009-06-01

We study the behavior of magnetorotational turbulence in shearing box simulations with a radial and azimuthal extent up to 10 scale heights. Maxwell and Reynolds stresses are found to increase by more than a factor of 2 when increasing the box size beyond two scale heights in the radial direction. Further increase of the box size has little or no effect on the statistical properties of the turbulence. An inverse cascade excites magnetic field structures at the largest scales of the box. The corresponding 10% variation in the Maxwell stress launches a zonal flow of alternating sub- and super-Keplerian velocity. This, in turn, generates a banded density structure in geostrophic balance between pressure and Coriolis forces. We present a simplified model for the appearance of zonal flows, in which stochastic forcing by the magnetic tension on short timescales creates zonal flow structures with lifetimes of several tens of orbits. We experiment with various improved shearing box algorithms to reduce the numerical diffusivity introduced by the supersonic shear flow. While a standard finite difference advection scheme shows signs of a suppression of turbulent activity near the edges of the box, this problem is eliminated by a new method where the Keplerian shear advection is advanced in time by interpolation in Fourier space.

Umbra (core)

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

Bradley, Jon David; Oppel III, Fred J.; Hart, Brian E.

Umbra is a flexible simulation framework for complex systems that can be used by itself for modeling, simulation, and analysis, or to create specific applications. It has been applied to many operations, primarily dealing with robotics and system of system simulations. This version, from 4.8 to 4.8.3b, incorporates bug fixes, refactored code, and new managed C++ wrapper code that can be used to bridge new applications written in C# to the C++ libraries. The new managed C++ wrapper code includes (project/directories) BasicSimulation, CSharpUmbraInterpreter, LogFileView, UmbraAboutBox, UmbraControls, UmbraMonitor and UmbraWrapper.

IMACS 󈨟: Proceedings of the IMACS World Congress on Computation and Applied Mathematics (13th) Held in Dublin, Ireland on July 22-26, 1991. Volume 4. Modelling and Simulation for Electrical, Electronic and Semiconductor Devices, Computation for Management Systems, Applications of Modelling and Simulation, Environmental Systems Simulation, Software Forum, Poster Sessions

DTIC Science & Technology

1991-07-01

synchronous machine case study . IEEE T rons. on For the ease nd -nq -2, four time scales trust be used And the A.C, Vol. 36. nul 3, March 1989. damnper... studied . A spot welded(Csse 3) * ss s i* r 0. or a line welded( Case 4) reinforcement plate is attached on the colliding surface of box beams arnd their...phased armature, is given on Figure 1. analytical field calculation in the machine magnetic structure. Il - MAGNETIC STRUCTURE MODELLING: In the case

Implementation of a 3D halo neutral model in the TRANSP code and application to projected NSTX-U plasmas

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

Medley, S. S.; Liu, D.; Gorelenkova, M. V.

2016-01-12

A 3D halo neutral code developed at the Princeton Plasma Physics Laboratory and implemented for analysis using the TRANSP code is applied to projected National Spherical Torus eXperiment-Upgrade (NSTX-U plasmas). The legacy TRANSP code did not handle halo neutrals properly since they were distributed over the plasma volume rather than remaining in the vicinity of the neutral beam footprint as is actually the case. The 3D halo neutral code uses a 'beam-in-a-box' model that encompasses both injected beam neutrals and resulting halo neutrals. Upon deposition by charge exchange, a subset of the full, one-half and one-third beam energy components producemore » first generation halo neutrals that are tracked through successive generations until an ionization event occurs or the descendant halos exit the box. The 3D halo neutral model and neutral particle analyzer (NPA) simulator in the TRANSP code have been benchmarked with the Fast-Ion D-Alpha simulation (FIDAsim) code, which provides Monte Carlo simulations of beam neutral injection, attenuation, halo generation, halo spatial diffusion, and photoemission processes. When using the same atomic physics database, TRANSP and FIDAsim simulations achieve excellent agreement on the spatial profile and magnitude of beam and halo neutral densities and the NPA energy spectrum. The simulations show that the halo neutral density can be comparable to the beam neutral density. These halo neutrals can double the NPA flux, but they have minor effects on the NPA energy spectrum shape. The TRANSP and FIDAsim simulations also suggest that the magnitudes of beam and halo neutral densities are relatively sensitive to the choice of the atomic physics databases.« less

Analogue modeling for science outreach: glacier flows at Antarctic National Museum, Italy

NASA Astrophysics Data System (ADS)

Zeoli, A.; Corti, G.; Folco, L.; Ossola, C.

2012-12-01

Comprehension of internal deformation and of ice flow in the Antarctic ice sheet in relation with the bedrock topography and with the thickness variation induced by climatic variations represent an important target for the scientific community. Analogue modelling technique aims to analyze geological or geomorphological processes through physical models built at a reduced geometrical scale in laboratory and deformed at reasonable scale of times. Corti et al. (2003 and 2008) have shown that this technique could also be used successfully for ice flow dynamic. Moreover, this technique gives a three-dimensional view of the processes. The models, that obviously simplify the geometry and rheology of natural processes, represent a geometrically, cinematically, dynamically and rheologically scaled analogue of the natural glacial environment. Following a procedure described in previous papers, proper materials have been selected to simulate the rheological behaviour of ice. In particular, during the experiments a Polydimethilsyloxane (PDMS) has been used to simulate glacial flow. PDMS is a transparent Newtonian silicone with a viscosity of 1.4 104 Pa s and a density of 965 kg m-3 (see material properties in Weijermars, 1986). The scaling of the model to natural conditions let to obtain reliable results for a correct comparison with the glacial processes under investigation. Models have been built with a with a geometrical scaling ratio of ~1.5 10-5, such that 1 cm in the model represents ~700 m in nature. The physical models have been deformed in terrestrial gravity field by allowing the PDMS to flow inside a Plexiglas box. In particular, the silicone has been poured inside the Plexiglas box and allowed to settle in order to obtain a flat free surface; the box has been then inclined of some degrees in order to allow the silicone to flow. Several boxes illustrating different glacial processes have been realized; each of them could be easily performed in short time and in standard laboratories. One of the main aims of the Antarctic National Museum in Siena (Italy) is to establish a strategy to deliver results to a broader scientific community. Time and spatial small scale of the experiments lead the analogue modeling technique easy to be shown to non-technical audiences through direct participation during Museum visits. All these experiments engage both teachers and students from primary and secondary schools and the general public.

Simulation of adaptive semi-active magnetorheological seat damper for vehicle occupant blast protection

NASA Astrophysics Data System (ADS)

Yoo, Jin-Hyeong; Murugan, Muthuvel; Wereley, Norman M.

2013-04-01

This study investigates a lumped-parameter human body model which includes lower leg in seated posture within a quarter-car model for blast injury assessment simulation. To simulate the shock acceleration of the vehicle, mine blast analysis was conducted on a generic land vehicle crew compartment (sand box) structure. For the purpose of simulating human body dynamics with non-linear parameters, a physical model of a lumped-parameter human body within a quarter car model was implemented using multi-body dynamic simulation software. For implementing the control scheme, a skyhook algorithm was made to work with the multi-body dynamic model by running a co-simulation with the control scheme software plug-in. The injury criteria and tolerance levels for the biomechanical effects are discussed for each of the identified vulnerable body regions, such as the relative head displacement and the neck bending moment. The desired objective of this analytical model development is to study the performance of adaptive semi-active magnetorheological damper that can be used for vehicle-occupant protection technology enhancements to the seat design in a mine-resistant military vehicle.

Identification of unique interactions between the flexible linker and the RecA-like domains of DEAD-box helicase Mss116

NASA Astrophysics Data System (ADS)

Zhang, Yuan; Palla, Mirkó; Sun, Andrew; Liao, Jung-Chi

2013-09-01

DEAD-box RNA helicases are ATP-dependent proteins implicated in nearly all aspects of RNA metabolism. The yeast DEAD-box helicase Mss116 is unique in its functions of splicing group I and group II introns and activating mRNA translation, but the structural understanding of why it performs these unique functions remains unclear. Here we used sequence analysis and molecular dynamics simulation to identify residues in the flexible linker specific for yeast Mss116, potentially associated with its unique functions. We first identified residues that are 100% conserved in Mss116 of different species of the Saccharomycetaceae family. The amino acids of these conserved residues were then compared with the amino acids of the corresponding residue positions of other RNA helicases to identify residues that have distinct amino acids from other DEAD-box proteins. Four residues in the flexible linker, i.e. N334, E335, P336 and H339, are conserved and Mss116-specific. Molecular dynamics simulation was conducted for the wild-type Mss116 structure and mutant models to examine mutational effects of the linker on the conformational equilibrium. Relatively short MD simulation runs (within 20 ns) were enough for us to observe mutational effects, suggesting serious structural perturbations by these mutations. The mutation of E335 depletes the interactions between E335 and K95 in domain 1. The interactions between N334/P336 and N496/I497 of domain 2 are also abolished by mutation. Our results suggest that tight interactions between the Mss116-specific flexible linker and the two RecA-like domains may be mechanically required to crimp RNA for the unique RNA processes of yeast Mss116.

Functional form and risk adjustment of hospital costs: Bayesian analysis of a Box-Cox random coefficients model.

PubMed

Hollenbeak, Christopher S

2005-10-15

While risk-adjusted outcomes are often used to compare the performance of hospitals and physicians, the most appropriate functional form for the risk adjustment process is not always obvious for continuous outcomes such as costs. Semi-log models are used most often to correct skewness in cost data, but there has been limited research to determine whether the log transformation is sufficient or whether another transformation is more appropriate. This study explores the most appropriate functional form for risk-adjusting the cost of coronary artery bypass graft (CABG) surgery. Data included patients undergoing CABG surgery at four hospitals in the midwest and were fit to a Box-Cox model with random coefficients (BCRC) using Markov chain Monte Carlo methods. Marginal likelihoods and Bayes factors were computed to perform model comparison of alternative model specifications. Rankings of hospital performance were created from the simulation output and the rankings produced by Bayesian estimates were compared to rankings produced by standard models fit using classical methods. Results suggest that, for these data, the most appropriate functional form is not logarithmic, but corresponds to a Box-Cox transformation of -1. Furthermore, Bayes factors overwhelmingly rejected the natural log transformation. However, the hospital ranking induced by the BCRC model was not different from the ranking produced by maximum likelihood estimates of either the linear or semi-log model. Copyright (c) 2005 John Wiley & Sons, Ltd.

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

Blansett, Ethan L.; Schroeppel, Richard Crabtree; Tang, Jason D.

With the build-out of large transport networks utilizing optical technologies, more and more capacity is being made available. Innovations in Dense Wave Division Multiplexing (DWDM) and the elimination of optical-electrical-optical conversions have brought on advances in communication speeds as we move into 10 Gigabit Ethernet and above. Of course, there is a need to encrypt data on these optical links as the data traverses public and private network backbones. Unfortunately, as the communications infrastructure becomes increasingly optical, advances in encryption (done electronically) have failed to keep up. This project examines the use of optical logic for implementing encryption in themore » photonic domain to achieve the requisite encryption rates. In order to realize photonic encryption designs, technology developed for electrical logic circuits must be translated to the photonic regime. This paper examines two classes of all optical logic (SEED, gain competition) and how each discrete logic element can be interconnected and cascaded to form an optical circuit. Because there is no known software that can model these devices at a circuit level, the functionality of the SEED and gain competition devices in an optical circuit were modeled in PSpice. PSpice allows modeling of the macro characteristics of the devices in context of a logic element as opposed to device level computational modeling. By representing light intensity as voltage, 'black box' models are generated that accurately represent the intensity response and logic levels in both technologies. By modeling the behavior at the systems level, one can incorporate systems design tools and a simulation environment to aid in the overall functional design. Each black box model of the SEED or gain competition device takes certain parameters (reflectance, intensity, input response), and models the optical ripple and time delay characteristics. These 'black box' models are interconnected and cascaded in an encrypting/scrambling algorithm based on a study of candidate encryption algorithms. We found that a low gate count, cascadable encryption algorithm is most feasible given device and processing constraints. The modeling and simulation of optical designs using these components is proceeding in parallel with efforts to perfect the physical devices and their interconnect. We have applied these techniques to the development of a 'toy' algorithm that may pave the way for more robust optical algorithms. These design/modeling/simulation techniques are now ready to be applied to larger optical designs in advance of our ability to implement such systems in hardware.« less

Maintenance Training Simulator Design and Acquisition.

DTIC Science & Technology

1980-08-01

7 ADA69 149 APPLIED SCIENCE ASSOCIATES INC VALENCIA PA F/6 5/9 MAINTENANCE TRAINING SIMULATOR DESIG AND ACOUISITION.(U) AUG 8O R J HRITZ. 6 R...TRAINING SIMULATOR DESIGN H AND ACQUISIIONII By Rohn J. Htz George R. Purifoy, Jr. M Applied Science Associates, Inc. Box 158A Valencia , Pennsylvania...related thereto. This report was submitted by Applied Science Associates, Inc., Box 158. Valencia . Pennsyvania 10059. under Contract F33015-78-C-409

Detection and classification of Breast Cancer in Wavelet Sub-bands of Fractal Segmented Cancerous Zones.

PubMed

Shirazinodeh, Alireza; Noubari, Hossein Ahmadi; Rabbani, Hossein; Dehnavi, Alireza Mehri

2015-01-01

Recent studies on wavelet transform and fractal modeling applied on mammograms for the detection of cancerous tissues indicate that microcalcifications and masses can be utilized for the study of the morphology and diagnosis of cancerous cases. It is shown that the use of fractal modeling, as applied to a given image, can clearly discern cancerous zones from noncancerous areas. In this paper, for fractal modeling, the original image is first segmented into appropriate fractal boxes followed by identifying the fractal dimension of each windowed section using a computationally efficient two-dimensional box-counting algorithm. Furthermore, using appropriate wavelet sub-bands and image Reconstruction based on modified wavelet coefficients, it is shown that it is possible to arrive at enhanced features for detection of cancerous zones. In this paper, we have attempted to benefit from the advantages of both fractals and wavelets by introducing a new algorithm. By using a new algorithm named F1W2, the original image is first segmented into appropriate fractal boxes, and the fractal dimension of each windowed section is extracted. Following from that, by applying a maximum level threshold on fractal dimensions matrix, the best-segmented boxes are selected. In the next step, the segmented Cancerous zones which are candidates are then decomposed by utilizing standard orthogonal wavelet transform and db2 wavelet in three different resolution levels, and after nullifying wavelet coefficients of the image at the first scale and low frequency band of the third scale, the modified reconstructed image is successfully utilized for detection of breast cancer regions by applying an appropriate threshold. For detection of cancerous zones, our simulations indicate the accuracy of 90.9% for masses and 88.99% for microcalcifications detection results using the F1W2 method. For classification of detected mictocalcification into benign and malignant cases, eight features are identified and utilized in radial basis function neural network. Our simulation results indicate the accuracy of 92% classification using F1W2 method.

Effectiveness Evaluation of Force Protection Training Using Computer-Based Instruction and X3d Simulation

DTIC Science & Technology

2007-09-01

behavior libraries selection box, Savage Tactics behavior sub-folder and hostile behavior sub-folder that contains the behavior that is being assigned to...21) applications. The interface allows users to select models (locations, friendly assets, hostile assets, neutral assets, etc) that will be used in...altitude, etc.) for each model and define their behaviors (friendly patrol craft, hostile explosive-laden vessel, etc). Once the models and their

Utilization of UARS Data in Validation of Photochemical and Dynamical Mechanisms in Stratospheric Models

NASA Technical Reports Server (NTRS)

Ko, M. K. W.; Rodriquez, J. M.; Hu, W.; Danilin, M. Y.; Shia, R.-L.

1998-01-01

The proposed work utilized Upper Atmosphere Research Satellite (UARS) measurements of short-lived and long-lived species, in conjunction with existing photochemical "box" models, trajectory models, and two-dimensional global models, to elucidate outstanding questions in our understanding of photochemical and dynamical mechanisms in the stratosphere. Particular emphasis was given to arriving at the best possible understanding of the chemical and dynamical contributions to the stratospheric ozone budget. Such understanding will increase confidence in the simulations carried out by assessment models.

Utilization of UARS Data in Validation of Photochemical and Dynamical Mechanisms in Stratospheric Models

NASA Technical Reports Server (NTRS)

Ko, Malcolm K. W.; Rodriquez, Jose M.; Hu, Wenjie; Danilin, Michael Y.; Shia, Run-Li

1998-01-01

The proposed work utilized Upper Atmosphere Research Satellite (UARS) measurements of short-lived and long-lived species, in conjunction with existing photochemical "box" models, trajectory models, and two-dimensional global models, to elucidate outstanding questions in our understanding of photochemical and dynamical mechanisms in the stratosphere. Particular emphasis was given to arriving at the best possible understanding of the chemical and dynamical contribution to the stratospheric ozone budget. Such understanding will increase confidence in the simulations carried out by assessment models.

Investigation of the quality of stored red blood cells after simulated air drop in the maritime environment.

PubMed

Meli, Athinoula; Hancock, Vicky; Doughty, Heidi; Smedley, Steve; Cardigan, Rebecca; Wiltshire, Michael

2018-02-01

Maritime medical capability may be compromised by blood resupply. Air-dropped red blood cells (RBCs) is a possible mitigation factor. This study set out to evaluate RBC storage variables after a simulated parachute air drop into the sea, as limited data exist. The air load construction for the air drop of blood was subject to static drop assessment to simulate a worst-case parachute drop scenario. One control and two test Golden Hour shipping containers were each packaged with 10 RBC units. The control box was not dropped; Test Boxes 1 and 2 were further reinforced with waterproof boxes and underwent a simulated air drop on Day 7 or Day 8 postdonation, respectively. One day after the drop and once a week thereafter until Day 43 of storage, RBCs from each box were sampled and tested for full blood counts, hemolysis, adenosine triphosphate, 2,3-diphosphoglycerate, pH, extracellular potassium, glucose, lactate, deformability, and RBC microvesicles. The packaging configuration completed the air drop with no water ingress or physical damage. All units met UK specifications for volume, hemoglobin, and hemolysis. There were no significant differences for any of the variables studied between RBCs in the control box compared to RBCs in Test Boxes 1 and 2 combined over storage. The test proved that the packaging solution and the impact of a maritime air drop as performed in this study, on Day 7 or Day 8 postdonation, did not affect the in vitro quality of RBCs in SAGM over storage for 35 days. © 2017 AABB.

Predicting patchy particle crystals: variable box shape simulations and evolutionary algorithms.

PubMed

Bianchi, Emanuela; Doppelbauer, Günther; Filion, Laura; Dijkstra, Marjolein; Kahl, Gerhard

2012-06-07

We consider several patchy particle models that have been proposed in literature and we investigate their candidate crystal structures in a systematic way. We compare two different algorithms for predicting crystal structures: (i) an approach based on Monte Carlo simulations in the isobaric-isothermal ensemble and (ii) an optimization technique based on ideas of evolutionary algorithms. We show that the two methods are equally successful and provide consistent results on crystalline phases of patchy particle systems.

An intermediate-complexity model for simulating marine biogeochemistry in deep time: Validation against the modern global ocean

NASA Astrophysics Data System (ADS)

Romaniello, Stephen J.; Derry, Louis A.

2010-08-01

We present a new high-resolution 1-D intermediate-complexity box model (ICBM) of ocean biogeochemical processes for paleoceanographic applications. The model contains 79 reservoirs in three regions that should be generally applicable throughout much of Earth history: (1) a stratified gyre region, (2) a high-latitude convective region, and (3) an upwelling region analogous to those found associated with eastern boundary currents. Transport processes are modeled as exchange fluxes between boxes and by eddy diffusion terms. Significant improvement in the representation of middepth oxygen budgets was achieved by implementing nonlocal mixing between the high-latitude surface and gyre thermocline reservoirs. The biogeochemical submodel simulates coupled C, N, P, O, and S systematics with explicit representation of microbial populations, using a process-based approach. Primary production follows Redfield stoichiometry, while water column remineralization is depth- and redox couple-dependent. Settling particulate organic matter is incorporated into a benthic submodel that accounts for burial and remineralization. The C/P ratio of burial depends on bottom water oxygen. Denitrification takes place both by classical and anammox pathways. The ICBM was tested against modern oceanographic observations from the Global Ocean Data Analysis Project, Joint Global Ocean Flux Study, and other databases. Comparisons of model output with circulation tracers including θ, salinity, CFC-12, and radiocarbon permit a test of the physical exchange scheme. Vertical profiles of biogeochemically reactive components in each of the three regions are in good agreement with observations. Under modern conditions the upwelling zone displays a pronounced oxygen minimum zone and water column denitrification, while these are not present in the high-latitude or gyre regions. Model-generated global fluxes also compare well to independent estimates of primary production, burial, and phosphorous and nitrogen cycling. The ICBM appears to adequately simulate the long-term (kyr) evolution of several biogeochemical cycles and improves on previous box models in several important ways. In a companion paper, the model's performance under euxinic conditions is tested against modern Black Sea data. The simple and adaptable structure of the model should make it applicable to a wide range of paleoceanographic problems. The model source code is available in MATLABTM 7 m-files provided as auxiliary material.

Optical scheme for simulating post-quantum nonlocality distillation.

PubMed

Chu, Wen-Jing; Yang, Ming; Pan, Guo-Zhu; Yang, Qing; Cao, Zhuo-Liang

2016-11-28

An optical scheme for simulating nonlocality distillation is proposed in post-quantum regime. The nonlocal boxes are simulated by measurements on appropriately pre- and post-selected polarization entangled photon pairs, i.e. post-quantum nonlocality is simulated by exploiting fair-sampling loophole in a Bell test. Mod 2 addition on the outputs of two nonlocal boxes combined with pre- and post-selection operations constitutes the key operation of simulating nonlocality distillation. This scheme provides a possible tool for the experimental study on the nonlocality in post-quantum regime and the exact physical principle precisely distinguishing physically realizable correlations from nonphysical ones.

Homemade laparoscopic simulators for surgical trainees.

PubMed

Khine, Myo; Leung, Edward; Morran, Chris; Muthukumarasamy, Giri

2011-06-01

Laparoscopic surgery has become increasingly popular in recent times. Laparoscopic skills and dexterity can be improved by using simulators. We provide a step-by-step guide with diagrams to build an individual homemade laparoscopic trainer box, which is easily available and affordable. We collected the required material for our homemade trainer box from a local DIY shop and purchased a high-definition (HD) webcam online. We used a 12-litre plastic storage box and mounted the webcam inside the lid of the plastic box. The ultraslim energy-saving fluorescent light was mounted behind the webcam. Holes were made in the plastic lid and patched with circular pieces of Neoprene to accommodate the insertion of laparoscopic instruments. The trainer box can be built in 3 hours. The trainer box weighs 1.2 kg with a light source, and is easily portable. It was demonstrated to a cohort of surgical trainees and they were very receptive, and liked the idea of an easy to assemble, low-cost trainer box with high-quality images. Our homemade trainer box offers HD vision that can be viewed on a personal computer, and the webcam is adjustable so it gives hands-free stability. It is built with a lightweight plastic box so it can be easily carried around by a trainee. This simple, inexpensive, easy-to-build trainer box makes a perfect solution for individuals who want to practise basic laparoscopic skills at home or in the workplace. © Blackwell Publishing Ltd 2011.

Self-organization in the limb: a Turing mechanism for digit development.

PubMed

Cooper, Kimberly L

2015-06-01

The statistician George E. P. Box stated, 'Essentially all models are wrong, but some are useful.' (Box GEP, Draper NR: Empirical Model-Building and Response Surfaces. Wiley; 1987). Modeling biological processes is challenging for many of the reasons classically trained developmental biologists often resist the idea that black and white equations can explain the grayscale subtleties of living things. Although a simplified mathematical model of development will undoubtedly fall short of precision, a good model is exceedingly useful if it raises at least as many testable questions as it answers. Self-organizing Turing models that simulate the pattern of digits in the hand replicate events that have not yet been explained by classical approaches. The union of theory and experimentation has recently identified and validated the minimal components of a Turing network for digit pattern and triggered a cascade of questions that will undoubtedly be well-served by the continued merging of disciplines. Copyright © 2015 Elsevier Ltd. All rights reserved.

X-ray clusters in a cold dark matter + lambda universe: A direct, large-scale, high-resolution, hydrodynamic simulation

NASA Technical Reports Server (NTRS)

Cen, Renyue; Ostriker, Jeremiah P.

1994-01-01

A new, three-dimensional, shock-capturing, hydrodynamic code is utilized to determine the distribution of hot gas in a cold dark matter (CDM) + lambda model universe. Periodic boundary conditions are assumed: a box with size 85/h Mpc, having cell size 0.31/h Mpc, is followed in a simulation with 270(exp 3) = 10(exp 7.3) cells. We adopt omega = 0.45, lambda = 0.55, h identically equal to H/100 km/s/Mpc = 0.6, and then, from the cosmic background explorer (COBE) and light element nucleosynthesis, sigma(sub 8) = 0.77, omega(sub b) = 0.043. We identify the X-ray emitting clusters in the simulation box, compute the luminosity function at several wavelength bands, the temperature function and estimated sizes, as well as the evolution of these quantities with redshift. This open model succeeds in matching local observations of clusters in contrast to the standard omega = 1, CDM model, which fails. It predicts an order of magnitude decline in the number density of bright (h nu = 2-10 keV) clusters from z = 0 to z = 2 in contrast to a slight increase in the number density for standard omega = 1, CDM model. This COBE-normalized CDM + lambda model produces approximately the same number of X-ray clusters having L(sub x) greater than 10(exp 43) erg/s as observed. The background radiation field at 1 keV due to clusters is approximately the observed background which, after correction for numerical effects, again indicates that the model is consistent with observations.

Root architecture simulation improves the inference from seedling root phenotyping towards mature root systems.

PubMed

Zhao, Jiangsan; Bodner, Gernot; Rewald, Boris; Leitner, Daniel; Nagel, Kerstin A; Nakhforoosh, Alireza

2017-02-01

Root phenotyping provides trait information for plant breeding. A shortcoming of high-throughput root phenotyping is the limitation to seedling plants and failure to make inferences on mature root systems. We suggest root system architecture (RSA) models to predict mature root traits and overcome the inference problem. Sixteen pea genotypes were phenotyped in (i) seedling (Petri dishes) and (ii) mature (sand-filled columns) root phenotyping platforms. The RSA model RootBox was parameterized with seedling traits to simulate the fully developed root systems. Measured and modelled root length, first-order lateral number, and root distribution were compared to determine key traits for model-based prediction. No direct relationship in root traits (tap, lateral length, interbranch distance) was evident between phenotyping systems. RootBox significantly improved the inference over phenotyping platforms. Seedling plant tap and lateral root elongation rates and interbranch distance were sufficient model parameters to predict genotype ranking in total root length with an RSpearman of 0.83. Parameterization including uneven lateral spacing via a scaling function substantially improved the prediction of architectures underlying the differently sized root systems. We conclude that RSA models can solve the inference problem of seedling root phenotyping. RSA models should be included in the phenotyping pipeline to provide reliable information on mature root systems to breeding research. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Crashworthiness Design for Bionic Bumper Structures Inspired by Cattail and Bamboo.

PubMed

Xu, Tao; Liu, Nian; Yu, Zhenglei; Xu, Tianshuang; Zou, Meng

2017-01-01

Many materials in nature exhibit excellent mechanical properties. In this study, we evaluated the bionic bumper structure models by using nonlinear finite element (FE) simulations for their crashworthiness under full-size impact loading. The structure contained the structural characteristics of cattail and bamboo. The results indicated that the bionic design enhances the specific energy absorption (SEA) of the bumper. The numerical results showed that the bionic cross-beam and bionic box of the bionic bumper have a significant effect on the crashworthiness of the structure. The crush deformation of bionic cross-beam and box bumper model was reduced by 33.33%, and the total weight was reduced by 44.44%. As the energy absorption capacity under lateral impact, the bionic design can be used in the future bumper body.

Crashworthiness Design for Bionic Bumper Structures Inspired by Cattail and Bamboo

PubMed Central

Xu, Tao; Liu, Nian

2017-01-01

Many materials in nature exhibit excellent mechanical properties. In this study, we evaluated the bionic bumper structure models by using nonlinear finite element (FE) simulations for their crashworthiness under full-size impact loading. The structure contained the structural characteristics of cattail and bamboo. The results indicated that the bionic design enhances the specific energy absorption (SEA) of the bumper. The numerical results showed that the bionic cross-beam and bionic box of the bionic bumper have a significant effect on the crashworthiness of the structure. The crush deformation of bionic cross-beam and box bumper model was reduced by 33.33%, and the total weight was reduced by 44.44%. As the energy absorption capacity under lateral impact, the bionic design can be used in the future bumper body. PMID:29118571

Computer Simulations of Epoxy Adhesive Monomer Interactions with Alumina Surfaces

DTIC Science & Technology

1992-08-01

using Sybyl"’ molecular modeling software 9 on a Digital Equipment Corporation microVAXw cluster. The Tripos force field was employed in the...Ave, N, Ft Leonard Wood, MO 65473-5000 1 ATM- Libary Commander, US. Army Enginer Waterways Expenment Station, P.O. Box 631, Vicksburg, MS 39180 1 ATTN

Atomic displacements in the charge ice pyrochlore Bi2Ti2O6O' studied by neutron total scattering

NASA Astrophysics Data System (ADS)

Shoemaker, Daniel P.; Seshadri, Ram; Hector, Andrew L.; Llobet, Anna; Proffen, Thomas; Fennie, Craig J.

2010-04-01

The oxide pyrochlore Bi2Ti2O6O' is known to be associated with large displacements of Bi and O' atoms from their ideal crystallographic positions. Neutron total scattering, analyzed in both reciprocal and real space, is employed here to understand the nature of these displacements. Rietveld analysis and maximum entropy methods are used to produce an average picture of the structural nonideality. Local structure is modeled via large-box reverse Monte Carlo simulations constrained simultaneously by the Bragg profile and real-space pair distribution function. Direct visualization and statistical analyses of these models show the precise nature of the static Bi and O' displacements. Correlations between neighboring Bi displacements are analyzed using coordinates from the large-box simulations. The framework of continuous symmetry measures has been applied to distributions of O'Bi4 tetrahedra to examine deviations from ideality. Bi displacements from ideal positions appear correlated over local length scales. The results are consistent with the idea that these nonmagnetic lone-pair containing pyrochlore compounds can be regarded as highly structurally frustrated systems.

Comparative Performance Evaluation of Rainfall-runoff Models, Six of Black-box Type and One of Conceptual Type, From The Galway Flow Forecasting System (gffs) Package, Applied On Two Irish Catchments

NASA Astrophysics Data System (ADS)

Goswami, M.; O'Connor, K. M.; Shamseldin, A. Y.

The "Galway Real-Time River Flow Forecasting System" (GFFS) is a software pack- age developed at the Department of Engineering Hydrology, of the National University of Ireland, Galway, Ireland. It is based on a selection of lumped black-box and con- ceptual rainfall-runoff models, all developed in Galway, consisting primarily of both the non-parametric (NP) and parametric (P) forms of two black-box-type rainfall- runoff models, namely, the Simple Linear Model (SLM-NP and SLM-P) and the seasonally-based Linear Perturbation Model (LPM-NP and LPM-P), together with the non-parametric wetness-index-based Linearly Varying Gain Factor Model (LVGFM), the black-box Artificial Neural Network (ANN) Model, and the conceptual Soil Mois- ture Accounting and Routing (SMAR) Model. Comprised of the above suite of mod- els, the system enables the user to calibrate each model individually, initially without updating, and it is capable also of producing combined (i.e. consensus) forecasts us- ing the Simple Average Method (SAM), the Weighted Average Method (WAM), or the Artificial Neural Network Method (NNM). The updating of each model output is achieved using one of four different techniques, namely, simple Auto-Regressive (AR) updating, Linear Transfer Function (LTF) updating, Artificial Neural Network updating (NNU), and updating by the Non-linear Auto-Regressive Exogenous-input method (NARXM). The models exhibit a considerable range of variation in degree of complexity of structure, with corresponding degrees of complication in objective func- tion evaluation. Operating in continuous river-flow simulation and updating modes, these models and techniques have been applied to two Irish catchments, namely, the Fergus and the Brosna. A number of performance evaluation criteria have been used to comparatively assess the model discharge forecast efficiency.

CatSim: a new computer assisted tomography simulation environment

NASA Astrophysics Data System (ADS)

De Man, Bruno; Basu, Samit; Chandra, Naveen; Dunham, Bruce; Edic, Peter; Iatrou, Maria; McOlash, Scott; Sainath, Paavana; Shaughnessy, Charlie; Tower, Brendon; Williams, Eugene

2007-03-01

We present a new simulation environment for X-ray computed tomography, called CatSim. CatSim provides a research platform for GE researchers and collaborators to explore new reconstruction algorithms, CT architectures, and X-ray source or detector technologies. The main requirements for this simulator are accurate physics modeling, low computation times, and geometrical flexibility. CatSim allows simulating complex analytic phantoms, such as the FORBILD phantoms, including boxes, ellipsoids, elliptical cylinders, cones, and cut planes. CatSim incorporates polychromaticity, realistic quantum and electronic noise models, finite focal spot size and shape, finite detector cell size, detector cross-talk, detector lag or afterglow, bowtie filtration, finite detector efficiency, non-linear partial volume, scatter (variance-reduced Monte Carlo), and absorbed dose. We present an overview of CatSim along with a number of validation experiments.

Partial molar enthalpies and reaction enthalpies from equilibrium molecular dynamics simulation

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

Schnell, Sondre K.; Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720; Department of Chemistry, Faculty of Natural Science and Technology, Norwegian University of Science and Technology, 4791 Trondheim

2014-10-14

We present a new molecular simulation technique for determining partial molar enthalpies in mixtures of gases and liquids from single simulations, without relying on particle insertions, deletions, or identity changes. The method can also be applied to systems with chemical reactions. We demonstrate our method for binary mixtures of Weeks-Chandler-Anderson particles by comparing with conventional simulation techniques, as well as for a simple model that mimics a chemical reaction. The method considers small subsystems inside a large reservoir (i.e., the simulation box), and uses the construction of Hill to compute properties in the thermodynamic limit from small-scale fluctuations. Results obtainedmore » with the new method are in excellent agreement with those from previous methods. Especially for modeling chemical reactions, our method can be a valuable tool for determining reaction enthalpies directly from a single MD simulation.« less

Saturation of the magnetorotational instability in the unstratified shearing box with zero net flux: convergence in taller boxes

NASA Astrophysics Data System (ADS)

Shi, Ji-Ming; Stone, James M.; Huang, Chelsea X.

2016-03-01

Previous studies of the non-linear regime of the magnetorotational instability in one particular type of shearing box model - unstratified with no net magnetic flux - find that without explicit dissipation (viscosity and resistivity) the saturation amplitude decreases with increasing numerical resolution. We show that this result is strongly dependent on the vertical aspect ratio of the computational domain Lz/Lx. When Lz/Lx ≲ 1, we recover previous results. However, when the vertical domain is extended Lz/Lx ≳ 2.5, we find the saturation level of the stress is greatly increased (giving a ratio of stress to pressure α ≳ 0.1), and moreover the results are independent of numerical resolution. Consistent with previous results, we find that saturation of the magnetorotational (MRI) in this regime is controlled by a cyclic dynamo which generates patches of strong toroidal field that switches sign on scales of Lx in the vertical direction. We speculate that when Lz/Lx ≲ 1, the dynamo is inhibited by the small size of the vertical domain, leading to the puzzling dependence of saturation amplitude on resolution. We show that previous toy models developed to explain the MRI dynamo are consistent with our results, and that the cyclic pattern of toroidal fields observed in stratified shearing box simulations (leading to the so-called butterfly diagram) may also be related. In tall boxes the saturation amplitude is insensitive to whether or not explicit dissipation is included in the calculations, at least for large magnetic Reynolds and Prandtl number. Finally, we show MRI turbulence in tall domains has a smaller critical Pmc, and an extended lifetime compared to Lz/Lx ≲ 1 boxes.

Granular Crater Formation

NASA Astrophysics Data System (ADS)

Clark, Abe; Behringer, Robert; Brandenburg, John

2009-11-01

This project characterizes crater formation in a granular material by a jet of gas impinging on a granular material, such as a retro-rocket landing on the moon. We have constructed a 2D model of a planetary surface, which consists of a thin, clear box partially filled with granular materials (sand, lunar and Mars simulants...). A metal pipe connected to a tank of nitrogen gas via a solenoid valve is inserted into the top of the box to model the rocket. The results are recorded using high-speed video. We process these images and videos in order to test existing models and develop new ones for describing crater formation. A similar set-up has been used by Metzger et al.footnotetextP. T. Metzger et al. Journal of Aerospace Engineering (2009) We find that the long-time shape of the crater is consistent with a predicted catenary shape (Brandenburg). The depth and width of the crater both evolve logarithmically in time, suggesting an analogy to a description in terms of an activated process: dD/dt = A (-aD) (D is the crater depth, a and A constants). This model provides a useful context to understand the role of the jet speed, as characterized by the pressure used to drive the flow. The box width also plays an important role in setting the width of the crater.

Operator’s Manual for Variable Weight, Variable C.G. Helmet Simulator

DTIC Science & Technology

1981-09-01

fdoestify by block nufber) - A variable weight, variable CG helmet simulator has been designed to measure the effect of US Army headgear on muscle...any variable weights in the boxes, is 2.5 lb, slightly less than the weight of most quality crash helmets made by reputable manufacturers. The addition...of variable weights to the boxes can alter the center of gravity to simulate the effect of equipment attached to the out- side of a helmet. The

Shadow: Running Tor in a Box for Accurate and Efficient Experimentation

DTIC Science & Technology

2011-09-23

Modeling the speed of a target CPU is done by running an OpenSSL [31] speed test on a real CPU of that type. This provides us with the raw CPU processing...rate, but we are also interested in the processing speed of an application. By running application 5 benchmarks on the same CPU as the OpenSSL speed test...simulation, saving CPU cy- cles on our simulation host machine. Shadow removes cryptographic processing by preloading the main OpenSSL [31] functions used

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

A theoretical and simulation study of the contact discontinuities based on a Vlasov simulation code

NASA Astrophysics Data System (ADS)

Tsai, T. C.; Lyu, L. H.; Chao, J. K.; Chen, M. Q.; Tsai, W. H.

2009-12-01

Contact discontinuity (CD) is the simplest solution that can be obtained from the magnetohydrodynamics (MHD) Rankine-Hugoniot jump conditions. Due to the limitations of the previous kinetic simulation models, the stability of the CD has become a controversial issue in the past 10 years. The stability of the CD is reexamined analytically and numerically. Our theoretical analysis shows that the electron temperature profile and the ion temperature profile must be out of phase across the CD if the CD structure is to be stable in the electron time scale and with zero electron heat flux on either side of the CD. Both a newly developed fourth-order implicit electrostatic Vlasov simulation code and an electromagnetic finite-size particle code are used to examine the stability and the electrostatic nature of the CD structure. Our theoretical prediction is verified by both simulations. Our results of Vlasov simulation also indicate that a simulation with initial electron temperature profile and ion temperature profile varying in phase across the CD will undergo very transient changes in the electron time scale but will relax into a quasi-steady CD structure within a few ion plasma oscillation periods if a real ion-electron mass ratio is used in the simulation and if the boundary conditions allow nonzero heat flux to be presented at the boundaries of the simulation box. The simulation results of this study indicate that the Vlasov simulation is a powerful tool to study nonlinear phenomena with nonperiodic boundary conditions and with nonzero heat flux at the boundaries of the simulation box.

Box- or Virtual-Reality Trainer: Which Tool Results in Better Transfer of Laparoscopic Basic Skills?-A Prospective Randomized Trial.

PubMed

Brinkmann, Christian; Fritz, Mathias; Pankratius, Ulrich; Bahde, Ralf; Neumann, Philipp; Schlueter, Steffen; Senninger, Norbert; Rijcken, Emile

Simulation training improves laparoscopic performance. Laparoscopic basic skills can be learned in simulators as box- or virtual-reality (VR) trainers. However, there is no clear recommendation for either box or VR trainers as the most appropriate tool for the transfer of acquired laparoscopic basic skills into a surgical procedure. Both training tools were compared, using validated and well-established curricula in the acquirement of basic skills, in a prospective randomized trial in a 5-day structured laparoscopic training course. Participants completed either a box- or VR-trainer curriculum and then applied the learned skills performing an ex situ laparoscopic cholecystectomy on a pig liver. The performance was recorded on video and evaluated offline by 4 blinded observers using the Global Operative Assessment of Laparoscopic Skills (GOALS) score. Learning curves of the various exercises included in the training course were compared and the improvement in each exercise was analyzed. Surgical Skills Lab of the Department of General and Visceral Surgery, University Hospital Muenster. Surgical novices without prior surgical experience (medical students, n = 36). Posttraining evaluation showed significant improvement compared with baseline in both groups, indicating acquisition of laparoscopic basic skills. Learning curves showed almost the same progression with no significant differences. In simulated laparoscopic cholecystectomy, total GOALS score was significantly higher for the box-trained group than the VR-trained group (box: 15.31 ± 3.61 vs. VR: 12.92 ± 3.06; p = 0.039; Hedge׳s g* = 0.699), indicating higher technical skill levels. Despite both systems having advantages and disadvantages, they can both be used for simulation training for laparoscopic skills. In the setting with 2 structured, validated and almost identical curricula, the box-trained group appears to be superior in the better transfer of basic skills into an experimental but structured surgical procedure. Copyright © 2017 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.

Electric Power Distribution System Model Simplification Using Segment Substitution

DOE PAGES

Reiman, Andrew P.; McDermott, Thomas E.; Akcakaya, Murat; ...

2017-09-20

Quasi-static time-series (QSTS) simulation is used to simulate the behavior of distribution systems over long periods of time (typically hours to years). The technique involves repeatedly solving the load-flow problem for a distribution system model and is useful for distributed energy resource (DER) planning. When a QSTS simulation has a small time step and a long duration, the computational burden of the simulation can be a barrier to integration into utility workflows. One way to relieve the computational burden is to simplify the system model. The segment substitution method of simplifying distribution system models introduced in this paper offers modelmore » bus reduction of up to 98% with a simplification error as low as 0.2% (0.002 pu voltage). Finally, in contrast to existing methods of distribution system model simplification, which rely on topological inspection and linearization, the segment substitution method uses black-box segment data and an assumed simplified topology.« less

Automated chemical kinetic modeling via hybrid reactive molecular dynamics and quantum chemistry simulations.

PubMed

Döntgen, Malte; Schmalz, Felix; Kopp, Wassja A; Kröger, Leif C; Leonhard, Kai

2018-06-13

An automated scheme for obtaining chemical kinetic models from scratch using reactive molecular dynamics and quantum chemistry simulations is presented. This methodology combines the phase space sampling of reactive molecular dynamics with the thermochemistry and kinetics prediction capabilities of quantum mechanics. This scheme provides the NASA polynomial and modified Arrhenius equation parameters for all species and reactions that are observed during the simulation and supplies them in the ChemKin format. The ab initio level of theory for predictions is easily exchangeable and the presently used G3MP2 level of theory is found to reliably reproduce hydrogen and methane oxidation thermochemistry and kinetics data. Chemical kinetic models obtained with this approach are ready-to-use for, e.g., ignition delay time simulations, as shown for hydrogen combustion. The presented extension of the ChemTraYzer approach can be used as a basis for methodologically advancing chemical kinetic modeling schemes and as a black-box approach to generate chemical kinetic models.

Electric Power Distribution System Model Simplification Using Segment Substitution

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

Reiman, Andrew P.; McDermott, Thomas E.; Akcakaya, Murat

Quasi-static time-series (QSTS) simulation is used to simulate the behavior of distribution systems over long periods of time (typically hours to years). The technique involves repeatedly solving the load-flow problem for a distribution system model and is useful for distributed energy resource (DER) planning. When a QSTS simulation has a small time step and a long duration, the computational burden of the simulation can be a barrier to integration into utility workflows. One way to relieve the computational burden is to simplify the system model. The segment substitution method of simplifying distribution system models introduced in this paper offers modelmore » bus reduction of up to 98% with a simplification error as low as 0.2% (0.002 pu voltage). Finally, in contrast to existing methods of distribution system model simplification, which rely on topological inspection and linearization, the segment substitution method uses black-box segment data and an assumed simplified topology.« less

A Monte-Carlo Analysis of Organic Volatility with Aerosol Microphysics

NASA Astrophysics Data System (ADS)

Gao, Chloe; Tsigaridis, Kostas; Bauer, Susanne E.

2017-04-01

A newly developed box model, MATRIX-VBS, includes the volatility-basis set (VBS) framework in an aerosol microphysical scheme MATRIX (Multiconfiguration Aerosol TRacker of mIXing state), which resolves aerosol mass and number concentrations and aerosol mixing state. The new scheme advanced the representation of organic aerosols in models by improving the traditional and simplistic treatment of organic aerosols as non-volatile and with a fixed size distribution. Further development includes adding the condensation of organics on coarse mode aerosols - dust and sea salt, thus making all organics in the system semi-volatile. To test and simplify the model, a Monte-Carlo analysis is performed to pin point which processes affect organics the most under varied chemical and meteorological conditions. Since the model's parameterizations have the ability to capture a very wide range of conditions, all possible scenarios on Earth across the whole parameter space, including temperature, humidity, location, emissions and oxidant levels, are examined. The Monte-Carlo simulations provide quantitative information on the sensitivity of the newly developed model and help us understand how organics are affecting the size distribution, mixing state and volatility distribution at varying levels of meteorological conditions and pollution levels. In addition, these simulations give information on which parameters play a critical role in the aerosol distribution and evolution in the atmosphere and which do not, that will facilitate the simplification of the box model, an important step in its implementation in the global model GISS ModelE as a module.

The Mind as Black Box: A Simulation of Theory Building in Psychology.

ERIC Educational Resources Information Center

Hildebrandt, Carolyn; Oliver, Jennifer

2000-01-01

Discusses an activity that uses the metaphor "the mind is a black box," in which students work in groups to discover what is inside a sealed, black, plastic box. States that the activity enables students to understand the need for theories in psychology and to comprehend how psychologists build, test, and refine those theories. (CMK)

Ureteroscopic skills with and without Roboflex Avicenna in the K-box® simulator.

PubMed

Proietti, Silvia; Dragos, Laurian; Emiliani, Esteban; Butticè, Salvatore; Talso, Michele; Baghdadi, Mohammed; Villa, Luca; Doizi, Steeve; Giusti, Guido; Traxer, Olivier

2017-01-01

The aim of this study was to evaluate the acquisition of basic ureteroscopic skills with and without Roboflex Avicenna by subjects with no prior surgical training. Ten medical students were divided in two groups: Group 1 was trained with Roboflex Avicenna and Group 2 with flexible ureteroscope alone, using the K-box ® simulator model. Participants were scored on their ability to perform or not two exercises, recording the time. In addition, the participants were evaluated on the quality of their performance for the following parameters: respect of the surrounding environment, flow of the operation, orientation, vision centering and stability. The first exercise was completed only by three and four out of five of students in Group 1 and Group 2, respectively. Stability with the scope was significantly more accurate in the first group compared with the second (P = 0.02). There were no differences in timing, flow or orientation between groups. Although not significant, a tendency of respecting the surrounding tissue and maintaining centered vision was perceived more in the first group. As for the second exercise, there were no differences between groups in regard of orientation, flow, respecting the surrounding tissue, stability or the ability of maintaining centered vision. Although not significant, the second group had a tendency of performing the exercise faster. According to these preliminary results, the acquisition of basic ureteroscopic skills with and without robotic fURS in the K-box ® simulator, by subjects with no prior surgical training, is similar.

Interpretable inference on the mixed effect model with the Box-Cox transformation.

PubMed

Maruo, K; Yamaguchi, Y; Noma, H; Gosho, M

2017-07-10

We derived results for inference on parameters of the marginal model of the mixed effect model with the Box-Cox transformation based on the asymptotic theory approach. We also provided a robust variance estimator of the maximum likelihood estimator of the parameters of this model in consideration of the model misspecifications. Using these results, we developed an inference procedure for the difference of the model median between treatment groups at the specified occasion in the context of mixed effects models for repeated measures analysis for randomized clinical trials, which provided interpretable estimates of the treatment effect. From simulation studies, it was shown that our proposed method controlled type I error of the statistical test for the model median difference in almost all the situations and had moderate or high performance for power compared with the existing methods. We illustrated our method with cluster of differentiation 4 (CD4) data in an AIDS clinical trial, where the interpretability of the analysis results based on our proposed method is demonstrated. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

A random effects meta-analysis model with Box-Cox transformation.

PubMed

Yamaguchi, Yusuke; Maruo, Kazushi; Partlett, Christopher; Riley, Richard D

2017-07-19

In a random effects meta-analysis model, true treatment effects for each study are routinely assumed to follow a normal distribution. However, normality is a restrictive assumption and the misspecification of the random effects distribution may result in a misleading estimate of overall mean for the treatment effect, an inappropriate quantification of heterogeneity across studies and a wrongly symmetric prediction interval. We focus on problems caused by an inappropriate normality assumption of the random effects distribution, and propose a novel random effects meta-analysis model where a Box-Cox transformation is applied to the observed treatment effect estimates. The proposed model aims to normalise an overall distribution of observed treatment effect estimates, which is sum of the within-study sampling distributions and the random effects distribution. When sampling distributions are approximately normal, non-normality in the overall distribution will be mainly due to the random effects distribution, especially when the between-study variation is large relative to the within-study variation. The Box-Cox transformation addresses this flexibly according to the observed departure from normality. We use a Bayesian approach for estimating parameters in the proposed model, and suggest summarising the meta-analysis results by an overall median, an interquartile range and a prediction interval. The model can be applied for any kind of variables once the treatment effect estimate is defined from the variable. A simulation study suggested that when the overall distribution of treatment effect estimates are skewed, the overall mean and conventional I 2 from the normal random effects model could be inappropriate summaries, and the proposed model helped reduce this issue. We illustrated the proposed model using two examples, which revealed some important differences on summary results, heterogeneity measures and prediction intervals from the normal random effects model. The random effects meta-analysis with the Box-Cox transformation may be an important tool for examining robustness of traditional meta-analysis results against skewness on the observed treatment effect estimates. Further critical evaluation of the method is needed.

A comparative study on the risk of second primary cancers in out-of-field organs associated with radiotherapy of localized prostate carcinoma using Monte Carlo-based accelerator and patient models

PubMed Central

Bednarz, Bryan; Athar, Basit; Xu, X. George

2010-01-01

Purpose: A physician’s decision regarding an ideal treatment approach (i.e., radiation, surgery, and∕or hormonal) for prostate carcinoma is traditionally based on a variety of metrics. One of these metrics is the risk of radiation-induced second primary cancer following radiation treatments. The aim of this study was to investigate the significance of second cancer risks in out-of-field organs from 3D-CRT and IMRT treatments of prostate carcinoma compared to baseline cancer risks in these organs. Methods: Monte Carlo simulations were performed using a detailed medical linear accelerator model and an anatomically realistic adult male whole-body phantom. A four-field box treatment, a four-field box treatment plus a six-field boost, and a seven-field IMRT treatment were simulated. Using BEIR VII risk models, the age-dependent lifetime attributable risks to various organs outside the primary beam with a known predilection for cancer were calculated using organ-averaged equivalent doses. Results: The four-field box treatment had the lowest treatment-related second primary cancer risks to organs outside the primary beam ranging from 7.3×10−9 to 2.54×10−5%∕MU depending on the patients age at exposure and second primary cancer site. The risks to organs outside the primary beam from the four-field box and six-field boost and the seven-field IMRT were nearly equivalent. The risks from the four-field box and six-field boost ranged from 1.39×10−8 to 1.80×10−5%∕MU, and from the seven-field IMRT ranged from 1.60×10−9 to 1.35×10−5%∕MU. The second cancer risks in all organs considered from each plan were below the baseline risks. Conclusions: The treatment-related second cancer risks in organs outside the primary beam due to 3D-CRT and IMRT is small. New risk assessment techniques need to be investigated to address the concern of radiation-induced second cancers from prostate treatments, particularly focusing on risks to organs inside the primary beam. PMID:20527532

Exploring global carbon turnover and radiocarbon cycling in terrestrial biosphere models

NASA Astrophysics Data System (ADS)

Graven, H. D.; Warren, H.

2017-12-01

The uptake of carbon into terrestrial ecosystems through net primary productivity (NPP) and the turnover of that carbon through various pathways are the fundamental drivers of changing carbon stocks on land, in addition to human-induced and natural disturbances. Terrestrial biosphere models use different formulations for carbon uptake and release, resulting in a range of values in NPP of 40-70 PgC/yr and biomass turnover times of about 25-40 years for the preindustrial period in current-generation models from CMIP5. Biases in carbon uptake and turnover impact simulated carbon uptake and storage in the historical period and later in the century under changing climate and CO2 concentration, however evaluating global-scale NPP and carbon turnover is challenging. Scaling up of plot-scale measurements involves uncertainty due to the large heterogeneity across ecosystems and biomass types, some of which are not well-observed. We are developing the modelling of radiocarbon in terrestrial biosphere models, with a particular focus on decadal 14C dynamics after the nuclear weapons testing in the 1950s-60s, including the impact of carbon flux trends and variability on 14C cycling. We use an estimate of the total inventory of excess 14C in the biosphere constructed by Naegler and Levin (2009) using a 14C budget approach incorporating estimates of total 14C produced by the weapons tests and atmospheric and oceanic 14C observations. By simulating radiocarbon in simple biosphere box models using carbon fluxes from the CMIP5 models, we find that carbon turnover is too rapid in many of the simple models - the models appear to take up too much 14C and release it too quickly. Therefore many CMIP5 models may also simulate carbon turnover that is too rapid. A caveat is that the simple box models we use may not adequately represent carbon dynamics in the full-scale models. Explicit simulation of radiocarbon in terrestrial biosphere models would allow more robust evaluation of biosphere models and the investigation of climate-carbon cycle feedbacks on various timescales. Explicit simulation of radiocarbon and carbon-13 in terrestrial biosphere models of Earth System Models, as well as in ocean models, is recommended by CMIP6 and supported by CMIP6 protocols and forcing datasets.

Computational Fluid Dynamics Analysis of Flexible Duct Junction Box Design

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

Beach, Robert; Prahl, Duncan; Lange, Rich

2013-12-01

IBACOS explored the relationships between pressure and physical configurations of flexible duct junction boxes by using computational fluid dynamics (CFD) simulations to predict individual box parameters and total system pressure, thereby ensuring improved HVAC performance. Current Air Conditioning Contractors of America (ACCA) guidance (Group 11, Appendix 3, ACCA Manual D, Rutkowski 2009) allows for unconstrained variation in the number of takeoffs, box sizes, and takeoff locations. The only variables currently used in selecting an equivalent length (EL) are velocity of air in the duct and friction rate, given the first takeoff is located at least twice its diameter away frommore » the inlet. This condition does not account for other factors impacting pressure loss across these types of fittings. For each simulation, the IBACOS team converted pressure loss within a box to an EL to compare variation in ACCA Manual D guidance to the simulated variation. IBACOS chose cases to represent flows reasonably correlating to flows typically encountered in the field and analyzed differences in total pressure due to increases in number and location of takeoffs, box dimensions, and velocity of air, and whether an entrance fitting is included. The team also calculated additional balancing losses for all cases due to discrepancies between intended outlet flows and natural flow splits created by the fitting. In certain asymmetrical cases, the balancing losses were significantly higher than symmetrical cases where the natural splits were close to the targets. Thus, IBACOS has shown additional design constraints that can ensure better system performance.« less

Rotational Diffusion Depends on Box Size in Molecular Dynamics Simulations.

PubMed

Linke, Max; Köfinger, Jürgen; Hummer, Gerhard

2018-06-07

We show that the rotational dynamics of proteins and nucleic acids determined from molecular dynamics simulations under periodic boundary conditions suffer from significant finite-size effects. We remove the box-size dependence of the rotational diffusion coefficients by adding a hydrodynamic correction k B T/6 ηV with k B Boltzmann's constant, T the absolute temperature, η the solvent shear viscosity, and V the box volume. We show that this correction accounts for the finite-size dependence of the rotational diffusion coefficients of horse-heart myoglobin and a B-DNA dodecamer in aqueous solution. The resulting hydrodynamic radii are in excellent agreement with experiment.

[Tools for laparoscopic skill development - available trainers and simulators].

PubMed

Jaksa, László; Haidegger, Tamás; Galambos, Péter; Kiss, Rita

2017-10-01

The laparoscopic minimally invasive surgical technique is widely employed on a global scale. However, the efficient and ethical teaching of this technique requires equipment for surgical simulation. These educational devices are present on the market in the form of box trainers and virtual reality simulators, or some combination of those. In this article, we present a systematic overview of commercially available surgical simulators describing the most important features of each product. Our overview elaborates on box trainers and virtual reality simulators, and also touches on surgical robotics simulators, together with operating room workflow simulators, for the sake of completeness. Apart from presenting educational tools, we evaluated the literature of laparoscopic surgical education and simulation, to provide a complete picture of the unfolding trends in this field. Orv Hetil. 2017; 158(40): 1570-1576.

Using the mind as a simulator: a randomized controlled trial of mental training.

PubMed

Eldred-Evans, David; Grange, Philippe; Cheang, Adrian; Yamamoto, Hidekazu; Ayis, Salma; Mulla, Mubashir; Immenroth, Marc; Sharma, Davendra; Reedy, Gabriel

2013-01-01

Laparoscopic simulators have been introduced as safe and effective methods of developing basic skills. Mental training is a novel training method likened to using the mind as a simulator to mentally rehearse the movements of a task or operation. It is widely used by professional athletes and musicians and has been suggested as a technique that could be used by surgical trainees. The purpose of this study was to assess the use of mental training in developing basic laparoscopic skills in novices. Sixty-four medical students without laparoscopic experience were randomized into 4 groups. The first 3 groups were trained to cut a circle on a box trainer. Group 1 received no additional training (BT), Group 2 received additional virtual reality training (BT + VRS), and Group 3 received additional mental training (BT + MT). The fourth group was trained on a virtual reality simulator with additional mental training (box-free). The following 4 assessment criterias: time, accuracy, precision and overall performance were measured on both the box-trainer and virtual simulator. The mental training group (BT + MT) demonstrated improved laparoscopic skills over both assessments. The improvement in skills in the VRS group (BT + VRS) was limited to VRS assessment and not observed in the box assessment. The fourth group (box-free) had the worst performance on both methods of assessment. The addition of mental training led to improved laparoscopic skills development. It is a flexible technique and has the potential to challenge VRS as a more cost-effective training method associated with lower capital investment. Given the benefits of mental training with further research, it could be considered for inclusion in training curricula. Copyright © 2013 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.

Ignorance is a bliss: Mathematical structure of many-box models

NASA Astrophysics Data System (ADS)

Tylec, Tomasz I.; Kuś, Marek

2018-03-01

We show that the propositional system of a many-box model is always a set-representable effect algebra. In particular cases of 2-box and 1-box models, it is an orthomodular poset and an orthomodular lattice, respectively. We discuss the relation of the obtained results with the so-called Local Orthogonality principle. We argue that non-classical properties of box models are the result of a dual enrichment of the set of states caused by the impoverishment of the set of propositions. On the other hand, quantum mechanical models always have more propositions as well as more states than the classical ones. Consequently, we show that the box models cannot be considered as generalizations of quantum mechanical models and seeking additional principles that could allow us to "recover quantum correlations" in box models are, at least from the fundamental point of view, pointless.

The Model Experiments and Finite Element Analysis on Deformation and Failure by Excavation of Grounds in Foregoing-roof Method

NASA Astrophysics Data System (ADS)

Sotokoba, Yasumasa; Okajima, Kenji; Iida, Toshiaki; Tanaka, Tadatsugu

We propose the trenchless box culvert construction method to construct box culverts in small covering soil layers while keeping roads or tracks open. When we use this construction method, it is necessary to clarify deformation and shear failure by excavation of grounds. In order to investigate the soil behavior, model experiments and elasto-plactic finite element analysis were performed. In the model experiments, it was shown that the shear failure was developed from the end of the roof to the toe of the boundary surface. In the finite element analysis, a shear band effect was introduced. Comparing the observed shear bands in model experiments with computed maximum shear strain contours, it was found that the observed direction of the shear band could be simulated reasonably by the finite element analysis. We may say that the finite element method used in this study is useful tool for this construction method.

Emissions from open burning of simulated military waste from forward operating bases.

PubMed

Aurell, Johanna; Gullett, Brian K; Yamamoto, Dirk

2012-10-16

Emissions from open burning of simulated military waste from forward operating bases (FOBs) were extensively characterized as an initial step in assessing potential inhalation exposure of FOB personnel and future disposal alternatives. Emissions from two different burning scenarios, so-called "burn piles/pits" and an air curtain burner/"burn box", were compared using simulated FOB waste from municipal and commercial sources. A comprehensive array of emissions was quantified, including CO(2), PM(2.5), volatile organic compounds (VOCs), polyaromatic hydrocarbons (PAHs), polychlorinated dibenzodioxins and -furans (PCDDs/PCDFs), polybrominated dibenzodioxins and -furans (PBDDs/PBDFs), and metals. In general, smoldering conditions in the burn box and the burn pile led to similar emissions. However, when the burn box underwent periodic waste charging to maintain sustained combustion, PM(2.5), VOCs, and PAH emissions dropped considerably compared to smoldering conditions and the overall burn pile results. The PCDD/PCDF and PBDD/PBDF emission factors for the burn piles were 50 times higher than those from the burn box likely due to the dominance of smoldering combustion in the burn piles.

Continuous assimilation of simulated Geosat altimetric sea level into an eddy-resolving numerical ocean model. I - Sea level differences. II - Referenced sea level differences

NASA Technical Reports Server (NTRS)

White, Warren B.; Tai, Chang-Kou; Holland, William R.

1990-01-01

The optimal interpolation method of Lorenc (1981) was used to conduct continuous assimilation of altimetric sea level differences from the simulated Geosat exact repeat mission (ERM) into a three-layer quasi-geostrophic eddy-resolving numerical ocean box model that simulates the statistics of mesoscale eddy activity in the western North Pacific. Assimilation was conducted continuously as the Geosat tracks appeared in simulated real time/space, with each track repeating every 17 days, but occurring at different times and locations within the 17-day period, as would have occurred in a realistic nowcast situation. This interpolation method was also used to conduct the assimilation of referenced altimetric sea level differences into the same model, performing the referencing of altimetric sea sevel differences by using the simulated sea level. The results of this dynamical interpolation procedure are compared with those of a statistical (i.e., optimum) interpolation procedure.

Prediction of PM 10 concentrations at urban traffic intersections using semi-empirical box modelling with instantaneous velocity and acceleration

NASA Astrophysics Data System (ADS)

He, Hong-di; Lu, Wei-Zhen; Xue, Yu

2009-12-01

At urban traffic intersections, vehicles frequently stop with idling engines during the red-light period and speed up rapidly during the green-light period. The changes of driving patterns (i.e., idle, acceleration, deceleration and cruising patterns) generally produce uncertain emission. Additionally, the movement of pedestrians and the influence of wind further result in the random dispersion of pollutants. It is, therefore, too complex to simulate the effects of such dynamics on the resulting emission using conventional deterministic causal models. For this reason, a modified semi-empirical box model for predicting the PM 10 concentrations on roadsides is proposed in this paper. The model constitutes three parts, i.e., traffic, emission and dispersion components. The traffic component is developed using a generalized force traffic model to obtain the instantaneous velocity and acceleration when vehicles move through intersections. Hence the distribution of vehicle emission in street canyon during the green-light period is calculated. Then the dispersion component is investigated using a semi-empirical box model combining average wind speed, box height and background concentrations. With these considerations, the proposed model is applied and evaluated using measured data at a busy traffic intersection in Mong Kok, Hong Kong. In order to test the performance of the model, two situations, i.e., the data sets within a sunny day and between two sunny days, were selected to examine the model performance. The predicted values are generally well coincident with the observed data during different time slots except several values are overestimated or underestimated. Moreover, two types of vehicles, i.e., buses and petrol cars, are separately taken into account in the study. Buses are verified to contribute most to the emission in street canyons, which may be useful in evaluating the impact of vehicle emissions on the ambient air quality when there is a significant change in a specific vehicular population.

Mesoscopic-microscopic spatial stochastic simulation with automatic system partitioning.

PubMed

Hellander, Stefan; Hellander, Andreas; Petzold, Linda

2017-12-21

The reaction-diffusion master equation (RDME) is a model that allows for efficient on-lattice simulation of spatially resolved stochastic chemical kinetics. Compared to off-lattice hard-sphere simulations with Brownian dynamics or Green's function reaction dynamics, the RDME can be orders of magnitude faster if the lattice spacing can be chosen coarse enough. However, strongly diffusion-controlled reactions mandate a very fine mesh resolution for acceptable accuracy. It is common that reactions in the same model differ in their degree of diffusion control and therefore require different degrees of mesh resolution. This renders mesoscopic simulation inefficient for systems with multiscale properties. Mesoscopic-microscopic hybrid methods address this problem by resolving the most challenging reactions with a microscale, off-lattice simulation. However, all methods to date require manual partitioning of a system, effectively limiting their usefulness as "black-box" simulation codes. In this paper, we propose a hybrid simulation algorithm with automatic system partitioning based on indirect a priori error estimates. We demonstrate the accuracy and efficiency of the method on models of diffusion-controlled networks in 3D.

A scale-invariant cellular-automata model for distributed seismicity

NASA Technical Reports Server (NTRS)

Barriere, Benoit; Turcotte, Donald L.

1991-01-01

In the standard cellular-automata model for a fault an element of stress is randomly added to a grid of boxes until a box has four elements, these are then redistributed to the adjacent boxes on the grid. The redistribution can result in one or more of these boxes having four or more elements in which case further redistributions are required. On the average added elements are lost from the edges of the grid. The model is modified so that the boxes have a scale-invariant distribution of sizes. The objective is to model a scale-invariant distribution of fault sizes. When a redistribution from a box occurs it is equivalent to a characteristic earthquake on the fault. A redistribution from a small box (a foreshock) can trigger an instability in a large box (the main shock). A redistribution from a large box always triggers many instabilities in the smaller boxes (aftershocks). The frequency-size statistics for both main shocks and aftershocks satisfy the Gutenberg-Richter relation with b = 0.835 for main shocks and b = 0.635 for aftershocks. Model foreshocks occur 28 percent of the time.

Coarse-Grain Molecular Dynamics Simulations To Investigate the Bulk Viscosity and Critical Micelle Concentration of the Ionic Surfactant Sodium Dodecyl Sulfate (SDS) in Aqueous Solution.

PubMed

Ruiz-Morales, Yosadara; Romero-Martínez, Ascención

2018-04-12

The first critical micelle concentration (CMC) of the ionic surfactant sodium dodecyl sulfate (SDS) in diluted aqueous solution has been determined at room temperature from the investigation of the bulk viscosity, at several concentrations of SDS, by means of coarse-grain molecular dynamics simulations. The coarse-grained model molecules at the mesoscale level are adopted. The bulk viscosity of SDS was calculated at several millimolar concentrations of SDS in water using the MARTINI force field by means of NVT shear Mesocite molecular dynamics. The definition of each bead in the MARTINI force field is established, as well as their radius, volume, and mass. The effect of the size of the simulation box on the obtained CMC has been investigated, as well as the effect of the number of SDS molecules, in the simulations, on the formation of aggregates. The CMC, which was obtained from a graph of the calculated viscosities versus concentration, is in good agreement with the reported experimental data and does not depend on the size of the box used in the simulation. The formation of a spherical micelle-like aggregate is observed, where the dodecyl sulfate tails point inward and the heads point outward the aggregation micelle, in accordance with experimental observations. The advantage of using coarse-grain molecular dynamics is the possibility of treating explicitly charged beads, applying a shear flow for viscosity calculation, and processing much larger spatial and temporal scales than atomistic molecular dynamics can. Furthermore, the CMC of SDS obtained with the coarse-grained model is in much better agreement with the experimental value than the value obtained with atomistic simulations.

Desktop chaotic systems: Intuition and visualization

NASA Technical Reports Server (NTRS)

Bright, Michelle M.; Melcher, Kevin J.; Qammar, Helen K.; Hartley, Tom T.

1993-01-01

This paper presents a dynamic study of the Wildwood Pendulum, a commercially available desktop system which exhibits a strange attractor. The purpose of studying this chaotic pendulum is twofold: to gain insight in the paradigmatic approach of modeling, simulating, and determining chaos in nonlinear systems; and to provide a desktop model of chaos as a visual tool. For this study, the nonlinear behavior of this chaotic pendulum is modeled, a computer simulation is performed, and an experimental performance is measured. An assessment of the pendulum in the phase plane shows the strange attractor. Through the use of a box-assisted correlation dimension methodology, the attractor dimension is determined for both the model and the experimental pendulum systems. Correlation dimension results indicate that the pendulum and the model are chaotic and their fractal dimensions are similar.

Impacts of bromine and iodine chemistry on tropospheric OH and HO2: comparing observations with box and global model perspectives

NASA Astrophysics Data System (ADS)

Stone, Daniel; Sherwen, Tomás; Evans, Mathew J.; Vaughan, Stewart; Ingham, Trevor; Whalley, Lisa K.; Edwards, Peter M.; Read, Katie A.; Lee, James D.; Moller, Sarah J.; Carpenter, Lucy J.; Lewis, Alastair C.; Heard, Dwayne E.

2018-03-01

The chemistry of the halogen species bromine and iodine has a range of impacts on tropospheric composition, and can affect oxidising capacity in a number of ways. However, recent studies disagree on the overall sign of the impacts of halogens on the oxidising capacity of the troposphere. We present simulations of OH and HO2 radicals for comparison with observations made in the remote tropical ocean boundary layer during the Seasonal Oxidant Study at the Cape Verde Atmospheric Observatory in 2009. We use both a constrained box model, using detailed chemistry derived from the Master Chemical Mechanism (v3.2), and the three-dimensional global chemistry transport model GEOS-Chem. Both model approaches reproduce the diurnal trends in OH and HO2. Absolute observed concentrations are well reproduced by the box model but are overpredicted by the global model, potentially owing to incomplete consideration of oceanic sourced radical sinks. The two models, however, differ in the impacts of halogen chemistry. In the box model, halogen chemistry acts to increase OH concentrations (by 9.8 % at midday at the Cape Verde Atmospheric Observatory), while the global model exhibits a small increase in OH at the Cape Verde Atmospheric Observatory (by 0.6 % at midday) but overall shows a decrease in the global annual mass-weighted mean OH of 4.5 %. These differences reflect the variety of timescales through which the halogens impact the chemical system. On short timescales, photolysis of HOBr and HOI, produced by reactions of HO2 with BrO and IO, respectively, increases the OH concentration. On longer timescales, halogen-catalysed ozone destruction cycles lead to lower primary production of OH radicals through ozone photolysis, and thus to lower OH concentrations. The global model includes more of the longer timescale responses than the constrained box model, and overall the global impact of the longer timescale response (reduced primary production due to lower O3 concentrations) overwhelms the shorter timescale response (enhanced cycling from HO2 to OH), and thus the global OH concentration decreases. The Earth system contains many such responses on a large range of timescales. This work highlights the care that needs to be taken to understand the full impact of any one process on the system as a whole.

Use of Collapsible Box Trainer as a Module for Resident Education

PubMed Central

Caban, Angel M.; Guido, Christopher; Silver, Michele; Rossidis, George; Sarosi, George

2013-01-01

Background and Objectives: We sought to determine whether training with a simple collapsible mobile box trainer leads to improved performance of fundamental laparoscopic skills (FLSs) during a 6-month interval versus validated laparoscopic box trainers and virtual-reality trainers, only accessible at a simulation training center. Methods: With institutional review board approval, 20 first- and second-year general surgery residents were randomized to scheduled training sessions in a surgical simulation laboratory or training in the use of a portable, collapsible Train Anywhere Skill Kit (TASKit) (Ethicon Endo-Surgery Cincinnati, OH, USA) trainer. Training was geared toward the FLS set for a skill assessment examination at a 6-month interval. Results: The residents who trained with the TASKit performed the peg-transfer, pattern-cut exercise, Endoloop, and intracorporeal knot-tying FLS tasks statistically more efficiently during their 6-month assessment versus their initial evaluation as compared with the group randomized to the simulation laboratory training. Conclusions: Using a simple collapsible mobile box trainer such as the TASKit can be a cost-effective method of training and preparing residents for FLS tasks considering the current cost associated with virtual and high-definition surgical trainers. This mode of surgical training allows residents to practice in their own time by removing barriers associated with simulation centers. PMID:24018083

Virtual suturing simulation based on commodity physics engine for medical learning.

PubMed

Choi, Kup-Sze; Chan, Sze-Ho; Pang, Wai-Man

2012-06-01

Development of virtual-reality medical applications is usually a complicated and labour intensive task. This paper explores the feasibility of using commodity physics engine to develop a suturing simulator prototype for manual skills training in the fields of nursing and medicine, so as to enjoy the benefits of rapid development and hardware-accelerated computation. In the prototype, spring-connected boxes of finite dimension are used to simulate soft tissues, whereas needle and thread are modelled with chained segments. Spherical joints are used to simulate suture's flexibility and to facilitate thread cutting. An algorithm is developed to simulate needle insertion and thread advancement through the tissue. Two-handed manipulations and force feedback are enabled with two haptic devices. Experiments on the closure of a wound show that the prototype is able to simulate suturing procedures at interactive rates. The simulator is also used to study a curvature-adaptive suture modelling technique. Issues and limitations of the proposed approach and future development are discussed.

Random access codes and nonlocal resources

NASA Astrophysics Data System (ADS)

Chaturvedi, Anubhav; Pawlowski, Marcin; Horodecki, Karol

2017-08-01

This work explores the notion of inter-convertibility between a cryptographic primitive: the random access code (RAC) and bipartite no-signaling nonlocal resources. To this end we introduce two generalizations of the Popescu-Rohrlich box (PR) and investigate their relation with the corresponding RACs. The first generalization is based on the number of Alice's input bits; we refer to it as the Bn-box. We show that the no-signaling condition imposes an equivalence between the Bn-box and the (n →1 ) RAC (encoding of n input bits to 1 bit of message). As an application we show that (n -1 ) PRs supplemented with one bit communication are necessary and sufficient to win a (n →1 ) RAC with certainty. Furthermore, we present a signaling instant of a perfectly working (n →1 ) RAC which cannot simulate the Bn-box, thus showing that it is weaker than its no-signaling counterpart. For the second generalization we replace Alice's input bits with d its (d -leveled classical systems); we call this the Bnd-box. In this case the no-signaling condition is not enough to enforce an equivalence between the Bnd-box and (n →1 ,d ) RAC (encoding of n input d its to 1 d it of message); i.e., while the Bnd-box can win a (n →1 ,d ) RAC with certainty, not all no-signaling instances of a (n →1 ,d ) RAC can simulate the Bnd-box. We use resource inequalities to quantitatively capture these results.

Identification and modeling of the electrohydraulic systems of the main gun of a main battle tank

NASA Astrophysics Data System (ADS)

Campos, Luiz C. A.; Menegaldo, Luciano L.

2012-11-01

The black-box mathematical models of the electrohydraulic systems responsible for driving the two degrees of freedom (elevation and azimuth) of the main gun of a main battle tank (MBT) were identified. Such systems respond to gunner's inputs while acquiring and tracking targets. Identification experiments were designed to collect simultaneous data from two inertial measurement units (IMU) installed at the gunner's handle (input) and at the center of rotation of the turret (output), for the identification of the azimuth system. For the elevation system, IMUs were installed at the gunner's handle (input) and at the breech of the gun (output). Linear accelerations and angular rates were collected for both input and output. Several black-box model architectures were investigated. As a result, nonlinear autoregressive with exogenous variables (NARX) second order model and nonlinear finite impulse response (NFIR) fourth order model, demonstrate to best fit the experimental data, with low computational costs. The derived models are being employed in a broader research, aiming to reproduce such systems in a laboratory virtual main gun simulator.

A model study of laboratory photooxidation experiments of mono- and sesquiterpenes

NASA Astrophysics Data System (ADS)

Capouet, M.; Vereecken, L.; Peeters, J.; Müller, J.

2006-12-01

The importance of monoterpenes in the atmosphere stems from their large emissions from plants, their high reactivity, and their role as precursors for Secondary Organic Aerosol (SOA) production. In order to quantify the impact of α-pinene oxidation (as representative of the monoterpenes) using a CTM, a detailed understanding of its oxidation mechanism is necessary. Past studies have investigated successfully the gas- phase OH-oxidation mechanism of α-pinene [Peeters et al., 2001; Vereecken and Peeters 2004; Capouet et al., 2004]. However, the SOA formation measured in laboratory experiments remains difficult to model, partly due to a poor understanding of the ozonolysis mechanism believed to be the dominant path to formation of condensable compounds. Very recently, Peeters and co-workers have developed a detailed mechanism for the α-pinene ozonolysis based on objective theoretical grounds. Both OH- and O3- oxidation mechanisms have been implemented in a box model and coupled to a module describing the gas/particle partitioning of the semi-volatile products on the basis of a vapour pressure prediction method [Capouet and Müller, 2006]. The photooxidation of primary products has been parameterized in order to evaluate the role of condensable compounds formed by secondary reactions. Simulations of a wide set of α-pinene photooxidation experiments reported in the literature have been performed. Results indicate that the calculated SOA contain a significant fraction of second generation products. Note in particular that our box model simulations as well as theoretical arguments contradict the gas-phase formation routes for pinic acid proposed in the literature and suggest a secondary origin for this compound. Contribution of the sesquiterpenes to biogenic non methane hydrocarbon emissions has been estimated from 9% to 28% in some regions in the U.S. Their high reactivity towards ozone and their complex chemistry make these compounds hardly accessible to theoretical and experimental study. Lately an increasing number of laboratory experiments have been performed and have reported that sesquiterpenes such as β- caryophyllene and α-humulene have much higher aerosol formation potentials than α-pinene on a mass basis. Using parameterizations similar to those developed previously for α-pinene, a simplified box model describing the oxidation of the sesquiterpenes and the related aerosol formation has been developed. Preliminary simulations of photooxidation experiments have been performed and are compared with the monoterpenes model results.

S-Boxes Based on Affine Mapping and Orbit of Power Function

NASA Astrophysics Data System (ADS)

Khan, Mubashar; Azam, Naveed Ahmed

2015-06-01

The demand of data security against computational attacks such as algebraic, differential, linear and interpolation attacks has been increased as a result of rapid advancement in the field of computation. It is, therefore, necessary to develop such cryptosystems which can resist current cryptanalysis and more computational attacks in future. In this paper, we present a multiple S-boxes scheme based on affine mapping and orbit of the power function used in Advanced Encryption Standard (AES). The proposed technique results in 256 different S-boxes named as orbital S-boxes. Rigorous tests and comparisons are performed to analyse the cryptographic strength of each of the orbital S-boxes. Furthermore, gray scale images are encrypted by using multiple orbital S-boxes. Results and simulations show that the encryption strength of the orbital S-boxes against computational attacks is better than that of the existing S-boxes.

Augmented twin-nonlinear two-box behavioral models for multicarrier LTE power amplifiers.

PubMed

Hammi, Oualid

2014-01-01

A novel class of behavioral models is proposed for LTE-driven Doherty power amplifiers with strong memory effects. The proposed models, labeled augmented twin-nonlinear two-box models, are built by cascading a highly nonlinear memoryless function with a mildly nonlinear memory polynomial with cross terms. Experimental validation on gallium nitride based Doherty power amplifiers illustrates the accuracy enhancement and complexity reduction achieved by the proposed models. When strong memory effects are observed, the augmented twin-nonlinear two-box models can improve the normalized mean square error by up to 3 dB for the same number of coefficients when compared to state-of-the-art twin-nonlinear two-box models. Furthermore, the augmented twin-nonlinear two-box models lead to the same performance as previously reported twin-nonlinear two-box models while requiring up to 80% less coefficients.

Accurate and general treatment of electrostatic interaction in Hamiltonian adaptive resolution simulations

NASA Astrophysics Data System (ADS)

Heidari, M.; Cortes-Huerto, R.; Donadio, D.; Potestio, R.

2016-10-01

In adaptive resolution simulations the same system is concurrently modeled with different resolution in different subdomains of the simulation box, thereby enabling an accurate description in a small but relevant region, while the rest is treated with a computationally parsimonious model. In this framework, electrostatic interaction, whose accurate treatment is a crucial aspect in the realistic modeling of soft matter and biological systems, represents a particularly acute problem due to the intrinsic long-range nature of Coulomb potential. In the present work we propose and validate the usage of a short-range modification of Coulomb potential, the Damped shifted force (DSF) model, in the context of the Hamiltonian adaptive resolution simulation (H-AdResS) scheme. This approach, which is here validated on bulk water, ensures a reliable reproduction of the structural and dynamical properties of the liquid, and enables a seamless embedding in the H-AdResS framework. The resulting dual-resolution setup is implemented in the LAMMPS simulation package, and its customized version employed in the present work is made publicly available.

Surgical resident evaluations of portable laparoscopic box trainers incorporated into a simulation-based minimally invasive surgery curriculum.

PubMed

Zapf, Matthew A C; Ujiki, Michael B

2015-02-01

Box trainers have been shown to be an effective tool for teaching laparoscopic skills; however, residents are challenged to find practice time. Portable trainers theoretically allow for extended hands on practice out of the hospital. We aimed to report resident experience with laparoscopic home box trainers. Over 2 years, all residents rotating through a minimally invasive service were given a portable trainer and access to a surgical simulation lab for practice. Each trainer contained a collapsible frame, a webcam with USB port, trocars, and laparoscopic instruments (needle driver, shears, Maryland and straight dissecting graspers) as well as Fundamentals of Laparoscopic Surgery skills testing materials. Residents were asked to log hours, usages, and their experience anonymously. Twenty-three residents received a portable trainer. Fifty percent of the participants found the trainer useful or very useful, 25% said it was not useful, and 25% did not access the trainer. Those that used the trainer during their rotation did so 3.1 ± 3.0 times for 2.9 ± 3.0 hours/week. After completing their rotation, 5 of 12 residents used their trainer for an average of 10.2 ± 9.4 hours. Forty-two percent of the responders liked the accessibility of the home box trainers, while 25% criticized the camera-computer interface. Portable box trainers are useful and can effectively supplement a laboratory-based surgical simulation curriculum; however, personal possession of a portable simulator does not result in voluntarily long-term practice. © The Author(s) 2014.

Mars Express radar deployment postponed

NASA Astrophysics Data System (ADS)

2004-04-01

New and improved computer models suggest that, during deployment, the radar booms may swing back and forth with larger amplitudes than previously expected. If this happened, the booms might come too close to delicate components of the spacecraft body. Further simulations and tests are under way to better understand the situation. The two main radar booms are 20-metre long hollow cylinders, of 2.5 centimetres diameter, folded up in a box like a concertina (accordion). When the box is opened, the elastic energy of the compressed glass-fibre booms will let them unfold like a jack-in-the-box. After the booms spring out, they will eventually lock in a straight line, taking up the shape that they had before being folded into the box. The deployment procedure of each boom is expected to last about 10 minutes. Simulations carried out four years ago by the radar boom's manufacturer, Astro Aerospace, California, USA, indicated that the deployment should be smooth, without significantly swinging back and forth. However, the radar team has now advised ESA that a new and refined analysis of the boom dynamics indicates that a sort of "backlash" might take place before the boom locks into its position. Although a successful deployment is not in question, Mars Express mission managers want to make sure that the booms are not subjected to excessive mechanical stress and that they do not interfere with the spacecraft as they deploy. The MARSIS team and their industrial contractors are now performing further tests and simulations to confirm that the deployment will have no impact on the safety of the spacecraft. These simulations will then be reviewed by ESA's experts. Based on the results, expected within a few weeks, ESA will decide when and how to activate MARSIS. MARSIS will study the sub-surface of Mars to a depth of a few kilometres. The instrument's antennas will send radio waves towards the planet and analyse how they are reflected by any surface that they encounter. In this way, MARSIS can investigate the sub-surface mineralogical composition and will reveal the presence of any underground reservoir of water or ice.

Efficient high-dimensional characterization of conductivity in a sand box using massive MRI-imaged concentration data

NASA Astrophysics Data System (ADS)

Lee, J. H.; Yoon, H.; Kitanidis, P. K.; Werth, C. J.; Valocchi, A. J.

2015-12-01

Characterizing subsurface properties, particularly hydraulic conductivity, is crucial for reliable and cost-effective groundwater supply management, contaminant remediation, and emerging deep subsurface activities such as geologic carbon storage and unconventional resources recovery. With recent advances in sensor technology, a large volume of hydro-geophysical and chemical data can be obtained to achieve high-resolution images of subsurface properties, which can be used for accurate subsurface flow and reactive transport predictions. However, subsurface characterization with a plethora of information requires high, often prohibitive, computational costs associated with "big data" processing and large-scale numerical simulations. As a result, traditional inversion techniques are not well-suited for problems that require coupled multi-physics simulation models with massive data. In this work, we apply a scalable inversion method called Principal Component Geostatistical Approach (PCGA) for characterizing heterogeneous hydraulic conductivity (K) distribution in a 3-D sand box. The PCGA is a Jacobian-free geostatistical inversion approach that uses the leading principal components of the prior information to reduce computational costs, sometimes dramatically, and can be easily linked with any simulation software. Sequential images of transient tracer concentrations in the sand box were obtained using magnetic resonance imaging (MRI) technique, resulting in 6 million tracer-concentration data [Yoon et. al., 2008]. Since each individual tracer observation has little information on the K distribution, the dimension of the data was reduced using temporal moments and discrete cosine transform (DCT). Consequently, 100,000 unknown K values consistent with the scale of MRI data (at a scale of 0.25^3 cm^3) were estimated by matching temporal moments and DCT coefficients of the original tracer data. Estimated K fields are close to the true K field, and even small-scale variability of the sand box was captured to highlight high K connectivity and contrasts between low and high K zones. Total number of 1,000 MODFLOW and MT3DMS simulations were required to obtain final estimates and corresponding estimation uncertainty, showing the efficiency and effectiveness of our method.

Indoor thermal performance evaluation of the SEPCO air collector

NASA Technical Reports Server (NTRS)

1977-01-01

The procedures used and the results obtained during the evaluation test program on the Solaron solar air collector, model EF-212, under simulated conditions for comparison with data collected in outdoor tests on the same collector are given. The test article was a single glazed collector with a nonsensitive absorber plate, aluminum box frame, and one inch isocyanurate foam insulation.

Evaluation of incremental reactivity and its uncertainty in Southern California.

PubMed

Martien, Philip T; Harley, Robert A; Milford, Jana B; Russell, Armistead G

2003-04-15

The incremental reactivity (IR) and relative incremental reactivity (RIR) of carbon monoxide and 30 individual volatile organic compounds (VOC) were estimated for the South Coast Air Basin using two photochemical air quality models: a 3-D, grid-based model and a vertically resolved trajectory model. Both models include an extended version of the SAPRC99 chemical mechanism. For the 3-D modeling, the decoupled direct method (DDM-3D) was used to assess reactivities. The trajectory model was applied to estimate uncertainties in reactivities due to uncertainties in chemical rate parameters, deposition parameters, and emission rates using Monte Carlo analysis with Latin hypercube sampling. For most VOC, RIRs were found to be consistent in rankings with those produced by Carter using a box model. However, 3-D simulations show that coastal regions, upwind of most of the emissions, have comparatively low IR but higher RIR than predicted by box models for C4-C5 alkenes and carbonyls that initiate the production of HOx radicals. Biogenic VOC emissions were found to have a lower RIR than predicted by box model estimates, because emissions of these VOC were mostly downwind of the areas of primary ozone production. Uncertainties in RIR of individual VOC were found to be dominated by uncertainties in the rate parameters of their primary oxidation reactions. The coefficient of variation (COV) of most RIR values ranged from 20% to 30%, whereas the COV of absolute incremental reactivity ranged from about 30% to 40%. In general, uncertainty and variability both decreased when relative rather than absolute reactivity metrics were used.

Evidence for renoxification in the tropical marine boundary layer

NASA Astrophysics Data System (ADS)

Reed, Chris; Evans, Mathew J.; Crilley, Leigh R.; Bloss, William J.; Sherwen, Tomás; Read, Katie A.; Lee, James D.; Carpenter, Lucy J.

2017-03-01

We present 2 years of NOx observations from the Cape Verde Atmospheric Observatory located in the tropical Atlantic boundary layer. We find that NOx mixing ratios peak around solar noon (at 20-30 pptV depending on season), which is counter to box model simulations that show a midday minimum due to OH conversion of NO2 to HNO3. Production of NOx via decomposition of organic nitrogen species and the photolysis of HNO3 appear insufficient to provide the observed noontime maximum. A rapid photolysis of nitrate aerosol to produce HONO and NO2, however, is able to simulate the observed diurnal cycle. This would make it the dominant source of NOx at this remote marine boundary layer site, overturning the previous paradigm according to which the transport of organic nitrogen species, such as PAN, is the dominant source. We show that observed mixing ratios (November-December 2015) of HONO at Cape Verde (˜ 3.5 pptV peak at solar noon) are consistent with this route for NOx production. Reactions between the nitrate radical and halogen hydroxides which have been postulated in the literature appear to improve the box model simulation of NOx. This rapid conversion of aerosol phase nitrate to NOx changes our perspective of the NOx cycling chemistry in the tropical marine boundary layer, suggesting a more chemically complex environment than previously thought.

Heart rate response during a simulated Olympic boxing match is predominantly above ventilatory threshold 2: a cross sectional study

PubMed Central

de Lira, Claudio Andre Barbosa; Peixinho-Pena, Luiz Fernando; Vancini, Rodrigo Luiz; de Freitas Guina Fachina, Rafael Júlio; de Almeida, Alexandre Aparecido; Andrade, Marília dos Santos; da Silva, Antonio Carlos

2013-01-01

The present study aimed to describe heart rate (HR) responses during a simulated Olympic boxing match and examine physiological parameters of boxing athletes. Ten highly trained Olympic boxing athletes (six men and four women) performed a maximal graded exercise test on a motorized treadmill to determine maximal oxygen uptake (52.2 mL · kg−1 · min−1 ± 7.2 mL · kg−1 · min−1) and ventilatory thresholds 1 and 2. Ventilatory thresholds 1 and 2 were used to classify the intensity of exercise based on respective HR during a boxing match. In addition, oxygen uptake (V̇O2) was estimated during the match based on the HR response and the HR-V̇O2 relationship obtained from a maximal graded exercise test for each participant. On a separate day, participants performed a boxing match lasting three rounds, 2 minutes each, with a 1-minute recovery period between each round, during which HR was measured. In this context, HR and V̇O2 were above ventilatory threshold 2 during 219.8 seconds ± 67.4 seconds. There was an increase in HR and V̇O2 as a function of round (round 3 < round 2 < round 1, P < 0.0001). These findings may direct individual training programs for boxing practitioners and other athletes. PMID:24379723

Heart rate response during a simulated Olympic boxing match is predominantly above ventilatory threshold 2: a cross sectional study.

PubMed

de Lira, Claudio Andre Barbosa; Peixinho-Pena, Luiz Fernando; Vancini, Rodrigo Luiz; de Freitas Guina Fachina, Rafael Júlio; de Almeida, Alexandre Aparecido; Andrade, Marília Dos Santos; da Silva, Antonio Carlos

2013-01-01

The present study aimed to describe heart rate (HR) responses during a simulated Olympic boxing match and examine physiological parameters of boxing athletes. Ten highly trained Olympic boxing athletes (six men and four women) performed a maximal graded exercise test on a motorized treadmill to determine maximal oxygen uptake (52.2 mL · kg(-1) · min(-1) ± 7.2 mL · kg(-1) · min(-1)) and ventilatory thresholds 1 and 2. Ventilatory thresholds 1 and 2 were used to classify the intensity of exercise based on respective HR during a boxing match. In addition, oxygen uptake (V̇O2) was estimated during the match based on the HR response and the HR-V̇O2 relationship obtained from a maximal graded exercise test for each participant. On a separate day, participants performed a boxing match lasting three rounds, 2 minutes each, with a 1-minute recovery period between each round, during which HR was measured. In this context, HR and V̇O2 were above ventilatory threshold 2 during 219.8 seconds ± 67.4 seconds. There was an increase in HR and V̇O2 as a function of round (round 3 < round 2 < round 1, P < 0.0001). These findings may direct individual training programs for boxing practitioners and other athletes.

A Tidally Averaged Sediment-Transport Model for San Francisco Bay, California

USGS Publications Warehouse

Lionberger, Megan A.; Schoellhamer, David H.

2009-01-01

A tidally averaged sediment-transport model of San Francisco Bay was incorporated into a tidally averaged salinity box model previously developed and calibrated using salinity, a conservative tracer (Uncles and Peterson, 1995; Knowles, 1996). The Bay is represented in the model by 50 segments composed of two layers: one representing the channel (>5-meter depth) and the other the shallows (0- to 5-meter depth). Calculations are made using a daily time step and simulations can be made on the decadal time scale. The sediment-transport model includes an erosion-deposition algorithm, a bed-sediment algorithm, and sediment boundary conditions. Erosion and deposition of bed sediments are calculated explicitly, and suspended sediment is transported by implicitly solving the advection-dispersion equation. The bed-sediment model simulates the increase in bed strength with depth, owing to consolidation of fine sediments that make up San Francisco Bay mud. The model is calibrated to either net sedimentation calculated from bathymetric-change data or measured suspended-sediment concentration. Specified boundary conditions are the tributary fluxes of suspended sediment and suspended-sediment concentration in the Pacific Ocean. Results of model calibration and validation show that the model simulates the trends in suspended-sediment concentration associated with tidal fluctuations, residual velocity, and wind stress well, although the spring neap tidal suspended-sediment concentration variability was consistently underestimated. Model validation also showed poor simulation of seasonal sediment pulses from the Sacramento-San Joaquin River Delta at Point San Pablo because the pulses enter the Bay over only a few days and the fate of the pulses is determined by intra-tidal deposition and resuspension that are not included in this tidally averaged model. The model was calibrated to net-basin sedimentation to calculate budgets of sediment and sediment-associated contaminants. While simulated net sedimentation in the four basins that comprise San Francisco Bay was correct, the simulations incorrectly eroded shallows while channels deposited because model surface-layer boxes span both shallows and channels, and neglect lateral variability of suspended-sediment concentration. Validation with recent (1983-2005) net sedimentation in South San Francisco Bay was poor, perhaps owing to poorly quantified sediment supply, and to invasive species that altered erosion and deposition processes. This demonstrates that deterministically predicting future sedimentation is difficult in this or any estuary for which boundary conditions are not stationary. The model would best be used as a tool for developing past and present sediment budgets, and for creating scenarios of future sedimentation that are compared to one another rather than considered a deterministic prediction.

A tale of two trainers: virtual reality versus a video trainer for acquisition of basic laparoscopic skills.

PubMed

Debes, Anders J; Aggarwal, Rajesh; Balasundaram, Indran; Jacobsen, Morten B

2010-06-01

This study aimed to assess the transferability of basic laparoscopic skills between a virtual reality simulator (MIST-VR) and a video trainer box (D-Box). Forty-six medical students were randomized into 2 groups, training on MIST-VR or D-Box. After training with one modality, a crossover assessment on the other was performed. When tested on MIST-VR, the MIST-VR group showed significantly shorter time (90.3 seconds vs 188.6 seconds, P <.001), better economy of movements (4.40 vs 7.50, P <.001), and lower score (224.7 vs 527.0, P <.001). However, when assessed on the D-Box, there was no difference between the groups for time (402.0 seconds vs 325.6 seconds, P = .152), total hand movements (THC) (289 vs 262, P = .792), or total path length (TPL) (34.9 m vs 34.6 m, P = .388). Both simulators provide significant improvement in performance. Our results indicate that skills learned on the MIST-VR are transferable to the D-Box, but the opposite cannot be demonstrated. Copyright 2010 Elsevier Inc. All rights reserved.

Laparoscopic virtual reality and box trainers: is one superior to the other?

PubMed

Munz, Y; Kumar, B D; Moorthy, K; Bann, S; Darzi, A

2004-03-01

Virtual reality (VR) simulators now have the potential to replace traditional methods of laparoscopic training. The aim of this study was to compare the VR simulator with the classical box trainer and determine whether one has advantages over the other. Twenty four novices were tested to determine their baseline laparoscopic skills and then randomized into the following three group: LapSim, box trainer, and no training (control). After 3 weekly training sessions lasting 30-min each, all subjects were reassessed. Assessment included motion analysis and error scores. Nonparametric tests were applied, and p < 0.05 was deemed significant. Both trained groups made significant improvements in all parameters measured ( p < 0.05). Compared to the controls, the box trainer group performed significantly better on most of the parameters, whereas the LapSim group performed significantly better on some parameters. There were no significant differences between the LapSim and box trainer groups. LapSim is effective in teaching skills that are transferable to a real laparoscopic task. However, there appear to be no substantial advantages of one system over the other.

Sensitivity and response of beryllium-10 in marine sediments to rapid production changes (geomagnetic events): A box model study

NASA Astrophysics Data System (ADS)

Christl, Marcus

2007-09-01

The response and the sensitivity of the marine beryllium-10 flux to abrupt production changes (e.g., caused by a geomagnetic event) are investigated by using a simple box model. The effect of mixing processes in the water column on the 10Be flux is simulated, and the influence of bioturbation on the sedimentary record is studied. While the effect of the oceanic residence time is found to be small, bioturbation can drastically change the shape and the amplitude of the modeled 10Be peak. The simulations indicate that 10Be production peaks persisting for more than 1500 years are recorded well in deep-sea sediments if bioturbation-induced integration times are small (tbio ≤ 1000 years), while sediment cores with tbio ≥ 1000 years are found to be not well suited for stratigraphic purposes. The results further show that the sedimentary 10Be peak lags initial signal. This time lag is almost independent of the event duration (for tbio ≤ 1000 years), ranging between about 400 and 600 years. Therefore the model results support the idea that marine 10Be peaks corresponding to geomagnetic events can be used as a global time marker to match marine, terrestrial, and ice core chronologies on the millennial and (if the time lag of (500 ± 100) years is considered) the submillennial timescale.

Use of Moderate-Resolution Imaging Spectroradiometer bidirectional reflectance distribution function products to enhance simulated surface albedos

NASA Astrophysics Data System (ADS)

Roesch, Andreas; Schaaf, Crystal; Gao, Feng

2004-06-01

Moderate-Resolution Imaging Spectroradiometer (MODIS) surface albedo at high spatial and spectral resolution is compared with other remotely sensed climatologies, ground-based data, and albedos simulated with the European Center/Hamburg 4 (ECHAM4) global climate model at T42 resolution. The study demonstrates the importance of MODIS data in assessing and improving albedo parameterizations in weather forecast and climate models. The remotely sensed PINKER surface albedo climatology follows the MODIS estimates fairly well in both the visible and near-infrared spectra, whereas ECHAM4 simulates high positive albedo biases over snow-covered boreal forests and the Himalayas. In contrast, the ECHAM4 albedo is probably too low over the Sahara sand desert and adjacent steppes. The study clearly indicates that neglecting albedo variations within T42 grid boxes leads to significant errors in the simulated regional climate and horizontal fluxes, mainly in mountainous and/or snow-covered regions. MODIS surface albedo at 0.05 resolution agrees quite well with in situ field measurements collected at Baseline Surface Radiation Network (BSRN) sites during snow-free periods, while significant positive biases are found under snow-covered conditions, mainly due to differences in the vegetation cover at the BSRN site (short grass) and the vegetation within the larger MODIS grid box. Black sky (direct beam) albedo from the MODIS bidirectional reflectance distribution function model captures the diurnal albedo cycle at BSRN sites with sufficient accuracy. The greatest negative biases are generally found when the Sun is low. A realistic approach for relating albedo and zenith angle has been proposed. Detailed evaluations have demonstrated that ignoring the zenith angle dependence may lead to significant errors in the surface energy balance.

Northern Indian Ocean Salt Transport (NIOST): Estimation of Fresh and Salt Water Transports in the Indian Ocean using Remote Sensing, Hydrographic Observations and HYCOM Simulations

DTIC Science & Technology

2014-09-30

Here we use the newly launched Aquarius satellite derived Sea Surface Salinity ( SSS ) data as well as Argo salinity profiles, model simulations and...dipolar sea surface salinity ( SSS ) structure with the salty Arabian Sea (AS) on the west and the fresher Bay of Bengal (BoB) on the east. At the surface...interconnected, region is quantified. PRELIMINARY RESULTS Figure 1 shows the mean Aquarius SSS during August 2011-May 2014 and several boxes that

Sampling Errors of SSM/I and TRMM Rainfall Averages: Comparison with Error Estimates from Surface Data and a Sample Model

NASA Technical Reports Server (NTRS)

Bell, Thomas L.; Kundu, Prasun K.; Kummerow, Christian D.; Einaudi, Franco (Technical Monitor)

2000-01-01

Quantitative use of satellite-derived maps of monthly rainfall requires some measure of the accuracy of the satellite estimates. The rainfall estimate for a given map grid box is subject to both remote-sensing error and, in the case of low-orbiting satellites, sampling error due to the limited number of observations of the grid box provided by the satellite. A simple model of rain behavior predicts that Root-mean-square (RMS) random error in grid-box averages should depend in a simple way on the local average rain rate, and the predicted behavior has been seen in simulations using surface rain-gauge and radar data. This relationship was examined using satellite SSM/I data obtained over the western equatorial Pacific during TOGA COARE. RMS error inferred directly from SSM/I rainfall estimates was found to be larger than predicted from surface data, and to depend less on local rain rate than was predicted. Preliminary examination of TRMM microwave estimates shows better agreement with surface data. A simple method of estimating rms error in satellite rainfall estimates is suggested, based on quantities that can be directly computed from the satellite data.

2010 Joint Chemical Biological Radiological Nuclear (CBRN) Conference and Exhibition (BRIEFING CHARTS)

DTIC Science & Technology

2010-06-24

control Defensive Test Chamber • Certified for Chem-Bio simulants • Man-in-simulant (MIST) testing Bang Box • Explosive material synthesis and testing...Explosive material synthesis and testing Bang Box –Peroxide Explosives Properties – HMTD, TATP, DADP –Peroxide Explosives as Initiators –TATP... Synthesis –HMTD Synthesis –RDX Synthesis –ANFO Mixture Mustang VILLAGE Approved for public release; distribution is unlimited. • Hotel, Post Office

Building dynamical models from data and prior knowledge: the case of the first period-doubling bifurcation.

PubMed

Aguirre, Luis Antonio; Furtado, Edgar Campos

2007-10-01

This paper reviews some aspects of nonlinear model building from data with (gray box) and without (black box) prior knowledge. The model class is very important because it determines two aspects of the final model, namely (i) the type of nonlinearity that can be accurately approximated and (ii) the type of prior knowledge that can be taken into account. Such features are usually in conflict when it comes to choosing the model class. The problem of model structure selection is also reviewed. It is argued that such a problem is philosophically different depending on the model class and it is suggested that the choice of model class should be performed based on the type of a priori available. A procedure is proposed to build polynomial models from data on a Poincaré section and prior knowledge about the first period-doubling bifurcation, for which the normal form is also polynomial. The final models approximate dynamical data in a least-squares sense and, by design, present the first period-doubling bifurcation at a specified value of parameters. The procedure is illustrated by means of simulated examples.

Avoiding fractional electrons in subsystem DFT based ab-initio molecular dynamics yields accurate models for liquid water and solvated OH radical

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

Genova, Alessandro, E-mail: alessandro.genova@rutgers.edu; Pavanello, Michele, E-mail: m.pavanello@rutgers.edu; Ceresoli, Davide, E-mail: davide.ceresoli@cnr.it

2016-06-21

In this work we achieve three milestones: (1) we present a subsystem DFT method capable of running ab-initio molecular dynamics simulations accurately and efficiently. (2) In order to rid the simulations of inter-molecular self-interaction error, we exploit the ability of semilocal frozen density embedding formulation of subsystem DFT to represent the total electron density as a sum of localized subsystem electron densities that are constrained to integrate to a preset, constant number of electrons; the success of the method relies on the fact that employed semilocal nonadditive kinetic energy functionals effectively cancel out errors in semilocal exchange–correlation potentials that aremore » linked to static correlation effects and self-interaction. (3) We demonstrate this concept by simulating liquid water and solvated OH{sup •} radical. While the bulk of our simulations have been performed on a periodic box containing 64 independent water molecules for 52 ps, we also simulated a box containing 256 water molecules for 22 ps. The results show that, provided one employs an accurate nonadditive kinetic energy functional, the dynamics of liquid water and OH{sup •} radical are in semiquantitative agreement with experimental results or higher-level electronic structure calculations. Our assessments are based upon comparisons of radial and angular distribution functions as well as the diffusion coefficient of the liquid.« less

Avoiding fractional electrons in subsystem DFT based ab-initio molecular dynamics yields accurate models for liquid water and solvated OH radical.

PubMed

Genova, Alessandro; Ceresoli, Davide; Pavanello, Michele

2016-06-21

In this work we achieve three milestones: (1) we present a subsystem DFT method capable of running ab-initio molecular dynamics simulations accurately and efficiently. (2) In order to rid the simulations of inter-molecular self-interaction error, we exploit the ability of semilocal frozen density embedding formulation of subsystem DFT to represent the total electron density as a sum of localized subsystem electron densities that are constrained to integrate to a preset, constant number of electrons; the success of the method relies on the fact that employed semilocal nonadditive kinetic energy functionals effectively cancel out errors in semilocal exchange-correlation potentials that are linked to static correlation effects and self-interaction. (3) We demonstrate this concept by simulating liquid water and solvated OH(•) radical. While the bulk of our simulations have been performed on a periodic box containing 64 independent water molecules for 52 ps, we also simulated a box containing 256 water molecules for 22 ps. The results show that, provided one employs an accurate nonadditive kinetic energy functional, the dynamics of liquid water and OH(•) radical are in semiquantitative agreement with experimental results or higher-level electronic structure calculations. Our assessments are based upon comparisons of radial and angular distribution functions as well as the diffusion coefficient of the liquid.

Augmented Twin-Nonlinear Two-Box Behavioral Models for Multicarrier LTE Power Amplifiers

PubMed Central

2014-01-01

A novel class of behavioral models is proposed for LTE-driven Doherty power amplifiers with strong memory effects. The proposed models, labeled augmented twin-nonlinear two-box models, are built by cascading a highly nonlinear memoryless function with a mildly nonlinear memory polynomial with cross terms. Experimental validation on gallium nitride based Doherty power amplifiers illustrates the accuracy enhancement and complexity reduction achieved by the proposed models. When strong memory effects are observed, the augmented twin-nonlinear two-box models can improve the normalized mean square error by up to 3 dB for the same number of coefficients when compared to state-of-the-art twin-nonlinear two-box models. Furthermore, the augmented twin-nonlinear two-box models lead to the same performance as previously reported twin-nonlinear two-box models while requiring up to 80% less coefficients. PMID:24624047

Thermal Response Of An Aerated Concrete Wall With Micro-Encapsulated Phase Change Material

NASA Astrophysics Data System (ADS)

Halúzová, Dušana

2015-06-01

For many years Phase Change Materials (PCM) have attracted attention due to their ability to store large amounts of thermal energy. This property makes them a candidate for the use of passive heat storage. In many applications, they are used to avoid the overheating of the temperature of an indoor environment. This paper describes the behavior of phase change materials that are inbuilt in aerated concrete blocks. Two building samples of an aerated concrete wall were measured in laboratory equipment called "twin-boxes". The first box consists of a traditional aerated concrete wall; the second one has additional PCM micro-encapsulated in the wall. The heat flux through the wall was measured and compared to simulation results modeled in the ESP-r program. This experimental measurement provides a foundation for a model that can be used to analyze further building constructions.

Confidence intervals for the first crossing point of two hazard functions.

PubMed

Cheng, Ming-Yen; Qiu, Peihua; Tan, Xianming; Tu, Dongsheng

2009-12-01

The phenomenon of crossing hazard rates is common in clinical trials with time to event endpoints. Many methods have been proposed for testing equality of hazard functions against a crossing hazards alternative. However, there has been relatively few approaches available in the literature for point or interval estimation of the crossing time point. The problem of constructing confidence intervals for the first crossing time point of two hazard functions is considered in this paper. After reviewing a recent procedure based on Cox proportional hazard modeling with Box-Cox transformation of the time to event, a nonparametric procedure using the kernel smoothing estimate of the hazard ratio is proposed. The proposed procedure and the one based on Cox proportional hazard modeling with Box-Cox transformation of the time to event are both evaluated by Monte-Carlo simulations and applied to two clinical trial datasets.

Analyzing the effect of carbon fiber reinforced polymer on the crashworthiness of aluminum square hollow beam for crash box application

NASA Astrophysics Data System (ADS)

Raman, R.; Jayanth, K.; Sarkar, I.; Ravi, K.

2017-11-01

Crashworthiness of a material is a measure of its ability to absorb energy during a crash. A well-designed crash box is instrumental in protecting the costly vehicle components. A square, hollow, hybrid beam of aluminum/CFRP was subjected to dynamic axial load to analyze the effect of five different lay-up sequences on its crashworthiness. The beam was placed between two plates. Boundary conditions were imposed on them to simulate a frontal body crash test model. Modeling and dynamic analysis of composite structures was done on ABAQUS. Different orientation of carbon fibers varies the crashworthiness of the hybrid beam. Addition of CFRP layer showed clear improvement in specific energy absorption and crush force efficiency compared to pure aluminum beam. Two layers of CFRP oriented at 90° on Aluminum showed 52% increase in CFE.

A white-box model of S-shaped and double S-shaped single-species population growth

PubMed Central

Kalmykov, Lev V.

2015-01-01

Complex systems may be mechanistically modelled by white-box modeling with using logical deterministic individual-based cellular automata. Mathematical models of complex systems are of three types: black-box (phenomenological), white-box (mechanistic, based on the first principles) and grey-box (mixtures of phenomenological and mechanistic models). Most basic ecological models are of black-box type, including Malthusian, Verhulst, Lotka–Volterra models. In black-box models, the individual-based (mechanistic) mechanisms of population dynamics remain hidden. Here we mechanistically model the S-shaped and double S-shaped population growth of vegetatively propagated rhizomatous lawn grasses. Using purely logical deterministic individual-based cellular automata we create a white-box model. From a general physical standpoint, the vegetative propagation of plants is an analogue of excitation propagation in excitable media. Using the Monte Carlo method, we investigate a role of different initial positioning of an individual in the habitat. We have investigated mechanisms of the single-species population growth limited by habitat size, intraspecific competition, regeneration time and fecundity of individuals in two types of boundary conditions and at two types of fecundity. Besides that, we have compared the S-shaped and J-shaped population growth. We consider this white-box modeling approach as a method of artificial intelligence which works as automatic hyper-logical inference from the first principles of the studied subject. This approach is perspective for direct mechanistic insights into nature of any complex systems. PMID:26038717

Laparoscopic skills acquisition: a study of simulation and traditional training.

PubMed

Marlow, Nicholas; Altree, Meryl; Babidge, Wendy; Field, John; Hewett, Peter; Maddern, Guy J

2014-12-01

Training in basic laparoscopic skills can be undertaken using traditional methods, where trainees are educated by experienced surgeons through a process of graduated responsibility or by simulation-based training. This study aimed to assess whether simulation trained individuals reach the same level of proficiency in basic laparoscopic skills as traditional trained participants when assessed in a simulated environment. A prospective study was undertaken. Participants were allocated to one of two cohorts according to surgical experience. Participants from the inexperienced cohort were randomized to receive training in basic laparoscopic skills on either a box trainer or a virtual reality simulator. They were then assessed on the simulator on which they did not receive training. Participants from the experienced cohort, considered to have received traditional training in basic laparoscopic skills, did not receive simulation training and were randomized to either the box trainer or virtual reality simulator for skills assessment. The assessment scores from different cohorts on either simulator were then compared. A total of 138 participants completed the assessment session, 101 in the inexperienced simulation-trained cohort and 37 on the experienced traditionally trained cohort. There was no statistically significant difference between the training outcomes of simulation and traditionally trained participants, irrespective of the simulator type used. The results demonstrated that participants trained on either a box trainer or virtual reality simulator achieved a level of basic laparoscopic skills assessed in a simulated environment that was not significantly different from participants who had been traditionally trained in basic laparoscopic skills. © 2013 Royal Australasian College of Surgeons.

The neglected nonlocal effects of deforestation

NASA Astrophysics Data System (ADS)

Winckler, Johannes; Reick, Christian; Pongratz, Julia

2017-04-01

Deforestation changes surface temperature locally via biogeophysical effects by changing the water, energy and momentum balance. Adding to these locally induced changes (local effects), deforestation at a given location can cause changes in temperature elsewhere (nonlocal effects). Most previous studies have not considered local and nonlocal effects separately, but investigated the total (local plus nonlocal) effects, for which global deforestation was found to cause a global mean cooling. Recent modeling and observational studies focused on the isolated local effects: The local effects are relevant for local living conditions, and they can be obtained from in-situ and satellite observations. Observational studies suggest that the local effects of potential deforestation cause a warming when averaged globally. This contrast between local warming and total cooling indicates that the nonlocal effects of deforestation are causing a cooling and thus counteract the local effects. It is still unclear how the nonlocal effects depend on the spatial scale of deforestation, and whether they still compensate the local warming in a more realistic spatial distribution of deforestation. To investigate this, we use a fully coupled climate model and separate local and nonlocal effects of deforestation in three steps: Starting from a forest world, we simulate deforestation in one out of four grid boxes using a regular spatial pattern and increase the number of deforestation grid boxes step-wise up to three out of four boxes in subsequent simulations. To compare these idealized spatial distributions of deforestation to a more realistic case, we separate local and nonlocal effects in a simulation where deforestation is applied in regions where it occurred historically. We find that the nonlocal effects scale nearly linearly with the number of deforested grid boxes, and the spatial distribution of the nonlocal effects is similar for the regular spatial distribution of deforestation and the more realistic pattern. Globally averaged, the deforestation-induced warming of the local effects is counteracted by the nonlocal effects, which are about three times as strong as the local effects (up to 0.1K local warming versus -0.3K nonlocal cooling). Thus, the nonlocal effects are more cooling than the local effects are warming, and this is valid not only for idealized simulations of large-scale deforestation, but also for a more realistic deforestation scenario. We conclude that the local effects of deforestation only yield an incomplete picture of the total climate effects by biogeophysical pathways. While the local effects capture the direct climatic response at the site of deforestation, the nonlocal effects have to be included if the biogeophysical effects of deforestation are considered for an implementation in climate policies.

Experimental and theoretical study of the operation of longitudinal sidewalls in reinforced concrete superstructures

NASA Astrophysics Data System (ADS)

Bokarev, Sergey; Efimov, Stefan

2017-11-01

In the present article, we report results of a laboratory experimental study of reinforced-concrete superstructure fragments with extended longitudinal boxing sidewalls. The study included laboratory tests and numerical experiments performed using a finite element model of fragments generated in specialized simulation software. The distribution of horizontal pressures over the height of longitudinal boxing sidewalls, the dependence of the bending moment in the root section of the sidewalls on the ballast-bed thickness under sleepers, and some other characteristics were examined. The results of the experimental and theoretical study have shown a good convergence of obtained data to each other and to the data obtained by an improved engineering calculation procedure proposed by the present authors.

A framework for optimization and quantification of uncertainty and sensitivity for developing carbon capture systems

DOE PAGES

Eslick, John C.; Ng, Brenda; Gao, Qianwen; ...

2014-12-31

Under the auspices of the U.S. Department of Energy’s Carbon Capture Simulation Initiative (CCSI), a Framework for Optimization and Quantification of Uncertainty and Sensitivity (FOQUS) has been developed. This tool enables carbon capture systems to be rapidly synthesized and rigorously optimized, in an environment that accounts for and propagates uncertainties in parameters and models. FOQUS currently enables (1) the development of surrogate algebraic models utilizing the ALAMO algorithm, which can be used for superstructure optimization to identify optimal process configurations, (2) simulation-based optimization utilizing derivative free optimization (DFO) algorithms with detailed black-box process models, and (3) rigorous uncertainty quantification throughmore » PSUADE. FOQUS utilizes another CCSI technology, the Turbine Science Gateway, to manage the thousands of simulated runs necessary for optimization and UQ. Thus, this computational framework has been demonstrated for the design and analysis of a solid sorbent based carbon capture system.« less

A neural-network-based model for the dynamic simulation of the tire/suspension system while traversing road irregularities.

PubMed

Guarneri, Paolo; Rocca, Gianpiero; Gobbi, Massimiliano

2008-09-01

This paper deals with the simulation of the tire/suspension dynamics by using recurrent neural networks (RNNs). RNNs are derived from the multilayer feedforward neural networks, by adding feedback connections between output and input layers. The optimal network architecture derives from a parametric analysis based on the optimal tradeoff between network accuracy and size. The neural network can be trained with experimental data obtained in the laboratory from simulated road profiles (cleats). The results obtained from the neural network demonstrate good agreement with the experimental results over a wide range of operation conditions. The NN model can be effectively applied as a part of vehicle system model to accurately predict elastic bushings and tire dynamics behavior. Although the neural network model, as a black-box model, does not provide a good insight of the physical behavior of the tire/suspension system, it is a useful tool for assessing vehicle ride and noise, vibration, harshness (NVH) performance due to its good computational efficiency and accuracy.

Nonconservative force model parameter estimation strategy for TOPEX/Poseidon precision orbit determination

NASA Technical Reports Server (NTRS)

Luthcke, S. B.; Marshall, J. A.

1992-01-01

The TOPEX/Poseidon spacecraft was launched on August 10, 1992 to study the Earth's oceans. To achieve maximum benefit from the altimetric data it is to collect, mission requirements dictate that TOPEX/Poseidon's orbit must be computed at an unprecedented level of accuracy. To reach our pre-launch radial orbit accuracy goals, the mismodeling of the radiative nonconservative forces of solar radiation, Earth albedo an infrared re-radiation, and spacecraft thermal imbalances cannot produce in combination more than a 6 cm rms error over a 10 day period. Similarly, the 10-day drag modeling error cannot exceed 3 cm rms. In order to satisfy these requirements, a 'box-wing' representation of the satellite has been developed in which, the satellite is modelled as the combination of flat plates arranged in the shape of a box and a connected solar array. The radiative/thermal nonconservative forces acting on each of the eight surfaces are computed independently, yielding vector accelerations which are summed to compute the total aggregate effect on the satellite center-of-mass. Select parameters associated with the flat plates are adjusted to obtain a better representation of the satellite acceleration history. This study analyzes the estimation of these parameters from simulated TOPEX/Poseidon laser data in the presence of both nonconservative and gravity model errors. A 'best choice' of estimated parameters is derived and the ability to meet mission requirements with the 'box-wing' model evaluated.

Investigation of processes controlling summertime gaseous elemental mercury oxidation at midlatitudinal marine, coastal, and inland sites

NASA Astrophysics Data System (ADS)

Ye, Zhuyun; Mao, Huiting; Lin, Che-Jen; Kim, Su Youn

2016-07-01

A box model incorporating a state-of-the-art chemical mechanism for atmospheric mercury (Hg) cycling was developed to investigate the oxidation of gaseous elemental mercury (GEM) at three locations in the northeastern United States: Appledore Island (AI; marine), Thompson Farm (TF; coastal, rural), and Pack Monadnock (PM; inland, rural, elevated). The chemical mechanism in this box model included the most up-to-date Hg and halogen chemistry. As a result, the box model was able to simulate reasonably the observed diurnal cycles of gaseous oxidized mercury (GOM) and chemical speciation bearing distinct differences between the three sites. In agreement with observations, simulated GOM diurnal cycles at AI and TF showed significant daytime peaks in the afternoon and nighttime minimums compared to flat GOM diurnal cycles at PM. Moreover, significant differences in the magnitude of GOM diurnal amplitude (AI > TF > PM) were captured in modeled results. At the coastal and inland sites, GEM oxidation was predominated by O3 and OH, contributing 80-99 % of total GOM production during daytime. H2O2-initiated GEM oxidation was significant (˜ 33 % of the total GOM) at the inland site during nighttime. In the marine boundary layer (MBL) atmosphere, Br and BrO became dominant GEM oxidants, with mixing ratios reaching 0.1 and 1 pptv, respectively, and contributing ˜ 70 % of the total GOM production during midday, while O3 dominated GEM oxidation (50-90 % of GOM production) over the remaining day when Br and BrO mixing ratios were diminished. The majority of HgBr produced from GEM+Br was oxidized by NO2 and HO2 to form brominated GOM species. Relative humidity and products of the CH3O2+BrO reaction possibly significantly affected the mixing ratios of Br or BrO radicals and subsequently GOM formation. Gas-particle partitioning could potentially be important in the production of GOM as well as Br and BrO at the marine site.

A sigmoidal model for biosorption of heavy metal cations from aqueous media.

PubMed

Özen, Rümeysa; Sayar, Nihat Alpagu; Durmaz-Sam, Selcen; Sayar, Ahmet Alp

2015-07-01

A novel multi-input single output (MISO) black-box sigmoid model is developed to simulate the biosorption of heavy metal cations by the fission yeast from aqueous medium. Validation and verification of the model is done through statistical chi-squared hypothesis tests and the model is evaluated by uncertainty and sensitivity analyses. The simulated results are in agreement with the data of the studied system in which Schizosaccharomyces pombe biosorbs Ni(II) cations at various process conditions. Experimental data is obtained originally for this work using dead cells of an adapted variant of S. Pombe and represented by Freundlich isotherms. A process optimization scheme is proposed using the present model to build a novel application of a cost-merit objective function which would be useful to predict optimal operation conditions. Copyright © 2015. Published by Elsevier Inc.

Generalized image charge solvation model for electrostatic interactions in molecular dynamics simulations of aqueous solutions

PubMed Central

Deng, Shaozhong; Xue, Changfeng; Baumketner, Andriy; Jacobs, Donald; Cai, Wei

2013-01-01

This paper extends the image charge solvation model (ICSM) [J. Chem. Phys. 131, 154103 (2009)], a hybrid explicit/implicit method to treat electrostatic interactions in computer simulations of biomolecules formulated for spherical cavities, to prolate spheroidal and triaxial ellipsoidal cavities, designed to better accommodate non-spherical solutes in molecular dynamics (MD) simulations. In addition to the utilization of a general truncated octahedron as the MD simulation box, central to the proposed extension is an image approximation method to compute the reaction field for a point charge placed inside such a non-spherical cavity by using a single image charge located outside the cavity. The resulting generalized image charge solvation model (GICSM) is tested in simulations of liquid water, and the results are analyzed in comparison with those obtained from the ICSM simulations as a reference. We find that, for improved computational efficiency due to smaller simulation cells and consequently a less number of explicit solvent molecules, the generalized model can still faithfully reproduce known static and dynamic properties of liquid water at least for systems considered in the present paper, indicating its great potential to become an accurate but more efficient alternative to the ICSM when bio-macromolecules of irregular shapes are to be simulated. PMID:23913979

Comparison of upconing under vertical and horizontal wells in freshwater lenses: sand-box experiments and numerical modeling

NASA Astrophysics Data System (ADS)

Stoeckl, Leonard; Stefan, Loeffler; Houben, Georg

2013-04-01

Freshwater lenses on islands and in inland areas are often the primary freshwater resource there. The fragile equilibrium between saline and fresh groundwater can be disrupted by excessive pumping, leading to an upward migration of the saline water underneath the well. Sand-box experiments were conducted to compare the upconing at vertical and horizontal wells pumping from a freshwater lens. Results were then compared to numerical simulations. To simulate the cross-section of an "infinite strip island", an acrylic box with a spacing of 5 cm was filled with coarse sand. After saturating the model with degassed saltwater from bottom to top, freshwater recharge was applied from above. By coloring the infiltrating freshwater with different tracer colors using uranine and indigotine we were able to visualize flow paths during pumping. A horizontal and a vertical well were placed at the left and right side of the symmetric island. Both had equal diameter, screen length, depth of placement, and distance to shore. Three increasing pumping rates were applied to each well successively and the electrical conductivity of the abstracted water was continuously measured using a through-flow cell. Results show that no saltwater entered the wells when pumping at the lowest rate. Still, slight saltwater upconing and a shift of the freshwater divide in the island were observed. At the second rate a clear saltwater breakthrough into the vertical well occurred, while the electrical conductivity remained nearly unchanged in the horizontal well. Applying the third (highest) abstraction rate to each of the wells saltwater entered both wells, exceeding drinking water standards in the vertical well. The described behavior indicates the advantage of horizontal over vertical wells on islands and in coastal zones prone to saltwater up-coning. Numerical simulations show similar patterns, even though deviations exist between the second and the third pumping rate, which are under and overestimated by the numerical simulation, respectively. Further investigations are necessary to investigate the dynamics of pumping from freshwater lenses under the influence of climate change (i.e. sea level rise).

Analysis of Environmental Applicability of HDPE Geomembrane by Simulated Applicability Testing for Waste Containment Construction

NASA Astrophysics Data System (ADS)

Jeon, Han-Yong

2016-10-01

Geosynthetic separation boxes made from recycled polymeric materials were designed to increase the waste landfill amount and develop the hydraulic performance in steep slope sides in the waste landfills. To evaluate the advantages of these geosynthetic separation boxes, index tests were conducted in order to compare the geonet composites and geosynthetic separation boxes. The tensile strength retention of the geosynthetic separation box plates exposed to UV light and leachate solutions was better than that of the geonet composites. The drainage performance of the geosynthetic separation boxes was compared with that of the geonet composites at a slope angle corresponding to a real waste landfill site. The drainage performance of the geosynthetic separation box plates was better than that of the geonet composites.

Coupling fast fluid dynamics and multizone airflow models in Modelica Buildings library to simulate the dynamics of HVAC systems

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

Tian, Wei; Sevilla, Thomas Alonso; Zuo, Wangda

Historically, multizone models are widely used in building airflow and energy performance simulations due to their fast computing speed. However, multizone models assume that the air in a room is well mixed, consequently limiting their application. In specific rooms where this assumption fails, the use of computational fluid dynamics (CFD) models may be an alternative option. Previous research has mainly focused on coupling CFD models and multizone models to study airflow in large spaces. While significant, most of these analyses did not consider the coupled simulation of the building airflow with the building's Heating, Ventilation, and Air-Conditioning (HVAC) systems. Thismore » paper tries to fill the gap by integrating the models for HVAC systems with coupled multizone and CFD simulations for airflows, using the Modelica simul ation platform. To improve the computational efficiency, we incorporated a simplified CFD model named fast fluid dynamics (FFD). We first introduce the data synchronization strategy and implementation in Modelica. Then, we verify the implementation using two case studies involving an isothermal and a non-isothermal flow by comparing model simulations to experiment data. Afterward, we study another three cases that are deemed more realistic. This is done by attaching a variable air volume (VAV) terminal box and a VAV system to previous flows to assess the capability of the models in studying the dynamic control of HVAC systems. Finally, we discuss further research needs on the coupled simulation using the models.« less

Applicability of Existing C3 (Command, Control and Communications) Vulnerability and Hardness Analyses to Sentry System Issues.

DTIC Science & Technology

1983-01-13

Naval .1 Ordnance Systems Command ) codes are detailed propagation simulations mostly at lower frequencies . These are combined with WEPH code phenomenology...AD B062349L. Scope /Abstract: This report describes a simple model for predicting the loads on box-like target structures subject to air blast. A... model and applying it to targets which can be approximated by a series of rectangular parallelopipeds. In this report the physical phenomena of high

Quasielastic neutron scattering measurements and ab initio MD-simulations on single ion motions in molten NaF

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

Demmel, F.; Mukhopadhyay, S.; Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ

2016-01-07

The ionic stochastic motions in the molten alkali halide NaF are investigated by quasielastic neutron scattering and first principles molecular dynamics simulation. Quasielastic neutron scattering was employed to extract the diffusion behavior of the sodium ions in the melt. An extensive first principles based simulation on a box of up to 512 particles has been performed to complement the experimental data. From that large box, a smaller 64-particle box has then been simulated over a runtime of 60 ps. A good agreement between calculated and neutron data on the level of spectral shape has been obtained. The obtained sodium diffusionmore » coefficients agree very well. The simulation predicts a fluorine diffusion coefficient similar to the sodium one. Applying the Nernst-Einstein equation, a remarkable large cross correlation between both ions can be deduced. The velocity cross correlations demonstrate a positive correlation between the ions over a period of 0.1 ps. That strong correlation is evidence that the unlike ions do not move completely statistically independent and have a strong association over a short period of time.« less

A Monte-Carlo Analysis of Organic Aerosol Volatility with Aerosol Microphysics

NASA Astrophysics Data System (ADS)

Gao, C. Y.; Tsigaridis, K.; Bauer, S. E.

2016-12-01

A newly developed box model scheme, MATRIX-VBS, includes the volatility-basis set (VBS) framework in an aerosol microphysical scheme MATRIX (Multiconfiguration Aerosol TRacker of mIXing state), which resolves aerosol mass and number concentrations and aerosol mixing state. The new scheme advanced the representation of organic aerosols in Earth system models by improving the traditional and simplistic treatment of organic aerosols as non-volatile and with a fixed size distribution. Further development includes adding the condensation of organics on coarse mode aerosols - dust and sea salt, thus making all organics in the system semi-volatile. To test and simplify the model, a Monte-Carlo analysis is performed to pin point which processes affect organics the most under which chemical and meteorological conditions. Since the model's parameterizations have the ability to capture a very wide range of conditions, from very clean to very polluted and for a wide range of meteorological conditions, all possible scenarios on Earth across the whole parameter space, including temperature, location, emissions and oxidant levels, are examined. The Monte-Carlo simulations provide quantitative information on the sensitivity of the newly developed model and help us understand how organics are affecting the size distribution, mixing state and volatility distribution at varying levels of meteorological conditions and pollution levels. In addition, these simulations give information on which parameters play a critical role in the aerosol distribution and evolution in the atmosphere and which do not, that will facilitate the simplification of the box model, an important step in its implementation in the global model.

The Nuclear Energy Advanced Modeling and Simulation Safeguards and Separations Reprocessing Plant Toolkit

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

McCaskey, Alex; Billings, Jay Jay; de Almeida, Valmor F

2011-08-01

This report details the progress made in the development of the Reprocessing Plant Toolkit (RPTk) for the DOE Nuclear Energy Advanced Modeling and Simulation (NEAMS) program. RPTk is an ongoing development effort intended to provide users with an extensible, integrated, and scalable software framework for the modeling and simulation of spent nuclear fuel reprocessing plants by enabling the insertion and coupling of user-developed physicochemical modules of variable fidelity. The NEAMS Safeguards and Separations IPSC (SafeSeps) and the Enabling Computational Technologies (ECT) supporting program element have partnered to release an initial version of the RPTk with a focus on software usabilitymore » and utility. RPTk implements a data flow architecture that is the source of the system's extensibility and scalability. Data flows through physicochemical modules sequentially, with each module importing data, evolving it, and exporting the updated data to the next downstream module. This is accomplished through various architectural abstractions designed to give RPTk true plug-and-play capabilities. A simple application of this architecture, as well as RPTk data flow and evolution, is demonstrated in Section 6 with an application consisting of two coupled physicochemical modules. The remaining sections describe this ongoing work in full, from system vision and design inception to full implementation. Section 3 describes the relevant software development processes used by the RPTk development team. These processes allow the team to manage system complexity and ensure stakeholder satisfaction. This section also details the work done on the RPTk ``black box'' and ``white box'' models, with a special focus on the separation of concerns between the RPTk user interface and application runtime. Section 4 and 5 discuss that application runtime component in more detail, and describe the dependencies, behavior, and rigorous testing of its constituent components.« less

Numerical analysis of experiments on the generation of shock waves in aluminium under indirect (X-ray) action on the Iskra-5 facility

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

Bondarenko, S V; Dolgoleva, G V; Novikova, E A

The dynamics of laser and X-ray radiation fields in experiments with cylindrical converter boxes (illuminators), which had earlier been carried out on the Iskra-5 laser facility (the second harmonic of iodine laser radiation, {lambda} = 0.66 {mu}m) was investigated in a sector approximation using the SND-LIRA numerical technique. In these experiments, the X-ray radiation temperature in the box was determined by measuring the velocity of the shock wave generated in the sample under investigation, which was located at the end of the cylindrical illuminator. Through simulations were made using the SND-LIRA code, which took into account the absorption of lasermore » driver radiation at the box walls, the production of quasithermal radiation, as well as the formation and propagation of the shock wave in the sample under investigation. An analysis of the experiments permits determining the electron thermal flux limiter f: for f = 0.03 it is possible to match the experimental scaling data for X-ray in-box radiation temperature to the data of our simulations. The shock velocities obtained from the simulations are also consistent with experimental data. In particular, in the experiment with six laser beams (and a laser energy E{sub L} = 1380 J introduced into the box) the velocity of the shock front (determined from the position of a laser mark) after passage through a 50-{mu}m thick base aluminium layer was equal to 35{+-}1.6 km s{sup -1}, and in simulations to 36 km s{sup -1}. In the experiment with four laser beams (for E{sub L} = 850 J) the shock velocity (measured from the difference of transit times through the base aluminium layer and an additional thin aluminium platelet) was equal to 30{+-}3.6 km s{sup -1}, and in simulations to 30 km s{sup -1}. (interaction of laser radiation with matter)« less

Performance assessment of Large Eddy Simulation (LES) for modeling dispersion in an urban street canyon with tree planting

NASA Astrophysics Data System (ADS)

Moonen, P.; Gromke, C.; Dorer, V.

2013-08-01

The potential of a Large Eddy Simulation (LES) model to reliably predict near-field pollutant dispersion is assessed. To that extent, detailed time-resolved numerical simulations of coupled flow and dispersion are conducted for a street canyon with tree planting. Different crown porosities are considered. The model performance is assessed in several steps, ranging from a qualitative comparison to measured concentrations, over statistical data analysis by means of scatter plots and box plots, up to the calculation of objective validation metrics. The extensive validation effort highlights and quantifies notable features and shortcomings of the model, which would otherwise remain unnoticed. The model performance is found to be spatially non-uniform. Closer agreement with measurement data is achieved near the canyon ends than for the central part of the canyon, and typical model acceptance criteria are satisfied more easily for the leeward than for the windward canyon wall. This demonstrates the need for rigorous model evaluation. Only quality-assured models can be used with confidence to support assessment, planning and implementation of pollutant mitigation strategies.

Fast Generation of Ensembles of Cosmological N-Body Simulations via Mode-Resampling

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

Schneider, M D; Cole, S; Frenk, C S

2011-02-14

We present an algorithm for quickly generating multiple realizations of N-body simulations to be used, for example, for cosmological parameter estimation from surveys of large-scale structure. Our algorithm uses a new method to resample the large-scale (Gaussian-distributed) Fourier modes in a periodic N-body simulation box in a manner that properly accounts for the nonlinear mode-coupling between large and small scales. We find that our method for adding new large-scale mode realizations recovers the nonlinear power spectrum to sub-percent accuracy on scales larger than about half the Nyquist frequency of the simulation box. Using 20 N-body simulations, we obtain a powermore » spectrum covariance matrix estimate that matches the estimator from Takahashi et al. (from 5000 simulations) with < 20% errors in all matrix elements. Comparing the rates of convergence, we determine that our algorithm requires {approx}8 times fewer simulations to achieve a given error tolerance in estimates of the power spectrum covariance matrix. The degree of success of our algorithm indicates that we understand the main physical processes that give rise to the correlations in the matter power spectrum. Namely, the large-scale Fourier modes modulate both the degree of structure growth through the variation in the effective local matter density and also the spatial frequency of small-scale perturbations through large-scale displacements. We expect our algorithm to be useful for noise modeling when constraining cosmological parameters from weak lensing (cosmic shear) and galaxy surveys, rescaling summary statistics of N-body simulations for new cosmological parameter values, and any applications where the influence of Fourier modes larger than the simulation size must be accounted for.« less

SLTCAP: A Simple Method for Calculating the Number of Ions Needed for MD Simulation.

PubMed

Schmit, Jeremy D; Kariyawasam, Nilusha L; Needham, Vince; Smith, Paul E

2018-04-10

An accurate depiction of electrostatic interactions in molecular dynamics requires the correct number of ions in the simulation box to capture screening effects. However, the number of ions that should be added to the box is seldom given by the bulk salt concentration because a charged biomolecule solute will perturb the local solvent environment. We present a simple method for calculating the number of ions that requires only the total solute charge, solvent volume, and bulk salt concentration as inputs. We show that the most commonly used method for adding salt to a simulation results in an effective salt concentration that is too high. These findings are confirmed using simulations of lysozyme. We have established a web server where these calculations can be readily performed to aid simulation setup.

Dynamical thresholding of pancake models: a promising variant of the HDM picture

NASA Astrophysics Data System (ADS)

Buchert, Thomas

Variants of pancake models are considered which allow for the construction of a phenomenological link to the galaxy formation process. A control parameter space is introduced which defines different scenarios of galaxy formation. The sensibility of statistical measures of the small-scale structure with respect to this parameter freedom is demonstrated. This property of the galaxy formation model, together with the consequences of enlarging the box size of the simulation to a `fair sample scale', form the basis of arguments to support the possible revival of the standard `Hot-Dark-Matter' model.

Development of a Pressure Box to Evaluate Reusable-Launch-Vehicle Cryogenic-Tank Panels

NASA Technical Reports Server (NTRS)

Ambur, Damodar R.; Sikora, Joseph; Maguire, James F.; Winn, Peter M.

1996-01-01

A cryogenic pressure-box test machine has been designed and is being developed to test full-scale reusable-launch-vehicle cryogenic-tank panels. This machine is equipped with an internal pressurization system, a cryogenic cooling system, and a heating system to simulate the mechanical and thermal loading conditions that are representative of a reusable-launch-vehicle mission profile. The cryogenic cooling system uses liquid helium and liquid nitrogen to simulate liquid hydrogen and liquid oxygen tank internal temperatures. A quartz lamp heating system is used for heating the external surface of the test panels to simulate cryogenic-tank external surface temperatures during re-entry of the launch vehicle. The pressurization system uses gaseous helium and is designed to be controlled independently of the cooling system. The tensile loads in the axial direction of the test panel are simulated by means of hydraulic actuators and a load control system. The hoop loads in the test panel are reacted by load-calibrated turnbuckles attached to the skin and frame elements of the test panel. The load distribution in the skin and frames can be adjusted to correspond to the tank structure by using these turnbuckles. The seal between the test panel and the cryogenic pressure box is made from a reinforced Teflon material which can withstand pressures greater than 52 psig at cryogenic temperatures. Analytical results and tests on prototype test components indicate that most of the cryogenic-tank loading conditions that occur in flight can be simulated in the cryogenic pressure-box test machine.

Effects of BOX engineering on analogue/RF and circuit performance of InGaAs-OI-Si MOSFET

NASA Astrophysics Data System (ADS)

Maity, Subir Kr.; Pandit, Soumya

2017-11-01

InGaAs is an attractive choice as alternate channel material in n-channel metal oxide semiconductor transistor for high-performance applications. However, electrostatic integrity of such device is poor. In this paper, we present a comprehensive technology computer-aided design simulation-based study of the effect of scaling the thickness of the buried oxide (BOX) region and varying the dielectric constant of BOX material on the electrostatic integrity, analogue/radio frequency (RF) performance and circuit performance of InGaAs-on-Insulator device. Device with thin BOX layer gives better drain-induced barrier lowering performance which enhances output resistance. The carrier mobility remains almost constant with thinning of BOX layer up to certain value. By lowering the dielectric constant of the BOX material, it is further possible to improve the analogue and RF performance. Effect of BOX thickness scaling and role of BOX dielectric material on gain-frequency response of common source amplifier is also studied. It is observed that frequency response of the amplifier improves for thin BOX and with low dielectric constant-based material.

Studies of Low Luminosity Active Galactic Nuclei with Monte Carlo and Magnetohydrodynamic Simulations

NASA Astrophysics Data System (ADS)

Hilburn, Guy Louis

Results from several studies are presented which detail explorations of the physical and spectral properties of low luminosity active galactic nuclei. An initial Sagittarius A* general relativistic magnetohydrodynamic simulation and Monte Carlo radiation transport model suggests accretion rate changes as the dominant flaring method. A similar study on M87 introduces new methods to the Monte Carlo model for increased consistency in highly energetic sources. Again, accretion rate variation seems most appropriate to explain spectral transients. To more closely resolve the methods of particle energization in active galactic nuclei accretion disks, a series of localized shearing box simulations explores the effect of numerical resolution on the development of current sheets. A particular focus on numerically describing converged current sheet formation will provide new methods for consideration of turbulence in accretion disks.

Use case driven approach to develop simulation model for PCS of APR1400 simulator

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

Dong Wook, Kim; Hong Soo, Kim; Hyeon Tae, Kang

2006-07-01

The full-scope simulator is being developed to evaluate specific design feature and to support the iterative design and validation in the Man-Machine Interface System (MMIS) design of Advanced Power Reactor (APR) 1400. The simulator consists of process model, control logic model, and MMI for the APR1400 as well as the Power Control System (PCS). In this paper, a use case driven approach is proposed to develop a simulation model for PCS. In this approach, a system is considered from the point of view of its users. User's view of the system is based on interactions with the system and themore » resultant responses. In use case driven approach, we initially consider the system as a black box and look at its interactions with the users. From these interactions, use cases of the system are identified. Then the system is modeled using these use cases as functions. Lower levels expand the functionalities of each of these use cases. Hence, starting from the topmost level view of the system, we proceeded down to the lowest level (the internal view of the system). The model of the system thus developed is use case driven. This paper will introduce the functionality of the PCS simulation model, including a requirement analysis based on use case and the validation result of development of PCS model. The PCS simulation model using use case will be first used during the full-scope simulator development for nuclear power plant and will be supplied to Shin-Kori 3 and 4 plant. The use case based simulation model development can be useful for the design and implementation of simulation models. (authors)« less

Source parameters of the 2013 Lushan, Sichuan, Ms7.0 earthquake and estimation of the near-fault strong ground motion

NASA Astrophysics Data System (ADS)

Meng, L.; Zhou, L.; Liu, J.

2013-12-01

Abstract: The April 20, 2013 Ms 7.0 earthquake in Lushan city, Sichuan province of China occurred as the result of east-west oriented reverse-type motion on a north-south striking fault. The source location suggests the event occurred on the Southern part of Longmenshan fault at a depth of 13km. The Lushan earthquake caused a great of loss of property and 196 deaths. The maximum intensity is up to VIII to IX at Boxing and Lushan city, which are located in the meizoseismal area. In this study, we analyzed the dynamic source process and calculated source spectral parameters, estimated the strong ground motion in the near-fault field based on the Brune's circle model at first. A dynamical composite source model (DCSM) has been developed further to simulate the near-fault strong ground motion with associated fault rupture properties at Boxing and Lushan city, respectively. The results indicate that the frictional undershoot behavior in the dynamic source process of Lushan earthquake, which is actually different from the overshoot activity of the Wenchuan earthquake. Based on the simulated results of the near-fault strong ground motion, described the intensity distribution of the Lushan earthquake field. The simulated intensity indicated that, the maximum intensity value is IX, and region with and above VII almost 16,000km2, which is consistence with observation intensity published online by China Earthquake Administration (CEA) on April 25. Moreover, the numerical modeling developed in this study has great application in the strong ground motion prediction and intensity estimation for the earthquake rescue purpose. In fact, the estimation methods based on the empirical relationship and numerical modeling developed in this study has great application in the strong ground motion prediction for the earthquake source process understand purpose. Keywords: Lushan, Ms7.0 earthquake; near-fault strong ground motion; DCSM; simulated intensity

Maestro and Castro: Simulation Codes for Astrophysical Flows

NASA Astrophysics Data System (ADS)

Zingale, Michael; Almgren, Ann; Beckner, Vince; Bell, John; Friesen, Brian; Jacobs, Adam; Katz, Maximilian P.; Malone, Christopher; Nonaka, Andrew; Zhang, Weiqun

2017-01-01

Stellar explosions are multiphysics problems—modeling them requires the coordinated input of gravity solvers, reaction networks, radiation transport, and hydrodynamics together with microphysics recipes to describe the physics of matter under extreme conditions. Furthermore, these models involve following a wide range of spatial and temporal scales, which puts tough demands on simulation codes. We developed the codes Maestro and Castro to meet the computational challenges of these problems. Maestro uses a low Mach number formulation of the hydrodynamics to efficiently model convection. Castro solves the fully compressible radiation hydrodynamics equations to capture the explosive phases of stellar phenomena. Both codes are built upon the BoxLib adaptive mesh refinement library, which prepares them for next-generation exascale computers. Common microphysics shared between the codes allows us to transfer a problem from the low Mach number regime in Maestro to the explosive regime in Castro. Importantly, both codes are freely available (https://github.com/BoxLib-Codes). We will describe the design of the codes and some of their science applications, as well as future development directions.Support for development was provided by NSF award AST-1211563 and DOE/Office of Nuclear Physics grant DE-FG02-87ER40317 to Stony Brook and by the Applied Mathematics Program of the DOE Office of Advance Scientific Computing Research under US DOE contract DE-AC02-05CH11231 to LBNL.

Self-inhibition can limit biologically enhanced TCE dissolution from a TCE DNAPL.

PubMed

Haest, P J; Springael, D; Seuntjens, P; Smolders, E

2012-11-01

Biodegradation of trichloroethene (TCE) near a Dense Non Aqueous Phase Liquid (DNAPL) can enhance the dissolution rate of the DNAPL by increasing the concentration gradient at the DNAPL-water interface. Two-dimensional flow-through sand boxes containing a TCE DNAPL and inoculated with a TCE dechlorinating consortium were set up to measure this bio-enhanced dissolution under anaerobic conditions. The total mass of TCE and daughter products in the effluent of the biotic boxes was 3-6 fold larger than in the effluent of the abiotic box. However, the mass of daughter products only accounted for 19-55% of the total mass of chlorinated compounds in the effluent, suggesting that bio-enhanced dissolution factors were maximally 1.3-2.2. The enhanced dissolution most likely primarily resulted from variable DNAPL distribution rather than biodegradation. Specific dechlorination rates previously determined in a stirred liquid medium were used in a reactive transport model to identify the rate limiting factors. The model adequately simulated the overall TCE degradation when predicted resident microbial numbers approached observed values and indicated an enhancement factor for TCE dissolution of 1.01. The model shows that dechlorination of TCE in the 2D box was limited due to the short residence time and the self-inhibition of the TCE degradation. A parameter sensitivity analysis predicts that the bio-enhanced dissolution factor for this TCE source zone can only exceed a value of 2 if the TCE self-inhibition is drastically reduced (when a TCE tolerant dehalogenating community is present) or if the DNAPL is located in a low-permeable layer with a small Darcy velocity. Copyright © 2012 Elsevier Ltd. All rights reserved.

Uncertain Representations of Sub-Grid Pollutant Transport in Chemistry-Transport Models and Impacts on Long-Range Transport and Global Composition

NASA Technical Reports Server (NTRS)

Pawson, Steven; Zhu, Z.; Ott, L. E.; Molod, A.; Duncan, B. N.; Nielsen, J. E.

2009-01-01

Sub-grid transport, by convection and turbulence, is known to play an important role in lofting pollutants from their source regions. Consequently, the long-range transport and climatology of simulated atmospheric composition are impacted. This study uses the Goddard Earth Observing System, Version 5 (GEOS-5) atmospheric model to study pollutant transport. The baseline model uses a Relaxed Arakawa-Schubert (RAS) scheme that represents convection through a sequence of linearly entraining cloud plumes characterized by unique detrainment levels. Thermodynamics, moisture and trace gases are transported in the same manner. Various approximate forms of trace-gas transport are implemented, in which the box-averaged cloud mass fluxes from RAS are used with different numerical approaches. Substantial impacts on forward-model simulations of CO (using a linearized chemistry) are evident. In particular, some aspects of simulations using a diffusive form of sub-grid transport bear more resemblance to space-biased CO observations than do the baseline simulations with RAS transport. Implications for transport in the real atmosphere will be discussed. Another issue of importance is that many adjoint/inversion computations use simplified representations of sub-grid transport that may be inconsistent with the forward models: implications will be discussed. Finally, simulations using a complex chemistry model in GEOS-5 (in place of the linearized CO model) are underway: noteworthy results from this simulation will be mentioned.

Simulation and comparison of the illuminance, uniformity, and efficiency of different forms of lighting used in basketball court illumination.

PubMed

Sun, Wen-Shing; Tien, Chuen-Lin; Tsuei, Chih-Hsuan; Pan, Jui-Wen

2014-10-10

We simulate and compare the illuminance, uniformity, and efficiency of metal-halide lamps, white LED light sources, and hybrid light box designs combining sunlight and white LED lighting used for indoor basketball court illumination. According to the optical simulation results and our examination of real situations, we find that hybrid light box designs combining sunlight and white LEDs do perform better than either metal-halide lamps or white LED lights. An evaluation of the sunlight concentrator system used in our inverted solar cell shows that the energy consumption of stadium lighting can be reduced significantly.

A satellite simulator for TRMM PR applied to climate model simulations

NASA Astrophysics Data System (ADS)

Spangehl, T.; Schroeder, M.; Bodas-Salcedo, A.; Hollmann, R.; Riley Dellaripa, E. M.; Schumacher, C.

2017-12-01

Climate model simulations have to be compared against observation based datasets in order to assess their skill in representing precipitation characteristics. Here we use a satellite simulator for TRMM PR in order to evaluate simulations performed with MPI-ESM (Earth system model of the Max Planck Institute for Meteorology in Hamburg, Germany) performed within the MiKlip project (https://www.fona-miklip.de/, funded by Federal Ministry of Education and Research in Germany). While classical evaluation methods focus on geophysical parameters such as precipitation amounts, the application of the satellite simulator enables an evaluation in the instrument's parameter space thereby reducing uncertainties on the reference side. The CFMIP Observation Simulator Package (COSP) provides a framework for the application of satellite simulators to climate model simulations. The approach requires the introduction of sub-grid cloud and precipitation variability. Radar reflectivities are obtained by applying Mie theory, with the microphysical assumptions being chosen to match the atmosphere component of MPI-ESM (ECHAM6). The results are found to be sensitive to the methods used to distribute the convective precipitation over the sub-grid boxes. Simple parameterization methods are used to introduce sub-grid variability of convective clouds and precipitation. In order to constrain uncertainties a comprehensive comparison with sub-grid scale convective precipitation variability which is deduced from TRMM PR observations is carried out.

Kinematic cues in perceptual weight judgement and their origins in box lifting

PubMed Central

Hamilton, A.; Joyce, D. W.; Flanagan, R.; Frith, C. D.; Wolpert, D. M.

2009-01-01

When accepting a parcel from another person, we are able to use information about that person’s movement to estimate in advance the weight of the parcel, that is, to judge its weight from observed action. Perceptual weight judgment provides a powerful method to study our interpretation of other people’s actions, but it is not known what sources of information are used in judging weight. We have manipulated full form videos to obtain precise control of the perceived kinematics of a box lifting action, and use this technique to explore the kinematic cues that affect weight judgment. We find that observers rely most on the duration of the lifting movement to judge weight, and make less use of the durations of the grasp phase, when the box is first gripped, or the place phase, when the box is put down. These findings can be compared to the kinematics of natural box lifting behaviour, where we find that the duration of the grasp component is the best predictor of true box weight. The lack of accord between the optimal cues predicted by the natural behaviour and the cues actually used in the perceptual task has implications for our understanding of action observation in terms of a motor simulation. The differences between perceptual and motor behaviour are evidence against a strong version of the motor simulation hypothesis. PMID:16311765

Global and Local Stress Analyses of McDonnell Douglas Stitched/RFI Composite Wing Stub Box

NASA Technical Reports Server (NTRS)

Wang, John T.

1996-01-01

This report contains results of structural analyses performed in support of the NASA structural testing of an all-composite stitched/RFI (resin film infusion) wing stub box. McDonnell Douglas Aerospace Company designed and fabricated the wing stub box. The analyses used a global/local approach. The global model contains the entire test article. It includes the all-composite stub box, a metallic load-transition box and a metallic wing-tip extension box. The two metallic boxes are connected to the inboard and outboard ends of the composite wing stub box, respectively. The load-transition box was attached to a steel and concrete vertical reaction structure and a load was applied at the tip of the extension box to bend the wing stub box upward. The local model contains an upper cover region surrounding three stringer runouts. In that region, a large nonlinear deformation was identified by the global analyses. A more detailed mesh was used for the local model to obtain more accurate analysis results near stringer runouts. Numerous analysis results such as deformed shapes, displacements at selected locations, and strains at critical locations are included in this report.

Benchmark of 3D halo neutral simulation in TRANSP and FIDASIM and application to projected neutral-beam-heated NSTX-U plasmas

NASA Astrophysics Data System (ADS)

Liu, D.; Medley, S. S.; Gorelenkova, M. V.; Heidbrink, W. W.; Stagner, L.

2014-10-01

A cloud of halo neutrals is created in the vicinity of beam footprint during the neutral beam injection and the halo neutral density can be comparable with beam neutral density. Proper modeling of halo neutrals is critical to correctly interpret neutral particle analyzers (NPA) and fast ion D-alpha (FIDA) signals since these signals strongly depend on local beam and halo neutral density. A 3D halo neutral model has been recently developed and implemented inside TRANSP code. The 3D halo neutral code uses a ``beam-in-a-box'' model that encompasses both injected beam neutrals and resulting halo neutrals. Upon deposition by charge exchange, a subset of the full, one-half and one-third beam energy components produce thermal halo neutrals that are tracked through successive halo neutral generations until an ionization event occurs or a descendant halo exits the box. A benchmark between 3D halo neural model in TRANSP and in FIDA/NPA synthetic diagnostic code FIDASIM is carried out. Detailed comparison of halo neutral density profiles from two codes will be shown. The NPA and FIDA simulations with and without 3D halos are applied to projections of plasma performance for the National Spherical Tours eXperiment-Upgrade (NSTX-U) and the effects of halo neutral density on NPA and FIDA signal amplitude and profile will be presented. Work supported by US DOE.

McSnow: A Monte-Carlo Particle Model for Riming and Aggregation of Ice Particles in a Multidimensional Microphysical Phase Space

NASA Astrophysics Data System (ADS)

Brdar, S.; Seifert, A.

2018-01-01

We present a novel Monte-Carlo ice microphysics model, McSnow, to simulate the evolution of ice particles due to deposition, aggregation, riming, and sedimentation. The model is an application and extension of the super-droplet method of Shima et al. (2009) to the more complex problem of rimed ice particles and aggregates. For each individual super-particle, the ice mass, rime mass, rime volume, and the number of monomers are predicted establishing a four-dimensional particle-size distribution. The sensitivity of the model to various assumptions is discussed based on box model and one-dimensional simulations. We show that the Monte-Carlo method provides a feasible approach to tackle this high-dimensional problem. The largest uncertainty seems to be related to the treatment of the riming processes. This calls for additional field and laboratory measurements of partially rimed snowflakes.

Elucidating the evolutionary conserved DNA-binding specificities of WRKY transcription factors by molecular dynamics and in vitro binding assays

PubMed Central

Brand, Luise H.; Fischer, Nina M.; Harter, Klaus; Kohlbacher, Oliver; Wanke, Dierk

2013-01-01

WRKY transcription factors constitute a large protein family in plants that is involved in the regulation of developmental processes and responses to biotic or abiotic stimuli. The question arises how stimulus-specific responses are mediated given that the highly conserved WRKY DNA-binding domain (DBD) exclusively recognizes the ‘TTGACY’ W-box consensus. We speculated that the W-box consensus might be more degenerate and yet undetected differences in the W-box consensus of WRKYs of different evolutionary descent exist. The phylogenetic analysis of WRKY DBDs suggests that they evolved from an ancestral group IIc-like WRKY early in the eukaryote lineage. A direct descent of group IIc WRKYs supports a monophyletic origin of all other group II and III WRKYs from group I by loss of an N-terminal DBD. Group I WRKYs are of paraphyletic descent and evolved multiple times independently. By homology modeling, molecular dynamics simulations and in vitro DNA–protein interaction-enzyme-linked immunosorbent assay with AtWRKY50 (IIc), AtWRKY33 (I) and AtWRKY11 (IId) DBDs, we revealed differences in DNA-binding specificities. Our data imply that other components are essentially required besides the W-box-specific binding to DNA to facilitate a stimulus-specific WRKY function. PMID:23975197

Dispersion of a Passive Scalar Within and Above an Urban Street Network

NASA Astrophysics Data System (ADS)

Goulart, E. V.; Coceal, O.; Belcher, S. E.

2018-03-01

The transport of a passive scalar from a continuous point-source release in an urban street network is studied using direct numerical simulation (DNS). Dispersion through the network is characterized by evaluating horizontal fluxes of scalar within and above the urban canopy and vertical exchange fluxes through the canopy top. The relative magnitude and balance of these fluxes are used to distinguish three different regions relative to the source location: a near-field region, a transition region and a far-field region. The partitioning of each of these fluxes into mean and turbulent parts is computed. It is shown that within the canopy the horizontal turbulent flux in the street network is small, whereas above the canopy it comprises a significant fraction of the total flux. Vertical fluxes through the canopy top are predominantly turbulent. The mean and turbulent fluxes are respectively parametrized in terms of an advection velocity and a detrainment velocity and the parametrization incorporated into a simple box-network model. The model treats the coupled dispersion problem within and above the street network in a unified way and predictions of mean concentrations compare well with the DNS data. This demonstrates the usefulness of the box-network approach for process studies and interpretation of results from more detailed numerical simulations.

Saturation of the magnetorotational instability at large Elsasser number

NASA Astrophysics Data System (ADS)

Jamroz, B.; Julien, K.; Knobloch, E.

2008-09-01

The magnetorotational instability is investigated within the shearing box approximation in the large Elsasser number regime. In this regime, which is of fundamental importance to astrophysical accretion disk theory, shear is the dominant source of energy, but the instability itself requires the presence of a weaker vertical magnetic field. Dissipative effects are weaker still but not negligible. The regime explored retains the condition that (viscous and ohmic) dissipative forces do not play a role in the leading order linear instability mechanism. However, they are sufficiently large to permit a nonlinear feedback mechanism whereby the turbulent stresses generated by the MRI act on and modify the local background shear in the angular velocity profile. To date this response has been omitted in shearing box simulations and is captured by a reduced pde model derived here from the global MHD fluid equations using multiscale asymptotic perturbation theory. Results from numerical simulations of the reduced pde model indicate a linear phase of exponential growth followed by a nonlinear adjustment to algebraic growth and decay in the fluctuating quantities. Remarkably, the velocity and magnetic field correlations associated with these algebraic growth and decay laws conspire to achieve saturation of the angular momentum transport. The inclusion of subdominant ohmic dissipation arrests the algebraic growth of the fluctuations on a longer, dissipative time scale.

Saturation of the Magnetorotational Instability at Large Elssaser Number

NASA Astrophysics Data System (ADS)

Julien, Keith; Jamroz, Benjamin; Knobloch, Edgar

2009-11-01

The MRI is believed to play an important role in accretion disk physics in extracting angular momentum from the disk and allowing accretion to take place. The instability is investigated within the shearing box approximation under conditions of fundamental importance to astrophysical accretion disk theory. The shear is taken to be the dominant source of energy, but the instability itself requires the presence of a weaker vertical magnetic field. Dissipative effects are suffiently weak that the Elsasser number is large. Thus dissipative forces do not play a role in the leading order linear instability mechanism. However, they are sufficiently large to permit a nonlinear feedback mechanism whereby the turbulent stresses generated by the MRI act on and modify the local background shear in the angular velocity profile. To date this response has been omitted in shearing box simulations and is captured by a reduced pde model derived from the global MHD fluid equations using multiscale asymptotic perturbation theory. Results from simulations of the model indicate a linear phase of exponential growth followed by a nonlinear adjustment to algebraic growth and decay in the fluctuating quantities. Remarkably, the velocity and magnetic field correlations associated with these growth and decay laws conspire to achieve saturation of angular momentum transport.

Learning basic laparoscopic skills: a randomized controlled study comparing box trainer, virtual reality simulator, and mental training.

PubMed

Mulla, Mubashir; Sharma, Davendra; Moghul, Masood; Kailani, Obeda; Dockery, Judith; Ayis, Salma; Grange, Philippe

2012-01-01

The objectives of this study were (1) to compare different methods of learning basic laparoscopic skills using box trainer (BT), virtual reality simulator (VRS) and mental training (MT); and (2) to determine the most effective method of learning laparoscopic skills. Randomized controlled trial. King's College, London. 41 medical students were included in the study. After randomization, they were divided into 5 groups. Group 1 was the control group without training; group 2 was box trained; group 3 was also box trained with an additional practice session; group 4 was VRS trained; and group 5 was solely mentally trained. The task was to cut out a circle marked on a stretchable material. All groups were assessed after 1 week on both BT and VRS. Four main parameters were assessed, namely time, precision, accuracy, and performance. Time: On BT assessment, the box-trained group with additional practice group 3 was the fastest, and the mental-trained group 5 was the slowest. On VRS assessment, the time difference between group 3 and the control group 1 was statistically significant. Precision: On BT assessment, the box-trained groups 2 and 3 scored high, and mental trained were low on precision. On VRS assessment, the VRS-trained group ranked at the top, and the MT group was at the bottom on precision. Accuracy: On BT assessment, the box-trained group 3 was best and the mental-trained group was last. On VRS assessment, the VRS-trained group 4 scored high closely followed by box-trained groups 2 and 3. Performance: On BT assessment, the box-trained group 3 ranked above all the other groups, and the mental-trained group ranked last. On VRS assessment, the VRS group 4 scored best, followed closely by box-trained groups 2 and 3. The skills learned on box training were reproducible on both VRS and BT. However, not all the skills learned on VRS were transferable to BT. Furthermore, VRS was found to be a reliable and the most convenient method of assessment. MT alone cannot replace conventional training. Copyright © 2012 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.

Removing systematic errors in interionic potentials of mean force computed in molecular simulations using reaction-field-based electrostatics

PubMed Central

Baumketner, Andrij

2009-01-01

The performance of reaction-field methods to treat electrostatic interactions is tested in simulations of ions solvated in water. The potential of mean force between sodium chloride pair of ions and between side chains of lysine and aspartate are computed using umbrella sampling and molecular dynamics simulations. It is found that in comparison with lattice sum calculations, the charge-group-based approaches to reaction-field treatments produce a large error in the association energy of the ions that exhibits strong systematic dependence on the size of the simulation box. The atom-based implementation of the reaction field is seen to (i) improve the overall quality of the potential of mean force and (ii) remove the dependence on the size of the simulation box. It is suggested that the atom-based truncation be used in reaction-field simulations of mixed media. PMID:19292522

A new high-performance 3D multiphase flow code to simulate volcanic blasts and pyroclastic density currents: example from the Boxing Day event, Montserrat

NASA Astrophysics Data System (ADS)

Ongaro, T. E.; Clarke, A.; Neri, A.; Voight, B.; Widiwijayanti, C.

2005-12-01

For the first time the dynamics of directed blasts from explosive lava-dome decompression have been investigated by means of transient, multiphase flow simulations in 2D and 3D. Multiphase flow models developed for the analysis of pyroclastic dispersal from explosive eruptions have been so far limited to 2D axisymmetric or Cartesian formulations which cannot properly account for important 3D features of the volcanic system such as complex morphology and fluid turbulence. Here we use a new parallel multiphase flow code, named PDAC (Pyroclastic Dispersal Analysis Code) (Esposti Ongaro et al., 2005), able to simulate the transient and 3D thermofluid-dynamics of pyroclastic dispersal produced by collapsing columns and volcanic blasts. The code solves the equations of the multiparticle flow model of Neri et al. (2003) on 3D domains extending up to several kilometres in 3D and includes a new description of the boundary conditions over topography which is automatically acquired from a DEM. The initial conditions are represented by a compact volume of gas and pyroclasts, with clasts of different sizes and densities, at high temperature and pressure. Different dome porosities and pressurization models were tested in 2D to assess the sensitivity of the results to the distribution of initial gas pressure, and to the total mass and energy stored in the dome, prior to 3D modeling. The simulations have used topographies appropriate for the 1997 Boxing Day directed blast on Montserrat, which eradicated the village of St. Patricks. Some simulations tested the runout of pyroclastic density currents over the ocean surface, corresponding to observations of over-water surges to several km distances at both locations. The PDAC code was used to perform 3D simulations of the explosive event on the actual volcano topography. The results highlight the strong topographic control on the propagation of the dense pyroclastic flows, the triggering of thermal instabilities, and the elutriation of finest particles, and demonstrated the formation of dense pyroclastic flows by drainage of clasts sedimented from dilute flows. Fundamental and accurate hazard information can be obtained from the simulations, and the 3D displays are readily comprehended by officials and the public, making them very effective tools for risk mitigation.

A New 3D Multi-fluid Dust Model: A Study of the Effects of Activity and Nucleus Rotation on Dust Grain Behavior at Comet 67P/Churyumov-Gerasimenko

NASA Astrophysics Data System (ADS)

Shou, Y.; Combi, M.; Toth, G.; Tenishev, V.; Fougere, N.; Jia, X.; Rubin, M.; Huang, Z.; Hansen, K.; Gombosi, T.

2017-11-01

Improving our capability to interpret observations of cometary dust is necessary to deepen our understanding of the role of dust in the formation of comets and in altering the cometary environments. Models including dust grains are in demand to interpret observations and test hypotheses. Several existing models have taken into account the gas-dust interaction, varying sizes of dust grains and the cometary gravitational force. In this work, we develop a multi-fluid dust model based on the BATS-R-US code. This model not only incorporates key features of previous dust models, but also has the capability of simulating time-dependent phenomena. Since the model is run in the rotating comet reference frame, the centrifugal and Coriolis forces are included. The boundary conditions on the nucleus surface can be set according to the distribution of activity and the solar illumination. The Sun revolves around the comet in this frame. A newly developed numerical mesh is also used to resolve the real-shaped nucleus in the center and to facilitate prescription of the outer boundary conditions that accommodate the rotating frame. The inner part of the mesh is a box composed of Cartesian cells and the outer surface is a smooth sphere, with stretched cells filled in between the box and the sphere. Our model achieved comparable results to the Direct Simulation Monte Carlo method and the Rosetta/OSIRIS observations. It is also applied to study the effects of the rotating nucleus and the cometary activity and offers interpretations of some dust observations of comet 67P/Churyumov-Gerasimenko.

Does box model training improve surgical dexterity and economy of movement during virtual reality laparoscopy? A randomised trial.

PubMed

Clevin, Lotte; Grantcharov, Teodor P

2008-01-01

Laparoscopic box model trainers have been used in training curricula for a long time, however data on their impact on skills acquisition is still limited. Our aim was to validate a low cost box model trainer as a tool for the training of skills relevant to laparoscopic surgery. Randomised, controlled trial (Canadian Task Force Classification I). University Hospital. Sixteen gynaecologic residents with limited laparoscopic experience were randomised to a group that received a structured box model training curriculum, and a control group. Performance before and after the training was assessed in a virtual reality laparoscopic trainer (LapSim and was based on objective parameters, registered by the computer system (time, error, and economy of motion scores). Group A showed significantly greater improvement in all performance parameters compared with the control group: economy of movement (p=0.001), time (p=0.001) and tissue damage (p=0.036), confirming the positive impact of box-trainer curriculum on laparoscopic skills acquisition. Structured laparoscopic skill training on a low cost box model trainer improves performance as assessed using the VR system. Trainees who used the box model trainer showed significant improvement compared to the control group. Box model trainers are valid tools for laparoscopic skills training and should be implemented in the comprehensive training curricula in gynaecology.

A Calculus for Boxes and Traits in a Java-Like Setting

NASA Astrophysics Data System (ADS)

Bettini, Lorenzo; Damiani, Ferruccio; de Luca, Marco; Geilmann, Kathrin; Schäfer, Jan

The box model is a component model for the object-oriented paradigm, that defines components (the boxes) with clear encapsulation boundaries. Having well-defined boundaries is crucial in component-based software development, because it enables to argue about the interference and interaction between a component and its context. In general, boxes contain several objects and inner boxes, of which some are local to the box and cannot be accessed from other boxes and some can be accessible by other boxes. A trait is a set of methods divorced from any class hierarchy. Traits can be composed together to form classes or other traits. We present a calculus for boxes and traits. Traits are units of fine-grained reuse, whereas boxes can be seen as units of coarse-grained reuse. The calculus is equipped with an ownership type system and allows us to combine coarse- and fine-grained reuse of code by maintaining encapsulation of components.

Effects of cumulus entrainment and multiple cloud types on a January global climate model simulation

NASA Technical Reports Server (NTRS)

Yao, Mao-Sung; Del Genio, Anthony D.

1989-01-01

An improved version of the GISS Model II cumulus parameterization designed for long-term climate integrations is used to study the effects of entrainment and multiple cloud types on the January climate simulation. Instead of prescribing convective mass as a fixed fraction of the cloud base grid-box mass, it is calculated based on the closure assumption that the cumulus convection restores the atmosphere to a neutral moist convective state at cloud base. This change alone significantly improves the distribution of precipitation, convective mass exchanges, and frequencies in the January climate. The vertical structure of the tropical atmosphere exhibits quasi-equilibrium behavior when this closure is used, even though there is no explicit constraint applied above cloud base.

The galaxy luminosity function around groups

NASA Astrophysics Data System (ADS)

González, R. E.; Padilla, N. D.; Galaz, G.; Infante, L.

2005-11-01

We present a study on the variations of the luminosity function of galaxies around clusters in a numerical simulation with semi-analytic galaxies, attempting to detect these variations in the 2dF Galaxy Redshift Survey. We subdivide the simulation box into equal-density regions around clusters, which we assume can be achieved by selecting objects at a given normalized distance (r/rrms, where rrms is an estimate of the halo radius) from the group centre. The semi-analytic model predicts important variations in the luminosity function out to r/rrms~= 5. In brief, variations in the mass function of haloes around clusters (large dark matter haloes with M > 1012h-1Msolar) lead to cluster central regions that present a high abundance of bright galaxies (high M* values) as well as low-luminosity galaxies (high α) at r/rrms~= 3 there is a lack of bright galaxies, which shows the depletion of galaxies in the regions surrounding clusters (minimum in M* and α), and a tendency to constant luminosity function parameters at larger cluster-centric distances. We take into account the observational biases present in the real data by reproducing the peculiar velocity effect on the redshifts of galaxies in the simulation box, and also by producing mock catalogues. We find that excluding from the analysis galaxies which in projection are close to the centres of the groups provides results that are qualitatively consistent with the full simulation box results. When we apply this method to mock catalogues of the 2dF Galaxy Redshift Survey (2dFGRS) and the 2PIGG catalogue of groups, we find that the variations in the luminosity function are almost completely erased by the Finger of God effect; only a lack of bright galaxies at r/rrms~= 3 can be marginally detected in the mock catalogues. The results from the real 2dFGRS data show a clearer detection of a dip in M* and α for r/rrms= 3, consistent with the semi-analytic predictions.

Tracking a Superstorm

NASA Image and Video Library

2017-12-08

Oct. 29, 2012 – A day before landfall, Sandy intensified into a Category 2 superstorm nearly 1,000 miles wide. Credit: NASA's Goddard Space Flight Center and NASA Center for Climate Simulation Video and images courtesy of NASA/GSFC/William Putman -- A NASA computer model simulates the astonishing track and forceful winds of Hurricane Sandy. Hurricane Sandy pummeled the East Coast late in 2012’s Atlantic hurricane season, causing 159 deaths and $70 billion in damages. Days before landfall, forecasts of its trajectory were still being made. Some computer models showed that a trough in the jet stream would kick the monster storm away from land and out to sea. Among the earliest to predict its true course was NASA’s GEOS-5 global atmosphere model. The model works by dividing Earth’s atmosphere into a virtual grid of stacked boxes. A supercomputer then solves mathematical equations inside each box to create a weather forecast predicting Sandy’s structure, path and other traits. The NASA model not only produced an accurate track of Sandy, but also captured fine-scale details of the storm’s changing intensity and winds. Watch the video to see it for yourself. For more information, please visit: gmao.gsfc.nasa.gov/research/atmosphericassim/tracking_hur... NASA image use policy. NASA Goddard Space Flight Center enables NASA’s mission through four scientific endeavors: Earth Science, Heliophysics, Solar System Exploration, and Astrophysics. Goddard plays a leading role in NASA’s accomplishments by contributing compelling scientific knowledge to advance the Agency’s mission. Follow us on Twitter Like us on Facebook Find us on Instagram

Parameter estimation of a pulp digester model with derivative-free optimization strategies

NASA Astrophysics Data System (ADS)

Seiça, João C.; Romanenko, Andrey; Fernandes, Florbela P.; Santos, Lino O.; Fernandes, Natércia C. P.

2017-07-01

The work concerns the parameter estimation in the context of the mechanistic modelling of a pulp digester. The problem is cast as a box bounded nonlinear global optimization problem in order to minimize the mismatch between the model outputs with the experimental data observed at a real pulp and paper plant. MCSFilter and Simulated Annealing global optimization methods were used to solve the optimization problem. While the former took longer to converge to the global minimum, the latter terminated faster at a significantly higher value of the objective function and, thus, failed to find the global solution.

Nonparametric Subgroup Identification by PRIM and CART: A Simulation and Application Study

PubMed Central

2017-01-01

Two nonparametric methods for the identification of subgroups with outstanding outcome values are described and compared to each other in a simulation study and an application to clinical data. The Patient Rule Induction Method (PRIM) searches for box-shaped areas in the given data which exceed a minimal size and average outcome. This is achieved via a combination of iterative peeling and pasting steps, where small fractions of the data are removed or added to the current box. As an alternative, Classification and Regression Trees (CART) prediction models perform sequential binary splits of the data to produce subsets which can be interpreted as subgroups of heterogeneous outcome. PRIM and CART were compared in a simulation study to investigate their strengths and weaknesses under various data settings, taking different performance measures into account. PRIM was shown to be superior in rather complex settings such as those with few observations, a smaller signal-to-noise ratio, and more than one subgroup. CART showed the best performance in simpler situations. A practical application of the two methods was illustrated using a clinical data set. For this application, both methods produced similar results but the higher amount of user involvement of PRIM became apparent. PRIM can be flexibly tuned by the user, whereas CART, although simpler to implement, is rather static. PMID:28611849

Nonparametric Subgroup Identification by PRIM and CART: A Simulation and Application Study.

PubMed

Ott, Armin; Hapfelmeier, Alexander

2017-01-01

Two nonparametric methods for the identification of subgroups with outstanding outcome values are described and compared to each other in a simulation study and an application to clinical data. The Patient Rule Induction Method (PRIM) searches for box-shaped areas in the given data which exceed a minimal size and average outcome. This is achieved via a combination of iterative peeling and pasting steps, where small fractions of the data are removed or added to the current box. As an alternative, Classification and Regression Trees (CART) prediction models perform sequential binary splits of the data to produce subsets which can be interpreted as subgroups of heterogeneous outcome. PRIM and CART were compared in a simulation study to investigate their strengths and weaknesses under various data settings, taking different performance measures into account. PRIM was shown to be superior in rather complex settings such as those with few observations, a smaller signal-to-noise ratio, and more than one subgroup. CART showed the best performance in simpler situations. A practical application of the two methods was illustrated using a clinical data set. For this application, both methods produced similar results but the higher amount of user involvement of PRIM became apparent. PRIM can be flexibly tuned by the user, whereas CART, although simpler to implement, is rather static.

The Fundamentals of Laparoscopic Surgery and LapVR evaluation metrics may not correlate with operative performance in a novice cohort

PubMed Central

Steigerwald, Sarah N.; Park, Jason; Hardy, Krista M.; Gillman, Lawrence; Vergis, Ashley S.

2015-01-01

Background Considerable resources have been invested in both low- and high-fidelity simulators in surgical training. The purpose of this study was to investigate if the Fundamentals of Laparoscopic Surgery (FLS, low-fidelity box trainer) and LapVR (high-fidelity virtual reality) training systems correlate with operative performance on the Global Operative Assessment of Laparoscopic Skills (GOALS) global rating scale using a porcine cholecystectomy model in a novice surgical group with minimal laparoscopic experience. Methods Fourteen postgraduate year 1 surgical residents with minimal laparoscopic experience performed tasks from the FLS program and the LapVR simulator as well as a live porcine laparoscopic cholecystectomy. Performance was evaluated using standardized FLS metrics, automatic computer evaluations, and a validated global rating scale. Results Overall, FLS score did not show an association with GOALS global rating scale score on the porcine cholecystectomy. None of the five LapVR task scores were significantly associated with GOALS score on the porcine cholecystectomy. Conclusions Neither the low-fidelity box trainer or the high-fidelity virtual simulator demonstrated significant correlation with GOALS operative scores. These findings offer caution against the use of these modalities for brief assessments of novice surgical trainees, especially for predictive or selection purposes. PMID:26641071

Force-Sensing Enhanced Simulation Environment (ForSense) for laparoscopic surgery training and assessment.

PubMed

Cundy, Thomas P; Thangaraj, Evelyn; Rafii-Tari, Hedyeh; Payne, Christopher J; Azzie, Georges; Sodergren, Mikael H; Yang, Guang-Zhong; Darzi, Ara

2015-04-01

Excessive or inappropriate tissue interaction force during laparoscopic surgery is a recognized contributor to surgical error, especially for robotic surgery. Measurement of force at the tool-tissue interface is, therefore, a clinically relevant skill assessment variable that may improve effectiveness of surgical simulation. Popular box trainer simulators lack the necessary technology to measure force. The aim of this study was to develop a force sensing unit that may be integrated easily with existing box trainer simulators and to (1) validate multiple force variables as objective measurements of laparoscopic skill, and (2) determine concurrent validity of a revised scoring metric. A base plate unit sensitized to a force transducer was retrofitted to a box trainer. Participants of 3 different levels of operative experience performed 5 repetitions of a peg transfer and suture task. Multiple outcome variables of force were assessed as well as a revised scoring metric that incorporated a penalty for force error. Mean, maximum, and overall magnitudes of force were significantly different among the 3 levels of experience, as well as force error. Experts were found to exert the least force and fastest task completion times, and vice versa for novices. Overall magnitude of force was the variable most correlated with experience level and task completion time. The revised scoring metric had similar predictive strength for experience level compared with the standard scoring metric. Current box trainer simulators can be adapted for enhanced objective measurements of skill involving force sensing. These outcomes are significantly influenced by level of expertise and are relevant to operative safety in laparoscopic surgery. Conventional proficiency standards that focus predominantly on task completion time may be integrated with force-based outcomes to be more accurately reflective of skill quality. Copyright © 2015 Elsevier Inc. All rights reserved.

Jump events in a 3D Edwards-Anderson spin glass

NASA Astrophysics Data System (ADS)

Mártin, Daniel A.; Iguain, José Luis

2017-11-01

The statistical properties of infrequent particle displacements, greater than a certain distance, are known as jump dynamics in the context of structural glass formers. We generalize the concept of a jump to the case of a spin glass, by dividing the system into small boxes, and considering the infrequent cooperative spin flips in each box. Jumps defined this way share similarities with jumps in structural glasses. We perform numerical simulations for the 3D Edwards-Anderson model, and study how the properties of these jumps depend on the waiting time after a quench. Similar to the results for structural glasses, we find that while jump frequency depends strongly on time, the jump duration and jump length are roughly stationary. At odds with some results reported on studies of structural glass formers, at long enough times, the rest time between jumps varies as the inverse of jump frequency. We give a possible explanation for this discrepancy. We also find that our results are qualitatively reproduced by a fully-connected trap model.

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

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

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

Alteration of Box-Jenkins methodology by implementing genetic algorithm method

NASA Astrophysics Data System (ADS)

Ismail, Zuhaimy; Maarof, Mohd Zulariffin Md; Fadzli, Mohammad

2015-02-01

A time series is a set of values sequentially observed through time. The Box-Jenkins methodology is a systematic method of identifying, fitting, checking and using integrated autoregressive moving average time series model for forecasting. Box-Jenkins method is an appropriate for a medium to a long length (at least 50) time series data observation. When modeling a medium to a long length (at least 50), the difficulty arose in choosing the accurate order of model identification level and to discover the right parameter estimation. This presents the development of Genetic Algorithm heuristic method in solving the identification and estimation models problems in Box-Jenkins. Data on International Tourist arrivals to Malaysia were used to illustrate the effectiveness of this proposed method. The forecast results that generated from this proposed model outperformed single traditional Box-Jenkins model.

A novel augmented reality simulator for skills assessment in minimal invasive surgery.

PubMed

Lahanas, Vasileios; Loukas, Constantinos; Smailis, Nikolaos; Georgiou, Evangelos

2015-08-01

Over the past decade, simulation-based training has come to the foreground as an efficient method for training and assessment of surgical skills in minimal invasive surgery. Box-trainers and virtual reality (VR) simulators have been introduced in the teaching curricula and have substituted to some extent the traditional model of training based on animals or cadavers. Augmented reality (AR) is a new technology that allows blending of VR elements and real objects within a real-world scene. In this paper, we present a novel AR simulator for assessment of basic laparoscopic skills. The components of the proposed system include: a box-trainer, a camera and a set of laparoscopic tools equipped with custom-made sensors that allow interaction with VR training elements. Three AR tasks were developed, focusing on basic skills such as perception of depth of field, hand-eye coordination and bimanual operation. The construct validity of the system was evaluated via a comparison between two experience groups: novices with no experience in laparoscopic surgery and experienced surgeons. The observed metrics included task execution time, tool pathlength and two task-specific errors. The study also included a feedback questionnaire requiring participants to evaluate the face-validity of the system. Between-group comparison demonstrated highly significant differences (<0.01) in all performance metrics and tasks denoting the simulator's construct validity. Qualitative analysis on the instruments' trajectories highlighted differences between novices and experts regarding smoothness and economy of motion. Subjects' ratings on the feedback questionnaire highlighted the face-validity of the training system. The results highlight the potential of the proposed simulator to discriminate groups with different expertise providing a proof of concept for the potential use of AR as a core technology for laparoscopic simulation training.

Unpredictable convection in a small box: Molecular-dynamics experiments

NASA Astrophysics Data System (ADS)

Rapaport, D. C.

1992-08-01

The Rayleigh-Bénard problem has been studied using discrete-particle simulation of a two-dimensional fluid in a square box. The presence of temporal periodicity in the convective roll structure was observed, but, more significantly, different simulation runs under identical conditions but with initial states that differed in ways that are seemingly irrelevant at the macroscopic level exhibited very different forms of pattern evolution. The final state always consisted of a horizontally adjacent pair of rolls, but not all initial states evolved to produce well-established periodic behavior, despite the fact that very long runs were undertaken. Results for both hard- and soft-disk fluids are described; the simulations included systems with over 105 particles.

Performance simulation of BaBar DIRC bar boxes in TORCH

NASA Astrophysics Data System (ADS)

Föhl, K.; Brook, N.; Castillo García, L.; Cussans, D.; Forty, R.; Frei, C.; Gao, R.; Gys, T.; Harnew, N.; Piedigrossi, D.; Rademacker, J.; Ros García, A.; van Dijk, M.

2017-12-01

TORCH is a large-area precision time-of-flight detector based on the DIRC principle. The DIRC bar boxes of the BaBar experiment at SLAC could possibly be reused to form a part of the TORCH detector time-of-flight wall area, proposed to provide positive particle identification of low momentum kaons in the LHCb experiment at CERN. For a potential integration of BaBar bar boxes into TORCH, new imaging readout optics are required. From the several designs of readout optics that have been considered, two are used in this paper to study the effect of BaBar bar optical imperfections on the detector reconstruction performance. The kaon-pion separation powers obtained from analysing simulated photon hit patterns show the performance reduction for a BaBar bar of non-square geometry compared to a perfectly rectangular cross section.

Manually locating physical and virtual reality objects.

PubMed

Chen, Karen B; Kimmel, Ryan A; Bartholomew, Aaron; Ponto, Kevin; Gleicher, Michael L; Radwin, Robert G

2014-09-01

In this study, we compared how users locate physical and equivalent three-dimensional images of virtual objects in a cave automatic virtual environment (CAVE) using the hand to examine how human performance (accuracy, time, and approach) is affected by object size, location, and distance. Virtual reality (VR) offers the promise to flexibly simulate arbitrary environments for studying human performance. Previously, VR researchers primarily considered differences between virtual and physical distance estimation rather than reaching for close-up objects. Fourteen participants completed manual targeting tasks that involved reaching for corners on equivalent physical and virtual boxes of three different sizes. Predicted errors were calculated from a geometric model based on user interpupillary distance, eye location, distance from the eyes to the projector screen, and object. Users were 1.64 times less accurate (p < .001) and spent 1.49 times more time (p = .01) targeting virtual versus physical box corners using the hands. Predicted virtual targeting errors were on average 1.53 times (p < .05) greater than the observed errors for farther virtual targets but not significantly different for close-up virtual targets. Target size, location, and distance, in addition to binocular disparity, affected virtual object targeting inaccuracy. Observed virtual box inaccuracy was less than predicted for farther locations, suggesting possible influence of cues other than binocular vision. Human physical interaction with objects in VR for simulation, training, and prototyping involving reaching and manually handling virtual objects in a CAVE are more accurate than predicted when locating farther objects.

Adhesives for assembly of lightweight wood containers

Treesearch

R. S. Kurtenacker

1964-01-01

This report discusses the screening of various adhesive and mastic systems for possible use in assembling lightweight wood containers. Results showed that dynamic tests of simulated box corners correlated reasonably well with rough handling evaluations of eight selected systems when used to assemble lightweight wood boxes made from a Group I container wood....

Modeling Polymer Stabilized Nano-scale Zero Valent Iron Transport Experiments in Porous Media to Understand the Transport Behavior

NASA Astrophysics Data System (ADS)

Mondal, P.; Krol, M.; Sleep, B. E.

2015-12-01

A wide variety of groundwater contaminants can be treated with nano-scale zero valent iron (nZVI). However, delivery of nZVI in the subsurface to the treatment zones is challenging as the bare nZVI particles have a higher tendency to agglomerate. The subsurface mobility of nZVI can be enhanced by stabilizing nZVI with polymer, such as carboxymethyl cellulose (CMC). In this study, numerical simulations were conducted to evaluate CMC stabilized nZVI transport behavior in porous media. The numerical simulations were based on a set of laboratory-scale transport experiments that were conducted in a two-dimensional water-saturated glass-walled sandbox (length - 55 cm; height - 45 cm; width - 1.4 cm), uniformly packed with silica sand. In the transport experiments: CMC stabilized nZVI and a non-reactive dye tracer Lissamine Green B (LGB) were used; water specific discharge and CMC concentration were varied; movements of LGB, and CMC-nZVI in the sandbox were tracked using a camera, a light source and a dark box. The concentrations of LGB, CMC, and CMC-nZVI at the sandbox outlet were analyzed. A 2D multiphase flow and transport model was applied to simulate experimental results. The images from LGB dye transport experiments were used to determine the pore water velocities and media permeabilities in various layers in the sand box. These permeability values were used in the subsequent simulations of CMC-nZVI transport. The 2D compositional simulator, modified to include colloid filtration theory (CFT), treated CMC as a solute and nZVI as a colloid. The simulator included composition dependent viscosity to account for CMC injection and mixing, and attachment efficiency as a fitting parameter for nZVI transport modeling. In the experiments, LGB and CMC recoveries were greater than 95%; however, CMC residence time was significantly higher than the LGB residence time and the higher CMC concentration caused higher pressure drops in the sandbox. The nZVI recovery was lower than 40% in all experiments. The simulation results were found to be in good agreement with the experimental results, implying that the compositional simulator including CFT-modified transport equations could be utilized for the estimation of CMC-stabilized nZVI transport in porous media and design of field scale implementations of CMC-nZVI for remediation.

Simulation System for Training in Laparoscopic Surgery

NASA Technical Reports Server (NTRS)

Basdogan, Cagatay; Ho, Chih-Hao

2003-01-01

A computer-based simulation system creates a visual and haptic virtual environment for training a medical practitioner in laparoscopic surgery. Heretofore, it has been common practice to perform training in partial laparoscopic surgical procedures by use of a laparoscopic training box that encloses a pair of laparoscopic tools, objects to be manipulated by the tools, and an endoscopic video camera. However, the surgical procedures simulated by use of a training box are usually poor imitations of the actual ones. The present computer-based system improves training by presenting a more realistic simulated environment to the trainee. The system includes a computer monitor that displays a real-time image of the affected interior region of the patient, showing laparoscopic instruments interacting with organs and tissues, as would be viewed by use of an endoscopic video camera and displayed to a surgeon during a laparoscopic operation. The system also includes laparoscopic tools that the trainee manipulates while observing the image on the computer monitor (see figure). The instrumentation on the tools consists of (1) position and orientation sensors that provide input data for the simulation and (2) actuators that provide force feedback to simulate the contact forces between the tools and tissues. The simulation software includes components that model the geometries of surgical tools, components that model the geometries and physical behaviors of soft tissues, and components that detect collisions between them. Using the measured positions and orientations of the tools, the software detects whether they are in contact with tissues. In the event of contact, the deformations of the tissues and contact forces are computed by use of the geometric and physical models. The image on the computer screen shows tissues deformed accordingly, while the actuators apply the corresponding forces to the distal ends of the tools. For the purpose of demonstration, the system has been set up to simulate the insertion of a flexible catheter in a bile duct. [As thus configured, the system can also be used to simulate other endoscopic procedures (e.g., bronchoscopy and colonoscopy) that include the insertion of flexible tubes into flexible ducts.] A hybrid approach has been followed in developing the software for real-time simulation of the visual and haptic interactions (1) between forceps and the catheter, (2) between the forceps and the duct, and (3) between the catheter and the duct. The deformations of the duct are simulated by finite-element and modalanalysis procedures, using only the most significant vibration modes of the duct for computing deformations and interaction forces. The catheter is modeled as a set of virtual particles uniformly distributed along the center line of the catheter and connected to each other via linear and torsional springs and damping elements. The interactions between the forceps and the duct as well as the catheter are simulated by use of a ray-based haptic-interaction- simulating technique in which the forceps are modeled as connected line segments.

A Randomized Controlled Trial Comparing Trainee-Directed Virtual Reality Simulation Training and Box Trainer on the Acquisition of Laparoscopic Suturing Skills.

PubMed

Ko, Jennifer K Y; Cheung, Vincent Y T; Pun, Ting Chung; Tung, Wai Kit

2018-03-01

To compare the proficiency of novices in acquiring laparoscopic suturing skills following training in a virtual reality simulator or box trainer compared to no training. This was a RCT in a university-affiliated teaching hospital recruiting participants who had no laparoscopic suturing experience to have suturing skill training in the virtual reality simulator, box trainer, or no training as control. Trainees were allowed to terminate training when they perceived competence in the procedure. Suturing skills were tested in the box trainer and scored using a modified Global Operative Assessment of Laparoscopic Skills questionnaire by their own self-evaluation and two experienced gynaecological laparoscopists. Of the 36 participants recruited, 27 (75%) had no laparoscopic experience. Participants with no laparoscopic experience took longer to complete training than those with experience (median 90 minutes [interquartile range (IQR) 80-115] vs. 55 min [IQR 40-65], respectively; P = 0.044). There were no differences in successful completion of the task (7/12 [58.3%], 10/12 [83.3%], 7/12 [58.3%]; P = 0.325), median suturing time in seconds (628 [IQR 460-835], 611 [IQR 434-691], 609 [IQR 540-837]; P = 0.702), mean subjective (mean ± SD 9.8 ± 1.8, 10.4 ± 2.8, 9.3 ± 2.4; P = 0.710), and objective (7.2 ± 1.8, 8.2 ± 2.1, 7.6 ± 1.7; P = 0.426) modified Global Operative Assessment of Laparoscopic Skills score in the simulator, pelvic trainer, and control groups, respectively. The intraclass correlation coefficient of the two reviewers was 0.422 (95% CI 0.159-0.717). Trainees were unable to accurately assess themselves as to skill level in laparoscopic suturing. A longer training time is required for novices to master laparoscopic suturing using a simulator or box trainer. Copyright © 2018 Society of Obstetricians and Gynaecologists of Canada. Published by Elsevier Inc. All rights reserved.

Size distributions of manure particles released under simulated rainfall.

PubMed

Pachepsky, Yakov A; Guber, Andrey K; Shelton, Daniel R; McCarty, Gregory W

2009-03-01

Manure and animal waste deposited on cropland and grazing lands serve as a source of microorganisms, some of which may be pathogenic. These microorganisms are released along with particles of dissolved manure during rainfall events. Relatively little if anything is known about the amounts and sizes of manure particles released during rainfall, that subsequently may serve as carriers, abode, and nutritional source for microorganisms. The objective of this work was to obtain and present the first experimental data on sizes of bovine manure particles released to runoff during simulated rainfall and leached through soil during subsequent infiltration. Experiments were conducted using 200 cm long boxes containing turfgrass soil sod; the boxes were designed so that rates of manure dissolution and subsequent infiltration and runoff could be monitored independently. Dairy manure was applied on the upper portion of boxes. Simulated rainfall (ca. 32.4 mm h(-1)) was applied for 90 min on boxes with stands of either live or dead grass. Electrical conductivity, turbidity, and particle size distributions obtained from laser diffractometry were determined in manure runoff and soil leachate samples. Turbidity of leachates and manure runoff samples decreased exponentially. Turbidity of manure runoff samples was on average 20% less than turbidity of soil leachate samples. Turbidity of leachate samples from boxes with dead grass was on average 30% less than from boxes with live grass. Particle size distributions in manure runoff and leachate suspensions remained remarkably stable after 15 min of runoff initiation, although the turbidity continued to decrease. Particles had the median diameter of 3.8 microm, and 90% of particles were between 0.6 and 17.8 microm. The particle size distributions were not affected by the grass status. Because manure particles are known to affect transport and retention of microbial pathogens in soil, more information needs to be collected about the concurrent release of pathogens and manure particles during rainfall events.

Opening Pandora's Box: The impact of open system modeling on interpretations of anoxia

NASA Astrophysics Data System (ADS)

Hotinski, Roberta M.; Kump, Lee R.; Najjar, Raymond G.

2000-06-01

The geologic record preserves evidence that vast regions of ancient oceans were once anoxic, with oxygen levels too low to sustain animal life. Because anoxic conditions have been postulated to foster deposition of petroleum source rocks and have been implicated as a kill mechanism in extinction events, the genesis of such anoxia has been an area of intense study. Most previous models of ocean oxygen cycling proposed, however, have either been qualitative or used closed-system approaches. We reexamine the question of anoxia in open-system box models in order to test the applicability of closed-system results over long timescales and find that open and closed-system modeling results may differ significantly on both short and long timescales. We also compare a scenario with basinwide diffuse upwelling (a three-box model) to a model with upwelling concentrated in the Southern Ocean (a four-box model). While a three-box modeling approach shows that only changes in high-latitude convective mixing rate and character of deepwater sources are likely to cause anoxia, four-box model experiments indicate that slowing of thermohaline circulation, a reduction in wind-driven upwelling, and changes in high-latitude export production may also cause dysoxia or anoxia in part of the deep ocean on long timescales. These results suggest that box models must capture the open-system and vertically stratified nature of the ocean to allow meaningful interpretations of long-lived episodes of anoxia.

Molecular dynamics simulations in hybrid particle-continuum schemes: Pitfalls and caveats

NASA Astrophysics Data System (ADS)

Stalter, S.; Yelash, L.; Emamy, N.; Statt, A.; Hanke, M.; Lukáčová-Medvid'ová, M.; Virnau, P.

2018-03-01

Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations typically pose a computational bottleneck, which we investigate in detail in this study. We find that it is preferable to simulate many small systems as opposed to a few large systems, and that a choice of a simple isokinetic thermostat is typically sufficient while thermostats such as Lowe-Andersen allow for simulations at elevated viscosity. We discuss suitable choices for time steps and finite-size effects which arise in the limit of very small simulation boxes. We also argue that if colloidal systems are considered as opposed to atomistic systems, the gap between microscopic and macroscopic simulations regarding time and length scales is significantly smaller. We propose a novel reduced-order technique for the coupling to the macroscopic solver, which allows us to approximate a non-linear stress-strain relation efficiently and thus further reduce computational effort of microscopic simulations.

Conventional box model training improves laparoscopic skills during salpingectomy on LapSim: a randomized trial.

PubMed

Akdemir, Ali; Ergenoğlu, Ahmet Mete; Yeniel, Ahmet Özgür; Sendağ, Fatih

2013-01-01

Box model trainers have been used for many years to facilitate the improvement of laparoscopic skills. However, there are limited data available on box trainers and their impact on skill acquisition, assessed by virtual reality systems. Twenty-two Postgraduate Year 1 gynecology residents with no laparoscopic experience were randomly divided into one group that received structured box model training and a control group. All residents performed a salpingectomy on LapSim before and after the training. Performances before and after the training were assessed using LapSim and were recorded using objective parameters, registered by a computer system (time, damage, and economy of motion scores). There were initially no differences between the two groups. The box trainer group showed significantly greater improvement in time (p=0.01) and economy of motion scores (p=0.001) compared with the control group post-training. The present study confirmed the positive effect of low cost box model training on laparoscopic skill acquisition as assessed using LapSim. Novice surgeons should obtain practice on box trainers and teaching centers should make efforts to establish training laboratories.

An Observationally Constrained Evaluation of the Oxidative Capacity in the Tropical Western Pacific Troposphere

NASA Technical Reports Server (NTRS)

Nicely, Julie M.; Anderson, Daniel C.; Canty, Timothy P.; Salawitch, Ross J.; Wolfe, Glenn M.; Apel, Eric C.; Arnold, Steve R.; Atlas, Elliot L.; Blake, Nicola J.; Bresch, James F.;

Optimization of process variables for decolorization of Disperse Yellow 211 by Bacillus subtilis using Box-Behnken design.

PubMed

Sharma, Praveen; Singh, Lakhvinder; Dilbaghi, Neeraj

2009-05-30

Decolorization of textile azo dye Disperse Yellow 211 (DY 211) was carried out from simulated aqueous solution by bacterial strain Bacillus subtilis. Response surface methodology (RSM), involving Box-Behnken design matrix in three most important operating variables; temperature, pH and initial dye concentration was successfully employed for the study and optimization of decolorization process. The total 17 experiments were conducted in the study towards the construction of a quadratic model. According to analysis of variance (ANOVA) results, the proposed model can be used to navigate the design space. Under optimized conditions the bacterial strain was able to decolorize DY 211 up to 80%. Model indicated that initial dye concentration of 100 mgl(-1), pH 7 and a temperature of 32.5 degrees C were found optimum for maximum % decolorization. Very high regression coefficient between the variables and the response (R(2)=0.9930) indicated excellent evaluation of experimental data by polynomial regression model. The combination of the three variables predicted through RSM was confirmed through confirmatory experiments, hence the bacterial strain holds a great potential for the treatment of colored textile effluents.

Simulation of plume dynamics by the Lattice Boltzmann Method

NASA Astrophysics Data System (ADS)

Mora, Peter; Yuen, David A.

2017-09-01

The Lattice Boltzmann Method (LBM) is a semi-microscopic method to simulate fluid mechanics by modelling distributions of particles moving and colliding on a lattice. We present 2-D simulations using the LBM of a fluid in a rectangular box being heated from below, and cooled from above, with a Rayleigh of Ra = 108, similar to current estimates of the Earth's mantle, and a Prandtl number of 5000. At this Prandtl number, the flow is found to be in the non-inertial regime where the inertial terms denoted I ≪ 1. Hence, the simulations presented lie within the regime of relevance for geodynamical problems. We obtain narrow upwelling plumes with mushroom heads and chutes of downwelling fluid as expected of a flow in the non-inertial regime. The method developed demonstrates that the LBM has great potential for simulating thermal convection and plume dynamics relevant to geodynamics, albeit with some limitations.

Cosmic reionization on computers. I. Design and calibration of simulations

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

Gnedin, Nickolay Y., E-mail: gnedin@fnal.gov

Cosmic Reionization On Computers is a long-term program of numerical simulations of cosmic reionization. Its goal is to model fully self-consistently (albeit not necessarily from the first principles) all relevant physics, from radiative transfer to gas dynamics and star formation, in simulation volumes of up to 100 comoving Mpc, and with spatial resolution approaching 100 pc in physical units. In this method paper, we describe our numerical method, the design of simulations, and the calibration of numerical parameters. Using several sets (ensembles) of simulations in 20 h {sup –1} Mpc and 40 h {sup –1} Mpc boxes with spatial resolutionmore » reaching 125 pc at z = 6, we are able to match the observed galaxy UV luminosity functions at all redshifts between 6 and 10, as well as obtain reasonable agreement with the observational measurements of the Gunn-Peterson optical depth at z < 6.« less

A simulated training model for laparoscopic pyloromyotomy: Is 3D printing the way of the future?

PubMed

Williams, Andrew; McWilliam, Morgan; Ahlin, James; Davidson, Jacob; Quantz, Mackenzie A; Bütter, Andreana

2018-05-01

Hypertrophic pyloric stenosis (HPS) is a common neonatal condition treated with open or laparoscopic pyloromyotomy. 3D-printed organs offer realistic simulations to practice surgical techniques. The purpose of this study was to validate a 3D HPS stomach model and assess model reliability and surgical realism. Medical students, general surgery residents, and adult and pediatric general surgeons were recruited from a single center. Participants were videotaped three times performing a laparoscopic pyloromyotomy using box trainers and 3D-printed stomachs. Attempts were graded independently by three reviewers using GOALS and Task Specific Assessments (TSA). Participants were surveyed using the Index of Agreement of Assertions on Model Accuracy (IAAMA). Participants reported their experience levels as novice (22%), inexperienced (26%), intermediate (19%), and experienced (33%). Interrater reliability was similar for overall average GOALS and TSA scores. There was a significant improvement in GOALS (p<0.0001) and TSA scores (p=0.03) between attempts and overall. Participants felt the model accurately simulated a laparoscopic pyloromyotomy (82%) and would be a useful tool for beginners (100%). A 3D-printed stomach model for simulated laparoscopic pyloromyotomy is a useful training tool for learners to improve laparoscopic skills. The GOALS and TSA provide reliable technical skills assessments. II. Copyright © 2018 Elsevier Inc. All rights reserved.

Sensitivity Analysis of the Sheet Metal Stamping Processes Based on Inverse Finite Element Modeling and Monte Carlo Simulation

NASA Astrophysics Data System (ADS)

Yu, Maolin; Du, R.

2005-08-01

Sheet metal stamping is one of the most commonly used manufacturing processes, and hence, much research has been carried for economic gain. Searching through the literatures, however, it is found that there are still a lots of problems unsolved. For example, it is well known that for a same press, same workpiece material, and same set of die, the product quality may vary owing to a number of factors, such as the inhomogeneous of the workpice material, the loading error, the lubrication, and etc. Presently, few seem able to predict the quality variation, not to mention what contribute to the quality variation. As a result, trial-and-error is still needed in the shop floor, causing additional cost and time delay. This paper introduces a new approach to predict the product quality variation and identify the sensitive design / process parameters. The new approach is based on a combination of inverse Finite Element Modeling (FEM) and Monte Carlo Simulation (more specifically, the Latin Hypercube Sampling (LHS) approach). With an acceptable accuracy, the inverse FEM (also called one-step FEM) requires much less computation load than that of the usual incremental FEM and hence, can be used to predict the quality variations under various conditions. LHS is a statistical method, through which the sensitivity analysis can be carried out. The result of the sensitivity analysis has clear physical meaning and can be used to optimize the die design and / or the process design. Two simulation examples are presented including drawing a rectangular box and drawing a two-step rectangular box.

Performance Aspects and Physiological Responses in Male Amateur Boxing Competitions: A Brief Review.

PubMed

Slimani, Maamer; Chaabène, Helmi; Davis, Philip; Franchini, Emerson; Cheour, Foued; Chamari, Karim

2017-04-01

Slimani, M, Chaabène, H, Davis, P, Franchini, E, Cheour, F, and Chamari, K. Performance aspects and physiological responses in male amateur boxing competitions: a brief review. J Strength Cond Res 31(4): 1132-1141, 2017-Boxing is one of the most popular striking combat sports in the world. The aim of this review was to present data concerning performance analysis (time-motion and technical-tactical analysis) and physiological responses (i.e., blood lactate concentration [BLC], heart rate, and oxygen consumption) during novice and elite male simulated and official amateur boxing competitions in any age category. The present review shows that boxing competition is a high-intensity intermittent striking combat sport. Typically, the activity-to-rest ratio was higher in elite (18:1) than in novice (9:1) boxers and significant differences were observed between rounds (first round = 16:1, second round = 8:1, and third round = 6:1) in novice boxers. Thus, total stop-time and total stop-frequency increased over subsequent rounds in novice boxers. The technical-tactical aspects in elite and novice boxing bouts were different between rounds and dependent on the match outcome (i.e., winners vs. losers). Particularly, the current review highlights that triple-punch combinations, total combinations, block- and counter-punch combinations, total punches to the head, technical performance effectiveness, and defensive- and offensive-skills effectiveness may have contributed to win in novice and elite boxing competitions. Higher frequencies of technical movements were also observed in elite compared with novice boxers. From a physiological point of view, BLC increased significantly from postround 1 compared with postround 3 in novice boxing match. BLC was also higher in official than in simulated elite boxing matches in senior compared with junior boxers and in medium heavy-weight category compared with light- and medium-weight categories in junior boxing competition. A higher percentage of maximal heart rate (%HRmax) and maximal oxygen uptake (V[Combining Dot Above]O2max) were reported in round 3 compared with rounds 2 and 1 in elite boxing competition. In conclusion, these data are useful for both technical-tactical and physical conditioning sessions. Coaches and fitness trainers are encouraged to adjust their training according to these particular characteristics, specifically in terms of age, participants' level, weight categories, and combat contest type.

Box-Cox transformation for QTL mapping.

PubMed

Yang, Runqing; Yi, Nengjun; Xu, Shizhong

2006-01-01

The maximum likelihood method of QTL mapping assumes that the phenotypic values of a quantitative trait follow a normal distribution. If the assumption is violated, some forms of transformation should be taken to make the assumption approximately true. The Box-Cox transformation is a general transformation method which can be applied to many different types of data. The flexibility of the Box-Cox transformation is due to a variable, called transformation factor, appearing in the Box-Cox formula. We developed a maximum likelihood method that treats the transformation factor as an unknown parameter, which is estimated from the data simultaneously along with the QTL parameters. The method makes an objective choice of data transformation and thus can be applied to QTL analysis for many different types of data. Simulation studies show that (1) Box-Cox transformation can substantially increase the power of QTL detection; (2) Box-Cox transformation can replace some specialized transformation methods that are commonly used in QTL mapping; and (3) applying the Box-Cox transformation to data already normally distributed does not harm the result.

The Use of Time Series Analysis and t Tests with Serially Correlated Data Tests.

ERIC Educational Resources Information Center

Nicolich, Mark J.; Weinstein, Carol S.

1981-01-01

Results of three methods of analysis applied to simulated autocorrelated data sets with an intervention point (varying in autocorrelation degree, variance of error term, and magnitude of intervention effect) are compared and presented. The three methods are: t tests; maximum likelihood Box-Jenkins (ARIMA); and Bayesian Box Jenkins. (Author/AEF)

Black-boxing and cause-effect power

PubMed Central

Albantakis, Larissa; Tononi, Giulio

2018-01-01

Reductionism assumes that causation in the physical world occurs at the micro level, excluding the emergence of macro-level causation. We challenge this reductionist assumption by employing a principled, well-defined measure of intrinsic cause-effect power–integrated information (Φ), and showing that, according to this measure, it is possible for a macro level to “beat” the micro level. Simple systems were evaluated for Φ across different spatial and temporal scales by systematically considering all possible black boxes. These are macro elements that consist of one or more micro elements over one or more micro updates. Cause-effect power was evaluated based on the inputs and outputs of the black boxes, ignoring the internal micro elements that support their input-output function. We show how black-box elements can have more common inputs and outputs than the corresponding micro elements, revealing the emergence of high-order mechanisms and joint constraints that are not apparent at the micro level. As a consequence, a macro, black-box system can have higher Φ than its micro constituents by having more mechanisms (higher composition) that are more interconnected (higher integration). We also show that, for a given micro system, one can identify local maxima of Φ across several spatiotemporal scales. The framework is demonstrated on a simple biological system, the Boolean network model of the fission-yeast cell-cycle, for which we identify stable local maxima during the course of its simulated biological function. These local maxima correspond to macro levels of organization at which emergent cause-effect properties of physical systems come into focus, and provide a natural vantage point for scientific inquiries. PMID:29684020

Screening for potentially hazardous PRTR chemicals in the Lake Biwa-Yodo River basin of Japan using a one-box multimedia model.

PubMed

Ariyadasa, B H A K T; Kondo, Akira; Inoue, Yoshio

2015-02-01

A system is needed to predict the behavior, fate, and occurrence of environmental pollutants for effective environmental monitoring. Available monitoring data and computational modeling were used to develop a one-box multimedia model based on the mass balance of the emitted chemicals. Eight physiochemical phenomena in the atmosphere, soil, water, and sediment were considered in this model. This study was carried out in the Lake Biwa-Yodo River basin which provides multiple land uses and also the natural water resource for nearly 13 million of population in the region. Annual emissions for 214 nonmetallic compounds were calculated using the chemical emission data on Japanese pollutant release and transfer registry and used for executing the model simulations for 1997, 2002, and 2008 as input data. The calculated chemical concentrations by the model for all the environmental media were analyzed to determine trends in concentration over this study span. The majority of the chemicals decreased in concentration over time. Among the 214 nonmetallic chemical pollutants, 36 chemicals did not decrease in concentration and were in the top 10 % for concentration on average. Of these 36 pollutants, 7 occur in all 4 environmental media and pose a potential health risk at humans in the Lake Biwa-Yodo River basin.

SimpleBox 4.0: Improving the model while keeping it simple….

PubMed

Hollander, Anne; Schoorl, Marian; van de Meent, Dik

2016-04-01

Chemical behavior in the environment is often modeled with multimedia fate models. SimpleBox is one often-used multimedia fate model, firstly developed in 1986. Since then, two updated versions were published. Based on recent scientific developments and experience with SimpleBox 3.0, a new version of SimpleBox was developed and is made public here: SimpleBox 4.0. In this new model, eight major changes were implemented: removal of the local scale and vegetation compartments, addition of lake compartments and deep ocean compartments (including the thermohaline circulation), implementation of intermittent rain instead of drizzle and of depth dependent soil concentrations, adjustment of the partitioning behavior for organic acids and bases as well as of the value for enthalpy of vaporization. In this paper, the effects of the model changes in SimpleBox 4.0 on the predicted steady-state concentrations of chemical substances were explored for different substance groups (neutral organic substances, acids, bases, metals) in a standard emission scenario. In general, the largest differences between the predicted concentrations in the new and the old model are caused by the implementation of layered ocean compartments. Undesirable high model complexity caused by vegetation compartments and a local scale were removed to enlarge the simplicity and user friendliness of the model. Copyright © 2016 Elsevier Ltd. All rights reserved.

Comparison of postbuckling model and finite element model with compression strength of corrugated boxes

Treesearch

Thomas J. Urbanik; Edmond P. Saliklis

2002-01-01

Conventional compression strength formulas for corrugated fiberboard boxes are limited to geometry and material that produce an elastic postbuckling failure. Inelastic postbuckling can occur in squatty boxes and trays, but a mechanistic rationale for unifying observed strength data is lacking. This study employs a finite element model, instead of actual experiments, to...

Magnetorotational Dynamo Action in the Shearing Box

NASA Astrophysics Data System (ADS)

Walker, Justin; Boldyrev, Stanislav

2017-10-01

Magnetic dynamo action caused by the magnetorotational instability is studied in the shearing-box approximation with no imposed net magnetic flux. Consistent with recent studies, the dynamo action is found to be sensitive to the aspect ratio of the box: it is much easier to obtain in tall boxes (stretched in the direction normal to the disk plane) than in long boxes (stretched in the radial direction). Our direct numerical simulations indicate that the dynamo is possible in both cases, given a large enough magnetic Reynolds number. To explain the relatively larger effort required to obtain the dynamo action in a long box, we propose that the turbulent eddies caused by the instability most efficiently fold and mix the magnetic field lines in the radial direction. As a result, in the long box the scale of the generated strong azimuthal (stream-wise directed) magnetic field is always comparable to the scale of the turbulent eddies. In contrast, in the tall box the azimuthal magnetic flux spreads in the vertical direction over a distance exceeding the scale of the turbulent eddies. As a result, different vertical sections of the tall box are permeated by large-scale nonzero azimuthal magnetic fluxes, facilitating the instability. NSF AGS-1261659, Vilas Associates Award, NSF-Teragrid Project TG-PHY110016.

Evolution of the Cosmic Web

NASA Astrophysics Data System (ADS)

Einasto, J.

2017-07-01

In the evolution of the cosmic web dark energy plays an important role. To understand the role of dark energy we investigate the evolution of superclusters in four cosmological models: standard model SCDM, conventional model LCDM, open model OCDM, and a hyper-dark-energy model HCDM. Numerical simulations of the evolution are performed in a box of size 1024 Mpc/h. Model superclusters are compared with superclusters found for Sloan Digital Sky Survey (SDSS). Superclusters are searched using density fields. LCDM superclusters have properties, very close to properties of observed SDSS superclusters. Standard model SCDM has about 2 times more superclusters than other models, but SCDM superclusters are smaller and have lower luminosities. Superclusters as principal structural elements of the cosmic web are present at all cosmological epochs.

Three-dimensional benchmark for variable-density flow and transport simulation: matching semi-analytic stability modes for steady unstable convection in an inclined porous box

USGS Publications Warehouse

Voss, Clifford I.; Simmons, Craig T.; Robinson, Neville I.

2010-01-01

This benchmark for three-dimensional (3D) numerical simulators of variable-density groundwater flow and solute or energy transport consists of matching simulation results with the semi-analytical solution for the transition from one steady-state convective mode to another in a porous box. Previous experimental and analytical studies of natural convective flow in an inclined porous layer have shown that there are a variety of convective modes possible depending on system parameters, geometry and inclination. In particular, there is a well-defined transition from the helicoidal mode consisting of downslope longitudinal rolls superimposed upon an upslope unicellular roll to a mode consisting of purely an upslope unicellular roll. Three-dimensional benchmarks for variable-density simulators are currently (2009) lacking and comparison of simulation results with this transition locus provides an unambiguous means to test the ability of such simulators to represent steady-state unstable 3D variable-density physics.

An Inexpensive Real-Time Interactive Three Dimensional Flight Simulation System.

DTIC Science & Technology

1987-06-01

irh ’.etp. the 4i, n. he Ii~ Pi~op 4’ WV o cl d m od 0 V d 0 i c IV 1 M A,.. wq li . .. . . . " VII. TARGET INTEGRATION A. GENERAL The primary ...kts 200 kts Direction 359.9 degrees 0 degrees From prelaunch 99 5* 0 0 4 5 @ G 2 3 00 ALT 01 Figure 9.6 IRIS Dial Box Fuctions 100 summary box for a...Description: The primary purpose of get tgt pos is to move the targets in the simulation. If the networking capability is in lise, the target positions for

MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing

PubMed Central

Diroma, Maria Angela; Santorsola, Mariangela; Guttà, Cristiano; Gasparre, Giuseppe; Picardi, Ernesto; Pesole, Graziano; Attimonelli, Marcella

2014-01-01

Motivation: The increasing availability of mitochondria-targeted and off-target sequencing data in whole-exome and whole-genome sequencing studies (WXS and WGS) has risen the demand of effective pipelines to accurately measure heteroplasmy and to easily recognize the most functionally important mitochondrial variants among a huge number of candidates. To this purpose, we developed MToolBox, a highly automated pipeline to reconstruct and analyze human mitochondrial DNA from high-throughput sequencing data. Results: MToolBox implements an effective computational strategy for mitochondrial genomes assembling and haplogroup assignment also including a prioritization analysis of detected variants. MToolBox provides a Variant Call Format file featuring, for the first time, allele-specific heteroplasmy and annotation files with prioritized variants. MToolBox was tested on simulated samples and applied on 1000 Genomes WXS datasets. Availability and implementation: MToolBox package is available at https://sourceforge.net/projects/mtoolbox/. Contact: marcella.attimonelli@uniba.it Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25028726

The influence of polarization on box air mass factors for UV/vis nadir satellite observations

NASA Astrophysics Data System (ADS)

Hilboll, Andreas; Richter, Andreas; Rozanov, Vladimir V.; Burrows, John P.

2015-04-01

Tropospheric abundances of pollutant trace gases like, e.g., NO2, are often derived by applying the differential optical absorption spectroscopy (DOAS) method to space-borne measurements of back-scattered and reflected solar radiation. The resulting quantity, the slant column density (SCD), subsequently has to be converted to more easily interpretable vertical column densities by means of the so-called box air mass factor (BAMF). The BAMF describes the ratio of SCD and VCD within one atmospheric layer and is calculated by a radiative transfer model. Current operational and scientific data products of satellite-derived trace gas VCDs do not include the effect of polarization in their radiative transfer models. However, the various scattering processes in the atmosphere do lead to a distinctive polarization pattern of the observed Earthshine spectra. This study investigates the influence of these polarization patterns on box air mass factors for satellite nadir DOAS measurements of NO2 in the UV/vis wavelength region. NO2 BAMFs have been simulated for a multitude of viewing geometries, surface albedos, and surface altitudes, using the radiative transfer model SCIATRAN. The results show a potentially large influence of polarization on the BAMF, which can reach 10% and more close to the surface. A simple correction for this effect seems not to be feasible, as it strongly depends on the specific measurement scenario and can lead to both high and low biases of the resulting NO2 VCD. We therefore conclude that all data products of NO2 VCDs derived from space-borne DOAS measurements should include polarization effects in their radiative transfer model calculations, or at least include the errors introduced by using linear models in their uncertainty estimates.

A Fast and Efficient Version of the TwO-Moment Aerosol Sectional (TOMAS) Global Aerosol Microphysics Model

NASA Technical Reports Server (NTRS)

Lee, Yunha; Adams, P. J.

2012-01-01

This study develops more computationally efficient versions of the TwO-Moment Aerosol Sectional (TOMAS) microphysics algorithms, collectively called Fast TOMAS. Several methods for speeding up the algorithm were attempted, but only reducing the number of size sections was adopted. Fast TOMAS models, coupled to the GISS GCM II-prime, require a new coagulation algorithm with less restrictive size resolution assumptions but only minor changes in other processes. Fast TOMAS models have been evaluated in a box model against analytical solutions of coagulation and condensation and in a 3-D model against the original TOMAS (TOMAS-30) model. Condensation and coagulation in the Fast TOMAS models agree well with the analytical solution but show slightly more bias than the TOMAS-30 box model. In the 3-D model, errors resulting from decreased size resolution in each process (i.e., emissions, cloud processing wet deposition, microphysics) are quantified in a series of model sensitivity simulations. Errors resulting from lower size resolution in condensation and coagulation, defined as the microphysics error, affect number and mass concentrations by only a few percent. The microphysics error in CN70CN100 (number concentrations of particles larger than 70100 nm diameter), proxies for cloud condensation nuclei, range from 5 to 5 in most regions. The largest errors are associated with decreasing the size resolution in the cloud processing wet deposition calculations, defined as cloud-processing error, and range from 20 to 15 in most regions for CN70CN100 concentrations. Overall, the Fast TOMAS models increase the computational speed by 2 to 3 times with only small numerical errors stemming from condensation and coagulation calculations when compared to TOMAS-30. The faster versions of the TOMAS model allow for the longer, multi-year simulations required to assess aerosol effects on cloud lifetime and precipitation.

Revisiting Antarctic Ozone Depletion

NASA Astrophysics Data System (ADS)

Grooß, Jens-Uwe; Tritscher, Ines; Müller, Rolf

2015-04-01

Antarctic ozone depletion is known for almost three decades and it has been well settled that it is caused by chlorine catalysed ozone depletion inside the polar vortex. However, there are still some details, which need to be clarified. In particular, there is a current debate on the relative importance of liquid aerosol and crystalline NAT and ice particles for chlorine activation. Particles have a threefold impact on polar chlorine chemistry, temporary removal of HNO3 from the gas-phase (uptake), permanent removal of HNO3 from the atmosphere (denitrification), and chlorine activation through heterogeneous reactions. We have performed simulations with the Chemical Lagrangian Model of the Stratosphere (CLaMS) employing a recently developed algorithm for saturation-dependent NAT nucleation for the Antarctic winters 2011 and 2012. The simulation results are compared with different satellite observations. With the help of these simulations, we investigate the role of the different processes responsible for chlorine activation and ozone depletion. Especially the sensitivity with respect to the particle type has been investigated. If temperatures are artificially forced to only allow cold binary liquid aerosol, the simulation still shows significant chlorine activation and ozone depletion. The results of the 3-D Chemical Transport Model CLaMS simulations differ from purely Lagrangian longtime trajectory box model simulations which indicates the importance of mixing processes.

CHEMICAL EVOLUTION LIBRARY FOR GALAXY FORMATION SIMULATION

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

Saitoh, Takayuki R., E-mail: saitoh@elsi.jp

We have developed a software library for chemical evolution simulations of galaxy formation under the simple stellar population (SSP) approximation. In this library, all of the necessary components concerning chemical evolution, such as initial mass functions, stellar lifetimes, yields from Type II and Type Ia supernovae, asymptotic giant branch stars, and neutron star mergers, are compiled from the literature. Various models are pre-implemented in this library so that users can choose their favorite combination of models. Subroutines of this library return released energy and masses of individual elements depending on a given event type. Since the redistribution manner of thesemore » quantities depends on the implementation of users’ simulation codes, this library leaves it up to the simulation code. As demonstrations, we carry out both one-zone, closed-box simulations and 3D simulations of a collapsing gas and dark matter system using this library. In these simulations, we can easily compare the impact of individual models on the chemical evolution of galaxies, just by changing the control flags and parameters of the library. Since this library only deals with the part of chemical evolution under the SSP approximation, any simulation codes that use the SSP approximation—namely, particle-base and mesh codes, as well as semianalytical models—can use it. This library is named “CELib” after the term “Chemical Evolution Library” and is made available to the community.« less

Speeding up N-body simulations of modified gravity: chameleon screening models

NASA Astrophysics Data System (ADS)

Bose, Sownak; Li, Baojiu; Barreira, Alexandre; He, Jian-hua; Hellwing, Wojciech A.; Koyama, Kazuya; Llinares, Claudio; Zhao, Gong-Bo

2017-02-01

We describe and demonstrate the potential of a new and very efficient method for simulating certain classes of modified gravity theories, such as the widely studied f(R) gravity models. High resolution simulations for such models are currently very slow due to the highly nonlinear partial differential equation that needs to be solved exactly to predict the modified gravitational force. This nonlinearity is partly inherent, but is also exacerbated by the specific numerical algorithm used, which employs a variable redefinition to prevent numerical instabilities. The standard Newton-Gauss-Seidel iterative method used to tackle this problem has a poor convergence rate. Our new method not only avoids this, but also allows the discretised equation to be written in a form that is analytically solvable. We show that this new method greatly improves the performance and efficiency of f(R) simulations. For example, a test simulation with 5123 particles in a box of size 512 Mpc/h is now 5 times faster than before, while a Millennium-resolution simulation for f(R) gravity is estimated to be more than 20 times faster than with the old method. Our new implementation will be particularly useful for running very high resolution, large-sized simulations which, to date, are only possible for the standard model, and also makes it feasible to run large numbers of lower resolution simulations for covariance analyses. We hope that the method will bring us to a new era for precision cosmological tests of gravity.

Atmospheric Turbulence Measurements in Support of Adaptive Optics Technology

DTIC Science & Technology

1989-03-01

Nieuwstadt and Brost (1986) performed a large eddy simulation model study of the decay of convective turbulence. We can use the TKE budget equation to...gradients and advections, M.S. thesis, Pennsylvania State University. Nieuwstadt, F.T.M., and R.A. Brost , 1986: The decay of convective turbulence. ,L...P.O Box 261 Puunene, Maui, HI 96784 AFWALIAAWW-3 ATTN: Mr. George Vogel Wright-Patterson AFB..OH 45433-6543 DL-4 Perkin-Elmer ATTN: Mr. NeufieLd GSO

Going Outside the TonB Box: Identification of Novel FepA-TonB Interactions In Vivo.

PubMed

Gresock, Michael G; Postle, Kathleen

2017-05-15

In Gram-negative bacteria, the cytoplasmic membrane protein TonB transmits energy derived from proton motive force to energize transport of important nutrients through TonB-dependent transporters in the outer membrane. Each transporter consists of a beta barrel domain and a lumen-occluding cork domain containing an essential sequence called the TonB box. To date, the only identified site of transporter-TonB interaction is between the TonB box and residues ∼158 to 162 of TonB. While the mechanism of ligand transport is a mystery, a current model based on site-directed spin labeling and molecular dynamics simulations is that, following ligand binding, the otherwise-sequestered TonB box extends into the periplasm for recognition by TonB, which mediates transport by pulling or twisting the cork. In this study, we tested that hypothesis with the outer membrane transporter FepA using in vivo photo-cross-linking to explore interactions of its TonB box and determine whether additional FepA-TonB interaction sites exist. We found numerous specific sites of FepA interaction with TonB on the periplasmic face of the FepA cork in addition to the TonB box. Two residues, T32 and A33, might constitute a ligand-sensitive conformational switch. The facts that some interactions were enhanced in the absence of ligand and that other interactions did not require the TonB box argued against the current model and suggested that the transport process is more complex than originally conceived, with subtleties that might provide a mechanism for discrimination among ligand-loaded transporters. These results constitute the first study on the dynamics of TonB-gated transporter interaction with TonB in vivo IMPORTANCE The TonB system of Gram-negative bacteria has a noncanonical active transport mechanism involving signal transduction and proteins integral to both membranes. To achieve transport, the cytoplasmic membrane protein TonB physically contacts outer membrane transporters such as FepA. Only one contact between TonB and outer membrane transporters has been identified to date: the TonB box at the transporter amino terminus. The TonB box has low information content, raising the question of how TonB can discriminate among multiple different TonB-dependent transporters present in the bacterium if it is the only means of contact. Here we identified several additional sites through which FepA contacts TonB in vivo , including two neighboring residues that may explain how FepA signals to TonB that ligand has bound. Copyright © 2017 American Society for Microbiology.

Mars Science Laboratory Rover System Thermal Test

NASA Technical Reports Server (NTRS)

Novak, Keith S.; Kempenaar, Joshua E.; Liu, Yuanming; Bhandari, Pradeep; Dudik, Brenda A.

2012-01-01

On November 26, 2011, NASA launched a large (900 kg) rover as part of the Mars Science Laboratory (MSL) mission to Mars. The MSL rover is scheduled to land on Mars on August 5, 2012. Prior to launch, the Rover was successfully operated in simulated mission extreme environments during a 16-day long Rover System Thermal Test (STT). This paper describes the MSL Rover STT, test planning, test execution, test results, thermal model correlation and flight predictions. The rover was tested in the JPL 25-Foot Diameter Space Simulator Facility at the Jet Propulsion Laboratory (JPL). The Rover operated in simulated Cruise (vacuum) and Mars Surface environments (8 Torr nitrogen gas) with mission extreme hot and cold boundary conditions. A Xenon lamp solar simulator was used to impose simulated solar loads on the rover during a bounding hot case and during a simulated Mars diurnal test case. All thermal hardware was exercised and performed nominally. The Rover Heat Rejection System, a liquid-phase fluid loop used to transport heat in and out of the electronics boxes inside the rover chassis, performed better than predicted. Steady state and transient data were collected to allow correlation of analytical thermal models. These thermal models were subsequently used to predict rover thermal performance for the MSL Gale Crater landing site. Models predict that critical hardware temperatures will be maintained within allowable flight limits over the entire 669 Sol surface mission.

Acquisition of fundamental laparoscopic skills: is a box really as good as a virtual reality trainer?

PubMed

Vitish-Sharma, P; Knowles, J; Patel, B

2011-01-01

Laparoscopic surgery requires working in a three-dimensional environment with a two-dimensional view. Skills such as depth perception, hand to eye co-ordination and bimanual manipulation are crucial to its efficacy. To compare the efficiency of training in laparoscopic skills on a VR simulator with a traditional box trainer. Twenty medical students were recruited. An initial training session on the relevant anatomy and steps of a laparoscopic cholecystectomy was given. Baseline skills were recorded using a pre-training laparoscopic cholecystectomy on the VR trainer. Parameters measured were: (1) total time taken (mins); (2) number of movements right and left instrument; (3) path length (cms) of right and left instrument was recorded. Ten students trained on a VR simulator, and ten on a box trainer, for three hours each. The box trainer group exercises were based on the Royal College of Surgeons core laparoscopic skills course, and the VR trainer exercises were based on the Simbionix LapMentor basic skills tasks. Following this both groups were reassessed by a laparoscopic cholecystectomy on the VR trainer. Both groups showed improvement in all measured parameters. A student T-test at 95% confidence interval showed no statistically significant difference between the two groups pre and post training. Both the VR and box trainer are effective in the acquisition of laparoscopic skills. Copyright © 2011 Surgical Associates Ltd. Published by Elsevier Ltd. All rights reserved.

Seasonal nutrient and plankton dynamics in a physical-biological model of Crater Lake

USGS Publications Warehouse

Fennel, K.; Collier, R.; Larson, G.; Crawford, G.; Boss, E.

2007-01-01

A coupled 1D physical-biological model of Crater Lake is presented. The model simulates the seasonal evolution of two functional phytoplankton groups, total chlorophyll, and zooplankton in good quantitative agreement with observations from a 10-year monitoring study. During the stratified period in summer and early fall the model displays a marked vertical structure: the phytoplankton biomass of the functional group 1, which represents diatoms and dinoflagellates, has its highest concentration in the upper 40 m; the phytoplankton biomass of group 2, which represents chlorophyta, chrysophyta, cryptomonads and cyanobacteria, has its highest concentrations between 50 and 80 m, and phytoplankton chlorophyll has its maximum at 120 m depth. A similar vertical structure is a reoccurring feature in the available data. In the model the key process allowing a vertical separation between biomass and chlorophyll is photoacclimation. Vertical light attenuation (i.e., water clarity) and the physiological ability of phytoplankton to increase their cellular chlorophyll-to-biomass ratio are ultimately determining the location of the chlorophyll maximum. The location of the particle maxima on the other hand is determined by the balance between growth and losses and occurs where growth and losses equal. The vertical particle flux simulated by our model agrees well with flux measurements from a sediment trap. This motivated us to revisit a previously published study by Dymond et al. (1996). Dymond et al. used a box model to estimate the vertical particle flux and found a discrepancy by a factor 2.5-10 between their model-derived flux and measured fluxes from a sediment trap. Their box model neglected the exchange flux of dissolved and suspended organic matter, which, as our model and available data suggests is significant for the vertical exchange of nitrogen. Adjustment of Dymond et al.'s assumptions to account for dissolved and suspended nitrogen yields a flux estimate that is consistent with sediment trap measurements and our model. ?? 2007 Springer Science+Business Media B.V.

Survival of foodborne pathogens on commercially packed table grapes under simulated refrigerated transit conditions.

PubMed

Carter, Michelle Qiu; Feng, Doris; Chapman, Mary H; Gabler, Franka

2018-06-01

We examined the survival of Listeria monocytogenes, Escherichia coli O157:H7, and Salmonella enterica Thompson inoculated on commercially packed table grapes under simulated refrigerated transit conditions (1.1 ± 0.5 °C; 90% RH). Grapes were placed in perforated polyethylene cluster bags, within a commercial expanded polystyrene box equipped with either a SO 2 -generating pad; a perforated polyethylene box liner; a SO 2 -generating pad and a box liner; or none of them. L. monocytogenes was most sensitive to SO 2 -generating pad. SO 2 -generating pad or SO 2 -generating pad with box liner inactivated this pathogen completely on day 12 following the inoculation. S. enterica Thompson displayed a similar cold sensitivity as L. monocytogenes, but was more resistant to SO 2 -generating pad than L. monocytogenes. While SO 2 -generating pad eliminated S. enterica Thompson on day 20, a combination of box liner with SO 2 -generating pad inactivated this pathogen completely on day 13. E. coli O157:H7 had the highest tolerance to transit temperature and to SO 2 -generating pad; SO 2 -generating pad inactivated this pathogen completely on Day 20. Our data suggest that use of SO 2 -generating pad combined with box liner is effective in reducing foodborne pathogens L. monocytogenes and S. enterica Thompson, while the use of SO 2 -generating pad alone was more effective on E. coli O157:H7. Published by Elsevier Ltd.

A generalized multivariate regression model for modelling ocean wave heights

NASA Astrophysics Data System (ADS)

Wang, X. L.; Feng, Y.; Swail, V. R.

2012-04-01

In this study, a generalized multivariate linear regression model is developed to represent the relationship between 6-hourly ocean significant wave heights (Hs) and the corresponding 6-hourly mean sea level pressure (MSLP) fields. The model is calibrated using the ERA-Interim reanalysis of Hs and MSLP fields for 1981-2000, and is validated using the ERA-Interim reanalysis for 2001-2010 and ERA40 reanalysis of Hs and MSLP for 1958-2001. The performance of the fitted model is evaluated in terms of Pierce skill score, frequency bias index, and correlation skill score. Being not normally distributed, wave heights are subjected to a data adaptive Box-Cox transformation before being used in the model fitting. Also, since 6-hourly data are being modelled, lag-1 autocorrelation must be and is accounted for. The models with and without Box-Cox transformation, and with and without accounting for autocorrelation, are inter-compared in terms of their prediction skills. The fitted MSLP-Hs relationship is then used to reconstruct historical wave height climate from the 6-hourly MSLP fields taken from the Twentieth Century Reanalysis (20CR, Compo et al. 2011), and to project possible future wave height climates using CMIP5 model simulations of MSLP fields. The reconstructed and projected wave heights, both seasonal means and maxima, are subject to a trend analysis that allows for non-linear (polynomial) trends.

Role of indirect readout mechanism in TATA box binding protein-DNA interaction.

PubMed

Mondal, Manas; Choudhury, Devapriya; Chakrabarti, Jaydeb; Bhattacharyya, Dhananjay

2015-03-01

Gene expression generally initiates from recognition of TATA-box binding protein (TBP) to the minor groove of DNA of TATA box sequence where the DNA structure is significantly different from B-DNA. We have carried out molecular dynamics simulation studies of TBP-DNA system to understand how the DNA structure alters for efficient binding. We observed rigid nature of the protein while the DNA of TATA box sequence has an inherent flexibility in terms of bending and minor groove widening. The bending analysis of the free DNA and the TBP bound DNA systems indicate presence of some similar structures. Principal coordinate ordination analysis also indicates some structural features of the protein bound and free DNA are similar. Thus we suggest that the DNA of TATA box sequence regularly oscillates between several alternate structures and the one suitable for TBP binding is induced further by the protein for proper complex formation.

Road crossing designs and their impact on fish assemblages of Great Plains streams

USGS Publications Warehouse

Bouska, Wesley W.; Paukert, Craig P.

2010-01-01

A mark-recapture field study was conducted to determine fish passage at 5 concrete box culverts and 5 low-water crossings (concrete slabs vented by culverts) as well as 10 control sites (below a natural riffle) in Flint Hills streams of northeastern Kansas. Additionally, we tested the upstream passage of four fish species native to Great Plains streams (Topeka shiner Notropis topeka, green sunfish Lepomis cyanellus, red shiner Cyprinella lutrensis, and southern redbelly dace Phoxinus erythrogaster) through three simulated crossing designs (box culverts, round corrugated culverts, and natural rock riffles) at water velocities of 0.1 to 1.1 m/s in an experimental stream. The field study indicated that cyprinids were twice as likely to move upstream of box culverts than low-water crossings and 1.4 times as likely to move upstream of control reaches than any crossing type. The best models indicated that the proportion of cyprinids that moved upstream increased with decreased culvert slope and length, perching, and increased culvert width. Our controlled experiment indicated that fish can move through velocities up to 1.1 m/s in a 1.86-m simulated stream and that the proportion of fish that moved upstream did not differ among crossing designs for southern redbelly dace, green sunfish, or Topeka shiner; however, natural rock riffles had lower proportional movements (mean = 0.19) than the box (0.38) or corrugated culvert designs (0.43) for red shiners. Water velocity did not affect the proportional upstream movement of any species except that of Topeka shiners, which increased with water velocity. Crossing design alone may not determine fish passage, and water velocities up to 1.1 m/s may not affect the passage of many Great Plains fishes. Barriers to fish movement may be the result of other factors (e.g., perching, slope, and crossing length). The use of properly designed and installed crossings has promise in conserving Great Plains stream fishes.

Approximate deconvolution model for the simulation of turbulent gas-solid flows: An a priori analysis

NASA Astrophysics Data System (ADS)

Schneiderbauer, Simon; Saeedipour, Mahdi

2018-02-01

Highly resolved two-fluid model (TFM) simulations of gas-solid flows in vertical periodic channels have been performed to study closures for the filtered drag force and the Reynolds-stress-like contribution stemming from the convective terms. An approximate deconvolution model (ADM) for the large-eddy simulation of turbulent gas-solid suspensions is detailed and subsequently used to reconstruct those unresolved contributions in an a priori manner. With such an approach, an approximation of the unfiltered solution is obtained by repeated filtering allowing the determination of the unclosed terms of the filtered equations directly. A priori filtering shows that predictions of the ADM model yield fairly good agreement with the fine grid TFM simulations for various filter sizes and different particle sizes. In particular, strong positive correlation (ρ > 0.98) is observed at intermediate filter sizes for all sub-grid terms. Additionally, our study reveals that the ADM results moderately depend on the choice of the filters, such as box and Gaussian filter, as well as the deconvolution order. The a priori test finally reveals that ADM is superior compared to isotropic functional closures proposed recently [S. Schneiderbauer, "A spatially-averaged two-fluid model for dense large-scale gas-solid flows," AIChE J. 63, 3544-3562 (2017)].

The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit.

PubMed

Cheng, Bingqing; Tribello, Gareth A; Ceriotti, Michele

2017-09-14

In this paper we discuss how the information contained in atomistic simulations of homogeneous nucleation should be used when fitting the parameters in macroscopic nucleation models. We show how the number of solid and liquid atoms in such simulations can be determined unambiguously by using a Gibbs dividing surface and how the free energy as a function of the number of solid atoms in the nucleus can thus be extracted. We then show that the parameters (the chemical potential, the interfacial free energy, and a Tolman correction) of a model based on classical nucleation theory can be fitted using the information contained in these free-energy profiles but that the parameters in such models are highly correlated. This correlation is unfortunate as it ensures that small errors in the computed free energy surface can give rise to large errors in the extrapolated properties of the fitted model. To resolve this problem we thus propose a method for fitting macroscopic nucleation models that uses simulations of planar interfaces and simulations of three-dimensional nuclei in tandem. We show that when the chemical potentials and the interface energy are pinned to their planar-interface values, more precise estimates for the Tolman length are obtained. Extrapolating the free energy profile obtained from small simulation boxes to larger nuclei is thus more reliable.

Turbulence Statistics in a Two-Dimensional Vortex Condensate.

PubMed

Frishman, Anna; Herbert, Corentin

2018-05-18

Disentangling the evolution of a coherent mean-flow and turbulent fluctuations, interacting through the nonlinearity of the Navier-Stokes equations, is a central issue in fluid mechanics. It affects a wide range of flows, such as planetary atmospheres, plasmas, or wall-bounded flows, and hampers turbulence models. We consider the special case of a two-dimensional flow in a periodic box, for which the mean flow, a pair of box-size vortices called "condensate," emerges from turbulence. As was recently shown, a perturbative closure describes correctly the condensate when turbulence is excited at small scales. In this context, we obtain explicit results for the statistics of turbulence, encoded in the Reynolds stress tensor. We demonstrate that the two components of the Reynolds stress, the momentum flux and the turbulent energy, are determined by different mechanisms. It was suggested previously that the momentum flux is fixed by a balance between forcing and mean-flow advection: using unprecedently long numerical simulations, we provide the first direct evidence supporting this prediction. By contrast, combining analytical computations with numerical simulations, we show that the turbulent energy is determined only by mean-flow advection and obtain for the first time a formula describing its profile in the vortex.

Turbulence Statistics in a Two-Dimensional Vortex Condensate

NASA Astrophysics Data System (ADS)

Frishman, Anna; Herbert, Corentin

2018-05-01

Disentangling the evolution of a coherent mean-flow and turbulent fluctuations, interacting through the nonlinearity of the Navier-Stokes equations, is a central issue in fluid mechanics. It affects a wide range of flows, such as planetary atmospheres, plasmas, or wall-bounded flows, and hampers turbulence models. We consider the special case of a two-dimensional flow in a periodic box, for which the mean flow, a pair of box-size vortices called "condensate," emerges from turbulence. As was recently shown, a perturbative closure describes correctly the condensate when turbulence is excited at small scales. In this context, we obtain explicit results for the statistics of turbulence, encoded in the Reynolds stress tensor. We demonstrate that the two components of the Reynolds stress, the momentum flux and the turbulent energy, are determined by different mechanisms. It was suggested previously that the momentum flux is fixed by a balance between forcing and mean-flow advection: using unprecedently long numerical simulations, we provide the first direct evidence supporting this prediction. By contrast, combining analytical computations with numerical simulations, we show that the turbulent energy is determined only by mean-flow advection and obtain for the first time a formula describing its profile in the vortex.

UEDGE Simulations for Power and Particle Flow Analysis of FRC Rocket

NASA Astrophysics Data System (ADS)

Zheng, Fred; Evans, Eugene S.; McGreivy, Nick; Kaptanoglu, Alan; Izacard, Olivier; Cohen, Samuel A.

2017-10-01

The field-reversed configuration (FRC) is under consideration for use in a direct fusion drive (DFD) rocket propulsion system for future space missions. To achieve a rocket configuration, the FRC is embedded within an asymmetric magnetic mirror, in which one end is closed and contains a gas box, and the other end is open and incorporates a magnetic nozzle. Neutral deuterium is injected into the gas box, and flows through the scrape-off layer (SOL) around the core plasma and out the magnetic nozzle, both cooling the core and serving as propellant. Previous studies have examined a range of operating conditions for the SOL of a DFD using UEDGE, a 2D fluid code; discrepancies on the order of 5% were found during the analysis of overall power balance. This work extends the analysis of the previously-studied SOL geometry by updating boundary conditions and conducting a detailed study of power and particle flows within the simulation with the goals of modeling electrical power generation instead of thrust and achieving higher specific impulse. This work was supported, in part, by DOE Contract Number DE-AC02-09CH11466 and Princeton Environmental Institute.

Simulation of the Predictive Control Algorithm for Container Crane Operation using Matlab Fuzzy Logic Tool Box

NASA Technical Reports Server (NTRS)

Richardson, Albert O.

1997-01-01

This research has investigated the use of fuzzy logic, via the Matlab Fuzzy Logic Tool Box, to design optimized controller systems. The engineering system for which the controller was designed and simulate was the container crane. The fuzzy logic algorithm that was investigated was the 'predictive control' algorithm. The plant dynamics of the container crane is representative of many important systems including robotic arm movements. The container crane that was investigated had a trolley motor and hoist motor. Total distance to be traveled by the trolley was 15 meters. The obstruction height was 5 meters. Crane height was 17.8 meters. Trolley mass was 7500 kilograms. Load mass was 6450 kilograms. Maximum trolley and rope velocities were 1.25 meters per sec. and 0.3 meters per sec., respectively. The fuzzy logic approach allowed the inclusion, in the controller model, of performance indices that are more effectively defined in linguistic terms. These include 'safety' and 'cargo swaying'. Two fuzzy inference systems were implemented using the Matlab simulation package, namely the Mamdani system (which relates fuzzy input variables to fuzzy output variables), and the Sugeno system (which relates fuzzy input variables to crisp output variable). It is found that the Sugeno FIS is better suited to including aspects of those plant dynamics whose mathematical relationships can be determined.

V-SUIT Model Validation Using PLSS 1.0 Test Results

NASA Technical Reports Server (NTRS)

Olthoff, Claas

2015-01-01

The dynamic portable life support system (PLSS) simulation software Virtual Space Suit (V-SUIT) has been under development at the Technische Universitat Munchen since 2011 as a spin-off from the Virtual Habitat (V-HAB) project. The MATLAB(trademark)-based V-SUIT simulates space suit portable life support systems and their interaction with a detailed and also dynamic human model, as well as the dynamic external environment of a space suit moving on a planetary surface. To demonstrate the feasibility of a large, system level simulation like V-SUIT, a model of NASA's PLSS 1.0 prototype was created. This prototype was run through an extensive series of tests in 2011. Since the test setup was heavily instrumented, it produced a wealth of data making it ideal for model validation. The implemented model includes all components of the PLSS in both the ventilation and thermal loops. The major components are modeled in greater detail, while smaller and ancillary components are low fidelity black box models. The major components include the Rapid Cycle Amine (RCA) CO2 removal system, the Primary and Secondary Oxygen Assembly (POS/SOA), the Pressure Garment System Volume Simulator (PGSVS), the Human Metabolic Simulator (HMS), the heat exchanger between the ventilation and thermal loops, the Space Suit Water Membrane Evaporator (SWME) and finally the Liquid Cooling Garment Simulator (LCGS). Using the created model, dynamic simulations were performed using same test points also used during PLSS 1.0 testing. The results of the simulation were then compared to the test data with special focus on absolute values during the steady state phases and dynamic behavior during the transition between test points. Quantified simulation results are presented that demonstrate which areas of the V-SUIT model are in need of further refinement and those that are sufficiently close to the test results. Finally, lessons learned from the modelling and validation process are given in combination with implications for the future development of other PLSS models in V-SUIT.

A Review of the Ginzburg-Syrovatskii's Galactic Cosmic-Ray Propagation Model and its Leaky-Box Limit

NASA Technical Reports Server (NTRS)

Barghouty, A. F.

2012-01-01

Phenomenological models of galactic cosmic-ray propagation are based on a diffusion equation known as the Ginzburg-Syrovatskii s equation, or variants (or limits) of this equation. Its one-dimensional limit in a homogeneous volume, known as the leaky-box limit or model, is sketched here. The justification, utility, limitations, and a typical numerical implementation of the leaky-box model are examined in some detail.

NCAR global model topography generation software for unstructured grids

NASA Astrophysics Data System (ADS)

Lauritzen, P. H.; Bacmeister, J. T.; Callaghan, P. F.; Taylor, M. A.

2015-06-01

It is the purpose of this paper to document the NCAR global model topography generation software for unstructured grids. Given a model grid, the software computes the fraction of the grid box covered by land, the gridbox mean elevation, and associated sub-grid scale variances commonly used for gravity wave and turbulent mountain stress parameterizations. The software supports regular latitude-longitude grids as well as unstructured grids; e.g. icosahedral, Voronoi, cubed-sphere and variable resolution grids. As an example application and in the spirit of documenting model development, exploratory simulations illustrating the impacts of topographic smoothing with the NCAR-DOE CESM (Community Earth System Model) CAM5.2-SE (Community Atmosphere Model version 5.2 - Spectral Elements dynamical core) are shown.

Projected Applications of a "Climate in a Box" Computing System at the NASA Short-Term Prediction Research and Transition (SPoRT) Center

NASA Technical Reports Server (NTRS)

Jedlovec, Gary J.; Molthan, Andrew L.; Zavodsky, Bradley; Case, Jonathan L.; LaFontaine, Frank J.

2010-01-01

The NASA Short-term Prediction Research and Transition (SPoRT) Center focuses on the transition of unique observations and research capabilities to the operational weather community, with a goal of improving short-term forecasts on a regional scale. Advances in research computing have lead to "Climate in a Box" systems, with hardware configurations capable of producing high resolution, near real-time weather forecasts, but with footprints, power, and cooling requirements that are comparable to desktop systems. The SPoRT Center has developed several capabilities for incorporating unique NASA research capabilities and observations with real-time weather forecasts. Planned utilization includes the development of a fully-cycled data assimilation system used to drive 36-48 hour forecasts produced by the NASA Unified version of the Weather Research and Forecasting (WRF) model (NU-WRF). The horsepower provided by the "Climate in a Box" system is expected to facilitate the assimilation of vertical profiles of temperature and moisture provided by the Atmospheric Infrared Sounder (AIRS) aboard the NASA Aqua satellite. In addition, the Moderate Resolution Imaging Spectroradiometer (MODIS) instruments aboard NASA s Aqua and Terra satellites provide high-resolution sea surface temperatures and vegetation characteristics. The development of MODIS normalized difference vegetation index (NVDI) composites for use within the NASA Land Information System (LIS) will assist in the characterization of vegetation, and subsequently the surface albedo and processes related to soil moisture. Through application of satellite simulators, NASA satellite instruments can be used to examine forecast model errors in cloud cover and other characteristics. Through the aforementioned application of the "Climate in a Box" system and NU-WRF capabilities, an end goal is the establishment of a real-time forecast system that fully integrates modeling and analysis capabilities developed within the NASA SPoRT Center, with benefits provided to the operational forecasting community.

Ontology-based coupled optimisation design method using state-space analysis for the spindle box system of large ultra-precision optical grinding machine

NASA Astrophysics Data System (ADS)

Wang, Qianren; Chen, Xing; Yin, Yuehong; Lu, Jian

2017-08-01

With the increasing complexity of mechatronic products, traditional empirical or step-by-step design methods are facing great challenges with various factors and different stages having become inevitably coupled during the design process. Management of massive information or big data, as well as the efficient operation of information flow, is deeply involved in the process of coupled design. Designers have to address increased sophisticated situations when coupled optimisation is also engaged. Aiming at overcoming these difficulties involved in conducting the design of the spindle box system of ultra-precision optical grinding machine, this paper proposed a coupled optimisation design method based on state-space analysis, with the design knowledge represented by ontologies and their semantic networks. An electromechanical coupled model integrating mechanical structure, control system and driving system of the motor is established, mainly concerning the stiffness matrix of hydrostatic bearings, ball screw nut and rolling guide sliders. The effectiveness and precision of the method are validated by the simulation results of the natural frequency and deformation of the spindle box when applying an impact force to the grinding wheel.

Importance of Resolving the Spectral Support of Beam-plasma Instabilities in Simulations

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

Shalaby, Mohamad; Broderick, Avery E.; Chang, Philip

2017-10-20

Many astrophysical plasmas are prone to beam-plasma instabilities. For relativistic and dilute beams, the spectral support of the beam-plasma instabilities is narrow, i.e., the linearly unstable modes that grow with rates comparable to the maximum growth rate occupy a narrow range of wavenumbers. This places stringent requirements on the box-sizes when simulating the evolution of the instabilities. We identify the implied lower limits on the box size imposed by the longitudinal beam plasma instability, i.e., typically the most stringent condition required to correctly capture the linear evolution of the instabilities in multidimensional simulations. We find that sizes many orders ofmore » magnitude larger than the resonant wavelength are typically required. Using one-dimensional particle-in-cell simulations, we show that the failure to sufficiently resolve the spectral support of the longitudinal instability yields slower growth and lower levels of saturation, potentially leading to erroneous physical conclusion.« less

Mechanical simulators for training for laparoscopic surgery in urology.

PubMed

Rassweiler, Jens; Klein, Jan; Teber, Dogu; Schulze, Michael; Frede, Thomas

2007-03-01

The introduction of laparoscopic surgery into urology has led to new training concepts differing significantly from previous concepts of training for open surgery. This paper focuses on the type and importance of mechanical simulators in laparoscopic training. On the basis of our own studies and experience with the development of various concepts of laparoscopic training, including different modules (i.e., Pelvi-trainer, animal models, clinical mentoring) since 1991, we reviewed the current literature concerning all types of simulators. We focused on training for laparoscopic ablative and reconstructive surgery using mechanical simulators. The principle of a mechanical simulator (i.e., a box with the possibility of trocar insertion) has not changed during the last decade. However, the types of Pelvi-trainers and the models used inside have been improved significantly. According to the task of the simulator, various sophisticated models have been developed, including standardized phantoms, animal organs, and even perfused segments of porcine organs. For laparoscopic suturing, various step-by-step training concepts have been presented. These can be used for determination of the ability of a physician with an interest in laparoscopic surgery, but also to classify the training status of a laparosopic surgeon. Training in laparoscopic surgery has become an important topic, not only in learning a procedure, but also in maintaining skills and preparing for the management of complications. For these purposes, mechanical simulators will definitely play an important role in the future.

Magnetorotational dynamo action in the shearing box

NASA Astrophysics Data System (ADS)

Walker, Justin; Boldyrev, Stanislav

2017-09-01

Magnetic dynamo action caused by the magnetorotational instability is studied in the shearing-box approximation with no imposed net magnetic flux. Consistent with recent studies, the dynamo action is found to be sensitive to the aspect ratio of the box: it is much easier to obtain in tall boxes (stretched in the direction normal to the disc plane) than in long boxes (stretched in the radial direction). Our direct numerical simulations indicate that the dynamo is possible in both cases, given a large enough magnetic Reynolds number. To explain the relatively larger effort required to obtain the dynamo action in a long box, we propose that the turbulent eddies caused by the instability most efficiently fold and mix the magnetic field lines in the radial direction. As a result, in the long box the scale of the generated strong azimuthal (stream-wise directed) magnetic field is always comparable to the scale of the turbulent eddies. In contrast, in the tall box the azimuthal magnetic flux spreads in the vertical direction over a distance exceeding the scale of the turbulent eddies. As a result, different vertical sections of the tall box are permeated by large-scale non-zero azimuthal magnetic fluxes, facilitating the instability. In agreement with this picture, the cases when the dynamo is efficient are characterized by a strong intermittency of the local azimuthal magnetic fluxes.

Determination of sample size for higher volatile data using new framework of Box-Jenkins model with GARCH: A case study on gold price

NASA Astrophysics Data System (ADS)

Roslindar Yaziz, Siti; Zakaria, Roslinazairimah; Hura Ahmad, Maizah

2017-09-01

The model of Box-Jenkins - GARCH has been shown to be a promising tool for forecasting higher volatile time series. In this study, the framework of determining the optimal sample size using Box-Jenkins model with GARCH is proposed for practical application in analysing and forecasting higher volatile data. The proposed framework is employed to daily world gold price series from year 1971 to 2013. The data is divided into 12 different sample sizes (from 30 to 10200). Each sample is tested using different combination of the hybrid Box-Jenkins - GARCH model. Our study shows that the optimal sample size to forecast gold price using the framework of the hybrid model is 1250 data of 5-year sample. Hence, the empirical results of model selection criteria and 1-step-ahead forecasting evaluations suggest that the latest 12.25% (5-year data) of 10200 data is sufficient enough to be employed in the model of Box-Jenkins - GARCH with similar forecasting performance as by using 41-year data.

Calibration of discrete element model parameters: soybeans

NASA Astrophysics Data System (ADS)

Ghodki, Bhupendra M.; Patel, Manish; Namdeo, Rohit; Carpenter, Gopal

2018-05-01

Discrete element method (DEM) simulations are broadly used to get an insight of flow characteristics of granular materials in complex particulate systems. DEM input parameters for a model are the critical prerequisite for an efficient simulation. Thus, the present investigation aims to determine DEM input parameters for Hertz-Mindlin model using soybeans as a granular material. To achieve this aim, widely acceptable calibration approach was used having standard box-type apparatus. Further, qualitative and quantitative findings such as particle profile, height of kernels retaining the acrylic wall, and angle of repose of experiments and numerical simulations were compared to get the parameters. The calibrated set of DEM input parameters includes the following (a) material properties: particle geometric mean diameter (6.24 mm); spherical shape; particle density (1220 kg m^{-3} ), and (b) interaction parameters such as particle-particle: coefficient of restitution (0.17); coefficient of static friction (0.26); coefficient of rolling friction (0.08), and particle-wall: coefficient of restitution (0.35); coefficient of static friction (0.30); coefficient of rolling friction (0.08). The results may adequately be used to simulate particle scale mechanics (grain commingling, flow/motion, forces, etc) of soybeans in post-harvest machinery and devices.

Effect of gasoline formulation on the formation of photosmog: a box model study.

PubMed

Geiger, Herald; Becker, Karl H; Wiesen, Peter

2003-04-01

Based on exhaust gas analyses from the combustion of five different types of gasoline in a passenger car operated on a chassis dynamometer, box model simulations of the irradiation of exhaust/NOx/air mixtures using an established chemical mechanism for a standardized photosmog scenario were performed. The fuel matrix used covered wide fractional ranges for paraffinic, olefinic, and aromatic hydrocarbons. Two fuels also contained methyl tertiary butyl ether (MTBE). The different O3 profiles calculated for each run were compared and interpreted. The O3 levels obtained were strongly influenced by the exhaust gas concentrations of aromatic and olefinic hydrocarbons. The higher exhaust content of these compounds caused higher O3 production in the smog system investigated. The conclusion of the present study is that the composition of gasoline cannot be taken directly for the estimation of the emissions' O3 creation potential from its combustion. Variation of the dilution in the different calculations showed evidence for an additional influence of transport effects. Accordingly, further detailed exhaust gas analyses followed by more complex modeling studies are necessary for a proper characterization of the relationship between fuel blend and gasoline combustion products.

Dissecting children's observational learning of complex actions through selective video displays.

PubMed

Flynn, Emma; Whiten, Andrew

2013-10-01

Children can learn how to use complex objects by watching others, yet the relative importance of different elements they may observe, such as the interactions of the individual parts of the apparatus, a model's movements, and desirable outcomes, remains unclear. In total, 140 3-year-olds and 140 5-year-olds participated in a study where they observed a video showing tools being used to extract a reward item from a complex puzzle box. Conditions varied according to the elements that could be seen in the video: (a) the whole display, including the model's hands, the tools, and the box; (b) the tools and the box but not the model's hands; (c) the model's hands and the tools but not the box; (d) only the end state with the box opened; and (e) no demonstration. Children's later attempts at the task were coded to establish whether they imitated the hierarchically organized sequence of the model's actions, the action details, and/or the outcome. Children's successful retrieval of the reward from the box and the replication of hierarchical sequence information were reduced in all but the whole display condition. Only once children had attempted the task and witnessed a second demonstration did the display focused on the tools and box prove to be better for hierarchical sequence information than the display focused on the tools and hands only. Copyright © 2013 Elsevier Inc. All rights reserved.

Large-eddy simulation of a turbulent mixing layer

NASA Technical Reports Server (NTRS)

Mansour, N. N.; Ferziger, J. H.; Reynolds, W. C.

1978-01-01

The three dimensional, time dependent (incompressible) vorticity equations were used to simulate numerically the decay of isotropic box turbulence and time developing mixing layers. The vorticity equations were spatially filtered to define the large scale turbulence field, and the subgrid scale turbulence was modeled. A general method was developed to show numerical conservation of momentum, vorticity, and energy. The terms that arise from filtering the equations were treated (for both periodic boundary conditions and no stress boundary conditions) in a fast and accurate way by using fast Fourier transforms. Use of vorticity as the principal variable is shown to produce results equivalent to those obtained by use of the primitive variable equations.

The thermochromism of the ET(30) betaine in a micro-heterogeneous medium: a spectral and dynamics simulation study.

PubMed

Aliaga, Carolina; Briones, Luis; Rezende, Marcos Caroli; Tirapegui, Cristián

2010-09-15

A spectral investigation of the thermochromic behavior of Reichardt's E(T)(30) betaine in aqueous solutions of block copolymers ("poloxamers") P407, P237 and P105 was carried out as a function of temperature and concentration. The betaine microenvironment at various stages of the micellization process in these systems was mimicked with the aid of molecular dynamics simulations of model systems. These consisted of the E(T)(30) probe in boxes of water molecules, in the presence of an isolated block copolymer of formula (PEO)(11)-(PPO)(16)-(PEO)(11), and of a micelle formed of 50 of these unimers. Copyright 2010 Elsevier Inc. All rights reserved.

Dose mapping using MCNP code and experiment for SVST-Co-60/B irradiator in Vietnam.

PubMed

Tran, Van Hung; Tran, Khac An

2010-06-01

By using MCNP code and ethanol-chlorobenzene (ECB) dosimeters the simulations and measurements of absorbed dose distribution in a tote-box of the Cobalt-60 irradiator, SVST-Co60/B at VINAGAMMA have been done. Based on the results Dose Uniformity Ratios (DUR), positions and values of minimum and maximum dose extremes in a tote-box, and efficiency of the irradiator for the different dummy densities have been gained. There is a good agreement between simulation and experimental results in comparison and they have valuable meanings for operation of the irradiator. Copyright 2010 Elsevier Ltd. All rights reserved.

GRAVOTURBULENT PLANETESIMAL FORMATION: THE POSITIVE EFFECT OF LONG-LIVED ZONAL FLOWS

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

Dittrich, K.; Klahr, H.; Johansen, A., E-mail: dittrich@mpia.de

2013-02-15

Recent numerical simulations have shown long-lived axisymmetric sub- and super-Keplerian flows in protoplanetary disks. These zonal flows are found in local as well as global simulations of disks unstable to the magnetorotational instability. This paper covers our study of the strength and lifetime of zonal flows and the resulting long-lived gas over- and underdensities as functions of the azimuthal and radial size of the local shearing box. We further investigate dust particle concentrations without feedback on the gas and without self-gravity. The strength and lifetime of zonal flows increase with the radial extent of the simulation box, but decrease withmore » the azimuthal box size. Our simulations support earlier results that zonal flows have a natural radial length scale of 5-7 gas pressure scale heights. This is the first study that combines three-dimensional MHD simulations of zonal flows and dust particles feeling the gas pressure. The pressure bumps trap particles with St = 1 very efficiently. We show that St = 0.1 particles (of some centimeters in size if at 5 AU in a minimum mass solar nebula) reach a hundred-fold higher density than initially. This opens the path for particles of St = 0.1 and dust-to-gas ratio of 0.01 or for particles of St {>=} 0.5 and dust-to-gas ratio 10{sup -4} to still reach densities that potentially trigger the streaming instability and thus gravoturbulent formation of planetesimals.« less

Modeling and optimization of trihalomethanes formation potential of surface water (a drinking water source) using Box-Behnken design.

PubMed

Singh, Kunwar P; Rai, Premanjali; Pandey, Priyanka; Sinha, Sarita

2012-01-01

The present research aims to investigate the individual and interactive effects of chlorine dose/dissolved organic carbon ratio, pH, temperature, bromide concentration, and reaction time on trihalomethanes (THMs) formation in surface water (a drinking water source) during disinfection by chlorination in a prototype laboratory-scale simulation and to develop a model for the prediction and optimization of THMs levels in chlorinated water for their effective control. A five-factor Box-Behnken experimental design combined with response surface and optimization modeling was used for predicting the THMs levels in chlorinated water. The adequacy of the selected model and statistical significance of the regression coefficients, independent variables, and their interactions were tested by the analysis of variance and t test statistics. The THMs levels predicted by the model were very close to the experimental values (R(2) = 0.95). Optimization modeling predicted maximum (192 μg/l) TMHs formation (highest risk) level in water during chlorination was very close to the experimental value (186.8 ± 1.72 μg/l) determined in laboratory experiments. The pH of water followed by reaction time and temperature were the most significant factors that affect the THMs formation during chlorination. The developed model can be used to determine the optimum characteristics of raw water and chlorination conditions for maintaining the THMs levels within the safe limit.

From field data to numerical models: application of the Box-Model to infer the dynamics of PDC generated during the AD 79 eruption of Somma-Vesuvio

NASA Astrophysics Data System (ADS)

Tadini, Alessandro; Neri, Augusto; Cioni, Raffaello; Bevilacqua, Andrea; Esposti Ongaro, Tomaso; Gurioli, Lucia

2017-04-01

The purpose of this work is to present a validation procedure for a physical and numerical model of Pyroclastic Density Currents (PDC) using feedbacks from well-known deposits emplaced by specific single eruptive units. The study is specifically focused on the PDCs generated during the overall famous AD 79 eruption of the Somma-Vesuvio volcano. To this purpose, values of the maximum runout, volumes and Total Grain Size Distributions have been estimated for two eruptive units (i.e. EU3pf and EU4; Cioni et al. 2000) of the AD 79 eruption. These units have been used to define the input volcanological parameters for testing the Box-Model of Dade and Huppert (1995), when reproducing one specific end-member of the complex spectrum of PDCs, that is the more dilute, turbulent part of the PDCs reconstructed in the Somma-Vesuvio record (stratified flows with concentration of solid particles in volume up to about 5%). The Box-Model is a kinematic approach, which calculates the flow density and velocity along time and the kinetic energy of the flow front. This can be compared with the potential energy needed to overcome topographic obstacles to estimate flow invasion across complex topographies. Validation of the model has been performed with respect to: i) the degree of overlapping between inundation areas given by the model and by field data; ii) the thickness of the deposit versus the thickness of the model output with distance; iii) the mass fractions of the different grain size classes with distance in the real deposit versus the model output. Several simulations have been performed considering i) polydisperse (with 10 grain size classes) and monodisperse (with the Mdφ values) systems; ii) a direct version (where the initial volume is released and the invasion area is computed) and an inverse version (where the initial collapsing volume is a function of an inundation area defined by the user); iii) axisymmetrical and asymmetrical collapses. Results allow to obtain first order estimates of the main variables characterizing the flow source and emplacement; among the two eruptive units chosen for model validation, the EU4 provided better results with only a minor empirical calibration of few parameters (i.e. settling velocity and initial volume fraction of solid particles), indicating that the Box Model can be suited to represent the kinematics of large (volume > 108 m^3, runout > 15 km) PDC at Somma-Vesuvio. Dade W. B., Huppert H. E. (1995) A box model for non-entraining, suspension-driven gravity surges on horizontal surfaces. Sedimentology 42 (3):453-470 Cioni R., Marianelli P., Santacroce R., Sbrana A. (2000). Plinian and subplinian eruptions. Encyclopedia of volcanoes. Academic, San Diego, 2000, 477-494.

The CEO's role in business model reinvention.

PubMed

Govindarajan, Vijay; Trimble, Chris

2011-01-01

Fending off new competitors is a perennial struggle for established companies. Govindarajan and Trimble, of Dartmouth's Tuck School of Business, explain why: Many corporations become too comfortable with their existing business models and neglect the necessary work of radically reinventing them. The authors map out an alternative in their "three boxes" framework. They argue that while a CEO manages the present (box 1), he or she must also selectively forget the past (box 2) in order to create the future (box 3). Infosys chairman N.R. Narayana Murthy mastered the three boxes to reinvigorate his company and greatly increased its changes of enduring for generations.

Simulation Based Optimization of Complex Monolithic Composite Structures Using Cellular Core Technology

NASA Astrophysics Data System (ADS)

Hickmott, Curtis W.

Cellular core tooling is a new technology which has the capability to manufacture complex integrated monolithic composite structures. This novel tooling method utilizes thermoplastic cellular cores as inner tooling. The semi-rigid nature of the cellular cores makes them convenient for lay-up, and under autoclave temperature and pressure they soften and expand providing uniform compaction on all surfaces including internal features such as ribs and spar tubes. This process has the capability of developing fully optimized aerospace structures by reducing or eliminating assembly using fasteners or bonded joints. The technology is studied in the context of evaluating its capabilities, advantages, and limitations in developing high quality structures. The complex nature of these parts has led to development of a model using the Finite Element Analysis (FEA) software Abaqus and the plug-in COMPRO Common Component Architecture (CCA) provided by Convergent Manufacturing Technologies. This model utilizes a "virtual autoclave" technique to simulate temperature profiles, resin flow paths, and ultimately deformation from residual stress. A model has been developed simulating the temperature profile during curing of composite parts made with the cellular core technology. While modeling of composites has been performed in the past, this project will look to take this existing knowledge and apply it to this new manufacturing method capable of building more complex parts and develop a model designed specifically for building large, complex components with a high degree of accuracy. The model development has been carried out in conjunction with experimental validation. A double box beam structure was chosen for analysis to determine the effects of the technology on internal ribs and joints. Double box beams were manufactured and sectioned into T-joints for characterization. Mechanical behavior of T-joints was performed using the T-joint pull-off test and compared to traditional tooling methods. Components made with the cellular core tooling method showed an improved strength at the joints. It is expected that this knowledge will help optimize the processing of complex, integrated structures and benefit applications in aerospace where lighter, structurally efficient components would be advantageous.

Microbial strengthening of loose sand.

PubMed

Banagan, B L; Wertheim, B M; Roth, M J S; Caslake, L F

2010-08-01

To test whether the addition of Flavobacterium johnsoniae could increase the strength of saturated Ottawa 30 sand. A box model was built that simulates groundwater-like flow through a main sand compartment. Strength tests were performed at seven locations and at two depths, 10.8 and 20.3 cm below the top of the tank, using a vane shear device before and after the addition of bacteria. After the addition of Fl. johnsoniae, sand samples were obtained from multiple sampling ports on the vertical sides of the box model. The presence of a bacterial biofilm was confirmed by staining these sand samples with SYTO-9 and Alexa Fluor 633 and viewing with a confocal microscope. The average shear strength increases after the addition of Fl. johnsoniae were 15.2-87.5%, depending on the experimental conditions. Flavobacterium johnsoniae caused a statistically significant increase in the strength of saturated Ottawa 30 sand. Biofilm-forming bacteria can increase the shear strength of saturated sand. The addition of biofilm-forming bacteria to a building site may be an alternate method to mitigate the effects of liquefaction.

A general Bayesian framework for calibrating and evaluating stochastic models of annual multi-site hydrological data

NASA Astrophysics Data System (ADS)

Frost, Andrew J.; Thyer, Mark A.; Srikanthan, R.; Kuczera, George

2007-07-01

SummaryMulti-site simulation of hydrological data are required for drought risk assessment of large multi-reservoir water supply systems. In this paper, a general Bayesian framework is presented for the calibration and evaluation of multi-site hydrological data at annual timescales. Models included within this framework are the hidden Markov model (HMM) and the widely used lag-1 autoregressive (AR(1)) model. These models are extended by the inclusion of a Box-Cox transformation and a spatial correlation function in a multi-site setting. Parameter uncertainty is evaluated using Markov chain Monte Carlo techniques. Models are evaluated by their ability to reproduce a range of important extreme statistics and compared using Bayesian model selection techniques which evaluate model probabilities. The case study, using multi-site annual rainfall data situated within catchments which contribute to Sydney's main water supply, provided the following results: Firstly, in terms of model probabilities and diagnostics, the inclusion of the Box-Cox transformation was preferred. Secondly the AR(1) and HMM performed similarly, while some other proposed AR(1)/HMM models with regionally pooled parameters had greater posterior probability than these two models. The practical significance of parameter and model uncertainty was illustrated using a case study involving drought security analysis for urban water supply. It was shown that ignoring parameter uncertainty resulted in a significant overestimate of reservoir yield and an underestimation of system vulnerability to severe drought.

General order parameter based correlation analysis of protein backbone motions between experimental NMR relaxation measurements and molecular dynamics simulations

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

Liu, Qing; Shi, Chaowei; Yu, Lu

Internal backbone dynamic motions are essential for different protein functions and occur on a wide range of time scales, from femtoseconds to seconds. Molecular dynamic (MD) simulations and nuclear magnetic resonance (NMR) spin relaxation measurements are valuable tools to gain access to fast (nanosecond) internal motions. However, there exist few reports on correlation analysis between MD and NMR relaxation data. Here, backbone relaxation measurements of {sup 15}N-labeled SH3 (Src homology 3) domain proteins in aqueous buffer were used to generate general order parameters (S{sup 2}) using a model-free approach. Simultaneously, 80 ns MD simulations of SH3 domain proteins in amore » defined hydrated box at neutral pH were conducted and the general order parameters (S{sup 2}) were derived from the MD trajectory. Correlation analysis using the Gromos force field indicated that S{sup 2} values from NMR relaxation measurements and MD simulations were significantly different. MD simulations were performed on models with different charge states for three histidine residues, and with different water models, which were SPC (simple point charge) water model and SPC/E (extended simple point charge) water model. S{sup 2} parameters from MD simulations with charges for all three histidines and with the SPC/E water model correlated well with S{sup 2} calculated from the experimental NMR relaxation measurements, in a site-specific manner. - Highlights: • Correlation analysis between NMR relaxation measurements and MD simulations. • General order parameter (S{sup 2}) as common reference between the two methods. • Different protein dynamics with different Histidine charge states in neutral pH. • Different protein dynamics with different water models.« less

Black-box Brain Experiments, Causal Mathematical Logic, and the Thermodynamics of Intelligence

NASA Astrophysics Data System (ADS)

Pissanetzky, Sergio; Lanzalaco, Felix

2013-12-01

Awareness of the possible existence of a yet-unknown principle of Physics that explains cognition and intelligence does exist in several projects of emulation, simulation, and replication of the human brain currently under way. Brain simulation projects define their success partly in terms of the emergence of non-explicitly programmed biophysical signals such as self-oscillation and spreading cortical waves. We propose that a recently discovered theory of Physics known as Causal Mathematical Logic (CML) that links intelligence with causality and entropy and explains intelligent behavior from first principles, is the missing link. We further propose the theory as a roadway to understanding more complex biophysical signals, and to explain the set of intelligence principles. The new theory applies to information considered as an entity by itself. The theory proposes that any device that processes information and exhibits intelligence must satisfy certain theoretical conditions irrespective of the substrate where it is being processed. The substrate can be the human brain, a part of it, a worm's brain, a motor protein that self-locomotes in response to its environment, a computer. Here, we propose to extend the causal theory to systems in Neuroscience, because of its ability to model complex systems without heuristic approximations, and to predict emerging signals of intelligence directly from the models. The theory predicts the existence of a large number of observables (or "signals"), all of which emerge and can be directly and mathematically calculated from non-explicitly programmed detailed causal models. This approach is aiming for a universal and predictive language for Neuroscience and AGI based on causality and entropy, detailed enough to describe the finest structures and signals of the brain, yet general enough to accommodate the versatility and wholeness of intelligence. Experiments are focused on a black-box as one of the devices described above of which both the input and the output are precisely known, but not the internal implementation. The same input is separately supplied to a causal virtual machine, and the calculated output is compared with the measured output. The virtual machine, described in a previous paper, is a computer implementation of CML, fixed for all experiments and unrelated to the device in the black box. If the two outputs are equivalent, then the experiment has quantitatively succeeded and conclusions can be drawn regarding details of the internal implementation of the device. Several small black-box experiments were successfully performed and demonstrated the emergence of non-explicitly programmed cognitive function in each case

Molecular dynamics simulation studies of caffeine aggregation in aqueous solution.

PubMed

Tavagnacco, Letizia; Schnupf, Udo; Mason, Philip E; Saboungi, Marie-Louise; Cesàro, Attilio; Brady, John W

2011-09-22

Molecular dynamics simulations were carried out on a system of eight independent caffeine molecules in a periodic box of water at 300 K, representing a solution near the solubility limit for caffeine at room temperature, using a newly developed CHARMM-type force field for caffeine in water. Simulations were also conducted for single caffeine molecules in water using two different water models (TIP3P and TIP4P). Water was found to structure in a complex fashion around the planar caffeine molecules, which was not sensitive to the water model used. As expected, extensive aggregation of the caffeine molecules was observed, with the molecules stacking their flat faces against one another like coins, with their methylene groups staggered to avoid steric clashes. A dynamic equilibrum was observed between large n-mers, including stacks with all eight solute molecules, and smaller clusters, with the calculated osmotic coefficient being in acceptable agreement with the experimental value. The insensitivity of the results to water model and the congruence with experimental thermodynamic data suggest that the observed stacking interactions are a realistic representation of the actual association mechanism in aqueous caffeine solutions.

CFD Simulations of the IHF Arc-Jet Flow: Compression-Pad/Separation Bolt Wedge Tests

NASA Technical Reports Server (NTRS)

Gokcen, Tahir; Skokova, Kristina A.

2017-01-01

This paper reports computational analyses in support of two wedge tests in a high enthalpy arc-jet facility at NASA Ames Research Center. These tests were conducted using two different wedge models, each placed in a free jet downstream of a corresponding different conical nozzle in the Ames 60-MW Interaction Heating Facility. Panel test articles included a metallic separation bolt imbedded in the compression-pad and heat shield materials, resulting in a circular protuberance over a flat plate. As part of the test calibration runs, surface pressure and heat flux measurements on water-cooled calibration plates integrated with the wedge models were also obtained. Surface heating distributions on the test articles as well as arc-jet test environment parameters for each test configuration are obtained through computational fluid dynamics simulations, consistent with the facility and calibration measurements. The present analysis comprises simulations of the non-equilibrium flow field in the facility nozzle, test box, and flow field over test articles, and comparisons with the measured calibration data.

Numerical simulation on the powder propellant pickup characteristics of feeding system at high pressure

NASA Astrophysics Data System (ADS)

Sun, Haijun; Hu, Chunbo; Zhu, Xiaofei

2017-10-01

A numerical study of powder propellant pickup progress at high pressure was presented in this paper by using two-fluid model with kinetic theory of granular flow in the computational fluid dynamics software package ANSYS/Fluent. Simulations were conducted to evaluate the effects of initial pressure, initial powder packing rate and mean particle diameter on the flow characteristics in terms of velocity vector distribution, granular temperature, pressure drop, particle velocity and volume. The numerical results of pressure drop were also compared with experiments to verify the TFM model. The simulated results show that the pressure drop value increases as the initial pressure increases, and the granular temperature under the conditions of different initial pressures and packing rates is almost the same in the area of throttling orifice plate. While there is an appropriate value for particle size and packing rate to form a ;core-annulus; structure in powder box, and the time-averaged velocity vector distribution of solid phase is inordinate.

Planetesimal and Protoplanet Dynamics in a Turbulent Protoplanetary Disk

NASA Astrophysics Data System (ADS)

Yang, Chao-Chin; Mac Low, M.; Menou, K.

2010-01-01

In core accretion scenario of planet formation, kilometer-sized planetesimals are the building blocks toward planetary cores. Their dynamics, however, are strongly influenced by their natal protoplanetary gas disks. It is generally believed that these disks are turbulent, most likely due to magnetorotational instability. The resulting density perturbations in the gas render the movement of the particles a random process. Depending on its strength, this process might cause several interesting consequences in the course of planet formation, specifically the survivability of objects under rapid inward type-I migration and/or collisional destruction. Using the local-shearing-box approximation, we conduct numerical simulations of planetesimals moving in a turbulent, magnetized gas disk, either unstratified or vertically stratified. We produce a fiducial disk model with turbulent accretion of Shakura-Sunyaev alpha about 10-2 and root-mean-square density perturbation of about 10% and statistically characterize the evolution of the orbital properties of the particles moving in the disk. These measurements result in accurate calibration of the random process of particle orbital change, indicating noticeably smaller magnitudes than predicted by global simulations, although the results may depend on the size of the shearing box. We apply these results to revisit the survivability of planetesimals under collisional destruction or protoplanets under type-I migration. Planetesimals are probably secure from collisional destruction, except for kilometer-sized objects situated in the outer regions of a young protoplanetary disk. On the other hand, we confirm earlier studies of local models in that type-I migration probably dominates diffusive migration due to stochastic torques for most planetary cores and terrestrial planets. Discrepancies in the derived magnitude of turbulence between local and global simulations of magnetorotationally unstable disks remains an open issue, with important consequences for planet formation scenarios.

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations.

PubMed

Anandakrishnan, Ramu; Aguilar, Boris; Onufriev, Alexey V

2012-07-01

The accuracy of atomistic biomolecular modeling and simulation studies depend on the accuracy of the input structures. Preparing these structures for an atomistic modeling task, such as molecular dynamics (MD) simulation, can involve the use of a variety of different tools for: correcting errors, adding missing atoms, filling valences with hydrogens, predicting pK values for titratable amino acids, assigning predefined partial charges and radii to all atoms, and generating force field parameter/topology files for MD. Identifying, installing and effectively using the appropriate tools for each of these tasks can be difficult for novice and time-consuming for experienced users. H++ (http://biophysics.cs.vt.edu/) is a free open-source web server that automates the above key steps in the preparation of biomolecular structures for molecular modeling and simulations. H++ also performs extensive error and consistency checking, providing error/warning messages together with the suggested corrections. In addition to numerous minor improvements, the latest version of H++ includes several new capabilities and options: fix erroneous (flipped) side chain conformations for HIS, GLN and ASN, include a ligand in the input structure, process nucleic acid structures and generate a solvent box with specified number of common ions for explicit solvent MD.

A Finite Element Solution of Lateral Periodic Poisson–Boltzmann Model for Membrane Channel Proteins

PubMed Central

Xu, Jingjie; Lu, Benzhuo

2018-01-01

Membrane channel proteins control the diffusion of ions across biological membranes. They are closely related to the processes of various organizational mechanisms, such as: cardiac impulse, muscle contraction and hormone secretion. Introducing a membrane region into implicit solvation models extends the ability of the Poisson–Boltzmann (PB) equation to handle membrane proteins. The use of lateral periodic boundary conditions can properly simulate the discrete distribution of membrane proteins on the membrane plane and avoid boundary effects, which are caused by the finite box size in the traditional PB calculations. In this work, we: (1) develop a first finite element solver (FEPB) to solve the PB equation with a two-dimensional periodicity for membrane channel proteins, with different numerical treatments of the singular charges distributions in the channel protein; (2) add the membrane as a dielectric slab in the PB model, and use an improved mesh construction method to automatically identify the membrane channel/pore region even with a tilt angle relative to the z-axis; and (3) add a non-polar solvation energy term to complete the estimation of the total solvation energy of a membrane protein. A mesh resolution of about 0.25 Å (cubic grid space)/0.36 Å (tetrahedron edge length) is found to be most accurate in linear finite element calculation of the PB solvation energy. Computational studies are performed on a few exemplary molecules. The results indicate that all factors, the membrane thickness, the length of periodic box, membrane dielectric constant, pore region dielectric constant, and ionic strength, have individually considerable influence on the solvation energy of a channel protein. This demonstrates the necessity to treat all of those effects in the PB model for membrane protein simulations. PMID:29495644

A Finite Element Solution of Lateral Periodic Poisson-Boltzmann Model for Membrane Channel Proteins.

PubMed

Ji, Nan; Liu, Tiantian; Xu, Jingjie; Shen, Longzhu Q; Lu, Benzhuo

2018-02-28

Membrane channel proteins control the diffusion of ions across biological membranes. They are closely related to the processes of various organizational mechanisms, such as: cardiac impulse, muscle contraction and hormone secretion. Introducing a membrane region into implicit solvation models extends the ability of the Poisson-Boltzmann (PB) equation to handle membrane proteins. The use of lateral periodic boundary conditions can properly simulate the discrete distribution of membrane proteins on the membrane plane and avoid boundary effects, which are caused by the finite box size in the traditional PB calculations. In this work, we: (1) develop a first finite element solver (FEPB) to solve the PB equation with a two-dimensional periodicity for membrane channel proteins, with different numerical treatments of the singular charges distributions in the channel protein; (2) add the membrane as a dielectric slab in the PB model, and use an improved mesh construction method to automatically identify the membrane channel/pore region even with a tilt angle relative to the z -axis; and (3) add a non-polar solvation energy term to complete the estimation of the total solvation energy of a membrane protein. A mesh resolution of about 0.25 Å (cubic grid space)/0.36 Å (tetrahedron edge length) is found to be most accurate in linear finite element calculation of the PB solvation energy. Computational studies are performed on a few exemplary molecules. The results indicate that all factors, the membrane thickness, the length of periodic box, membrane dielectric constant, pore region dielectric constant, and ionic strength, have individually considerable influence on the solvation energy of a channel protein. This demonstrates the necessity to treat all of those effects in the PB model for membrane protein simulations.

Coupled Particle Transport and Pattern Formation in a Nonlinear Leaky-Box Model

NASA Technical Reports Server (NTRS)

Barghouty, A. F.; El-Nemr, K. W.; Baird, J. K.

2009-01-01

Effects of particle-particle coupling on particle characteristics in nonlinear leaky-box type descriptions of the acceleration and transport of energetic particles in space plasmas are examined in the framework of a simple two-particle model based on the Fokker-Planck equation in momentum space. In this model, the two particles are assumed coupled via a common nonlinear source term. In analogy with a prototypical mathematical system of diffusion-driven instability, this work demonstrates that steady-state patterns with strong dependence on the magnetic turbulence but a rather weak one on the coupled particles attributes can emerge in solutions of a nonlinearly coupled leaky-box model. The insight gained from this simple model may be of wider use and significance to nonlinearly coupled leaky-box type descriptions in general.

Molecular dynamics simulations elucidate the mode of protein recognition by Skp1 and the F-box domain in the SCF complex.

PubMed

Chandra Dantu, Sarath; Nathubhai Kachariya, Nitin; Kumar, Ashutosh

2016-01-01

Polyubiquitination of the target protein by a ubiquitin transferring machinery is key to various cellular processes. E3 ligase Skp1-Cul1-F-box (SCF) is one such complex which plays crucial role in substrate recognition and transfer of the ubiquitin molecule. Previous computational studies have focused on S-phase kinase-associated protein 2 (Skp2), cullin, and RING-finger proteins of this complex, but the roles of the adapter protein Skp1 and F-box domain of Skp2 have not been determined. Using sub-microsecond molecular dynamics simulations of full-length Skp1, unbound Skp2, Skp2-Cks1 (Cks1: Cyclin-dependent kinases regulatory subunit 1), Skp1-Skp2, and Skp1-Skp2-Cks1 complexes, we have elucidated the function of Skp1 and the F-box domain of Skp2. We found that the L16 loop of Skp1, which was deleted in previous X-ray crystallography studies, can offer additional stability to the ternary complex via its interactions with the C-terminal tail of Skp2. Moreover, Skp1 helices H6, H7, and H8 display vivid conformational flexibility when not bound to Skp2, suggesting that these helices can recognize and lock the F-box proteins. Furthermore, we observed that the F-box domain could rotate (5°-129°), and that the binding partner determined the degree of conformational flexibility. Finally, Skp1 and Skp2 were found to execute a domain motion in Skp1-Skp2 and Skp1-Skp2-Cks1 complexes that could decrease the distance between ubiquitination site of the substrate and the ubiquitin molecule by 3 nm. Thus, we propose that both the F-box domain of Skp2 and Skp1-Skp2 domain motions displaying preferential conformational control can together facilitate polyubiquitination of a wide variety of substrates. © 2015 Wiley Periodicals, Inc.

Phase equilibrium in argon films stabilized by homogeneous surfaces and thermodynamics of two-stage melting transition.

PubMed

Ustinov, E A

2014-02-21

Freezing of gases adsorbed on open surfaces (e.g., graphite) and in narrow pores is a widespread phenomenon which is a subject of a large number of publications. Modeling of the gas/liquid-solid transition is usually accomplished with a molecular simulation technique. However, quantitative analysis of the gas/liquid-solid coexistence and thermodynamic properties of the solid layer still encounters serious difficulties. This is mainly due to the effect of simulation box size on the lattice constant. Since the lattice constant is a function of loading and temperature, once the ordering transition has occurred, the simulation box size must be corrected in the course of simulation according to the Gibbs-Duhem equation. A significant problem is also associated with accurate prediction of the two-dimensional liquid-solid coexistence because of a small difference in densities of coexisting phases. The aim of this study is thermodynamic analysis of the two-dimensional phase coexistence in systems involving crystal-like free of defects layers in narrow slit pores. A special attention was paid to the determination of triple point temperatures. It is shown that intrinsic properties of argon monolayer adsorbed on the graphite surface are similar to those of isolated monolayer accommodated in the slit pore having width of two argon collision diameters. Analysis of the latter system is shown to be clearer and less time-consuming than the former one, which has allowed for explanation of the experimentally observed two-stage melting transition of argon monolayer on graphite without invoking the periodic surface potential modulation and orientational transition.

Phase equilibrium in argon films stabilized by homogeneous surfaces and thermodynamics of two-stage melting transition

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

Ustinov, E. A., E-mail: eustinov@mail.wplus.net

Freezing of gases adsorbed on open surfaces (e.g., graphite) and in narrow pores is a widespread phenomenon which is a subject of a large number of publications. Modeling of the gas/liquid–solid transition is usually accomplished with a molecular simulation technique. However, quantitative analysis of the gas/liquid–solid coexistence and thermodynamic properties of the solid layer still encounters serious difficulties. This is mainly due to the effect of simulation box size on the lattice constant. Since the lattice constant is a function of loading and temperature, once the ordering transition has occurred, the simulation box size must be corrected in the coursemore » of simulation according to the Gibbs–Duhem equation. A significant problem is also associated with accurate prediction of the two-dimensional liquid–solid coexistence because of a small difference in densities of coexisting phases. The aim of this study is thermodynamic analysis of the two-dimensional phase coexistence in systems involving crystal-like free of defects layers in narrow slit pores. A special attention was paid to the determination of triple point temperatures. It is shown that intrinsic properties of argon monolayer adsorbed on the graphite surface are similar to those of isolated monolayer accommodated in the slit pore having width of two argon collision diameters. Analysis of the latter system is shown to be clearer and less time-consuming than the former one, which has allowed for explanation of the experimentally observed two-stage melting transition of argon monolayer on graphite without invoking the periodic surface potential modulation and orientational transition.« less

Application of molecular dynamics simulations in molecular property prediction II: diffusion coefficient.

PubMed

Wang, Junmei; Hou, Tingjun

2011-12-01

In this work, we have evaluated how well the general assisted model building with energy refinement (AMBER) force field performs in studying the dynamic properties of liquids. Diffusion coefficients (D) have been predicted for 17 solvents, five organic compounds in aqueous solutions, four proteins in aqueous solutions, and nine organic compounds in nonaqueous solutions. An efficient sampling strategy has been proposed and tested in the calculation of the diffusion coefficients of solutes in solutions. There are two major findings of this study. First of all, the diffusion coefficients of organic solutes in aqueous solution can be well predicted: the average unsigned errors and the root mean square errors are 0.137 and 0.171 × 10(-5) cm(-2) s(-1), respectively. Second, although the absolute values of D cannot be predicted, good correlations have been achieved for eight organic solvents with experimental data (R(2) = 0.784), four proteins in aqueous solutions (R(2) = 0.996), and nine organic compounds in nonaqueous solutions (R(2) = 0.834). The temperature dependent behaviors of three solvents, namely, TIP3P water, dimethyl sulfoxide, and cyclohexane have been studied. The major molecular dynamics (MD) settings, such as the sizes of simulation boxes and with/without wrapping the coordinates of MD snapshots into the primary simulation boxes have been explored. We have concluded that our sampling strategy that averaging the mean square displacement collected in multiple short-MD simulations is efficient in predicting diffusion coefficients of solutes at infinite dilution. Copyright © 2011 Wiley Periodicals, Inc.

A Three-Pulse Release Tablet for Amoxicillin: Preparation, Pharmacokinetic Study and Physiologically Based Pharmacokinetic Modeling.

PubMed

Li, Jin; Chai, Hongyu; Li, Yang; Chai, Xuyu; Zhao, Yan; Zhao, Yunfan; Tao, Tao; Xiang, Xiaoqiang

2016-01-01

Amoxicillin is a commonly used antibiotic which has a short half-life in human. The frequent administration of amoxicillin is often required to keep the plasma drug level in an effective range. The short dosing interval of amoxicillin could also cause some side effects and drug resistance, and impair its therapeutic efficacy and patients' compliance. Therefore, a three-pulse release tablet of amoxicillin is desired to generate sustained release in vivo, and thus to avoid the above mentioned disadvantages. The pulsatile release tablet consists of three pulsatile components: one immediate-release granule and two delayed release pellets, all containing amoxicillin. The preparation of a pulsatile release tablet of amoxicillin mainly includes wet granulation craft, extrusion/spheronization craft, pellet coating craft, mixing craft, tablet compression craft and film coating craft. Box-Behnken design, Scanning Electron Microscope and in vitro drug release test were used to help the optimization of formulations. A crossover pharmacokinetic study was performed to compare the pharmacokinetic profile of our in-house pulsatile tablet with that of commercial immediate release tablet. The pharmacokinetic profile of this pulse formulation was simulated by physiologically based pharmacokinetic (PBPK) model with the help of Simcyp®. Single factor experiments identify four important factors of the formulation, namely, coating weight of Eudragit L30 D-55 (X1), coating weight of AQOAT AS-HF (X2), the extrusion screen aperture (X3) and compression forces (X4). The interrelations of the four factors were uncovered by a Box-Behnken design to help to determine the optimal formulation. The immediate-release granule, two delayed release pellets, together with other excipients, namely, Avicel PH 102, colloidal silicon dioxide, polyplasdone and magnesium stearate were mixed, and compressed into tablets, which was subsequently coated with Opadry® film to produce pulsatile tablet of amoxicillin. In vitro release study firstly indicated a three-pulse release profile of the tablet. Later the pulse tablet was found to generate the sustained release of amoxicillin in beagle dogs. Furthermore, the Simcyp® software was used to simulate the in vivo concentration time curve model of the three-pulse release tablet for amoxicillin in both human and beagle dog. The prediction by PBPK model nicely fitted the observation in human and beagle dog. This study has demonstrated the interrelation of factors affecting the pulsatile formulation of amoxicillin using a Box-Behnken design. The three-pulse release tablets of amoxicillin were proven to generate pulsatile release in vitro and sustained release in vivo. This formulation was also found to extend the effective plasma concentration in human compared to the tablet of immediate release based on the simulation data by PBPK modeling. This study provides an example of using PBPK to guide the development of pulsatile dosage forms.

Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects

PubMed Central

Rocklin, Gabriel J.; Mobley, David L.; Dill, Ken A.; Hünenberger, Philippe H.

2013-01-01

The calculation of a protein-ligand binding free energy based on molecular dynamics (MD) simulations generally relies on a thermodynamic cycle in which the ligand is alchemically inserted into the system, both in the solvated protein and free in solution. The corresponding ligand-insertion free energies are typically calculated in nanoscale computational boxes simulated under periodic boundary conditions and considering electrostatic interactions defined by a periodic lattice-sum. This is distinct from the ideal bulk situation of a system of macroscopic size simulated under non-periodic boundary conditions with Coulombic electrostatic interactions. This discrepancy results in finite-size effects, which affect primarily the charging component of the insertion free energy, are dependent on the box size, and can be large when the ligand bears a net charge, especially if the protein is charged as well. This article investigates finite-size effects on calculated charging free energies using as a test case the binding of the ligand 2-amino-5-methylthiazole (net charge +1 e) to a mutant form of yeast cytochrome c peroxidase in water. Considering different charge isoforms of the protein (net charges −5, 0, +3, or +9 e), either in the absence or the presence of neutralizing counter-ions, and sizes of the cubic computational box (edges ranging from 7.42 to 11.02 nm), the potentially large magnitude of finite-size effects on the raw charging free energies (up to 17.1 kJ mol−1) is demonstrated. Two correction schemes are then proposed to eliminate these effects, a numerical and an analytical one. Both schemes are based on a continuum-electrostatics analysis and require performing Poisson-Boltzmann (PB) calculations on the protein-ligand system. While the numerical scheme requires PB calculations under both non-periodic and periodic boundary conditions, the latter at the box size considered in the MD simulations, the analytical scheme only requires three non-periodic PB calculations for a given system, its dependence on the box size being analytical. The latter scheme also provides insight into the physical origin of the finite-size effects. These two schemes also encompass a correction for discrete solvent effects that persists even in the limit of infinite box sizes. Application of either scheme essentially eliminates the size dependence of the corrected charging free energies (maximal deviation of 1.5 kJ mol−1). Because it is simple to apply, the analytical correction scheme offers a general solution to the problem of finite-size effects in free-energy calculations involving charged solutes, as encountered in calculations concerning, e.g., protein-ligand binding, biomolecular association, residue mutation, pKa and redox potential estimation, substrate transformation, solvation, and solvent-solvent partitioning. PMID:24320250

Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects.

PubMed

Rocklin, Gabriel J; Mobley, David L; Dill, Ken A; Hünenberger, Philippe H

2013-11-14

The calculation of a protein-ligand binding free energy based on molecular dynamics (MD) simulations generally relies on a thermodynamic cycle in which the ligand is alchemically inserted into the system, both in the solvated protein and free in solution. The corresponding ligand-insertion free energies are typically calculated in nanoscale computational boxes simulated under periodic boundary conditions and considering electrostatic interactions defined by a periodic lattice-sum. This is distinct from the ideal bulk situation of a system of macroscopic size simulated under non-periodic boundary conditions with Coulombic electrostatic interactions. This discrepancy results in finite-size effects, which affect primarily the charging component of the insertion free energy, are dependent on the box size, and can be large when the ligand bears a net charge, especially if the protein is charged as well. This article investigates finite-size effects on calculated charging free energies using as a test case the binding of the ligand 2-amino-5-methylthiazole (net charge +1 e) to a mutant form of yeast cytochrome c peroxidase in water. Considering different charge isoforms of the protein (net charges -5, 0, +3, or +9 e), either in the absence or the presence of neutralizing counter-ions, and sizes of the cubic computational box (edges ranging from 7.42 to 11.02 nm), the potentially large magnitude of finite-size effects on the raw charging free energies (up to 17.1 kJ mol(-1)) is demonstrated. Two correction schemes are then proposed to eliminate these effects, a numerical and an analytical one. Both schemes are based on a continuum-electrostatics analysis and require performing Poisson-Boltzmann (PB) calculations on the protein-ligand system. While the numerical scheme requires PB calculations under both non-periodic and periodic boundary conditions, the latter at the box size considered in the MD simulations, the analytical scheme only requires three non-periodic PB calculations for a given system, its dependence on the box size being analytical. The latter scheme also provides insight into the physical origin of the finite-size effects. These two schemes also encompass a correction for discrete solvent effects that persists even in the limit of infinite box sizes. Application of either scheme essentially eliminates the size dependence of the corrected charging free energies (maximal deviation of 1.5 kJ mol(-1)). Because it is simple to apply, the analytical correction scheme offers a general solution to the problem of finite-size effects in free-energy calculations involving charged solutes, as encountered in calculations concerning, e.g., protein-ligand binding, biomolecular association, residue mutation, pKa and redox potential estimation, substrate transformation, solvation, and solvent-solvent partitioning.

Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects

NASA Astrophysics Data System (ADS)

Rocklin, Gabriel J.; Mobley, David L.; Dill, Ken A.; Hünenberger, Philippe H.

2013-11-01

The calculation of a protein-ligand binding free energy based on molecular dynamics (MD) simulations generally relies on a thermodynamic cycle in which the ligand is alchemically inserted into the system, both in the solvated protein and free in solution. The corresponding ligand-insertion free energies are typically calculated in nanoscale computational boxes simulated under periodic boundary conditions and considering electrostatic interactions defined by a periodic lattice-sum. This is distinct from the ideal bulk situation of a system of macroscopic size simulated under non-periodic boundary conditions with Coulombic electrostatic interactions. This discrepancy results in finite-size effects, which affect primarily the charging component of the insertion free energy, are dependent on the box size, and can be large when the ligand bears a net charge, especially if the protein is charged as well. This article investigates finite-size effects on calculated charging free energies using as a test case the binding of the ligand 2-amino-5-methylthiazole (net charge +1 e) to a mutant form of yeast cytochrome c peroxidase in water. Considering different charge isoforms of the protein (net charges -5, 0, +3, or +9 e), either in the absence or the presence of neutralizing counter-ions, and sizes of the cubic computational box (edges ranging from 7.42 to 11.02 nm), the potentially large magnitude of finite-size effects on the raw charging free energies (up to 17.1 kJ mol-1) is demonstrated. Two correction schemes are then proposed to eliminate these effects, a numerical and an analytical one. Both schemes are based on a continuum-electrostatics analysis and require performing Poisson-Boltzmann (PB) calculations on the protein-ligand system. While the numerical scheme requires PB calculations under both non-periodic and periodic boundary conditions, the latter at the box size considered in the MD simulations, the analytical scheme only requires three non-periodic PB calculations for a given system, its dependence on the box size being analytical. The latter scheme also provides insight into the physical origin of the finite-size effects. These two schemes also encompass a correction for discrete solvent effects that persists even in the limit of infinite box sizes. Application of either scheme essentially eliminates the size dependence of the corrected charging free energies (maximal deviation of 1.5 kJ mol-1). Because it is simple to apply, the analytical correction scheme offers a general solution to the problem of finite-size effects in free-energy calculations involving charged solutes, as encountered in calculations concerning, e.g., protein-ligand binding, biomolecular association, residue mutation, pKa and redox potential estimation, substrate transformation, solvation, and solvent-solvent partitioning.

EPA EcoBox

EPA Pesticide Factsheets

This tool box of ecological risk assessment (Eco-box) includes over 400+ links to tools, models, and databases found within EPA and our Government partners designed that can aid risk assessors with performing exposure assessments.

Heart Rate and Liking During "Kinect Boxing" Versus "Wii Boxing": The Potential for Enjoyable Vigorous Physical Activity Videogames.

PubMed

Sanders, Gabriel J; Peacock, Corey A; Barkley, Jacob E; Gish, Brian; Brock, Scott; Volpenhein, Josh

2015-08-01

Nintendo(®) (Kyoto, Japan) "Wii™ Sports Boxing" ("Wii Boxing") and Xbox(®) (Microsoft, Redmond, WA) "Kinect(®) Sports Boxing" ("Kinect Boxing") are both boxing simulation videogames that are available for two different active videogame (AVG) systems. Although these AVGs are similar, the style of gameplay required is different (i.e., upper body only versus total body movements) and may alter physical activity intensity and one's preference for playing one game over the other. AVGs that elicit the greatest physiologic challenge and are preferred by users should be identified in an effort to enhance the efficacy of physical activity interventions and programs that include AVGs. The mean heart rate (HRmean) and peak heart rate (HRpeak) for 27 adults (22.7±4.2 years old) were recorded during four 10-minute conditions: seated rest, treadmill walking at 3 miles/hour, "Wii Boxing," and "Kinect Boxing." Upon completion of all four conditions, participants indicated which condition they preferred, and HRmean and HRpeak were calculated as a percentage of age-predicted maximum heart rate to classify physical activity intensity for the three activity conditions (treadmill, "Wii Boxing," and "Kinect Boxing"). "Kinect Boxing" significantly (P<0.001) increased percentage HRmean (64.1±1.6 percent of age-predicted maximum) and percentage HRpeak (76.5±1.9 percent) above all other conditions: Wii HRmean, 53.0±1.2 percent; Wii HRpeak, 61.8±1.5 percent; treadmill HRmean, 52.4±1.2 percent; treadmill HRpeak, 55.2±2.2 percent. Percentage HRpeak for "Kinect Boxing" was great enough to be considered a vigorous-intensity physical activity. There was no difference (P=0.55) in percentage HRmean between "Wii Boxing" and treadmill walking. Participants also preferred "Kinect Boxing" (P<0.001; n=26) to all other conditions ("Wii Boxing," n=1; treadmill n=0). "Kinect Boxing" was the most preferred and the only condition that was physiologically challenging enough to be classified as a vigorous-intensity physical activity.

Modeling the Lyα Forest in Collisionless Simulations

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

Sorini, Daniele; Oñorbe, José; Lukić, Zarija

2016-08-11

Cosmological hydrodynamic simulations can accurately predict the properties of the intergalactic medium (IGM), but only under the condition of retaining the high spatial resolution necessary to resolve density fluctuations in the IGM. This resolution constraint prohibits simulating large volumes, such as those probed by BOSS and future surveys, like DESI and 4MOST. To overcome this limitation, we present in this paper "Iteratively Matched Statistics" (IMS), a novel method to accurately model the Lyα forest with collisionless N-body simulations, where the relevant density fluctuations are unresolved. We use a small-box, high-resolution hydrodynamic simulation to obtain the probability distribution function (PDF) andmore » the power spectrum of the real-space Lyα forest flux. These two statistics are iteratively mapped onto a pseudo-flux field of an N-body simulation, which we construct from the matter density. We demonstrate that our method can reproduce the PDF, line of sight and 3D power spectra of the Lyα forest with good accuracy (7%, 4%, and 7% respectively). We quantify the performance of the commonly used Gaussian smoothing technique and show that it has significantly lower accuracy (20%–80%), especially for N-body simulations with achievable mean inter-particle separations in large-volume simulations. Finally, in addition, we show that IMS produces reasonable and smooth spectra, making it a powerful tool for modeling the IGM in large cosmological volumes and for producing realistic "mock" skies for Lyα forest surveys.« less

MODELING THE Ly α FOREST IN COLLISIONLESS SIMULATIONS

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

Sorini, Daniele; Oñorbe, José; Hennawi, Joseph F.

2016-08-20

Cosmological hydrodynamic simulations can accurately predict the properties of the intergalactic medium (IGM), but only under the condition of retaining the high spatial resolution necessary to resolve density fluctuations in the IGM. This resolution constraint prohibits simulating large volumes, such as those probed by BOSS and future surveys, like DESI and 4MOST. To overcome this limitation, we present “Iteratively Matched Statistics” (IMS), a novel method to accurately model the Ly α forest with collisionless N -body simulations, where the relevant density fluctuations are unresolved. We use a small-box, high-resolution hydrodynamic simulation to obtain the probability distribution function (PDF) and themore » power spectrum of the real-space Ly α forest flux. These two statistics are iteratively mapped onto a pseudo-flux field of an N -body simulation, which we construct from the matter density. We demonstrate that our method can reproduce the PDF, line of sight and 3D power spectra of the Ly α forest with good accuracy (7%, 4%, and 7% respectively). We quantify the performance of the commonly used Gaussian smoothing technique and show that it has significantly lower accuracy (20%–80%), especially for N -body simulations with achievable mean inter-particle separations in large-volume simulations. In addition, we show that IMS produces reasonable and smooth spectra, making it a powerful tool for modeling the IGM in large cosmological volumes and for producing realistic “mock” skies for Ly α forest surveys.« less

The reference cube: A new ballistic model to generate staining in firearm barrels.

PubMed

Schyma, Christian; Bauer, Kristina; Brünig, Julia

2017-06-01

After contact shots to the head biological traces can be found inside firearm barrels. So far silicone coated, gelatin filled box models were used to generate such staining according to the triple contrast method (mixture of acrylic paint, barium sulfate and blood sealed in a thin foil bag). This study was conducted to develop a transparent ballistic model allowing contact shots. Gelatin filled polyethylene bottles with and without a silicone coat were tested in comparison to non-covered gelatin blocks. Finally, thin foil bags of 5 cm × 5 cm dimension were glued on a synthetic absorbent kitchen wipe on top of which 1 L 10% gelatin solution was molded to create blocks of 8.5 cm length. A kitchen wipe with a paint pad on its inside formed the front of the cube. Three contact shots each with a 9 mm Luger pistol and a .38 special revolver were performed on all model variations. The staining was documented by endoscopy and swabs gathered from both ends of the barrel were analyzed by quantitative PCR. Reliable staining was achieved using the front covered gelatin block with comparable results to the silicone coated box model used before. For further research using ballistic models to simulate a human head a symmetric form of the gelatin block such as a cube is recommended.

Unconventional bearing capacity analysis and optimization of multicell box girders.

PubMed

Tepic, Jovan; Doroslovacki, Rade; Djelosevic, Mirko

2014-01-01

This study deals with unconventional bearing capacity analysis and the procedure of optimizing a two-cell box girder. The generalized model which enables the local stress-strain analysis of multicell girders was developed based on the principle of cross-sectional decomposition. The applied methodology is verified using the experimental data (Djelosevic et al., 2012) for traditionally formed box girders. The qualitative and quantitative evaluation of results obtained for the two-cell box girder is realized based on comparative analysis using the finite element method (FEM) and the ANSYS v12 software. The deflection function obtained by analytical and numerical methods was found consistent provided that the maximum deviation does not exceed 4%. Multicell box girders are rationally designed support structures characterized by much lower susceptibility of their cross-sectional elements to buckling and higher specific capacity than traditionally formed box girders. The developed local stress model is applied for optimizing the cross section of a two-cell box carrier. The author points to the advantages of implementing the model of local stresses in the optimization process and concludes that the technological reserve of bearing capacity amounts to 20% at the same girder weight and constant load conditions.

[Existing laparoscopic simulators and their benefit for the surgeon].

PubMed

Kalvach, J; Ryska, O; Ryska, M

2016-01-01

Nowadays, laparoscopic operations are a common part of surgical practice. However, they have their own characteristics and require a specific method of preparation. Recently, simulation techniques have been increasingly used for the training of skills. The aim of this review is to provide a summary of available literature on the topic of laparoscopic simulators, to assess their contribution to the training of surgeons, and to identify the most effective type of simulation. PubMed database, Web of Science and Cochrane Library were used to search for relevant publications. The keywords "laparoscopy, simulator, surgery, assessment" were used in the search. The search was limited to prospective studies published in the last 5 years in the English language. From a total of 354 studies found, we included in the survey 26 that matched our criteria. Nine studies compared individual simulators to one another. Five studies evaluated "high and low fidelity" (a virtual box simulator) as equally effective (EBM 2a). In three cases the "low fidelity" box simulator was found to be more efficient (EBM 2a3b). Only one study preferred the virtual simulator (VR) (EBM2b).Thirteen studies evaluated the benefits of simulators for practice. Twelve found training on a simulator to be an effective method of preparation (EBM 1b3b). In contrast, one study did not find any difference between the training simulator and traditional preparation (EBM 3b). Nine studies evaluated directly one of the methods of evaluating laparoscopic skills. Three studies evaluated VR simulator as a useful assessment tool. Other studies evaluated as successful the scoring system GOALS-GH. The hand motion analysis model was successful in one case. Most studies were observational (EBM 3b) and only 2 studies were of higher quality (EBM 2b). Simulators are an effective tool for practicing laparoscopic techniques (EBM: 1b). It cannot be determined based on available data which of the simulators is most effective. The virtual simulator, however, still remains the most self-sufficient unit suitable for teaching as well as evaluation of laparoscopic techniques (EBM 2b3b). Further studies are needed to find an effective system and parameters for an objective evaluation of skills. laparoscopy - simulator - surgery assessment.

Roles of bulk viscosity on Rayleigh-Taylor instability: Non-equilibrium thermodynamics due to spatio-temporal pressure fronts

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

Sengupta, Tapan K., E-mail: tksen@iitk.ac.in; Bhole, Ashish; Shruti, K. S.

Direct numerical simulations of Rayleigh-Taylor instability (RTI) between two air masses with a temperature difference of 70 K is presented using compressible Navier-Stokes formulation in a non-equilibrium thermodynamic framework. The two-dimensional flow is studied in an isolated box with non-periodic walls in both vertical and horizontal directions. The non-conducting interface separating the two air masses is impulsively removed at t = 0 (depicting a heaviside function). No external perturbation has been used at the interface to instigate the instability at the onset. Computations have been carried out for rectangular and square cross sections. The formulation is free of Boussinesq approximationmore » commonly used in many Navier-Stokes formulations for RTI. Effect of Stokes’ hypothesis is quantified, by using models from acoustic attenuation measurement for the second coefficient of viscosity from two experiments. Effects of Stokes’ hypothesis on growth of mixing layer and evolution of total entropy for the Rayleigh-Taylor system are reported. The initial rate of growth is observed to be independent of Stokes’ hypothesis and the geometry of the box. Following this stage, growth rate is dependent on the geometry of the box and is sensitive to the model used. As a consequence of compressible formulation, we capture pressure wave-packets with associated reflection and rarefaction from the non-periodic walls. The pattern and frequency of reflections of pressure waves noted specifically at the initial stages are reflected in entropy variation of the system.« less

Numerical investigation of supersonic turbulent boundary layers with high wall temperature

NASA Technical Reports Server (NTRS)

Guo, Y.; Adams, N. A.

1994-01-01

A direct numerical approach has been developed to simulate supersonic turbulent boundary layers. The mean flow quantities are obtained by solving the parabolized Reynolds-averaged Navier-Stokes equations (globally). Fluctuating quantities are computed locally with a temporal direct numerical simulation approach, in which nonparallel effects of boundary layers are partially modeled. Preliminary numerical results obtained at the free-stream Mach numbers 3, 4.5, and 6 with hot-wall conditions are presented. Approximately 5 million grid points are used in all three cases. The numerical results indicate that compressibility effects on turbulent kinetic energy, in terms of dilatational dissipation and pressure-dilatation correlation, are small. Due to the hot-wall conditions the results show significant low Reynolds number effects and large streamwise streaks. Further simulations with a bigger computational box or a cold-wall condition are desirable.

Evaluation of subgrid-scale turbulence models using a fully simulated turbulent flow

NASA Technical Reports Server (NTRS)

Clark, R. A.; Ferziger, J. H.; Reynolds, W. C.

1977-01-01

An exact turbulent flow field was calculated on a three-dimensional grid with 64 points on a side. The flow simulates grid-generated turbulence from wind tunnel experiments. In this simulation, the grid spacing is small enough to include essentially all of the viscous energy dissipation, and the box is large enough to contain the largest eddy in the flow. The method is limited to low-turbulence Reynolds numbers, in our case R sub lambda = 36.6. To complete the calculation using a reasonable amount of computer time with reasonable accuracy, a third-order time-integration scheme was developed which runs at about the same speed as a simple first-order scheme. It obtains this accuracy by saving the velocity field and its first-time derivative at each time step. Fourth-order accurate space-differencing is used.

The MassiveBlack-II simulation: The evolution of haloes and galaxies to z ~ 0

DOE PAGES

Khandai, Nishikanta; Di Matteo, Tiziana; Croft, Rupert; ...

2015-04-24

We investigate the properties and clustering of halos, galaxies and blackholes to z = 0 in the high resolution hydrodynamical simulation MassiveBlack-II (MBII). MBII evolves a ΛCDM cosmology in a cubical comoving volume V box = (100Mpc/h)³. It is the highest resolution simulation of this size which includes a self-consistent model for star formation, black hole accretion and associated feedback. We provide a simulation browser web application which enables interactive search and tagging of the halos, subhalos and their properties and publicly release our galaxy catalogs to the scientific community. Our analysis of the halo mass function in MBII revealsmore » that baryons have strong effects with changes in the halo abundance of 20–35% below the knee of the mass function (M halo 10 13.2 M ⊙ h at z = 0) when compared to dark-matter-only simulations. We provide a fitting function for the halo MF out to redshift z = 11 and discuss its limitations.« less

ASIS v1.0: an adaptive solver for the simulation of atmospheric chemistry

NASA Astrophysics Data System (ADS)

Cariolle, Daniel; Moinat, Philippe; Teyssèdre, Hubert; Giraud, Luc; Josse, Béatrice; Lefèvre, Franck

2017-04-01

This article reports on the development and tests of the adaptive semi-implicit scheme (ASIS) solver for the simulation of atmospheric chemistry. To solve the ordinary differential equation systems associated with the time evolution of the species concentrations, ASIS adopts a one-step linearized implicit scheme with specific treatments of the Jacobian of the chemical fluxes. It conserves mass and has a time-stepping module to control the accuracy of the numerical solution. In idealized box-model simulations, ASIS gives results similar to the higher-order implicit schemes derived from the Rosenbrock's and Gear's methods and requires less computation and run time at the moderate precision required for atmospheric applications. When implemented in the MOCAGE chemical transport model and the Laboratoire de Météorologie Dynamique Mars general circulation model, the ASIS solver performs well and reveals weaknesses and limitations of the original semi-implicit solvers used by these two models. ASIS can be easily adapted to various chemical schemes and further developments are foreseen to increase its computational efficiency, and to include the computation of the concentrations of the species in aqueous-phase in addition to gas-phase chemistry.

Black Box Testing: Experiments with Runway Incursion Advisory Alerting System

NASA Technical Reports Server (NTRS)

Mukkamala, Ravi

2005-01-01

This report summarizes our research findings on the Black box testing of Runway Incursion Advisory Alerting System (RIAAS) and Runway Safety Monitor (RSM) system. Developing automated testing software for such systems has been a problem because of the extensive information that has to be processed. Customized software solutions have been proposed. However, they are time consuming to develop. Here, we present a less expensive, and a more general test platform that is capable of performing complete black box testing. The technique is based on the classification of the anomalies that arise during Monte Carlo simulations. In addition, we also discuss a generalized testing tool (prototype) that we have developed.

No significant impact of Foxf1 siRNA treatment in acute and chronic CCl4 liver injury.

PubMed

Abshagen, Kerstin; Rotberg, Tobias; Genz, Berit; Vollmar, Brigitte

2017-08-01

Chronic liver injury of any etiology is the main trigger of fibrogenic responses and thought to be mediated by hepatic stellate cells. Herein, activating transcription factors like forkhead box f1 are described to stimulate pro-fibrogenic genes in hepatic stellate cells. By using a liver-specific siRNA delivery system (DBTC), we evaluated whether forkhead box f1 siRNA treatment exhibit beneficial effects in murine models of acute and chronic CCl 4 -induced liver injury. Systemic administration of DBTC-forkhead box f1 siRNA in mice was only sufficient to silence forkhead box f1 in acute CCl 4 model, but was not able to attenuate liver injury as measured by liver enzymes and necrotic liver cell area. Therapeutic treatment of mice with DBTC-forkhead box f1 siRNA upon chronic CCl 4 exposition failed to inhibit forkhead box f1 expression and hence lacked to diminish hepatic stellate cells activation or fibrosis development. As a conclusion, DBTC-forkhead box f1 siRNA reduced forkhead box f1 expression in a model of acute but not chronic toxic liver injury and showed no positive effects in either of these mice models. Impact statement As liver fibrosis is a worldwide health problem, antifibrotic therapeutic strategies are urgently needed. Therefore, further developments of new technologies including validation in different experimental models of liver disease are essential. Since activation of hepatic stellate cells is a key event upon liver injury, the activating transcription factor forkhead box f1 (Foxf1) represents a potential target gene. Previously, we evaluated Foxf1 silencing by a liver-specific siRNA delivery system (DBTC), exerting beneficial effects in cholestasis. The present study was designed to confirm the therapeutic potential of Foxf1 siRNA in models of acute and chronic CCl 4 -induced liver injury. DBTC-Foxf1 siRNA was only sufficient to silence Foxf1 in acute CCl 4 model and did not ameliorate liver injury or fibrogenesis. This underlines the significance of the experimental model used. Each model displays specific characteristics in the pathogenic nature, time course and severity of fibrosis and the optimal time point for starting a therapy.

Comparison of Global Cloud Fraction and TOA Radiation Budgets between the NASA GISS AR5 GCM Simulations and CERES-MODIS Observations

NASA Astrophysics Data System (ADS)

Stanfield, R. E.; Dong, X.; Xi, B.; Del Genio, A. D.; Minnis, P.; Doelling, D.; Loeb, N. G.

2011-12-01

To better advise policymakers, it is necessary for climate models to provide credible predictions of future climates. Meeting this goal requires climate models to successfully simulate the present and past climates. The past, current and future Earth climate has been simulated by the NASA GISS ModelE climate model and has been summarized by the Fourth Assessment Report of the Intergovernmental Panel on Climate Change (IPCC, AR4, 2007). New simulations from the updated AR5 version of the NASA GISS ModelE GCM have been released to the public community and will be included in the IPCC AR5 ensemble of simulations. Due to the recent nature of these simulations, however, they have yet to be extensively validated against observations. To evaluate the GISS AR5 simulated global clouds and TOA radiation budgets, we have collected and processed the NASA CERES and MODIS observations during the period 2000-2005. In detail, the 1ox1o resolution monthly averaged SYN1 product has been used with combined observations from both Terra and Aqua satellites, and degraded to a 2ox2.5o grid box to match the GCM spatial resolution. These observations are temporally interpolated and fit to data from geostationary satellites to provide time continuity. The GISS AR5 products were downloaded from the CMIP5 (Coupled Model Intercomparison Project Phase 5) for the IPCC-AR5. Preliminary comparisons between GISS AR5 simulations and CERES-MODIS observations have shown that although their annual and seasonal mean CFs agree within a few percent, there are significant differences in several climatic regions. For example, the modeled CFs have positive biases in the Arctic, Antarctic, Tropics, and Sahara Desert, but negative biases over the southern middle latitudes (30-65 oS). The OLR, albedo and NET radiation comparisons are similar to the CF comparison.

Structured box training improves stability of retraction while multitasking in colorectal surgery simulation.

PubMed

Kobiela, Jarek; Spychalski, Piotr; Łaski, Dariusz; Błażyńska-Spychalska, Agata; Łachiński, Andrzej J; Śledziński, Zbigniew; Hull, Tracy

2018-09-01

Laparoscopic colorectal surgery has an established role. The ability to multitask (use a retraction tool with one hand and navigate a laparoscopic camera with the other) is desired for efficient laparoscopic surgery. Surgical trainees must learn this skill to perform advanced laparoscopic tasks. The aim was to determine whether a box-training protocol improves the stability of retraction while multitasking in colorectal surgery simulation. Fifty-eight medical students were recruited to attend a basic laparoscopic box-training course. Ability to perform steady retraction with and without multitasking was measured initially and at the conclusion of the course. Before training, students demonstrated a decrease in performance while multitasking with a greater maximal exerted force, a greater range of force, and a greater standard deviation for traction and minimal exerted force, range of force and a greater standard deviation for countertraction. Statistically significant improvement (lower maximal exerted force and lower range of force) was observed for traction while multitasking after training. After the training, no statistically significant differences were found when the student performed a single task versus multitasking, both for traction and countertraction. A structured box-training curriculum improved the stability of retraction while multitasking in this colorectal surgery simulation. Although it did not improve stability of retraction as a single task, it did improve stability of retraction while multitasking. After training, this enables the trainee to retract as efficiently while operating the camera as they retract when only focusing on retraction as a single task. Copyright © 2018 Elsevier Inc. All rights reserved.

Numerical Simulation of Multiphase Magnetohydrodynamic Flow and Deformation of Electrolyte-Metal Interface in Aluminum Electrolysis Cells

NASA Astrophysics Data System (ADS)

Hua, Jinsong; Rudshaug, Magne; Droste, Christian; Jorgensen, Robert; Giskeodegard, Nils-Haavard

2018-06-01

A computational fluid dynamics based multiphase magnetohydrodynamic (MHD) flow model for simulating the melt flow and bath-metal interface deformation in realistic aluminum reduction cells is presented. The model accounts for the complex physics of the MHD problem in aluminum reduction cells by coupling two immiscible fluids, electromagnetic field, Lorentz force, flow turbulence, and complex cell geometry with large length scale. Especially, the deformation of bath-metal interface is tracked directly in the simulation, and the condition of constant anode-cathode distance (ACD) is maintained by moving anode bottom dynamically with the deforming bath-metal interface. The metal pad deformation and melt flow predicted by the current model are compared to the predictions using a simplified model where the bath-metal interface is assumed flat. The effects of the induced electric current due to fluid flow and the magnetic field due to the interior cell current on the metal pad deformation and melt flow are investigated. The presented model extends the conventional simplified box model by including detailed cell geometry such as the ledge profile and all channels (side, central, and cross-channels). The simulations show the model sensitivity to different side ledge profiles and the cross-channel width by comparing the predicted melt flow and metal pad heaving. In addition, the model dependencies upon the reduction cell operation conditions such as ACD, current distribution on cathode surface and open/closed channel top, are discussed.

What Is More Important for Fourth-Grade Primary School Students for Transforming Their Potential into Achievement: The Individual or the Environmental Box in Multidimensional Conceptions of Giftedness?

ERIC Educational Resources Information Center

Stoeger, Heidrun; Steinbach, Julia; Obergriesser, Stefanie; Matthes, Benjamin

2014-01-01

Multidimensional models of giftedness specify individual and environmental moderators or catalysts that help transform potential into achievement. However, these models do not state whether the importance of the "individual boxes" and the "environmental boxes" changes during this process. The present study examines whether,…

Analysis of key technologies for virtual instruments metrology

NASA Astrophysics Data System (ADS)

Liu, Guixiong; Xu, Qingui; Gao, Furong; Guan, Qiuju; Fang, Qiang

2008-12-01

Virtual instruments (VIs) require metrological verification when applied as measuring instruments. Owing to the software-centered architecture, metrological evaluation of VIs includes two aspects: measurement functions and software characteristics. Complexity of software imposes difficulties on metrological testing of VIs. Key approaches and technologies for metrology evaluation of virtual instruments are investigated and analyzed in this paper. The principal issue is evaluation of measurement uncertainty. The nature and regularity of measurement uncertainty caused by software and algorithms can be evaluated by modeling, simulation, analysis, testing and statistics with support of powerful computing capability of PC. Another concern is evaluation of software features like correctness, reliability, stability, security and real-time of VIs. Technologies from software engineering, software testing and computer security domain can be used for these purposes. For example, a variety of black-box testing, white-box testing and modeling approaches can be used to evaluate the reliability of modules, components, applications and the whole VI software. The security of a VI can be assessed by methods like vulnerability scanning and penetration analysis. In order to facilitate metrology institutions to perform metrological verification of VIs efficiently, an automatic metrological tool for the above validation is essential. Based on technologies of numerical simulation, software testing and system benchmarking, a framework for the automatic tool is proposed in this paper. Investigation on implementation of existing automatic tools that perform calculation of measurement uncertainty, software testing and security assessment demonstrates the feasibility of the automatic framework advanced.

Bayesian spatial transformation models with applications in neuroimaging data

PubMed Central

Miranda, Michelle F.; Zhu, Hongtu; Ibrahim, Joseph G.

2013-01-01

Summary The aim of this paper is to develop a class of spatial transformation models (STM) to spatially model the varying association between imaging measures in a three-dimensional (3D) volume (or 2D surface) and a set of covariates. Our STMs include a varying Box-Cox transformation model for dealing with the issue of non-Gaussian distributed imaging data and a Gaussian Markov Random Field model for incorporating spatial smoothness of the imaging data. Posterior computation proceeds via an efficient Markov chain Monte Carlo algorithm. Simulations and real data analysis demonstrate that the STM significantly outperforms the voxel-wise linear model with Gaussian noise in recovering meaningful geometric patterns. Our STM is able to reveal important brain regions with morphological changes in children with attention deficit hyperactivity disorder. PMID:24128143

Description and Evaluation of IAP-AACM: A Global-regional Aerosol Chemistry Model for the Earth System Model CAS-ESM

NASA Astrophysics Data System (ADS)

Wei, Y.; Chen, X.

2017-12-01

We present a first description and evaluation of the IAP Atmospheric Aerosol Chemistry Model (IAP-AACM) which has been integrated into the earth system model CAS-ESM. In this way it is possible to research into interaction of clouds and aerosol by its two-way coupling with the IAP Atmospheric General Circulation Model (IAP-AGCM). The model has a nested global-regional grid based on the Global Environmental Atmospheric Transport Model (GEATM) and the Nested Air Quality Prediction Modeling System (NAQPMS). The AACM provides two optional gas chemistry schemes, the CBM-Z gas chemistry as well as a sulfur oxidize box designed specifically for the CAS-ESM. Now the model driven by AGCM has been applied to a 1-year simulation of tropospheric chemistry both on global and regional scales for 2014, and been evaluated against various observation datasets, including aerosol precursor gas concentration, aerosol mass and number concentrations. Furthermore, global budgets in AACM are compared with other global aerosol models. Generally, the AACM simulations are within the range of other global aerosol model predictions, and the model has a reasonable agreement with observations of gases and particles concentration both on global and regional scales.

The suppression effect of a periodic surface with semicircular grooves on the high power microwave long pill-box window multipactor phenomenon

NASA Astrophysics Data System (ADS)

Zhang, Xue; Wang, Yong; Fan, Junjie; Zhong, Yong; Zhang, Rui

2014-09-01

To improve the transmitting power in an S-band klystron, a long pill-box window that has a disk with grooves with a semicircular cross section is theoretically investigated and simulated. A Monte-Carlo algorithm is used to track the secondary electron trajectories and analyze the multipactor scenario in the long pill-box window and on the grooved surface. Extending the height of the long-box window can decrease the normal electric field on the surface of the window disk, but the single surface multipactor still exists. It is confirmed that the window disk with periodic semicircular grooves can explicitly suppress the multipactor and predominantly depresses the local field enhancement and the bottom continuous multipactor. The difference between semicircular and sharp boundary grooves is clarified numerically and analytically.

What boxing-related stimuli reveal about response behaviour.

PubMed

Ottoboni, Giovanni; Russo, Gabriele; Tessari, Alessia

2015-01-01

When two athletes meet inside the ropes of the boxing ring to fight, their cognitive systems have to respond as quickly as possible to a manifold of stimuli to assure victory. In the present work, we studied the pre-attentive mechanisms, which form the basis of an athlete's ability in reacting to an opponent's punches. Expert boxers, beginner boxers and people with no experience of boxing performed a Simon-like task where they judged the colour of the boxing gloves worn by athletes in attack postures by pressing two lateralised keys. Although participants were not instructed to pay attention to the direction of the punches, beginner boxers' responses resembled a defence-related pattern, expert boxers' resembled counterattacks, whereas non-athletes' responses were not influenced by the unrelated task information. Results are discussed in the light of an expertise-related action simulation account.

Hydrology and numerical simulation of groundwater flow and streamflow depletion by well withdrawals in the Malad-Lower Bear River Area, Box Elder County, Utah

USGS Publications Warehouse

Stolp, Bernard J.; Brooks, Lynette E.; Solder, John

2017-03-28

The Malad-Lower Bear River study area in Box Elder County, Utah, consists of a valley bounded by mountain ranges and is mostly agricultural or undeveloped. The Bear and Malad Rivers enter the study area with a combined average flow of about 1,100,000 acre-feet per year (acre-ft/yr), and this surface water dominates the hydrology. Groundwater occurs in consolidated rock and basin fill. Groundwater recharge occurs from precipitation in the mountains and moves through consolidated rock to the basin fill. Recharge occurs in the valley from irrigation. Groundwater discharge occurs to rivers, springs and diffuse seepage areas, evapotranspiration, field drains, and wells. Groundwater, including springs, is a source for municipal and domestic water supply. Although withdrawal from wells is a small component of the groundwater budget, there is concern that additional groundwater development will reduce the amount of flow in the Malad River. Historical records of surface-water diversions, land use, and groundwater levels indicate relatively stable hydrologic conditions from the 1960s to the 2010s, and that current groundwater development has had little effect on the groundwater system. Average annual recharge to and discharge from the groundwater flow system are estimated to be 164,000 and 228,000 acre-ft/yr, respectively. The imbalance between recharge and discharge represents uncertainties resulting from system complexities, and the possibility of groundwater inflow from surrounding basins.This study reassesses the hydrologic system, refines the groundwater budget, and creates a numerical groundwater flow model that is used to analyze the effects of groundwater withdrawals on surface water. The model uses the detailed catalog of locations and amounts of groundwater recharge and discharge defined during this study. Calibrating the model to adequately simulate recharge, discharge, and groundwater levels results in simulated aquifer properties that can be used to understand the relation between pumping and the reduction in discharge to rivers, springs, natural vegetation, and field drains. Simulations run by the calibrated model were used to calculate the reduction of groundwater discharge to the Malad River (stream depletion) in response to a well withdrawal of 360 acre-ft/yr at any location within the study area. Modeling results show that streamflow depletion in the Malad River depends on both depth and location of groundwater withdrawal, and varies from less than 1 percent to 96 percent of the well withdrawal. The relation between simulated withdrawal and reductions in Malad River streamflow, Bear River streamflow, and spring discharge are shown on capture maps.

A photosynthesis-based two-leaf canopy stomatal ...

EPA Pesticide Factsheets

A coupled photosynthesis-stomatal conductance model with single-layer sunlit and shaded leaf canopy scaling is implemented and evaluated in a diagnostic box model with the Pleim-Xiu land surface model (PX LSM) and ozone deposition model components taken directly from the meteorology and air quality modeling system—WRF/CMAQ (Weather Research and Forecast model and Community Multiscale Air Quality model). The photosynthesis-based model for PX LSM (PX PSN) is evaluated at a FLUXNET site for implementation against different parameterizations and the current PX LSM approach with a simple Jarvis function (PX Jarvis). Latent heat flux (LH) from PX PSN is further evaluated at five FLUXNET sites with different vegetation types and landscape characteristics. Simulated ozone deposition and flux from PX PSN are evaluated at one of the sites with ozone flux measurements. Overall, the PX PSN simulates LH as well as the PX Jarvis approach. The PX PSN, however, shows distinct advantages over the PX Jarvis approach for grassland that likely result from its treatment of C3 and C4 plants for CO2 assimilation. Simulations using Moderate Resolution Imaging Spectroradiometer (MODIS) leaf area index (LAI) rather than LAI measured at each site assess how the model would perform with grid averaged data used in WRF/CMAQ. MODIS LAI estimates degrade model performance at all sites but one site having exceptionally old and tall trees. Ozone deposition velocity and ozone flux along with LH

Using box models to quantify zonal distributions and emissions of halocarbons in the background atmosphere.

NASA Astrophysics Data System (ADS)

Elkins, J. W.; Nance, J. D.; Dutton, G. S.; Montzka, S. A.; Hall, B. D.; Miller, B.; Butler, J. H.; Mondeel, D. J.; Siso, C.; Moore, F. L.; Hintsa, E. J.; Wofsy, S. C.; Rigby, M. L.

2015-12-01

The Halocarbons and other Atmospheric Trace Species (HATS) of NOAA's Global Monitoring Division started measurements of the major chlorofluorocarbons and nitrous oxide in 1977 from flask samples collected at five remote sites around the world. Our program has expanded to over 40 compounds at twelve sites, which includes six in situ instruments and twelve flask sites. The Montreal Protocol for Substances that Deplete the Ozone Layer and its subsequent amendments has helped to decrease the concentrations of many of the ozone depleting compounds in the atmosphere. Our goal is to provide zonal emission estimates for these trace gases from multi-box models and their estimated atmospheric lifetimes in this presentation and make the emission values available on our web site. We plan to use our airborne measurements to calibrate the exchange times between the boxes for 5-box and 12-box models using sulfur hexafluoride where emissions are better understood.

High-Fidelity Computational Aerodynamics of the Elytron 4S UAV

NASA Technical Reports Server (NTRS)

Ventura Diaz, Patricia; Yoon, Seokkwan; Theodore, Colin R.

2018-01-01

High-fidelity Computational Fluid Dynamics (CFD) have been carried out for the Elytron 4S Unmanned Aerial Vehicle (UAV), also known as the converticopter "proto12". It is the scaled wind tunnel model of the Elytron 4S, an Urban Air Mobility (UAM) concept, a tilt-wing, box-wing rotorcraft capable of Vertical Take-Off and Landing (VTOL). The three-dimensional unsteady Navier-Stokes equations are solved on overset grids employing high-order accurate schemes, dual-time stepping, and a hybrid turbulence model using NASA's CFD code OVERFLOW. The Elytron 4S UAV has been simulated in airplane mode and in helicopter mode.

A photosynthesis-based two-leaf canopy stomatal conductance model for meteorology and air quality modeling with WRF/CMAQ PX LSM

NASA Astrophysics Data System (ADS)

Ran, Limei; Pleim, Jonathan; Song, Conghe; Band, Larry; Walker, John T.; Binkowski, Francis S.

2017-02-01

A coupled photosynthesis-stomatal conductance model with single-layer sunlit and shaded leaf canopy scaling is implemented and evaluated in a diagnostic box model with the Pleim-Xiu land surface model (PX LSM) and ozone deposition model components taken directly from the meteorology and air quality modeling system - WRF/CMAQ (Weather Research and Forecast model and Community Multiscale Air Quality model). The photosynthesis-based model for PX LSM (PX PSN) is evaluated at a FLUXNET site for implementation against different parameterizations and the current PX LSM approach with a simple Jarvis function (PX Jarvis). Latent heat flux (LH) from PX PSN is further evaluated at five FLUXNET sites with different vegetation types and landscape characteristics. Simulated ozone deposition and flux from PX PSN are evaluated at one of the sites with ozone flux measurements. Overall, the PX PSN simulates LH as well as the PX Jarvis approach. The PX PSN, however, shows distinct advantages over the PX Jarvis approach for grassland that likely result from its treatment of C3 and C4 plants for CO2 assimilation. Simulations using Moderate Resolution Imaging Spectroradiometer (MODIS) leaf area index (LAI) rather than LAI measured at each site assess how the model would perform with grid averaged data used in WRF/CMAQ. MODIS LAI estimates degrade model performance at all sites but one site having exceptionally old and tall trees. Ozone deposition velocity and ozone flux along with LH are simulated especially well by the PX PSN compared to significant overestimation by the PX Jarvis for a grassland site.

Coupling Field Theory with Mesoscopic Dynamical Simulations of Multicomponent Lipid Bilayers

PubMed Central

McWhirter, J. Liam; Ayton, Gary; Voth, Gregory A.

2004-01-01

A method for simulating a two-component lipid bilayer membrane in the mesoscopic regime is presented. The membrane is modeled as an elastic network of bonded points; the spring constants of these bonds are parameterized by the microscopic bulk modulus estimated from earlier atomistic nonequilibrium molecular dynamics simulations for several bilayer mixtures of DMPC and cholesterol. The modulus depends on the composition of a point in the elastic membrane model. The dynamics of the composition field is governed by the Cahn-Hilliard equation where a free energy functional models the coupling between the composition and curvature fields. The strength of the bonds in the elastic network are then modulated noting local changes in the composition and using a fit to the nonequilibrium molecular dynamics simulation data. Estimates for the magnitude and sign of the coupling parameter in the free energy model are made treating the bending modulus as a function of composition. A procedure for assigning the remaining parameters in the free energy model is also outlined. It is found that the square of the mean curvature averaged over the entire simulation box is enhanced if the strength of the bonds in the elastic network are modulated in response to local changes in the composition field. We suggest that this simulation method could also be used to determine if phase coexistence affects the stress response of the membrane to uniform dilations in area. This response, measured in the mesoscopic regime, is already known to be conditioned or renormalized by thermal undulations. PMID:15347594

Variation of the NMVOC speciation in the solvent sector and the sensitivity of modelled tropospheric ozone

NASA Astrophysics Data System (ADS)

von Schneidemesser, E.; Coates, J.; Denier van der Gon, H. A. C.; Visschedijk, A. J. H.; Butler, T. M.

2016-06-01

Non-methane volatile organic compounds (NMVOCs) are detrimental to human health owing to the toxicity of many of the NMVOC species, as well as their role in the formation of secondary air pollutants such as tropospheric ozone (O3) and secondary organic aerosol. The speciation and amount of NMVOCs emitted into the troposphere are represented in emission inventories (EIs) for input to chemical transport models that predict air pollutant levels. Much of the information in EIs pertaining to speciation of NMVOCs is likely outdated, but before taking on the task of providing an up-to-date and highly speciated EI, a better understanding of the sensitivity of models to the change in NMVOC input would be highly beneficial. According to the EIs, the solvent sector is the most important sector for NMVOC emissions. Here, the sensitivity of modelled tropospheric O3 to NMVOC emission inventory speciation was investigated by comparing the maximum potential difference in O3 produced using a variety of reported solvent sector EI speciations in an idealized study using a box model. The sensitivity was tested using three chemical mechanisms that describe O3 production chemistry, typically employed for different types of modelling scales - point (MCM v3.2), regional (RADM2), and global (MOZART-4). In the box model simulations, a maximum difference of 15 ppbv (ca. 22% of the mean O3 mixing ratio of 69 ppbv) between the different EI speciations of the solvent sector was calculated. In comparison, for the same EI speciation, but comparing the three different mechanisms, a maximum difference of 6.7 ppbv was observed. Relationships were found between the relative contribution of NMVOC compound classes (alkanes and oxygenated species) in the speciations to the amount of Ox produced in the box model. These results indicate that modelled tropospheric O3 is sensitive to the speciation of NMVOCs as specified by emission inventories, suggesting that detailed updates to the EI speciation information would be warranted. Furthermore, modelled tropospheric O3 was also sensitive to the choice of chemical mechanism and further evaluation of both of these sensitivities in more realistic chemical-transport models is needed.

Risk Reduction and Training using Simulation Based Tools - 12180

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

Hall, Irin P.

2012-07-01

Process Modeling and Simulation (M and S) has been used for many years in manufacturing and similar domains, as part of an industrial engineer's tool box. Traditionally, however, this technique has been employed in small, isolated projects where models were created from scratch, often making it time and cost prohibitive. Newport News Shipbuilding (NNS) has recognized the value of this predictive technique and what it offers in terms of risk reduction, cost avoidance and on-schedule performance of highly complex work. To facilitate implementation, NNS has been maturing a process and the software to rapidly deploy and reuse M and Smore » based decision support tools in a variety of environments. Some examples of successful applications by NNS of this technique in the nuclear domain are a reactor refueling simulation based tool, a fuel handling facility simulation based tool and a tool for dynamic radiation exposure tracking. The next generation of M and S applications include expanding simulation based tools into immersive and interactive training. The applications discussed here take a tool box approach to creating simulation based decision support tools for maximum utility and return on investment. This approach involves creating a collection of simulation tools that can be used individually or integrated together for a larger application. The refueling simulation integrates with the fuel handling facility simulation to understand every aspect and dependency of the fuel handling evolutions. This approach translates nicely to other complex domains where real system experimentation is not feasible, such as nuclear fuel lifecycle and waste management. Similar concepts can also be applied to different types of simulation techniques. For example, a process simulation of liquid waste operations may be useful to streamline and plan operations, while a chemical model of the liquid waste composition is an important tool for making decisions with respect to waste disposition. Integrating these tools into a larger virtual system provides a tool for making larger strategic decisions. The key to integrating and creating these virtual environments is the software and the process used to build them. Although important steps in the direction of using simulation based tools for nuclear domain, the applications described here represent only a small cross section of possible benefits. The next generation of applications will, likely, focus on situational awareness and adaptive planning. Situational awareness refers to the ability to visualize in real time the state of operations. Some useful tools in this area are Geographic Information Systems (GIS), which help monitor and analyze geographically referenced information. Combined with such situational awareness capability, simulation tools can serve as the platform for adaptive planning tools. These are the tools that allow the decision maker to react to the changing environment in real time by synthesizing massive amounts of data into easily understood information. For the nuclear domains, this may mean creation of Virtual Nuclear Systems, from Virtual Waste Processing Plants to Virtual Nuclear Reactors. (authors)« less

Lack of transfer of skills after virtual reality simulator training with haptic feedback.

PubMed

Våpenstad, Cecilie; Hofstad, Erlend Fagertun; Bø, Lars Eirik; Kuhry, Esther; Johnsen, Gjermund; Mårvik, Ronald; Langø, Thomas; Hernes, Toril Nagelhus

2017-12-01

Virtual reality (VR) simulators enrich surgical training and offer training possibilities outside of the operating room (OR). In this study, we created a criterion-based training program on a VR simulator with haptic feedback and tested it by comparing the performances of a simulator group against a control group. Medical students with no experience in laparoscopy were randomly assigned to a simulator group or a control group. In the simulator group, the candidates trained until they reached predefined criteria on the LapSim ® VR simulator (Surgical Science AB, Göteborg, Sweden) with haptic feedback (Xitact TM IHP, Mentice AB, Göteborg, Sweden). All candidates performed a cholecystectomy on a porcine organ model in a box trainer (the clinical setting). The performances were video rated by two surgeons blinded to subject training status. In total, 30 students performed the cholecystectomy and had their videos rated (N = 16 simulator group, N = 14 control group). The control group achieved better video rating scores than the simulator group (p < .05). The criterion-based training program did not transfer skills to the clinical setting. Poor mechanical performance of the simulated haptic feedback is believed to have resulted in a negative training effect.

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

Bose, Sownak; Li, Baojiu; He, Jian-hua

We describe and demonstrate the potential of a new and very efficient method for simulating certain classes of modified gravity theories, such as the widely studied f ( R ) gravity models. High resolution simulations for such models are currently very slow due to the highly nonlinear partial differential equation that needs to be solved exactly to predict the modified gravitational force. This nonlinearity is partly inherent, but is also exacerbated by the specific numerical algorithm used, which employs a variable redefinition to prevent numerical instabilities. The standard Newton-Gauss-Seidel iterative method used to tackle this problem has a poor convergencemore » rate. Our new method not only avoids this, but also allows the discretised equation to be written in a form that is analytically solvable. We show that this new method greatly improves the performance and efficiency of f ( R ) simulations. For example, a test simulation with 512{sup 3} particles in a box of size 512 Mpc/ h is now 5 times faster than before, while a Millennium-resolution simulation for f ( R ) gravity is estimated to be more than 20 times faster than with the old method. Our new implementation will be particularly useful for running very high resolution, large-sized simulations which, to date, are only possible for the standard model, and also makes it feasible to run large numbers of lower resolution simulations for covariance analyses. We hope that the method will bring us to a new era for precision cosmological tests of gravity.« less

A comparison between skeleton and bounding box models for falling direction recognition

NASA Astrophysics Data System (ADS)

Narupiyakul, Lalita; Srisrisawang, Nitikorn

2017-12-01

Falling is an injury that can lead to a serious medical condition in every range of the age of people. However, in the case of elderly, the risk of serious injury is much higher. Due to the fact that one way of preventing serious injury is to treat the fallen person as soon as possible, several works attempted to implement different algorithms to recognize the fall. Our work compares the performance of two models based on features extraction: (i) Body joint data (Skeleton Data) which are the joint's positions in 3 axes and (ii) Bounding box (Box-size Data) covering all body joints. Machine learning algorithms that were chosen are Decision Tree (DT), Naïve Bayes (NB), K-nearest neighbors (KNN), Linear discriminant analysis (LDA), Voting Classification (VC), and Gradient boosting (GB). The results illustrate that the models trained with Skeleton data are performed far better than those trained with Box-size data (with an average accuracy of 94-81% and 80-75%, respectively). KNN shows the best performance in both Body joint model and Bounding box model. In conclusion, KNN with Body joint model performs the best among the others.

Unifying Model-Based and Reactive Programming within a Model-Based Executive

NASA Technical Reports Server (NTRS)

Williams, Brian C.; Gupta, Vineet; Norvig, Peter (Technical Monitor)

1999-01-01

Real-time, model-based, deduction has recently emerged as a vital component in AI's tool box for developing highly autonomous reactive systems. Yet one of the current hurdles towards developing model-based reactive systems is the number of methods simultaneously employed, and their corresponding melange of programming and modeling languages. This paper offers an important step towards unification. We introduce RMPL, a rich modeling language that combines probabilistic, constraint-based modeling with reactive programming constructs, while offering a simple semantics in terms of hidden state Markov processes. We introduce probabilistic, hierarchical constraint automata (PHCA), which allow Markov processes to be expressed in a compact representation that preserves the modularity of RMPL programs. Finally, a model-based executive, called Reactive Burton is described that exploits this compact encoding to perform efficIent simulation, belief state update and control sequence generation.

Inferring the unobserved chemical state of the atmosphere: idealized data assimilation experiments

NASA Astrophysics Data System (ADS)

Knote, C. J.; Barré, J.; Eckl, M.; Hornbrook, R. S.; Wiedinmyer, C.; Emmons, L. K.; Orlando, J. J.; Tyndall, G. S.; Arellano, A. F.

2015-12-01

Chemical data assimilation in numerical models of the atmosphere is a venture into uncharted territory, into a world populated by a vast zoo of chemical compounds with strongly non-linear interactions. Commonly assimilated observations exist for only a selected few of those key gas phase compounds (CO, O3, NO2), and assimilating those in models assuming linearity begs the question of: To what extent we can infer the remainder to create a new state of the atmosphere that is chemically sound and optimal? In our work we present the first systematic investigation of sensitivities that exist between chemical compounds under varying ambient conditions in order to inform scientists on the potential pitfalls when assimilating single/few chemical compounds into complex 3D chemistry transport models. In order to do this, we developed a box-modeling tool (BOXMOX) based on the Kinetic PreProcessor (KPP, http://people.cs.vt.edu/~asandu/Software/Kpp/) in which we can conduct simulations with a suite of 'mechanisms', sets of differential equations describing atmospheric photochemistry. The box modeling approach allows us to sample a large variety of atmospheric conditions (urban, rural, biogenically dominated, biomass burning plumes) to capture the range of chemical conditions that typically exist in the atmosphere. Included in our suite are 'lumped' mechanisms typically used in regional and global chemistry transport models (MOZART, RACM, RADM2, SAPRC99, CB05, CBMZ) as well as the Master Chemical Mechanism (MCM, U. Leeds). We will use an Observing System Simulation Experiment approach with the MCM prediction as 'nature' or 'true' state, assimilating idealized synthetic observations (from MCM) into the different ‚lumped' mechanisms under various environments. Two approaches to estimate the sensitivity of the chemical system will be compared: 1) adjoint: using Jacobians computed by KPP and 2) ensemble: by perturbing emissions, temperature, photolysis rates, entrainment, etc., in order to create gain matrices to infer the unobserved part of the photochemical system.

Finite-volume and partial quenching effects in the magnetic polarizability of the neutron

NASA Astrophysics Data System (ADS)

Hall, J. M. M.; Leinweber, D. B.; Young, R. D.

2014-03-01

There has been much progress in the experimental measurement of the electric and magnetic polarizabilities of the nucleon. Similarly, lattice QCD simulations have recently produced dynamical QCD results for the magnetic polarizability of the neutron approaching the chiral regime. In order to compare the lattice simulations with experiment, calculation of partial quenching and finite-volume effects is required prior to an extrapolation in quark mass to the physical point. These dependencies are described using chiral effective field theory. Corrections to the partial quenching effects associated with the sea-quark-loop electric charges are estimated by modeling corrections to the pion cloud. These are compared to the uncorrected lattice results. In addition, the behavior of the finite-volume corrections as a function of pion mass is explored. Box sizes of approximately 7 fm are required to achieve a result within 5% of the infinite-volume result at the physical pion mass. A variety of extrapolations are shown at different box sizes, providing a benchmark to guide future lattice QCD calculations of the magnetic polarizabilities. A relatively precise value for the physical magnetic polarizability of the neutron is presented, βn=1.93(11)stat(11)sys×10-4 fm3, which is in agreement with current experimental results.

Multigrid contact detection method

NASA Astrophysics Data System (ADS)

He, Kejing; Dong, Shoubin; Zhou, Zhaoyao

2007-03-01

Contact detection is a general problem of many physical simulations. This work presents a O(N) multigrid method for general contact detection problems (MGCD). The multigrid idea is integrated with contact detection problems. Both the time complexity and memory consumption of the MGCD are O(N) . Unlike other methods, whose efficiencies are influenced strongly by the object size distribution, the performance of MGCD is insensitive to the object size distribution. We compare the MGCD with the no binary search (NBS) method and the multilevel boxing method in three dimensions for both time complexity and memory consumption. For objects with similar size, the MGCD is as good as the NBS method, both of which outperform the multilevel boxing method regarding memory consumption. For objects with diverse size, the MGCD outperform both the NBS method and the multilevel boxing method. We use the MGCD to solve the contact detection problem for a granular simulation system based on the discrete element method. From this granular simulation, we get the density property of monosize packing and binary packing with size ratio equal to 10. The packing density for monosize particles is 0.636. For binary packing with size ratio equal to 10, when the number of small particles is 300 times as the number of big particles, the maximal packing density 0.824 is achieved.

Occupancy modeling reveals territory-level effects of nest boxes on the presence, colonization, and persistence of a declining raptor in a fruit-growing region.

PubMed

Shave, Megan E; Lindell, Catherine A

2017-01-01

Nest boxes for predators in agricultural regions are an easily implemented tool to improve local habitat quality with potential benefits for both conservation and agriculture. The potential for nest boxes to increase raptor populations in agricultural regions is of particular interest given their positions as top predators. This study examined the effects of cherry orchard nest boxes on the local breeding population of a declining species, the American Kestrel (Falco sparverius), in a fruit-growing region of Michigan. During the 2013-2016 study, we added a total of 23 new nest boxes in addition to 24 intact boxes installed previously; kestrels used up to 100% of our new boxes each season. We conducted temporally-replicated surveys along four roadside transects divided into 1.6 km × 500 m sites. We developed a multi-season occupancy model under a Bayesian framework and found that nest boxes had strong positive effects on first-year site occupancy, site colonization, and site persistence probabilities. The estimated number of occupied sites increased between 2013 and 2016, which correlated with the increase in number of sites with boxes. Kestrel detections decreased with survey date but were not affected by time of day or activity at the boxes themselves. These results indicate that nest boxes determined the presence of kestrels at our study sites and support the conclusion that the local kestrel population is likely limited by nest site availability. Furthermore, our results are highly relevant to the farmers on whose properties the boxes were installed, for we can conclude that installing a nest box in an orchard resulted in a high probability of kestrels occupying that orchard or the areas adjacent to it.

Ab initio modeling of steady-state and time-dependent charge transport in hole-only α-NPD devices

NASA Astrophysics Data System (ADS)

Liu, Feilong; Massé, Andrea; Friederich, Pascal; Symalla, Franz; Nitsche, Robert; Wenzel, Wolfgang; Coehoorn, Reinder; Bobbert, Peter A.

2016-12-01

We present an ab initio modeling study of steady-state and time-dependent charge transport in hole-only devices of the amorphous molecular semiconductor α-NPD [N ,N'-Di(1 -naphthyl)-N ,N'-diphenyl-(1 ,1'-biphenyl)-4 ,4'-diamine] . The study is based on the microscopic information obtained from atomistic simulations of the morphology and density functional theory calculations of the molecular hole energies, reorganization energies, and transfer integrals. Using stochastic approaches, the microscopic information obtained in simulation boxes at a length scale of ˜10 nm is expanded and employed in one-dimensional (1D) and three-dimensional (3D) master-equation modeling of the charge transport at the device scale of ˜100 nm. Without any fit parameter, predicted current density-voltage and impedance spectroscopy data obtained with the 3D modeling are in very good agreement with measured data on devices with different α-NPD layer thicknesses in a wide range of temperatures, bias voltages, and frequencies. Similarly good results are obtained with the computationally much more efficient 1D modeling after optimizing a hopping prefactor.

Dynamics and Solubility of He and CO 2 in Brine

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

Ho, Tuan Anh; Tenney, Craig M.

2016-09-01

Molecular dynamics simulation was implemented using LAMMPS simulation package (1) to study the diffusivity of He 3 and CO 2 in NaCl aqueous solution. To simulate at infinite dilute gas concentration, we placed one He 3 or CO 2 molecule in an initial simulation box of 24x24x33Å 3 containing 512 water molecules and a certain number of NaCl molecules depending on the concentration. Initial configuration was set up by placing water, NaCl, and gas molecules into different regions in the simulation box. Calculating diffusion coefficient for one He or CO 2 molecule consistently yields poor results. To overcome this, formore » each simulation at specific conditions (i.e., temperature, pressure, and NaCl concentration), we conducted 50 simulations initiated from 50 different configurations. These configurations are obtained by performing the simulation starting from the initial configuration mentioned above in the NVE ensemble (i.e., constant number of particles, volume, and energy). for 100,000 time steps and collecting one configuration every 2,000 times step. The output temperature of this simulation is about 500K. The collected configurations were then equilibrated for 2ns in the NPT ensemble (i.e., constant number of particles, pressure, and temperature) followed by 9ns simulations in the NVT ensemble (i.e., constant number of particles, volume, and temperature). The time step is 1fs for all simulations.« less

Construction of an evidence-based, graduated training curriculum for D-box, a webcam-based laparoscopic basic skills trainer box.

PubMed

Debes, Anders J; Aggarwal, Rajesh; Balasundaram, Indran; Jacobsen, Morten B J

2012-06-01

Surgical training programs are now including simulators as training tools for teaching laparoscopic surgery. The aim of this study was to develop a standardized, graduated, and evidence-based curriculum for the newly developed D-box (D-box Medical, Lier, Norway) for training basic laparoscopic skills. Eighteen interns with no laparoscopic experience completed a training program on the D-box consisting of 8 sessions of 5 tasks with assessment on a sixth task. Performance was measured by the use of 3-dimensional electromagnetic tracking of hand movements, path length, and time taken. Ten experienced surgeons (>100 laparoscopic surgeries, median 250) were recruited for establishing benchmark criteria. Significant learning curves were obtained for all construct valid parameters for tasks 4 (P < .005) and 5 (P < .005) and reached plateau levels between the fifth and sixth session. Within the 8 sessions of this study, between 50% and 89% of the interns reached benchmark criteria on tasks 4 and 5. Benchmark criteria and an evidence-based curriculum have been developed for the D-box. The curriculum is aimed at training and assessing surgical novices in basic laparoscopic skills. Copyright © 2012 Elsevier Inc. All rights reserved.

Non-local boxes and their implementation in Minecraft

NASA Astrophysics Data System (ADS)

Simnacher, Timo Yannick

PR-boxes are binary devices connecting two remote parties satisfying x AND y = a + b mod 2, where x and y denote the binary inputs and a and b are the respective outcomes without signaling. These devices are named after their inventors Sandu Popescu and Daniel Rohrlich and saturate the Clauser-Horne-Shimony-Holt (CHSH) inequality. This Bell-like inequality bounds the correlation that can exist between two remote, non-signaling, classical systems described by local hidden variable theories. Experiments have now convincingly shown that quantum entanglement cannot be explained by local hidden variable theories. Furthermore, the CHSH inequality provides a method to distinguish quantum systems from super-quantum correlations. The correlation between the outputs of the PR-box goes beyond any quantum entanglement. Though PR-boxes would have impressive consequences, as far as we know they are not physically realizable. However, by introducing PR-boxes to Minecraft as part of the redstone system, which simulates the electrical components for binary computing, we can experience the consequences of super-quantum correlations. For instance, Wim van Dam proved that two parties can use a sufficient number of PR-boxes to compute any Boolean function f(x,y) with only one bit of communication.

Sensitivity of Polar Stratospheric Ozone Loss to Uncertainties in Chemical Reaction Kinetics

NASA Technical Reports Server (NTRS)

Kawa, S. Randolph; Stolarski, Richard S.; Douglass, Anne R.; Newman, Paul A.

2008-01-01

Several recent observational and laboratory studies of processes involved in polar stratospheric ozone loss have prompted a reexamination of aspect of out understanding for this key indicator of global change. To a large extent, our confidence in understanding and projecting changes in polar and global ozone is based on our ability to to simulate these process in numerical models of chemistry and transport. These models depend on laboratory-measured kinetic reaction rates and photlysis cross section to simulate molecular interactions. In this study we use a simple box-model scenario for Antarctic ozone to estimate the uncertainty in loss attributable to known reaction kinetic uncertainties. Following the method of earlier work, rates and uncertainties from the latest laboratory evaluation are applied in random combinations. We determine the key reaction and rates contributing the largest potential errors and compare the results to observations to evaluate which combinations are consistent with atmospheric data. Implications for our theoretical and practical understanding of polar ozone loss will be assessed.

Nano-Indentation of Aluminium Reinforced Metallic Glass Composites: A Molecular Dynamics Study

NASA Astrophysics Data System (ADS)

Yadav, D.; Gupta, P.; Yedla, N.

2018-03-01

Molecular dynamics (MD) simulations are performed for nanoindentation on metal (Al)-metallic glass (Cu50Zr50) reinforced composites to investigate the mechanical properties and the effects of volume percentage on behavior of the load-displacement curves. The interaction among Al-Cu-Zr is modelled using a EAM (Embedded Atom Method) potential. Simulation box size of 100 Å (x) × 100 Å (y) × 100 Å (z) is modelled for investigating the properties of the sintered models by altering the volume percentage on the scale of 5%-20%. Nanoindentation is done along y-direction with a spherical diamond indenter at temperature of 300 K with constant indentation speed of 100 m/s. NVT ensemble is used with a timestep of 0.002 ps. Investigations on the effect of volume percentage show that as volume percentage of Metallic Glass (MG) increases, the corresponding Load required to penetrate inside the sample also increases. As a result of this Hardness also increase as volume percentage varies from 5% to 20%.

Stream-water storage in the ocean using an impermeable membrane

NASA Astrophysics Data System (ADS)

Murabayashi, E. T.; Asuka, M.; Yamada, R.; Fok, Y. S.; Gee, H. K.

1983-05-01

The conceptual feasibility of storing fresh water in the ocean was investigated using a plastic membrane as the reservoir liner. In the initial phase, two physical hydraulic models were constructed to test the concept. The first was a water-filled, glass-sided box to observe the movement and reaction of the membrane to various simulated effects of currents, waves, and sediment deposition. The second was a 1:400-scale model (6.7 x 6.1 m) of West Loch, Pearl Harbor (a potential field application site), with 1:24 vertical exaggeration for similitude. The curtain method was used because it can enclose a large water body. The effect of wind, waves, tides, and currents on the curtain were simulated and the reactions observed. Although modeling is a useful tool for investigating initial concepts, its direct field application is limited because of scaling. Curtains, floating reservoirs, and bags were constructed of polyethylene sheets and deployed. All worked well after modifications were made following initial testing.

Optimization of black-box models with uncertain climatic inputs—Application to sunflower ideotype design

PubMed Central

Picheny, Victor; Trépos, Ronan; Casadebaig, Pierre

2017-01-01

Accounting for the interannual climatic variations is a well-known issue for simulation-based studies of environmental systems. It often requires intensive sampling (e.g., averaging the simulation outputs over many climatic series), which hinders many sequential processes, in particular optimization algorithms. We propose here an approach based on a subset selection in a large basis of climatic series, using an ad-hoc similarity function and clustering. A non-parametric reconstruction technique is introduced to estimate accurately the distribution of the output of interest using only the subset sampling. The proposed strategy is non-intrusive and generic (i.e. transposable to most models with climatic data inputs), and can be combined to most “off-the-shelf” optimization solvers. We apply our approach to sunflower ideotype design using the crop model SUNFLO. The underlying optimization problem is formulated as a multi-objective one to account for risk-aversion. Our approach achieves good performances even for limited computational budgets, outperforming significantly standard strategies. PMID:28542198

Thermodynamic modeling of small scale biomass gasifiers: Development and assessment of the ''Multi-Box'' approach.

PubMed

Vakalis, Stergios; Patuzzi, Francesco; Baratieri, Marco

2016-04-01

Modeling can be a powerful tool for designing and optimizing gasification systems. Modeling applications for small scale/fixed bed biomass gasifiers have been interesting due to their increased commercial practices. Fixed bed gasifiers are characterized by a wide range of operational conditions and are multi-zoned processes. The reactants are distributed in different phases and the products from each zone influence the following process steps and thus the composition of the final products. The present study aims to improve the conventional 'Black-Box' thermodynamic modeling by means of developing multiple intermediate 'boxes' that calculate two phase (solid-vapor) equilibriums in small scale gasifiers. Therefore the model is named ''Multi-Box''. Experimental data from a small scale gasifier have been used for the validation of the model. The returned results are significantly closer with the actual case study measurements in comparison to single-stage thermodynamic modeling. Copyright © 2016 Elsevier Ltd. All rights reserved.

Development and initial validation of an endoscopic part-task training box.

PubMed

Thompson, Christopher C; Jirapinyo, Pichamol; Kumar, Nitin; Ou, Amy; Camacho, Andrew; Lengyel, Balazs; Ryan, Michele B

2014-09-01

There is currently no objective and validated methodology available to assess the progress of endoscopy trainees or to determine when technical competence has been achieved. The aims of the current study were to develop an endoscopic part-task simulator and to assess scoring system validity. Fundamental endoscopic skills were determined via kinematic analysis, literature review, and expert interviews. Simulator prototypes and scoring systems were developed to reflect these skills. Validity evidence for content, internal structure, and response process was evaluated. The final training box consisted of five modules (knob control, torque, retroflexion, polypectomy, and navigation and loop reduction). A total of 5 minutes were permitted per module with extra points for early completion. Content validity index (CVI)-realism was 0.88, CVI-relevance was 1.00, and CVI-representativeness was 0.88, giving a composite CVI of 0.92. Overall, 82 % of participants considered the simulator to be capable of differentiating between ability levels, and 93 % thought the simulator should be used to assess ability prior to performing procedures in patients. Inter-item assessment revealed correlations from 0.67 to 0.93, suggesting that tasks were sufficiently correlated to assess the same underlying construct, with each task remaining independent. Each module represented 16.0 % - 26.1 % of the total score, suggesting that no module contributed disproportionately to the composite score. Average box scores were 272.6 and 284.4 (P = 0.94) when performed sequentially, and average score for all participants with proctor 1 was 297.6 and 308.1 with proctor 2 (P = 0.94), suggesting reproducibility and minimal error associated with test administration. A part-task training box and scoring system were developed to assess fundamental endoscopic skills, and validity evidence regarding content, internal structure, and response process was demonstrated. © Georg Thieme Verlag KG Stuttgart · New York.

Graphical User Interface for Simulink Integrated Performance Analysis Model

NASA Technical Reports Server (NTRS)

Durham, R. Caitlyn

2009-01-01

The J-2X Engine (built by Pratt & Whitney Rocketdyne,) in the Upper Stage of the Ares I Crew Launch Vehicle, will only start within a certain range of temperature and pressure for Liquid Hydrogen and Liquid Oxygen propellants. The purpose of the Simulink Integrated Performance Analysis Model is to verify that in all reasonable conditions the temperature and pressure of the propellants are within the required J-2X engine start boxes. In order to run the simulation, test variables must be entered at all reasonable values of parameters such as heat leak and mass flow rate. To make this testing process as efficient as possible in order to save the maximum amount of time and money, and to show that the J-2X engine will start when it is required to do so, a graphical user interface (GUI) was created to allow the input of values to be used as parameters in the Simulink Model, without opening or altering the contents of the model. The GUI must allow for test data to come from Microsoft Excel files, allow those values to be edited before testing, place those values into the Simulink Model, and get the output from the Simulink Model. The GUI was built using MATLAB, and will run the Simulink simulation when the Simulate option is activated. After running the simulation, the GUI will construct a new Microsoft Excel file, as well as a MATLAB matrix file, using the output values for each test of the simulation so that they may graphed and compared to other values.

Backscattered electron simulations to evaluate sensitivity against electron dosage of buried semiconductor features

NASA Astrophysics Data System (ADS)

Mukhtar, Maseeh; Thiel, Bradley

2018-03-01

In fabrication, overlay measurements of semiconductor device patterns have conventionally been performed using optical methods. Beginning with image-based techniques using box-in-box to the more recent diffraction-based overlay (DBO). Alternatively, use of SEM overlay is under consideration for in-device overlay. Two main application spaces are measurement features from multiple mask levels on the same surface and buried features. Modern CD-SEMs are adept at measuring overlay for cases where all features are on the surface. In order to measure overlay of buried features, HV-SEM is needed. Gate-to-fin and BEOL overlay are important use cases for this technique. A JMONSEL simulation exercise was performed for these two cases using 10 nm line/space gratings of graduated increase in depth of burial. Backscattered energy loss results of these simulations were used to calculate the sensitivity measurements of buried features versus electron dosage for an array of electron beam voltages.

Type-I cosmic-string network

NASA Astrophysics Data System (ADS)

Hiramatsu, Takashi; Sendouda, Yuuiti; Takahashi, Keitaro; Yamauchi, Daisuke; Yoo, Chul-Moon

2013-10-01

We study the network of Type-I cosmic strings using the field-theoretic numerical simulations in the Abelian-Higgs model. For Type-I strings, the gauge field plays an important role, and thus we find that the correlation length of the strings is strongly dependent upon the parameter β, the ratio between the masses of the scalar field and the gauge field, namely, β=mφ2/mA2. In particular, if we take the cosmic expansion into account, the network becomes densest in the comoving box for a specific value of β for β<1.

Transport Properties of Water and Sodium Dodecyl Sulfate (Postprint)

DTIC Science & Technology

2013-08-01

and dihedrals, while the intermolecular interac- tions are modeled by the long-range Lennard-Jones and Coulomb interactions. At each simulation step...in the same periodic water box, then the de - pendence of DL on the length L is given by DL ¼ D0 2:837kBT 6pgL (2) In Eq. (2), g is the shear...Renewable Sustainable Energy Rev., 16(6), pp. 3917–3938. [27] Mingzheng, Z., Guodong, X., Jian, L., Lei , C., and Lijun, Z., 2012, “Analysis of Factors

[A test of the focusing hypothesis for category judgment: an explanation using the mental-box model].

PubMed

Hatori, Tsuyoshi; Takemura, Kazuhisa; Fujii, Satoshi; Ideno, Takashi

2011-06-01

This paper presents a new model of category judgment. The model hypothesizes that, when more attention is focused on a category, the psychological range of the category gets narrower (category-focusing hypothesis). We explain this hypothesis by using the metaphor of a "mental-box" model: the more attention that is focused on a mental box (i.e., a category set), the smaller the size of the box becomes (i.e., a cardinal number of the category set). The hypothesis was tested in an experiment (N = 40), where the focus of attention on prescribed verbal categories was manipulated. The obtained data gave support to the hypothesis: category-focusing effects were found in three experimental tasks (regarding the category of "food", "height", and "income"). The validity of the hypothesis was discussed based on the results.

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

Tang, Jason D.; Schroeppel, Richard Crabtree; Robertson, Perry J.

With the build-out of large transport networks utilizing optical technologies, more and more capacity is being made available. Innovations in Dense Wave Division Multiplexing (DWDM) and the elimination of optical-electrical-optical conversions have brought on advances in communication speeds as we move into 10 Gigabit Ethernet and above. Of course, there is a need to encrypt data on these optical links as the data traverses public and private network backbones. Unfortunately, as the communications infrastructure becomes increasingly optical, advances in encryption (done electronically) have failed to keep up. This project examines the use of optical logic for implementing encryption in themore » photonic domain to achieve the requisite encryption rates. This paper documents the innovations and advances of work first detailed in 'Photonic Encryption using All Optical Logic,' [1]. A discussion of underlying concepts can be found in SAND2003-4474. In order to realize photonic encryption designs, technology developed for electrical logic circuits must be translated to the photonic regime. This paper examines S-SEED devices and how discrete logic elements can be interconnected and cascaded to form an optical circuit. Because there is no known software that can model these devices at a circuit level, the functionality of S-SEED devices in an optical circuit was modeled in PSpice. PSpice allows modeling of the macro characteristics of the devices in context of a logic element as opposed to device level computational modeling. By representing light intensity as voltage, 'black box' models are generated that accurately represent the intensity response and logic levels in both technologies. By modeling the behavior at the systems level, one can incorporate systems design tools and a simulation environment to aid in the overall functional design. Each black box model takes certain parameters (reflectance, intensity, input response), and models the optical ripple and time delay characteristics. These 'black box' models are interconnected and cascaded in an encrypting/scrambling algorithm based on a study of candidate encryption algorithms. Demonstration circuits show how these logic elements can be used to form NAND, NOR, and XOR functions. This paper also presents functional analysis of a serial, low gate count demonstration algorithm suitable for scrambling/encryption using S-SEED devices.« less

Numerical investigation for formability of aluminum 6016 alloy under non-isothermal warm forming process

NASA Astrophysics Data System (ADS)

Hu, P.; Dai, M. H.; Ying, L.; Shi, D. Y.; Zhao, K. M.; Lu, J. D.

2013-05-01

The warm forming technology of aluminum alloy has attracted attention from worldwide automotive engineering sector in recent years, with which the complex geometry parts can be realized at elevated temperature. A non-isothermal warm forming process for the heat treatable aluminum can quickly carry out its application on traditional production line by adding a furnace to heat up the aluminum alloy sheet. The 6000 aluminum alloy was investigated by numerical simulation and experiment using the Nakajima test model in this paper. A modified Fields-Backofen model was introduced into numerical simulation process to describe the thermo-mechanical flow behavior of a 6000 series aluminum alloy. The experimental data was obtained by conducting thermal-mechanical uniaxial tensile experiment in temperatures range of 25˜400°C to guarantee the numerical simulation more accurate. The numerical simulation was implemented with LS_DYNA software in terms of coupled dynamic explicit method for investigating the effect of initial forming temperature and the Binder Holder Force (BHF), which are critical process parameters in non-isothermal warm forming. The results showed that the optimal initial forming temperature range was 300°C˜350°C. By means of conducting numerical simulation in deep drawing box model, the forming window of BHF and temperature around the optimal initial forming temperature (275°, 300° and 325°) are investigated, which can provide guidance to actual experiment.

The suppression effect of a periodic surface with semicircular grooves on the high power microwave long pill-box window multipactor phenomenon

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

Zhang, Xue, E-mail: zhangxue.iecas@yahoo.com; Wang, Yong; Fan, Junjie

2014-09-15

To improve the transmitting power in an S-band klystron, a long pill-box window that has a disk with grooves with a semicircular cross section is theoretically investigated and simulated. A Monte-Carlo algorithm is used to track the secondary electron trajectories and analyze the multipactor scenario in the long pill-box window and on the grooved surface. Extending the height of the long-box window can decrease the normal electric field on the surface of the window disk, but the single surface multipactor still exists. It is confirmed that the window disk with periodic semicircular grooves can explicitly suppress the multipactor and predominantlymore » depresses the local field enhancement and the bottom continuous multipactor. The difference between semicircular and sharp boundary grooves is clarified numerically and analytically.« less

The two-box model of climate: limitations and applications to planetary habitability and maximum entropy production studies.

PubMed

Lorenz, Ralph D

2010-05-12

The 'two-box model' of planetary climate is discussed. This model has been used to demonstrate consistency of the equator-pole temperature gradient on Earth, Mars and Titan with what would be predicted from a principle of maximum entropy production (MEP). While useful for exposition and for generating first-order estimates of planetary heat transports, it has too low a resolution to investigate climate systems with strong feedbacks. A two-box MEP model agrees well with the observed day : night temperature contrast observed on the extrasolar planet HD 189733b.

Models for nearly every occasion: Part I - One box models.

PubMed

Hewett, Paul; Ganser, Gary H

2017-01-01

The standard "well mixed room," "one box" model cannot be used to predict occupational exposures whenever the scenario involves the use of local controls. New "constant emission" one box models are proposed that permit either local exhaust or local exhaust with filtered return, coupled with general room ventilation or the recirculation of a portion of the general room exhaust. New "two box" models are presented in Part II of this series. Both steady state and transient models were developed. The steady state equation for each model, including the standard one box steady state model, is augmented with an additional factor reflecting the fraction of time the substance was generated during each task. This addition allows the easy calculation of the average exposure for cyclic and irregular emission patterns, provided the starting and ending concentrations are zero or near zero, or the cumulative time across all tasks is long (e.g., several tasks to a full shift). The new models introduce additional variables, such as the efficiency of the local exhaust to immediately capture freshly generated contaminant and the filtration efficiency whenever filtered exhaust is returned to the workspace. Many of the model variables are knowable (e.g., room volume and ventilation rate). A structured procedure for calibrating a model to a work scenario is introduced that can be applied to both continuous and cyclic processes. The "calibration" procedure generates estimates of the generation rate and all of remaining unknown model variables.

Air/water exchange of mercury in the Everglades I: the behavior of dissolved gaseous mercury in the Everglades Nutrient Removal Project

PubMed

Zhang; Lindberg

2000-10-02

From 1996 to 1998 we determined dissolved gaseous mercury (DGM) in waters of the Everglades Nutrient Removal Project (ENR), a constructed wetlands. The concentrations of DGM measured in these waters (mean 7.3 +/- 9.5 pg l(-1)) are among the lowest reported in the literature, and suggest a system often near or slightly above equilibrium with Hg in ambient air. DGM exhibited both seasonal and diel trends, peaking at midday and during the summer. A simple box budget model of DGM in waters of the Everglades was developed using an interactive spreadsheet based on a mass balance among light-induced reduction of HgII (production of DGM), Hg0 oxidation (removal), and Hg0 evasion in a box (water column) consisting of a surface region with sunlight available and a lower dark region. The modeling results suggest high sensitivity of hourly DGM concentrations to DGM production rates and initial DGM levels. The sensitivity to Hg oxidation is lower than the sensitivity to DGM production. The model performance demonstrates successful simulations of a variety of DGM trends in the Everglades. In particular, it clearly demonstrates how it is possible to measure comparable rates of evasion over several Everglades sites with different DGM concentrations.

Laparoscopic simulation training in gynaecology: Current provision and staff attitudes - a cross-sectional survey.

PubMed

Burden, Christy; Fox, Robert; Hinshaw, Kim; Draycott, Timothy J; James, Mark

2016-01-01

The objectives of this study were to explore current provision of laparoscopic simulation training, and to determine attitudes of trainers and trainees to the role of simulators in surgical training across the UK. An anonymous cross-sectional survey with cluster sampling was developed and circulated. All Royal College of Obstetricians and Gynaecologists (RCOG) Training Programme Directors (TPD), College Tutors (RCT) and Trainee representatives (TR) across the UK were invited to participate. One hundred and ninety-six obstetricians and gynaecologists participated. Sixty-three percent of hospitals had at least one box trainer, and 14.6% had least one virtual-reality simulator. Only 9.3% and 3.6% stated that trainees used a structured curriculum on box and virtual-reality simulators, respectively. Respondents working in a Large/Teaching hospital (p = 0.008) were more likely to agree that simulators enhance surgical training. Eighty-nine percent agreed that simulators improve the quality of training, and should be mandatory or desirable for junior trainees. Consultants (p = 0.003) and respondents over 40 years (p = 0.011) were more likely to hold that a simulation test should be undertaken before live operation. Our data demonstrated, therefore, that availability of laparoscopic simulators is inconsistent, with limited use of mandatory structured curricula. In contrast, both trainers and trainees recognise a need for greater use of laparoscopic simulation for surgical training.

Validation of an intermediate-complexity model for simulating marine biogeochemistry under anoxic conditions in the modern Black Sea

NASA Astrophysics Data System (ADS)

Romaniello, Stephen J.; Derry, Louis A.

2010-08-01

We test the ability of a new 1-D intermediate-complexity box model (ICBM) that includes process-based C, N, P, O, and S biogeochemistry to simulate profiles and fluxes of biogeochemically reactive species across a wide range of ocean redox states. The ICBM was developed to simulate whole ocean processes for paleoceanographic applications and has been tested with data from the modern global ocean. Here we adapt the circulation submodel of the ICBM to simulate water mass exchange and eddy diffusion processes in the Black Sea but make only very minor changes to the biogeochemical submodel. We force the model with estimated natural and anthropogenic inputs of tracers and nutrients to the Black Sea and compare the results of the simulations to modern observations. Ventilation of the Black Sea is modeled by depth-dependent entrainment of Cold Intermediate Layer water into Bosphorus plume water and subsequent intrusion into deep layers. The simulated profiles of circulation tracers θ, salinity, CFC-12, and radiocarbon agree well with available data, suggesting that the model does a reasonable job of representing physical exchange. Vertical profiles of biogeochemically active components are in good overall agreement with observations. The lack of trace metal (Mn and Fe) cycling in the model results in some discrepancies between the simulated profiles and observation across the suboxic zone; however, the overall redox balance is not sensitive to this difference. We compare modeled basin-wide biogeochemical fluxes to available estimates, but in a number of cases uncertainties in modern budgets limit our ability to test the model rigorously. In agreement with earlier work we find that fixed N losses via thiodenitrification are likely a major pathway in the Black Sea N cycle. Overall, the same biogeochemical submodel used to simulate the modern global ocean appears to perform well in simulating Black Sea processes without requiring significant modification. The ability of a single model to perform across a wide range of redox states is an important prerequisite for applying the ICBM to deep time paleoceanographic problems. The model source code is available as MATLAB™ 7 m-files provided as auxiliary material.

A Multi-Paradigm Modeling Framework to Simulate Dynamic Reciprocity in a Bioreactor

PubMed Central

Kaul, Himanshu; Cui, Zhanfeng; Ventikos, Yiannis

2013-01-01

Despite numerous technology advances, bioreactors are still mostly utilized as functional black-boxes where trial and error eventually leads to the desirable cellular outcome. Investigators have applied various computational approaches to understand the impact the internal dynamics of such devices has on overall cell growth, but such models cannot provide a comprehensive perspective regarding the system dynamics, due to limitations inherent to the underlying approaches. In this study, a novel multi-paradigm modeling platform capable of simulating the dynamic bidirectional relationship between cells and their microenvironment is presented. Designing the modeling platform entailed combining and coupling fully an agent-based modeling platform with a transport phenomena computational modeling framework. To demonstrate capability, the platform was used to study the impact of bioreactor parameters on the overall cell population behavior and vice versa. In order to achieve this, virtual bioreactors were constructed and seeded. The virtual cells, guided by a set of rules involving the simulated mass transport inside the bioreactor, as well as cell-related probabilistic parameters, were capable of displaying an array of behaviors such as proliferation, migration, chemotaxis and apoptosis. In this way the platform was shown to capture not only the impact of bioreactor transport processes on cellular behavior but also the influence that cellular activity wields on that very same local mass transport, thereby influencing overall cell growth. The platform was validated by simulating cellular chemotaxis in a virtual direct visualization chamber and comparing the simulation with its experimental analogue. The results presented in this paper are in agreement with published models of similar flavor. The modeling platform can be used as a concept selection tool to optimize bioreactor design specifications. PMID:23555740

Multiscale modelling of precipitation in concentrated alloys: from atomistic Monte Carlo simulations to cluster dynamics I thermodynamics

NASA Astrophysics Data System (ADS)

Lépinoux, J.; Sigli, C.

2018-01-01

In a recent paper, the authors showed how the clusters free energies are constrained by the coagulation probability, and explained various anomalies observed during the precipitation kinetics in concentrated alloys. This coagulation probability appeared to be a too complex function to be accurately predicted knowing only the cluster distribution in Cluster Dynamics (CD). Using atomistic Monte Carlo (MC) simulations, it is shown that during a transformation at constant temperature, after a short transient regime, the transformation occurs at quasi-equilibrium. It is proposed to use MC simulations until the system quasi-equilibrates then to switch to CD which is mean field but not limited by a box size like MC. In this paper, we explain how to take into account the information available before the quasi-equilibrium state to establish guidelines to safely predict the cluster free energies.

Reproducibility of the Internal Load and Performance-Based Responses to Simulated Amateur Boxing.

PubMed

Thomson, Edward D; Lamb, Kevin L

2017-12-01

Thomson, ED and Lamb, KL. Reproducibility of the internal load and performance-based responses to simulated amateur boxing. J Strength Cond Res 31(12): 3396-3402, 2017-The aim of this study was to examine the reproducibility of the internal load and performance-based responses to repeated bouts of a three-round amateur boxing simulation protocol (boxing conditioning and fitness test [BOXFIT]). Twenty-eight amateur boxers completed 2 familiarization trials before performing 2 complete trials of the BOXFIT, separated by 4-7 days. To characterize the internal load, mean (HRmean) and peak (HRpeak) heart rate, breath-by-breath oxygen uptake (V[Combining Dot Above]O2), aerobic energy expenditure, excess carbon dioxide production (CO2excess), and ratings of perceived exertion were recorded throughout each round, and blood lactate determined post-BOXFIT. Additionally, an indication of the performance-based demands of the BOXFIT was provided by a measure of acceleration of the punches thrown in each round. Analyses revealed there were no significant differences (p > 0.05) between repeated trials in any round for all dependent measures. The typical error (coefficient variation %) for all but 1 marker of internal load (CO2excess) was 1.2-16.5% and reflected a consistency that was sufficient for the detection of moderate changes in variables owing to an intervention. The reproducibility of the punch accelerations was high (coefficient of variance % range = 2.1-2.7%). In general, these findings suggest that the internal load and performance-based efforts recorded during the BOXFIT are reproducible and, thereby, offer practitioners a method by which meaningful changes impacting on performance could be identified.

Study of Linear and Nonlinear Waves in Plasma Crystals Using the Box_Tree Code

NASA Astrophysics Data System (ADS)

Qiao, K.; Hyde, T.; Barge, L.

Dusty plasma systems play an important role in both astrophysical and planetary environments (protostellar clouds, planetary ring systems and magnetospheres, cometary environments) and laboratory settings (plasma processing or nanofabrication). Recent research has focussed on defining (both theoretically and experimentally) the different types of wave mode propagations, which are possible within plasma crystals. This is an important topic since several of the fundamental quantities for characterizing such crystals can be obtained directly from an analysis of the wave propagation/dispersion. This paper will discuss a num rical model fore 2D-monolayer plasma crystals, which was established using a modified box tree code. Different wave modes were examined by adding a time dependent potential to the code designed to simulate a laser radiation perturbation as has been applied in many experiments. Both linear waves (for example, longitudinal and transverse dust lattice waves) and nonlinear waves (solitary waves) are examined. The output data will also be compared with the results of corresponding experiments and discussed.

Modeling out-of-plane actuation in thin-film nematic polymer networks: From chiral ribbons to auto-origami boxes via twist and topology

PubMed Central

Gimenez-Pinto, Vianney; Ye, Fangfu; Mbanga, Badel; Selinger, Jonathan V.; Selinger, Robin L. B.

2017-01-01

Various experimental and theoretical studies demonstrate that complex stimulus-responsive out-of-plane distortions such as twist of different chirality, emergence of cones, simple and anticlastic bending can be engineered and pre-programmed in a liquid crystalline rubbery material given a well-controlled director microstructure. Via 3-d finite element simulation studies, we demonstrate director-encoded chiral shape actuation in thin-film nematic polymer networks under external stimulus. Furthermore, we design two complex director fields with twisted nematic domains and nematic disclinations that encode a pattern of folds for an auto-origami box. This actuator will be flat at a reference nematic state and form four well-controlled bend distortions as orientational order changes. Device fabrication is applicable via current experimental techniques. These results are in qualitative agreement with theoretical predictions, provide insight into experimental observations, and demonstrate the value of finite element methods at the continuum level for designing and engineering liquid crystal polymeric devices. PMID:28349949

Complexation behavior of oppositely charged polyelectrolytes: Effect of charge distribution

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

Zhao, Mingtian; Li, Baohui, E-mail: dliang@pku.edu.cn, E-mail: baohui@nankai.edu.cn; Zhou, Jihan

Complexation behavior of oppositely charged polyelectrolytes in a solution is investigated using a combination of computer simulations and experiments, focusing on the influence of polyelectrolyte charge distributions along the chains on the structure of the polyelectrolyte complexes. The simulations are performed using Monte Carlo with the replica-exchange algorithm for three model systems where each system is composed of a mixture of two types of oppositely charged model polyelectrolyte chains (EGEG){sub 5}/(KGKG){sub 5}, (EEGG){sub 5}/(KKGG){sub 5}, and (EEGG){sub 5}/(KGKG){sub 5}, in a solution including explicit solvent molecules. Among the three model systems, only the charge distributions along the chains are notmore » identical. Thermodynamic quantities are calculated as a function of temperature (or ionic strength), and the microscopic structures of complexes are examined. It is found that the three systems have different transition temperatures, and form complexes with different sizes, structures, and densities at a given temperature. Complex microscopic structures with an alternating arrangement of one monolayer of E/K monomers and one monolayer of G monomers, with one bilayer of E and K monomers and one bilayer of G monomers, and with a mixture of monolayer and bilayer of E/K monomers in a box shape and a trilayer of G monomers inside the box are obtained for the three mixture systems, respectively. The experiments are carried out for three systems where each is composed of a mixture of two types of oppositely charged peptide chains. Each peptide chain is composed of Lysine (K) and glycine (G) or glutamate (E) and G, in solution, and the chain length and amino acid sequences, and hence the charge distribution, are precisely controlled, and all of them are identical with those for the corresponding model chain. The complexation behavior and complex structures are characterized through laser light scattering and atomic force microscopy measurements. The order of the apparent weight-averaged molar mass and the order of density of complexes observed from the three experimental systems are qualitatively in agreement with those predicted from the simulations.« less

Atomic Oxygen Exposure of Polyimide Foam for International Space Station Solar Array Wing Blanket Box

NASA Technical Reports Server (NTRS)

Finckenor, M. M.; Albyn, K. C.; Watts, E. W.

2006-01-01

Onorbit photos of the International Space Station (ISS) solar array blanket box foam pad assembly indicate degradation of the Kapton film covering the foam, leading to atomic oxygen (AO) exposure of the foam. The purpose of this test was to determine the magnitude of particulate generation caused by low-Earth orbital environment exposure of the foam and also by compression of the foam during solar array wing retraction. The polyimide foam used in the ISS solar array wing blanket box assembly is susceptible to significant AO erosion. The foam sample in this test lost one-third of its mass after exposure to the equivalent of 22 mo onorbit. Some particulate was generated by exposure to simulated orbital conditions and the simulated solar array retraction (compression test). However, onorbit, these particles would also be eroded by AO. The captured particles were generally <1 mm, and the particles shaken free of the sample had a maximum size of 4 mm. The foam sample maintained integrity after a compression load of 2.5 psi.

Bayesian spatial transformation models with applications in neuroimaging data.

PubMed

Miranda, Michelle F; Zhu, Hongtu; Ibrahim, Joseph G

2013-12-01

The aim of this article is to develop a class of spatial transformation models (STM) to spatially model the varying association between imaging measures in a three-dimensional (3D) volume (or 2D surface) and a set of covariates. The proposed STM include a varying Box-Cox transformation model for dealing with the issue of non-Gaussian distributed imaging data and a Gaussian Markov random field model for incorporating spatial smoothness of the imaging data. Posterior computation proceeds via an efficient Markov chain Monte Carlo algorithm. Simulations and real data analysis demonstrate that the STM significantly outperforms the voxel-wise linear model with Gaussian noise in recovering meaningful geometric patterns. Our STM is able to reveal important brain regions with morphological changes in children with attention deficit hyperactivity disorder. © 2013, The International Biometric Society.

CFD Simulations of the IHF Arc-Jet Flow: Compression-Pad Separation Bolt Wedge Tests

NASA Technical Reports Server (NTRS)

Gokcen, Tahir; Skokova, Kristina A.

2017-01-01

This paper reports computational analyses in support of two wedge tests in a high enthalpy arc-jet facility at NASA Ames Research Center. These tests were conducted using two different wedge models, each placed in a free jet downstream of a corresponding different conical nozzle in the Ames 60-MW Interaction Heating Facility. Each panel test article included a metallic separation bolt imbedded in Orion compression-pad and heatshield materials, resulting in a circular protuberance over a flat plate. The protuberances produce complex model flowfields, containing shock-shock and shock-boundary layer interactions, and multiple augmented heating regions on the test plate. As part of the test calibration runs, surface pressure and heat flux measurements on water-cooled calibration plates integrated with the wedge models were also obtained. Surface heating distributions on the test articles as well as arc-jet test environment parameters for each test configuration are obtained through computational fluid dynamics simulations, consistent with the facility and calibration measurements. The present analysis comprises simulations of the non-equilibrium flow field in the facility nozzle, test box, and flow field over test articles, and comparisons with the measured calibration data.

CFD Simulations of the IHF Arc-Jet Flow: Compression-Pad/Separation Bolt Wedge Tests

NASA Technical Reports Server (NTRS)

Goekcen, Tahir; Skokova, Kristina A.

2017-01-01

This paper reports computational analyses in support of two wedge tests in a high enthalpy arc-jet facility at NASA Ames Research Center. These tests were conducted using two different wedge models, each placed in a free jet downstream of a corresponding different conical nozzle in the Ames 60-MW Interaction Heating Facility. Each panel test article included a metallic separation bolt imbedded in Orion compression-pad and heatshield materials, resulting in a circular protuberance over a flat plate. The protuberances produce complex model flowfields, containing shock-shock and shock-boundary layer interactions, and multiple augmented heating regions on the test plate. As part of the test calibration runs, surface pressure and heat flux measurements on water-cooled calibration plates integrated with the wedge models were also obtained. Surface heating distributions on the test articles as well as arc-jet test environment parameters for each test configuration are obtained through computational fluid dynamics simulations, consistent with the facility and calibration measurements. The present analysis comprises simulations of the nonequilibrium flowfield in the facility nozzle, test box, and flowfield over test articles, and comparisons with the measured calibration data.

Molecular Dynamics Simulation Studies of Caffeine Aggregation in Aqueous Solution

PubMed Central

Tavagnacco, Letizia; Schnupf, Udo; Mason, Philip E.; Saboungi, Marie-Louise; Cesàro, Attilio; Brady, John W.

2011-01-01

Molecular dynamics simulations were carried out on a system of eight independent caffeine molecules in a periodic box of water at 300 K, representing a solution near the solubility limit for caffeine at room temperature, using a newly-developed CHARMM-type force field for caffeine in water. Simulations were also conducted for single caffeine molecules in water using two different water models (TIP3P and TIP4P). Water was found to structure in a complex fashion around the planar caffeine molecules, which was not sensitive to the water model used. As expected, extensive aggregation of the caffeine molecules was observed, with the molecules stacking their flat faces against one another like coins, with their methylene groups staggered to avoid steric clashes. A dynamic equilibrum was observed between large n-mers, including stacks with all eight solute molecules, and smaller clusters, with the calculated osmotic coefficient being in acceptable agreement with the experimental value. The insensitivity of the results to water model and the congruence with experimental thermodynamic data suggest that the observed stacking interactions are a realistic representation of the actual association mechanism in aqueous caffeine solutions. PMID:21812485

Fast Virtual Stenting with Active Contour Models in Intracranical Aneurysm

PubMed Central

Zhong, Jingru; Long, Yunling; Yan, Huagang; Meng, Qianqian; Zhao, Jing; Zhang, Ying; Yang, Xinjian; Li, Haiyun

2016-01-01

Intracranial stents are becoming increasingly a useful option in the treatment of intracranial aneurysms (IAs). Image simulation of the releasing stent configuration together with computational fluid dynamics (CFD) simulation prior to intervention will help surgeons optimize intervention scheme. This paper proposed a fast virtual stenting of IAs based on active contour model (ACM) which was able to virtually release stents within any patient-specific shaped vessel and aneurysm models built on real medical image data. In this method, an initial stent mesh was generated along the centerline of the parent artery without the need for registration between the stent contour and the vessel. Additionally, the diameter of the initial stent volumetric mesh was set to the maximum inscribed sphere diameter of the parent artery to improve the stenting accuracy and save computational cost. At last, a novel criterion for terminating virtual stent expanding that was based on the collision detection of the axis aligned bounding boxes was applied, making the stent expansion free of edge effect. The experiment results of the virtual stenting and the corresponding CFD simulations exhibited the efficacy and accuracy of the ACM based method, which are valuable to intervention scheme selection and therapy plan confirmation. PMID:26876026

Process fault detection and nonlinear time series analysis for anomaly detection in safeguards

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

Burr, T.L.; Mullen, M.F.; Wangen, L.E.

In this paper we discuss two advanced techniques, process fault detection and nonlinear time series analysis, and apply them to the analysis of vector-valued and single-valued time-series data. We investigate model-based process fault detection methods for analyzing simulated, multivariate, time-series data from a three-tank system. The model-predictions are compared with simulated measurements of the same variables to form residual vectors that are tested for the presence of faults (possible diversions in safeguards terminology). We evaluate two methods, testing all individual residuals with a univariate z-score and testing all variables simultaneously with the Mahalanobis distance, for their ability to detect lossmore » of material from two different leak scenarios from the three-tank system: a leak without and with replacement of the lost volume. Nonlinear time-series analysis tools were compared with the linear methods popularized by Box and Jenkins. We compare prediction results using three nonlinear and two linear modeling methods on each of six simulated time series: two nonlinear and four linear. The nonlinear methods performed better at predicting the nonlinear time series and did as well as the linear methods at predicting the linear values.« less

Brane boxes, anomalies, bending, and tadpoles

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

Leigh, R.G.; Rozali, M.

1999-01-01

Certain classes of chiral four-dimensional gauge theories may be obtained as the world volume theories of D5-branes are suspended between networks of NS5-branes, the so-called brane box models. In this paper, we derive the stringy consistency conditions placed on these models, and show that they are equivalent to an anomaly cancellation of the gauge theories. We derive these conditions in the orbifold theories which are {ital T} dual to the elliptic brane box models. Specifically, we show that the expression for tadpoles for unphysical twisted Ramond-Ramond 4-form fields in the orbifold theory are proportional to the gauge anomalies of themore » brane box theory. Thus string consistency is equivalent to world volume gauge anomaly cancellation. Furthermore, we find additional cylinder amplitudes which give the {beta} functions of the gauge theory. We show how these correspond to bending of the NS-branes in the brane box theory. {copyright} {ital 1998} {ital The American Physical Society}« less

Secondary formation of nitrated phenols: insights from observations during the Uintah Basin Winter Ozone Study (UBWOS) 2014

NASA Astrophysics Data System (ADS)

Yuan, B.; Liggio, J.; Wentzell, J.; Li, S.-M.; Stark, H.; Roberts, J. M.; Gilman, J.; Lerner, B.; Warneke, C.; Li, R.; Leithead, A.; Osthoff, H. D.; Wild, R.; Brown, S. S.; de Gouw, J. A.

2015-10-01

We describe the results from online measurements of nitrated phenols using a time of flight chemical ionization mass spectrometer (ToF-CIMS) with acetate as reagent ion in an oil and gas production region in January and February of 2014. Strong diurnal profiles were observed for nitrated phenols, with concentration maxima at night. Based on known markers (CH4, NOx, CO2), primary emissions of nitrated phenols were not important in this study. A box model was used to simulate secondary formation of phenol, nitrophenol (NP) and dinitrophenols (DNP). The box model results indicate that oxidation of aromatics in the gas phase can explain the observed concentrations of NP and DNP in this study. Photolysis was the most efficient loss pathway for NP in the gas phase. We show that aqueous-phase reactions and heterogeneous reactions were minor sources of nitrated phenols in our study. This study demonstrates that the emergence of new ToF-CIMS (including PTR-TOF) techniques allows for the measurement of intermediate oxygenates at low levels and these measurements improve our understanding of the evolution of primary VOCs in the atmosphere.

Secondary formation of nitrated phenols: insights from observations during the Uintah Basin Winter Ozone Study (UBWOS) 2014

NASA Astrophysics Data System (ADS)

Yuan, Bin; Liggio, John; Wentzell, Jeremy; Li, Shao-Meng; Stark, Harald; Roberts, James M.; Gilman, Jessica; Lerner, Brian; Warneke, Carsten; Li, Rui; Leithead, Amy; Osthoff, Hans D.; Wild, Robert; Brown, Steven S.; de Gouw, Joost A.

2016-02-01

We describe the results from online measurements of nitrated phenols using a time-of-flight chemical ionization mass spectrometer (ToF-CIMS) with acetate as reagent ion in an oil and gas production region in January and February of 2014. Strong diurnal profiles were observed for nitrated phenols, with concentration maxima at night. Based on known markers (CH4, NOx, CO2), primary emissions of nitrated phenols were not important in this study. A box model was used to simulate secondary formation of phenol, nitrophenol (NP), and dinitrophenols (DNP). The box model results indicate that oxidation of aromatics in the gas phase can explain the observed concentrations of NP and DNP in this study. Photolysis was the most efficient loss pathway for NP in the gas phase. We show that aqueous-phase reactions and heterogeneous reactions were minor sources of nitrated phenols in our study. This study demonstrates that the emergence of new ToF-CIMS (including PTR-TOF) techniques allows for the measurement of intermediate oxygenates at low levels and these measurements improve our understanding on the evolution of primary VOCs in the atmosphere.

A Landing Gear Noise Reduction Study Based on Computational Simulations

NASA Technical Reports Server (NTRS)

Khorrami, Mehdi R.; Lockard, David P.

2006-01-01

Landing gear is one of the more prominent airframe noise sources. Techniques that diminish gear noise and suppress its radiation to the ground are highly desirable. Using a hybrid computational approach, this paper investigates the noise reduction potential of devices added to a simplified main landing gear model without small scale geometric details. The Ffowcs Williams and Hawkings equation is used to predict the noise at far-field observer locations from surface pressure data provided by unsteady CFD calculations. Because of the simplified nature of the model, most of the flow unsteadiness is restricted to low frequencies. The wheels, gear boxes, and oleo appear to be the primary sources of unsteadiness at these frequencies. The addition of fairings around the gear boxes and wheels, and the attachment of a splitter plate on the downstream side of the oleo significantly reduces the noise over a wide range of frequencies, but a dramatic increase in noise is observed at one frequency. The increased flow velocities, a consequence of the more streamlined bodies, appear to generate extra unsteadiness around other parts giving rise to the additional noise. Nonetheless, the calculations demonstrate the capability of the devices to improve overall landing gear noise.

The Messy Aerosol Submodel MADE3 (v2.0b): Description and a Box Model Test

NASA Technical Reports Server (NTRS)

Kaiser, J. C.; Hendricks, J.; Righi, M.; Riemer, N.; Zaveri, R. A.; Metzger, S.; Aquila, Valentina

2014-01-01

We introduce MADE3 (Modal Aerosol Dynamics model for Europe, adapted for global applications, 3rd generation), an aerosol dynamics submodel for application within the MESSy framework (Modular Earth Submodel System). MADE3 builds on the predecessor aerosol submodels MADE and MADE-in. Its main new features are the explicit representation of coarse particle interactions both with other particles and with condensable gases, and the inclusion of hydrochloric acid (HCl)chloride (Cl) partitioning between the gas and condensed phases. The aerosol size distribution is represented in the new submodel as a superposition of nine lognormal modes: one for fully soluble particles, one for insoluble particles, and one for mixed particles in each of three size ranges (Aitken, accumulation, and coarse mode size ranges). In order to assess the performance of MADE3 we compare it to its predecessor MADE and to the much more detailed particle-resolved aerosol model PartMC-MOSAIC in a box model simulation of an idealized marine boundary layer test case. MADE3 and MADE results are very similar, except in the coarse mode, where the aerosol is dominated by sea spray particles. Cl is reduced in MADE3 with respect to MADE due to the HClCl partitioning that leads to Cl removal from the sea spray aerosol in our test case. Additionally, aerosol nitrate concentration is higher in MADE3 due to the condensation of nitric acid on coarse particles. MADE3 and PartMC- MOSAIC show substantial differences in the fine particle size distributions (sizes about 2 micrometers) that could be relevant when simulating climate effects on a global scale. Nevertheless, the agreement between MADE3 and PartMC-MOSAIC is very good when it comes to coarse particle size distribution, and also in terms of aerosol composition. Considering these results and the well-established ability of MADE in reproducing observed aerosol loadings and composition, MADE3 seems suitable for application within a global model.

Intracellular antibody signalling is regulated by phosphorylation of the Fc receptor TRIM21

PubMed Central

Vaysburd, Marina; Yang, Ji-Chun; Mallery, Donna L; Zeng, Jingwei; Johnson, Christopher M; McLaughlin, Stephen H; Skehel, Mark; Maslen, Sarah; Cruickshank, James; Huguenin-Dezot, Nicolas; Chin, Jason W; Neuhaus, David

2018-01-01

Cell surface Fc receptors activate inflammation and are tightly controlled to prevent autoimmunity. Antibodies also simulate potent immune signalling from inside the cell via the cytosolic antibody receptor TRIM21, but how this is regulated is unknown. Here we show that TRIM21 signalling is constitutively repressed by its B-Box domain and activated by phosphorylation. The B-Box occupies an E2 binding site on the catalytic RING domain by mimicking E2-E3 interactions, inhibiting TRIM21 ubiquitination and preventing immune activation. TRIM21 is derepressed by IKKβ and TBK1 phosphorylation of an LxxIS motif in the RING domain, at the interface with the B-Box. Incorporation of phosphoserine or a phosphomimetic within this motif relieves B-Box inhibition, promoting E2 binding, RING catalysis, NF-κB activation and cytokine transcription upon infection with DNA or RNA viruses. These data explain how intracellular antibody signalling is regulated and reveal that the B-Box is a critical regulator of RING E3 ligase activity. PMID:29667579

Demographic consequences of nest box use for Red-footed Falcons Falco vespertinus in Central Asia

USGS Publications Warehouse

Bragin, Evgeny A.; Bragin, Alexander E.; Katzner, Todd

2017-01-01

Nest box programs are frequently implemented for the conservation of cavity-nesting birds, but their effectiveness is rarely evaluated in comparison to birds not using nest boxes. In the European Palearctic, Red-footed Falcon Falco vespertinus populations are both of high conservation concern and are strongly associated with nest box programs in heavily managed landscapes. We used a 21-year monitoring dataset collected on 753 nesting attempts by Red-footed Falcons in unmanaged natural or semi-natural habitats to provide basic information on this poorly known species; to evaluate long-term demographic trends; and to evaluate response of demographic parameters of Red-footed Falcons to environmental factors including use of nest boxes. We observed significant differences among years in laying date, offspring loss, and numbers of fledglings produced, but not in egg production. Of these four parameters, offspring loss and, to a lesser extent, number of fledglings exhibited directional trends over time. Variation in laying date and in numbers of eggs were not well explained by any one model, but instead by combinations of models, each with informative terms for nest type. Nevertheless, laying in nest boxes occurred 2.10 ± 0.70 days earlier than in natural nests. In contrast, variation in both offspring loss and numbers of fledglings produced were fairly well explained by a single model including terms for nest type, nest location, and an interaction between the two parameters (65% and 81% model weights respectively), with highest offspring loss in nest boxes on forest edges. Because, for other species, earlier laying dates are associated with more fit individuals, this interaction highlighted a possible ecological trap, whereby birds using nest boxes on forest edges lay eggs earlier but suffer greater offspring loss and produce lower numbers of fledglings than do those in other nesting settings. If nest boxes increase offspring loss for Red-footed Falcons in heavily managed landscapes where populations are at greater risk, or for the many other species of rare or endangered birds supported by nest box programs, these processes could have important demographic and conservation consequences.

Standard Model and New physics for ɛ'k/ɛk

NASA Astrophysics Data System (ADS)

Kitahara, Teppei

2018-05-01

The first result of the lattice simulation and improved perturbative calculations have pointed to a discrepancy between data on ɛ'k/ɛk and the standard-model (SM) prediction. Several new physics (NP) models can explain this discrepancy, and such NP models are likely to predict deviations of ℬ(K → πvv) from the SM predictions, which can be probed precisely in the near future by NA62 and KOTO experiments. We present correlations between ɛ'k/ɛk and ℬ(K → πvv) in two types of NP scenarios: a box dominated scenario and a Z-penguin dominated one. It is shown that different correlations are predicted and the future precision measurements of K → πvv can distinguish both scenarios.

Structure of an E3:E2~Ub Complex Reveals an Allosteric Mechanism Shared among RING/U-box Ligases

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

Pruneda, Jonathan N.; Littlefield, Peter J.; Soss, Sarah E.

2012-09-28

Despite the widespread importance of RING/U-box E3 ubiquitin ligases in ubiquitin (Ub) signaling, the mechanismby which this class of enzymes facilitates Ub transfer remains enigmatic. Here, we present a structural model for a RING/U-box E3:E2~Ub complex poised for Ub transfer. The model and additional analyses reveal that E3 binding biases dynamic E2~Ub ensembles toward closed conformations with enhanced reactivity for substrate lysines. We identify a key hydrogen bond between a highly conserved E3 side chain and an E2 backbone carbonyl, observed in all structures of active RING/ U-Box E3/E2 pairs, as the linchpin for allosteric activation of E2~Ub. The conformationalmore » biasing mechanism is generalizable across diverse E2s and RING/U-box E3s, but is not shared by HECT-type E3s. The results provide a structural model for a RING/ U-box E3:E2~Ub ligase complex and identify the long sought-after source of allostery for RING/UBox activation of E2~Ub conjugates.« less

Low Power S-Box Architecture for AES Algorithm using Programmable Second Order Reversible Cellular Automata: An Application to WBAN.

PubMed

Gangadari, Bhoopal Rao; Ahamed, Shaik Rafi

2016-12-01

In this paper, we presented a novel approach of low energy consumption architecture of S-Box used in Advanced Encryption Standard (AES) algorithm using programmable second order reversible cellular automata (RCA 2 ). The architecture entails a low power implementation with minimal delay overhead and the performance of proposed RCA 2 based S-Box in terms of security is evaluated using the cryptographic properties such as nonlinearity, correlation immunity bias, strict avalanche criteria, entropy and also found that the proposed architecture is secure enough for cryptographic applications. Moreover, the proposed AES algorithm architecture simulation studies show that energy consumption of 68.726 nJ, power dissipation of 3.856 mW for 0.18- μm at 13.69 MHz and energy consumption of 29.408 nJ, power dissipation of 1.65 mW for 0.13- μm at 13.69 MHz. The proposed AES algorithm with RCA 2 based S-Box shows a reduction power consumption by 50 % and energy consumption by 5 % compared to best classical S-Box and composite field arithmetic based AES algorithm. Apart from that, it is also shown that RCA 2 based S-Boxes are dynamic in nature, invertible, low power dissipation compared to that of LUT based S-Box and hence suitable for Wireless Body Area Network (WBAN) applications.

PIC Simulations of Hypersonic Plasma Instabilities

NASA Astrophysics Data System (ADS)

Niehoff, D.; Ashour-Abdalla, M.; Niemann, C.; Decyk, V.; Schriver, D.; Clark, E.

2013-12-01

The plasma sheaths formed around hypersonic aircraft (Mach number, M > 10) are relatively unexplored and of interest today to both further the development of new technologies and solve long-standing engineering problems. Both laboratory experiments and analytical/numerical modeling are required to advance the understanding of these systems; it is advantageous to perform these tasks in tandem. There has already been some work done to study these plasmas by experiments that create a rapidly expanding plasma through ablation of a target with a laser. In combination with a preformed magnetic field, this configuration leads to a magnetic "bubble" formed behind the front as particles travel at about Mach 30 away from the target. Furthermore, the experiment was able to show the generation of fast electrons which could be due to instabilities on electron scales. To explore this, future experiments will have more accurate diagnostics capable of observing time- and length-scales below typical ion scales, but simulations are a useful tool to explore these plasma conditions theoretically. Particle in Cell (PIC) simulations are necessary when phenomena are expected to be observed at these scales, and also have the advantage of being fully kinetic with no fluid approximations. However, if the scales of the problem are not significantly below the ion scales, then the initialization of the PIC simulation must be very carefully engineered to avoid unnecessary computation and to select the minimum window where structures of interest can be studied. One method of doing this is to seed the simulation with either experiment or ion-scale simulation results. Previous experiments suggest that a useful configuration for studying hypersonic plasma configurations is a ring of particles rapidly expanding transverse to an external magnetic field, which has been simulated on the ion scale with an ion-hybrid code. This suggests that the PIC simulation should have an equivalent configuration; however, modeling a plasma expanding radially in every direction is computationally expensive. In order to reduce the computational expense, we use a radial density profile from the hybrid simulation results to seed a self-consistent PIC simulation in one direction (x), while creating a current in the direction (y) transverse to both the drift velocity and the magnetic field (z) to create the magnetic bubble observed in experiment. The simulation will be run in two spatial dimensions but retain three velocity dimensions, and the results will be used to explore the growth of micro-instabilities present in hypersonic plasmas in the high-density region as it moves through the simulation box. This will still require a significantly large box in order to compare with experiment, as the experiments are being performed over distances of 104 λDe and durations of 105 ωpe-1.

Quantifying the Physical Response to a Contemporary Amateur Boxing Simulation.

PubMed

Finlay, Mitchell J; Greig, Matt; Page, Richard M

2018-04-01

Finlay, MJ, Greig, M, and Page, RM. Quantifying the physical response to a contemporary amateur boxing simulation. J Strength Cond Res 32(4): 1005-1012, 2018-This study examined the physical response to a contemporary boxing-specific exercise protocol (BSEP), based on notational analysis of amateur boxing. Nine male senior elite amateur boxers completed a 3 × 3-minute BSEP, with a 1-minute passive recovery period interspersing each round. Average (HRave) and peak (HRpeak) heart rates, average (V[Combining Dot Above]O2ave) and peak oxygen consumptions (V[Combining Dot Above]O2peak), blood lactate (BLa) concentrations, rating of perceived exertion, and both triaxial and uniaxial PlayerLoad metrics were recorded during the completion of the BSEP. Blood lactate concentration increased significantly in each round (Round 1 = 2.4 ± 1.3 mmol·L; Round 2 = 3.3 ± 1.7 mmol·L; Round 3 = 4.3 ± 2.6 mmol·L). Significantly lower HRave and HRpeak values were found in the first round (HRave: 150 ± 15 b·min; HRpeak: 162 ± 12 b·min) when compared with the second (HRave: 156 ± 16 b·min; HRpeak: 166 ± 13 b·min) and third (HRave: 150 ± 15 b·min; HRpeak: 169 ± 14 b·min). No significant differences were found in any of the V[Combining Dot Above]O2 or PlayerLoad metrics recorded during the BSEP. The BSEP based on notational analysis elicited a fatigue response across rounds, confirming its validity. The BSEP can be used as a training tool for boxing-specific conditioning with implications for reduced injury risk, and to assess the physical response to boxing-specific interventions. Moreover, the BSEP can also be manipulated to suit all levels of participants or training phases, with practical applications in performance monitoring and microcycle periodization.

Training on an inexpensive tablet-based device is equally effective as on a standard laparoscopic box trainer

PubMed Central

Montanari, Eliana; Schwameis, Richard; Louridas, Marisa; Göbl, Christian; Kuessel, Lorenz; Polterauer, Stephan; Husslein, Heinrich

2016-01-01

Abstract Background: The aim of the study was to assess whether an inexpensive tablet-based box trainer (TBT) is at least equally effective compared with a standard box trainer (SBT) to learn basic laparoscopic skills (BLS). BLS training outside the operating room has been shown to be beneficial for surgical residency. However, simulation trainers are expensive and are not consistently available in all training centers. Therefore, TBT and other homemade box trainers were developed. Methods: Medical students were randomized to either a TBT or an SBT and trained 4 fundamentals of laparoscopic surgery (FLS) tasks for 1 hour twice a week for 4 weeks. A baseline test before the training period and a posttraining test were performed. All students then completed a questionnaire to assess their assigned box trainer. The primary outcome measure was the improvement in total test scores. Improvement in the scores for the 4 individual FLS tasks was chosen as a secondary outcome measure. Results: Thirty-two medical students were recruited. Baseline test scores did not differ significantly between the groups. BLS improved significantly in both groups for the total score and for all 4 tasks separately. Participants in the TBT group showed a greater improvement of total scores than those in the SBT group, although this did not reach statistical significance; noninferiority of the TBT compared with the SBT concerning the improvement of total scores could be demonstrated. Regarding the individual FLS tasks, noninferiority of the TBT could be shown for the pattern cutting and the suturing with intracorporeal knot-tying task. The acceptance of the TBT by the trainees was very good. Conclusion: Learning BLS on a homemade TBT is at least equally effective as on an SBT, with the advantage of being very cost saving. Therefore, this readily available box trainer may be used as an effective, flexible training device outside the operating room to improve accessibility to simulation training. PMID:27684813

PyFLOWGO: An open-source platform for simulation of channelized lava thermo-rheological properties

NASA Astrophysics Data System (ADS)

Chevrel, Magdalena Oryaëlle; Labroquère, Jérémie; Harris, Andrew J. L.; Rowland, Scott K.

2018-02-01

Lava flow advance can be modeled through tracking the evolution of the thermo-rheological properties of a control volume of lava as it cools and crystallizes. An example of such a model was conceived by Harris and Rowland (2001) who developed a 1-D model, FLOWGO, in which the velocity of a control volume flowing down a channel depends on rheological properties computed following the thermal path estimated via a heat balance box model. We provide here an updated version of FLOWGO written in Python that is an open-source, modern and flexible language. Our software, named PyFLOWGO, allows selection of heat fluxes and rheological models of the user's choice to simulate the thermo-rheological evolution of the lava control volume. We describe its architecture which offers more flexibility while reducing the risk of making error when changing models in comparison to the previous FLOWGO version. Three cases are tested using actual data from channel-fed lava flow systems and results are discussed in terms of model validation and convergence. PyFLOWGO is open-source and packaged in a Python library to be imported and reused in any Python program (https://github.com/pyflowgo/pyflowgo)

Bounded diffusion impedance characterization of battery electrodes using fractional modeling

NASA Astrophysics Data System (ADS)

Gabano, Jean-Denis; Poinot, Thierry; Huard, Benoît

2017-06-01

This article deals with the ability of fractional modeling to describe the bounded diffusion behavior encountered in modern thin film and nanoparticles lithium battery electrodes. Indeed, the diffusion impedance of such batteries behaves as a half order integrator characterized by the Warburg impedance at high frequencies and becomes a classical integrator described by a capacitor at low frequencies. The transition between these two behaviors depends on the particles geometry. Three of them will be considered in this paper: planar, cylindrical and spherical ones. The fractional representation proposed is a gray box model able to perfectly fit the low and high frequency diffusive impedance behaviors while optimizing the frequency response transition. Identification results are provided using frequential simulation data considering the three electrochemical diffusion models based on the particles geometry. Furthermore, knowing this geometry allows to estimate the diffusion ionic resistance and time constant using the relationships linking these physical parameters to the structural fractional model parameters. Finally, other simulations using Randles impedance models including the charge transfer impedance and the external resistance demonstrate the interest of fractional modeling in order to identify properly not only the charge transfer impedance but also the diffusion physical parameters whatever the particles geometry.

Computational Analysis of Arc-Jet Wedge Tests Including Ablation and Shape Change

NASA Technical Reports Server (NTRS)

Goekcen, Tahir; Chen, Yih-Kanq; Skokova, Kristina A.; Milos, Frank S.

2010-01-01

Coupled fluid-material response analyses of arc-jet wedge ablation tests conducted in a NASA Ames arc-jet facility are considered. These tests were conducted using blunt wedge models placed in a free jet downstream of the 6-inch diameter conical nozzle in the Ames 60-MW Interaction Heating Facility. The fluid analysis includes computational Navier-Stokes simulations of the nonequilibrium flowfield in the facility nozzle and test box as well as the flowfield over the models. The material response analysis includes simulation of two-dimensional surface ablation and internal heat conduction, thermal decomposition, and pyrolysis gas flow. For ablating test articles undergoing shape change, the material response and fluid analyses are coupled in order to calculate the time dependent surface heating and pressure distributions that result from shape change. The ablating material used in these arc-jet tests was Phenolic Impregnated Carbon Ablator. Effects of the test article shape change on fluid and material response simulations are demonstrated, and computational predictions of surface recession, shape change, and in-depth temperatures are compared with the experimental measurements.

Preliminary analysis on hybrid Box-Jenkins - GARCH modeling in forecasting gold price

NASA Astrophysics Data System (ADS)

Yaziz, Siti Roslindar; Azizan, Noor Azlinna; Ahmad, Maizah Hura; Zakaria, Roslinazairimah; Agrawal, Manju; Boland, John

2015-02-01

Gold has been regarded as a valuable precious metal and the most popular commodity as a healthy return investment. Hence, the analysis and prediction of gold price become very significant to investors. This study is a preliminary analysis on gold price and its volatility that focuses on the performance of hybrid Box-Jenkins models together with GARCH in analyzing and forecasting gold price. The Box-Cox formula is used as the data transformation method due to its potential best practice in normalizing data, stabilizing variance and reduces heteroscedasticity using 41-year daily gold price data series starting 2nd January 1973. Our study indicates that the proposed hybrid model ARIMA-GARCH with t-innovation can be a new potential approach in forecasting gold price. This finding proves the strength of GARCH in handling volatility in the gold price as well as overcomes the non-linear limitation in the Box-Jenkins modeling.

Impact of pollution controls in Beijing on atmospheric oxygenated volatile organic compounds (OVOCs) during the 2008 Olympic Games: observation and modeling implications

NASA Astrophysics Data System (ADS)

Liu, Y.; Yuan, B.; Li, X.; Shao, M.; Lu, S.; Li, Y.; Chang, C.-C.; Zhu, T.

2014-10-01

Oxygenated volatile organic compounds (OVOCs) are important products of the photo-oxidation of hydrocarbons. They influence the oxidizing capacity and the ozone forming potential of the atmosphere. In the summer of 2008 two months' emission restrictions were enforced in Beijing to improve air quality during the Olympic Games. Observation evidence has been reported in related studies that these control measures were efficient in reducing the concentrations of primary anthropogenic pollutants (CO, NOx and non-methane hydrocarbons, i.e. NMHCs) by 30-40%. In this study, the influence of the emission restrictions on ambient levels of OVOCs was explored using a neural network analysis with consideration of meteorological conditions. Statistically significant reductions in formaldehyde (HCHO), acetaldehyde (CH3CHO), methyl ethyl ketone (MEK) and methanol were found to be 12.9, 15.8, 17.1 and 19.6%, respectively, when the restrictions were in place. The effect of emission control on acetone was not detected in neural network simulations, probably due to pollution transport from surrounding areas outside Beijing. Although the ambient levels of most NMHCs were decreased by ~35% during the full control period, the emission ratios of reactive hydrocarbons attributed to vehicular emissions did not present obvious difference. A zero-dimensional box model based on Master Chemical Mechanism version 3.2 (MCM3.2) was applied to evaluate how OVOCs productions respond to the reduced precursors during the emission controlled period. On average, secondary HCHO was produced from the oxidation of anthropogenic alkenes (54%), isoprene (30%) and aromatics (15%). The importance of biogenic source for the total HCHO formation was almost on a par with that of anthropogenic alkenes during the daytime. Anthropogenic alkenes and alkanes dominated the photochemical production of other OVOCs such as acetaldehyde, acetone and MEK. The relative changes of modelled aldehydes, methyl vinyl ketone and methacrolein (MVK + MACR) before and during the pollution controlled period were comparable to the estimated reductions in the neural network, reflecting that current mechanisms can largely explain secondary production of those species under urban conditions. However, it is worthy to notice that the box model overestimated the measured concentrations of aldehydes by a factor of 1.4-1.7, and simulated MEK was in good agreement with the measurements when primary sources were taken into consideration. These results suggest that the understanding of OVOCs budget in the box model remains incomplete, there is still considerable uncertainty in particular missing sinks (unknown chemical reactions and physical dilution processes) for aldehydes and absence of direct emissions for ketones.

Source parameters of the 2013, Ms 7.0, Lushan earthquake and the characteristics of the near-fault strong ground motion

NASA Astrophysics Data System (ADS)

Zhao, Fengfan; Meng, Lingyuan

2016-04-01

The April 20, 2013 Ms 7.0, earthquake in Lushan city, Sichuan province of China occurred as the result of east-west oriented reverse-type motion on a north-south striking fault. The source location suggests the event occurred on the Southern part of Longmenshan fault at a depth of 13km. The maximum intensity is up to VIII to IX at Boxing and Lushan city, which are located in the meizoseismal area. In this study, we analyzed the dynamic source process with the source mechanism and empirical relationships, estimated the strong ground motion in the near-fault field based on the Brune's circle model. A dynamical composite source model (DCSM) has been developed to simulate the near-fault strong ground motion with associated fault rupture properties at Boxing and Lushan city, respectively. The results indicate that the frictional undershoot behavior in the dynamic source process of Lushan earthquake, which is actually different from the overshoot activity of the Wenchuan earthquake. Moreover, we discussed the characteristics of the strong ground motion in the near-fault field, that the broadband synthetic seismogram ground motion predictions for Boxing and Lushan city produced larger peak values, shorter durations and higher frequency contents. It indicates that the factors in near-fault strong ground motion was under the influence of higher effect stress drop and asperity slip distributions on the fault plane. This work is financially supported by the Natural Science Foundation of China (Grant No. 41404045) and by Science for Earthquake Resilience of CEA (XH14055Y).

Pore water pressure variations in Subpermafrost groundwater : Numerical modeling compared with experimental modeling

NASA Astrophysics Data System (ADS)

Rivière, Agnès.; Goncalves, Julio; Jost, Anne; Font, Marianne

2010-05-01

Development and degradation of permafrost directly affect numerous hydrogeological processes such as thermal regime, exchange between river and groundwater, groundwater flows patterns and groundwater recharge (Michel, 1994). Groundwater in permafrost area is subdivided into two zones: suprapermafrost and subpermafrost which are separated by permafrost. As a result of the volumetric expansion of water upon freezing and assuming ice lenses and frost heave do not form freezing in a saturated aquifer, the progressive formation of permafrost leads to the pressurization of the subpermafrost groundwater (Wang, 2006). Therefore disappearance or aggradation of permafrost modifies the confined or unconfined state of subpermafrost groundwater. Our study focuses on modifications of pore water pressure of subpermafrost groundwater which could appear during thawing and freezing of soil. Numerical simulation allows elucidation of some of these processes. Our numerical model accounts for phase changes for coupled heat transport and variably saturated flow involving cycles of freezing and thawing. The flow model is a combination of a one-dimensional channel flow model which uses Manning-Strickler equation and a two-dimensional vertically groundwater flow model using Richards equation. Numerical simulation of heat transport consisted in a two dimensional model accounting for the effects of latent heat of phase change of water associated with melting/freezing cycles which incorporated the advection-diffusion equation describing heat-transfer in porous media. The change of hydraulic conductivity and thermal conductivity are considered by our numerical model. The model was evaluated by comparing predictions with data from laboratory freezing experiments. Experimental design was undertaken at the Laboratory M2C (Univesité de Caen-Basse Normandie, CNRS, France). The device consisted of a Plexiglas box insulated on all sides except on the top. Precipitation and ambient temperature are imposed. The Plexiglas box is filled with glass beads of which hydraulics and thermal parameters are known. All parameters required for our numerical model are controlled and continuous monitoring of soil temperatures and pore water pressure are reported. Our results of experimental model allow us to test the relevance of processes described by our numerical simulation and to quantify the impact of permafrost on pore water pressure of subpermafrost groundwater during a cycle of freezing and thawing. Michel, Frederick A. and Van Everdingen, Robert O. 1994. Changes in hydrogeologic regimes in permafrost regions due to climatic change. Permafrost and Periglacial Processes, 5: 191-195. Wang, Chi-yuen and Manga, Michael and Hanna, Jeffrey C. 2006. Can freezing cause floods on Mars? Geophysical Research Letters, 33

Simulating Cosmic Reionization and Its Observable Consequences

NASA Astrophysics Data System (ADS)

Shapiro, Paul

2017-01-01

I summarize recent progress in modelling the epoch of reionization by large- scale simulations of cosmic structure formation, radiative transfer and their interplay, which trace the ionization fronts that swept across the IGM, to predict observable signatures. Reionization by starlight from early galaxies affected their evolution, impacting reionization, itself, and imprinting the galaxies with a memory of reionization. Star formation suppression, e.g., may explain the observed underabundance of Local Group dwarfs relative to N-body predictions for Cold Dark Matter. I describe CoDa (''Cosmic Dawn''), the first fully-coupled radiation-hydrodynamical simulation of reionization and galaxy formation in the Local Universe, in a volume large enough to model reionization globally but with enough resolving power to follow all the atomic-cooling galactic halos in that volume. A 90 Mpc box was simulated from a constrained realization of primordial fluctuations, chosen to reproduce present-day features of the Local Group, including the Milky Way and M31, and the local universe beyond, including the Virgo cluster. The new RAMSES-CUDATON hybrid CPU-GPU code took 11 days to perform this simulation on the Titan supercomputer at Oak Ridge National Laboratory, with 4096-cubed N-body particles for the dark matter and 4096-cubed cells for the atomic gas and ionizing radiation.

The importance of terrestrial weathering for climate system modelling on extended timescales: a study with the UVic ESCM

NASA Astrophysics Data System (ADS)

Brault, Marc-Olivier; Matthews, Damon; Mysak, Lawrence

2016-04-01

The chemical erosion of carbonate and silicate rocks is a key process in the global carbon cycle and, through its coupling with calcium carbonate deposition in the ocean, is the primary sink of carbon on geologic timescales. The dynamic interdependence of terrestrial weathering rates with atmospheric temperature and carbon dioxide concentrations is crucial to the regulation of Earth's climate over multi-millennial timescales. However any attempts to develop a modeling context for terrestrial weathering as part of a dynamic climate system are limited, mostly because of the difficulty in adapting the multi-millennial timescales of the implied negative feedback mechanism with those of the atmosphere and ocean. Much of the earlier work on this topic is therefore based on box-model approaches, abandoning spatial variability for the sake of computational efficiency and the possibility to investigate the impact of weathering on climate change over time frames much longer than those allowed by traditional climate system models. As a result we still have but a rudimentary understanding of the chemical weathering feedback mechanism and its effects on ocean biogeochemistry and atmospheric CO2. Here, we introduce a spatially-explicit, rock weathering model into the University of Victoria Earth System Climate Model (UVic ESCM). We use a land map which takes into account a number of different rock lithologies, changes in sea level, as well as an empirical model of the temperature and NPP dependency of weathering rates for the different rock types. We apply this new model to the last deglacial period (c. 21000BP to 13000BP) as well as a future climate change scenario (c. 1800AD to 6000AD+), comparing the results of our 2-D version of the weathering feedback mechanism to simulations using only the box-model parameterizations of Meissner et al. [2012]. These simulations reveal the importance of two-dimensional factors (i.e., changes in sea level and rock type distribution) in the role of the weathering negative feedback mechanism on multi-millennial timescales.

A Physics-driven Neural Networks-based Simulation System (PhyNNeSS) for multimodal interactive virtual environments involving nonlinear deformable objects

PubMed Central

De, Suvranu; Deo, Dhannanjay; Sankaranarayanan, Ganesh; Arikatla, Venkata S.

2012-01-01

Background While an update rate of 30 Hz is considered adequate for real time graphics, a much higher update rate of about 1 kHz is necessary for haptics. Physics-based modeling of deformable objects, especially when large nonlinear deformations and complex nonlinear material properties are involved, at these very high rates is one of the most challenging tasks in the development of real time simulation systems. While some specialized solutions exist, there is no general solution for arbitrary nonlinearities. Methods In this work we present PhyNNeSS - a Physics-driven Neural Networks-based Simulation System - to address this long-standing technical challenge. The first step is an off-line pre-computation step in which a database is generated by applying carefully prescribed displacements to each node of the finite element models of the deformable objects. In the next step, the data is condensed into a set of coefficients describing neurons of a Radial Basis Function network (RBFN). During real-time computation, these neural networks are used to reconstruct the deformation fields as well as the interaction forces. Results We present realistic simulation examples from interactive surgical simulation with real time force feedback. As an example, we have developed a deformable human stomach model and a Penrose-drain model used in the Fundamentals of Laparoscopic Surgery (FLS) training tool box. Conclusions A unique computational modeling system has been developed that is capable of simulating the response of nonlinear deformable objects in real time. The method distinguishes itself from previous efforts in that a systematic physics-based pre-computational step allows training of neural networks which may be used in real time simulations. We show, through careful error analysis, that the scheme is scalable, with the accuracy being controlled by the number of neurons used in the simulation. PhyNNeSS has been integrated into SoFMIS (Software Framework for Multimodal Interactive Simulation) for general use. PMID:22629108

Exact solution for the time evolution of network rewiring models

NASA Astrophysics Data System (ADS)

Evans, T. S.; Plato, A. D. K.

2007-05-01

We consider the rewiring of a bipartite graph using a mixture of random and preferential attachment. The full mean-field equations for the degree distribution and its generating function are given. The exact solution of these equations for all finite parameter values at any time is found in terms of standard functions. It is demonstrated that these solutions are an excellent fit to numerical simulations of the model. We discuss the relationship between our model and several others in the literature, including examples of urn, backgammon, and balls-in-boxes models, the Watts and Strogatz rewiring problem, and some models of zero range processes. Our model is also equivalent to those used in various applications including cultural transmission, family name and gene frequencies, glasses, and wealth distributions. Finally some Voter models and an example of a minority game also show features described by our model.

Improved method for calibration of exchange flows for a physical transport box model of Tampa Bay, FL USA

EPA Science Inventory

Results for both sequential and simultaneous calibration of exchange flows between segments of a 10-box, one-dimensional, well-mixed, bifurcated tidal mixing model for Tampa Bay are reported. Calibrations were conducted for three model options with different mathematical expressi...

Time Series ARIMA Models of Undergraduate Grade Point Average.

ERIC Educational Resources Information Center

Rogers, Bruce G.

The Auto-Regressive Integrated Moving Average (ARIMA) Models, often referred to as Box-Jenkins models, are regression methods for analyzing sequential dependent observations with large amounts of data. The Box-Jenkins approach, a three-stage procedure consisting of identification, estimation and diagnosis, was used to select the most appropriate…

Numerical simulation for horizontal subsurface flow constructed wetlands: A short review including geothermal effects and solution bounding in biodegradation procedures

NASA Astrophysics Data System (ADS)

Liolios, K.; Tsihrintzis, V.; Angelidis, P.; Georgiev, K.; Georgiev, I.

2016-10-01

Current developments on modeling of groundwater flow and contaminant transport and removal in the porous media of Horizontal Subsurface Flow Constructed Wetlands (HSF CWs) are first reviewed in a short way. The two usual environmental engineering approaches, the black-box and the process-based one, are briefly presented. Next, recent research results obtained by using these two approaches are briefly discussed as application examples, where emphasis is given to the evaluation of the optimal design and operation parameters concerning HSF CWs. For the black-box approach, the use of Artificial Neural Networks is discussed for the formulation of models, which predict the removal performance of HSF CWs. A novel mathematical prove is presented, which concerns the dependence of the first-order removal coefficient on the Temperature and the Hydraulic Residence Time. For the process-based approach, an application example is first discussed which concerns procedures to evaluate the optimal range of values for the removal coefficient, dependent on either the Temperature or the Hydraulic Residence Time. This evaluation is based on simulating available experimental results of pilot-scale units operated in Democritus University of Thrace, Xanthi, Greece. Further, in a second example, a novel enlargement of the system of Partial Differential Equations is presented, in order to include geothermal effects. Finally, in a third example, the case of parameters uncertainty concerning biodegradation procedures is considered and the use of upper and a novel approach is presented, which concerns the upper and the lower solution bound for the practical draft design of HSF CWs.

The Impact of Three-Dimensional Effects on the Simulation of Turbulence Kinetic Energy in a Major Alpine Valley

NASA Astrophysics Data System (ADS)

Goger, Brigitta; Rotach, Mathias W.; Gohm, Alexander; Fuhrer, Oliver; Stiperski, Ivana; Holtslag, Albert A. M.

2018-02-01

The correct simulation of the atmospheric boundary layer (ABL) is crucial for reliable weather forecasts in truly complex terrain. However, common assumptions for model parametrizations are only valid for horizontally homogeneous and flat terrain. Here, we evaluate the turbulence parametrization of the numerical weather prediction model COSMO with a horizontal grid spacing of Δ x = 1.1 km for the Inn Valley, Austria. The long-term, high-resolution turbulence measurements of the i-Box measurement sites provide a useful data pool of the ABL structure in the valley and on slopes. We focus on days and nights when ABL processes dominate and a thermally-driven circulation is present. Simulations are performed for case studies with both a one-dimensional turbulence parametrization, which only considers the vertical turbulent exchange, and a hybrid turbulence parametrization, also including horizontal shear production and advection in the budget of turbulence kinetic energy (TKE). We find a general underestimation of TKE by the model with the one-dimensional turbulence parametrization. In the simulations with the hybrid turbulence parametrization, the modelled TKE has a more realistic structure, especially in situations when the TKE production is dominated by shear related to the afternoon up-valley flow, and during nights, when a stable ABL is present. The model performance also improves for stations on the slopes. An estimation of the horizontal shear production from the observation network suggests that three-dimensional effects are a relevant part of TKE production in the valley.

The Impact of Three-Dimensional Effects on the Simulation of Turbulence Kinetic Energy in a Major Alpine Valley

NASA Astrophysics Data System (ADS)

Goger, Brigitta; Rotach, Mathias W.; Gohm, Alexander; Fuhrer, Oliver; Stiperski, Ivana; Holtslag, Albert A. M.

2018-07-01

The correct simulation of the atmospheric boundary layer (ABL) is crucial for reliable weather forecasts in truly complex terrain. However, common assumptions for model parametrizations are only valid for horizontally homogeneous and flat terrain. Here, we evaluate the turbulence parametrization of the numerical weather prediction model COSMO with a horizontal grid spacing of Δ x = 1.1 km for the Inn Valley, Austria. The long-term, high-resolution turbulence measurements of the i-Box measurement sites provide a useful data pool of the ABL structure in the valley and on slopes. We focus on days and nights when ABL processes dominate and a thermally-driven circulation is present. Simulations are performed for case studies with both a one-dimensional turbulence parametrization, which only considers the vertical turbulent exchange, and a hybrid turbulence parametrization, also including horizontal shear production and advection in the budget of turbulence kinetic energy (TKE). We find a general underestimation of TKE by the model with the one-dimensional turbulence parametrization. In the simulations with the hybrid turbulence parametrization, the modelled TKE has a more realistic structure, especially in situations when the TKE production is dominated by shear related to the afternoon up-valley flow, and during nights, when a stable ABL is present. The model performance also improves for stations on the slopes. An estimation of the horizontal shear production from the observation network suggests that three-dimensional effects are a relevant part of TKE production in the valley.

HAM2D: 2D Shearing Box Model

NASA Astrophysics Data System (ADS)

Gammie, Charles F.; Guan, Xiaoyue

2012-10-01

HAM solves non-relativistic hyperbolic partial differential equations in conservative form using high-resolution shock-capturing techniques. This version of HAM has been configured to solve the magnetohydrodynamic equations of motion in axisymmetry to evolve a shearing box model.

Bayesian inference for multivariate meta-analysis Box-Cox transformation models for individual patient data with applications to evaluation of cholesterol lowering drugs

PubMed Central

Kim, Sungduk; Chen, Ming-Hui; Ibrahim, Joseph G.; Shah, Arvind K.; Lin, Jianxin

2013-01-01

In this paper, we propose a class of Box-Cox transformation regression models with multidimensional random effects for analyzing multivariate responses for individual patient data (IPD) in meta-analysis. Our modeling formulation uses a multivariate normal response meta-analysis model with multivariate random effects, in which each response is allowed to have its own Box-Cox transformation. Prior distributions are specified for the Box-Cox transformation parameters as well as the regression coefficients in this complex model, and the Deviance Information Criterion (DIC) is used to select the best transformation model. Since the model is quite complex, a novel Monte Carlo Markov chain (MCMC) sampling scheme is developed to sample from the joint posterior of the parameters. This model is motivated by a very rich dataset comprising 26 clinical trials involving cholesterol lowering drugs where the goal is to jointly model the three dimensional response consisting of Low Density Lipoprotein Cholesterol (LDL-C), High Density Lipoprotein Cholesterol (HDL-C), and Triglycerides (TG) (LDL-C, HDL-C, TG). Since the joint distribution of (LDL-C, HDL-C, TG) is not multivariate normal and in fact quite skewed, a Box-Cox transformation is needed to achieve normality. In the clinical literature, these three variables are usually analyzed univariately: however, a multivariate approach would be more appropriate since these variables are correlated with each other. A detailed analysis of these data is carried out using the proposed methodology. PMID:23580436

Bayesian inference for multivariate meta-analysis Box-Cox transformation models for individual patient data with applications to evaluation of cholesterol-lowering drugs.

PubMed

Kim, Sungduk; Chen, Ming-Hui; Ibrahim, Joseph G; Shah, Arvind K; Lin, Jianxin

2013-10-15

In this paper, we propose a class of Box-Cox transformation regression models with multidimensional random effects for analyzing multivariate responses for individual patient data in meta-analysis. Our modeling formulation uses a multivariate normal response meta-analysis model with multivariate random effects, in which each response is allowed to have its own Box-Cox transformation. Prior distributions are specified for the Box-Cox transformation parameters as well as the regression coefficients in this complex model, and the deviance information criterion is used to select the best transformation model. Because the model is quite complex, we develop a novel Monte Carlo Markov chain sampling scheme to sample from the joint posterior of the parameters. This model is motivated by a very rich dataset comprising 26 clinical trials involving cholesterol-lowering drugs where the goal is to jointly model the three-dimensional response consisting of low density lipoprotein cholesterol (LDL-C), high density lipoprotein cholesterol (HDL-C), and triglycerides (TG) (LDL-C, HDL-C, TG). Because the joint distribution of (LDL-C, HDL-C, TG) is not multivariate normal and in fact quite skewed, a Box-Cox transformation is needed to achieve normality. In the clinical literature, these three variables are usually analyzed univariately; however, a multivariate approach would be more appropriate because these variables are correlated with each other. We carry out a detailed analysis of these data by using the proposed methodology. Copyright © 2013 John Wiley & Sons, Ltd.

Rosin-Rammler Distributions in ANSYS Fluent

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

Dunham, Ryan Q.

In Health Physics monitoring, particles need to be collected and tracked. One method is to predict the motion of potential health hazards with computer models. Particles released from various sources within a glove box can become a respirable health hazard if released into the area surrounding a glove box. The goal of modeling the aerosols in a glove box is to reduce the hazards associated with a leak in the glove box system. ANSYS Fluent provides a number of tools for modeling this type of environment. Particles can be released using injections into the flow path with turbulent properties. Themore » models of particle tracks can then be used to predict paths and concentrations of particles within the flow. An attempt to understand and predict the handling of data by Fluent was made, and results iteratively tracked. Trends in data were studied to comprehend the final results. The purpose of the study was to allow a better understanding of the operation of Fluent for aerosol modeling for future application in many fields.« less

Molecular envelope and atomic model of an anti-terminated glyQS T-box regulator in complex with tRNAGly

PubMed Central

Chetnani, Bhaskar

2017-01-01

Abstract A T-box regulator or riboswitch actively monitors the levels of charged/uncharged tRNA and participates in amino acid homeostasis by regulating genes involved in their utilization or biosynthesis. It has an aptamer domain for cognate tRNA recognition and an expression platform to sense the charge state and modulate gene expression. These two conserved domains are connected by a variable linker that harbors additional secondary structural elements, such as Stem III. The structural basis for specific tRNA binding is known, but the structural basis for charge sensing and the role of other elements remains elusive. To gain new structural insights on the T-box mechanism, a molecular envelope was calculated from small angle X-ray scattering data for the Bacillus subtilis glyQS T-box riboswitch in complex with an uncharged tRNAGly. A structural model of an anti-terminated glyQS T-box in complex with its cognate tRNAGly was derived based on the molecular envelope. It shows the location and relative orientation of various secondary structural elements. The model was validated by comparing the envelopes of the wild-type complex and two variants. The structural model suggests that in addition to a possible regulatory role, Stem III could aid in preferential stabilization of the T-box anti-terminated state allowing read-through of regulated genes. PMID:28531275

System load forecasts for an electric utility. [Hourly loads using Box-Jenkins method

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

Uri, N.D.

This paper discusses forecasting hourly system load for an electric utility using Box-Jenkins time-series analysis. The results indicate that a model based on the method of Box and Jenkins, given its simplicity, gives excellent results over the forecast horizon.

Virtual reality simulator training of laparoscopic cholecystectomies - a systematic review.

PubMed

Ikonen, T S; Antikainen, T; Silvennoinen, M; Isojärvi, J; Mäkinen, E; Scheinin, T M

2012-01-01

Simulators are widely used in occupations where practice in authentic environments would involve high human or economic risks. Surgical procedures can be simulated by increasingly complex and expensive techniques. This review gives an update on computer-based virtual reality (VR) simulators in training for laparoscopic cholecystectomies. From leading databases (Medline, Cochrane, Embase), randomised or controlled trials and the latest systematic reviews were systematically searched and reviewed. Twelve randomised trials involving simulators were identified and analysed, as well as four controlled studies. Furthermore, seven studies comparing black boxes and simulators were included. The results indicated any kind of simulator training (black box, VR) to be beneficial at novice level. After VR training, novice surgeons seemed to be able to perform their first live cholecystectomies with fewer errors, and in one trial the positive effect remained during the first ten cholecystectomies. No clinical follow-up data were found. Optimal learning requires skills training to be conducted as part of a systematic training program. No data on the cost-benefit of simulators were found, the price of a VR simulator begins at EUR 60 000. Theoretical background to learning and limited research data support the use of simulators in the early phases of surgical training. The cost of buying and using simulators is justified if the risk of injuries and complications to patients can be reduced. Developing surgical skills requires repeated training. In order to achieve optimal learning a validated training program is needed.

Sensitivity and spin-up times of cohesive sediment transport models used to simulate bathymetric change: Chapter 31

USGS Publications Warehouse

Schoellhamer, D.H.; Ganju, N.K.; Mineart, P.R.; Lionberger, M.A.; Kusuda, T.; Yamanishi, H.; Spearman, J.; Gailani, J. Z.

2008-01-01

Bathymetric change in tidal environments is modulated by watershed sediment yield, hydrodynamic processes, benthic composition, and anthropogenic activities. These multiple forcings combine to complicate simple prediction of bathymetric change; therefore, numerical models are necessary to simulate sediment transport. Errors arise from these simulations, due to inaccurate initial conditions and model parameters. We investigated the response of bathymetric change to initial conditions and model parameters with a simplified zero-dimensional cohesive sediment transport model, a two-dimensional hydrodynamic/sediment transport model, and a tidally averaged box model. The zero-dimensional model consists of a well-mixed control volume subjected to a semidiurnal tide, with a cohesive sediment bed. Typical cohesive sediment parameters were utilized for both the bed and suspended sediment. The model was run until equilibrium in terms of bathymetric change was reached, where equilibrium is defined as less than the rate of sea level rise in San Francisco Bay (2.17 mm/year). Using this state as the initial condition, model parameters were perturbed 10% to favor deposition, and the model was resumed. Perturbed parameters included, but were not limited to, maximum tidal current, erosion rate constant, and critical shear stress for erosion. Bathymetric change was most sensitive to maximum tidal current, with a 10% perturbation resulting in an additional 1.4 m of deposition over 10 years. Re-establishing equilibrium in this model required 14 years. The next most sensitive parameter was the critical shear stress for erosion; when increased 10%, an additional 0.56 m of sediment was deposited and 13 years were required to re-establish equilibrium. The two-dimensional hydrodynamic/sediment transport model was calibrated to suspended-sediment concentration, and despite robust solution of hydrodynamic conditions it was unable to accurately hindcast bathymetric change. The tidally averaged box model was calibrated to bathymetric change data and shows rapidly evolving bathymetry in the first 10-20 years, though sediment supply and hydrodynamic forcing did not vary greatly. This initial burst of bathymetric change is believed to be model adjustment to initial conditions, and suggests a spin-up time of greater than 10 years. These three diverse modeling approaches reinforce the sensitivity of cohesive sediment transport models to initial conditions and model parameters, and highlight the importance of appropriate calibration data. Adequate spin-up time of the order of years is required to initialize models, otherwise the solution will contain bathymetric change that is not due to environmental forcings, but rather improper specification of initial conditions and model parameters. Temporally intensive bathymetric change data can assist in determining initial conditions and parameters, provided they are available. Computational effort may be reduced by selectively updating hydrodynamics and bathymetry, thereby allowing time for spin-up periods. reserved.

Validation of a noninvasive system for measuring head acceleration for use during boxing competition.

PubMed

Beckwith, Jonathan G; Chu, Jeffrey J; Greenwald, Richard M

2007-08-01

Although the epidemiology and mechanics of concussion in sports have been investigated for many years, the biomechanical factors that contribute to mild traumatic brain injury remain unclear because of the difficulties in measuring impact events in the field. The purpose of this study was to validate an instrumented boxing headgear (IBH) that can be used to measure impact severity and location during play. The instrumented boxing headgear data were processed to determine linear and rotational acceleration at the head center of gravity, impact location, and impact severity metrics, such as the Head Injury Criterion (HIC) and Gadd Severity Index (GSI). The instrumented boxing headgear was fitted to a Hybrid III (HIII) head form and impacted with a weighted pendulum to characterize accuracy and repeatability. Fifty-six impacts over 3 speeds and 5 locations were used to simulate blows most commonly observed in boxing. A high correlation between the HIII and instrumented boxing headgear was established for peak linear and rotational acceleration (r2= 0.91), HIC (r2 = 0.88), and GSI (r2 = 0.89). Mean location error was 9.7 +/- 5.2 masculine. Based on this study, the IBH is a valid system for measuring head acceleration and impact location that can be integrated into training and competition.

Total OH reactivity as a constraint of model calculated peroxy radical production, and the catalytic efficiency of NOx in O3 production in a boreal forest environment.

NASA Astrophysics Data System (ADS)

Javed, M. U.; Hens, K.; Martinez, M.; Kubistin, D.; Novelli, A.; Beygi, Z. H.; Axinte, R.; Nölscher, A. C.; Sinha, V.; Song, W.; Johnson, A. M.; Auld, J.; Bohn, B.; Sander, R.; Taraborrelli, D.; Williams, J.; Fischer, H.; Lelieveld, J.; Harder, H.

2016-12-01

Peroxy radicals play a key role in ozone (O3) production and hydroxyl (OH) recycling influencing the self-cleansing capacity and air quality. Organic peroxy radical (RO2) concentrations are estimated by three different approaches for a boreal forest, based on the field campaign HUMPPA-COPEC 2010 in Southern Finland. RO2 concentrations were simulated by a box model constrained by the comprehensive dataset from the campaign and cross-checked against the photostationary state (PSS) of NOx [= nitric oxide (NO) + nitrogen dioxide (NO2)] calculations. The model simulated RO2 concentrations appear too low to explain the measured PSS of NOx. As the atmospheric RO2 production is proportional to OH loss, the total OH loss rate frequency (total OH reactivity) in the model is underestimated compared to the measurements. The total OH reactivity of the model is tuned to match the observed total OH reactivity by increasing the biogenic volatile organic compound (BVOCs) concentrations for the model simulations. The new-found simulated RO2 concentrations based on the tuned OH reactivity explain the measured PSS of NOx reasonably well. Furthermore, the sensitivity of the NOx lifetime and the catalytic efficiency of NOx (CE) in O3 production, in the context of organic alkyl nitrate (RONO2) formation, was also investigated. Based on the campaign data, it was found that the lifetime of NOx and the CE are reduced and are sensitive to the RONO2 formation under low-NOx conditions, which matches a previous model-based study.

Salt tectonics in an experimental turbiditic tank

NASA Astrophysics Data System (ADS)

Sellier, Nicolas; Vendeville, Bruno

2010-05-01

We modelled the effect of the deposition of clastic sediments wedges along passive margin by combining two different experimental approaches. The first approach, which uses flume experiments in order to model turbiditic transport and deposition, had focused, so far mainly on the stratigraphic architecture and flow properties. But most experiments have not accounted for the impact of syndepositional deformation. The second approach is the classic tectonic modelling (sand-box experiments) is aimed essentially at understanding deformation, for example the deformation of a sediment wedge deposited onto a mobile salt layer. However, with this approach, the sediment transport processes are crudely modelled by adding each sediment layer uniformly, regardless of the potential influence of the sea-floor bathymetry on the depositional pattern. We designed a new tectono-stratigraphic modelling tank, which combines modelling of the turbiditic transport and deposition, and salt-related deformation driven by sediment loading. The set-up comprises a channel connected to a main water tank. A deformation box is placed at the mouth of the channel, on the base of the tank. The base of the box can be filled with various kinds of substrates either rigid (sand) or viscous (silicone polymer, simulating mobile salt layer having varying length and thickness). A mixture of fine-grained powder and water is maintained in suspension in a container, and then released and channelled toward the basin, generating an analogue of basin-floor fans or lobes. We investigated the effect of depositing several consecutive turbiditic lobes on the deformation of the salt body and its overburden. The dynamics of experimental turbidity currents lead to deposits whose thickness varied gradually laterally: the lobe is thick in the proximal region and thins progressively distally, thus creating a very gentle regional surface slope. As the fan grows by episodic deposition of successive turbiditic lobes, the model deforms spontaneously by vertical collapse and lateral spreading of the entire overburden. We conducted a series of systematic experiments varying the length and thickness of the salt body, as well as the sediment input and nature.

Ferrite HOM Absorber for the RHIC ERL

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

Hahn,H.; Choi, E.M.; Hammons, L.

A superconducting Energy Recovery Linac is under construction at Brookhaven National Laboratory to serve as test bed for RHIC upgrades. The damping of higher-order modes in the superconducting five-cell cavity for the Energy-Recovery linac at RHIC is performed exclusively by two ferrite absorbers. The ferrite properties have been measured in ferrite-loaded pill box cavities resulting in the permeability values given by a first-order Debye model for the tiled absorber structure and an equivalent permeability value for computer simulations with solid ring dampers. Measured and simulated results for the higher-order modes in the prototype copper cavity are discussed. First room-temperature measurementsmore » of the finished niobium cavity are presented which confirm the effective damping of higher-order modes in the ERL. by the ferrite absorbers.« less

A direct comparison of U.S. Environmental Protection Agency's method 304B and batch tests for determining activated-sludge biodegradation rate constants for volatile organic compounds

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

Cano, M.L.; Wilcox, M.E.; Compernolle, R. van

Biodegradation rate constants for volatile organic compounds (VOCs) in activated-sludge systems are needed to quantify emissions. One current US environmental Protection Agency method for determining a biodegradation rate constant is Method 304B. In this approach, a specific activated-sludge unit is simulated by a continuous biological treatment system with a sealed headspace. Batch experiments, however, can be alternatives to Method 304B. Two of these batch methods are the batch test that uses oxygen addition (BOX) and the serum bottle test (SBT). In this study, Method 304B was directly compared to BOX and SBT experiments. A pilot-scale laboratory reactor was constructed tomore » serve as the Method 304B unit. Biomass from the unit was also used to conduct BOX and modified SBT experiments (modification involved use of a sealed draft-tube reactor with a headspace recirculation pump instead of a serum bottle) for 1,2-dichloroethane, diisopropyl ether, methyl tertiary butyl ether, and toluene. Three experimental runs--each consisting of one Method 304B experiment, one BOX experiment, and one modified SBT experiment--were completed. The BOX and SBT data for each run were analyzed using a Monod model, and best-fit biodegradation kinetic parameters were determined for each experiment, including a first-order biodegradation rate constant (K{sub 1}). Experimental results suggest that for readily biodegradable VOCs the two batch techniques can provide improved means of determining biodegradation rate constants compared with Method 304B. In particular, these batch techniques avoid the Method 304B problem associated with steady-state effluent concentrations below analytical detection limits. However, experimental results also suggest that the two batch techniques should not be used to determine biodegradation rate constants for slowly degraded VOCs (i.e., K{sub 1} {lt} 0.1 L/g VSS-h).« less

Gene transfer of high-mobility group box 1 box-A domain in a rat acute liver failure model.

PubMed

Tanaka, Masayuki; Shinoda, Masahiro; Takayanagi, Atsushi; Oshima, Go; Nishiyama, Ryo; Fukuda, Kazumasa; Yagi, Hiroshi; Hayashida, Tetsu; Masugi, Yohei; Suda, Koichi; Yamada, Shingo; Miyasho, Taku; Hibi, Taizo; Abe, Yuta; Kitago, Minoru; Obara, Hideaki; Itano, Osamu; Takeuchi, Hiroya; Sakamoto, Michiie; Tanabe, Minoru; Maruyama, Ikuro; Kitagawa, Yuko

2015-04-01

High-mobility group box 1 (HMGB1) has recently been identified as an important mediator of various kinds of acute and chronic inflammation. The protein encoded by the box-A domain of the HMGB1 gene is known to act as a competitive inhibitor of HMGB1. In this study, we investigated whether box-A gene transfer results in box-A protein production in rats and assessed therapeutic efficacy in vivo using an acute liver failure (ALF) model. Three types of adenovirus vectors were constructed-a wild type and two mutants-and a mutant vector was then selected based on the secretion from HeLa cells. The secreted protein was subjected to a tumor necrosis factor (TNF) production inhibition test in vitro. The vector was injected via the portal vein in healthy Wistar rats to confirm box-A protein production in the liver. The vector was then injected via the portal vein in rats with ALF. Western blot analysis showed enhanced expression of box-A protein in HeLa cells transfected with one of the mutant vectors. The culture supernatant from HeLa cells transfected with the vector inhibited TNF-α production from macrophages. Expression of box-A protein was confirmed in the transfected liver at 72 h after transfection. Transfected rats showed decreased hepatic enzymes, plasma HMGB1, and hepatic TNF-α messenger RNA levels, and histologic findings and survival were significantly improved. HMGB1 box-A gene transfer results in box-A protein production in the liver and appears to have a beneficial effect on ALF in rats. Copyright © 2015 Elsevier Inc. All rights reserved.

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

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

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

Tail reconnection in the global magnetospheric context: Vlasiator first results

NASA Astrophysics Data System (ADS)

Palmroth, Minna; Hoilijoki, Sanni; Juusola, Liisa; Pulkkinen, Tuija I.; Hietala, Heli; Pfau-Kempf, Yann; Ganse, Urs; von Alfthan, Sebastian; Vainio, Rami; Hesse, Michael

2017-11-01

The key dynamics of the magnetotail have been researched for decades and have been associated with either three-dimensional (3-D) plasma instabilities and/or magnetic reconnection. We apply a global hybrid-Vlasov code, Vlasiator, to simulate reconnection self-consistently in the ion kinetic scales in the noon-midnight meridional plane, including both dayside and nightside reconnection regions within the same simulation box. Our simulation represents a numerical experiment, which turns off the 3-D instabilities but models ion-scale reconnection physically accurately in 2-D. We demonstrate that many known tail dynamics are present in the simulation without a full description of 3-D instabilities or without the detailed description of the electrons. While multiple reconnection sites can coexist in the plasma sheet, one reconnection point can start a global reconfiguration process, in which magnetic field lines become detached and a plasmoid is released. As the simulation run features temporally steady solar wind input, this global reconfiguration is not associated with sudden changes in the solar wind. Further, we show that lobe density variations originating from dayside reconnection may play an important role in stabilising tail reconnection.

Nonparametric autocovariance estimation from censored time series by Gaussian imputation.

PubMed

Park, Jung Wook; Genton, Marc G; Ghosh, Sujit K

2009-02-01

One of the most frequently used methods to model the autocovariance function of a second-order stationary time series is to use the parametric framework of autoregressive and moving average models developed by Box and Jenkins. However, such parametric models, though very flexible, may not always be adequate to model autocovariance functions with sharp changes. Furthermore, if the data do not follow the parametric model and are censored at a certain value, the estimation results may not be reliable. We develop a Gaussian imputation method to estimate an autocovariance structure via nonparametric estimation of the autocovariance function in order to address both censoring and incorrect model specification. We demonstrate the effectiveness of the technique in terms of bias and efficiency with simulations under various rates of censoring and underlying models. We describe its application to a time series of silicon concentrations in the Arctic.

Cscibox: A Software System for Age-Model Construction and Evaluation

NASA Astrophysics Data System (ADS)

Bradley, E.; Anderson, K. A.; Marchitto, T. M., Jr.; de Vesine, L. R.; White, J. W. C.; Anderson, D. M.

2014-12-01

CSciBox is an integrated software system for the construction and evaluation of age models of paleo-environmetal archives, both directly dated and cross dated. The time has come to encourage cross-pollinization between earth science and computer science in dating paleorecords. This project addresses that need. The CSciBox code, which is being developed by a team of computer scientists and geoscientists, is open source and freely available on github. The system employs modern database technology to store paleoclimate proxy data and analysis results in an easily accessible and searchable form. This makes it possible to do analysis on the whole core at once, in an interactive fashion, or to tailor the analysis to a subset of the core without loading the entire data file. CSciBox provides a number of 'components' that perform the common steps in age-model construction and evaluation: calibrations, reservoir-age correction, interpolations, statistics, and so on. The user employs these components via a graphical user interface (GUI) to go from raw data to finished age model in a single tool: e.g., an IntCal09 calibration of 14C data from a marine sediment core, followed by a piecewise-linear interpolation. CSciBox's GUI supports plotting of any measurement in the core against any other measurement, or against any of the variables in the calculation of the age model-with or without explicit error representations. Using the GUI, CSciBox's user can import a new calibration curve or other background data set and define a new module that employs that information. Users can also incorporate other software (e.g., Calib, BACON) as 'plug ins.' In the case of truly large data or significant computational effort, CSciBox is parallelizable across modern multicore processors, or clusters, or even the cloud. The next generation of the CSciBox code, currently in the testing stages, includes an automated reasoning engine that supports a more-thorough exploration of plausible age models and cross-dating scenarios.

A new finite element and finite difference hybrid method for computing electrostatics of ionic solvated biomolecule

NASA Astrophysics Data System (ADS)

Ying, Jinyong; Xie, Dexuan

2015-10-01

The Poisson-Boltzmann equation (PBE) is one widely-used implicit solvent continuum model for calculating electrostatics of ionic solvated biomolecule. In this paper, a new finite element and finite difference hybrid method is presented to solve PBE efficiently based on a special seven-overlapped box partition with one central box containing the solute region and surrounded by six neighboring boxes. In particular, an efficient finite element solver is applied to the central box while a fast preconditioned conjugate gradient method using a multigrid V-cycle preconditioning is constructed for solving a system of finite difference equations defined on a uniform mesh of each neighboring box. Moreover, the PBE domain, the box partition, and an interface fitted tetrahedral mesh of the central box can be generated adaptively for a given PQR file of a biomolecule. This new hybrid PBE solver is programmed in C, Fortran, and Python as a software tool for predicting electrostatics of a biomolecule in a symmetric 1:1 ionic solvent. Numerical results on two test models with analytical solutions and 12 proteins validate this new software tool, and demonstrate its high performance in terms of CPU time and memory usage.