Challenges in Reproducibility, Replicability, and Comparability of Computational Models and Tools for Neuronal and Glial Networks, Cells, and Subcellular Structures.

PubMed

Manninen, Tiina; Aćimović, Jugoslava; Havela, Riikka; Teppola, Heidi; Linne, Marja-Leena

2018-01-01

The possibility to replicate and reproduce published research results is one of the biggest challenges in all areas of science. In computational neuroscience, there are thousands of models available. However, it is rarely possible to reimplement the models based on the information in the original publication, let alone rerun the models just because the model implementations have not been made publicly available. We evaluate and discuss the comparability of a versatile choice of simulation tools: tools for biochemical reactions and spiking neuronal networks, and relatively new tools for growth in cell cultures. The replicability and reproducibility issues are considered for computational models that are equally diverse, including the models for intracellular signal transduction of neurons and glial cells, in addition to single glial cells, neuron-glia interactions, and selected examples of spiking neuronal networks. We also address the comparability of the simulation results with one another to comprehend if the studied models can be used to answer similar research questions. In addition to presenting the challenges in reproducibility and replicability of published results in computational neuroscience, we highlight the need for developing recommendations and good practices for publishing simulation tools and computational models. Model validation and flexible model description must be an integral part of the tool used to simulate and develop computational models. Constant improvement on experimental techniques and recording protocols leads to increasing knowledge about the biophysical mechanisms in neural systems. This poses new challenges for computational neuroscience: extended or completely new computational methods and models may be required. Careful evaluation and categorization of the existing models and tools provide a foundation for these future needs, for constructing multiscale models or extending the models to incorporate additional or more detailed biophysical mechanisms. Improving the quality of publications in computational neuroscience, enabling progressive building of advanced computational models and tools, can be achieved only through adopting publishing standards which underline replicability and reproducibility of research results.

Challenges in Reproducibility, Replicability, and Comparability of Computational Models and Tools for Neuronal and Glial Networks, Cells, and Subcellular Structures

PubMed Central

Manninen, Tiina; Aćimović, Jugoslava; Havela, Riikka; Teppola, Heidi; Linne, Marja-Leena

2018-01-01

The possibility to replicate and reproduce published research results is one of the biggest challenges in all areas of science. In computational neuroscience, there are thousands of models available. However, it is rarely possible to reimplement the models based on the information in the original publication, let alone rerun the models just because the model implementations have not been made publicly available. We evaluate and discuss the comparability of a versatile choice of simulation tools: tools for biochemical reactions and spiking neuronal networks, and relatively new tools for growth in cell cultures. The replicability and reproducibility issues are considered for computational models that are equally diverse, including the models for intracellular signal transduction of neurons and glial cells, in addition to single glial cells, neuron-glia interactions, and selected examples of spiking neuronal networks. We also address the comparability of the simulation results with one another to comprehend if the studied models can be used to answer similar research questions. In addition to presenting the challenges in reproducibility and replicability of published results in computational neuroscience, we highlight the need for developing recommendations and good practices for publishing simulation tools and computational models. Model validation and flexible model description must be an integral part of the tool used to simulate and develop computational models. Constant improvement on experimental techniques and recording protocols leads to increasing knowledge about the biophysical mechanisms in neural systems. This poses new challenges for computational neuroscience: extended or completely new computational methods and models may be required. Careful evaluation and categorization of the existing models and tools provide a foundation for these future needs, for constructing multiscale models or extending the models to incorporate additional or more detailed biophysical mechanisms. Improving the quality of publications in computational neuroscience, enabling progressive building of advanced computational models and tools, can be achieved only through adopting publishing standards which underline replicability and reproducibility of research results. PMID:29765315

Validation of a Monte Carlo simulation of the Inveon PET scanner using GATE

NASA Astrophysics Data System (ADS)

Lu, Lijun; Zhang, Houjin; Bian, Zhaoying; Ma, Jianhua; Feng, Qiangjin; Chen, Wufan

2016-08-01

The purpose of this study is to validate the application of GATE (Geant4 Application for Tomographic Emission) Monte Carlo simulation toolkit in order to model the performance characteristics of Siemens Inveon small animal PET system. The simulation results were validated against experimental/published data in accordance with the NEMA NU-4 2008 protocol for standardized evaluation of spatial resolution, sensitivity, scatter fraction (SF) and noise equivalent counting rate (NECR) of a preclinical PET system. An agreement of less than 18% was obtained between the radial, tangential and axial spatial resolutions of the simulated and experimental results. The simulated peak NECR of mouse-size phantom agreed with the experimental result, while for the rat-size phantom simulated value was higher than experimental result. The simulated and experimental SFs of mouse- and rat- size phantom both reached an agreement of less than 2%. It has been shown the feasibility of our GATE model to accurately simulate, within certain limits, all major performance characteristics of Inveon PET system.

Publishing a Simulation Game.

ERIC Educational Resources Information Center

Gohring, Ralph J.

1979-01-01

A case study describing the process involved in publishing a personally developed simulation game including finding a publisher, obtaining a copyright, negotiating the contract, controlling front-end costs, marketing the product, and receiving feedback from users. (CMV)

Publishing and sharing of hydrologic models through WaterHUB

NASA Astrophysics Data System (ADS)

Merwade, V.; Ruddell, B. L.; Song, C.; Zhao, L.; Kim, J.; Assi, A.

2011-12-01

Most hydrologists use hydrologic models to simulate the hydrologic processes to understand hydrologic pathways and fluxes for research, decision making and engineering design. Once these tasks are complete including publication of results, the models generally are not published or made available to the public for further use and improvement. Although publication or sharing of models is not required for journal publications, sharing of models may open doors for new collaborations, and avoids duplication of efforts if other researchers are interested in simulating a particular watershed for which a model already exists. For researchers, who are interested in sharing models, there are limited avenues to publishing their models to the wider community. Towards filling this gap, a prototype cyberinfrastructure (CI), called WaterHUB, is developed for sharing hydrologic data and modeling tools in an interactive environment. To test the utility of WaterHUB for sharing hydrologic models, a system to publish and share SWAT (Soil Water Assessment Tool) is developed. Users can utilize WaterHUB to search and download existing SWAT models, and also upload new SWAT models. Metadata such as the name of the watershed, name of the person or agency who developed the model, simulation period, time step, and list of calibrated parameters also published with individual model.

Modeling variably saturated subsurface solute transport with MODFLOW-UZF and MT3DMS.

PubMed

Morway, Eric D; Niswonger, Richard G; Langevin, Christian D; Bailey, Ryan T; Healy, Richard W

2013-03-01

The MT3DMS groundwater solute transport model was modified to simulate solute transport in the unsaturated zone by incorporating the unsaturated-zone flow (UZF1) package developed for MODFLOW. The modified MT3DMS code uses a volume-averaged approach in which Lagrangian-based UZF1 fluid fluxes and storage changes are mapped onto a fixed grid. Referred to as UZF-MT3DMS, the linked model was tested against published benchmarks solved analytically as well as against other published codes, most frequently the U.S. Geological Survey's Variably-Saturated Two-Dimensional Flow and Transport Model. Results from a suite of test cases demonstrate that the modified code accurately simulates solute advection, dispersion, and reaction in the unsaturated zone. Two- and three-dimensional simulations also were investigated to ensure unsaturated-saturated zone interaction was simulated correctly. Because the UZF1 solution is analytical, large-scale flow and transport investigations can be performed free from the computational and data burdens required by numerical solutions to Richards' equation. Results demonstrate that significant simulation runtime savings can be achieved with UZF-MT3DMS, an important development when hundreds or thousands of model runs are required during parameter estimation and uncertainty analysis. Three-dimensional variably saturated flow and transport simulations revealed UZF-MT3DMS to have runtimes that are less than one tenth of the time required by models that rely on Richards' equation. Given its accuracy and efficiency, and the wide-spread use of both MODFLOW and MT3DMS, the added capability of unsaturated-zone transport in this familiar modeling framework stands to benefit a broad user-ship. Published 2012. This article is a U.S. Government work and is in the public domain in the USA.

Finite element modelling for mode-I fracture behaviour of CFRP

NASA Astrophysics Data System (ADS)

Chetan, H. C.; Kattimani, Subhaschandra; Murigendrappa, S. M.

2018-04-01

Debonding is a major failure mechanism in Carbon Fiber Reinforced Polymer (CFRP) due to presence of many adhesion joins, in between many layers. In the current study a finite element simulation is carried out using Virtual Crack Closure Technique (VCCT) and Cohesive Zone Modelling (CZM) using Abaqus as analysis tool. A comparative study is performed in to order analyze convergence of results from CZM and VCCT. It was noted that CZM results matched well with published literature. The results from VCCT were also in good comparison with experimental data of published literature, but were seen to be overestimated. Parametric study is performed to evaluate the variation of input parameters like initial stiffness, element size, peak stress and energy release rate `G'. From the numerical evaluation, it was noted that CZM simulation relies largely on element size and peak stress.

Medical Simulation Practices 2010 Survey Results

NASA Technical Reports Server (NTRS)

McCrindle, Jeffrey J.

2011-01-01

Medical Simulation Centers are an essential component of our learning infrastructure to prepare doctors and nurses for their careers. Unlike the military and aerospace simulation industry, very little has been published regarding the best practices currently in use within medical simulation centers. This survey attempts to provide insight into the current simulation practices at medical schools, hospitals, university nursing programs and community college nursing programs. Students within the MBA program at Saint Joseph's University conducted a survey of medical simulation practices during the summer 2010 semester. A total of 115 institutions responded to the survey. The survey resus discuss overall effectiveness of current simulation centers as well as the tools and techniques used to conduct the simulation activity

Hierarchical CAD Tools for Radiation Hardened Mixed Signal Electronic Circuits

DTIC Science & Technology

2005-01-28

11 Figure 3: Schematic of Analog and Digital Components 12 Figure 4: Dose Rate Syntax 14 Figure 5: Single Event Effects (SEE) Syntax 15 Figure 6...Harmony-AMS simulation of a Digital Phase Locked Loop 19 Figure 10: SEE results from DPLL Simulation 20 Figure 11: Published results used for validation...analog and digital circuitry. Combining the analog and digital elements onto a single chip has several advantages, but also creates unique challenges

Twenty Years On!: Updating the IEA BESTEST Building Thermal Fabric Test Cases for ASHRAE Standard 140

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

Judkoff, R.; Neymark, J.

2013-07-01

ANSI/ASHRAE Standard 140, Standard Method of Test for the Evaluation of Building Energy Analysis Computer Programs applies the IEA BESTEST building thermal fabric test cases and example simulation results originally published in 1995. These software accuracy test cases and their example simulation results, which comprise the first test suite adapted for the initial 2001 version of Standard 140, are approaching their 20th anniversary. In response to the evolution of the state of the art in building thermal fabric modeling since the test cases and example simulation results were developed, work is commencing to update the normative test specification and themore » informative example results.« less

Twenty Years On!: Updating the IEA BESTEST Building Thermal Fabric Test Cases for ASHRAE Standard 140: Preprint

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

Judkoff, R.; Neymark, J.

2013-07-01

ANSI/ASHRAE Standard 140, Standard Method of Test for the Evaluation of Building Energy Analysis Computer Programs applies the IEA BESTEST building thermal fabric test cases and example simulation results originally published in 1995. These software accuracy test cases and their example simulation results, which comprise the first test suite adapted for the initial 2001 version of Standard 140, are approaching their 20th anniversary. In response to the evolution of the state of the art in building thermal fabric modeling since the test cases and example simulation results were developed, work is commencing to update the normative test specification and themore » informative example results.« less

Development of a Dependency Theory Toolbox for Database Design.

DTIC Science & Technology

1987-12-01

published algorithms and theorems , and hand simulating these algorithms can be a tedious and error prone chore. Additionally, since the process of...to design and study relational databases exists in the form of published algorithms and theorems . However, hand simulating these algorithms can be a...published algorithms and theorems . Hand simulating these algorithms can be a tedious and error prone chore. Therefore, a toolbox of algorithms and

Neuronvisio: A Graphical User Interface with 3D Capabilities for NEURON.

PubMed

Mattioni, Michele; Cohen, Uri; Le Novère, Nicolas

2012-01-01

The NEURON simulation environment is a commonly used tool to perform electrical simulation of neurons and neuronal networks. The NEURON User Interface, based on the now discontinued InterViews library, provides some limited facilities to explore models and to plot their simulation results. Other limitations include the inability to generate a three-dimensional visualization, no standard mean to save the results of simulations, or to store the model geometry within the results. Neuronvisio (http://neuronvisio.org) aims to address these deficiencies through a set of well designed python APIs and provides an improved UI, allowing users to explore and interact with the model. Neuronvisio also facilitates access to previously published models, allowing users to browse, download, and locally run NEURON models stored in ModelDB. Neuronvisio uses the matplotlib library to plot simulation results and uses the HDF standard format to store simulation results. Neuronvisio can be viewed as an extension of NEURON, facilitating typical user workflows such as model browsing, selection, download, compilation, and simulation. The 3D viewer simplifies the exploration of complex model structure, while matplotlib permits the plotting of high-quality graphs. The newly introduced ability of saving numerical results allows users to perform additional analysis on their previous simulations.

Atmospheric Dispersion Modeling of the February 2014 Waste Isolation Pilot Plant Release

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

Nasstrom, John; Piggott, Tom; Simpson, Matthew

2015-07-22

This report presents the results of a simulation of the atmospheric dispersion and deposition of radioactivity released from the Waste Isolation Pilot Plant (WIPP) site in New Mexico in February 2014. These simulations were made by the National Atmospheric Release Advisory Center (NARAC) at Lawrence Livermore National Laboratory (LLNL), and supersede NARAC simulation results published in a previous WIPP report (WIPP, 2014). The results presented in this report use additional, more detailed data from WIPP on the specific radionuclides released, radioactivity release amounts and release times. Compared to the previous NARAC simulations, the new simulation results in this report aremore » based on more detailed modeling of the winds, turbulence, and particle dry deposition. In addition, the initial plume rise from the exhaust vent was considered in the new simulations, but not in the previous NARAC simulations. The new model results show some small differences compared to previous results, but do not change the conclusions in the WIPP (2014) report. Presented are the data and assumptions used in these model simulations, as well as the model-predicted dose and deposition on and near the WIPP site. A comparison of predicted and measured radionuclide-specific air concentrations is also presented.« less

Gryphon: A Hybrid Agent-Based Modeling and Simulation Platform for Infectious Diseases

NASA Astrophysics Data System (ADS)

Yu, Bin; Wang, Jijun; McGowan, Michael; Vaidyanathan, Ganesh; Younger, Kristofer

In this paper we present Gryphon, a hybrid agent-based stochastic modeling and simulation platform developed for characterizing the geographic spread of infectious diseases and the effects of interventions. We study both local and non-local transmission dynamics of stochastic simulations based on the published parameters and data for SARS. The results suggest that the expected numbers of infections and the timeline of control strategies predicted by our stochastic model are in reasonably good agreement with previous studies. These preliminary results indicate that Gryphon is able to characterize other future infectious diseases and identify endangered regions in advance.

Evaluation of near surface ozone and particulate matter in air ...

EPA Pesticide Factsheets

In this study, techniques typically used for future air quality projections are applied to a historical 11-year period to assess the performance of the modeling system when the driving meteorological conditions are obtained using dynamical downscaling of coarse-scale fields without correcting toward higher-resolution observations. The Weather Research and Forecasting model and the Community Multiscale Air Quality model are used to simulate regional climate and air quality over the contiguous United States for 2000–2010. The air quality simulations for that historical period are then compared to observations from four national networks. Comparisons are drawn between defined performance metrics and other published modeling results for predicted ozone, fine particulate matter, and speciated fine particulate matter. The results indicate that the historical air quality simulations driven by dynamically downscaled meteorology are typically within defined modeling performance benchmarks and are consistent with results from other published modeling studies using finer-resolution meteorology. This indicates that the regional climate and air quality modeling framework utilized here does not introduce substantial bias, which provides confidence in the method’s use for future air quality projections. This paper shows that if emissions inputs and coarse-scale meteorological inputs are reasonably accurate, then air quality can be simulated with acceptable accuracy even wi

Case Studies Comparing System Advisor Model (SAM) Results to Real Performance Data: Preprint

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

Blair, N.; Dobos, A.; Sather, N.

2012-06-01

NREL has completed a series of detailed case studies comparing the simulations of the System Advisor Model (SAM) and measured performance data or published performance expectations. These case studies compare PV measured performance data with simulated performance data using appropriate weather data. The measured data sets were primarily taken from NREL onsite PV systems and weather monitoring stations.

Direct numerical simulation of cellular-scale blood flow in microvascular networks

NASA Astrophysics Data System (ADS)

Balogh, Peter; Bagchi, Prosenjit

2017-11-01

A direct numerical simulation method is developed to study cellular-scale blood flow in physiologically realistic microvascular networks that are constructed in silico following published in vivo images and data, and are comprised of bifurcating, merging, and winding vessels. The model resolves large deformation of individual red blood cells (RBC) flowing in such complex networks. The vascular walls and deformable interfaces of the RBCs are modeled using the immersed-boundary methods. Time-averaged hemodynamic quantities obtained from the simulations agree quite well with published in vivo data. Our simulations reveal that in several vessels the flow rates and pressure drops could be negatively correlated. The flow resistance and hematocrit are also found to be negatively correlated in some vessels. These observations suggest a deviation from the classical Poiseuille's law in such vessels. The cells are observed to frequently jam at vascular bifurcations resulting in reductions in hematocrit and flow rate in the daughter and mother vessels. We find that RBC jamming results in several orders of magnitude increase in hemodynamic resistance, and thus provides an additional mechanism of increased in vivo blood viscosity as compared to that determined in vitro. Funded by NSF CBET 1604308.

Optical ensemble analysis of intraocular lens performance through a simulated clinical trial with ZEMAX.

PubMed

Zhao, Huawei

2009-01-01

A ZEMAX model was constructed to simulate a clinical trial of intraocular lenses (IOLs) based on a clinically oriented Monte Carlo ensemble analysis using postoperative ocular parameters. The purpose of this model is to test the feasibility of streamlining and optimizing both the design process and the clinical testing of IOLs. This optical ensemble analysis (OEA) is also validated. Simulated pseudophakic eyes were generated by using the tolerancing and programming features of ZEMAX optical design software. OEA methodology was verified by demonstrating that the results of clinical performance simulations were consistent with previously published clinical performance data using the same types of IOLs. From these results we conclude that the OEA method can objectively simulate the potential clinical trial performance of IOLs.

Skin hydration analysis by experiment and computer simulations and its implications for diapered skin.

PubMed

Saadatmand, M; Stone, K J; Vega, V N; Felter, S; Ventura, S; Kasting, G; Jaworska, J

2017-11-01

Experimental work on skin hydration is technologically challenging, and mostly limited to observations where environmental conditions are constant. In some cases, like diapered baby skin, such work is practically unfeasible, yet it is important to understand potential effects of diapering on skin condition. To overcome this challenge, in part, we developed a computer simulation model of reversible transient skin hydration effects. Skin hydration model by Li et al. (Chem Eng Sci, 138, 2015, 164) was further developed to simulate transient exposure conditions where relative humidity (RH), wind velocity, air, and skin temperature can be any function of time. Computer simulations of evaporative water loss (EWL) decay after different occlusion times were compared with experimental data to calibrate the model. Next, we used the model to investigate EWL and SC thickness in different diapering scenarios. Key results from the experimental work were: (1) For occlusions by RH=100% and free water longer than 30 minutes the absorbed amount of water is almost the same; (2) Longer occlusion times result in higher water absorption by the SC. The EWL decay and skin water content predictions were in agreement with experimental data. Simulations also revealed that skin under occlusion hydrates mainly because the outflux is blocked, not because it absorbs water from the environment. Further, simulations demonstrated that hydration level is sensitive to time, RH and/or free water on skin. In simulated diapering scenarios, skin maintained hydration content very close to the baseline conditions without a diaper for the entire duration of a 24 hours period. Different diapers/diaper technologies are known to have different profiles in terms of their ability to provide wetness protection, which can result in consumer-noticeable differences in wetness. Simulation results based on published literature using data from a number of different diapers suggest that diapered skin hydrates within ranges considered reversible. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Estimation of wear in total hip replacement using a ten station hip simulator.

PubMed

Brummitt, K; Hardaker, C S

1996-01-01

The results of hip simulator tests on a total of 16 total hip joints, all of them 22.25 mm Charnley designs, are presented. Wear at up to 6.75 million cycles was assessed by using a coordinate measuring machine. The results gave good agreement with clinical estimates of wear rate on the same design of joint replacement from a number of sources. Good agreement was also obtained when comparison was made with the published results from more sophisticated simulators. The major source of variation in the results was found to occur in the first million cycles where creep predominates. The results of this study support the use of this type of simplified simulator for estimating wear in a total hip prosthesis. The capability to test a significant number of joints simultaneously may make this mechanism preferable to more complex machines in many cases.

Hybrid Particle-Element Simulation of Impact on Composite Orbital Debris Shields

NASA Technical Reports Server (NTRS)

Fahrenthold, Eric P.

2004-01-01

This report describes the development of new numerical methods and new constitutive models for the simulation of hypervelocity impact effects on spacecraft. The research has included parallel implementation of the numerical methods and material models developed under the project. Validation work has included both one dimensional simulations, for comparison with exact solutions, and three dimensional simulations of published hypervelocity impact experiments. The validated formulations have been applied to simulate impact effects in a velocity and kinetic energy regime outside the capabilities of current experimental methods. The research results presented here allow for the expanded use of numerical simulation, as a complement to experimental work, in future design of spacecraft for hypervelocity impact effects.

Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC).

PubMed

Galindo-Murillo, Rodrigo; Roe, Daniel R; Cheatham, Thomas E

2015-05-01

The structure and dynamics of DNA are critically related to its function. Molecular dynamics simulations augment experiment by providing detailed information about the atomic motions. However, to date the simulations have not been long enough for convergence of the dynamics and structural properties of DNA. Molecular dynamics simulations performed with AMBER using the ff99SB force field with the parmbsc0 modifications, including ensembles of independent simulations, were compared to long timescale molecular dynamics performed with the specialized Anton MD engine on the B-DNA structure d(GCACGAACGAACGAACGC). To assess convergence, the decay of the average RMSD values over longer and longer time intervals was evaluated in addition to assessing convergence of the dynamics via the Kullback-Leibler divergence of principal component projection histograms. These molecular dynamics simulations-including one of the longest simulations of DNA published to date at ~44μs-surprisingly suggest that the structure and dynamics of the DNA helix, neglecting the terminal base pairs, are essentially fully converged on the ~1-5μs timescale. We can now reproducibly converge the structure and dynamics of B-DNA helices, omitting the terminal base pairs, on the μs time scale with both the AMBER and CHARMM C36 nucleic acid force fields. Results from independent ensembles of simulations starting from different initial conditions, when aggregated, match the results from long timescale simulations on the specialized Anton MD engine. With access to large-scale GPU resources or the specialized MD engine "Anton" it is possible for a variety of molecular systems to reproducibly and reliably converge the conformational ensemble of sampled structures. This article is part of a Special Issue entitled: Recent developments of molecular dynamics. Copyright © 2014. Published by Elsevier B.V.

SEIR model simulation for Hepatitis B

NASA Astrophysics Data System (ADS)

Side, Syafruddin; Irwan, Mulbar, Usman; Sanusi, Wahidah

2017-09-01

Mathematical modelling and simulation for Hepatitis B discuss in this paper. Population devided by four variables, namely: Susceptible, Exposed, Infected and Recovered (SEIR). Several factors affect the population in this model is vaccination, immigration and emigration that occurred in the population. SEIR Model obtained Ordinary Differential Equation (ODE) non-linear System 4-D which then reduces to 3-D. SEIR model simulation undertaken to predict the number of Hepatitis B cases. The results of the simulation indicates the number of Hepatitis B cases will increase and then decrease for several months. The result of simulation using the number of case in Makassar also found the basic reproduction number less than one, that means, Makassar city is not an endemic area of Hepatitis B. With approval from the proceedings editor article 020185 titled, "SEIR model simulation for Hepatitis B," is retracted from the public record, as it is a duplication of article 020198 published in the same volume.

Impact of revised and potential future albedo estimates on CCSM3 simulations of growing-season surface temperature fields for North America

Treesearch

Warren E. Heilman; David Y. Hollinger; Xiuping Li; Xindi Bain; Shiyuan. Zhong

2010-01-01

Recently published albedo research has resulted in improved growing-season albedo estimates for forest and grassland vegetation. The impact of these improved estimates on the ability of climate models to simulate growing-season surface temperature patterns is unknown. We have developed a set of current-climate surface temperature scenarios for North America using the...

Assessment of the neutron dose field around a biomedical cyclotron: FLUKA simulation and experimental measurements.

PubMed

Infantino, Angelo; Cicoria, Gianfranco; Lucconi, Giulia; Pancaldi, Davide; Vichi, Sara; Zagni, Federico; Mostacci, Domiziano; Marengo, Mario

2016-12-01

In the planning of a new cyclotron facility, an accurate knowledge of the radiation field around the accelerator is fundamental for the design of shielding, the protection of workers, the general public and the environment. Monte Carlo simulations can be very useful in this process, and their use is constantly increasing. However, few data have been published so far as regards the proper validation of Monte Carlo simulation against experimental measurements, particularly in the energy range of biomedical cyclotrons. In this work a detailed model of an existing installation of a GE PETtrace 16.5MeV cyclotron was developed using FLUKA. An extensive measurement campaign of the neutron ambient dose equivalent H ∗ (10) in marked positions around the cyclotron was conducted using a neutron rem-counter probe and CR39 neutron detectors. Data from a previous measurement campaign performed by our group using TLDs were also re-evaluated. The FLUKA model was then validated by comparing the results of high-statistics simulations with experimental data. In 10 out of 12 measurement locations, FLUKA simulations were in agreement within uncertainties with all the three different sets of experimental data; in the remaining 2 positions, the agreement was with 2/3 of the measurements. Our work allows to quantitatively validate our FLUKA simulation setup and confirms that Monte Carlo technique can produce accurate results in the energy range of biomedical cyclotrons. Copyright © 2016 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Undergraduate interprofessional education using high-fidelity paediatric simulation.

PubMed

Stewart, Moira; Kennedy, Neil; Cuene-Grandidier, Hazel

2010-06-01

High-fidelity simulation is becoming increasingly important in the delivery of teaching and learning to health care professionals within a safe environment. Its use in an interprofessional context and at undergraduate level has the potential to facilitate the learning of good communication and teamworking, in addition to clinical knowledge and skills. Interprofessional teaching and learning workshops using high-fidelity paediatric simulation were developed and delivered to undergraduate medical and nursing students at Queen's University Belfast. Learning outcomes common to both professions, and essential in the clinical management of sick children, included basic competencies, communication and teamworking skills. Quantitative and qualitative evaluation was undertaken using published questionnaires. Quantitative results - the 32-item questionnaire was analysed for reliability using spss. Responses were positive for both groups of students across four domains - acquisition of knowledge and skills, communication and teamworking, professional identity and role awareness, and attitudes to shared learning. Qualitative results - thematic content analysis was used to analyse open-ended responses. Students from both groups commented that an interprofessional education (IPE) approach to paediatric simulation improved clinical and practice-based skills, and provided a safe learning environment. Students commented that there should be more interprofessional and simulation learning opportunities. High-fidelity paediatric simulation, used in an interprofessional context, has the potential to meet the requirements of undergraduate medical and nursing curricula. Further research is needed into the long-term benefits for patient care, and its generalisability to other areas within health care teaching and learning. © Blackwell Publishing Ltd 2010.

Simulation of Flood Profiles for Fivemile Creek at Tarrant, Alabama, 2006

USGS Publications Warehouse

Lee, K.G.; Hedgecock, T.S.

2007-01-01

A one-dimensional step-backwater model was used to simulate flooding conditions for Fivemile Creek at Tarrant, Alabama. The 100-year flood stage published in the current flood insurance study for Tarrant by the Federal Emergency Management Agency was significantly exceeded by the March 2000 and May 2003 floods in this area. A peak flow of 14,100 cubic feet per second was computed by the U.S. Geological Survey for the May 2003 flood in the vicinity of Lawson Road. Using this estimated peak flow, flood-plain surveys with associated roughness coefficients, and the surveyed high-water profile for the May 2003 flood, a flow model was calibrated to closely match this known event. The calibrated model was then used to simulate flooding for the 10-, 50-, 100-, and 500-year recurrence interval floods. The results indicate that for the 100-year recurrence interval, the flood profile is about 2.5 feet higher, on average, than the profile published by the Federal Emergency Management Agency. The absolute maximum and minimum difference is 6.80 feet and 0.67 foot, respectively. All water-surface elevations computed for the 100-year flood are higher than those published by the Federal Emergency Management Agency, except for cross section H. The results of this study provide the community with flood-profile information that can be used for existing flood-plain mitigation, future development, and safety plans for the city.

LBflow: An extensible lattice Boltzmann framework for the simulation of geophysical flows. Part II: usage and validation

NASA Astrophysics Data System (ADS)

Llewellin, E. W.

2010-02-01

LBflow is a flexible, extensible implementation of the lattice Boltzmann method, developed with geophysical applications in mind. The theoretical basis for LBflow, and its implementation, are presented in the companion paper, 'Part I'. This article covers the practical usage of LBflow and presents guidelines for obtaining optimal results from available computing power. The relationships among simulation resolution, accuracy, runtime and memory requirements are investigated in detail. Particular attention is paid to the origin, quantification and minimization of errors. LBflow is validated against analytical, numerical and experimental results for a range of three-dimensional flow geometries. The fluid conductance of prismatic pipes with various cross sections is calculated with LBflow and found to be in excellent agreement with published results. Simulated flow along sinusoidally constricted pipes gives good agreement with experimental data for a wide range of Reynolds number. The permeability of packs of spheres is determined and shown to be in excellent agreement with analytical results. The accuracy of internal flow patterns within the investigated geometries is also in excellent quantitative agreement with published data. The development of vortices within a sinusoidally constricted pipe with increasing Reynolds number is shown, demonstrating the insight that LBflow can offer as a 'virtual laboratory' for fluid flow.

The ISI distribution of the stochastic Hodgkin-Huxley neuron.

PubMed

Rowat, Peter F; Greenwood, Priscilla E

2014-01-01

The simulation of ion-channel noise has an important role in computational neuroscience. In recent years several approximate methods of carrying out this simulation have been published, based on stochastic differential equations, and all giving slightly different results. The obvious, and essential, question is: which method is the most accurate and which is most computationally efficient? Here we make a contribution to the answer. We compare interspike interval histograms from simulated data using four different approximate stochastic differential equation (SDE) models of the stochastic Hodgkin-Huxley neuron, as well as the exact Markov chain model simulated by the Gillespie algorithm. One of the recent SDE models is the same as the Kurtz approximation first published in 1978. All the models considered give similar ISI histograms over a wide range of deterministic and stochastic input. Three features of these histograms are an initial peak, followed by one or more bumps, and then an exponential tail. We explore how these features depend on deterministic input and on level of channel noise, and explain the results using the stochastic dynamics of the model. We conclude with a rough ranking of the four SDE models with respect to the similarity of their ISI histograms to the histogram of the exact Markov chain model.

Simulation of Decomposition Kinetics of Supercooled Austenite in Powder Steel

NASA Astrophysics Data System (ADS)

Tsyganova, M. S.; Ivashko, A. G.; Polyshuk, I. N.; Nabatov, R. I.; Tsyganova, A. I.

2017-10-01

To approve heat treatment of steel modes, quantitative data on austenite decomposition are required. Gaining these data experimentally appears to be extremely complicated. In present work, few approaches to simulate the phase transformation process are proposed considering structure characteristics of powder steels. Results of comparative analysis of these approaches are also given. Predicting the transformation kinetics by simulation is verified for PK40N2M (0.38% C, 2.10% Ni, 0.40% Mo) steel with 3% porosity and PK80 (0.80% C) steel with different porosity using published experimental data.

Chinks in Solar Dynamo Theory: Turbulent Diffusion, Dynamo Waves and Magnetic Helicity

NASA Technical Reports Server (NTRS)

DeLuca, E. E.; Wagner, William J. (Technical Monitor)

2001-01-01

We have investigated the generation of magnetic fields in the Sun using two-dimensional and three-dimensional numerical simulations. The results of our investigations have been presented at scientific meetings and published.

Revised simulation model does not predict rebound in gonorrhoea prevalence where core groups are treated in the presence of antimicrobial resistance.

PubMed

Trecker, Molly A; Hogan, Daniel J; Waldner, Cheryl L; Dillon, Jo-Anne R; Osgood, Nathaniel D

2015-06-01

To determine the effects of using discrete versus continuous quantities of people in a compartmental model examining the contribution of antimicrobial resistance (AMR) to rebound in the prevalence of gonorrhoea. A previously published transmission model was reconfigured to represent the occurrence of gonorrhoea in discrete persons, rather than allowing fractions of infected individuals during simulations. In the revised model, prevalence only rebounded under scenarios reproduced from the original paper when AMR occurrence was increased by 10(5) times. In such situations, treatment of high-risk individuals yielded outcomes very similar to those resulting from treatment of low-risk and intermediate-risk individuals. Otherwise, in contrast with the original model, prevalence was the lowest when the high-risk group was treated, supporting the current policy of targeting treatment to high-risk groups. Simulation models can be highly sensitive to structural features. Small differences in structure and parameters can substantially influence predicted outcomes and policy prescriptions, and must be carefully considered. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

A review of training research and virtual reality simulators for the da Vinci surgical system.

PubMed

Liu, May; Curet, Myriam

2015-01-01

PHENOMENON: Virtual reality simulators are the subject of several recent studies of skills training for robot-assisted surgery. Yet no consensus exists regarding what a core skill set comprises or how to measure skill performance. Defining a core skill set and relevant metrics would help surgical educators evaluate different simulators. This review draws from published research to propose a core technical skill set for using the da Vinci surgeon console. Publications on three commercial simulators were used to evaluate the simulators' content addressing these skills and associated metrics. An analysis of published research suggests that a core technical skill set for operating the surgeon console includes bimanual wristed manipulation, camera control, master clutching to manage hand position, use of third instrument arm, activating energy sources, appropriate depth perception, and awareness of forces applied by instruments. Validity studies of three commercial virtual reality simulators for robot-assisted surgery suggest that all three have comparable content and metrics. However, none have comprehensive content and metrics for all core skills. INSIGHTS: Virtual reality simulation remains a promising tool to support skill training for robot-assisted surgery, yet existing commercial simulator content is inadequate for performing and assessing a comprehensive basic skill set. The results of this evaluation help identify opportunities and challenges that exist for future developments in virtual reality simulation for robot-assisted surgery. Specifically, the inclusion of educational experts in the development cycle alongside clinical and technological experts is recommended.

Comparison of Geant4-DNA simulation of S-values with other Monte Carlo codes

NASA Astrophysics Data System (ADS)

André, T.; Morini, F.; Karamitros, M.; Delorme, R.; Le Loirec, C.; Campos, L.; Champion, C.; Groetz, J.-E.; Fromm, M.; Bordage, M.-C.; Perrot, Y.; Barberet, Ph.; Bernal, M. A.; Brown, J. M. C.; Deleuze, M. S.; Francis, Z.; Ivanchenko, V.; Mascialino, B.; Zacharatou, C.; Bardiès, M.; Incerti, S.

2014-01-01

Monte Carlo simulations of S-values have been carried out with the Geant4-DNA extension of the Geant4 toolkit. The S-values have been simulated for monoenergetic electrons with energies ranging from 0.1 keV up to 20 keV, in liquid water spheres (for four radii, chosen between 10 nm and 1 μm), and for electrons emitted by five isotopes of iodine (131, 132, 133, 134 and 135), in liquid water spheres of varying radius (from 15 μm up to 250 μm). The results have been compared to those obtained from other Monte Carlo codes and from other published data. The use of the Kolmogorov-Smirnov test has allowed confirming the statistical compatibility of all simulation results.

Surgical simulators in cataract surgery training.

PubMed

Sikder, Shameema; Tuwairqi, Khaled; Al-Kahtani, Eman; Myers, William G; Banerjee, Pat

2014-02-01

Virtual simulators have been widely implemented in medical and surgical training, including ophthalmology. The increasing number of published articles in this field mandates a review of the available results to assess current technology and explore future opportunities. A PubMed search was conducted and a total of 10 articles were reviewed. Virtual simulators have shown construct validity in many modules, successfully differentiating user experience levels during simulated phacoemulsification surgery. Simulators have also shown improvements in wet-lab performance. The implementation of simulators in the residency training has been associated with a decrease in cataract surgery complication rates. Virtual reality simulators are an effective tool in measuring performance and differentiating trainee skill level. Additionally, they may be useful in improving surgical skill and patient outcomes in cataract surgery. Future opportunities rely on taking advantage of technical improvements in simulators for education and research.

Numerical Simulation of Liquids Draining From a Tank Using OpenFOAM

NASA Astrophysics Data System (ADS)

Sakri, Fadhilah Mohd; Sukri Mat Ali, Mohamed; Zaki Shaikh Salim, Sheikh Ahmad; Muhamad, Sallehuddin

2017-08-01

Accurate simulation of liquids draining is a challenging task. It involves two phases flow, i.e. liquid and air. In this study draining a liquid from a cylindrical tank is numerically simulated using OpenFOAM. OpenFOAM is an open source CFD package and it becomes increasingly popular among the academician and also industries. Comparisons with theoretical and results from previous published data confirmed that OpenFOAM is able to simulate the liquids draining very well. This is done using the gas-liquid interface solver available in the standard library of OpenFOAM. Additionally, this study was also able to explain the physics flow of the draining tank.

Computer simulated modeling of healthy and diseased right ventricular and pulmonary circulation.

PubMed

Chou, Jody; Rinehart, Joseph B

2018-01-12

We have previously developed a simulated cardiovascular physiology model for in-silico testing and validation of novel closed-loop controllers. To date, a detailed model of the right heart and pulmonary circulation was not needed, as previous controllers were not intended for use in patients with cardiac or pulmonary pathology. With new development of controllers for vasopressors, and looking forward, for combined vasopressor-fluid controllers, modeling of right-sided and pulmonary pathology is now relevant to further in-silico validation, so we aimed to expand our existing simulation platform to include these elements. Our hypothesis was that the completed platform could be tuned and stabilized such that the distributions of a randomized sample of simulated patients' baseline characteristics would be similar to reported population values. Our secondary outcomes were to further test the system in representing acute right heart failure and pulmonary artery hypertension. After development and tuning of the right-sided circulation, the model was validated against clinical data from multiple previously published articles. The model was considered 'tuned' when 100% of generated randomized patients converged to stability (steady, physiologically-plausible compartmental volumes, flows, and pressures) and 'valid' when the means for the model data in each health condition were contained within the standard deviations for the published data for the condition. A fully described right heart and pulmonary circulation model including non-linear pressure/volume relationships and pressure dependent flows was created over a 6-month span. The model was successfully tuned such that 100% of simulated patients converged into a steady state within 30 s. Simulation results in the healthy state for central venous volume (3350 ± 132 ml) pulmonary blood volume (405 ± 39 ml), pulmonary artery pressures (systolic 20.8 ± 4.1 mmHg and diastolic 9.4 ± 1.8 mmHg), left atrial pressure (4.6 ± 0.8 mmHg), PVR (1.0 ± 0.2 wood units), and CI (3.8 ± 0.5 l/min/m 2 ) all met criteria for acceptance of the model, though the standard deviations of LAP and CI were somewhat narrower than published comparators. The simulation results for right ventricular infarction also fell within the published ranges: pulmonary blood volume (727 ± 102 ml), pulmonary arterial pressures (30 ± 4 mmHg systolic, 12 ± 2 mmHg diastolic), left atrial pressure (13 ± 2 mmHg), PVR (1.6 ± 0.3 wood units), and CI (2.0 ± 0.4 l/min/m 2 ) all fell within one standard deviation of the reported population values and vice-versa. In the pulmonary hypertension model, pulmonary blood volume of 615 ± 90 ml, pulmonary arterial pressures of 80 ± 14 mmHg systolic, 36 ± 7 mmHg diastolic, and the left atrial pressure of 11 ± 2 mmHg all met criteria for acceptance. For CI, the simulated value of 2.8 ± 0.4 l/min/m 2 once again had a narrower spread than most of the published data, but fell inside of the SD of all published data, and the PVR value of 7.5 ± 1.6 wood units fell in the middle of the four published studies. The right-ventricular and pulmonary circulation simulation appears to be a reasonable approximation of the right-sided circulation for healthy physiology as well as the pathologic conditions tested.

Testing prediction methods: Earthquake clustering versus the Poisson model

USGS Publications Warehouse

Michael, A.J.

1997-01-01

Testing earthquake prediction methods requires statistical techniques that compare observed success to random chance. One technique is to produce simulated earthquake catalogs and measure the relative success of predicting real and simulated earthquakes. The accuracy of these tests depends on the validity of the statistical model used to simulate the earthquakes. This study tests the effect of clustering in the statistical earthquake model on the results. Three simulation models were used to produce significance levels for a VLF earthquake prediction method. As the degree of simulated clustering increases, the statistical significance drops. Hence, the use of a seismicity model with insufficient clustering can lead to overly optimistic results. A successful method must pass the statistical tests with a model that fully replicates the observed clustering. However, a method can be rejected based on tests with a model that contains insufficient clustering. U.S. copyright. Published in 1997 by the American Geophysical Union.

Comparison of Austenite Decomposition Models During Finite Element Simulation of Water Quenching and Air Cooling of AISI 4140 Steel

NASA Astrophysics Data System (ADS)

Babu, K.; Prasanna Kumar, T. S.

2014-08-01

An indigenous, non-linear, and coupled finite element (FE) program has been developed to predict the temperature field and phase evolution during heat treatment of steels. The diffusional transformations during continuous cooling of steels were modeled using Johnson-Mehl-Avrami-Komogorov equation, and the non-diffusion transformation was modeled using Koistinen-Marburger equation. Cylindrical quench probes made of AISI 4140 steel of 20-mm diameter and 50-mm long were heated to 1123 K (850 °C), quenched in water, and cooled in air. The temperature history during continuous cooling was recorded at the selected interior locations of the quench probes. The probes were then sectioned at the mid plane and resultant microstructures were observed. The process of water quenching and air cooling of AISI 4140 steel probes was simulated with the heat flux boundary condition in the FE program. The heat flux for air cooling process was calculated through the inverse heat conduction method using the cooling curve measured during air cooling of a stainless steel 304L probe as an input. The heat flux for the water quenching process was calculated from a surface heat flux model proposed for quenching simulations. The isothermal transformation start and finish times of different phases were taken from the published TTT data and were also calculated using Kirkaldy model and Li model and used in the FE program. The simulated cooling curves and phases using the published TTT data had a good agreement with the experimentally measured values. The computation results revealed that the use of published TTT data was more reliable in predicting the phase transformation during heat treatment of low alloy steels than the use of the Kirkaldy or Li model.

Finite element analysis of pedestrian lower limb fractures by direct force: the result of being run over or impact?

PubMed

Li, Zhengdong; Zou, Donghua; Liu, Ningguo; Zhong, Liangwei; Shao, Yu; Wan, Lei; Huang, Ping; Chen, Yijiu

2013-06-10

The elucidation and prediction of the biomechanics of lower limb fractures could serve as a useful tool in forensic practices. Finite element (FE) analysis could potentially help in the understanding of the fracture mechanisms of lower limb fractures frequently caused by car-pedestrian accidents. Our aim was (1) to develop and validate a FE model of the human lower limb, (2) to assess the biomechanics of specific injuries concerning run-over and impact loading conditions, and (3) to reconstruct one real car-pedestrian collision case using the model created in this study. We developed a novel lower limb FE model and simulated three different loading scenarios. The geometry of the model was reconstructed using Mimics 13.0 based on computed tomography (CT) scans from an actual traffic accident. The material properties were based upon a synthesis of data found in published literature. The FE model validation and injury reconstruction were conducted using the LS-DYNA code. The FE model was validated by a comparison of the simulation results of three-point bending, overall lateral impact tests and published postmortem human surrogate (PMHS) results. Simulated loading scenarios of running-over the thigh with a wheel, the impact on the upper leg, and impact on the lower thigh were conducted with velocities of 10 m/s, 20 m/s, and 40 m/s, respectively. We compared the injuries resulting from one actual case with the simulated results in order to explore the possible fracture bio-mechanism. The peak fracture forces, maximum bending moments, and energy lost ratio exhibited no significant differences between the FE simulations and the literature data. Under simulated run-over conditions, the segmental fracture pattern was formed and the femur fracture patterns and mechanisms were consistent with the actual injury features of the case. Our study demonstrated that this simulation method could potentially be effective in identifying forensic cases and exploring of the injury mechanisms of lower limb fractures encountered due to inflicted lesions. This model can also help to distinguish between possible and impossible scenarios. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Population models and simulation methods: The case of the Spearman rank correlation.

PubMed

Astivia, Oscar L Olvera; Zumbo, Bruno D

2017-11-01

The purpose of this paper is to highlight the importance of a population model in guiding the design and interpretation of simulation studies used to investigate the Spearman rank correlation. The Spearman rank correlation has been known for over a hundred years to applied researchers and methodologists alike and is one of the most widely used non-parametric statistics. Still, certain misconceptions can be found, either explicitly or implicitly, in the published literature because a population definition for this statistic is rarely discussed within the social and behavioural sciences. By relying on copula distribution theory, a population model is presented for the Spearman rank correlation, and its properties are explored both theoretically and in a simulation study. Through the use of the Iman-Conover algorithm (which allows the user to specify the rank correlation as a population parameter), simulation studies from previously published articles are explored, and it is found that many of the conclusions purported in them regarding the nature of the Spearman correlation would change if the data-generation mechanism better matched the simulation design. More specifically, issues such as small sample bias and lack of power of the t-test and r-to-z Fisher transformation disappear when the rank correlation is calculated from data sampled where the rank correlation is the population parameter. A proof for the consistency of the sample estimate of the rank correlation is shown as well as the flexibility of the copula model to encompass results previously published in the mathematical literature. © 2017 The British Psychological Society.

IgSimulator: a versatile immunosequencing simulator.

PubMed

Safonova, Yana; Lapidus, Alla; Lill, Jennie

2015-10-01

The recent introduction of next-generation sequencing technologies to antibody studies have resulted in a growing number of immunoinformatics tools for antibody repertoire analysis. However, benchmarking these newly emerging tools remains problematic since the gold standard datasets that are needed to validate these tools are typically not available. Since simulating antibody repertoires is often the only feasible way to benchmark new immunoinformatics tools, we developed the IgSimulator tool that addresses various complications in generating realistic antibody repertoires. IgSimulator's code has modular structure and can be easily adapted to new requirements to simulation. IgSimulator is open source and freely available as a C++ and Python program running on all Unix-compatible platforms. The source code is available from yana-safonova.github.io/ig_simulator. safonova.yana@gmail.com Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

The Elastic Behaviour of Sintered Metallic Fibre Networks: A Finite Element Study by Beam Theory

PubMed Central

Bosbach, Wolfram A.

2015-01-01

Background The finite element method has complimented research in the field of network mechanics in the past years in numerous studies about various materials. Numerical predictions and the planning efficiency of experimental procedures are two of the motivational aspects for these numerical studies. The widespread availability of high performance computing facilities has been the enabler for the simulation of sufficiently large systems. Objectives and Motivation In the present study, finite element models were built for sintered, metallic fibre networks and validated by previously published experimental stiffness measurements. The validated models were the basis for predictions about so far unknown properties. Materials and Methods The finite element models were built by transferring previously published skeletons of fibre networks into finite element models. Beam theory was applied as simplification method. Results and Conclusions The obtained material stiffness isn’t a constant but rather a function of variables such as sample size and boundary conditions. Beam theory offers an efficient finite element method for the simulated fibre networks. The experimental results can be approximated by the simulated systems. Two worthwhile aspects for future work will be the influence of size and shape and the mechanical interaction with matrix materials. PMID:26569603

A method to investigate the diffusion properties of nuclear calcium.

PubMed

Queisser, Gillian; Wittum, Gabriel

2011-10-01

Modeling biophysical processes in general requires knowledge about underlying biological parameters. The quality of simulation results is strongly influenced by the accuracy of these parameters, hence the identification of parameter values that the model includes is a major part of simulating biophysical processes. In many cases, secondary data can be gathered by experimental setups, which are exploitable by mathematical inverse modeling techniques. Here we describe a method for parameter identification of diffusion properties of calcium in the nuclei of rat hippocampal neurons. The method is based on a Gauss-Newton method for solving a least-squares minimization problem and was formulated in such a way that it is ideally implementable in the simulation platform uG. Making use of independently published space- and time-dependent calcium imaging data, generated from laser-assisted calcium uncaging experiments, here we could identify the diffusion properties of nuclear calcium and were able to validate a previously published model that describes nuclear calcium dynamics as a diffusion process.

Laboratory simulation of field-aligned currents

NASA Technical Reports Server (NTRS)

Wessel, Frank J.; Rostoker, Norman

1993-01-01

A summary of progress during the period Apr. 1992 to Mar. 1993 is provided. Objectives of the research are (1) to simulate, via laboratory experiments, the three terms of the field-aligned current equation; (2) to simulate auroral-arc formation processes by configuring the boundary conditions of the experimental chamber and plasma parameters to produce highly localized return currents at the end of a field-aligned current system; and (3) to extrapolate these results, using theoretical and computational techniques, to the problem of magnetospheric-ionospheric coupling and to compare them with published literature signatures of auroral-arc phenomena.

Simulation optimization of PSA-threshold based prostate cancer screening policies

PubMed Central

Zhang, Jingyu; Denton, Brian T.; Shah, Nilay D.; Inman, Brant A.

2013-01-01

We describe a simulation optimization method to design PSA screening policies based on expected quality adjusted life years (QALYs). Our method integrates a simulation model in a genetic algorithm which uses a probabilistic method for selection of the best policy. We present computational results about the efficiency of our algorithm. The best policy generated by our algorithm is compared to previously recommended screening policies. Using the policies determined by our model, we present evidence that patients should be screened more aggressively but for a shorter length of time than previously published guidelines recommend. PMID:22302420

Compatible topologies and parameters for NMR structure determination of carbohydrates by simulated annealing.

PubMed

Feng, Yingang

2017-01-01

The use of NMR methods to determine the three-dimensional structures of carbohydrates and glycoproteins is still challenging, in part because of the lack of standard protocols. In order to increase the convenience of structure determination, the topology and parameter files for carbohydrates in the program Crystallography & NMR System (CNS) were investigated and new files were developed to be compatible with the standard simulated annealing protocols for proteins and nucleic acids. Recalculating the published structures of protein-carbohydrate complexes and glycosylated proteins demonstrates that the results are comparable to the published structures which employed more complex procedures for structure calculation. Integrating the new carbohydrate parameters into the standard structure calculation protocol will facilitate three-dimensional structural study of carbohydrates and glycosylated proteins by NMR spectroscopy.

Compatible topologies and parameters for NMR structure determination of carbohydrates by simulated annealing

PubMed Central

2017-01-01

The use of NMR methods to determine the three-dimensional structures of carbohydrates and glycoproteins is still challenging, in part because of the lack of standard protocols. In order to increase the convenience of structure determination, the topology and parameter files for carbohydrates in the program Crystallography & NMR System (CNS) were investigated and new files were developed to be compatible with the standard simulated annealing protocols for proteins and nucleic acids. Recalculating the published structures of protein-carbohydrate complexes and glycosylated proteins demonstrates that the results are comparable to the published structures which employed more complex procedures for structure calculation. Integrating the new carbohydrate parameters into the standard structure calculation protocol will facilitate three-dimensional structural study of carbohydrates and glycosylated proteins by NMR spectroscopy. PMID:29232406

Virtual reality aided visualization of fluid flow simulations with application in medical education and diagnostics.

PubMed

Djukic, Tijana; Mandic, Vesna; Filipovic, Nenad

2013-12-01

Medical education, training and preoperative diagnostics can be drastically improved with advanced technologies, such as virtual reality. The method proposed in this paper enables medical doctors and students to visualize and manipulate three-dimensional models created from CT or MRI scans, and also to analyze the results of fluid flow simulations. Simulation of fluid flow using the finite element method is performed, in order to compute the shear stress on the artery walls. The simulation of motion through the artery is also enabled. The virtual reality system proposed here could shorten the length of training programs and make the education process more effective. © 2013 Published by Elsevier Ltd.

CAG12 - A CSCM based procedure for flow of an equilibrium chemically reacting gas

NASA Technical Reports Server (NTRS)

Green, M. J.; Davy, W. C.; Lombard, C. K.

1985-01-01

The Conservative Supra Characteristic Method (CSCM), an implicit upwind Navier-Stokes algorithm, is extended to the numerical simulation of flows in chemical equilibrium. The resulting computer code known as Chemistry and Gasdynamics Implicit - Version 2 (CAG12) is described. First-order accurate results are presented for inviscid and viscous Mach 20 flows of air past a hemisphere-cylinder. The solution procedure captures the bow shock in a chemically reacting gas, a technique that is needed for simulating high altitude, rarefied flows. In an initial effort to validate the code, the inviscid results are compared with published gasdynamic and chemistry solutions and satisfactorily agreement is obtained.

Qualitative modeling of normal blood coagulation and its pathological states using stochastic activity networks.

PubMed

Mounts, W M; Liebman, M N

1997-07-01

We have developed a method for representing biological pathways and simulating their behavior based on the use of stochastic activity networks (SANs). SANs, an extension of the original Petri net, have been used traditionally to model flow systems including data-communications networks and manufacturing processes. We apply the methodology to the blood coagulation cascade, a biological flow system, and present the representation method as well as results of simulation studies based on published experimental data. In addition to describing the dynamic model, we also present the results of its utilization to perform simulations of clinical states including hemophilia's A and B as well as sensitivity analysis of individual factors and their impact on thrombin production.

Physics-based agent to simulant correlations for vapor phase mass transport.

PubMed

Willis, Matthew P; Varady, Mark J; Pearl, Thomas P; Fouse, Janet C; Riley, Patrick C; Mantooth, Brent A; Lalain, Teri A

2013-12-15

Chemical warfare agent simulants are often used as an agent surrogate to perform environmental testing, mitigating exposure hazards. This work specifically addresses the assessment of downwind agent vapor concentration resulting from an evaporating simulant droplet. A previously developed methodology was used to estimate the mass diffusivities of the chemical warfare agent simulants methyl salicylate, 2-chloroethyl ethyl sulfide, di-ethyl malonate, and chloroethyl phenyl sulfide. Along with the diffusivity of the chemical warfare agent bis(2-chloroethyl) sulfide, the simulant diffusivities were used in an advection-diffusion model to predict the vapor concentrations downwind from an evaporating droplet of each chemical at various wind velocities and temperatures. The results demonstrate that the simulant-to-agent concentration ratio and the corresponding vapor pressure ratio are equivalent under certain conditions. Specifically, the relationship is valid within ranges of measurement locations relative to the evaporating droplet and observation times. The valid ranges depend on the relative transport properties of the agent and simulant, and whether vapor transport is diffusion or advection dominant. Published by Elsevier B.V.

INACSL Standards of Best Practice for Simulation: Past, Present, and Future.

PubMed

Sittner, Barbara J; Aebersold, Michelle L; Paige, Jane B; Graham, Leslie L M; Schram, Andrea Parsons; Decker, Sharon I; Lioce, Lori

2015-01-01

To describe the historical evolution of the International Nursing Association for Clinical Simulation and Learning's (INACSL) Standards of Best Practice: Simulation. The establishment of simulation standards began as a concerted effort by the INACSL Board of Directors in 2010 to provide best practices to design, conduct, and evaluate simulation activities in order to advance the science of simulation as a teaching methodology. A comprehensive review of the evolution of INACSL Standards of Best Practice: Simulation was conducted using journal publications, the INACSL website, INACSL member survey, and reports from members of the INACSL Standards Committee. The initial seven standards, published in 2011, were reviewed and revised in 2013. Two new standards were published in 2015. The standards will continue to evolve as the science of simulation advances. As the use of simulation-based experiences increases, the INACSL Standards of Best Practice: Simulation are foundational to standardizing language, behaviors, and curricular design for facilitators and learners.

FEM design and simulation of a short, 10 MV, S-band Linac with Monte Carlo dose simulations.

PubMed

Baillie, Devin; St Aubin, J; Fallone, B G; Steciw, S

2015-04-01

Current commercial 10 MV Linac waveguides are 1.5 m. The authors' current 6 MV linear accelerator-magnetic resonance imager (Linac-MR) system fits in typical radiotherapy vaults. To allow 10 MV treatments with the Linac-MR and still fit within typical vaults, the authors design a 10 MV Linac with an accelerator waveguide of the same length (27.5 cm) as current 6 MV Linacs. The first design stage is to design a cavity such that a specific experimental measurement for breakdown is applicable to the cavity. This is accomplished through the use of finite element method (FEM) simulations to match published shunt impedance, Q factor, and ratio of peak to mean-axial electric field strength from an electric breakdown study. A full waveguide is then designed and tuned in FEM simulations based on this cavity design. Electron trajectories are computed through the resulting radio frequency fields, and the waveguide geometry is modified by shifting the first coupling cavity in order to optimize the electron beam properties until the energy spread and mean energy closely match values published for an emulated 10 MV Linac. Finally, Monte Carlo dose simulations are used to compare the resulting photon beam depth dose profile and penumbra with that produced by the emulated 10 MV Linac. The shunt impedance, Q factor, and ratio of peak to mean-axial electric field strength are all matched to within 0.1%. A first coupling cavity shift of 1.45 mm produces an energy spectrum width of 0.347 MeV, very close to the published value for the emulated 10 MV of 0.315 MeV, and a mean energy of 10.53 MeV, nearly identical to the published 10.5 MeV for the emulated 10 MV Linac. The depth dose profile produced by their new Linac is within 1% of that produced by the emulated 10 MV spectrum for all depths greater than 1.5 cm. The penumbra produced is 11% narrower, as measured from 80% to 20% of the central axis dose. The authors have successfully designed and simulated an S-band waveguide of length of 27.5 cm capable of producing a 10 MV photon beam. This waveguide operates well within the breakdown threshold determined for the cavity geometry used. The designed Linac produces depth dose profiles similar to those of the emulated 10 MV Linac (waveguide-length of 1.5 m) but yields a narrower penumbra.

Molecular dynamics simulations of membrane proteins and their interactions: from nanoscale to mesoscale.

PubMed

Chavent, Matthieu; Duncan, Anna L; Sansom, Mark Sp

2016-10-01

Molecular dynamics simulations provide a computational tool to probe membrane proteins and systems at length scales ranging from nanometers to close to a micrometer, and on microsecond timescales. All atom and coarse-grained simulations may be used to explore in detail the interactions of membrane proteins and specific lipids, yielding predictions of lipid binding sites in good agreement with available structural data. Building on the success of protein-lipid interaction simulations, larger scale simulations reveal crowding and clustering of proteins, resulting in slow and anomalous diffusional dynamics, within realistic models of cell membranes. Current methods allow near atomic resolution simulations of small membrane organelles, and of enveloped viruses to be performed, revealing key aspects of their structure and functionally important dynamics. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Simulations of material mixing in laser-driven reshock experiments

NASA Astrophysics Data System (ADS)

Haines, Brian M.; Grinstein, Fernando F.; Welser-Sherrill, Leslie; Fincke, James R.

2013-02-01

We perform simulations of a laser-driven reshock experiment [Welser-Sherrill et al., High Energy Density Phys. (unpublished)] in the strong-shock high energy-density regime to better understand material mixing driven by the Richtmyer-Meshkov instability. Validation of the simulations is based on direct comparison of simulation and radiographic data. Simulations are also compared with published direct numerical simulation and the theory of homogeneous isotropic turbulence. Despite the fact that the flow is neither homogeneous, isotropic nor fully turbulent, there are local regions in which the flow demonstrates characteristics of homogeneous isotropic turbulence. We identify and isolate these regions by the presence of high levels of turbulent kinetic energy (TKE) and vorticity. After reshock, our analysis shows characteristics consistent with those of incompressible isotropic turbulence. Self-similarity and effective Reynolds number assessments suggest that the results are reasonably converged at the finest resolution. Our results show that in shock-driven transitional flows, turbulent features such as self-similarity and isotropy only fully develop once de-correlation, characteristic vorticity distributions, and integrated TKE, have decayed significantly. Finally, we use three-dimensional simulation results to test the performance of two-dimensional Reynolds-averaged Navier-Stokes simulations. In this context, we also test a presumed probability density function turbulent mixing model extensively used in combustion applications.

The use of molecular dynamics simulations to evaluate the DNA sequence-selectivity of G-A cross-linking PBD-duocarmycin dimers.

PubMed

Jackson, Paul J M; Rahman, Khondaker M; Thurston, David E

2017-01-01

The pyrrolobenzodiazepine (PBD) and duocarmycin families are DNA-interactive agents that covalently bond to guanine (G) and adenine (A) bases, respectively, and that have been joined together to create synthetic dimers capable of cross-linking G-G, A-A, and G-A bases. Three G-A alkylating dimers have been reported in publications to date, with defined DNA-binding sites proposed for two of them. In this study we have used molecular dynamics simulations to elucidate preferred DNA-binding sites for the three published molecular types. For the PBD-CPI dimer UTA-6026 (1), our simulations correctly predicted its favoured binding site (i.e., 5'-C(G)AATTA-3') as identified by DNA cleavage studies. However, for the PBD-CI molecule ('Compound 11', 3), we were unable to reconcile the results of our simulations with the reported preferred cross-linking sequence (5'-ATTTTCC(G)-3'). We found that the molecule is too short to span the five base pairs between the A and G bases as claimed, but should target instead a sequence such as 5'-ATTTC(G)-3' with two less base pairs between the reacting G and A residues. Our simulation results for this hybrid dimer are also in accord with the very low interstrand cross-linking and in vitro cytotoxicity activities reported for it. Although a preferred cross-linking sequence was not reported for the third hybrid dimer ('27eS', 2), our simulations predict that it should span two base pairs between covalently reacting G and A bases (e.g., 5'-GTAT(A)-3'). Copyright © 2016. Published by Elsevier Ltd.

Modeling variably saturated subsurface solute transport with MODFLOW-UZF and MT3DMS

USGS Publications Warehouse

Morway, Eric D.; Niswonger, Richard G.; Langevin, Christian D.; Bailey, Ryan T.; Healy, Richard W.

2013-01-01

The MT3DMS groundwater solute transport model was modified to simulate solute transport in the unsaturated zone by incorporating the unsaturated-zone flow (UZF1) package developed for MODFLOW. The modified MT3DMS code uses a volume-averaged approach in which Lagrangian-based UZF1 fluid fluxes and storage changes are mapped onto a fixed grid. Referred to as UZF-MT3DMS, the linked model was tested against published benchmarks solved analytically as well as against other published codes, most frequently the U.S. Geological Survey's Variably-Saturated Two-Dimensional Flow and Transport Model. Results from a suite of test cases demonstrate that the modified code accurately simulates solute advection, dispersion, and reaction in the unsaturated zone. Two- and three-dimensional simulations also were investigated to ensure unsaturated-saturated zone interaction was simulated correctly. Because the UZF1 solution is analytical, large-scale flow and transport investigations can be performed free from the computational and data burdens required by numerical solutions to Richards' equation. Results demonstrate that significant simulation runtime savings can be achieved with UZF-MT3DMS, an important development when hundreds or thousands of model runs are required during parameter estimation and uncertainty analysis. Three-dimensional variably saturated flow and transport simulations revealed UZF-MT3DMS to have runtimes that are less than one tenth of the time required by models that rely on Richards' equation. Given its accuracy and efficiency, and the wide-spread use of both MODFLOW and MT3DMS, the added capability of unsaturated-zone transport in this familiar modeling framework stands to benefit a broad user-ship.

Photoresist and stochastic modeling

NASA Astrophysics Data System (ADS)

Hansen, Steven G.

2018-01-01

Analysis of physical modeling results can provide unique insights into extreme ultraviolet stochastic variation, which augment, and sometimes refute, conclusions based on physical intuition and even wafer experiments. Simulations verify the primacy of "imaging critical" counting statistics (photons, electrons, and net acids) and the image/blur-dependent dose sensitivity in describing the local edge or critical dimension variation. But the failure of simple counting when resist thickness is varied highlights a limitation of this exact analytical approach, so a calibratable empirical model offers useful simplicity and convenience. Results presented here show that a wide range of physical simulation results can be well matched by an empirical two-parameter model based on blurred image log-slope (ILS) for lines/spaces and normalized ILS for holes. These results are largely consistent with a wide range of published experimental results; however, there is some disagreement with the recently published dataset of De Bisschop. The present analysis suggests that the origin of this model failure is an unexpected blurred ILS:dose-sensitivity relationship failure in that resist process. It is shown that a photoresist mechanism based on high photodecomposable quencher loading and high quencher diffusivity can give rise to pitch-dependent blur, which may explain the discrepancy.

Computer Simulation Shows the Effect of Communication on Day of Surgery Patient Flow.

PubMed

Taaffe, Kevin; Fredendall, Lawrence; Huynh, Nathan; Franklin, Jennifer

2015-07-01

To improve patient flow in a surgical environment, practitioners and academicians often use process mapping and simulation as tools to evaluate and recommend changes. We used simulations to help staff visualize the effect of communication and coordination delays that occur on the day of surgery. Perioperative services staff participated in tabletop exercises in which they chose the delays that were most important to eliminate. Using a day-of-surgery computer simulation model, the elimination of delays was tested and the results were shared with the group. This exercise, repeated for multiple groups of staff, provided an understanding of not only the dynamic events taking place, but also how small communication delays can contribute to a significant loss in efficiency and the ability to provide timely care. Survey results confirmed these understandings. Copyright © 2015 AORN, Inc. Published by Elsevier Inc. All rights reserved.

Integrating open-source software applications to build molecular dynamics systems.

PubMed

Allen, Bruce M; Predecki, Paul K; Kumosa, Maciej

2014-04-05

Three open-source applications, NanoEngineer-1, packmol, and mis2lmp are integrated using an open-source file format to quickly create molecular dynamics (MD) cells for simulation. The three software applications collectively make up the open-source software (OSS) suite known as MD Studio (MDS). The software is validated through software engineering practices and is verified through simulation of the diglycidyl ether of bisphenol-a and isophorone diamine (DGEBA/IPD) system. Multiple simulations are run using the MDS software to create MD cells, and the data generated are used to calculate density, bulk modulus, and glass transition temperature of the DGEBA/IPD system. Simulation results compare well with published experimental and numerical results. The MDS software prototype confirms that OSS applications can be analyzed against real-world research requirements and integrated to create a new capability. Copyright © 2014 Wiley Periodicals, Inc.

Terrain Portrayal for Synthetic Vision Systems Head-Down Displays Evaluation Results: Compilation of Pilot Transcripts

NASA Technical Reports Server (NTRS)

Hughes, Monica F.; Glaab, Louis J.

2007-01-01

The Terrain Portrayal for Head-Down Displays (TP-HDD) simulation experiment addressed multiple objectives involving twelve display concepts (two baseline concepts without terrain and ten synthetic vision system (SVS) variations), four evaluation maneuvers (two en route and one approach maneuver, plus a rare-event scenario), and three pilot group classifications. The TP-HDD SVS simulation was conducted in the NASA Langley Research Center's (LaRC's) General Aviation WorkStation (GAWS) facility. The results from this simulation establish the relationship between terrain portrayal fidelity and pilot situation awareness, workload, stress, and performance and are published in the NASA TP entitled Terrain Portrayal for Synthetic Vision Systems Head-Down Displays Evaluation Results. This is a collection of pilot comments during each run of the TP-HDD simulation experiment. These comments are not the full transcripts, but a condensed version where only the salient remarks that applied to the scenario, the maneuver, or the actual research itself were compiled.

MARIKA - A model revision system using qualitative analysis of simulations. [of human orientation system

NASA Technical Reports Server (NTRS)

Groleau, Nicolas; Frainier, Richard; Colombano, Silvano; Hazelton, Lyman; Szolovits, Peter

1993-01-01

This paper describes portions of a novel system called MARIKA (Model Analysis and Revision of Implicit Key Assumptions) to automatically revise a model of the normal human orientation system. The revision is based on analysis of discrepancies between experimental results and computer simulations. The discrepancies are calculated from qualitative analysis of quantitative simulations. The experimental and simulated time series are first discretized in time segments. Each segment is then approximated by linear combinations of simple shapes. The domain theory and knowledge are represented as a constraint network. Incompatibilities detected during constraint propagation within the network yield both parameter and structural model alterations. Interestingly, MARIKA diagnosed a data set from the Massachusetts Eye and Ear Infirmary Vestibular Laboratory as abnormal though the data was tagged as normal. Published results from other laboratories confirmed the finding. These encouraging results could lead to a useful clinical vestibular tool and to a scientific discovery system for space vestibular adaptation.

Semi-physiologic model validation and bioequivalence trials simulation to select the best analyte for acetylsalicylic acid.

PubMed

Cuesta-Gragera, Ana; Navarro-Fontestad, Carmen; Mangas-Sanjuan, Victor; González-Álvarez, Isabel; García-Arieta, Alfredo; Trocóniz, Iñaki F; Casabó, Vicente G; Bermejo, Marival

2015-07-10

The objective of this paper is to apply a previously developed semi-physiologic pharmacokinetic model implemented in NONMEM to simulate bioequivalence trials (BE) of acetyl salicylic acid (ASA) in order to validate the model performance against ASA human experimental data. ASA is a drug with first-pass hepatic and intestinal metabolism following Michaelis-Menten kinetics that leads to the formation of two main metabolites in two generations (first and second generation metabolites). The first aim was to adapt the semi-physiological model for ASA in NOMMEN using ASA pharmacokinetic parameters from literature, showing its sequential metabolism. The second aim was to validate this model by comparing the results obtained in NONMEM simulations with published experimental data at a dose of 1000 mg. The validated model was used to simulate bioequivalence trials at 3 dose schemes (100, 1000 and 3000 mg) and with 6 test formulations with decreasing in vivo dissolution rate constants versus the reference formulation (kD 8-0.25 h (-1)). Finally, the third aim was to determine which analyte (parent drug, first generation or second generation metabolite) was more sensitive to changes in formulation performance. The validation results showed that the concentration-time curves obtained with the simulations reproduced closely the published experimental data, confirming model performance. The parent drug (ASA) was the analyte that showed to be more sensitive to the decrease in pharmaceutical quality, with the highest decrease in Cmax and AUC ratio between test and reference formulations. Copyright © 2015 Elsevier B.V. All rights reserved.

Simulation model of a single-stage lithium bromide-water absorption cooling unit

NASA Technical Reports Server (NTRS)

Miao, D.

1978-01-01

A computer model of a LiBr-H2O single-stage absorption machine was developed. The model, utilizing a given set of design data such as water-flow rates and inlet or outlet temperatures of these flow rates but without knowing the interior characteristics of the machine (heat transfer rates and surface areas), can be used to predict or simulate off-design performance. Results from 130 off-design cases for a given commercial machine agree with the published data within 2 percent.

Parser for Sabin-to-Mahoney Transition Model of Quasispecies Replication

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

Ecale Zhou, Carol

2016-01-03

This code is a data parse for preparing output from the Qspp agent-based stochastic simulation model for plotting in Excel. This code is specific to a set of simulations that were run for the purpose of preparing data for a publication. It is necessary to make this code open-source in order to publish the model code (Qspp), which has already been released. There is a necessity of assuring that results from using Qspp for a publication

Frequency domain phase noise analysis of dual injection-locked optoelectronic oscillators.

PubMed

Jahanbakht, Sajad

2016-10-01

Dual injection-locked optoelectronic oscillators (DIL-OEOs) have been introduced as a means to achieve very low-noise microwave oscillations while avoiding the large spurious peaks that occur in the phase noise of the conventional single-loop OEOs. In these systems, two OEOs are inter-injection locked to each other. The OEO with the longer optical fiber delay line is called the master OEO, and the other is called the slave OEO. Here, a frequency domain approach for simulating the phase noise spectrum of each of the OEOs in a DIL-OEO system and based on the conversion matrix approach is presented. The validity of the new approach is verified by comparing its results with previously published data in the literature. In the new approach, first, in each of the master or slave OEOs, the power spectral densities (PSDs) of two white and 1/f noise sources are optimized such that the resulting simulated phase noise of any of the master or slave OEOs in the free-running state matches the measured phase noise of that OEO. After that, the proposed approach is able to simulate the phase noise PSD of both OEOs at the injection-locked state. Because of the short run-time requirements, especially compared to previously proposed time domain approaches, the new approach is suitable for optimizing the power injection ratios (PIRs), and potentially other circuit parameters, in order to achieve good performance regarding the phase noise in each of the OEOs. Through various numerical simulations, the optimum PIRs for achieving good phase noise performance are presented and discussed; they are in agreement with the previously published results. This further verifies the applicability of the new approach. Moreover, some other interesting results regarding the spur levels are also presented.

Simulation technology for resuscitation training: a systematic review and meta-analysis.

PubMed

Mundell, William C; Kennedy, Cassie C; Szostek, Jason H; Cook, David A

2013-09-01

To summarize current available data on simulation-based training in resuscitation for health care professionals. MEDLINE, EMBASE, CINAHL, PsycINFO, ERIC, Web of Science, Scopus and reference lists of published reviews. Published studies of any language or date that enrolled health professions' learners to investigate the use of technology-enhanced simulation to teach resuscitation in comparison with no intervention or alternative training. Data were abstracted in duplicate. We identified themes examining different approaches to curriculum design. We pooled results using random effects meta-analysis. 182 studies were identified involving 16,636 participants. Overall, simulation-based training of resuscitation skills, in comparison to no intervention, appears effective regardless of assessed outcome, level of learner, study design, or specific task trained. In comparison to no intervention, simulation training improved outcomes of knowledge (Hedges' g) 1.05 (95% confidence interval, 0.81-1.29), process skill 1.13 (0.99-1.27), product skill 1.92 (1.26-2.60), time skill 1.77 (1.13-2.42) and patient outcomes 0.26 (0.047-0.48). In comparison with non-simulation intervention, learner satisfaction 0.79 (0.27-1.31) and process skill 0.35 (0.12-0.59) outcomes favored simulation. Studies investigating how to optimize simulation training found higher process skill outcomes in courses employing "booster" practice 0.13 (0.03-0.22), team/group dynamics 0.51 (0.06-0.97), distraction 1.76 (1.02-2.50) and integrated feedback 0.49 (0.17-0.80) compared to courses without these features. Most analyses reflected high between-study inconsistency (I(2) values >50%). Simulation-based training for resuscitation is highly effective. Design features of "booster" practice, team/group dynamics, distraction and integrated feedback improve effectiveness. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Implementation of new physics models for low energy electrons in liquid water in Geant4-DNA.

PubMed

Bordage, M C; Bordes, J; Edel, S; Terrissol, M; Franceries, X; Bardiès, M; Lampe, N; Incerti, S

2016-12-01

A new alternative set of elastic and inelastic cross sections has been added to the very low energy extension of the Geant4 Monte Carlo simulation toolkit, Geant4-DNA, for the simulation of electron interactions in liquid water. These cross sections have been obtained from the CPA100 Monte Carlo track structure code, which has been a reference in the microdosimetry community for many years. They are compared to the default Geant4-DNA cross sections and show better agreement with published data. In order to verify the correct implementation of the CPA100 cross section models in Geant4-DNA, simulations of the number of interactions and ranges were performed using Geant4-DNA with this new set of models, and the results were compared with corresponding results from the original CPA100 code. Good agreement is observed between the implementations, with relative differences lower than 1% regardless of the incident electron energy. Useful quantities related to the deposited energy at the scale of the cell or the organ of interest for internal dosimetry, like dose point kernels, are also calculated using these new physics models. They are compared with results obtained using the well-known Penelope Monte Carlo code. Copyright © 2016 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Modeling integrated fixed-film activated sludge and moving-bed biofilm reactor systems II: evaluation.

PubMed

Boltz, Joshua P; Johnson, Bruce R; Daigger, Glen T; Sandino, Julian; Elenter, Deborah

2009-06-01

A steady-state model presented by Boltz, Johnson, Daigger, and Sandino (2009) describing integrated fixed-film activated sludge (IFAS) and moving-bed biofilm reactor (MBBR) systems has been demonstrated to simulate, with reasonable accuracy, four wastewater treatment configurations with published operational data. Conditions simulated include combined carbon oxidation and nitrification (both IFAS and MBBR), tertiary nitrification MBBR, and post denitrification IFAS with methanol addition as the external carbon source. Simulation results illustrate that the IFAS/MBBR model is sufficiently accurate for describing ammonia-nitrogen reduction, nitrate/nitrite-nitrogen reduction and production, biofilm and suspended biomass distribution, and sludge production.

Simulation of Structural Transformations in Heating of Alloy Steel

NASA Astrophysics Data System (ADS)

Kurkin, A. S.; Makarov, E. L.; Kurkin, A. B.; Rubtsov, D. E.; Rubtsov, M. E.

2017-07-01

Amathematical model for computer simulation of structural transformations in an alloy steel under the conditions of the thermal cycle of multipass welding is presented. The austenitic transformation under the heating and the processes of decomposition of bainite and martensite under repeated heating are considered. Amethod for determining the necessary temperature-time parameters of the model from the chemical composition of the steel is described. Published data are processed and the results used to derive regression models of the temperature ranges and parameters of transformation kinetics of alloy steels. The method developed is used in computer simulation of the process of multipass welding of pipes by the finite-element method.

Investigation of Different Constituent Encoders in a Turbo-code Scheme for Reduced Decoder Complexity

NASA Technical Reports Server (NTRS)

Kwatra, S. C.

1998-01-01

A large number of papers have been published attempting to give some analytical basis for the performance of Turbo-codes. It has been shown that performance improves with increased interleaver length. Also procedures have been given to pick the best constituent recursive systematic convolutional codes (RSCC's). However testing by computer simulation is still required to verify these results. This thesis begins by describing the encoding and decoding schemes used. Next simulation results on several memory 4 RSCC's are shown. It is found that the best BER performance at low E(sub b)/N(sub o) is not given by the RSCC's that were found using the analytic techniques given so far. Next the results are given from simulations using a smaller memory RSCC for one of the constituent encoders. Significant reduction in decoding complexity is obtained with minimal loss in performance. Simulation results are then given for a rate 1/3 Turbo-code with the result that this code performed as well as a rate 1/2 Turbo-code as measured by the distance from their respective Shannon limits. Finally the results of simulations where an inaccurate noise variance measurement was used are given. From this it was observed that Turbo-decoding is fairly stable with regard to noise variance measurement.

Saffman-Taylor Instability and the Inner Splitting Mechanism

NASA Astrophysics Data System (ADS)

Oliveira, Rafael; Meiburg, Eckart

2017-11-01

The classical miscible displacement experiments of Wooding (1969) exhibit an inner splitting phenomenon that remained unexplained for over 40 years. 3D Navier-Stokes simulations presented in, were the first ones to reproduce these experimental observations numerically, and to demonstrate that they are linked to concentrated streamwise vortices. The origin of these concentrated streamwise vortices remained a mystery, however. The current investigation, published at, finally resolves this long-standing issue. Towards this end, we compare 3D Navier-Stokes simulation results for neutrally buoyant, viscously unstable displacements and gravitationally unstable, constant viscosity ones. Only the former exhibit the generation of streamwise vorticity. The simulation results present conclusive evidence that it is caused by the lateral displacement of the more viscous fluid by the less viscous one, with the variable viscosity terms playing a dominant role.

A Journey in Standard Development: The Core Manufacturing Simulation Data (CMSD) Information Model.

PubMed

Lee, Yung-Tsun Tina

2015-01-01

This report documents a journey "from research to an approved standard" of a NIST-led standard development activity. That standard, Core Manufacturing Simulation Data (CMSD) information model, provides neutral structures for the efficient exchange of manufacturing data in a simulation environment. The model was standardized under the auspices of the international Simulation Interoperability Standards Organization (SISO). NIST started the research in 2001 and initiated the standardization effort in 2004. The CMSD standard was published in two SISO Products. In the first Product, the information model was defined in the Unified Modeling Language (UML) and published in 2010 as SISO-STD-008-2010. In the second Product, the information model was defined in Extensible Markup Language (XML) and published in 2013 as SISO-STD-008-01-2012. Both SISO-STD-008-2010 and SISO-STD-008-01-2012 are intended to be used together.

Development of a device to simulate tooth mobility.

PubMed

Erdelt, Kurt-Jürgen; Lamper, Timea

2010-10-01

The testing of new materials under simulation of oral conditions is essential in medicine. For simulation of fracture strength different simulation devices are used for test set-up. The results of these in vitro tests differ because there is no standardization of tooth mobility in simulation devices. The aim of this study is to develop a simulation device that depicts the tooth mobility curve as accurately as possible and creates reproducible and scalable mobility curves. With the aid of published literature and with the help of dentists, average forms of tooth classes were generated. Based on these tooth data, different abutment tooth shapes and different simulation devices were designed with a CAD system and were generated with a Rapid Prototyping system. Then, for all simulation devices the displacement curves were created with a universal testing machine and compared with the tooth mobility curve. With this new information, an improved adapted simulation device was constructed. A simulations device that is able to simulate the mobility curve of natural teeth with high accuracy and where mobility is reproducible and scalable was developed.

Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language.

PubMed

Waltemath, Dagmar; Adams, Richard; Bergmann, Frank T; Hucka, Michael; Kolpakov, Fedor; Miller, Andrew K; Moraru, Ion I; Nickerson, David; Sahle, Sven; Snoep, Jacky L; Le Novère, Nicolas

2011-12-15

The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools. In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions. With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from different fields of research can be accurately described and combined.

Virtual reality training in laparoscopic surgery: A systematic review & meta-analysis.

PubMed

Alaker, Medhat; Wynn, Greg R; Arulampalam, Tan

2016-05-01

Laparoscopic surgery requires a different and sometimes more complex skill set than does open surgery. Shortened working hours, less training times, and patient safety issues necessitates that these skills need to be acquired outside the operating room. Virtual reality simulation in laparoscopic surgery is a growing field, and many studies have been published to determine its effectiveness. This systematic review and meta-analysis aims to evaluate virtual reality simulation in laparoscopic abdominal surgery in comparison to other simulation models and to no training. A systematic literature search was carried out until January 2014 in full adherence to PRISMA guidelines. All randomised controlled studies comparing virtual reality training to other models of training or to no training were included. Only studies utilizing objective and validated assessment tools were included. Thirty one randomised controlled trials that compare virtual reality training to other models of training or to no training were included. The results of the meta-analysis showed that virtual reality simulation is significantly more effective than video trainers, and at least as good as box trainers. The use of Proficiency-based VR training, under supervision with prompt instructions and feedback, and the use of haptic feedback, has proven to be the most effective way of delivering the virtual reality training. The incorporation of virtual reality training into surgical training curricula is now necessary. A unified platform of training needs to be established. Further studies to assess the impact on patient outcomes and on hospital costs are necessary. (PROSPERO Registration number: CRD42014010030). Copyright © 2016 IJS Publishing Group Ltd. Published by Elsevier Ltd. All rights reserved.

WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions.

PubMed

Karr, Jonathan R; Phillips, Nolan C; Covert, Markus W

2014-01-01

Mechanistic 'whole-cell' models are needed to develop a complete understanding of cell physiology. However, extracting biological insights from whole-cell models requires running and analyzing large numbers of simulations. We developed WholeCellSimDB, a database for organizing whole-cell simulations. WholeCellSimDB was designed to enable researchers to search simulation metadata to identify simulations for further analysis, and quickly slice and aggregate simulation results data. In addition, WholeCellSimDB enables users to share simulations with the broader research community. The database uses a hybrid relational/hierarchical data format architecture to efficiently store and retrieve both simulation setup metadata and results data. WholeCellSimDB provides a graphical Web-based interface to search, browse, plot and export simulations; a JavaScript Object Notation (JSON) Web service to retrieve data for Web-based visualizations; a command-line interface to deposit simulations; and a Python API to retrieve data for advanced analysis. Overall, we believe WholeCellSimDB will help researchers use whole-cell models to advance basic biological science and bioengineering. http://www.wholecellsimdb.org SOURCE CODE REPOSITORY: URL: http://github.com/CovertLab/WholeCellSimDB. © The Author(s) 2014. Published by Oxford University Press.

CFD: A Castle in the Sand?

NASA Technical Reports Server (NTRS)

Kleb, William L.; Wood, William A.

2004-01-01

The computational simulation community is not routinely publishing independently verifiable tests to accompany new models or algorithms. A survey reveals that only 22% of new models published are accompanied by tests suitable for independently verifying the new model. As the community develops larger codes with increased functionality, and hence increased complexity in terms of the number of building block components and their interactions, it becomes prohibitively expensive for each development group to derive the appropriate tests for each component. Therefore, the computational simulation community is building its collective castle on a very shaky foundation of components with unpublished and unrepeatable verification tests. The computational simulation community needs to begin publishing component level verification tests before the tide of complexity undermines its foundation.

Simulation of Low-Intensity Ultrasound Propagating in a Beagle Dog Dentoalveolar Structure to Investigate the Relations between Ultrasonic Parameters and Cementum Regeneration.

PubMed

Vafaeian, Behzad; Al-Daghreer, Saleh; El-Rich, Marwan; Adeeb, Samer; El-Bialy, Tarek

2015-08-01

The therapeutic effect of low-intensity pulsed ultrasound on orthodontically induced inflammatory root resorption is believed to be brought about through mechanical signals induced by the low-intensity pulsed ultrasound. However, the stimulatory mechanism triggering dental cell response has not been clearly identified yet. The aim of this study was to evaluate possible relations between the amounts of new cementum regeneration and ultrasonic parameters such as pressure amplitude and time-averaged energy density. We used the finite-element method to simulate the previously published experiment on ultrasonic wave propagation in the dentoalveolar structure of beagle dogs. Qualitative relations between the thickness of the regenerated cementum in the experiment and the ultrasonic parameters were observed. Our results indicated that the areas of the root surface with greater ultrasonic pressure were associated with larger amounts of cementum regeneration. However, the establishment of reliable quantitative correlations between ultrasound parameters and cementum regeneration requires more experimental data and simulations. Copyright © 2015 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

FEM design and simulation of a short, 10 MV, S-band Linac with Monte Carlo dose simulations

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

Baillie, Devin; Aubin, J. St.; Steciw, S., E-mail: ssteciw@ualberta.ca

2015-04-15

Purpose: Current commercial 10 MV Linac waveguides are 1.5 m. The authors’ current 6 MV linear accelerator–magnetic resonance imager (Linac–MR) system fits in typical radiotherapy vaults. To allow 10 MV treatments with the Linac–MR and still fit within typical vaults, the authors design a 10 MV Linac with an accelerator waveguide of the same length (27.5 cm) as current 6 MV Linacs. Methods: The first design stage is to design a cavity such that a specific experimental measurement for breakdown is applicable to the cavity. This is accomplished through the use of finite element method (FEM) simulations to match publishedmore » shunt impedance, Q factor, and ratio of peak to mean-axial electric field strength from an electric breakdown study. A full waveguide is then designed and tuned in FEM simulations based on this cavity design. Electron trajectories are computed through the resulting radio frequency fields, and the waveguide geometry is modified by shifting the first coupling cavity in order to optimize the electron beam properties until the energy spread and mean energy closely match values published for an emulated 10 MV Linac. Finally, Monte Carlo dose simulations are used to compare the resulting photon beam depth dose profile and penumbra with that produced by the emulated 10 MV Linac. Results: The shunt impedance, Q factor, and ratio of peak to mean-axial electric field strength are all matched to within 0.1%. A first coupling cavity shift of 1.45 mm produces an energy spectrum width of 0.347 MeV, very close to the published value for the emulated 10 MV of 0.315 MeV, and a mean energy of 10.53 MeV, nearly identical to the published 10.5 MeV for the emulated 10 MV Linac. The depth dose profile produced by their new Linac is within 1% of that produced by the emulated 10 MV spectrum for all depths greater than 1.5 cm. The penumbra produced is 11% narrower, as measured from 80% to 20% of the central axis dose. Conclusions: The authors have successfully designed and simulated an S-band waveguide of length of 27.5 cm capable of producing a 10 MV photon beam. This waveguide operates well within the breakdown threshold determined for the cavity geometry used. The designed Linac produces depth dose profiles similar to those of the emulated 10 MV Linac (waveguide-length of 1.5 m) but yields a narrower penumbra.« less

Monte Carlo decision curve analysis using aggregate data.

PubMed

Hozo, Iztok; Tsalatsanis, Athanasios; Djulbegovic, Benjamin

2017-02-01

Decision curve analysis (DCA) is an increasingly used method for evaluating diagnostic tests and predictive models, but its application requires individual patient data. The Monte Carlo (MC) method can be used to simulate probabilities and outcomes of individual patients and offers an attractive option for application of DCA. We constructed a MC decision model to simulate individual probabilities of outcomes of interest. These probabilities were contrasted against the threshold probability at which a decision-maker is indifferent between key management strategies: treat all, treat none or use predictive model to guide treatment. We compared the results of DCA with MC simulated data against the results of DCA based on actual individual patient data for three decision models published in the literature: (i) statins for primary prevention of cardiovascular disease, (ii) hospice referral for terminally ill patients and (iii) prostate cancer surgery. The results of MC DCA and patient data DCA were identical. To the extent that patient data DCA were used to inform decisions about statin use, referral to hospice or prostate surgery, the results indicate that MC DCA could have also been used. As long as the aggregate parameters on distribution of the probability of outcomes and treatment effects are accurately described in the published reports, the MC DCA will generate indistinguishable results from individual patient data DCA. We provide a simple, easy-to-use model, which can facilitate wider use of DCA and better evaluation of diagnostic tests and predictive models that rely only on aggregate data reported in the literature. © 2017 Stichting European Society for Clinical Investigation Journal Foundation.

Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language

PubMed Central

2011-01-01

Background The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools. Results In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions. Conclusions With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from different fields of research can be accurately described and combined. PMID:22172142

Survey of student attitudes towards digital simulation technologies at a dental school in China.

PubMed

Ren, Q; Wang, Y; Zheng, Q; Ye, L; Zhou, X D; Zhang, L L

2017-08-01

Digital simulation technologies have become widespread in healthcare education, especially in dentistry; these technologies include digital X-ray images, digital microscopes, virtual pathology slides and other types of simulation. This study aimed to assess students' attitudes towards digital simulation technologies at a large, top-ranked dental school in China, as well as find out how students compare the digital technologies with traditional training methods. In April 2015, a custom-designed questionnaire was distributed to a total of 389 students who had received digital technology and simulation-based training in West China Dental School during 2012-2014. Results of a cross-sectional survey show that most students accept digital simulation technology; they report that the technology is stimulating and facilitates self-directed and self-paced learning. These findings, together with the objective advantages of digital technology, suggest that digital simulation training offers significant potential for dental education, highlighting the need for further research and more widespread implementation. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Modeling and simulation of different and representative engineering problems using Network Simulation Method

PubMed Central

2018-01-01

Mathematical models simulating different and representative engineering problem, atomic dry friction, the moving front problems and elastic and solid mechanics are presented in the form of a set of non-linear, coupled or not coupled differential equations. For different parameters values that influence the solution, the problem is numerically solved by the network method, which provides all the variables of the problems. Although the model is extremely sensitive to the above parameters, no assumptions are considered as regards the linearization of the variables. The design of the models, which are run on standard electrical circuit simulation software, is explained in detail. The network model results are compared with common numerical methods or experimental data, published in the scientific literature, to show the reliability of the model. PMID:29518121

Modeling and simulation of different and representative engineering problems using Network Simulation Method.

PubMed

Sánchez-Pérez, J F; Marín, F; Morales, J L; Cánovas, M; Alhama, F

2018-01-01

Mathematical models simulating different and representative engineering problem, atomic dry friction, the moving front problems and elastic and solid mechanics are presented in the form of a set of non-linear, coupled or not coupled differential equations. For different parameters values that influence the solution, the problem is numerically solved by the network method, which provides all the variables of the problems. Although the model is extremely sensitive to the above parameters, no assumptions are considered as regards the linearization of the variables. The design of the models, which are run on standard electrical circuit simulation software, is explained in detail. The network model results are compared with common numerical methods or experimental data, published in the scientific literature, to show the reliability of the model.

Validation of Finite Element Crash Test Dummy Models for Predicting Orion Crew Member Injuries During a Simulated Vehicle Landing

NASA Technical Reports Server (NTRS)

Tabiei, Al; Lawrence, Charles; Fasanella, Edwin L.

2009-01-01

A series of crash tests were conducted with dummies during simulated Orion crew module landings at the Wright-Patterson Air Force Base. These tests consisted of several crew configurations with and without astronaut suits. Some test results were collected and are presented. In addition, finite element models of the tests were developed and are presented. The finite element models were validated using the experimental data, and the test responses were compared with the computed results. Occupant crash data, such as forces, moments, and accelerations, were collected from the simulations and compared with injury criteria to assess occupant survivability and injury. Some of the injury criteria published in the literature is summarized for completeness. These criteria were used to determine potential injury during crew impact events.

Developing a molecular dynamics force field for both folded and disordered protein states.

PubMed

Robustelli, Paul; Piana, Stefano; Shaw, David E

2018-05-07

Molecular dynamics (MD) simulation is a valuable tool for characterizing the structural dynamics of folded proteins and should be similarly applicable to disordered proteins and proteins with both folded and disordered regions. It has been unclear, however, whether any physical model (force field) used in MD simulations accurately describes both folded and disordered proteins. Here, we select a benchmark set of 21 systems, including folded and disordered proteins, simulate these systems with six state-of-the-art force fields, and compare the results to over 9,000 available experimental data points. We find that none of the tested force fields simultaneously provided accurate descriptions of folded proteins, of the dimensions of disordered proteins, and of the secondary structure propensities of disordered proteins. Guided by simulation results on a subset of our benchmark, however, we modified parameters of one force field, achieving excellent agreement with experiment for disordered proteins, while maintaining state-of-the-art accuracy for folded proteins. The resulting force field, a99SB- disp , should thus greatly expand the range of biological systems amenable to MD simulation. A similar approach could be taken to improve other force fields. Copyright © 2018 the Author(s). Published by PNAS.

1-D blood flow modelling in a running human body.

PubMed

Szabó, Viktor; Halász, Gábor

2017-07-01

In this paper an attempt was made to simulate blood flow in a mobile human arterial network, specifically, in a running human subject. In order to simulate the effect of motion, a previously published immobile 1-D model was modified by including an inertial force term into the momentum equation. To calculate inertial force, gait analysis was performed at different levels of speed. Our results show that motion has a significant effect on the amplitudes of the blood pressure and flow rate but the average values are not effected significantly.

The benefits of being a video gamer in laparoscopic surgery.

PubMed

Sammut, Matthew; Sammut, Mark; Andrejevic, Predrag

2017-09-01

Video games are mainly considered to be of entertainment value in our society. Laparoscopic surgery and video games are activities similarly requiring eye-hand and visual-spatial skills. Previous studies have not conclusively shown a positive correlation between video game experience and improved ability to accomplish visual-spatial tasks in laparoscopic surgery. This study was an attempt to investigate this relationship. The aim of the study was to investigate whether previous video gaming experience affects the baseline performance on a laparoscopic simulator trainer. Newly qualified medical officers with minimal experience in laparoscopic surgery were invited to participate in the study and assigned to the following groups: gamers (n = 20) and non-gamers (n = 20). Analysis included participants' demographic data and baseline video gaming experience. Laparoscopic skills were assessed using a laparoscopic simulator trainer. There were no significant demographic differences between the two groups. Each participant performed three laparoscopic tasks and mean scores between the two groups were compared. The gamer group had statistically significant better results in maintaining the laparoscopic camera horizon ± 15° (p value = 0.009), in the complex ball manipulation accuracy rates (p value = 0.024) and completed the complex laparoscopic simulator task in a significantly shorter time period (p value = 0.001). Although prior video gaming experience correlated with better results, there were no significant differences for camera accuracy rates (p value = 0.074) and in a two-handed laparoscopic exercise task accuracy rates (p value = 0.092). The results show that previous video-gaming experience improved the baseline performance in laparoscopic simulator skills. Copyright © 2017 IJS Publishing Group Ltd. Published by Elsevier Ltd. All rights reserved.

Monte Carlo kinetics simulations of ice-mantle formation on interstellar grains

NASA Astrophysics Data System (ADS)

Garrod, Robin

2015-08-01

The majority of interstellar dust-grain chemical kinetics models use rate equations, or alternative population-based simulation methods, to trace the time-dependent formation of grain-surface molecules and ice mantles. Such methods are efficient, but are incapable of considering explicitly the morphologies of the dust grains, the structure of the ices formed thereon, or the influence of local surface composition on the chemistry.A new Monte Carlo chemical kinetics model, MIMICK, is presented here, whose prototype results were published recently (Garrod 2013, ApJ, 778, 158). The model calculates the strengths and positions of the potential mimima on the surface, on the fly, according to the individual pair-wise (van der Waals) bonds between surface species, allowing the structure of the ice to build up naturally as surface diffusion and chemistry occur. The prototype model considered contributions to a surface particle's potential only from contiguous (or "bonded") neighbors; the full model considers contributions from surface constituents from short to long range. Simulations are conducted on a fully 3-D user-generated dust-grain with amorphous surface characteristics. The chemical network has also been extended from the simple water system previously published, and now includes 33 chemical species and 55 reactions. This allows the major interstellar ice components to be simulated, such as water, methane, ammonia and methanol, as well as a small selection of more complex molecules, including methyl formate (HCOOCH3).The new model results indicate that the porosity of interstellar ices are dependent on multiple variables, including gas density, the dust temperature, and the relative accretion rates of key gas-phase species. The results presented also have implications for the formation of complex organic molecules on dust-grain surfaces at very low temperatures.

Development and application of a crossbreeding simulation model for goat production systems in tropical regions.

PubMed

Tsukahara, Y; Oishi, K; Hirooka, H

2011-12-01

A deterministic simulation model was developed to estimate biological production efficiency and to evaluate goat crossbreeding systems under tropical conditions. The model involves 5 production systems: pure indigenous, first filial generations (F1), backcross (BC), composite breeds of F1 (CMP(F1)), and BC (CMP(BC)). The model first simulates growth, reproduction, lactation, and energy intakes of a doe and a kid on a 1-d time step at the individual level and thereafter the outputs are integrated into the herd dynamics program. The ability of the model to simulate individual performances was tested under a base situation. The simulation results represented daily BW changes, ME requirements, and milk yield and the estimates were within the range of published data. Two conventional goat production scenarios (an intensive milk production scenario and an integrated goat and oil palm production scenario) in Malaysia were examined. The simulation results of the intensive milk production scenario showed the greater production efficiency of the CMP(BC) and CMP(F1) systems and decreased production efficiency of the F1 and BC systems. The results of the integrated goat and oil palm production scenario showed that the production efficiency and stocking rate were greater for the indigenous goats than for the crossbreeding systems.

Modeling the liquid filling in capillary well microplates for analyte preconcentration.

PubMed

Yu, Yang; Wang, Xuewei; Ng, Tuck Wah

2012-06-15

An attractive advantage of the capillary well microplate approach is the ability to conduct evaporative analyte preconcentration. We advance the use of hydrophobic materials for the wells which apart from reducing material loss through wetting also affords self entry into the well when the droplet size reduces below a critical value. Using Surface Evolver simulation without gravity, we find the critical diameters D(c) fitting very well with theoretical results. When simulating the critical diameters D(c)(G) with gravity included, the gravitational effect could only be ignored when the liquid volumes were small (difference of 5.7% with 5 μL of liquid), but not when the liquid volumes were large (differences of more than 22% with 50 μL of liquid). From this, we developed a modifying equation from a series of simulation results made to describe the gravitational effect. This modifying equation fitted the simulation results well in our simulation range (100°≤θ≤135° and 1 μL≤V≤200 μL). In simulating the condition of multiple wells underneath each droplet, we found that having more holes did not alter the critical diameters significantly. Consequently, the modifying relation should also generally express the critical diameter for multiple wells under a droplet. Crown Copyright © 2012. Published by Elsevier Inc. All rights reserved.

Molecular dynamics simulation of a piston driven shock wave in a hard sphere gas. Final Contractor ReportPh.D. Thesis

NASA Technical Reports Server (NTRS)

Woo, Myeung-Jouh; Greber, Isaac

1995-01-01

Molecular dynamics simulation is used to study the piston driven shock wave at Mach 1.5, 3, and 10. A shock tube, whose shape is a circular cylinder, is filled with hard sphere molecules having a Maxwellian thermal velocity distribution and zero mean velocity. The piston moves and a shock wave is generated. All collisions are specular, including those between the molecules and the computational boundaries, so that the shock development is entirely causal, with no imposed statistics. The structure of the generated shock is examined in detail, and the wave speed; profiles of density, velocity, and temperature; and shock thickness are determined. The results are compared with published results of other methods, especially the direct simulation Monte-Carlo method. Property profiles are similar to those generated by direct simulation Monte-Carlo method. The shock wave thicknesses are smaller than the direct simulation Monte-Carlo results, but larger than those of the other methods. Simulation of a shock wave, which is one-dimensional, is a severe test of the molecular dynamics method, which is always three-dimensional. A major challenge of the thesis is to examine the capability of the molecular dynamics methods by choosing a difficult task.

SS-mPMG and SS-GA: tools for finding pathways and dynamic simulation of metabolic networks.

PubMed

Katsuragi, Tetsuo; Ono, Naoaki; Yasumoto, Keiichi; Altaf-Ul-Amin, Md; Hirai, Masami Y; Sriyudthsak, Kansuporn; Sawada, Yuji; Yamashita, Yui; Chiba, Yukako; Onouchi, Hitoshi; Fujiwara, Toru; Naito, Satoshi; Shiraishi, Fumihide; Kanaya, Shigehiko

2013-05-01

Metabolomics analysis tools can provide quantitative information on the concentration of metabolites in an organism. In this paper, we propose the minimum pathway model generator tool for simulating the dynamics of metabolite concentrations (SS-mPMG) and a tool for parameter estimation by genetic algorithm (SS-GA). SS-mPMG can extract a subsystem of the metabolic network from the genome-scale pathway maps to reduce the complexity of the simulation model and automatically construct a dynamic simulator to evaluate the experimentally observed behavior of metabolites. Using this tool, we show that stochastic simulation can reproduce experimentally observed dynamics of amino acid biosynthesis in Arabidopsis thaliana. In this simulation, SS-mPMG extracts the metabolic network subsystem from published databases. The parameters needed for the simulation are determined using a genetic algorithm to fit the simulation results to the experimental data. We expect that SS-mPMG and SS-GA will help researchers to create relevant metabolic networks and carry out simulations of metabolic reactions derived from metabolomics data.

Gray: a ray tracing-based Monte Carlo simulator for PET

NASA Astrophysics Data System (ADS)

Freese, David L.; Olcott, Peter D.; Buss, Samuel R.; Levin, Craig S.

2018-05-01

Monte Carlo simulation software plays a critical role in PET system design. Performing complex, repeated Monte Carlo simulations can be computationally prohibitive, as even a single simulation can require a large amount of time and a computing cluster to complete. Here we introduce Gray, a Monte Carlo simulation software for PET systems. Gray exploits ray tracing methods used in the computer graphics community to greatly accelerate simulations of PET systems with complex geometries. We demonstrate the implementation of models for positron range, annihilation acolinearity, photoelectric absorption, Compton scatter, and Rayleigh scatter. For validation, we simulate the GATE PET benchmark, and compare energy, distribution of hits, coincidences, and run time. We show a speedup using Gray, compared to GATE for the same simulation, while demonstrating nearly identical results. We additionally simulate the Siemens Biograph mCT system with both the NEMA NU-2 scatter phantom and sensitivity phantom. We estimate the total sensitivity within % when accounting for differences in peak NECR. We also estimate the peak NECR to be kcps, or within % of published experimental data. The activity concentration of the peak is also estimated within 1.3%.

Monte Carlo calculations of lung dose in ORNL phantom for boron neutron capture therapy.

PubMed

Krstic, D; Markovic, V M; Jovanovic, Z; Milenkovic, B; Nikezic, D; Atanackovic, J

2014-10-01

Monte Carlo simulations were performed to evaluate dose for possible treatment of cancers by boron neutron capture therapy (BNCT). The computational model of male Oak Ridge National Laboratory (ORNL) phantom was used to simulate tumours in the lung. Calculations have been performed by means of the MCNP5/X code. In this simulation, two opposite neutron beams were considered, in order to obtain uniform neutron flux distribution inside the lung. The obtained results indicate that the lung cancer could be treated by BNCT under the assumptions of calculations. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Simulation of Flood Profiles for Catoma Creek near Montgomery, Alabama, 2008

USGS Publications Warehouse

Lee, K.G.; Hedgecock, T.S.

2008-01-01

A one-dimensional step-backwater model was used to simulate flooding conditions for Catoma Creek near Montgomery, Alabama. A peak flow of 50,000 cubic feet per second was computed by the U.S. Geological Survey for the March 1990 flood at the Norman Bridge Road gaging station. Using this estimated peak flow, flood-plain surveys with associated roughness coefficients, and surveyed high-water marks for the March 1990 flood, a flow model was calibrated to closely match the known event. The calibrated model then was used to simulate flooding for the 10-, 50-, 100-, and 500-year recurrence-interval floods. The 100-year flood stage for the Alabama River also was computed in the vicinity of the Catoma Creek confluence using observed high-water profiles from the 1979 and 1990 floods and gaging-station data. The results indicate that the 100-year flood profile for Catoma Creek within the 15-mile study reach is about 2.5 feet higher, on average, than the profile published by the Federal Emergency Management Agency. The maximum and minimum differences are 6.0 feet and 0.8 foot, respectively. All water-surface elevations computed for the 100-year flood are higher than those published by the Federal Emergency Management Agency. The 100-year flood stage computed for the Alabama River in the vicinity of the Catoma Creek confluence was about 4.5 feet lower than the elevation published by the Federal Emergency Management Agency. The results of this study provide the community with flood-profile information that can be used for flood-plain mitigation, future development, and safety plans for the city.

3-D VPIC simulation of an vortex-induced reconnection event observed by MMS

DOE Data Explorer

Nakamura, Takuma; Daughton, William

2016-01-01

The data set consists of a 3-D fully kinetic (VPIC) simulation of an in-situ observation event at the Earth's magnetopause by the NASA MMS spacecraft on September 8, 2015. The results show a turbulent development of magnetic reconnection induced by the Kelvin-Helmohltz vortex, and resulting significantly efficient plasma mixing across the magnetopause. The vortex-induced reconnection signatures are well consistent with the MMS observations. These results are published in some scientific journals such as Nature Communications. Fortran unformatted files with 1024x1536x512 cells, which have been compressed from original ones with 2048x3072x1024 cells, are archived for selected time slices of field and moment data shown in these papers.

MODFLOW-based coupled surface water routing and groundwater-flow simulation

USGS Publications Warehouse

Hughes, Joseph D.; Langevin, Christian D.; White, Jeremy T.

2015-01-01

In this paper, we present a flexible approach for simulating one- and two-dimensional routing of surface water using a numerical surface water routing (SWR) code implicitly coupled to the groundwater-flow process in MODFLOW. Surface water routing in SWR can be simulated using a diffusive-wave approximation of the Saint-Venant equations and/or a simplified level-pool approach. SWR can account for surface water flow controlled by backwater conditions caused by small water-surface gradients or surface water control structures. A number of typical surface water control structures, such as culverts, weirs, and gates, can be represented, and it is possible to implement operational rules to manage surface water stages and streamflow. The nonlinear system of surface water flow equations formulated in SWR is solved by using Newton methods and direct or iterative solvers. SWR was tested by simulating the (1) Lal axisymmetric overland flow, (2) V-catchment, and (3) modified Pinder-Sauer problems. Simulated results for these problems compare well with other published results and indicate that SWR provides accurate results for surface water-only and coupled surface water/groundwater problems. Results for an application of SWR and MODFLOW to the Snapper Creek area of Miami-Dade County, Florida, USA are also presented and demonstrate the value of coupled surface water and groundwater simulation in managed, low-relief coastal settings.

Simulation of granular and gas-solid flows using discrete element method

NASA Astrophysics Data System (ADS)

Boyalakuntla, Dhanunjay S.

2003-10-01

In recent years there has been increased research activity in the experimental and numerical study of gas-solid flows. Flows of this type have numerous applications in the energy, pharmaceuticals, and chemicals process industries. Typical applications include pulverized coal combustion, flow and heat transfer in bubbling and circulating fluidized beds, hopper and chute flows, pneumatic transport of pharmaceutical powders and pellets, and many more. The present work addresses the study of gas-solid flows using computational fluid dynamics (CFD) techniques and discrete element simulation methods (DES) combined. Many previous studies of coupled gas-solid flows have been performed assuming the solid phase as a continuum with averaged properties and treating the gas-solid flow as constituting of interpenetrating continua. Instead, in the present work, the gas phase flow is simulated using continuum theory and the solid phase flow is simulated using DES. DES treats each solid particle individually, thus accounting for its dynamics due to particle-particle interactions, particle-wall interactions as well as fluid drag and buoyancy. The present work involves developing efficient DES methods for dense granular flow and coupling this simulation to continuum simulations of the gas phase flow. Simulations have been performed to observe pure granular behavior in vibrating beds. Benchmark cases have been simulated and the results obtained match the published literature. The dimensionless acceleration amplitude and the bed height are the parameters governing bed behavior. Various interesting behaviors such as heaping, round and cusp surface standing waves, as well as kinks, have been observed for different values of the acceleration amplitude for a given bed height. Furthermore, binary granular mixtures (granular mixtures with two particle sizes) in a vibrated bed have also been studied. Gas-solid flow simulations have been performed to study fluidized beds. Benchmark 2D fluidized bed simulations have been performed and the results have been shown to satisfactorily compare with those published in the literature. A comprehensive study of the effect of drag correlations on the simulation of fluidized beds has been performed. It has been found that nearly all the drag correlations studied make similar predictions of global quantities such as the time-dependent pressure drop, bubbling frequency and growth. In conclusion, discrete element simulation has been successfully coupled to continuum gas-phase. Though all the results presented in the thesis are two-dimensional, the present implementation is completely three dimensional and can be used to study 3D fluidized beds to aid in better design and understanding. Other industrially important phenomena like particle coating, coal gasification etc., and applications in emerging areas such as nano-particle/fluid mixtures can also be studied through this type of simulation. (Abstract shortened by UMI.)

A simulation model to estimate cost-offsets for a disease-management program for chronic kidney disease.

PubMed

Gandjour, Afschin; Tschulena, Ulrich; Steppan, Sonja; Gatti, Emanuele

2015-04-01

The aim of this paper is to develop a simulation model that analyzes cost-offsets of a hypothetical disease management program (DMP) for patients with chronic kidney disease (CKD) in Germany compared to no such program. A lifetime Markov model with simulated 65-year-old patients with CKD was developed using published data on costs and health status and simulating the progression to end-stage renal disease (ESRD), cardiovascular disease and death. A statutory health insurance perspective was adopted. This modeling study shows considerable potential for cost-offsets from a DMP for patients with CKD. The potential for cost-offsets increases with relative risk reduction by the DMP and baseline glomerular filtration rate. Results are most sensitive to the cost of dialysis treatment. This paper presents a general 'prototype' simulation model for the prevention of ESRD. The model allows for further modification and adaptation in future applications.

Qualitative, semi-quantitative, and quantitative simulation of the osmoregulation system in yeast.

PubMed

Pang, Wei; Coghill, George M

2015-05-01

In this paper we demonstrate how Morven, a computational framework which can perform qualitative, semi-quantitative, and quantitative simulation of dynamical systems using the same model formalism, is applied to study the osmotic stress response pathway in yeast. First the Morven framework itself is briefly introduced in terms of the model formalism employed and output format. We then built a qualitative model for the biophysical process of the osmoregulation in yeast, and a global qualitative-level picture was obtained through qualitative simulation of this model. Furthermore, we constructed a Morven model based on existing quantitative model of the osmoregulation system. This model was then simulated qualitatively, semi-quantitatively, and quantitatively. The obtained simulation results are presented with an analysis. Finally the future development of the Morven framework for modelling the dynamic biological systems is discussed. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Coarse-grained simulations of protein-protein association: an energy landscape perspective.

PubMed

Ravikumar, Krishnakumar M; Huang, Wei; Yang, Sichun

2012-08-22

Understanding protein-protein association is crucial in revealing the molecular basis of many biological processes. Here, we describe a theoretical simulation pipeline to study protein-protein association from an energy landscape perspective. First, a coarse-grained model is implemented and its applications are demonstrated via molecular dynamics simulations for several protein complexes. Second, an enhanced search method is used to efficiently sample a broad range of protein conformations. Third, multiple conformations are identified and clustered from simulation data and further projected on a three-dimensional globe specifying protein orientations and interacting energies. Results from several complexes indicate that the crystal-like conformation is favorable on the energy landscape even if the landscape is relatively rugged with metastable conformations. A closer examination on molecular forces shows that the formation of associated protein complexes can be primarily electrostatics-driven, hydrophobics-driven, or a combination of both in stabilizing specific binding interfaces. Taken together, these results suggest that the coarse-grained simulations and analyses provide an alternative toolset to study protein-protein association occurring in functional biomolecular complexes. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Virtual planning for craniomaxillofacial surgery--7 years of experience.

PubMed

Adolphs, Nicolai; Haberl, Ernst-Johannes; Liu, Weichen; Keeve, Erwin; Menneking, Horst; Hoffmeister, Bodo

2014-07-01

Contemporary computer-assisted surgery systems more and more allow for virtual simulation of even complex surgical procedures with increasingly realistic predictions. Preoperative workflows are established and different commercially software solutions are available. Potential and feasibility of virtual craniomaxillofacial surgery as an additional planning tool was assessed retrospectively by comparing predictions and surgical results. Since 2006 virtual simulation has been performed in selected patient cases affected by complex craniomaxillofacial disorders (n = 8) in addition to standard surgical planning based on patient specific 3d-models. Virtual planning could be performed for all levels of the craniomaxillofacial framework within a reasonable preoperative workflow. Simulation of even complex skeletal displacements corresponded well with the real surgical result and soft tissue simulation proved to be helpful. In combination with classic 3d-models showing the underlying skeletal pathology virtual simulation improved planning and transfer of craniomaxillofacial corrections. Additional work and expenses may be justified by increased possibilities of visualisation, information, instruction and documentation in selected craniomaxillofacial procedures. Copyright © 2013 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

TRANSPORT, AIR-SURFACE EXCHANGE AND LANDSCAPE ACCUMULATION OF AIRBORNE POLLUTANTS DEPOSITED ONTO RURAL CATCHMENTS: THE CASE OF MERCURY

EPA Science Inventory

This paper presents a modeling analysis of airborne mercury fate in rural catchments by coupling components of simulation models developed and published previously by the authors. Results for individual rural catchments are presented and discussed, with a focus on the major mercu...

The role of moisture content in above-ground leaching

Treesearch

Stan Lebow; Patricia Lebow

2007-01-01

This paper reviews previous reports on the moisture content of wood exposed above ground and compares those values to moisture contents obtained using simulated rainfall and immersion methods. Laboratory leaching trials with CCA-treated specimens were also conducted and the results compared to published values for leaching of CCA-treated specimens exposed above ground...

Computational characterization of fracture healing under reduced gravity loading conditions.

PubMed

Gadomski, Benjamin C; Lerner, Zachary F; Browning, Raymond C; Easley, Jeremiah T; Palmer, Ross H; Puttlitz, Christian M

2016-07-01

The literature is deficient with regard to how the localized mechanical environment of skeletal tissue is altered during reduced gravitational loading and how these alterations affect fracture healing. Thus, a finite element model of the ovine hindlimb was created to characterize the local mechanical environment responsible for the inhibited fracture healing observed under experimental simulated hypogravity conditions. Following convergence and verification studies, hydrostatic pressure and strain within a diaphyseal fracture of the metatarsus were evaluated for models under both 1 and 0.25 g loading environments and compared to results of a related in vivo study. Results of the study suggest that reductions in hydrostatic pressure and strain of the healing fracture for animals exposed to reduced gravitational loading conditions contributed to an inhibited healing process, with animals exposed to the simulated hypogravity environment subsequently initiating an intramembranous bone formation process rather than the typical endochondral ossification healing process experienced by animals healing in a 1 g gravitational environment. © 2015 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 34:1206-1215, 2016. © 2015 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

Early assessment of proarrhythmic risk of drugs using the in vitro data and single-cell-based in silico models: proof of concept.

PubMed

Abbasi, Mitra; Small, Ben G; Patel, Nikunjkumar; Jamei, Masoud; Polak, Sebastian

2017-02-01

To determine the predictive performance of in silico models using drug-specific preclinical cardiac electrophysiology data to investigate drug-induced arrhythmia risk (e.g. Torsade de pointes (TdP)) in virtual human subjects. To assess drug proarrhythmic risk, we used a set of in vitro electrophysiological measurements describing ion channel inhibition triggered by the investigated drugs. The Cardiac Safety Simulator version 2.0 (CSS; Simcyp, Sheffield, UK) platform was used to simulate human left ventricular cardiac myocyte action potential models. This study shows the impact of drug concentration changes on particular ionic currents by using available experimental data. The simulation results display safety threshold according to drug concentration threshold and log (threshold concentration/ effective therapeutic plasma concentration (ETPC)). We reproduced the underlying biophysical characteristics of cardiac cells resulted in effects of drugs associated with cardiac arrhythmias (action potential duration (APD) and QT prolongation and TdP) which were observed in published 3D simulations, yet with much less computational burden.

Geant4 simulation of the CERN-EU high-energy reference field (CERF) facility.

PubMed

Prokopovich, D A; Reinhard, M I; Cornelius, I M; Rosenfeld, A B

2010-09-01

The CERN-EU high-energy reference field facility is used for testing and calibrating both active and passive radiation dosemeters for radiation protection applications in space and aviation. Through a combination of a primary particle beam, target and a suitable designed shielding configuration, the facility is able to reproduce the neutron component of the high altitude radiation field relevant to the jet aviation industry. Simulations of the facility using the GEANT4 (GEometry ANd Tracking) toolkit provide an improved understanding of the neutron particle fluence as well as the particle fluence of other radiation components present. The secondary particle fluence as a function of the primary particle fluence incident on the target and the associated dose equivalent rates were determined at the 20 designated irradiation positions available at the facility. Comparisons of the simulated results with previously published simulations obtained using the FLUKA Monte Carlo code, as well as with experimental results of the neutron fluence obtained with a Bonner sphere spectrometer, are made.

Analysis of simulated advanced spaceborne thermal emission and reflection (ASTER) radiometer data of the Iron Hill, Colorado, study area for mapping lithologies

USGS Publications Warehouse

Rowan, L.C.

1998-01-01

The advanced spaceborne thermal emission and reflection (ASTER) radiometer was designed to record reflected energy in nine channels with 15 or 30 m resolution, including stereoscopic images, and emitted energy in five channels with 90 m resolution from the NASA Earth Observing System AM1 platform. A simulated ASTER data set was produced for the Iron Hill, Colorado, study area by resampling calibrated, registered airborne visible/infrared imaging spectrometer (AVIRIS) data, and thermal infrared multispectral scanner (TIMS) data to the appropriate spatial and spectral parameters. A digital elevation model was obtained to simulate ASTER-derived topographic data. The main lithologic units in the area are granitic rocks and felsite into which a carbonatite stock and associated alkalic igneous rocks were intruded; these rocks are locally covered by Jurassic sandstone, Tertiary rhyolitic tuff, and colluvial deposits. Several methods were evaluated for mapping the main lithologic units, including the unsupervised classification and spectral curve-matching techniques. In the five thermal-infrared (TIR) channels, comparison of the results of linear spectral unmixing and unsupervised classification with published geologic maps showed that the main lithologic units were mapped, but large areas with moderate to dense tree cover were not mapped in the TIR data. Compared to TIMS data, simulated ASTER data permitted slightly less discrimination in the mafic alkalic rock series, and carbonatite was not mapped in the TIMS nor in the simulated ASTER TIR data. In the nine visible and near-infrared channels, unsupervised classification did not yield useful results, but both the spectral linear unmixing and the matched filter techniques produced useful results, including mapping calcitic and dolomitic carbonatite exposures, travertine in hot spring deposits, kaolinite in argillized sandstone and tuff, and muscovite in sericitized granite and felsite, as well as commonly occurring illite/muscovite. However, the distinction made in AVIRIS data between calcite and dolomite was not consistently feasible in the simulated ASTER data. Comparison of the lithologic information produced by spectral analysis of the simulated ASTER data to a photogeologic interpretation of a simulated ASTER color image illustrates the high potential of spectral analysis of ASTER data to geologic interpretation. This paper is not subject to U.S. copyright. Published in 1998 by the American Geophysical Union.

Diurnal Forcing of Planetary Atmospheres

NASA Technical Reports Server (NTRS)

Houben, Howard C.

1997-01-01

Much progress has been made on calculations of the Martian seasonal water cycle using the Mars Climate Model developed for this purpose. Two papers, documenting the model and the water transport results obtained with it have been published in the Journal of Geophysical Research - Planets. An additional paper describing results related to the evolution of the seasonal water cycle as a result of orbital changes was published in Advances in Space Research. Since that time, further studies have concentrated on the consequences of the soil adsorption required to match the observed water cycle and its relation to the stability of ground ice and other potential water reservoirs. Earth-related studies have concentrated on incorporating an efficient and realistic microphysical model into the Ames Stratospheric General Circulation Model used to simulate the spread of the ML Pinatubo and other volcanic clouds in the stratosphere. In addition, visualizations of the simulations are being incorporated into a video describing the UARS mission. A paper describing the new stratospheric aerosol microphysics package (and its consequences for volcanic cloud evolution) will be submitted in the near future. The paper will discuss the relative importance of condensation and coagulation to early particle growth and the separation of the cloud by sedimentation of the larger particles. A more general paper which highlights the observation that particle number densities did not increase dramatically after the ML Pinatubo eruption is planned. Simulations of atmospheric transport will be extended to include studies of terrestrial tropospheric tracers using the Fifth-Generation Penn State/NCAR Mesoscale Model.

Epidermal Homeostasis and Radiation Responses in a Multiscale Tissue Modeling Framework

NASA Technical Reports Server (NTRS)

Hu, Shaowen; Cucinotta, Francis A.

2013-01-01

The surface of skin is lined with several thin layers of epithelial cells that are maintained throughout life time by a small population of stem cells. High dose radiation exposures could injure and deplete the underlying proliferative cells and induce cutaneous radiation syndrome. In this work we propose a multiscale computational model for skin epidermal dynamics that links phenomena occurring at the subcellular, cellular, and tissue levels of organization, to simulate the experimental data of the radiation response of swine epidermis, which is closely similar to human epidermis. Incorporating experimentally measured histological and cell kinetic parameters, we obtain results of population kinetics and proliferation indexes comparable to observations in unirradiated and acutely irradiated swine experiments. At the sub-cellular level, several recently published Wnt signaling controlled cell-cycle models are applied and the roles of key components and parameters are analyzed. Based on our simulation results, we demonstrate that a moderate increase of proliferation rate for the survival proliferative cells is sufficient to fully repopulate the area denuded by high dose radiation, as long as the integrity of underlying basement membrane is maintained. Our work highlights the importance of considering proliferation kinetics as well as the spatial organization of tissues when conducting in vivo investigations of radiation responses. This integrated model allow us to test the validity of several basic biological rules at the cellular level and sub-cellular mechanisms by qualitatively comparing simulation results with published research, and enhance our understanding of the pathophysiological effects of ionizing radiation on skin.

Reaction modeling of drainage quality in the Duluth Complex, northern Minnesota, USA

USGS Publications Warehouse

Seal, Robert; Lapakko, Kim; Piatak, Nadine; Woodruff, Laurel G.

2015-01-01

Reaction modeling can be a valuable tool in predicting the long-term behavior of waste material if representative rate constants can be derived from long-term leaching tests or other approaches. Reaction modeling using the REACT program of the Geochemist’s Workbench was conducted to evaluate long-term drainage quality affected by disseminated Cu-Ni-(Co-)-PGM sulfide mineralization in the basal zone of the Duluth Complex where significant resources have been identified. Disseminated sulfide minerals, mostly pyrrhotite and Cu-Fe sulfides, are hosted by clinopyroxene-bearing troctolites. Carbonate minerals are scarce to non-existent. Long-term simulations of up to 20 years of weathering of tailings used two different sets of rate constants: one based on published laboratory single-mineral dissolution experiments, and one based on leaching experiments using bulk material from the Duluth Complex conducted by the Minnesota Department of Natural Resources (MNDNR). The simulations included only plagioclase, olivine, clinopyroxene, pyrrhotite, and water as starting phases. Dissolved oxygen concentrations were assumed to be in equilibrium with atmospheric oxygen. The simulations based on the published single-mineral rate constants predicted that pyrrhotite would be effectively exhausted in less than two years and pH would rise accordingly. In contrast, only 20 percent of the pyrrhotite was depleted after two years using the MNDNR rate constants. Predicted pyrrhotite depletion by the simulation based on the MNDNR rate constant matched well with published results of laboratory tests on tailings. Modeling long-term weathering of mine wastes also can provide important insights into secondary reactions that may influence the permeability of tailings and thereby affect weathering behavior. Both models predicted the precipitation of a variety of secondary phases including goethite, gibbsite, and clay (nontronite).

Coupled thermochemical, isotopic evolution and heat transfer simulations in highly irradiated UO2 nuclear fuel

NASA Astrophysics Data System (ADS)

Piro, M. H. A.; Banfield, J.; Clarno, K. T.; Simunovic, S.; Besmann, T. M.; Lewis, B. J.; Thompson, W. T.

2013-10-01

Predictive capabilities for simulating irradiated nuclear fuel behavior are enhanced in the current work by coupling thermochemistry, isotopic evolution and heat transfer. Thermodynamic models that are incorporated into this framework not only predict the departure from stoichiometry of UO2, but also consider dissolved fission and activation products in the fluorite oxide phase, noble metal inclusions, secondary oxides including uranates, zirconates, molybdates and the gas phase. Thermochemical computations utilize the spatial and temporal evolution of the fission and activation product inventory in the pellet, which is typically neglected in nuclear fuel performance simulations. Isotopic computations encompass the depletion, decay and transmutation of more than 2000 isotopes that are calculated at every point in space and time. These computations take into consideration neutron flux depression and the increased production of fissile plutonium near the fuel pellet periphery (i.e., the so-called “rim effect”). Thermochemical and isotopic predictions are in very good agreement with reported experimental measurements of highly irradiated UO2 fuel with an average burnup of 102 GW d t(U)-1. Simulation results demonstrate that predictions are considerably enhanced when coupling thermochemical and isotopic computations in comparison to empirical correlations. Notice: This manuscript has been authored by UT-Battelle, LLC, under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes.

Effectiveness of patient simulation in nursing education: meta-analysis.

PubMed

Shin, Sujin; Park, Jin-Hwa; Kim, Jung-Hee

2015-01-01

The use of simulation as an educational tool is becoming increasingly prevalent in nursing education, and a variety of simulators are utilized. Based on the results of these studies, nursing facilitators must find ways to promote effective learning among students in clinical practice and classrooms. To identify the best available evidence about the effects of patient simulation in nursing education through a meta-analysis. This study explores quantitative evidence published in the electronic databases: EBSCO, Medline, ScienceDirect, and ERIC. Using a search strategy, we identified 2503 potentially relevant articles. Twenty studies were included in the final analysis. We found significant post-intervention improvements in various domains for participants who received simulation education compared to the control groups, with a pooled random-effects standardized mean difference of 0.71, which is a medium-to-large effect size. In the subgroup analysis, we found that simulation education in nursing had benefits, in terms of effect sizes, when the effects were evaluated through performance, the evaluation outcome was psychomotor skills, the subject of learning was clinical, learners were clinical nurses and senior undergraduate nursing students, and simulators were high fidelity. These results indicate that simulation education demonstrated medium to large effect sizes and could guide nurse educators with regard to the conditions under which patient simulation is more effective than traditional learning methods. Copyright © 2014 Elsevier Ltd. All rights reserved.

An efficient soil water balance model based on hybrid numerical and statistical methods

NASA Astrophysics Data System (ADS)

Mao, Wei; Yang, Jinzhong; Zhu, Yan; Ye, Ming; Liu, Zhao; Wu, Jingwei

2018-04-01

Most soil water balance models only consider downward soil water movement driven by gravitational potential, and thus cannot simulate upward soil water movement driven by evapotranspiration especially in agricultural areas. In addition, the models cannot be used for simulating soil water movement in heterogeneous soils, and usually require many empirical parameters. To resolve these problems, this study derives a new one-dimensional water balance model for simulating both downward and upward soil water movement in heterogeneous unsaturated zones. The new model is based on a hybrid of numerical and statistical methods, and only requires four physical parameters. The model uses three governing equations to consider three terms that impact soil water movement, including the advective term driven by gravitational potential, the source/sink term driven by external forces (e.g., evapotranspiration), and the diffusive term driven by matric potential. The three governing equations are solved separately by using the hybrid numerical and statistical methods (e.g., linear regression method) that consider soil heterogeneity. The four soil hydraulic parameters required by the new models are as follows: saturated hydraulic conductivity, saturated water content, field capacity, and residual water content. The strength and weakness of the new model are evaluated by using two published studies, three hypothetical examples and a real-world application. The evaluation is performed by comparing the simulation results of the new model with corresponding results presented in the published studies, obtained using HYDRUS-1D and observation data. The evaluation indicates that the new model is accurate and efficient for simulating upward soil water flow in heterogeneous soils with complex boundary conditions. The new model is used for evaluating different drainage functions, and the square drainage function and the power drainage function are recommended. Computational efficiency of the new model makes it particularly suitable for large-scale simulation of soil water movement, because the new model can be used with coarse discretization in space and time.

High performance computing in biology: multimillion atom simulations of nanoscale systems

PubMed Central

Sanbonmatsu, K. Y.; Tung, C.-S.

2007-01-01

Computational methods have been used in biology for sequence analysis (bioinformatics), all-atom simulation (molecular dynamics and quantum calculations), and more recently for modeling biological networks (systems biology). Of these three techniques, all-atom simulation is currently the most computationally demanding, in terms of compute load, communication speed, and memory load. Breakthroughs in electrostatic force calculation and dynamic load balancing have enabled molecular dynamics simulations of large biomolecular complexes. Here, we report simulation results for the ribosome, using approximately 2.64 million atoms, the largest all-atom biomolecular simulation published to date. Several other nanoscale systems with different numbers of atoms were studied to measure the performance of the NAMD molecular dynamics simulation program on the Los Alamos National Laboratory Q Machine. We demonstrate that multimillion atom systems represent a 'sweet spot' for the NAMD code on large supercomputers. NAMD displays an unprecedented 85% parallel scaling efficiency for the ribosome system on 1024 CPUs. We also review recent targeted molecular dynamics simulations of the ribosome that prove useful for studying conformational changes of this large biomolecular complex in atomic detail. PMID:17187988

Velocity segregation and systematic biases in velocity dispersion estimates with the SPT-GMOS spectroscopic survey

DOE PAGES

Bayliss, Matthew. B.; Zengo, Kyle; Ruel, Jonathan; ...

2017-03-07

The velocity distribution of galaxies in clusters is not universal; rather, galaxies are segregated according to their spectral type and relative luminosity. We examine the velocity distributions of different populations of galaxies within 89 Sunyaev Zel'dovich (SZ) selected galaxy clusters spanningmore » $ 0.28 < z < 1.08$. Our sample is primarily draw from the SPT-GMOS spectroscopic survey, supplemented by additional published spectroscopy, resulting in a final spectroscopic sample of 4148 galaxy spectra---2868 cluster members. The velocity dispersion of star-forming cluster galaxies is $$17\\pm4$$% greater than that of passive cluster galaxies, and the velocity dispersion of bright ($$m < m^{*}-0.5$$) cluster galaxies is $$11\\pm4$$% lower than the velocity dispersion of our total member population. We find good agreement with simulations regarding the shape of the relationship between the measured velocity dispersion and the fraction of passive vs. star-forming galaxies used to measure it, but we find a small offset between this relationship as measured in data and simulations in which suggests that our dispersions are systematically low by as much as 3\\% relative to simulations. We argue that this offset could be interpreted as a measurement of the effective velocity bias that describes the ratio of our observed velocity dispersions and the intrinsic velocity dispersion of dark matter particles in a published simulation result. Here, by measuring velocity bias in this way suggests that large spectroscopic surveys can improve dispersion-based mass-observable scaling relations for cosmology even in the face of velocity biases, by quantifying and ultimately calibrating them out.« less

Velocity segregation and systematic biases in velocity dispersion estimates with the SPT-GMOS spectroscopic survey

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

Bayliss, Matthew. B.; Zengo, Kyle; Ruel, Jonathan

The velocity distribution of galaxies in clusters is not universal; rather, galaxies are segregated according to their spectral type and relative luminosity. We examine the velocity distributions of different populations of galaxies within 89 Sunyaev Zel'dovich (SZ) selected galaxy clusters spanningmore » $ 0.28 < z < 1.08$. Our sample is primarily draw from the SPT-GMOS spectroscopic survey, supplemented by additional published spectroscopy, resulting in a final spectroscopic sample of 4148 galaxy spectra---2868 cluster members. The velocity dispersion of star-forming cluster galaxies is $$17\\pm4$$% greater than that of passive cluster galaxies, and the velocity dispersion of bright ($$m < m^{*}-0.5$$) cluster galaxies is $$11\\pm4$$% lower than the velocity dispersion of our total member population. We find good agreement with simulations regarding the shape of the relationship between the measured velocity dispersion and the fraction of passive vs. star-forming galaxies used to measure it, but we find a small offset between this relationship as measured in data and simulations in which suggests that our dispersions are systematically low by as much as 3\\% relative to simulations. We argue that this offset could be interpreted as a measurement of the effective velocity bias that describes the ratio of our observed velocity dispersions and the intrinsic velocity dispersion of dark matter particles in a published simulation result. Here, by measuring velocity bias in this way suggests that large spectroscopic surveys can improve dispersion-based mass-observable scaling relations for cosmology even in the face of velocity biases, by quantifying and ultimately calibrating them out.« less

A web platform for integrated surface water - groundwater modeling and data management

NASA Astrophysics Data System (ADS)

Fatkhutdinov, Aybulat; Stefan, Catalin; Junghanns, Ralf

2016-04-01

Model-based decision support systems are considered to be reliable and time-efficient tools for resources management in various hydrology related fields. However, searching and acquisition of the required data, preparation of the data sets for simulations as well as post-processing, visualization and publishing of the simulations results often requires significantly more work and time than performing the modeling itself. The purpose of the developed software is to combine data storage facilities, data processing instruments and modeling tools in a single platform which potentially can reduce time required for performing simulations, hence decision making. The system is developed within the INOWAS (Innovative Web Based Decision Support System for Water Sustainability under a Changing Climate) project. The platform integrates spatially distributed catchment scale rainfall - runoff, infiltration and groundwater flow models with data storage, processing and visualization tools. The concept is implemented in a form of a web-GIS application and is build based on free and open source components, including the PostgreSQL database management system, Python programming language for modeling purposes, Mapserver for visualization and publishing the data, Openlayers for building the user interface and others. Configuration of the system allows performing data input, storage, pre- and post-processing and visualization in a single not disturbed workflow. In addition, realization of the decision support system in the form of a web service provides an opportunity to easily retrieve and share data sets as well as results of simulations over the internet, which gives significant advantages for collaborative work on the projects and is able to significantly increase usability of the decision support system.

Velocity Segregation and Systematic Biases In Velocity Dispersion Estimates with the SPT-GMOS Spectroscopic Survey

NASA Astrophysics Data System (ADS)

Bayliss, Matthew. B.; Zengo, Kyle; Ruel, Jonathan; Benson, Bradford A.; Bleem, Lindsey E.; Bocquet, Sebastian; Bulbul, Esra; Brodwin, Mark; Capasso, Raffaella; Chiu, I.-non; McDonald, Michael; Rapetti, David; Saro, Alex; Stalder, Brian; Stark, Antony A.; Strazzullo, Veronica; Stubbs, Christopher W.; Zenteno, Alfredo

2017-03-01

The velocity distribution of galaxies in clusters is not universal; rather, galaxies are segregated according to their spectral type and relative luminosity. We examine the velocity distributions of different populations of galaxies within 89 Sunyaev Zel’dovich (SZ) selected galaxy clusters spanning 0.28< z< 1.08. Our sample is primarily draw from the SPT-GMOS spectroscopic survey, supplemented by additional published spectroscopy, resulting in a final spectroscopic sample of 4148 galaxy spectra—2868 cluster members. The velocity dispersion of star-forming cluster galaxies is 17 ± 4% greater than that of passive cluster galaxies, and the velocity dispersion of bright (m< {m}* -0.5) cluster galaxies is 11 ± 4% lower than the velocity dispersion of our total member population. We find good agreement with simulations regarding the shape of the relationship between the measured velocity dispersion and the fraction of passive versus star-forming galaxies used to measure it, but we find a small offset between this relationship as measured in data and simulations, which suggests that our dispersions are systematically low by as much as 3% relative to simulations. We argue that this offset could be interpreted as a measurement of the effective velocity bias that describes the ratio of our observed velocity dispersions and the intrinsic velocity dispersion of dark matter particles in a published simulation result. Measuring velocity bias in this way suggests that large spectroscopic surveys can improve dispersion-based mass-observable scaling relations for cosmology even in the face of velocity biases, by quantifying and ultimately calibrating them out.

Large eddy simulation and experimental study on vented gasoline-air mixture explosions in a semi-confined obstructed pipe.

PubMed

Li, Guoqing; Du, Yang; Wang, Shimao; Qi, Sheng; Zhang, Peili; Chen, Wenzhuo

2017-10-05

In this work, LES simulation coupled with a TFC sub-grid combustion model has been performed in a semi-confined pipe (L/D=10, V=10L) in the presence of four hollow-square obstacles (BR=49.8%) with circular hollow cross-section, in order to study the premixed gasoline-air mixture explosions. The comparisons between simulated results and experimental results have been conducted. It was found that the simulated results were in good agreement with experimental data in terms of flame structures, flame locations and overpressure time histories. Moreover, the interaction between flame propagation process and obstacles, overpressure dynamics were analyzed. In addition, the effects of initial gasoline vapor concentration (lean (ϕ=1.3%), stoichiometric (ϕ=1.7%) and rich (ϕ=2.1%)), and the number of obstacles (from 1 to 4) were also investigated by experiments. Some of the experimental results have been compared with the literature data. It is found that the explosion parameters of gasoline-air mixtures (e.g. the maximum overpressure peaks, average overpressure growth rates, etc.) are different from some other fuels such as hydrogen, methane and LPG, etc. Copyright © 2017. Published by Elsevier B.V.

Peridynamic Applications for Orthotropic Materials

DTIC Science & Technology

2012-09-26

test and a vibration excitation of a laminated beam. An SEN (single edge notch) test of a 0° laminated plate was simulated by peridynamics and the...computational results matched very well with published experimental results. Fracture initiation and crack path of laminated plates with different fiber...Dwivedi [1] modeled the propagation of single-edge notch (SEN) in 0° laminated plate using cohesizve zone method. Xu [2] and Hu [3] proposed a two

Building a Virtual Model of a Baleen Whale: Phase 2

DTIC Science & Technology

2015-09-30

example, the biosonar signal generation mechanism and the formation of an acoustic transmission beam, or to measure the amplitude differences and...from simulations with published results from live animal biosonar research (Cranford and Krysl, 2013). Collectively, our research results butress the...2004). " Biosonar pulse production in odontocetes: The state of our knowledge," in Echolocation in bats and dolphins, edited by J. A. Thomas, C. F

Exploring the use of high-fidelity simulation training to enhance clinical skills.

PubMed

Ann Kirkham, Lucy

2018-02-07

The use of interprofessional simulation training to enhance nursing students' performance of technical and non-technical clinical skills is becoming increasingly common. Simulation training can involve the use of role play, virtual reality or patient simulator manikins to replicate clinical scenarios and assess the nursing student's ability to, for example, undertake clinical observations or work as part of a team. Simulation training enables nursing students to practise clinical skills in a safe environment. Effective simulation training requires extensive preparation, and debriefing is necessary following a simulated training session to review any positive or negative aspects of the learning experience. This article discusses a high-fidelity simulated training session that was used to assess a group of third-year nursing students and foundation level 1 medical students. This involved the use of a patient simulator manikin in a scenario that required the collaborative management of a deteriorating patient. ©2018 RCN Publishing Company Ltd. All rights reserved. Not to be copied, transmitted or recorded in any way, in whole or part, without prior permission of the publishers.

The Ongoing and Open-Ended Simulation

ERIC Educational Resources Information Center

Cohen, Alexander

2016-01-01

This case study explores a novel form of classroom simulation that differs from published examples in two important respects. First, it is ongoing. While most simulations represent a single learning episode embedded within a course, the ongoing simulation is a continuous set of interrelated events and decisions that accompany learning throughout…

Simulation of the right-angle car collision based on identified parameters

NASA Astrophysics Data System (ADS)

Kostek, R.; Aleksandrowicz, P.

2017-10-01

This article presents an influence of contact parameters on the collision pattern of vehicles. In this case a crash of two Fiat Cinquecentos with perpendicular median planes was simulated. The first vehicle was driven with a speed 50 km/h and crashed into the other one, standing still. It is a typical collision at junctions. For the first simulation, the default parameters of the V-SIM simulation program were assumed and then the parameters identified from the crash test of a Fiat Cinquecento, published by ADAC (Allgemeiner Deutscher Automobil-Club) were used. Various post-impact movements were observed for both simulations, which demonstrates a sensitivity of the simulation results to the assumed parameters. Applying the default parameters offered by the program can lead to inadequate evaluation of the collision part due to its only approximate reconstruction, which in consequence, influences the court decision. It was demonstrated how complex it is to reconstruct the pattern of the vehicles’ crash and what problems are faced by expert witnesses who tend to use default parameters.

Current status and future challenges in T-cell receptor/peptide/MHC molecular dynamics simulations.

PubMed

Knapp, Bernhard; Demharter, Samuel; Esmaielbeiki, Reyhaneh; Deane, Charlotte M

2015-11-01

The interaction between T-cell receptors (TCRs) and major histocompatibility complex (MHC)-bound epitopes is one of the most important processes in the adaptive human immune response. Several hypotheses on TCR triggering have been proposed. Many of them involve structural and dynamical adjustments in the TCR/peptide/MHC interface. Molecular Dynamics (MD) simulations are a computational technique that is used to investigate structural dynamics at atomic resolution. Such simulations are used to improve understanding of signalling on a structural level. Here we review how MD simulations of the TCR/peptide/MHC complex have given insight into immune system reactions not achievable with current experimental methods. Firstly, we summarize methods of TCR/peptide/MHC complex modelling and TCR/peptide/MHC MD trajectory analysis methods. Then we classify recently published simulations into categories and give an overview of approaches and results. We show that current studies do not come to the same conclusions about TCR/peptide/MHC interactions. This discrepancy might be caused by too small sample sizes or intrinsic differences between each interaction process. As computational power increases future studies will be able to and should have larger sample sizes, longer runtimes and additional parts of the immunological synapse included. © The Author 2015. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods to estimate the between‐study variance and its uncertainty in meta‐analysis†

PubMed Central

Jackson, Dan; Viechtbauer, Wolfgang; Bender, Ralf; Bowden, Jack; Knapp, Guido; Kuss, Oliver; Higgins, Julian PT; Langan, Dean; Salanti, Georgia

2015-01-01

Meta‐analyses are typically used to estimate the overall/mean of an outcome of interest. However, inference about between‐study variability, which is typically modelled using a between‐study variance parameter, is usually an additional aim. The DerSimonian and Laird method, currently widely used by default to estimate the between‐study variance, has been long challenged. Our aim is to identify known methods for estimation of the between‐study variance and its corresponding uncertainty, and to summarise the simulation and empirical evidence that compares them. We identified 16 estimators for the between‐study variance, seven methods to calculate confidence intervals, and several comparative studies. Simulation studies suggest that for both dichotomous and continuous data the estimator proposed by Paule and Mandel and for continuous data the restricted maximum likelihood estimator are better alternatives to estimate the between‐study variance. Based on the scenarios and results presented in the published studies, we recommend the Q‐profile method and the alternative approach based on a ‘generalised Cochran between‐study variance statistic’ to compute corresponding confidence intervals around the resulting estimates. Our recommendations are based on a qualitative evaluation of the existing literature and expert consensus. Evidence‐based recommendations require an extensive simulation study where all methods would be compared under the same scenarios. © 2015 The Authors. Research Synthesis Methods published by John Wiley & Sons Ltd. PMID:26332144

Monte Carlo reference data sets for imaging research: Executive summary of the report of AAPM Research Committee Task Group 195.

PubMed

Sechopoulos, Ioannis; Ali, Elsayed S M; Badal, Andreu; Badano, Aldo; Boone, John M; Kyprianou, Iacovos S; Mainegra-Hing, Ernesto; McMillan, Kyle L; McNitt-Gray, Michael F; Rogers, D W O; Samei, Ehsan; Turner, Adam C

2015-10-01

The use of Monte Carlo simulations in diagnostic medical imaging research is widespread due to its flexibility and ability to estimate quantities that are challenging to measure empirically. However, any new Monte Carlo simulation code needs to be validated before it can be used reliably. The type and degree of validation required depends on the goals of the research project, but, typically, such validation involves either comparison of simulation results to physical measurements or to previously published results obtained with established Monte Carlo codes. The former is complicated due to nuances of experimental conditions and uncertainty, while the latter is challenging due to typical graphical presentation and lack of simulation details in previous publications. In addition, entering the field of Monte Carlo simulations in general involves a steep learning curve. It is not a simple task to learn how to program and interpret a Monte Carlo simulation, even when using one of the publicly available code packages. This Task Group report provides a common reference for benchmarking Monte Carlo simulations across a range of Monte Carlo codes and simulation scenarios. In the report, all simulation conditions are provided for six different Monte Carlo simulation cases that involve common x-ray based imaging research areas. The results obtained for the six cases using four publicly available Monte Carlo software packages are included in tabular form. In addition to a full description of all simulation conditions and results, a discussion and comparison of results among the Monte Carlo packages and the lessons learned during the compilation of these results are included. This abridged version of the report includes only an introductory description of the six cases and a brief example of the results of one of the cases. This work provides an investigator the necessary information to benchmark his/her Monte Carlo simulation software against the reference cases included here before performing his/her own novel research. In addition, an investigator entering the field of Monte Carlo simulations can use these descriptions and results as a self-teaching tool to ensure that he/she is able to perform a specific simulation correctly. Finally, educators can assign these cases as learning projects as part of course objectives or training programs.

Bistable behavior of the lac operon in E. coli when induced with a mixture of lactose and TMG.

PubMed

Díaz-Hernández, Orlando; Santillán, Moisés

2010-01-01

In this work we investigate multistability in the lac operon of Escherichia coli when it is induced by a mixture of lactose and the non-metabolizable thiomethyl galactoside (TMG). In accordance with previously published experimental results and computer simulations, our simulations predict that: (1) when the system is induced by TMG, the system shows a discernible bistable behavior while, (2) when the system is induced by lactose, bistability does not disappear but excessively high concentrations of lactose would be required to observe it. Finally, our simulation results predict that when a mixture of lactose and TMG is used, the bistability region in the extracellular glucose concentration vs. extracellular lactose concentration parameter space changes in such a way that the model predictions regarding bistability could be tested experimentally. These experiments could help to solve a recent controversy regarding the existence of bistability in the lac operon under natural conditions.

A new optimal sliding mode controller design using scalar sign function.

PubMed

Singla, Mithun; Shieh, Leang-San; Song, Gangbing; Xie, Linbo; Zhang, Yongpeng

2014-03-01

This paper presents a new optimal sliding mode controller using the scalar sign function method. A smooth, continuous-time scalar sign function is used to replace the discontinuous switching function in the design of a sliding mode controller. The proposed sliding mode controller is designed using an optimal Linear Quadratic Regulator (LQR) approach. The sliding surface of the system is designed using stable eigenvectors and the scalar sign function. Controller simulations are compared with another existing optimal sliding mode controller. To test the effectiveness of the proposed controller, the controller is implemented on an aluminum beam with piezoceramic sensor and actuator for vibration control. This paper includes the control design and stability analysis of the new optimal sliding mode controller, followed by simulation and experimental results. The simulation and experimental results show that the proposed approach is very effective. © 2013 ISA. Published by Elsevier Ltd. All rights reserved.

Modeling and analysis of fractional order DC-DC converter.

PubMed

Radwan, Ahmed G; Emira, Ahmed A; AbdelAty, Amr M; Azar, Ahmad Taher

2017-07-11

Due to the non-idealities of commercial inductors, the demand for a better model that accurately describe their dynamic response is elevated. So, the fractional order models of Buck, Boost and Buck-Boost DC-DC converters are presented in this paper. The detailed analysis is made for the two most common modes of converter operation: Continuous Conduction Mode (CCM) and Discontinuous Conduction Mode (DCM). Closed form time domain expressions are derived for inductor currents, voltage gain, average current, conduction time and power efficiency where the effect of the fractional order inductor is found to be strongly present. For example, the peak inductor current at steady state increases with decreasing the inductor order. Advanced Design Systems (ADS) circuit simulations are used to verify the derived formulas, where the fractional order inductor is simulated using Valsa Constant Phase Element (CPE) approximation and Generalized Impedance Converter (GIC). Different simulation results are introduced with good matching to the theoretical formulas for the three DC-DC converter topologies under different fractional orders. A comprehensive comparison with the recently published literature is presented to show the advantages and disadvantages of each approach. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

LES of Temporally Evolving Mixing Layers by Three High Order Schemes

NASA Astrophysics Data System (ADS)

Yee, H.; Sjögreen, B.; Hadjadj, A.

2011-10-01

The performance of three high order shock-capturing schemes is compared for large eddy simulations (LES) of temporally evolving mixing layers for different convective Mach number (Mc) ranging from the quasi-incompressible regime to highly compressible supersonic regime. The considered high order schemes are fifth-order WENO (WENO5), seventh-order WENO (WENO7), and the associated eighth-order central spatial base scheme with the dissipative portion of WENO7 as a nonlinear post-processing filter step (WENO7fi). This high order nonlinear filter method (Yee & Sjögreen 2009) is designed for accurate and efficient simulations of shock-free compressible turbulence, turbulence with shocklets and turbulence with strong shocks with minimum tuning of scheme parameters. The LES results by WENO7fi using the same scheme parameter agree well with experimental results of Barone et al. (2006), and published direct numerical simulations (DNS) by Rogers & Moser (1994) and Pantano & Sarkar (2002), whereas results by WENO5 and WENO7 compare poorly with experimental data and DNS computations.

A Short Study on the Validity of Miller's Theorem Applied to Transistor Amplifier High-Frequency Performance

ERIC Educational Resources Information Center

Schubert, T. F., Jr.; Kim, E. M.

2009-01-01

The use of Miller's Theorem in the determination of the high-frequency cutoff frequency of transistor amplifiers was recently challenged by a paper published in this TRANSACTIONS. Unfortunately, that paper provided no simulation or experimental results to bring credence to the challenge or to validate the alternate method of determination…

Teaching the Growth, Ripening, and Agglomeration of Nanostructures in Computer Experiments

ERIC Educational Resources Information Center

Meyburg, Jan Philipp; Diesing, Detlef

2017-01-01

This article describes the implementation and application of a metal deposition and surface diffusion Monte Carlo simulation in a physical chemistry lab course. Here the self-diffusion of Ag atoms on a Ag(111) surface is modeled and compared to published experimental results. Both the thin-film homoepitaxial growth during adatom deposition onto a…

Neuron splitting in compute-bound parallel network simulations enables runtime scaling with twice as many processors.

PubMed

Hines, Michael L; Eichner, Hubert; Schürmann, Felix

2008-08-01

Neuron tree topology equations can be split into two subtrees and solved on different processors with no change in accuracy, stability, or computational effort; communication costs involve only sending and receiving two double precision values by each subtree at each time step. Splitting cells is useful in attaining load balance in neural network simulations, especially when there is a wide range of cell sizes and the number of cells is about the same as the number of processors. For compute-bound simulations load balance results in almost ideal runtime scaling. Application of the cell splitting method to two published network models exhibits good runtime scaling on twice as many processors as could be effectively used with whole-cell balancing.

Evaluating Simulation Methodologies to Determine Best Strategies to Maximize Student Learning.

PubMed

Scherer, Yvonne K; Foltz-Ramos, Kelly; Fabry, Donna; Chao, Ying-Yu

2016-01-01

Limited evidence exists as to the most effective ways to provide simulation experiences to maximize student learning. This quasi-experimental study investigated 2 different strategies repeated versus 1 exposure and participation versus observation on student outcomes following exposure to a high-fidelity acute asthma exacerbation of asthma scenario. Immediate repeated exposure resulted in significantly higher scores on knowledge, student satisfaction and self-confidence, and clinical performance measures than a single exposure. Significant intergroup differences were found on participants' satisfaction and self-confidence as compared with observers. Implications for nurse educators include expanding the observer role when designing repeated exposure to simulations and integrating technical, cognitive, and behavioral outcomes as a way for faculty to evaluate students' clinical performance. Published by Elsevier Inc.

Simulation of drop movement over an inclined surface using smoothed particle hydrodynamics.

PubMed

Das, Arup K; Das, Prasanta K

2009-10-06

Smoothed particle hydrodynamics (SPH) is used to numerically simulate the movement of drops down an inclined plane. Diffuse interfaces have been assumed for tracking the motion of the contact line. The asymmetric shape of the three-dimensional drop and the variation of contact angle along its periphery can be calculated using the simulation. During the motion of a liquid drop down an inclined plane, an internal circulation of liquid particles is observed due to gravitational pull which causes periodic change in the drop shape. The critical angle of inclination required for the inception of drop motion is also evaluated for different fluids as a function of drop volume. The numerical predictions exhibit a good agreement with the published experimental results.

Use of computational fluid dynamics in respiratory medicine.

PubMed

Fernández Tena, Ana; Casan Clarà, Pere

2015-06-01

Computational Fluid Dynamics (CFD) is a computer-based tool for simulating fluid movement. The main advantages of CFD over other fluid mechanics studies include: substantial savings in time and cost, the analysis of systems or conditions that are very difficult to simulate experimentally (as is the case of the airways), and a practically unlimited level of detail. We used the Ansys-Fluent CFD program to develop a conducting airway model to simulate different inspiratory flow rates and the deposition of inhaled particles of varying diameters, obtaining results consistent with those reported in the literature using other procedures. We hope this approach will enable clinicians to further individualize the treatment of different respiratory diseases. Copyright © 2014 SEPAR. Published by Elsevier Espana. All rights reserved.

Monte Carlo simulation of chemistry following radiolysis with TOPAS-nBio

NASA Astrophysics Data System (ADS)

Ramos-Méndez, J.; Perl, J.; Schuemann, J.; McNamara, A.; Paganetti, H.; Faddegon, B.

2018-05-01

Simulation of water radiolysis and the subsequent chemistry provides important information on the effect of ionizing radiation on biological material. The Geant4 Monte Carlo toolkit has added chemical processes via the Geant4-DNA project. The TOPAS tool simplifies the modeling of complex radiotherapy applications with Geant4 without requiring advanced computational skills, extending the pool of users. Thus, a new extension to TOPAS, TOPAS-nBio, is under development to facilitate the configuration of track-structure simulations as well as water radiolysis simulations with Geant4-DNA for radiobiological studies. In this work, radiolysis simulations were implemented in TOPAS-nBio. Users may now easily add chemical species and their reactions, and set parameters including branching ratios, dissociation schemes, diffusion coefficients, and reaction rates. In addition, parameters for the chemical stage were re-evaluated and updated from those used by default in Geant4-DNA to improve the accuracy of chemical yields. Simulation results of time-dependent and LET-dependent primary yields Gx (chemical species per 100 eV deposited) produced at neutral pH and 25 °C by short track-segments of charged particles were compared to published measurements. The LET range was 0.05–230 keV µm‑1. The calculated Gx values for electrons satisfied the material balance equation within 0.3%, similar for protons albeit with long calculation time. A smaller geometry was used to speed up proton and alpha simulations, with an acceptable difference in the balance equation of 1.3%. Available experimental data of time-dependent G-values for agreed with simulated results within 7%  ±  8% over the entire time range; for over the full time range within 3%  ±  4% for H2O2 from 49%  ±  7% at earliest stages and 3%  ±  12% at saturation. For the LET-dependent Gx, the mean ratios to the experimental data were 1.11  ±  0.98, 1.21  ±  1.11, 1.05  ±  0.52, 1.23  ±  0.59 and 1.49  ±  0.63 (1 standard deviation) for , , H2, H2O2 and , respectively. In conclusion, radiolysis and subsequent chemistry with Geant4-DNA has been successfully incorporated in TOPAS-nBio. Results are in reasonable agreement with published measured and simulated data.

14 CFR Appendix H to Part 121 - Advanced Simulation

Code of Federal Regulations, 2014 CFR

2014-01-01

... 14 Aeronautics and Space 3 2014-01-01 2014-01-01 false Advanced Simulation H Appendix H to Part... Simulation Link to an amendment published at 78 FR 67846, Nov. 12, 2013. This appendix provides guidelines... Simulation Training Program For an operator to conduct Level C or D training under this appendix all required...

Using Microcomputers Simulations in the Classroom: Examples from Undergraduate and Faculty Computer Literacy Courses.

ERIC Educational Resources Information Center

Hart, Jeffrey A.

1985-01-01

Presents a discussion of how computer simulations are used in two undergraduate social science courses and a faculty computer literacy course on simulations and artificial intelligence. Includes a list of 60 simulations for use on mainframes and microcomputers. Entries include type of hardware required, publisher's address, and cost. Sample…

14 CFR 121.409 - Training courses using airplane simulators and other training devices.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 14 Aeronautics and Space 3 2014-01-01 2014-01-01 false Training courses using airplane simulators... Program § 121.409 Training courses using airplane simulators and other training devices. Link to an amendment published at 78 FR 67837, Nov. 12, 2013. (a) Training courses utilizing airplane simulators and...

Using the Everest Team Simulation to Teach Threshold Concepts

ERIC Educational Resources Information Center

Nichols, Elizabeth; Wright, April L.

2015-01-01

This resource review focuses on "Leadership and Team Simulation: Everest V2" released by Harvard Business Publishing. The review describes the simulation's story line of a commercial team expedition climbing to the summit of Mount Everest along with the simulation's architecture and key features. Building on Wright and Gilmore's (2012)…

Design and validation of inert homemade explosive simulants for ground penetrating radar

NASA Astrophysics Data System (ADS)

VanderGaast, Brian W.; McFee, John E.; Russell, Kevin L.; Faust, Anthony A.

2015-05-01

The Canadian Armed Forces (CAF) identified a requirement for inert simulants to act as improvised, or homemade, explosives (IEs) when training on, or evaluating, ground penetrating radar (GPR) systems commonly used in the detection of buried landmines and improvised explosive devices (IEDs). In response, Defence R and D Canada (DRDC) initiated a project to develop IE simulant formulations using commonly available inert materials. These simulants are intended to approximate the expected GPR response of common ammonium nitrate-based IEs, in particular ammonium nitrate/fuel oil (ANFO) and ammonium nitrate/aluminum (ANAl). The complex permittivity over the range of electromagnetic frequencies relevant to standard GPR systems was measured for bulk quantities of these three IEs that had been fabricated at DRDC Suffield Research Centre. Following these measurements, published literature was examined to find benign materials with both a similar complex permittivity, as well as other physical properties deemed desirable - such as low-toxicity, thermal stability, and commercial availability - in order to select candidates for subsequent simulant formulation. Suitable simulant formulations were identified for ANFO, with resulting complex permittivities measured to be within acceptable limits of target values. These IE formulations will now undergo end-user trials with CAF operators in order to confirm their utility. Investigations into ANAl simulants continues. This progress report outlines the development program, simulant design, and current validation results.

Does virtual reality simulation have a role in training trauma and orthopaedic surgeons?

PubMed

Bartlett, J D; Lawrence, J E; Stewart, M E; Nakano, N; Khanduja, V

2018-05-01

Aims The aim of this study was to assess the current evidence relating to the benefits of virtual reality (VR) simulation in orthopaedic surgical training, and to identify areas of future research. Materials and Methods A literature search using the MEDLINE, Embase, and Google Scholar databases was performed. The results' titles, abstracts, and references were examined for relevance. Results A total of 31 articles published between 2004 and 2016 and relating to the objective validity and efficacy of specific virtual reality orthopaedic surgical simulators were identified. We found 18 studies demonstrating the construct validity of 16 different orthopaedic virtual reality simulators by comparing expert and novice performance. Eight studies have demonstrated skill acquisition on a simulator by showing improvements in performance with repeated use. A further five studies have demonstrated measurable improvements in operating theatre performance following a period of virtual reality simulator training. Conclusion The demonstration of 'real-world' benefits from the use of VR simulation in knee and shoulder arthroscopy is promising. However, evidence supporting its utility in other forms of orthopaedic surgery is lacking. Further studies of validity and utility should be combined with robust analyses of the cost efficiency of validated simulators to justify the financial investment required for their use in orthopaedic training. Cite this article: Bone Joint J 2018;100-B:559-65.

Agent-based modeling and systems dynamics model reproduction.

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

North, M. J.; Macal, C. M.

2009-01-01

Reproducibility is a pillar of the scientific endeavour. We view computer simulations as laboratories for electronic experimentation and therefore as tools for science. Recent studies have addressed model reproduction and found it to be surprisingly difficult to replicate published findings. There have been enough failed simulation replications to raise the question, 'can computer models be fully replicated?' This paper answers in the affirmative by reporting on a successful reproduction study using Mathematica, Repast and Swarm for the Beer Game supply chain model. The reproduction process was valuable because it demonstrated the original result's robustness across modelling methodologies and implementation environments.

Impact of Neutrino Opacities on Core-collapse Supernova Simulations

NASA Astrophysics Data System (ADS)

Kotake, Kei; Takiwaki, Tomoya; Fischer, Tobias; Nakamura, Ko; Martínez-Pinedo, Gabriel

2018-02-01

The accurate description of neutrino opacities is central to both the core-collapse supernova (CCSN) phenomenon and the validity of the explosion mechanism itself. In this work, we study in a systematic fashion the role of a variety of well-selected neutrino opacities in CCSN simulations where the multi-energy, three-flavor neutrino transport is solved using the isotropic diffusion source approximation (IDSA) scheme. To verify our code, we first present results from one-dimensional (1D) simulations following the core collapse, bounce, and ∼250 ms postbounce of a 15 {M}ȯ star using a standard set of neutrino opacities by Bruenn. A detailed comparison with published results supports the reliability of our three-flavor IDSA scheme using the standard opacity set. We then investigate in 1D simulations how individual opacity updates lead to differences with the baseline run with the standard opacity set. Through detailed comparisons with previous work, we check the validity of our implementation of each update in a step-by-step manner. Individual neutrino opacities with the largest impact on the overall evolution in 1D simulations are selected for systematic comparisons in our two-dimensional (2D) simulations. Special attention is given to the criterion of explodability in the 2D models. We discuss the implications of these results as well as its limitations and the requirements for future, more elaborate CCSN modeling.

A virtual source model for Monte Carlo simulation of helical tomotherapy.

PubMed

Yuan, Jiankui; Rong, Yi; Chen, Quan

2015-01-08

The purpose of this study was to present a Monte Carlo (MC) simulation method based on a virtual source, jaw, and MLC model to calculate dose in patient for helical tomotherapy without the need of calculating phase-space files (PSFs). Current studies on the tomotherapy MC simulation adopt a full MC model, which includes extensive modeling of radiation source, primary and secondary jaws, and multileaf collimator (MLC). In the full MC model, PSFs need to be created at different scoring planes to facilitate the patient dose calculations. In the present work, the virtual source model (VSM) we established was based on the gold standard beam data of a tomotherapy unit, which can be exported from the treatment planning station (TPS). The TPS-generated sinograms were extracted from the archived patient XML (eXtensible Markup Language) files. The fluence map for the MC sampling was created by incorporating the percentage leaf open time (LOT) with leaf filter, jaw penumbra, and leaf latency contained from sinogram files. The VSM was validated for various geometry setups and clinical situations involving heterogeneous media and delivery quality assurance (DQA) cases. An agreement of < 1% was obtained between the measured and simulated results for percent depth doses (PDDs) and open beam profiles for all three jaw settings in the VSM commissioning. The accuracy of the VSM leaf filter model was verified in comparing the measured and simulated results for a Picket Fence pattern. An agreement of < 2% was achieved between the presented VSM and a published full MC model for heterogeneous phantoms. For complex clinical head and neck (HN) cases, the VSM-based MC simulation of DQA plans agreed with the film measurement with 98% of planar dose pixels passing on the 2%/2 mm gamma criteria. For patient treatment plans, results showed comparable dose-volume histograms (DVHs) for planning target volumes (PTVs) and organs at risk (OARs). Deviations observed in this study were consistent with literature. The VSM-based MC simulation approach can be feasibly built from the gold standard beam model of a tomotherapy unit. The accuracy of the VSM was validated against measurements in homogeneous media, as well as published full MC model in heterogeneous media.

A virtual source model for Monte Carlo simulation of helical tomotherapy

PubMed Central

Yuan, Jiankui; Rong, Yi

2015-01-01

The purpose of this study was to present a Monte Carlo (MC) simulation method based on a virtual source, jaw, and MLC model to calculate dose in patient for helical tomotherapy without the need of calculating phase‐space files (PSFs). Current studies on the tomotherapy MC simulation adopt a full MC model, which includes extensive modeling of radiation source, primary and secondary jaws, and multileaf collimator (MLC). In the full MC model, PSFs need to be created at different scoring planes to facilitate the patient dose calculations. In the present work, the virtual source model (VSM) we established was based on the gold standard beam data of a tomotherapy unit, which can be exported from the treatment planning station (TPS). The TPS‐generated sinograms were extracted from the archived patient XML (eXtensible Markup Language) files. The fluence map for the MC sampling was created by incorporating the percentage leaf open time (LOT) with leaf filter, jaw penumbra, and leaf latency contained from sinogram files. The VSM was validated for various geometry setups and clinical situations involving heterogeneous media and delivery quality assurance (DQA) cases. An agreement of <1% was obtained between the measured and simulated results for percent depth doses (PDDs) and open beam profiles for all three jaw settings in the VSM commissioning. The accuracy of the VSM leaf filter model was verified in comparing the measured and simulated results for a Picket Fence pattern. An agreement of <2% was achieved between the presented VSM and a published full MC model for heterogeneous phantoms. For complex clinical head and neck (HN) cases, the VSM‐based MC simulation of DQA plans agreed with the film measurement with 98% of planar dose pixels passing on the 2%/2 mm gamma criteria. For patient treatment plans, results showed comparable dose‐volume histograms (DVHs) for planning target volumes (PTVs) and organs at risk (OARs). Deviations observed in this study were consistent with literature. The VSM‐based MC simulation approach can be feasibly built from the gold standard beam model of a tomotherapy unit. The accuracy of the VSM was validated against measurements in homogeneous media, as well as published full MC model in heterogeneous media. PACS numbers: 87.53.‐j, 87.55.K‐ PMID:25679157

Gray: a ray tracing-based Monte Carlo simulator for PET.

PubMed

Freese, David L; Olcott, Peter D; Buss, Samuel R; Levin, Craig S

2018-05-21

Monte Carlo simulation software plays a critical role in PET system design. Performing complex, repeated Monte Carlo simulations can be computationally prohibitive, as even a single simulation can require a large amount of time and a computing cluster to complete. Here we introduce Gray, a Monte Carlo simulation software for PET systems. Gray exploits ray tracing methods used in the computer graphics community to greatly accelerate simulations of PET systems with complex geometries. We demonstrate the implementation of models for positron range, annihilation acolinearity, photoelectric absorption, Compton scatter, and Rayleigh scatter. For validation, we simulate the GATE PET benchmark, and compare energy, distribution of hits, coincidences, and run time. We show a [Formula: see text] speedup using Gray, compared to GATE for the same simulation, while demonstrating nearly identical results. We additionally simulate the Siemens Biograph mCT system with both the NEMA NU-2 scatter phantom and sensitivity phantom. We estimate the total sensitivity within [Formula: see text]% when accounting for differences in peak NECR. We also estimate the peak NECR to be [Formula: see text] kcps, or within [Formula: see text]% of published experimental data. The activity concentration of the peak is also estimated within 1.3%.

Online model checking approach based parameter estimation to a neuronal fate decision simulation model in Caenorhabditis elegans with hybrid functional Petri net with extension.

PubMed

Li, Chen; Nagasaki, Masao; Koh, Chuan Hock; Miyano, Satoru

2011-05-01

Mathematical modeling and simulation studies are playing an increasingly important role in helping researchers elucidate how living organisms function in cells. In systems biology, researchers typically tune many parameters manually to achieve simulation results that are consistent with biological knowledge. This severely limits the size and complexity of simulation models built. In order to break this limitation, we propose a computational framework to automatically estimate kinetic parameters for a given network structure. We utilized an online (on-the-fly) model checking technique (which saves resources compared to the offline approach), with a quantitative modeling and simulation architecture named hybrid functional Petri net with extension (HFPNe). We demonstrate the applicability of this framework by the analysis of the underlying model for the neuronal cell fate decision model (ASE fate model) in Caenorhabditis elegans. First, we built a quantitative ASE fate model containing 3327 components emulating nine genetic conditions. Then, using our developed efficient online model checker, MIRACH 1.0, together with parameter estimation, we ran 20-million simulation runs, and were able to locate 57 parameter sets for 23 parameters in the model that are consistent with 45 biological rules extracted from published biological articles without much manual intervention. To evaluate the robustness of these 57 parameter sets, we run another 20 million simulation runs using different magnitudes of noise. Our simulation results concluded that among these models, one model is the most reasonable and robust simulation model owing to the high stability against these stochastic noises. Our simulation results provide interesting biological findings which could be used for future wet-lab experiments.

GATE Monte Carlo simulation in a cloud computing environment

NASA Astrophysics Data System (ADS)

Rowedder, Blake Austin

The GEANT4-based GATE is a unique and powerful Monte Carlo (MC) platform, which provides a single code library allowing the simulation of specific medical physics applications, e.g. PET, SPECT, CT, radiotherapy, and hadron therapy. However, this rigorous yet flexible platform is used only sparingly in the clinic due to its lengthy calculation time. By accessing the powerful computational resources of a cloud computing environment, GATE's runtime can be significantly reduced to clinically feasible levels without the sizable investment of a local high performance cluster. This study investigated a reliable and efficient execution of GATE MC simulations using a commercial cloud computing services. Amazon's Elastic Compute Cloud was used to launch several nodes equipped with GATE. Job data was initially broken up on the local computer, then uploaded to the worker nodes on the cloud. The results were automatically downloaded and aggregated on the local computer for display and analysis. Five simulations were repeated for every cluster size between 1 and 20 nodes. Ultimately, increasing cluster size resulted in a decrease in calculation time that could be expressed with an inverse power model. Comparing the benchmark results to the published values and error margins indicated that the simulation results were not affected by the cluster size and thus that integrity of a calculation is preserved in a cloud computing environment. The runtime of a 53 minute long simulation was decreased to 3.11 minutes when run on a 20-node cluster. The ability to improve the speed of simulation suggests that fast MC simulations are viable for imaging and radiotherapy applications. With high power computing continuing to lower in price and accessibility, implementing Monte Carlo techniques with cloud computing for clinical applications will continue to become more attractive.

Numerical simulation of fluid flow and heat transfer in enhanced copper tube

NASA Astrophysics Data System (ADS)

Rahman, M. M.; Zhen, T.; Kadir, A. K.

2013-06-01

Inner grooved tube is enhanced with grooves by increasing the inner surface area. Due to its high efficiency of heat transfer, it is used widely in power generation, air conditioning and many other applications. Heat exchanger is one of the example that uses inner grooved tube to enhance rate heat transfer. Precision in production of inner grooved copper tube is very important because it affects the tube's performance due to various tube parameters. Therefore, it is necessary to carry out analysis in optimizing tube performance prior to production in order to avoid unnecessary loss. The analysis can be carried out either through experimentation or numerical simulation. However, experimental study is too costly and takes longer time in gathering necessary information. Therefore, numerical simulation is conducted instead of experimental research. Firstly, the model of inner grooved tube was generated using SOLIDWORKS. Then it was imported into GAMBIT for healing, followed by meshing, boundary types and zones settings. Next, simulation was done in FLUENT where all the boundary conditions are set. The simulation results were observed and compared with published experimental results. It showed that heat transfer enhancement in range of 649.66% to 917.22% of inner grooved tube compared to plain tube.

A Monte Carlo analysis of breast screening randomized trials.

PubMed

Zamora, Luis I; Forastero, Cristina; Guirado, Damián; Lallena, Antonio M

2016-12-01

To analyze breast screening randomized trials with a Monte Carlo simulation tool. A simulation tool previously developed to simulate breast screening programmes was adapted for that purpose. The history of women participating in the trials was simulated, including a model for survival after local treatment of invasive cancers. Distributions of time gained due to screening detection against symptomatic detection and the overall screening sensitivity were used as inputs. Several randomized controlled trials were simulated. Except for the age range of women involved, all simulations used the same population characteristics and this permitted to analyze their external validity. The relative risks obtained were compared to those quoted for the trials, whose internal validity was addressed by further investigating the reasons of the disagreements observed. The Monte Carlo simulations produce results that are in good agreement with most of the randomized trials analyzed, thus indicating their methodological quality and external validity. A reduction of the breast cancer mortality around 20% appears to be a reasonable value according to the results of the trials that are methodologically correct. Discrepancies observed with Canada I and II trials may be attributed to a low mammography quality and some methodological problems. Kopparberg trial appears to show a low methodological quality. Monte Carlo simulations are a powerful tool to investigate breast screening controlled randomized trials, helping to establish those whose results are reliable enough to be extrapolated to other populations and to design the trial strategies and, eventually, adapting them during their development. Copyright © 2016 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Parallel STEPS: Large Scale Stochastic Spatial Reaction-Diffusion Simulation with High Performance Computers

PubMed Central

Chen, Weiliang; De Schutter, Erik

2017-01-01

Stochastic, spatial reaction-diffusion simulations have been widely used in systems biology and computational neuroscience. However, the increasing scale and complexity of models and morphologies have exceeded the capacity of any serial implementation. This led to the development of parallel solutions that benefit from the boost in performance of modern supercomputers. In this paper, we describe an MPI-based, parallel operator-splitting implementation for stochastic spatial reaction-diffusion simulations with irregular tetrahedral meshes. The performance of our implementation is first examined and analyzed with simulations of a simple model. We then demonstrate its application to real-world research by simulating the reaction-diffusion components of a published calcium burst model in both Purkinje neuron sub-branch and full dendrite morphologies. Simulation results indicate that our implementation is capable of achieving super-linear speedup for balanced loading simulations with reasonable molecule density and mesh quality. In the best scenario, a parallel simulation with 2,000 processes runs more than 3,600 times faster than its serial SSA counterpart, and achieves more than 20-fold speedup relative to parallel simulation with 100 processes. In a more realistic scenario with dynamic calcium influx and data recording, the parallel simulation with 1,000 processes and no load balancing is still 500 times faster than the conventional serial SSA simulation. PMID:28239346

Parallel STEPS: Large Scale Stochastic Spatial Reaction-Diffusion Simulation with High Performance Computers.

PubMed

Chen, Weiliang; De Schutter, Erik

2017-01-01

Stochastic, spatial reaction-diffusion simulations have been widely used in systems biology and computational neuroscience. However, the increasing scale and complexity of models and morphologies have exceeded the capacity of any serial implementation. This led to the development of parallel solutions that benefit from the boost in performance of modern supercomputers. In this paper, we describe an MPI-based, parallel operator-splitting implementation for stochastic spatial reaction-diffusion simulations with irregular tetrahedral meshes. The performance of our implementation is first examined and analyzed with simulations of a simple model. We then demonstrate its application to real-world research by simulating the reaction-diffusion components of a published calcium burst model in both Purkinje neuron sub-branch and full dendrite morphologies. Simulation results indicate that our implementation is capable of achieving super-linear speedup for balanced loading simulations with reasonable molecule density and mesh quality. In the best scenario, a parallel simulation with 2,000 processes runs more than 3,600 times faster than its serial SSA counterpart, and achieves more than 20-fold speedup relative to parallel simulation with 100 processes. In a more realistic scenario with dynamic calcium influx and data recording, the parallel simulation with 1,000 processes and no load balancing is still 500 times faster than the conventional serial SSA simulation.

Critical Parameters of the Initiation Zone for Spontaneous Dynamic Rupture Propagation

NASA Astrophysics Data System (ADS)

Galis, M.; Pelties, C.; Kristek, J.; Moczo, P.; Ampuero, J. P.; Mai, P. M.

2014-12-01

Numerical simulations of rupture propagation are used to study both earthquake source physics and earthquake ground motion. Under linear slip-weakening friction, artificial procedures are needed to initiate a self-sustained rupture. The concept of an overstressed asperity is often applied, in which the asperity is characterized by its size, shape and overstress. The physical properties of the initiation zone may have significant impact on the resulting dynamic rupture propagation. A trial-and-error approach is often necessary for successful initiation because 2D and 3D theoretical criteria for estimating the critical size of the initiation zone do not provide general rules for designing 3D numerical simulations. Therefore, it is desirable to define guidelines for efficient initiation with minimal artificial effects on rupture propagation. We perform an extensive parameter study using numerical simulations of 3D dynamic rupture propagation assuming a planar fault to examine the critical size of square, circular and elliptical initiation zones as a function of asperity overstress and background stress. For a fixed overstress, we discover that the area of the initiation zone is more important for the nucleation process than its shape. Comparing our numerical results with published theoretical estimates, we find that the estimates by Uenishi & Rice (2004) are applicable to configurations with low background stress and small overstress. None of the published estimates are consistent with numerical results for configurations with high background stress. We therefore derive new equations to estimate the initiation zone size in environments with high background stress. Our results provide guidelines for defining the size of the initiation zone and overstress with minimal effects on the subsequent spontaneous rupture propagation.

Monte Carlo modeling of the Siemens Optifocus multileaf collimator.

PubMed

Laliena, Victor; García-Romero, Alejandro

2015-05-01

We have developed a new component module for the BEAMnrc software package, called SMLC, which models the tongue-and-groove structure of the Siemens Optifocus multileaf collimator. The ultimate goal is to perform accurate Monte Carlo simulations of the IMRT treatments carried out with Optifocus. SMLC has been validated by direct geometry checks and by comparing quantitatively the results of simulations performed with it and with the component module VARMLC. Measurements and Monte Carlo simulations of absorbed dose distributions of radiation fields sensitive to the tongue-and-groove effect have been performed to tune the free parameters of SMLC. The measurements cannot be accurately reproduced with VARMLC. Finally, simulations of a typical IMRT field showed that SMLC improves the agreement with experimental measurements with respect to VARMLC in clinically relevant cases. 87.55. K. Copyright © 2015 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Extension of the dielectric breakdown model for simulation of viscous fingering at finite viscosity ratios.

PubMed

Doorwar, Shashvat; Mohanty, Kishore K

2014-07-01

Immiscible displacement of viscous oil by water in a petroleum reservoir is often hydrodynamically unstable. Due to similarities between the physics of dielectric breakdown and immiscible flow in porous media, we extend the existing dielectric breakdown model to simulate viscous fingering patterns for a wide range of viscosity ratios (μ(r)). At low values of power-law index η, the system behaves like a stable Eden growth model and as the value of η is increased to unity, diffusion limited aggregation-like fractals appear. This model is compared with our two-dimensional (2D) experiments to develop a correlation between the viscosity ratio and the power index, i.e., η = 10(-5)μ(r)(0.8775). The 2D and three-dimensional (3D) simulation data appear scalable. The fingering pattern in 3D simulations at finite viscosity ratios appear qualitatively similar to the few experimental results published in the literature.

Surgical clothing systems in laminar airflow operating room: a numerical assessment.

PubMed

Sadrizadeh, Sasan; Holmberg, Sture

2014-01-01

This study compared two different laminar airflow distribution strategies - horizontal and vertical - and investigated the effectiveness of both ventilation systems in terms of reducing the sedimentation and distribution of bacteria-carrying particles. Three different staff clothing systems, which resulted in source strengths of 1.5, 4 and 5 CFU/s per person, were considered. The exploration was conducted numerically using a computational fluid dynamics technique. Active and passive air sampling methods were simulated in addition to recovery tests, and the results were compared. Model validation was performed through comparisons with measurement data from the published literature. The recovery test yielded a value of 8.1 min for the horizontal ventilation scenario and 11.9 min for the vertical ventilation system. Fewer particles were captured by the slit sampler and in sedimentation areas with the horizontal ventilation system. The simulated results revealed that under identical conditions in the examined operating room, the horizontal laminar ventilation system performed better than the vertical option. The internal constellation of lamps, the surgical team and objects could have a serious effect on the movement of infectious particles and therefore on postoperative surgical site infections. Copyright © 2014 King Saud Bin Abdulaziz University for Health Sciences. Published by Elsevier Ltd. All rights reserved.

Neighbourhood food, physical activity, and educational environments and black/white disparities in obesity: a complex systems simulation analysis.

PubMed

Orr, Mark G; Kaplan, George A; Galea, Sandro

2016-09-01

Multiple approaches that can contribute to reducing obesity have been proposed. These policies may share overlapping pathways, and may have unanticipated consequences, creating considerable complexity. Aiming to illuminate the use of agent-based models to explore the consequences of key policies, this paper simulates the effects of increasing neighbourhood availability of good food stores, physical activity infrastructure and higher school quality on the reduction of black/white disparities in body mass index (BMI) in the USA. We used an agent-based model, with parameters derived from the empirical literature, which included individual and neighbourhood characteristics over the life course as determinants of behaviours thought to impact BMI. We systematically varied the strength of the 3 policy interventions, examining the impact of 125 different policy scenarios on black/white BMI disparities. In the absence of any of these policies, black/white BMI disparities generally increased over time. However, we found that some combinations of these policies resulted in reductions in BMI, yielding decreases in the black/white BMI disparity as large as a 90%. Within the structure of relationships captured in this simulation model, there is support for the further use of agent-based simulation models to explore upstream policies as plausible candidates for the reduction of black/white disparities in BMI. These results highlight the potential insights into important public health problems, such as obesity, that can come from uniting the systems science approach with policy analysis. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Docking simulation analysis of range data requirements for the orbital maneuvering vehicle

NASA Technical Reports Server (NTRS)

Micheal, J. D.; Vinz, F. L.

1985-01-01

The results of an initial study are reported assess the controllability of the Orbital Maneuvering Vehicle (OMV) for terminal closure and docking are reported. The vehicle characteristics used in this study are those of the Marshall Space Flight Center (MSFC) baseline OMV which were published with the request for proposals for preliminary design of this vehicle. This simulation was conducted at MSFC using the Target Motion Simulator. The study focused on the OMV manual mode capability to accommodate both stabilized and tumbling target engagements with varying complements of range and range rate data displayed to the OMV operator. Four trained test subjects performed over 400 simulated orbital dockings during this study. A firm requirement for radar during the terminal closure and dock phase of the OMV mission was not established by these simulations. Fifteen pound thrusters recommended in the MSFC baseline design were found to be advantageous for initial rate matching maneuvers with unstabilized targets; however, lower thrust levels were desirable for making the final docking maneuvers.

Absorption and folding of melittin onto lipid bilayer membranes via unbiased atomic detail microsecond molecular dynamics simulation.

PubMed

Chen, Charles H; Wiedman, Gregory; Khan, Ayesha; Ulmschneider, Martin B

2014-09-01

Unbiased molecular simulation is a powerful tool to study the atomic details driving functional structural changes or folding pathways of highly fluid systems, which present great challenges experimentally. Here we apply unbiased long-timescale molecular dynamics simulation to study the ab initio folding and partitioning of melittin, a template amphiphilic membrane active peptide. The simulations reveal that the peptide binds strongly to the lipid bilayer in an unstructured configuration. Interfacial folding results in a localized bilayer deformation. Akin to purely hydrophobic transmembrane segments the surface bound native helical conformer is highly resistant against thermal denaturation. Circular dichroism spectroscopy experiments confirm the strong binding and thermostability of the peptide. The study highlights the utility of molecular dynamics simulations for studying transient mechanisms in fluid lipid bilayer systems. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova. Copyright © 2014. Published by Elsevier B.V.

Tackling force-field bias in protein folding simulations: folding of Villin HP35 and Pin WW domains in explicit water.

PubMed

Mittal, Jeetain; Best, Robert B

2010-08-04

The ability to fold proteins on a computer has highlighted the fact that existing force fields tend to be biased toward a particular type of secondary structure. Consequently, force fields for folding simulations are often chosen according to the native structure, implying that they are not truly "transferable." Here we show that, while the AMBER ff03 potential is known to favor helical structures, a simple correction to the backbone potential (ff03( *)) results in an unbiased energy function. We take as examples the 35-residue alpha-helical Villin HP35 and 37 residue beta-sheet Pin WW domains, which had not previously been folded with the same force field. Starting from unfolded configurations, simulations of both proteins in Amber ff03( *) in explicit solvent fold to within 2.0 A RMSD of the experimental structures. This demonstrates that a simple backbone correction results in a more transferable force field, an important requirement if simulations are to be used to interpret folding mechanism. 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

The R package 'RLumModel': Simulating charge transfer in quartz

NASA Astrophysics Data System (ADS)

Friedrich, Johannes; Kreutzer, Sebastian; Schmidt, Christoph

2017-04-01

Kinetic models of quartz luminescence have gained an important role for predicting experimental results and for understanding charge transfers in (natural) quartz as well as for other dosimetric materials, e.g., Al2O3:C. We present the R package 'RLumModel', offering an easy-to-use tool for simulating quartz luminescence signals (TL, OSL, LM-OSL and RF) based on five integrated and published parameter sets as well as the possibility to use own parameters. Simulation commands can be created (a) using the Risø Sequence Editor, (b) a built-in SAR sequence generator or (c) self-explanatory keywords for customised sequences. Results can be analysed seamlessly using the R package 'Luminescence' along with a visualisation of concentrations of electrons and holes in every trap/centre as well as in the valence and conduction band during all stages of the simulation. Modelling luminescence signals can help understanding charge transfer processes occurring in nature or during measurements in the laboratory. This will lead to a better understanding of several processes concerning geoscientific questions, because quartz is the second most abundant mineral in the Earth's continental crust.

Relativistic Astrophysics in Black Hole and Low-Mass Neutron Star X-ray Binaries

NASA Technical Reports Server (NTRS)

2000-01-01

During the five-year period, our study of "Relativistic Astrophysics in Black Hole and Low-Mass Neutron Star X-ray Binaries" has been focused on the following aspects: observations, data analysis, Monte-Carlo simulations, numerical calculations, and theoretical modeling. Most of the results of our study have been published in refereed journals and conference presentations.

Towards identifying nurse educator competencies required for simulation-based learning: A systemised rapid review and synthesis.

PubMed

Topping, Anne; Bøje, Rikke Buus; Rekola, Leena; Hartvigsen, Tina; Prescott, Stephen; Bland, Andrew; Hope, Angela; Haho, Paivi; Hannula, Leena

2015-11-01

This paper presents the results of a systemised rapid review and synthesis of the literature undertaken to identify competencies required by nurse educators to facilitate simulation-based learning (SBL). An international collaboration undertook a protocol-based search, retrieval and critical review. Web of Science, PubMed, CINAHL Plus, PsycInfo, ERIC, the Cochrane Library and Science Direct. The search was limited to articles published in English, 2002-2012. The search terms used: nurse*, learn*, facilitator, simula*, lecturer, competence, skill*, qualificat*, educator, health care, "patient simulation", "nursing education" and "faculty". The search yielded 2156 "hits", following a review of the abstracts, 72 full-text articles were extracted. These were screened against predetermined inclusion/exclusion criteria and nine articles were retained. Following critical appraisal, the articles were analyzed using an inductive approach to extract statements for categorization and synthesis as competency statements. This review confirmed that there was a modest amount of empirical evidence on which to base a competency framework. Those papers that provided descriptions of educator preparation identified simulation-based workshops, or experiential training, as the most common approaches for enhancing skills. SBL was not associated with any one theoretical perspective. Delivery of SBL appeared to demand competencies associated with planning and designing simulations, facilitating learning in "safe" environments, expert nursing knowledge based on credible clinical realism, reference to evidence-based knowledge and demonstration of professional values and identity. This review derived a preliminary competency framework. This needs further development as a model for educators delivering SBL as part of nursing curricula. Copyright © 2015. Published by Elsevier Ltd.

Computer modeling of obesity links theoretical energetic measures with experimental measures of fuel use for lean and obese men.

PubMed

Rossow, Heidi A; Calvert, C Chris

2014-10-01

The goal of this research was to use a computational model of human metabolism to predict energy metabolism for lean and obese men. The model is composed of 6 state variables representing amino acids, muscle protein, visceral protein, glucose, triglycerides, and fatty acids (FAs). Differential equations represent carbohydrate, amino acid, and FA uptake and output by tissues based on ATP creation and use for both lean and obese men. Model parameterization is based on data from previous studies. Results from sensitivity analyses indicate that model predictions of resting energy expenditure (REE) and respiratory quotient (RQ) are dependent on FA and glucose oxidation rates with the highest sensitivity coefficients (0.6, 0.8 and 0.43, 0.15, respectively, for lean and obese models). Metabolizable energy (ME) is influenced by ingested energy intake with a sensitivity coefficient of 0.98, and a phosphate-to-oxygen ratio by FA oxidation rate and amino acid oxidation rate (0.32, 0.24 and 0.55, 0.65 for lean and obese models, respectively). Simulations of previously published studies showed that the model is able to predict ME ranging from 6.6 to 9.3 with 0% differences between published and model values, and RQ ranging from 0.79 to 0.86 with 1% differences between published and model values. REEs >7 MJ/d are predicted with 6% differences between published and model values. Glucose oxidation increases by ∼0.59 mol/d, RQ increases by 0.03, REE increases by 2 MJ/d, and heat production increases by 1.8 MJ/d in the obese model compared with lean model simulations. Increased FA oxidation results in higher changes in RQ and lower relative changes in REE. These results suggest that because fat mass is directly related to REE and rate of FA oxidation, body fat content could be used as a predictor of RQ. © 2014 American Society for Nutrition.

Business Simulations in Language Teaching.

ERIC Educational Resources Information Center

Westerfield, Kay J.; And Others

This paper describes a pilot project, conducted within the American English Institute at the University of Oregon, on the use of a published business-oriented management simulation in English language training for university-bound international students. The management game simulated competition among a group of manufacturing companies to acquire…

Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC)

PubMed Central

Galindo-Murillo, Rodrigo; Roe, Daniel R.; Cheatham, Thomas E.

2014-01-01

Background The structure and dynamics of DNA are critically related to its function. Molecular dynamics (MD) simulations augment experiment by providing detailed information about the atomic motions. However, to date the simulations have not been long enough for convergence of the dynamics and structural properties of DNA. Methods MD simulations performed with AMBER using the ff99SB force field with the parmbsc0 modifications, including ensembles of independent simulations, were compared to long timescale MD performed with the specialized Anton MD engine on the B-DNA structure d(GCACGAACGAACGAACGC). To assess convergence, the decay of the average RMSD values over longer and longer time intervals was evaluated in addition to assessing convergence of the dynamics via the Kullback-Leibler divergence of principal component projection histograms. Results These MD simulations —including one of the longest simulations of DNA published to date at ~44 μs—surprisingly suggest that the structure and dynamics of the DNA helix, neglecting the terminal base pairs, are essentially fully converged on the ~1–5 μs timescale. Conclusions We can now reproducibly converge the structure and dynamics of B-DNA helices, omitting the terminal base pairs, on the μs time scale with both the AMBER and CHARMM C36 nucleic acid force fields. Results from independent ensembles of simulations starting from different initial conditions, when aggregated, match the results from long timescale simulations on the specialized Anton MD engine. General Significance With access to large-scale GPU resources or the specialized MD engine “Anton” it is possibly for a variety of molecular systems to reproducibly and reliably converge the conformational ensemble of sampled structures. PMID:25219455

Simulating the role of visual selective attention during the development of perceptual completion.

PubMed

Schlesinger, Matthew; Amso, Dima; Johnson, Scott P

2012-11-01

We recently proposed a multi-channel, image-filtering model for simulating the development of visual selective attention in young infants (Schlesinger, Amso & Johnson, 2007). The model not only captures the performance of 3-month-olds on a visual search task, but also implicates two cortical regions that may play a role in the development of visual selective attention. In the current simulation study, we used the same model to simulate 3-month-olds' performance on a second measure, the perceptual unity task. Two parameters in the model - corresponding to areas in the occipital and parietal cortices - were systematically varied while the gaze patterns produced by the model were recorded and subsequently analyzed. Three key findings emerged from the simulation study. First, the model successfully replicated the performance of 3-month-olds on the unity perception task. Second, the model also helps to explain the improved performance of 2-month-olds when the size of the occluder in the unity perception task is reduced. Third, in contrast to our previous simulation results, variation in only one of the two cortical regions simulated (i.e. recurrent activity in posterior parietal cortex) resulted in a performance pattern that matched 3-month-olds. These findings provide additional support for our hypothesis that the development of perceptual completion in early infancy is promoted by progressive improvements in visual selective attention and oculomotor skill. © 2012 Blackwell Publishing Ltd.

Evaluation of simulated corn yields and associated uncertainty in different climate zones of China using Daycent Model

NASA Astrophysics Data System (ADS)

Fu, A.; Xue, Y.

2017-12-01

Corn is one of most important agricultural production in China. Research on the simulation of corn yields and the impacts of climate change and agricultural management practices on corn yields is important in maintaining the stable corn production. After climatic data including daily temperature, precipitation, solar radiation, relative humidity, and wind speed from 1948 to 2010, soil properties, observed corn yields, and farmland management information were collected, corn yields grown in humidity and hot environment (Sichuang province) and cold and dry environment (Hebei province) in China in the past 63 years were simulated by Daycent, and the results was evaluated based on published yield record. The relationship between regional climate change, global warming and corn yield were analyzed, the uncertainties of simulation derived from agricultural management practices by changing fertilization levels, land fertilizer maintenance and tillage methods were reported. The results showed that: (1) Daycent model is capable to simulate corn yields under the different climatic background in China. (2) When studying the relationship between regional climate change and corn yields, it has been found that observed and simulated corn yields increased along with total regional climate change. (3) When studying the relationship between the global warming and corn yields, It was discovered that newly-simulated corn yields after removing the global warming trend of original temperature data were lower than before.

Evaluation of cloud-resolving and limited area model intercomparison simulations using TWP-ICE observations: 1. Deep convective updraft properties: Eval. of TWP-ICE CRMs and LAMs Pt. 1

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

Varble, Adam; Zipser, Edward J.; Fridlind, Ann M.

2014-12-18

Ten 3D cloud-resolving model (CRM) simulations and four 3D limited area model (LAM) simulations of an intense mesoscale convective system observed on 23-24 January 2006 during the Tropical Warm Pool – International Cloud Experiment (TWP-ICE) are compared with each other and with observed radar reflectivity fields and dual-Doppler retrievals of vertical wind speeds in an attempt to explain published results showing a high bias in simulated convective radar reflectivity aloft. This high bias results from ice water content being large, which is a product of large, strong convective updrafts, although hydrometeor size distribution assumptions modulate the size of this bias.more » Making snow mass more realistically proportional to D2 rather than D3 eliminates unrealistically large snow reflectivities over 40 dBZ in some simulations. Graupel, unlike snow, produces high biased reflectivity in all simulations, which is partly a result of parameterized microphysics, but also partly a result of overly intense simulated updrafts. Peak vertical velocities in deep convective updrafts are greater than dual-Doppler retrieved values, especially in the upper troposphere. Freezing of liquid condensate, often rain, lofted above the freezing level in simulated updraft cores greatly contributes to these excessive upper tropospheric vertical velocities. The strongest simulated updraft cores are nearly undiluted, with some of the strongest showing supercell characteristics during the multicellular (pre-squall) stage of the event. Decreasing horizontal grid spacing from 900 to 100 meters slightly weakens deep updraft vertical velocity and moderately decreases the amount of condensate aloft, but not enough to match observational retrievals. Therefore, overly intense simulated updrafts may additionally be a product of unrealistic interactions between convective dynamics, parameterized microphysics, and the large-scale model forcing that promote different convective strengths than observed.« less

Study of Viability and Challenges of using SiPMs as an Alternative to PMT’s in Scintillation Detectors for Nuclear Safeguards

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

Iliev, Metodi

The goals of this project are to identify fundamental and practical problems and features with SiPMs as they relate to IAEA detector needs, Identify published results and implementations of scintillation detectors tat use SiPMs that are of interest to IAEA, asses how effectively the fundamental problems were addresses, and perform simulations and experiments as needed to reproduce crucial results and make recommendations.

Simulation Models for Socioeconomic Inequalities in Health: A Systematic Review

PubMed Central

Speybroeck, Niko; Van Malderen, Carine; Harper, Sam; Müller, Birgit; Devleesschauwer, Brecht

2013-01-01

Background: The emergence and evolution of socioeconomic inequalities in health involves multiple factors interacting with each other at different levels. Simulation models are suitable for studying such complex and dynamic systems and have the ability to test the impact of policy interventions in silico. Objective: To explore how simulation models were used in the field of socioeconomic inequalities in health. Methods: An electronic search of studies assessing socioeconomic inequalities in health using a simulation model was conducted. Characteristics of the simulation models were extracted and distinct simulation approaches were identified. As an illustration, a simple agent-based model of the emergence of socioeconomic differences in alcohol abuse was developed. Results: We found 61 studies published between 1989 and 2013. Ten different simulation approaches were identified. The agent-based model illustration showed that multilevel, reciprocal and indirect effects of social determinants on health can be modeled flexibly. Discussion and Conclusions: Based on the review, we discuss the utility of using simulation models for studying health inequalities, and refer to good modeling practices for developing such models. The review and the simulation model example suggest that the use of simulation models may enhance the understanding and debate about existing and new socioeconomic inequalities of health frameworks. PMID:24192788

Antiskid braking system

NASA Technical Reports Server (NTRS)

Pazdera, J. S.

1974-01-01

Published report describes analytical development and simulation of braking system. System prevents wheels from skidding when brakes are applied, significantly reducing stopping distance. Report also presents computer simulation study on system as applied to aircraft.

Reanalysis of Mariner 9 UV spectrometer data for ozone, cloud, and dust abundances, and their interaction over climate timescales

NASA Technical Reports Server (NTRS)

Lindner, Bernhard Lee

1992-01-01

Research activities to date are discussed. Selected Mariner 9 UV spectra were obtained. Radiative transfer models were updated and then exercised to simulate spectra. Simulated and observed spectra compare favorably. It is noted that large amounts of ozone are currently not retrieved with reflectance spectroscopy, raising large doubts about earlier published ozone abundances. As these published abundances have been used as a benchmark for all theoretical photochemical models of Mars, this deserves further exploration. Three manuscripts were published, and one is in review. Papers were presented and published at three conferences, and are planned for five more conferences in the next six months. The research plan for the next reporting period is discussed and involves continuing studies of reflectance spectroscopy, further examination of Mariner 9 data, and climate change studies of ozone.

Mercury and methylmercury stream concentrations in a Coastal Plain watershed: a multi-scale simulation analysis.

PubMed

Knightes, C D; Golden, H E; Journey, C A; Davis, G M; Conrads, P A; Marvin-DiPasquale, M; Brigham, M E; Bradley, P M

2014-04-01

Mercury is a ubiquitous global environmental toxicant responsible for most US fish advisories. Processes governing mercury concentrations in rivers and streams are not well understood, particularly at multiple spatial scales. We investigate how insights gained from reach-scale mercury data and model simulations can be applied at broader watershed scales using a spatially and temporally explicit watershed hydrology and biogeochemical cycling model, VELMA. We simulate fate and transport using reach-scale (0.1 km(2)) study data and evaluate applications to multiple watershed scales. Reach-scale VELMA parameterization was applied to two nested sub-watersheds (28 km(2) and 25 km(2)) and the encompassing watershed (79 km(2)). Results demonstrate that simulated flow and total mercury concentrations compare reasonably to observations at different scales, but simulated methylmercury concentrations are out-of-phase with observations. These findings suggest that intricacies of methylmercury biogeochemical cycling and transport are under-represented in VELMA and underscore the complexity of simulating mercury fate and transport. Published by Elsevier Ltd.

Current Status of Simulation-based Training Tools in Orthopedic Surgery: A Systematic Review.

PubMed

Morgan, Michael; Aydin, Abdullatif; Salih, Alan; Robati, Shibby; Ahmed, Kamran

To conduct a systematic review of orthopedic training and assessment simulators with reference to their level of evidence (LoE) and level of recommendation. Medline and EMBASE library databases were searched for English language articles published between 1980 and 2016, describing orthopedic simulators or validation studies of these models. All studies were assessed for LoE, and each model was subsequently awarded a level of recommendation using a modified Oxford Centre for Evidence-Based Medicine classification, adapted for education. A total of 76 articles describing orthopedic simulators met the inclusion criteria, 47 of which described at least 1 validation study. The most commonly identified models (n = 34) and validation studies (n = 26) were for knee arthroscopy. Construct validation was the most frequent validation study attempted by authors. In all, 62% (47 of 76) of the simulator studies described arthroscopy simulators, which also contained validation studies with the highest LoE. Orthopedic simulators are increasingly being subjected to validation studies, although the LoE of such studies generally remain low. There remains a lack of focus on nontechnical skills and on cost analyses of orthopedic simulators. Copyright © 2017 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.

Simulation Games: Practical References, Potential Use, Selected Bibliography.

ERIC Educational Resources Information Center

Kidder, Steven J.

Several recently published books on simulation and games are briefly discussed. Selected research studies and demonstration projects are examined to show the potential of simulation and gaming for teaching and training and for the study of social and psychological processes. The bibliography lists 113 publications which should lead the reader to…

Gemini Capsule and Rendezvous Docking Simulator

NASA Image and Video Library

1962-12-19

Practicing with a full-scale model of the Gemini Capsule in Langley's Rendezvous Docking Simulator. -- Caption and photograph published in Winds of Change, 75th Anniversary NASA publication, (page 89), by James Schultz.

Antibiotic Dosing in Continuous Renal Replacement Therapy.

PubMed

Shaw, Alexander R; Mueller, Bruce A

2017-07-01

Appropriate antibiotic dosing is critical to improve outcomes in critically ill patients with sepsis. The addition of continuous renal replacement therapy makes achieving appropriate antibiotic dosing more difficult. The lack of continuous renal replacement therapy standardization results in treatment variability between patients and may influence whether appropriate antibiotic exposure is achieved. The aim of this study was to determine if continuous renal replacement therapy effluent flow rate impacts attaining appropriate antibiotic concentrations when conventional continuous renal replacement therapy antibiotic doses were used. This study used Monte Carlo simulations to evaluate the effect of effluent flow rate variance on pharmacodynamic target attainment for cefepime, ceftazidime, levofloxacin, meropenem, piperacillin, and tazobactam. Published demographic and pharmacokinetic parameters for each antibiotic were used to develop a pharmacokinetic model. Monte Carlo simulations of 5000 patients were evaluated for each antibiotic dosing regimen at the extremes of Kidney Disease: Improving Global Outcomes guidelines recommended effluent flow rates (20 and 35 mL/kg/h). The probability of target attainment was calculated using antibiotic-specific pharmacodynamic targets assessed over the first 72 hours of therapy. Most conventional published antibiotic dosing recommendations, except for levofloxacin, reach acceptable probability of target attainment rates when effluent rates of 20 or 35 mL/kg/h are used. Copyright © 2017 National Kidney Foundation, Inc. Published by Elsevier Inc. All rights reserved.

X-ray system simulation software tools for radiology and radiography education.

PubMed

Kengyelics, Stephen M; Treadgold, Laura A; Davies, Andrew G

2018-02-01

To develop x-ray simulation software tools to support delivery of radiological science education for a range of learning environments and audiences including individual study, lectures, and tutorials. Two software tools were developed; one simulated x-ray production for a simple two dimensional radiographic system geometry comprising an x-ray source, beam filter, test object and detector. The other simulated the acquisition and display of two dimensional radiographic images of complex three dimensional objects using a ray casting algorithm through three dimensional mesh objects. Both tools were intended to be simple to use, produce results accurate enough to be useful for educational purposes, and have an acceptable simulation time on modest computer hardware. The radiographic factors and acquisition geometry could be altered in both tools via their graphical user interfaces. A comparison of radiographic contrast measurements of the simulators to a real system was performed. The contrast output of the simulators had excellent agreement with measured results. The software simulators were deployed to 120 computers on campus. The software tools developed are easy-to-use, clearly demonstrate important x-ray physics and imaging principles, are accessible within a standard University setting and could be used to enhance the teaching of x-ray physics to undergraduate students. Current approaches to teaching x-ray physics in radiological science lack immediacy when linking theory with practice. This method of delivery allows students to engage with the subject in an experiential learning environment. Copyright © 2017. Published by Elsevier Ltd.

Antenna gain of actively compensated free-space optical communication systems under strong turbulence conditions.

PubMed

Juarez, Juan C; Brown, David M; Young, David W

2014-05-19

Current Strehl ratio models for actively compensated free-space optical communications terminals do not accurately predict system performance under strong turbulence conditions as they are based on weak turbulence theory. For evaluation of compensated systems, we present an approach for simulating the Strehl ratio with both low-order (tip/tilt) and higher-order (adaptive optics) correction. Our simulation results are then compared to the published models and their range of turbulence validity is assessed. Finally, we propose a new Strehl ratio model and antenna gain equation that are valid for general turbulence conditions independent of the degree of compensation.

Galileo and optical illusion

NASA Astrophysics Data System (ADS)

Parker, Gary D.

1986-03-01

Galileo's earliest telescopic measurements are of sufficient quality that their detailed analysis yields scientifically interesting and pedagogically useful results. An optical illusion strongly influences Galileo's observations of Jupiter's moons, as published in the Starry Messenger. A simple procedure identifies individual satellites with sufficient reliability to demonstrate that Galileo regularly underestimated satellite brightness and overestimated elongation when a satellite was very close to Jupiter. The probability of underestimation is a monotonically decreasing function of separation angle, both for Galileo and for viewers of a laboratory simulation of the Jupiter ``starfield'' viewed by Galileo. Analysis of Galileo's records and a simple simulation experiment appropriate to undergraduate courses clarify the scientific problems facing Galileo in interpreting his observations.

A web-based rapid assessment tool for production publishing solutions

NASA Astrophysics Data System (ADS)

Sun, Tong

2010-02-01

Solution assessment is a critical first-step in understanding and measuring the business process efficiency enabled by an integrated solution package. However, assessing the effectiveness of any solution is usually a very expensive and timeconsuming task which involves lots of domain knowledge, collecting and understanding the specific customer operational context, defining validation scenarios and estimating the expected performance and operational cost. This paper presents an intelligent web-based tool that can rapidly assess any given solution package for production publishing workflows via a simulation engine and create a report for various estimated performance metrics (e.g. throughput, turnaround time, resource utilization) and operational cost. By integrating the digital publishing workflow ontology and an activity based costing model with a Petri-net based workflow simulation engine, this web-based tool allows users to quickly evaluate any potential digital publishing solutions side-by-side within their desired operational contexts, and provides a low-cost and rapid assessment for organizations before committing any purchase. This tool also benefits the solution providers to shorten the sales cycles, establishing a trustworthy customer relationship and supplement the professional assessment services with a proven quantitative simulation and estimation technology.

Antibody humanization by molecular dynamics simulations-in-silico guided selection of critical backmutations.

PubMed

Margreitter, Christian; Mayrhofer, Patrick; Kunert, Renate; Oostenbrink, Chris

2016-06-01

Monoclonal antibodies represent the fastest growing class of biotherapeutic proteins. However, as they are often initially derived from rodent organisms, there is a severe risk of immunogenic reactions, hampering their applicability. The humanization of these antibodies remains a challenging task in the context of rational drug design. "Superhumanization" describes the direct transfer of the complementarity determining regions to a human germline framework, but this humanization approach often results in loss of binding affinity. In this study, we present a new approach for predicting promising backmutation sites using molecular dynamics simulations of the model antibody Ab2/3H6. The simulation method was developed in close conjunction with novel specificity experiments. Binding properties of mAb variants were evaluated directly from crude supernatants and confirmed using established binding affinity assays for purified antibodies. Our approach provides access to the dynamical features of the actual binding sites of an antibody, based solely on the antibody sequence. Thus we do not need structural data on the antibody-antigen complex and circumvent cumbersome methods to assess binding affinities. © 2016 The Authors Journal of Molecular Recognition Published by John Wiley & Sons Ltd. © 2016 The Authors Journal of Molecular Recognition Published by John Wiley & Sons Ltd.

Simulated Driving Assessment (SDA) for teen drivers: results from a validation study.

PubMed

McDonald, Catherine C; Kandadai, Venk; Loeb, Helen; Seacrist, Thomas S; Lee, Yi-Ching; Winston, Zachary; Winston, Flaura K

2015-06-01

Driver error and inadequate skill are common critical reasons for novice teen driver crashes, yet few validated, standardised assessments of teen driving skills exist. The purpose of this study is to evaluate the construct and criterion validity of a newly developed Simulated Driving Assessment (SDA) for novice teen drivers. The SDA's 35 min simulated drive incorporates 22 variations of the most common teen driver crash configurations. Driving performance was compared for 21 inexperienced teens (age 16-17 years, provisional license ≤90 days) and 17 experienced adults (age 25-50 years, license ≥5 years, drove ≥100 miles per week, no collisions or moving violations ≤3 years). SDA driving performance (Error Score) was based on driving safety measures derived from simulator and eye-tracking data. Negative driving outcomes included simulated collisions or run-off-the-road incidents. A professional driving evaluator/instructor (DEI Score) reviewed videos of SDA performance. The SDA demonstrated construct validity: (1) teens had a higher Error Score than adults (30 vs. 13, p=0.02); (2) For each additional error committed, the RR of a participant's propensity for a simulated negative driving outcome increased by 8% (95% CI 1.05 to 1.10, p<0.01). The SDA-demonstrated criterion validity: Error Score was correlated with DEI Score (r=-0.66, p<0.001). This study supports the concept of validated simulated driving tests like the SDA to assess novice driver skill in complex and hazardous driving scenarios. The SDA, as a standard protocol to evaluate teen driver performance, has the potential to facilitate screening and assessment of teen driving readiness and could be used to guide targeted skill training. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Blunt forehead trauma and optic canal involvement: finite element analysis of anterior skull base and orbit on causes of vision impairment.

PubMed

Huempfner-Hierl, Heike; Bohne, Alexander; Wollny, Gert; Sterker, Ina; Hierl, Thomas

2015-10-01

Clinical studies report on vision impairment after blunt frontal head trauma. A possible cause is damage to the optic nerve bundle within the optic canal due to microfractures of the anterior skull base leading to indirect traumatic optic neuropathy. A finite element study simulating impact forces on the paramedian forehead in different grades was initiated. The set-up consisted of a high-resolution skull model with about 740 000 elements, a blunt impactor and was solved in a transient time-dependent simulation. Individual bone material parameters were calculated for each volume element to increase realism. Results showed stress propagation from the frontal impact towards the optic foramen and the chiasm even at low-force fist-like impacts. Higher impacts produced stress patterns corresponding to typical fracture patterns of the anterior skull base including the optic canal. Transient simulation discerned two stress peaks equalling oscillation. It can be concluded that even comparatively low stresses and oscillation in the optic foramen may cause micro damage undiscerned by CT or MRI explaining consecutive vision loss. Higher impacts lead to typical comminuted fractures, which may affect the integrity of the optic canal. Finite element simulation can be effectively used in studying head trauma and its clinical consequences. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Corn stover harvest increases herbicide movement to subsurface drains - Root Zone Water Quality Model simulations.

PubMed

Shipitalo, Martin J; Malone, Robert W; Ma, Liwang; Nolan, Bernard T; Kanwar, Rameshwar S; Shaner, Dale L; Pederson, Carl H

2016-06-01

Crop residue removal for bioenergy production can alter soil hydrologic properties and the movement of agrochemicals to subsurface drains. The Root Zone Water Quality Model (RZWQM), previously calibrated using measured flow and atrazine concentrations in drainage from a 0.4 ha chisel-tilled plot, was used to investigate effects of 50 and 100% corn (Zea mays L.) stover harvest and the accompanying reductions in soil crust hydraulic conductivity and total macroporosity on transport of atrazine, metolachlor and metolachlor oxanilic acid (OXA). The model accurately simulated field-measured metolachlor transport in drainage. A 3 year simulation indicated that 50% residue removal reduced subsurface drainage by 31% and increased atrazine and metolachlor transport in drainage 4-5-fold when surface crust conductivity and macroporosity were reduced by 25%. Based on its measured sorption coefficient, approximately twofold reductions in OXA losses were simulated with residue removal. The RZWQM indicated that, if corn stover harvest reduces crust conductivity and soil macroporosity, losses of atrazine and metolachlor in subsurface drainage will increase owing to reduced sorption related to more water moving through fewer macropores. Losses of the metolachlor degradation product OXA will decrease as a result of the more rapid movement of the parent compound into the soil. Published 2015. This article is a U.S. Government work and is in the public domain in the USA. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.

Structured water in polyelectrolyte dendrimers: Understanding small angle neutron scattering results through atomistic simulation

NASA Astrophysics Data System (ADS)

Wu, Bin; Kerkeni, Boutheïna; Egami, Takeshi; Do, Changwoo; Liu, Yun; Wang, Yongmei; Porcar, Lionel; Hong, Kunlun; Smith, Sean C.; Liu, Emily L.; Smith, Gregory S.; Chen, Wei-Ren

2012-04-01

Based on atomistic molecular dynamics (MD) simulations, the small angle neutron scattering (SANS) intensity behavior of a single generation-4 polyelectrolyte polyamidoamine starburst dendrimer is investigated at different levels of molecular protonation. The SANS form factor, P(Q), and Debye autocorrelation function, γ(r), are calculated from the equilibrium MD trajectory based on a mathematical approach proposed in this work. The consistency found in comparison against previously published experimental findings (W.-R. Chen, L. Porcar, Y. Liu, P. D. Butler, and L. J. Magid, Macromolecules 40, 5887 (2007)) leads to a link between the neutron scattering experiment and MD computation, and fresh perspectives. The simulations enable scattering calculations of not only the hydrocarbons but also the contribution from the scattering length density fluctuations caused by structured, confined water within the dendrimer. Based on our computational results, we explore the validity of using radius of gyration RG for microstructure characterization of a polyelectrolyte dendrimer from the scattering perspective.

Application of ADM1 for modeling of biogas production from anaerobic digestion of Hydrilla verticillata.

PubMed

Chen, Xiaojuan; Chen, Zhihua; Wang, Xun; Huo, Chan; Hu, Zhiquan; Xiao, Bo; Hu, Mian

2016-07-01

The present study focused on the application of anaerobic digestion model no. 1 (ADM1) to simulate biogas production from Hydrilla verticillata. Model simulation was carried out by implementing ADM1 in AQUASIM 2.0 software. Sensitivity analysis was used to select the most sensitive parameters for estimation using the absolute-relative sensitivity function. Among all the kinetic parameters, disintegration constant (kdis), hydrolysis constant of protein (khyd_pr), Monod maximum specific substrate uptake rate (km_aa, km_ac, km_h2) and half-saturation constants (Ks_aa, Ks_ac) affect biogas production significantly, which were optimized by fitting of the model equations to the data obtained from batch experiments. The ADM1 model after parameter estimation was able to well predict the experimental results of daily biogas production and biogas composition. The simulation results of evolution of organic acids, bacteria concentrations and inhibition effects also helped to get insight into the reaction mechanisms. Copyright © 2016. Published by Elsevier Ltd.

The Lake Tahoe Basin Land Use Simulation Model

USGS Publications Warehouse

Forney, William M.; Oldham, I. Benson

2011-01-01

This U.S. Geological Survey Open-File Report describes the final modeling product for the Tahoe Decision Support System project for the Lake Tahoe Basin funded by the Southern Nevada Public Land Management Act and the U.S. Geological Survey's Geographic Analysis and Monitoring Program. This research was conducted by the U.S. Geological Survey Western Geographic Science Center. The purpose of this report is to describe the basic elements of the novel Lake Tahoe Basin Land Use Simulation Model, publish samples of the data inputs, basic outputs of the model, and the details of the Python code. The results of this report include a basic description of the Land Use Simulation Model, descriptions and summary statistics of model inputs, two figures showing the graphical user interface from the web-based tool, samples of the two input files, seven tables of basic output results from the web-based tool and descriptions of their parameters, and the fully functional Python code.

Bistable Behavior of the Lac Operon in E. Coli When Induced with a Mixture of Lactose and TMG

PubMed Central

Díaz-Hernández, Orlando; Santillán, Moisés

2010-01-01

In this work we investigate multistability in the lac operon of Escherichia coli when it is induced by a mixture of lactose and the non-metabolizable thiomethyl galactoside (TMG). In accordance with previously published experimental results and computer simulations, our simulations predict that: (1) when the system is induced by TMG, the system shows a discernible bistable behavior while, (2) when the system is induced by lactose, bistability does not disappear but excessively high concentrations of lactose would be required to observe it. Finally, our simulation results predict that when a mixture of lactose and TMG is used, the bistability region in the extracellular glucose concentration vs. extracellular lactose concentration parameter space changes in such a way that the model predictions regarding bistability could be tested experimentally. These experiments could help to solve a recent controversy regarding the existence of bistability in the lac operon under natural conditions. PMID:21423364

INVESTIGATION OF THE HUMIDITY EFFECT ON THE FAC-IR-300 IONIZATION CHAMBER RESPONSE.

PubMed

Mohammadi, Seyed Mostafa; Tavakoli-Anbaran, Hossein

2018-02-01

The free-air ionization chamber is communicating with the ambient air, therefore, the atmospheric parameters such as temperature, pressure and humidity effect on the ionization chamber performance. The free-air ionization chamber, entitled as FAC-IR-300, that design at the Atomic Energy Organization of Iran, AEOI, is required the atmospheric correction factors for correct the chamber reading. In this article, the effect of humidity on the ionization chamber response was investigated. For this reason, was introduced the humidity correction factor, kh. In this article, the Monte Carlo simulation was used to determine the kh factor. The simulation results show in relative humidities between 30% to 80%, the kh factor is equal 0.9970 at 20°C and 0.9975 at 22°C. From the simulation results, at low energy the energy dependence of the kh factor is significant and with increasing energy this dependence is negligible. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Assessing impacts of simulated oil spills on the Northeast Arctic cod fishery.

PubMed

Carroll, JoLynn; Vikebø, Frode; Howell, Daniel; Broch, Ole Jacob; Nepstad, Raymond; Augustine, Starrlight; Skeie, Geir Morten; Bast, Radovan; Juselius, Jonas

2018-01-01

We simulate oil spills of 1500 and 4500m 3 /day lasting 14, 45, and 90days in the spawning grounds of the commercial fish species, Northeast Arctic cod. Modeling the life history of individual fish eggs and larvae, we predict deviations from the historical pattern of recruitment to the adult population due to toxic oil exposures. Reductions in survival for pelagic stages of cod were 0-10%, up to a maximum of 43%. These reductions resulted in a decrease in adult cod biomass of <3% for most scenarios, up to a maximum of 12%. In all simulations, the adult population remained at full reproductive potential with a sufficient number of juveniles surviving to replenish the population. The diverse age distribution helps protect the adult cod population from reductions in a single year's recruitment after a major oil spill. These results provide insights to assist in managing oil spill impacts on fisheries. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

LES of Temporally Evolving Mixing Layers by an Eighth-Order Filter Scheme

NASA Technical Reports Server (NTRS)

Hadjadj, A; Yee, H. C.; Sjogreen, B.

2011-01-01

An eighth-order filter method for a wide range of compressible flow speeds (H.C. Yee and B. Sjogreen, Proceedings of ICOSAHOM09, June 22-26, 2009, Trondheim, Norway) are employed for large eddy simulations (LES) of temporally evolving mixing layers (TML) for different convective Mach numbers (Mc) and Reynolds numbers. The high order filter method is designed for accurate and efficient simulations of shock-free compressible turbulence, turbulence with shocklets and turbulence with strong shocks with minimum tuning of scheme parameters. The value of Mc considered is for the TML range from the quasi-incompressible regime to the highly compressible supersonic regime. The three main characteristics of compressible TML (the self similarity property, compressibility effects and the presence of large-scale structure with shocklets for high Mc) are considered for the LES study. The LES results using the same scheme parameters for all studied cases agree well with experimental results of Barone et al. (2006), and published direct numerical simulations (DNS) work of Rogers & Moser (1994) and Pantano & Sarkar (2002).

Evaluation of protective shielding thickness for diagnostic radiology rooms: theory and computer simulation.

PubMed

Costa, Paulo R; Caldas, Linda V E

2002-01-01

This work presents the development and evaluation using modern techniques to calculate radiation protection barriers in clinical radiographic facilities. Our methodology uses realistic primary and scattered spectra. The primary spectra were computer simulated using a waveform generalization and a semiempirical model (the Tucker-Barnes-Chakraborty model). The scattered spectra were obtained from published data. An analytical function was used to produce attenuation curves from polychromatic radiation for specified kVp, waveform, and filtration. The results of this analytical function are given in ambient dose equivalent units. The attenuation curves were obtained by application of Archer's model to computer simulation data. The parameters for the best fit to the model using primary and secondary radiation data from different radiographic procedures were determined. They resulted in an optimized model for shielding calculation for any radiographic room. The shielding costs were about 50% lower than those calculated using the traditional method based on Report No. 49 of the National Council on Radiation Protection and Measurements.

Improved Atomistic Monte Carlo Simulations Demonstrate that Poly-L-Proline Adopts Heterogeneous Ensembles of Conformations of Semi-Rigid Segments Interrupted by Kinks

PubMed Central

Radhakrishnan, Aditya; Vitalis, Andreas; Mao, Albert H.; Steffen, Adam T.; Pappu, Rohit V.

2012-01-01

Poly-L-proline (PLP) polymers are useful mimics of biologically relevant proline-rich sequences. Biophysical and computational studies of PLP polymers in aqueous solutions are challenging because of the diversity of length scales and the slow time scales for conformational conversions. We describe an atomistic simulation approach that combines an improved ABSINTH implicit solvation model, with conformational sampling based on standard and novel Metropolis Monte Carlo moves. Refinements to forcefield parameters were guided by published experimental data for proline-rich systems. We assessed the validity of our simulation results through quantitative comparisons to experimental data that were not used in refining the forcefield parameters. Our analysis shows that PLP polymers form heterogeneous ensembles of conformations characterized by semi-rigid, rod-like segments interrupted by kinks, which result from a combination of internal cis peptide bonds, flexible backbone ψ-angles, and the coupling between ring puckering and backbone degrees of freedom. PMID:22329658

Monte Carlo simulation of chemistry following radiolysis with TOPAS-nBio.

PubMed

Ramos-Méndez, J; Perl, J; Schuemann, J; McNamara, A; Paganetti, H; Faddegon, B

2018-05-17

Simulation of water radiolysis and the subsequent chemistry provides important information on the effect of ionizing radiation on biological material. The Geant4 Monte Carlo toolkit has added chemical processes via the Geant4-DNA project. The TOPAS tool simplifies the modeling of complex radiotherapy applications with Geant4 without requiring advanced computational skills, extending the pool of users. Thus, a new extension to TOPAS, TOPAS-nBio, is under development to facilitate the configuration of track-structure simulations as well as water radiolysis simulations with Geant4-DNA for radiobiological studies. In this work, radiolysis simulations were implemented in TOPAS-nBio. Users may now easily add chemical species and their reactions, and set parameters including branching ratios, dissociation schemes, diffusion coefficients, and reaction rates. In addition, parameters for the chemical stage were re-evaluated and updated from those used by default in Geant4-DNA to improve the accuracy of chemical yields. Simulation results of time-dependent and LET-dependent primary yields G x (chemical species per 100 eV deposited) produced at neutral pH and 25 °C by short track-segments of charged particles were compared to published measurements. The LET range was 0.05-230 keV µm -1 . The calculated G x values for electrons satisfied the material balance equation within 0.3%, similar for protons albeit with long calculation time. A smaller geometry was used to speed up proton and alpha simulations, with an acceptable difference in the balance equation of 1.3%. Available experimental data of time-dependent G-values for [Formula: see text] agreed with simulated results within 7%  ±  8% over the entire time range; for [Formula: see text] over the full time range within 3%  ±  4%; for H 2 O 2 from 49%  ±  7% at earliest stages and 3%  ±  12% at saturation. For the LET-dependent G x , the mean ratios to the experimental data were 1.11  ±  0.98, 1.21  ±  1.11, 1.05  ±  0.52, 1.23  ±  0.59 and 1.49  ±  0.63 (1 standard deviation) for [Formula: see text], [Formula: see text], H 2 , H 2 O 2 and [Formula: see text], respectively. In conclusion, radiolysis and subsequent chemistry with Geant4-DNA has been successfully incorporated in TOPAS-nBio. Results are in reasonable agreement with published measured and simulated data.

Comparative Study of Three High Order Schemes for LES of Temporally Evolving Mixing Layers

NASA Technical Reports Server (NTRS)

Yee, Helen M. C.; Sjogreen, Biorn Axel; Hadjadj, C.

2012-01-01

Three high order shock-capturing schemes are compared for large eddy simulations (LES) of temporally evolving mixing layers (TML) for different convective Mach numbers (Mc) ranging from the quasi-incompressible regime to highly compressible supersonic regime. The considered high order schemes are fifth-order WENO (WENO5), seventh-order WENO (WENO7) and the associated eighth-order central spatial base scheme with the dissipative portion of WENO7 as a nonlinear post-processing filter step (WENO7fi). This high order nonlinear filter method (H.C. Yee and B. Sjogreen, Proceedings of ICOSAHOM09, June 22-26, 2009, Trondheim, Norway) is designed for accurate and efficient simulations of shock-free compressible turbulence, turbulence with shocklets and turbulence with strong shocks with minimum tuning of scheme parameters. The LES results by WENO7fi using the same scheme parameter agree well with experimental results of Barone et al. (2006), and published direct numerical simulations (DNS) work of Rogers & Moser (1994) and Pantano & Sarkar (2002), whereas results by WENO5 and WENO7 compare poorly with experimental data and DNS computations.

Chance performance and floor effects: threats to the validity of the Wechsler Memory Scale--fourth edition designs subtest.

PubMed

Martin, Phillip K; Schroeder, Ryan W

2014-06-01

The Designs subtest allows for accumulation of raw score points by chance alone, creating the potential for artificially inflated performances, especially in older patients. A random number generator was used to simulate the random selection and placement of cards by 100 test naive participants, resulting in a mean raw score of 36.26 (SD = 3.86). This resulted in relatively high-scaled scores in the 45-54, 55-64, and 65-69 age groups on Designs II. In the latter age group, in particular, the mean simulated performance resulted in a scaled score of 7, with scores 1 SD below and above the performance mean translating to scaled scores of 5 and 8, respectively. The findings indicate that clinicians should use caution when interpreting Designs II performance in these age groups, as our simulations demonstrated that low average to average range scores occur frequently when patients are relying solely on chance performance. © The Author 2014. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Simulated sudden increase in geomagnetic activity and its effect on heart rate variability: Experimental verification of correlation studies.

PubMed

Caswell, Joseph M; Singh, Manraj; Persinger, Michael A

2016-08-01

Previous research investigating the potential influence of geomagnetic factors on human cardiovascular state has tended to converge upon similar inferences although the results remain relatively controversial. Furthermore, previous findings have remained essentially correlational without accompanying experimental verification. An exception to this was noted for human brain activity in a previous study employing experimental simulation of sudden geomagnetic impulses in order to assess correlational results that had demonstrated a relationship between geomagnetic perturbations and neuroelectrical parameters. The present study employed the same equipment in a similar procedure in order to validate previous findings of a geomagnetic-cardiovascular dynamic with electrocardiography and heart rate variability measures. Results indicated that potential magnetic field effects on frequency components of heart rate variability tended to overlap with previous correlational studies where low frequency power and the ratio between low and high frequency components of heart rate variability appeared affected. In the present study, a significant increase in these particular parameters was noted during geomagnetic simulation compared to baseline recordings. Copyright © 2016 The Committee on Space Research (COSPAR). Published by Elsevier Ltd. All rights reserved.

Study protocol for a framework analysis using video review to identify latent safety threats: trauma resuscitation using in situ simulation team training (TRUST).

PubMed

Fan, Mark; Petrosoniak, Andrew; Pinkney, Sonia; Hicks, Christopher; White, Kari; Almeida, Ana Paula Siquiera Silva; Campbell, Douglas; McGowan, Melissa; Gray, Alice; Trbovich, Patricia

2016-11-07

Errors in trauma resuscitation are common and have been attributed to breakdowns in the coordination of system elements (eg, tools/technology, physical environment and layout, individual skills/knowledge, team interaction). These breakdowns are triggered by unique circumstances and may go unrecognised by trauma team members or hospital administrators; they can be described as latent safety threats (LSTs). Retrospective approaches to identifying LSTs (ie, after they occur) are likely to be incomplete and prone to bias. To date, prospective studies have not used video review as the primary mechanism to identify any and all LSTs in trauma resuscitation. A series of 12 unannounced in situ simulations (ISS) will be conducted to prospectively identify LSTs at a level 1 Canadian trauma centre (over 800 dedicated trauma team activations annually). 4 scenarios have already been designed as part of this protocol based on 5 recurring themes found in the hospital's mortality and morbidity process. The actual trauma team will be activated to participate in the study. Each simulation will be audio/video recorded from 4 different camera angles and transcribed to conduct a framework analysis. Video reviewers will code the videos deductively based on a priori themes of LSTs identified from the literature, and/or inductively based on the events occurring in the simulation. LSTs will be prioritised to target interventions in future work. Institutional research ethics approval has been acquired (SMH REB #15-046). Results will be published in peer-reviewed journals and presented at relevant conferences. Findings will also be presented to key institutional stakeholders to inform mitigation strategies for improved patient safety. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Dynamic analysis of fixed-free single-walled carbon nanotube-based bio-sensors because of various viruses.

PubMed

Gupta, A; Joshi, A Y; Sharma, S C; Harsha, S P

2012-09-01

In the present study, the vibrations of the fixed-free single-walled carbon nanotube (SWCNT) with attached bacterium/virus on the tip have been investigated. To explore the suitability of the SWCNT as a bacterium/virus detector device, first the various types of virus have been taken for the study and then the resonant frequencies of fixed-free SWCNT with attachment of those viruses have been simulated. These resonant frequencies are compared with the published analytical data, and it is shown that the finite element method (FEM) simulation results are in good agreement with the analytical data. The results showed the sensitivity and suitability of the SWCNT having different length and different masses (attached at the tip SWCNT) to identify the bacterium or virus.

New and Improved? A Comparison of the Original and Revised Versions of the Structured Interview of Reported Symptoms

ERIC Educational Resources Information Center

Green, Debbie; Rosenfeld, Barry; Belfi, Brian

2013-01-01

The current study evaluated the accuracy of the Structured Interview of Reported Symptoms, Second Edition (SIRS-2) in a criterion-group study using a sample of forensic psychiatric patients and a community simulation sample, comparing it to the original SIRS and to results published in the SIRS-2 manual. The SIRS-2 yielded an impressive…

Analysis of steady-state salt-water upconing with application at Truro well field, Cape Cod, Massachusetts

USGS Publications Warehouse

Reilly, T.E.; Frimpter, M.H.; LeBlanc, D.R.; Goodman, A.S.

1987-01-01

Sharp interface methods have been used successfully to describe the physics of upconing. A finite-element model is developed to simulate a sharp interface for determination of the steady-state position of the interface and maximum permissible well discharges. The model developed is compared to previous published electric-analog model results of Bennett and others (1968). -from Authors

Hybrid Techniques for Quantum Circuit Simulation

DTIC Science & Technology

2014-02-01

Detailed theorems and proofs describing these results are included in our published manuscript [10]. Embedding of stabilizer geometry in the Hilbert ...space. We also describe how the discrete embedding of stabilizer geometry in Hilbert space complicates several natural geometric tasks. As described...the Hilbert space in which they are embedded, and that they are arranged in a fairly uniform pattern. These factors suggest that, if one seeks a

A Cost-Effectiveness Analysis of Clopidogrel for Patients with Non-ST-Segment Elevation Acute Coronary Syndrome in China.

PubMed

Cui, Ming; Tu, Chen Chen; Chen, Er Zhen; Wang, Xiao Li; Tan, Seng Chuen; Chen, Can

2016-09-01

There are a number of economic evaluation studies of clopidogrel for patients with non-ST-segment elevation acute coronary syndrome (NSTEACS) published from the perspective of multiple countries in recent years. However, relevant research is quite limited in China. We aimed to estimate the long-term cost effectiveness for up to 1-year treatment with clopidogrel plus acetylsalicylic acid (ASA) versus ASA alone for NSTEACS from the public payer perspective in China. This analysis used a Markov model to simulate a cohort of patients for quality-adjusted life years (QALYs) gained and incremental cost for lifetime horizon. Based on the primary event rates, adherence rate, and mortality derived from the CURE trial, hazard functions obtained from published literature were used to extrapolate the overall survival to lifetime horizon. Resource utilization, hospitalization, medication costs, and utility values were estimated from official reports, published literature, and analysis of the patient-level insurance data in China. To assess the impact of parameters' uncertainty on cost-effectiveness results, one-way sensitivity analyses were undertaken for key parameters, and probabilistic sensitivity analysis (PSA) was conducted using the Monte Carlo simulation. The therapy of clopidogrel plus ASA is a cost-effective option in comparison with ASA alone for the treatment of NSTEACS in China, leading to 0.0548 life years (LYs) and 0.0518 QALYs gained per patient. From the public payer perspective in China, clopidogrel plus ASA is associated with an incremental cost of 43,340 China Yuan (CNY) per QALY gained and 41,030 CNY per LY gained (discounting at 3.5% per year). PSA results demonstrated that 88% of simulations were lower than the cost-effectiveness threshold of 150,721 CYN per QALY gained. Based on the one-way sensitivity analysis, results are most sensitive to price of clopidogrel, but remain well below this threshold. This analysis suggests that treatment with clopidogrel plus ASA for up to 1 year for patients with NSTEACS is cost effective in the local context of China from a public payers' perspective. Sanofi China.

Evaluating the Effect of Virtual Reality Temporal Bone Simulation on Mastoidectomy Performance: A Meta-analysis.

PubMed

Lui, Justin T; Hoy, Monica Y

2017-06-01

Background The increasing prevalence of virtual reality simulation in temporal bone surgery warrants an investigation to assess training effectiveness. Objectives To determine if temporal bone simulator use improves mastoidectomy performance. Data Sources Ovid Medline, Embase, and PubMed databases were systematically searched per the PRISMA guidelines. Review Methods Inclusion criteria were peer-reviewed publications that utilized quantitative data of mastoidectomy performance following the use of a temporal bone simulator. The search was restricted to human studies published in English. Studies were excluded if they were in non-peer-reviewed format, were descriptive in nature, or failed to provide surgical performance outcomes. Meta-analysis calculations were then performed. Results A meta-analysis based on the random-effects model revealed an improvement in overall mastoidectomy performance following training on the temporal bone simulator. A standardized mean difference of 0.87 (95% CI, 0.38-1.35) was generated in the setting of a heterogeneous study population ( I 2 = 64.3%, P < .006). Conclusion In the context of a diverse population of virtual reality simulation temporal bone surgery studies, meta-analysis calculations demonstrate an improvement in trainee mastoidectomy performance with virtual simulation training.

Simulation of guided-wave ultrasound propagation in composite laminates: Benchmark comparisons of numerical codes and experiment.

PubMed

Leckey, Cara A C; Wheeler, Kevin R; Hafiychuk, Vasyl N; Hafiychuk, Halyna; Timuçin, Doğan A

2018-03-01

Ultrasonic wave methods constitute the leading physical mechanism for nondestructive evaluation (NDE) and structural health monitoring (SHM) of solid composite materials, such as carbon fiber reinforced polymer (CFRP) laminates. Computational models of ultrasonic wave excitation, propagation, and scattering in CFRP composites can be extremely valuable in designing practicable NDE and SHM hardware, software, and methodologies that accomplish the desired accuracy, reliability, efficiency, and coverage. The development and application of ultrasonic simulation approaches for composite materials is an active area of research in the field of NDE. This paper presents comparisons of guided wave simulations for CFRP composites implemented using four different simulation codes: the commercial finite element modeling (FEM) packages ABAQUS, ANSYS, and COMSOL, and a custom code executing the Elastodynamic Finite Integration Technique (EFIT). Benchmark comparisons are made between the simulation tools and both experimental laser Doppler vibrometry data and theoretical dispersion curves. A pristine and a delamination type case (Teflon insert in the experimental specimen) is studied. A summary is given of the accuracy of simulation results and the respective computational performance of the four different simulation tools. Published by Elsevier B.V.

Modeling Wettability Alteration using Chemical EOR Processes in Naturally Fractured Reservoirs

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

Mojdeh Delshad; Gary A. Pope; Kamy Sepehrnoori

2007-09-30

The objective of our search is to develop a mechanistic simulation tool by adapting UTCHEM to model the wettability alteration in both conventional and naturally fractured reservoirs. This will be a unique simulator that can model surfactant floods in naturally fractured reservoir with coupling of wettability effects on relative permeabilities, capillary pressure, and capillary desaturation curves. The capability of wettability alteration will help us and others to better understand and predict the oil recovery mechanisms as a function of wettability in naturally fractured reservoirs. The lack of a reliable simulator for wettability alteration means that either the concept that hasmore » already been proven to be effective in the laboratory scale may never be applied commercially to increase oil production or the process must be tested in the field by trial and error and at large expense in time and money. The objective of Task 1 is to perform a literature survey to compile published data on relative permeability, capillary pressure, dispersion, interfacial tension, and capillary desaturation curve as a function of wettability to aid in the development of petrophysical property models as a function of wettability. The new models and correlations will be tested against published data. The models will then be implemented in the compositional chemical flooding reservoir simulator, UTCHEM. The objective of Task 2 is to understand the mechanisms and develop a correlation for the degree of wettability alteration based on published data. The objective of Task 3 is to validate the models and implementation against published data and to perform 3-D field-scale simulations to evaluate the impact of uncertainties in the fracture and matrix properties on surfactant alkaline and hot water floods.« less

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

DOE PAGES

Lee, Jumin; Cheng, Xi; Swails, Jason M.; ...

2015-11-12

Here we report that proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The use of the CHARMM36 force field (C36 FF) in different MD simulation programs can result in disagreements with published simulations performed with CHARMM due to differences in the protocols used to treat the long-range and 1-4 nonbonded interactions. In this study, we systematically test the use of the C36 lipid FF in NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM. A wide range of Lennard-Jones (LJ) cutoff schemes and integrator algorithms were tested to find themore » optimal simulation protocol to best match bilayer properties of six lipids with varying acyl chain saturation and head groups. MD simulations of a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer were used to obtain the optimal protocol for each program. MD simulations with all programs were found to reasonably match the DPPC bilayer properties (surface area per lipid, chain order parameters, and area compressibility modulus) obtained using the standard protocol used in CHARMM as well as from experiments. The optimal simulation protocol was then applied to the other five lipid simulations and resulted in excellent agreement between results from most simulation programs as well as with experimental data. AMBER compared least favorably with the expected membrane properties, which appears to be due to its use of the hard-truncation in the LJ potential versus a force-based switching function used to smooth the LJ potential as it approaches the cutoff distance. The optimal simulation protocol for each program has been implemented in CHARMM-GUI. This protocol is expected to be applicable to the remainder of the additive C36 FF including the proteins, nucleic acids, carbohydrates, and small molecules.« less

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field.

PubMed

Lee, Jumin; Cheng, Xi; Swails, Jason M; Yeom, Min Sun; Eastman, Peter K; Lemkul, Justin A; Wei, Shuai; Buckner, Joshua; Jeong, Jong Cheol; Qi, Yifei; Jo, Sunhwan; Pande, Vijay S; Case, David A; Brooks, Charles L; MacKerell, Alexander D; Klauda, Jeffery B; Im, Wonpil

2016-01-12

Proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The use of the CHARMM36 force field (C36 FF) in different MD simulation programs can result in disagreements with published simulations performed with CHARMM due to differences in the protocols used to treat the long-range and 1-4 nonbonded interactions. In this study, we systematically test the use of the C36 lipid FF in NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM. A wide range of Lennard-Jones (LJ) cutoff schemes and integrator algorithms were tested to find the optimal simulation protocol to best match bilayer properties of six lipids with varying acyl chain saturation and head groups. MD simulations of a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer were used to obtain the optimal protocol for each program. MD simulations with all programs were found to reasonably match the DPPC bilayer properties (surface area per lipid, chain order parameters, and area compressibility modulus) obtained using the standard protocol used in CHARMM as well as from experiments. The optimal simulation protocol was then applied to the other five lipid simulations and resulted in excellent agreement between results from most simulation programs as well as with experimental data. AMBER compared least favorably with the expected membrane properties, which appears to be due to its use of the hard-truncation in the LJ potential versus a force-based switching function used to smooth the LJ potential as it approaches the cutoff distance. The optimal simulation protocol for each program has been implemented in CHARMM-GUI. This protocol is expected to be applicable to the remainder of the additive C36 FF including the proteins, nucleic acids, carbohydrates, and small molecules.

The ability of healthy volunteers to simulate a neurologic field defect on automated perimetry.

PubMed

Ghate, Deepta; Bodnarchuk, Brian; Sanders, Sheila; Deokule, Sunil; Kedar, Sachin

2014-03-01

To determine if volunteers can simulate and reproduce 3 types of neurologic field defects: hemianopia, quadrantanopia, and central scotoma. Cross-sectional study. Thirty healthy volunteers new to perimetry (including automated perimetry). After informed consent, volunteers were randomized to 1 of the 3 visual field defects listed above. All visual field testing was performed on the right eye using the Humphrey Field Analyzer (HFA; Carl Zeiss Meditec, Dublin, CA) SITA Fast 24-2 protocol. Each volunteer was provided with standard new patient instructions and was shown a diagram of the defect to be simulated. Two sets of visual fields were performed on the right eye with 10 minutes between tests. Three experts used the Ocular Hypertension Treatment Study reading center criteria and determined if the simulation was successful. Proportion of volunteers able to simulate the assigned visual field. All 10 volunteers (100%) successfully simulated a hemianopia on the first and second fields. All 10 volunteers (100%) simulated a quadrantanopia on the first field and 9 (90%) did so on the second field. Eight volunteers (80%) successfully simulated a central scotoma in the first field and all 10 (100%) did so on in the second field. Reliability criteria were excellent. Forty-seven fields (78%) had 0 fixation losses, 48 (80%) had 0 false-positive results, and 44 (73%) had 0 false-negative results. It is easy to simulate reproducible and reliable neurologic field defects on automated perimetry using HFA. Copyright © 2014 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.

Managing emergency department overcrowding via ambulance diversion: a discrete event simulation model.

PubMed

Lin, Chih-Hao; Kao, Chung-Yao; Huang, Chong-Ye

2015-01-01

Ambulance diversion (AD) is considered one of the possible solutions to relieve emergency department (ED) overcrowding. Study of the effectiveness of various AD strategies is prerequisite for policy-making. Our aim is to develop a tool that quantitatively evaluates the effectiveness of various AD strategies. A simulation model and a computer simulation program were developed. Three sets of simulations were executed to evaluate AD initiating criteria, patient-blocking rules, and AD intervals, respectively. The crowdedness index, the patient waiting time for service, and the percentage of adverse patients were assessed to determine the effect of various AD policies. Simulation results suggest that, in a certain setting, the best timing for implementing AD is when the crowdedness index reaches the critical value, 1.0 - an indicator that ED is operating at its maximal capacity. The strategy to divert all patients transported by ambulance is more effective than to divert either high-acuity patients only or low-acuity patients only. Given a total allowable AD duration, implementing AD multiple times with short intervals generally has better effect than having a single AD with maximal allowable duration. An input-throughput-output simulation model is proposed for simulating ED operation. Effectiveness of several AD strategies on relieving ED overcrowding was assessed via computer simulations based on this model. By appropriate parameter settings, the model can represent medical resource providers of different scales. It is also feasible to expand the simulations to evaluate the effect of AD strategies on a community basis. The results may offer insights for making effective AD policies. Copyright © 2012. Published by Elsevier B.V.

Development of an alkaline/surfactant/polymer compositional reservoir simulator

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

Bhuyan, D.

1989-01-01

The mathematical formulation of a generalized three-dimensional compositional reservoir simulator for high-pH chemical flooding processes is presented in this work. The model assumes local thermodynamic equilibrium with respect to both reaction chemistry and phase behavior and calculates equilibrium electrolyte and phase compositions as a function of time and position. The reaction chemistry considers aqueous electrolytic chemistry, precipitation/dissolution of minerals, ion exchange reactions on matrix surface, reaction of acidic components of crude oil with the bases in the aqueous solution and cation exchange reactions with the micelles. The simulator combines this detailed reaction chemistry associated with these processes with the extensivemore » physical and flow property modeling schemes of an existing chemical flood simulator (UTCHEM) to model the multiphase, multidimensional displacement processes. The formulation of the chemical equilibrium model is quite general and is adaptable to simulate a variety of chemical descriptions. In addition to its use in the simulation of high-pH chemical flooding processes, the model will find application in the simulation of other reactive flow problems like the ground water contamination, reinjection of produced water, chemical waste disposal, etc. in one, two or three dimensions and under multiphase flow conditions. In this work, the model is used to simulate several hypothetical cases of high-pH chemical floods, which include cases from a simple alkaline preflush of a micellar/polymer flood to surfactant enhanced alkaline-polymer flooding and the results are analyzed. Finally, a few published alkaline, alkaline-polymer and surfactant-alkaline-polymer corefloods are simulated and compared with the experimental results.« less

Modeling digital breast tomosynthesis imaging systems for optimization studies

NASA Astrophysics Data System (ADS)

Lau, Beverly Amy

Digital breast tomosynthesis (DBT) is a new imaging modality for breast imaging. In tomosynthesis, multiple images of the compressed breast are acquired at different angles, and the projection view images are reconstructed to yield images of slices through the breast. One of the main problems to be addressed in the development of DBT is the optimal parameter settings to obtain images ideal for detection of cancer. Since it would be unethical to irradiate women multiple times to explore potentially optimum geometries for tomosynthesis, it is ideal to use a computer simulation to generate projection images. Existing tomosynthesis models have modeled scatter and detector without accounting for oblique angles of incidence that tomosynthesis introduces. Moreover, these models frequently use geometry-specific physical factors measured from real systems, which severely limits the robustness of their algorithms for optimization. The goal of this dissertation was to design the framework for a computer simulation of tomosynthesis that would produce images that are sensitive to changes in acquisition parameters, so an optimization study would be feasible. A computer physics simulation of the tomosynthesis system was developed. The x-ray source was modeled as a polychromatic spectrum based on published spectral data, and inverse-square law was applied. Scatter was applied using a convolution method with angle-dependent scatter point spread functions (sPSFs), followed by scaling using an angle-dependent scatter-to-primary ratio (SPR). Monte Carlo simulations were used to generate sPSFs for a 5-cm breast with a 1-cm air gap. Detector effects were included through geometric propagation of the image onto layers of the detector, which were blurred using depth-dependent detector point-spread functions (PRFs). Depth-dependent PRFs were calculated every 5-microns through a 200-micron thick CsI detector using Monte Carlo simulations. Electronic noise was added as Gaussian noise as a last step of the model. The sPSFs and detector PRFs were verified to match published data, and noise power spectrum (NPS) from simulated flat field images were shown to match empirically measured data from a digital mammography unit. A novel anthropomorphic software breast phantom was developed for 3D imaging simulation. Projection view images of the phantom were shown to have similar structure as real breasts in the spatial frequency domain, using the power-law exponent beta to quantify tissue complexity. The physics simulation and computer breast phantom were used together, following methods from a published study with real tomosynthesis images of real breasts. The simulation model and 3D numerical breast phantoms were able to reproduce the trends in the experimental data. This result demonstrates the ability of the tomosynthesis physics model to generate images sensitive to changes in acquisition parameters.

Comparing the Cost-Effectiveness of Simulation Modalities: A Case Study of Peripheral Intravenous Catheterization Training

ERIC Educational Resources Information Center

Isaranuwatchai, Wanrudee; Brydges, Ryan; Carnahan, Heather; Backstein, David; Dubrowski, Adam

2014-01-01

While the ultimate goal of simulation training is to enhance learning, cost-effectiveness is a critical factor. Research that compares simulation training in terms of educational- and cost-effectiveness will lead to better-informed curricular decisions. Using previously published data we conducted a cost-effectiveness analysis of three…

Combining Simulation and Optimization Models for Hardwood Lumber Production

Treesearch

G.A. Mendoza; R.J. Meimban; W.G. Luppold; Philip A. Araman

1991-01-01

Published literature contains a number of optimization and simulation models dealing with the primary processing of hardwood and softwood logs. Simulation models have been developed primarily as descriptive models for characterizing the general operations and performance of a sawmill. Optimization models, on the other hand, were developed mainly as analytical tools for...

A Scoping Review: Conceptualizations and Pedagogical Models of Learning in Nursing Simulation

ERIC Educational Resources Information Center

Poikela, Paula; Teräs, Marianne

2015-01-01

Simulations have been implemented globally in nursing education for years with diverse conceptual foundations. The aim of this scoping review is to examine the literature regarding the conceptualizations of learning and pedagogical models in nursing simulations. A scoping review of peer-reviewed articles published between 2000 and 2013 was…

Assessing the Optimal Position for Vedolizumab in the Treatment of Ulcerative Colitis: A Simulation Model.

PubMed

Scott, Frank I; Shah, Yash; Lasch, Karen; Luo, Michelle; Lewis, James D

2018-01-18

Vedolizumab, an α4β7 integrin monoclonal antibody inhibiting gut lymphocyte trafficking, is an effective treatment for ulcerative colitis (UC). We evaluated the optimal position of vedolizumab in the UC treatment paradigm. Using Markov modeling, we assessed multiple algorithms for the treatment of UC. The base case was a 35-year-old male with steroid-dependent moderately to severely active UC without previous immunomodulator or biologic use. The model included 4 different algorithms over 1 year, with vedolizumab use prior to: initiating azathioprine (Algorithm 1), combination therapy with infliximab and azathioprine (Algorithm 2), combination therapy with an alternative anti-tumor necrosis factor (anti-TNF) and azathioprine (Algorithm 3), and colectomy (Algorithm 4). Transition probabilities and quality-adjusted life-year (QALY) estimates were derived from the published literature. Primary analyses included simulating 100 trials of 100,000 individuals, assessing clinical outcomes, and QALYs. Sensitivity analyses employed longer time horizons and ranges for all variables. Algorithm 1 (vedolizumab use prior to all other therapies) was the preferred strategy, resulting in 8981 additional individuals in remission, 18 fewer cases of lymphoma, and 1087 fewer serious infections per 100,000 patients compared with last-line use (A4). Algorithm 1 also resulted in 0.0197 to 0.0205 more QALYs compared with other algorithms. This benefit increased with longer time horizons. Algorithm 1 was preferred in all sensitivity analyses. The model suggests that treatment algorithms positioning vedolizumab prior to other therapies should be considered for individuals with moderately to severely active steroid-dependent UC. Further prospective research is needed to confirm these simulated results. © 2018 Crohn’s & Colitis Foundation of America. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

The Bebig Valencia-type skin applicators: Dosimetric study and implementation of a dosimetric hybrid technique.

PubMed

Anagnostopoulos, Georgios; Andrássy, Michael; Baltas, Dimos

To determine the relative dose rate distribution in water for the Bebig 20 mm and 30 mm skin applicators and report results in a form suitable for potential clinical use. Results for both skin applicators are also provided in the form of a hybrid Task Group 43 (TG-43) dosimetry technique. Furthermore, the radiation leakage around both skin applicators from the radiation protection point of view and the impact of the geometrical source position uncertainties are studied and reported. Monte Carlo simulations were performed using the MCNP 6.1 general purpose code, which was benchmarked against published dosimetry data for the Bebig Ir2.A85-2 high-dose-rate iridium-192 source, as well as the dosimetry data for the two Elekta skin applicators. Both Bebig skin applicators were modeled, and the dose rate distributions in a water phantom were calculated. The dosimetric quantities derived according to a hybrid TG-43 dosimetry technique are provided with their corresponding uncertainty values. The air kerma rate in air was simulated in the vicinity of each skin applicator to assess the radiation leakage. Results from the Monte Carlo simulations of both skin applicators are presented in the form of figures and relative dose rate tables, and additionally with the aid of the quantities defined in the hybrid TG-43 dosimetry technique and their corresponding uncertainty values. Their output factors, flatness, and penumbra values were found comparable to the Elekta skin applicators. The radiation shielding was evaluated to be adequate. The effect of potential uncertainties in source positioning on dosimetry should be investigated as part of applicator commissioning. Copyright © 2017 American Brachytherapy Society. Published by Elsevier Inc. All rights reserved.

Computing the total atmospheric refraction for real-time optical imaging sensor simulation

NASA Astrophysics Data System (ADS)

Olson, Richard F.

2015-05-01

Fast and accurate computation of light path deviation due to atmospheric refraction is an important requirement for real-time simulation of optical imaging sensor systems. A large body of existing literature covers various methods for application of Snell's Law to the light path ray tracing problem. This paper provides a discussion of the adaptation to real time simulation of atmospheric refraction ray tracing techniques used in mid-1980's LOWTRAN releases. The refraction ray trace algorithm published in a LOWTRAN-6 technical report by Kneizys (et. al.) has been coded in MATLAB for development, and in C-language for simulation use. To this published algorithm we have added tuning parameters for variable path segment lengths, and extensions for Earth grazing and exoatmospheric "near Earth" ray paths. Model atmosphere properties used to exercise the refraction algorithm were obtained from tables published in another LOWTRAN-6 related report. The LOWTRAN-6 based refraction model is applicable to atmospheric propagation at wavelengths in the IR and visible bands of the electromagnetic spectrum. It has been used during the past two years by engineers at the U.S. Army Aviation and Missile Research, Development and Engineering Center (AMRDEC) in support of several advanced imaging sensor simulations. Recently, a faster (but sufficiently accurate) method using Gauss-Chebyshev Quadrature integration for evaluating the refraction integral was adopted.

Simulation of local ion transport in lamellar block copolymer electrolytes based on electron micrographs

DOE PAGES

Chintapalli, Mahati; Higa, Kenneth; Chen, X. Chelsea; ...

2016-12-19

A method is presented in this paper to relate local morphology and ionic conductivity in a solid, lamellar block copolymer electrolyte for lithium batteries, by simulating conductivity through transmission electron micrographs. The electrolyte consists of polystyrene-block-poly(ethylene oxide) mixed with lithium bis(trifluoromethanesulfonyl) imide salt (SEO/LiTFSI), where the polystyrene phase is structural phase and the poly(ethylene oxide)/LiTFSI phase is ionically conductive. The electric potential distribution is simulated in binarized micrographs by solving the Laplace equation with constant potential boundary conditions. A morphology factor, f, is reported for each image by calculating the effective conductivity relative to a homogenous conductor. Images from twomore » samples are examined, one annealed with large lamellar grains and one unannealed with small grains. The average value off is 0.45 ± 0.04 for the annealed sample, and 0.37 ± 0.03 for the unannealed sample, both close to the value predicted by effective medium theory, 1/2. Simulated conductivities are compared to published experimental conductivities. The value of f Unannealed/f Annealed is 0.82 for simulations and 6.2 for experiments. Simulation results correspond well to predictions by effective medium theory but do not explain the experimental measurements. Finally, observation of nanoscale morphology over length scales greater than the size of the micrographs (~1 μm) may be required to explain the experimental results.« less

Simulation of local ion transport in lamellar block copolymer electrolytes based on electron micrographs

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

Chintapalli, Mahati; Higa, Kenneth; Chen, X. Chelsea

A method is presented in this paper to relate local morphology and ionic conductivity in a solid, lamellar block copolymer electrolyte for lithium batteries, by simulating conductivity through transmission electron micrographs. The electrolyte consists of polystyrene-block-poly(ethylene oxide) mixed with lithium bis(trifluoromethanesulfonyl) imide salt (SEO/LiTFSI), where the polystyrene phase is structural phase and the poly(ethylene oxide)/LiTFSI phase is ionically conductive. The electric potential distribution is simulated in binarized micrographs by solving the Laplace equation with constant potential boundary conditions. A morphology factor, f, is reported for each image by calculating the effective conductivity relative to a homogenous conductor. Images from twomore » samples are examined, one annealed with large lamellar grains and one unannealed with small grains. The average value off is 0.45 ± 0.04 for the annealed sample, and 0.37 ± 0.03 for the unannealed sample, both close to the value predicted by effective medium theory, 1/2. Simulated conductivities are compared to published experimental conductivities. The value of f Unannealed/f Annealed is 0.82 for simulations and 6.2 for experiments. Simulation results correspond well to predictions by effective medium theory but do not explain the experimental measurements. Finally, observation of nanoscale morphology over length scales greater than the size of the micrographs (~1 μm) may be required to explain the experimental results.« less

Effects of simulated microgravity on Streptococcus mutans physiology and biofilm structure.

PubMed

Cheng, Xingqun; Xu, Xin; Chen, Jing; Zhou, Xuedong; Cheng, Lei; Li, Mingyun; Li, Jiyao; Wang, Renke; Jia, Wenxiang; Li, Yu-Qing

2014-10-01

Long-term spaceflights will eventually become an inevitable occurrence. Previous studies have indicated that oral infectious diseases, including dental caries, were more prevalent in astronauts due to the effect of microgravity. However, the impact of the space environment, especially the microgravity environment, on the virulence factors of Streptococcus mutans, a major caries-associated bacterium, is yet to be explored. In the present study, we investigated the impact of simulated microgravity on the physiology and biofilm structure of S. mutans. We also explored the dual-species interaction between S. mutans and Streptococcus sanguinis under a simulated microgravity condition. Results indicated that the simulated microgravity condition can enhance the acid tolerance ability, modify the biofilm architecture and extracellular polysaccharide distribution of S. mutans, and increase the proportion of S. mutans within a dual-species biofilm, probably through the regulation of various gene expressions. We hypothesize that the enhanced competitiveness of S. mutans under simulated microgravity may cause a multispecies micro-ecological imbalance, which would result in the initiation of dental caries. Our current findings are consistent with previous studies, which revealed a higher astronaut-associated incidence of caries. Further research is required to explore the detailed mechanisms. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Fracture simulation of restored teeth using a continuum damage mechanics failure model.

PubMed

Li, Haiyan; Li, Jianying; Zou, Zhenmin; Fok, Alex Siu-Lun

2011-07-01

The aim of this paper is to validate the use of a finite-element (FE) based continuum damage mechanics (CDM) failure model to simulate the debonding and fracture of restored teeth. Fracture testing of plastic model teeth, with or without a standard Class-II MOD (mesial-occusal-distal) restoration, was carried out to investigate their fracture behavior. In parallel, 2D FE models of the teeth are constructed and analyzed using the commercial FE software ABAQUS. A CDM failure model, implemented into ABAQUS via the user element subroutine (UEL), is used to simulate the debonding and/or final fracture of the model teeth under a compressive load. The material parameters needed for the CDM model to simulate fracture are obtained through separate mechanical tests. The predicted results are then compared with the experimental data of the fracture tests to validate the failure model. The failure processes of the intact and restored model teeth are successfully reproduced by the simulation. However, the fracture parameters obtained from testing small specimens need to be adjusted to account for the size effect. The results indicate that the CDM model is a viable model for the prediction of debonding and fracture in dental restorations. Copyright © 2011 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

Computer-assisted preoperative simulation for positioning and fixation of plate in 2-stage procedure combining maxillary advancement by distraction technique and mandibular setback surgery.

PubMed

Suenaga, Hideyuki; Taniguchi, Asako; Yonenaga, Kazumichi; Hoshi, Kazuto; Takato, Tsuyoshi

2016-01-01

Computer-assisted preoperative simulation surgery is employed to plan and interact with the 3D images during the orthognathic procedure. It is useful for positioning and fixation of maxilla by a plate. We report a case of maxillary retrusion by a bilateral cleft lip and palate, in which a 2-stage orthognathic procedure (maxillary advancement by distraction technique and mandibular setback surgery) was performed following a computer-assisted preoperative simulation planning to achieve the positioning and fixation of the plate. A high accuracy was achieved in the present case. A 21-year-old male patient presented to our department with a complaint of maxillary retrusion following bilateral cleft lip and palate. Computer-assisted preoperative simulation with 2-stage orthognathic procedure using distraction technique and mandibular setback surgery was planned. The preoperative planning of the procedure resulted in good aesthetic outcomes. The error of the maxillary position was less than 1mm. The implementation of the computer-assisted preoperative simulation for the positioning and fixation of plate in 2-stage orthognathic procedure using distraction technique and mandibular setback surgery yielded good results. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Pseudo hard-sphere potential for use in continuous molecular-dynamics simulation of spherical and chain molecules

NASA Astrophysics Data System (ADS)

Jover, J.; Haslam, A. J.; Galindo, A.; Jackson, G.; Müller, E. A.

2012-10-01

We present a continuous pseudo-hard-sphere potential based on a cut-and-shifted Mie (generalized Lennard-Jones) potential with exponents (50, 49). Using this potential one can mimic the volumetric, structural, and dynamic properties of the discontinuous hard-sphere potential over the whole fluid range. The continuous pseudo potential has the advantage that it may be incorporated directly into off-the-shelf molecular-dynamics code, allowing the user to capitalise on existing hardware and software advances. Simulation results for the compressibility factor of the fluid and solid phases of our pseudo hard spheres are presented and compared both to the Carnahan-Starling equation of state of the fluid and published data, the differences being indistinguishable within simulation uncertainty. The specific form of the potential is employed to simulate flexible chains formed from these pseudo hard spheres at contact (pearl-necklace model) for mc = 4, 5, 7, 8, 16, 20, 100, 201, and 500 monomer segments. The compressibility factor of the chains per unit of monomer, mc, approaches a limiting value at reasonably small values, mc < 50, as predicted by Wertheim's first order thermodynamic perturbation theory. Simulation results are also presented for highly asymmetric mixtures of pseudo hard spheres, with diameter ratios of 3:1, 5:1, 20:1 over the whole composition range.

Energy efficient strategy for throughput improvement in wireless sensor networks.

PubMed

Jabbar, Sohail; Minhas, Abid Ali; Imran, Muhammad; Khalid, Shehzad; Saleem, Kashif

2015-01-23

Network lifetime and throughput are one of the prime concerns while designing routing protocols for wireless sensor networks (WSNs). However, most of the existing schemes are either geared towards prolonging network lifetime or improving throughput. This paper presents an energy efficient routing scheme for throughput improvement in WSN. The proposed scheme exploits multilayer cluster design for energy efficient forwarding node selection, cluster heads rotation and both inter- and intra-cluster routing. To improve throughput, we rotate the role of cluster head among various nodes based on two threshold levels which reduces the number of dropped packets. We conducted simulations in the NS2 simulator to validate the performance of the proposed scheme. Simulation results demonstrate the performance efficiency of the proposed scheme in terms of various metrics compared to similar approaches published in the literature.

Energy Efficient Strategy for Throughput Improvement in Wireless Sensor Networks

PubMed Central

Jabbar, Sohail; Minhas, Abid Ali; Imran, Muhammad; Khalid, Shehzad; Saleem, Kashif

2015-01-01

Network lifetime and throughput are one of the prime concerns while designing routing protocols for wireless sensor networks (WSNs). However, most of the existing schemes are either geared towards prolonging network lifetime or improving throughput. This paper presents an energy efficient routing scheme for throughput improvement in WSN. The proposed scheme exploits multilayer cluster design for energy efficient forwarding node selection, cluster heads rotation and both inter- and intra-cluster routing. To improve throughput, we rotate the role of cluster head among various nodes based on two threshold levels which reduces the number of dropped packets. We conducted simulations in the NS2 simulator to validate the performance of the proposed scheme. Simulation results demonstrate the performance efficiency of the proposed scheme in terms of various metrics compared to similar approaches published in the literature. PMID:25625902

Scale Rules for Macrosegregation during Direct-Chill Casting of Aluminum Alloys

NASA Astrophysics Data System (ADS)

Eskin, Dmitry G.; Du, Qiang; Katgerman, Laurens

2008-05-01

An analysis of published experimental and numerical results shows that there is a scaling relationship between the magnitude and direction of centerline segregation in direct-chill (DC) cast billets from aluminum alloys and the process parameters, i.e., billet diameter and casting speed. It seems that there is always a range of these process parameters where the centerline segregation is positive, and there is a threshold when the centerline segregation vanishes. Numerical simulations of macrosegregation during DC casting of a binary Al-Cu alloy were performed at different ratios of casting speed and billet diameter. The macrosegregation model takes into account only two mechanisms of macrosegregation, i.e., thermosolutal convection and shrinkage-induced flow. The results of these computer simulations fit well to the dependence obtained using numerous reference data. The results are discussed in terms of the contribution of different mechanisms of macrosegregation and the shape of the billet sump.

Performance, Capacity and Limitations of AMSS Communications

NASA Technical Reports Server (NTRS)

Ripamonti, Claudio; Konangi, Vijay K.; Kerczewski, robert J.

2002-01-01

This paper reports on the performance of Aeronautical Mobile Satellite Service (AMSS), based on simulation results, when incorporated into the Aeronautical Telecommunications Network (ATN). A comparison between its performance under current data traffic load and under future ATN traffic load was used to determine the reliability of AMSS in providing continuous communications between the ground and the aircraft over remote regions of the globe. The simulation involved modeling AMSS through the use of the published standards to ensure the accuracy of the results. Although the results indicated that there is indeed a reduced capacity (to about one-fourth) and efficiency of the system at the increased traffic load, the reduction in performance does not lead to the conclusion that an alternative to AMSS must be found. On the contrary, some modifications to the protocols controlling the operation of AMSS and updating the system with new technologies, would make it as valid a solution to the problem as it is today.

Simulations and phantom evaluations of magnetic resonance electrical impedance tomography (MREIT) for breast cancer detection

NASA Astrophysics Data System (ADS)

Sadleir, Rosalind J.; Sajib, Saurav Z. K.; Kim, Hyung Joong; Kwon, Oh In; Woo, Eung Je

2013-05-01

MREIT is a new imaging modality that can be used to reconstruct high-resolution conductivity images of the human body. Since conductivity values of cancerous tissues in the breast are significantly higher than those of surrounding normal tissues, breast imaging using MREIT may provide a new noninvasive way of detecting early stage of cancer. In this paper, we present results of experimental and numerical simulation studies of breast MREIT. We built a realistic three-dimensional model of the human breast connected to a simplified model of the chest including the heart and evaluated the ability of MREIT to detect cancerous anomalies in a background material with similar electrical properties to breast tissue. We performed numerical simulations of various scenarios in breast MREIT including assessment of the effects of fat inclusions and effects related to noise levels, such as changing the amplitude of injected currents, effect of added noise and number of averages. Phantom results showed straightforward detection of cancerous anomalies in a background was possible with low currents and few averages. The simulation results showed it should be possible to detect a cancerous anomaly in the breast, while restricting the maximal current density in the heart below published levels for nerve excitation.

The Separation of Blood Components Using Standing Surface Acoustic Waves (SSAWs) Microfluidic Devices: Analysis and Simulation.

PubMed

Soliman, Ahmed M; Eldosoky, Mohamed A; Taha, Taha E

2017-03-29

The separation of blood components (WBCs, RBCs, and platelets) is important for medical applications. Recently, standing surface acoustic wave (SSAW) microfluidic devices are used for the separation of particles. In this paper, the design analysis of SSAW microfluidics is presented. Also, the analysis of SSAW force with Rayleigh angle effect and its attenuation in liquid-loaded substrate, viscous drag force, hydrodynamic force, and diffusion force are explained and analyzed. The analyses are provided for selecting the piezoelectric material, width of the main microchannel, working area of SAW, wavelength, minimum input power required for the separation process, and widths of outlet collecting microchannels. The design analysis of SSAW microfluidics is provided for determining the minimum input power required for the separation process with appropriated the displacement contrast of the particles.The analyses are applied for simulation the separation of blood components. The piezoelectric material, width of the main microchannel, working area of SAW, wavelength, and minimum input power required for the separation process are selected as LiNbO₃, 120 μm, 1.08 mm², 300 μm, 371 mW. The results are compared to other published results. The results of these simulations achieve minimum power consumption, less complicated setup, and high collecting efficiency. All simulation programs are built by MATLAB.

The Separation of Blood Components Using Standing Surface Acoustic Waves (SSAWs) Microfluidic Devices: Analysis and Simulation

PubMed Central

Soliman, Ahmed M.; Eldosoky, Mohamed A.; Taha, Taha E.

2017-01-01

The separation of blood components (WBCs, RBCs, and platelets) is important for medical applications. Recently, standing surface acoustic wave (SSAW) microfluidic devices are used for the separation of particles. In this paper, the design analysis of SSAW microfluidics is presented. Also, the analysis of SSAW force with Rayleigh angle effect and its attenuation in liquid-loaded substrate, viscous drag force, hydrodynamic force, and diffusion force are explained and analyzed. The analyses are provided for selecting the piezoelectric material, width of the main microchannel, working area of SAW, wavelength, minimum input power required for the separation process, and widths of outlet collecting microchannels. The design analysis of SSAW microfluidics is provided for determining the minimum input power required for the separation process with appropriated the displacement contrast of the particles.The analyses are applied for simulation the separation of blood components. The piezoelectric material, width of the main microchannel, working area of SAW, wavelength, and minimum input power required for the separation process are selected as LiNbO3, 120 μm, 1.08 mm2, 300 μm, 371 mW. The results are compared to other published results. The results of these simulations achieve minimum power consumption, less complicated setup, and high collecting efficiency. All simulation programs are built by MATLAB. PMID:28952506

Optimised in vitro applicable loads for the simulation of lateral bending in the lumbar spine.

PubMed

Dreischarf, Marcel; Rohlmann, Antonius; Bergmann, Georg; Zander, Thomas

2012-07-01

In in vitro studies of the lumbar spine simplified loading modes (compressive follower force, pure moment) are usually employed to simulate the standard load cases flexion-extension, axial rotation and lateral bending of the upper body. However, the magnitudes of these loads vary widely in the literature. Thus the results of current studies may lead to unrealistic values and are hardly comparable. It is still unknown which load magnitudes lead to a realistic simulation of maximum lateral bending. A validated finite element model of the lumbar spine was used in an optimisation study to determine which magnitudes of the compressive follower force and bending moment deliver results that fit best with averaged in vivo data. The best agreement with averaged in vivo measured data was found for a compressive follower force of 700 N and a lateral bending moment of 7.8 Nm. These results show that loading modes that differ strongly from the optimised one may not realistically simulate maximum lateral bending. The simplified but in vitro applicable loading cannot perfectly mimic the in vivo situation. However, the optimised magnitudes are those which agree best with averaged in vivo measured data. Its consequent application would lead to a better comparability of different investigations. Copyright © 2012 IPEM. Published by Elsevier Ltd. All rights reserved.

[Benchmark experiment to verify radiation transport calculations for dosimetry in radiation therapy].

PubMed

Renner, Franziska

2016-09-01

Monte Carlo simulations are regarded as the most accurate method of solving complex problems in the field of dosimetry and radiation transport. In (external) radiation therapy they are increasingly used for the calculation of dose distributions during treatment planning. In comparison to other algorithms for the calculation of dose distributions, Monte Carlo methods have the capability of improving the accuracy of dose calculations - especially under complex circumstances (e.g. consideration of inhomogeneities). However, there is a lack of knowledge of how accurate the results of Monte Carlo calculations are on an absolute basis. A practical verification of the calculations can be performed by direct comparison with the results of a benchmark experiment. This work presents such a benchmark experiment and compares its results (with detailed consideration of measurement uncertainty) with the results of Monte Carlo calculations using the well-established Monte Carlo code EGSnrc. The experiment was designed to have parallels to external beam radiation therapy with respect to the type and energy of the radiation, the materials used and the kind of dose measurement. Because the properties of the beam have to be well known in order to compare the results of the experiment and the simulation on an absolute basis, the benchmark experiment was performed using the research electron accelerator of the Physikalisch-Technische Bundesanstalt (PTB), whose beam was accurately characterized in advance. The benchmark experiment and the corresponding Monte Carlo simulations were carried out for two different types of ionization chambers and the results were compared. Considering the uncertainty, which is about 0.7 % for the experimental values and about 1.0 % for the Monte Carlo simulation, the results of the simulation and the experiment coincide. Copyright © 2015. Published by Elsevier GmbH.

Simulation-Based Bronchoscopy Training

PubMed Central

Kennedy, Cassie C.; Maldonado, Fabien

2013-01-01

Background: Simulation-based bronchoscopy training is increasingly used, but effectiveness remains uncertain. We sought to perform a comprehensive synthesis of published work on simulation-based bronchoscopy training. Methods: We searched MEDLINE, EMBASE, CINAHL, PsycINFO, ERIC, Web of Science, and Scopus for eligible articles through May 11, 2011. We included all original studies involving health professionals that evaluated, in comparison with no intervention or an alternative instructional approach, simulation-based training for flexible or rigid bronchoscopy. Study selection and data abstraction were performed independently and in duplicate. We pooled results using random effects meta-analysis. Results: From an initial pool of 10,903 articles, we identified 17 studies evaluating simulation-based bronchoscopy training. In comparison with no intervention, simulation training was associated with large benefits on skills and behaviors (pooled effect size, 1.21 [95% CI, 0.82-1.60]; n = 8 studies) and moderate benefits on time (0.62 [95% CI, 0.12-1.13]; n = 7). In comparison with clinical instruction, behaviors with real patients showed nonsignificant effects favoring simulation for time (0.61 [95% CI, −1.47 to 2.69]) and process (0.33 [95% CI, −1.46 to 2.11]) outcomes (n = 2 studies each), although variation in training time might account for these differences. Four studies compared alternate simulation-based training approaches. Inductive analysis to inform instructional design suggested that longer or more structured training is more effective, authentic clinical context adds value, and animal models and plastic part-task models may be superior to more costly virtual-reality simulators. Conclusions: Simulation-based bronchoscopy training is effective in comparison with no intervention. Comparative effectiveness studies are few. PMID:23370487

Virtual milk for modelling and simulation of dairy processes.

PubMed

Munir, M T; Zhang, Y; Yu, W; Wilson, D I; Young, B R

2016-05-01

The modeling of dairy processing using a generic process simulator suffers from shortcomings, given that many simulators do not contain milk components in their component libraries. Recently, pseudo-milk components for a commercial process simulator were proposed for simulation and the current work extends this pseudo-milk concept by studying the effect of both total milk solids and temperature on key physical properties such as thermal conductivity, density, viscosity, and heat capacity. This paper also uses expanded fluid and power law models to predict milk viscosity over the temperature range from 4 to 75°C and develops a succinct regressed model for heat capacity as a function of temperature and fat composition. The pseudo-milk was validated by comparing the simulated and actual values of the physical properties of milk. The milk thermal conductivity, density, viscosity, and heat capacity showed differences of less than 2, 4, 3, and 1.5%, respectively, between the simulated results and actual values. This work extends the capabilities of the previously proposed pseudo-milk and of a process simulator to model dairy processes, processing different types of milk (e.g., whole milk, skim milk, and concentrated milk) with different intrinsic compositions, and to predict correct material and energy balances for dairy processes. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Simulation of white light generation and near light bullets using a novel numerical technique

NASA Astrophysics Data System (ADS)

Zia, Haider

2018-01-01

An accurate and efficient simulation has been devised, employing a new numerical technique to simulate the derivative generalised non-linear Schrödinger equation in all three spatial dimensions and time. The simulation models all pertinent effects such as self-steepening and plasma for the non-linear propagation of ultrafast optical radiation in bulk material. Simulation results are compared to published experimental spectral data of an example ytterbium aluminum garnet system at 3.1 μm radiation and fits to within a factor of 5. The simulation shows that there is a stability point near the end of the 2 mm crystal where a quasi-light bullet (spatial temporal soliton) is present. Within this region, the pulse is collimated at a reduced diameter (factor of ∼2) and there exists a near temporal soliton at the spatial center. The temporal intensity within this stable region is compressed by a factor of ∼4 compared to the input. This study shows that the simulation highlights new physical phenomena based on the interplay of various linear, non-linear and plasma effects that go beyond the experiment and is thus integral to achieving accurate designs of white light generation systems for optical applications. An adaptive error reduction algorithm tailor made for this simulation will also be presented in appendix.

Program Code Generator for Cardiac Electrophysiology Simulation with Automatic PDE Boundary Condition Handling

PubMed Central

Punzalan, Florencio Rusty; Kunieda, Yoshitoshi; Amano, Akira

2015-01-01

Clinical and experimental studies involving human hearts can have certain limitations. Methods such as computer simulations can be an important alternative or supplemental tool. Physiological simulation at the tissue or organ level typically involves the handling of partial differential equations (PDEs). Boundary conditions and distributed parameters, such as those used in pharmacokinetics simulation, add to the complexity of the PDE solution. These factors can tailor PDE solutions and their corresponding program code to specific problems. Boundary condition and parameter changes in the customized code are usually prone to errors and time-consuming. We propose a general approach for handling PDEs and boundary conditions in computational models using a replacement scheme for discretization. This study is an extension of a program generator that we introduced in a previous publication. The program generator can generate code for multi-cell simulations of cardiac electrophysiology. Improvements to the system allow it to handle simultaneous equations in the biological function model as well as implicit PDE numerical schemes. The replacement scheme involves substituting all partial differential terms with numerical solution equations. Once the model and boundary equations are discretized with the numerical solution scheme, instances of the equations are generated to undergo dependency analysis. The result of the dependency analysis is then used to generate the program code. The resulting program code are in Java or C programming language. To validate the automatic handling of boundary conditions in the program code generator, we generated simulation code using the FHN, Luo-Rudy 1, and Hund-Rudy cell models and run cell-to-cell coupling and action potential propagation simulations. One of the simulations is based on a published experiment and simulation results are compared with the experimental data. We conclude that the proposed program code generator can be used to generate code for physiological simulations and provides a tool for studying cardiac electrophysiology. PMID:26356082

A High-Resolution Spatially Explicit Monte-Carlo Simulation Approach to Commercial and Residential Electricity and Water Demand Modeling

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

Morton, April M; McManamay, Ryan A; Nagle, Nicholas N

Abstract As urban areas continue to grow and evolve in a world of increasing environmental awareness, the need for high resolution spatially explicit estimates for energy and water demand has become increasingly important. Though current modeling efforts mark significant progress in the effort to better understand the spatial distribution of energy and water consumption, many are provided at a course spatial resolution or rely on techniques which depend on detailed region-specific data sources that are not publicly available for many parts of the U.S. Furthermore, many existing methods do not account for errors in input data sources and may thereforemore » not accurately reflect inherent uncertainties in model outputs. We propose an alternative and more flexible Monte-Carlo simulation approach to high-resolution residential and commercial electricity and water consumption modeling that relies primarily on publicly available data sources. The method s flexible data requirement and statistical framework ensure that the model is both applicable to a wide range of regions and reflective of uncertainties in model results. Key words: Energy Modeling, Water Modeling, Monte-Carlo Simulation, Uncertainty Quantification Acknowledgment This manuscript has been authored by employees of UT-Battelle, LLC, under contract DE-AC05-00OR22725 with the U.S. Department of Energy. Accordingly, the United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes.« less

Author Correction: Emission budgets and pathways consistent with limiting warming to 1.5 °C

NASA Astrophysics Data System (ADS)

Millar, Richard J.; Fuglestvedt, Jan S.; Friedlingstein, Pierre; Rogelj, Joeri; Grubb, Michael J.; Matthews, H. Damon; Skeie, Ragnhild B.; Forster, Piers M.; Frame, David J.; Allen, Myles R.

2018-06-01

In the version of this Article originally published, a coding error resulted in the erroneous inclusion of a subset of RCP4.5 and RCP8.5 simulations in the sets used for RCP2.6 and RCP6, respectively, leading to an incorrect depiction of the data of the latter two sets in Fig. 1b and RCP2.6 in Table 2. This coding error has now been corrected. The graphic and quantitative changes in the corrected Fig. 1b and Table 2 are contrasted with the originally published display items below. The core conclusions of the paper are not affected, but some numerical values and statements have also been updated as a result; these are listed below. All these errors have now been corrected in the online versions of this Article.

14 CFR 121.407 - Training program: Approval of airplane simulators and other training devices.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 14 Aeronautics and Space 3 2014-01-01 2014-01-01 false Training program: Approval of airplane... Program § 121.407 Training program: Approval of airplane simulators and other training devices. Link to an amendment published at 78 FR 67836, Nov. 12, 2013. (a) Each airplane simulator and other training device...

Overreliance on auditory feedback may lead to sound/syllable repetitions: simulations of stuttering and fluency-inducing conditions with a neural model of speech production

PubMed Central

Civier, Oren; Tasko, Stephen M.; Guenther, Frank H.

2010-01-01

This paper investigates the hypothesis that stuttering may result in part from impaired readout of feedforward control of speech, which forces persons who stutter (PWS) to produce speech with a motor strategy that is weighted too much toward auditory feedback control. Over-reliance on feedback control leads to production errors which, if they grow large enough, can cause the motor system to “reset” and repeat the current syllable. This hypothesis is investigated using computer simulations of a “neurally impaired” version of the DIVA model, a neural network model of speech acquisition and production. The model’s outputs are compared to published acoustic data from PWS’ fluent speech, and to combined acoustic and articulatory movement data collected from the dysfluent speech of one PWS. The simulations mimic the errors observed in the PWS subject’s speech, as well as the repairs of these errors. Additional simulations were able to account for enhancements of fluency gained by slowed/prolonged speech and masking noise. Together these results support the hypothesis that many dysfluencies in stuttering are due to a bias away from feedforward control and toward feedback control. PMID:20831971

Strong control of Southern Ocean cloud reflectivity by ice-nucleating particles.

PubMed

Vergara-Temprado, Jesús; Miltenberger, Annette K; Furtado, Kalli; Grosvenor, Daniel P; Shipway, Ben J; Hill, Adrian A; Wilkinson, Jonathan M; Field, Paul R; Murray, Benjamin J; Carslaw, Ken S

2018-03-13

Large biases in climate model simulations of cloud radiative properties over the Southern Ocean cause large errors in modeled sea surface temperatures, atmospheric circulation, and climate sensitivity. Here, we combine cloud-resolving model simulations with estimates of the concentration of ice-nucleating particles in this region to show that our simulated Southern Ocean clouds reflect far more radiation than predicted by global models, in agreement with satellite observations. Specifically, we show that the clouds that are most sensitive to the concentration of ice-nucleating particles are low-level mixed-phase clouds in the cold sectors of extratropical cyclones, which have previously been identified as a main contributor to the Southern Ocean radiation bias. The very low ice-nucleating particle concentrations that prevail over the Southern Ocean strongly suppress cloud droplet freezing, reduce precipitation, and enhance cloud reflectivity. The results help explain why a strong radiation bias occurs mainly in this remote region away from major sources of ice-nucleating particles. The results present a substantial challenge to climate models to be able to simulate realistic ice-nucleating particle concentrations and their effects under specific meteorological conditions. Copyright © 2018 the Author(s). Published by PNAS.

Disadvantages of interfragmentary shear on fracture healing--mechanical insights through numerical simulation.

PubMed

Steiner, Malte; Claes, Lutz; Ignatius, Anita; Simon, Ulrich; Wehner, Tim

2014-07-01

The outcome of secondary fracture healing processes is strongly influenced by interfragmentary motion. Shear movement is assumed to be more disadvantageous than axial movement, however, experimental results are contradictory. Numerical fracture healing models allow simulation of the fracture healing process with variation of single input parameters and under comparable, normalized mechanical conditions. Thus, a comparison of the influence of different loading directions on the healing process is possible. In this study we simulated fracture healing under several axial compressive, and translational and torsional shear movement scenarios, and compared their respective healing times. Therefore, we used a calibrated numerical model for fracture healing in sheep. Numerous variations of movement amplitudes and musculoskeletal loads were simulated for the three loading directions. Our results show that isolated axial compression was more beneficial for the fracture healing success than both isolated shearing conditions for load and displacement magnitudes which were identical as well as physiological different, and even for strain-based normalized comparable conditions. Additionally, torsional shear movements had less impeding effects than translational shear movements. Therefore, our findings suggest that osteosynthesis implants can be optimized, in particular, to limit translational interfragmentary shear under musculoskeletal loading. © 2014 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

Blood-plasma separation in Y-shaped bifurcating microfluidic channels: A dissipative particle dynamics simulation study

PubMed Central

Li, Xuejin; Popel, Aleksander S.; Karniadakis, George Em

2012-01-01

The motion of a suspension of red blood cells (RBCs) flowing in a Y-shaped bifurcating microfluidic channel is investigated using a validated low-dimensional RBC (LD-RBC) model based on dissipative particle dynamics (DPD). Specifically, the RBC is represented as a closed torus-like ring of ten colloidal particles, which leads to efficient simulations of blood flow in microcirculation over a wide range of hematocrits. Adaptive no-slip wall boundary conditions were implemented to model hydrodynamic flow within a specific wall structure of diverging 3D microfluidic channels, paying attention to controlling density fluctuations. Plasma skimming and the all-or-nothing phenomenon of RBCs in a bifurcating microfluidic channel have been investigated in our simulations for healthy and diseased blood, including the size of cell-free layer on the daughter branches. The feed hematocrit level in the parent channel has considerable influence on blood-plasma separation. Compared to the blood-plasma separation efficiencies of healthy RBCs, malaria-infected stiff RBCs (iRBCs) have a tendency to travel into the low flowrate daughter branch because of their different initial distribution in the parent channel. Our simulation results are consistent with previously published experimental results and theoretical predictions. PMID:22476709

Organ radiation exposure with EOS: GATE simulations versus TLD measurements

NASA Astrophysics Data System (ADS)

Clavel, A. H.; Thevenard-Berger, P.; Verdun, F. R.; Létang, J. M.; Darbon, A.

2016-03-01

EOS® is an innovative X-ray imaging system allowing the acquisition of two simultaneous images of a patient in the standing position, during the vertical scan of two orthogonal fan beams. This study aimed to compute organs radiation exposure to a patient, in the particular geometry of this system. Two different positions of the patient in the machine were studied, corresponding to postero-anterior plus left lateral projections (PA-LLAT) and antero-posterior plus right lateral projections (AP-RLAT). To achieve this goal, a Monte-Carlo simulation was developed based on a GATE environment. To model the physical properties of the patient, a computational phantom was produced based on computed tomography scan data of an anthropomorphic phantom. The simulations provided several organs doses, which were compared to previously published dose results measured with Thermo Luminescent Detectors (TLD) in the same conditions and with the same phantom. The simulation results showed a good agreement with measured doses at the TLD locations, for both AP-RLAT and PA-LLAT projections. This study also showed that the organ dose assessed only from a sample of locations, rather than considering the whole organ, introduced significant bias, depending on organs and projections.

Computational model of in vivo human energy metabolism during semi-starvation and re-feeding

PubMed Central

Hall, Kevin D.

2008-01-01

Changes of body weight and composition are the result of complex interactions among metabolic fluxes contributing to macronutrient balances. To better understand these interactions, a mathematical model was constructed that used the measured dietary macronutrient intake during semi-starvation and re-feeding as model inputs and computed whole-body energy expenditure, de novo lipogenesis, gluconeogenesis, as well as turnover and oxidation of carbohydrate, fat and protein. Published in vivo human data provided the basis for the model components which were integrated by fitting a few unknown parameters to the classic Minnesota human starvation experiment. The model simulated the measured body weight and fat mass changes during semi-starvation and re-feeding and predicted the unmeasured metabolic fluxes underlying the body composition changes. The resting metabolic rate matched the experimental measurements and required a model of adaptive thermogenesis. Re-feeding caused an elevation of de novo lipogenesis which, along with increased fat intake, resulted in a rapid repletion and overshoot of body fat. By continuing the computer simulation with the pre-starvation diet and physical activity, the original body weight and composition was eventually restored, but body fat mass was predicted to take more than one additional year to return to within 5% of its original value. The model was validated by simulating a recently published short-term caloric restriction experiment without changing the model parameters. The predicted changes of body weight, fat mass, resting metabolic rate, and nitrogen balance matched the experimental measurements thereby providing support for the validity of the model. PMID:16449298

Report of the Working Group on the Composition of Ultra High Energy Cosmic Rays

NASA Astrophysics Data System (ADS)

Abbasi, R.; Bellido, J.; Belz, J.; de Souza, V.; Hanlon, W.; Ikeda, D.; Lundquist, J. P.; Sokolskypt, P.; Stroman, T.; Tameda, Y.; Tsunesada, Y.; Unger, M.; Yushkov, A.

For the first time a proper comparison of the average depth of shower maximum (Xmax) published by the Pierre Auger and Telescope Array Observatories is presented. The Xmax distributions measured by the Pierre Auger Observatory were fit using simulated events initiated by four primaries (proton, helium, nitrogen and iron). The primary abundances which best describe the Auger data were simulated through the Telescope Array (TA) Middle Drum (MD) fluorescence and surface detector array. The simulated events were analyzed by the TA Collaboration using the same procedure as applied to their data. The result is a simulated version of the Auger data as it would be observed by TA. This analysis allows a direct comparison of the evolution of < Xmax > with energy of both data sets. The < Xmax > measured by TA-MD is consistent with a preliminary simulation of the Auger data through the TA detector and the average difference between the two data sets was found to be (2.9 ± 2.7 (stat.) ± 18 (syst.)) g/cm2.

Interventional Radiation Oncology (IRO): Transition of a magnetic resonance simulator to a brachytherapy suite.

PubMed

Anderson, Roberta; Armour, Elwood; Beeckler, Courtney; Briner, Valerie; Choflet, Amanda; Cox, Andrea; Fader, Amanda N; Hannah, Marie N; Hobbs, Robert; Huang, Ellen; Kiely, Marilyn; Lee, Junghoon; Morcos, Marc; McMillan, Paige E; Miller, Dave; Ng, Sook Kien; Prasad, Rashmi; Souranis, Annette; Thomsen, Robert; DeWeese, Theodore L; Viswanathan, Akila N

As a core component of a new gynecologic cancer radiation program, we envisioned, structured, and implemented a novel Interventional Radiation Oncology (IRO) unit and magnetic resonance (MR)-brachytherapy environment in an existing MR simulator. We describe the external and internal processes required over a 6-8 month time frame to develop a clinical and research program for gynecologic brachytherapy and to successfully convert an MR simulator into an IRO unit. Support of the institution and department resulted in conversion of an MR simulator to a procedural suite. Development of the MR gynecologic brachytherapy program required novel equipment, staffing, infrastructural development, and cooperative team development with anesthetists, nurses, therapists, physicists, and physicians to ensure a safe and functional environment. Creation of a separate IRO unit permitted a novel billing structure. The creation of an MR-brachytherapy environment in an MR simulator is feasible. Developing infrastructure includes several collaborative elements. Unique to the field of radiation oncology, formalizing the space as an Interventional Radiation Oncology unit permits a sustainable financial structure. Copyright © 2018 American Brachytherapy Society. Published by Elsevier Inc. All rights reserved.

Assessment of the Draft AIAA S-119 Flight Dynamic Model Exchange Standard

NASA Technical Reports Server (NTRS)

Jackson, E. Bruce; Murri, Daniel G.; Hill, Melissa A.; Jessick, Matthew V.; Penn, John M.; Hasan, David A.; Crues, Edwin Z.; Falck, Robert D.; McCarthy, Thomas G.; Vuong, Nghia;

Effect of interstitial and substitution alloying elements on the intrinsic stacking fault energy of nanocrystalline fcc-iron by atomistic simulation study

NASA Astrophysics Data System (ADS)

Mohammadzadeh, Mina; Mohammadzadeh, Roghayeh

2017-11-01

The stacking fault energy (SFE) is an important parameter in the deformation mechanism of face centered cubic (fcc) iron-based alloy. In this study, the effect of interstitial (C and N) and substitution (Nb and Ti) alloying elements on the intrinsic SFE (ISFE) of nanocrystalline iron were investigated via molecular dynamics (MD) simulation. The modified embedded atom method (MEAM) inter-atomic potential was used in the MD simulations. The results demonstrate a strong dependence of ISFE with addition of interstitial alloying elements but only a mild increase in ISFE with addition of substitution alloying elements in the composition range of 0 < {CNb, CTi} < 3 (at%). Moreover, it is shown that alloying of fcc iron with N decreases ISFE, whereas it increases significantly by addition of carbon element [0 < {CC, CN} < 3.5 (at%)]. The simulation method employed in this work shows reasonable agreement with some published experimental/calculated data.

Simulation of neutron production using MCNPX+MCUNED.

PubMed

Erhard, M; Sauvan, P; Nolte, R

2014-10-01

In standard MCNPX, the production of neutrons by ions cannot be modelled efficiently. The MCUNED patch applied to MCNPX 2.7.0 allows to model the production of neutrons by light ions down to energies of a few kiloelectron volts. This is crucial for the simulation of neutron reference fields. The influence of target properties, such as the diffusion of reactive isotopes into the target backing or the effect of energy and angular straggling, can be studied efficiently. In this work, MCNPX/MCUNED calculations are compared with results obtained with the TARGET code for simulating neutron production. Furthermore, MCUNED incorporates more effective variance reduction techniques and a coincidence counting tally. This allows the simulation of a TCAP experiment being developed at PTB. In this experiment, 14.7-MeV neutrons will be produced by the reaction T(d,n)(4)He. The neutron fluence is determined by counting alpha particles, independently of the reaction cross section. © The Author 2013. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Eddy Resolving Global Ocean Prediction including Tides

DTIC Science & Technology

2013-09-30

atlantic meridional overturning circulation in the subpolar North Atlantic . Journal of Geophysical Research vol 118, doi:10.1002/jgrc,20065. [published, refereed] ...global ocean circulation model was examined using results from years 2005-2009 of a seven and a half year 1/12.5° global simulation that resolves...internal tides, along with barotropic tides and the eddying general circulation . We examined tidal amplitudes computed using 18 183-day windows that

Predicting unfolding thermodynamics and stable intermediates for alanine-rich helical peptides with the aid of coarse-grained molecular simulation.

PubMed

Calero-Rubio, Cesar; Paik, Bradford; Jia, Xinqiao; Kiick, Kristi L; Roberts, Christopher J

2016-10-01

This report focuses on the molecular-level processes and thermodynamics of unfolding of a series of helical peptides using a coarse-grained (CG) molecular model. The CG model was refined to capture thermodynamics and structural changes as a function of temperature for a set of published peptide sequences. Circular dichroism spectroscopy (CD) was used to experimentally monitor the temperature-dependent conformational changes and stability of published peptides and new sequences introduced here. The model predictions were quantitatively or semi-quantitatively accurate in all cases. The simulations and CD results showed that, as expected, in most cases the unfolding of helical peptides is well described by a simply 2-state model, and conformational stability increased with increased length of the helices. A notable exception in a 19-residue helix was when two Ala residues were each replaced with Phe. This stabilized a partly unfolded intermediate state via hydrophobic contacts, and also promoted aggregates at higher peptide concentrations. Copyright © 2016 Elsevier B.V. All rights reserved.

Validation of a finite element method framework for cardiac mechanics applications

NASA Astrophysics Data System (ADS)

Danan, David; Le Rolle, Virginie; Hubert, Arnaud; Galli, Elena; Bernard, Anne; Donal, Erwan; Hernández, Alfredo I.

2017-11-01

Modeling cardiac mechanics is a particularly challenging task, mainly because of the poor understanding of the underlying physiology, the lack of observability and the complexity of the mechanical properties of myocardial tissues. The choice of cardiac mechanic solvers, especially, implies several difficulties, notably due to the potential instability arising from the nonlinearities inherent to the large deformation framework. Furthermore, the verification of the obtained simulations is a difficult task because there is no analytic solutions for these kinds of problems. Hence, the objective of this work is to provide a quantitative verification of a cardiac mechanics implementation based on two published benchmark problems. The first problem consists in deforming a bar whereas the second problem concerns the inflation of a truncated ellipsoid-shaped ventricle, both in the steady state case. Simulations were obtained by using the finite element software GETFEM++. Results were compared to the consensus solution published by 11 groups and the proposed solutions were indistinguishable. The validation of the proposed mechanical model implementation is an important step toward the proposition of a global model of cardiac electro-mechanical activity.

Modeling Np and Pu transport with a surface complexation model and spatially variant sorption capacities: Implications for reactive transport modeling and performance assessments of nuclear waste disposal sites

USGS Publications Warehouse

Glynn, P.D.

2003-01-01

One-dimensional (1D) geochemical transport modeling is used to demonstrate the effects of speciation and sorption reactions on the ground-water transport of Np and Pu, two redox-sensitive elements. Earlier 1D simulations (Reardon, 1981) considered the kinetically limited dissolution of calcite and its effect on ion-exchange reactions (involving 90Sr, Ca, Na, Mg and K), and documented the spatial variation of a 90Sr partition coefficient under both transient and steady-state chemical conditions. In contrast, the simulations presented here assume local equilibrium for all reactions, and consider sorption on constant potential, rather than constant charge, surfaces. Reardon's (1981) seminal findings on the spatial and temporal variability of partitioning (of 90Sr) are reexamined and found partially caused by his assumption of a kinetically limited reaction. In the present work, sorption is assumed the predominant retardation process controlling Pu and Np transport, and is simulated using a diffuse-double-layer-surface-complexation (DDLSC) model. Transport simulations consider the infiltration of Np- and Pu-contaminated waters into an initially uncontaminated environment, followed by the cleanup of the resultant contamination with uncontaminated water. Simulations are conducted using different spatial distributions of sorption capacities (with the same total potential sorption capacity, but with different variances and spatial correlation structures). Results obtained differ markedly from those that would be obtained in transport simulations using constant Kd, Langmuir or Freundlich sorption models. When possible, simulation results (breakthrough curves) are fitted to a constant K d advection-dispersion transport model and compared. Functional differences often are great enough that they prevent a meaningful fit of the simulation results with a constant K d (or even a Langmuir or Freundlich) model, even in the case of Np, a weakly sorbed radionuclide under the simulation conditions. Functional behaviors that cannot be fit include concentration trend reversals and radionuclide desorption spikes. Other simulation results are fit successfully but the fitted parameters (Kd and dispersivity) vary significantly depending on simulation conditions (e.g. "infiltration" vs. "cleanup" conditions). Notably, an increase in the variance of the specified sorption capacities results in a marked increase in the dispersion of the radionuclides. The results presented have implications for the simulation of radionuclide migration in performance assessments of nuclear waste-disposal sites, for the future monitoring of those sites, and more generally for modeling contaminant transport in ground-water environments. ?? 2003 Published by Elsevier Science Ltd.

Mechanical Properties and Simulated Aging of Silicone Maxillofacial Elastomers: Advancements in the Past 45 Years.

PubMed

Hatamleh, Muhanad M; Polyzois, Gregory L; Nuseir, Amjad; Hatamleh, Khaldoun; Alnazzawi, Ahmad

2016-07-01

To identify and discuss the findings of publications on mechanical behavior of maxillofacial prosthetic materials published since 1969. Original experimental articles reporting on mechanical properties of maxillofacial prosthetic materials were included. A two-stage search of the literature, electronic and hand search, identified relevant published studies up to May 2015. An extensive electronic search was conducted of databases including PubMed, Embase, Scopus, and Google Scholar. Included primary studies (n = 63) reported on tensile strength, tear strength, and hardness of maxillofacial prosthetic materials at baseline and after aging. The search revealed 63 papers, with more than 28 papers being published in the past 10 years, which shows an increased number of publications when compared to only 6 papers published in the 1970s. The increase is linear with significant correlation (r = 0.85). Such an increase reflects great awareness and continued developments and warrants more research in the field of maxillofacial prosthetic materials properties; however, it is difficult to directly compare results, as studies varied in maxillofacial prosthetic materials tested with various silicone elastomers being heavily investigated, standards followed in preparing test specimens, experimental testing protocols, and parameters used in setting simulated aging conditionings. It is imperative to overcome the existing variability by establishing unified national or international standards/specifications for maxillofacial prosthetic materials. Standardization organizations or bodies, the scientific community, and academia need to be coordinated to achieve this goal. In the meantime and despite all of these theoretically significant alternatives, clinical practice still faces problems with serviceability of maxillofacial prostheses. © 2016 by the American College of Prosthodontists.

Pore-scale and Continuum Simulations of Solute Transport Micromodel Benchmark Experiments

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

Oostrom, Martinus; Mehmani, Yashar; Romero Gomez, Pedro DJ

Four sets of micromodel nonreactive solute transport experiments were conducted with flow velocity, grain diameter, pore-aspect ratio, and flow focusing heterogeneity as the variables. The data sets were offered to pore-scale modeling groups to test their simulators. Each set consisted of two learning experiments, for which all results was made available, and a challenge experiment, for which only the experimental description and base input parameters were provided. The experimental results showed a nonlinear dependence of the dispersion coefficient on the Peclet number, a negligible effect of the pore-aspect ratio on transverse mixing, and considerably enhanced mixing due to flow focusing.more » Five pore-scale models and one continuum-scale model were used to simulate the experiments. Of the pore-scale models, two used a pore-network (PN) method, two others are based on a lattice-Boltzmann (LB) approach, and one employed a computational fluid dynamics (CFD) technique. The learning experiments were used by the PN models to modify the standard perfect mixing approach in pore bodies into approaches to simulate the observed incomplete mixing. The LB and CFD models used these experiments to appropriately discretize the grid representations. The continuum model use published non-linear relations between transverse dispersion coefficients and Peclet numbers to compute the required dispersivity input values. Comparisons between experimental and numerical results for the four challenge experiments show that all pore-scale models were all able to satisfactorily simulate the experiments. The continuum model underestimated the required dispersivity values and, resulting in less dispersion. The PN models were able to complete the simulations in a few minutes, whereas the direct models needed up to several days on supercomputers to resolve the more complex problems.« less

Strong scaling and speedup to 16,384 processors in cardiac electro-mechanical simulations.

PubMed

Reumann, Matthias; Fitch, Blake G; Rayshubskiy, Aleksandr; Keller, David U J; Seemann, Gunnar; Dossel, Olaf; Pitman, Michael C; Rice, John J

2009-01-01

High performance computing is required to make feasible simulations of whole organ models of the heart with biophysically detailed cellular models in a clinical setting. Increasing model detail by simulating electrophysiology and mechanical models increases computation demands. We present scaling results of an electro - mechanical cardiac model of two ventricles and compare them to our previously published results using an electrophysiological model only. The anatomical data-set was given by both ventricles of the Visible Female data-set in a 0.2 mm resolution. Fiber orientation was included. Data decomposition for the distribution onto the distributed memory system was carried out by orthogonal recursive bisection. Load weight ratios for non-tissue vs. tissue elements used in the data decomposition were 1:1, 1:2, 1:5, 1:10, 1:25, 1:38.85, 1:50 and 1:100. The ten Tusscher et al. (2004) electrophysiological cell model was used and the Rice et al. (1999) model for the computation of the calcium transient dependent force. Scaling results for 512, 1024, 2048, 4096, 8192 and 16,384 processors were obtained for 1 ms simulation time. The simulations were carried out on an IBM Blue Gene/L supercomputer. The results show linear scaling from 512 to 16,384 processors with speedup factors between 1.82 and 2.14 between partitions. The most optimal load ratio was 1:25 for on all partitions. However, a shift towards load ratios with higher weight for the tissue elements can be recognized as can be expected when adding computational complexity to the model while keeping the same communication setup. This work demonstrates that it is potentially possible to run simulations of 0.5 s using the presented electro-mechanical cardiac model within 1.5 hours.

Predictions of the electro-mechanical response of conductive CNT-polymer composites

NASA Astrophysics Data System (ADS)

Matos, Miguel A. S.; Tagarielli, Vito L.; Baiz-Villafranca, Pedro M.; Pinho, Silvestre T.

2018-05-01

We present finite element simulations to predict the conductivity, elastic response and strain-sensing capability of conductive composites comprising a polymeric matrix and carbon nanotubes. Realistic representative volume elements (RVE) of the microstructure are generated and both constituents are modelled as linear elastic solids, with resistivity independent of strain; the electrical contact between nanotubes is represented by a new element which accounts for quantum tunnelling effects and captures the sensitivity of conductivity to separation. Monte Carlo simulations are conducted and the sensitivity of the predictions to RVE size is explored. Predictions of modulus and conductivity are found in good agreement with published results. The strain-sensing capability of the material is explored for multiaxial strain states.

A numerical simulation of finite-length Taylor-Couette flow

NASA Technical Reports Server (NTRS)

Streett, C. L.; Hussaini, M. Y.

1987-01-01

The processes leading to laminar-turbulent transition in finite-channel-length Taylor-Couette flow are investigated analytically, solving the unsteady incompressible Navier-Stokes equations by spectral-collocation methods. A time-split algorithm, implementable in both axisymmetric and fully three-dimensional time-accurate versions, and an algorithm based on the staggered-mesh discretization of Bernardi and Maday (1986) are described in detail, and results obtained by applying the axisymmetric version of the first algorithm and a steady-state version of the second are presented graphically and compared with published experimental data. The feasibility of full three-dimensional simulations of the progression through chaotic states to turbulence under the constraints of Taylor-Couette flow is demonstrated.

Lattice QCD and heavy ion collisions: a review of recent progress.

PubMed

Ratti, Claudia

2018-04-04

In the last few years, numerical simulations of QCD on the lattice have reached a new level of accuracy. A wide range of thermodynamic quantities is now available in the continuum limit and for physical quark masses. This allows a comparison with measurements from heavy ion collisions for the first time. Furthermore, calculations of dynamical quantities are also becoming available. The combined effort from first principles and experiment allows us to gain an unprecedented understanding of the properties of quark-gluon plasma. I will review the state-of-the-art results from lattice simulations and connect them to the experimental information from RHIC and the LHC. © 2018 IOP Publishing Ltd.

Monte Carlo simulation tool for online treatment monitoring in hadrontherapy with in-beam PET: A patient study.

PubMed

Fiorina, E; Ferrero, V; Pennazio, F; Baroni, G; Battistoni, G; Belcari, N; Cerello, P; Camarlinghi, N; Ciocca, M; Del Guerra, A; Donetti, M; Ferrari, A; Giordanengo, S; Giraudo, G; Mairani, A; Morrocchi, M; Peroni, C; Rivetti, A; Da Rocha Rolo, M D; Rossi, S; Rosso, V; Sala, P; Sportelli, G; Tampellini, S; Valvo, F; Wheadon, R; Bisogni, M G

2018-05-07

Hadrontherapy is a method for treating cancer with very targeted dose distributions and enhanced radiobiological effects. To fully exploit these advantages, in vivo range monitoring systems are required. These devices measure, preferably during the treatment, the secondary radiation generated by the beam-tissue interactions. However, since correlation of the secondary radiation distribution with the dose is not straightforward, Monte Carlo (MC) simulations are very important for treatment quality assessment. The INSIDE project constructed an in-beam PET scanner to detect signals generated by the positron-emitting isotopes resulting from projectile-target fragmentation. In addition, a FLUKA-based simulation tool was developed to predict the corresponding reference PET images using a detailed scanner model. The INSIDE in-beam PET was used to monitor two consecutive proton treatment sessions on a patient at the Italian Center for Oncological Hadrontherapy (CNAO). The reconstructed PET images were updated every 10 s providing a near real-time quality assessment. By half-way through the treatment, the statistics of the measured PET images were already significant enough to be compared with the simulations with average differences in the activity range less than 2.5 mm along the beam direction. Without taking into account any preferential direction, differences within 1 mm were found. In this paper, the INSIDE MC simulation tool is described and the results of the first in vivo agreement evaluation are reported. These results have justified a clinical trial, in which the MC simulation tool will be used on a daily basis to study the compliance tolerances between the measured and simulated PET images. Copyright © 2018 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

The use of Monte Carlo simulations for accurate dose determination with thermoluminescence dosemeters in radiation therapy beams.

PubMed

Mobit, P

2002-01-01

The energy responses of LiF-TLDs irradiated in megavoltage electron and photon beams have been determined experimentally by many investigators over the past 35 years but the results vary considerably. General cavity theory has been used to model some of the experimental findings but the predictions of these cavity theories differ from each other and from measurements by more than 13%. Recently, two groups or investigators using Monte Carlo simulations and careful experimental techniques showed that the energy response of 1 mm or 2 mm thick LiF-TLD irradiated by megavoltage photon and electron beams is not more than 5% less than unity for low-Z phantom materials like water or Perspex. However, when the depth of irradiation is significantly different from dmax and the TLD size is more than 5 mm, then the energy response is up to 12% less than unity for incident electron beams. Monte Carlo simulations of some of the experiments reported in the literature showed that some of the contradictory experimental results are reproducible with Monte Carlo simulations. Monte Carlo simulations show that the energy response of LiF-TLDs depends on the size of detector used in electron beams, the depth of irradiation and the incident electron energy. Other differences can be attributed to absolute dose determination and precision of the TL technique. Monte Carlo simulations have also been used to evaluate some of the published general cavity theories. The results show that some of the parameters used to evaluate Burlin's general cavity theory are wrong by factor of 3. Despite this, the estimation of the energy response for most clinical situations using Burlin's cavity equation agrees with Monte Carlo simulations within 1%.

An Agent-Based Model of a Hepatic Inflammatory Response to Salmonella: A Computational Study under a Large Set of Experimental Data.

PubMed

Shi, Zhenzhen; Chapes, Stephen K; Ben-Arieh, David; Wu, Chih-Hang

2016-01-01

We present an agent-based model (ABM) to simulate a hepatic inflammatory response (HIR) in a mouse infected by Salmonella that sometimes progressed to problematic proportions, known as "sepsis". Based on over 200 published studies, this ABM describes interactions among 21 cells or cytokines and incorporates 226 experimental data sets and/or data estimates from those reports to simulate a mouse HIR in silico. Our simulated results reproduced dynamic patterns of HIR reported in the literature. As shown in vivo, our model also demonstrated that sepsis was highly related to the initial Salmonella dose and the presence of components of the adaptive immune system. We determined that high mobility group box-1, C-reactive protein, and the interleukin-10: tumor necrosis factor-α ratio, and CD4+ T cell: CD8+ T cell ratio, all recognized as biomarkers during HIR, significantly correlated with outcomes of HIR. During therapy-directed silico simulations, our results demonstrated that anti-agent intervention impacted the survival rates of septic individuals in a time-dependent manner. By specifying the infected species, source of infection, and site of infection, this ABM enabled us to reproduce the kinetics of several essential indicators during a HIR, observe distinct dynamic patterns that are manifested during HIR, and allowed us to test proposed therapy-directed treatments. Although limitation still exists, this ABM is a step forward because it links underlying biological processes to computational simulation and was validated through a series of comparisons between the simulated results and experimental studies.

An Agent-Based Model of a Hepatic Inflammatory Response to Salmonella: A Computational Study under a Large Set of Experimental Data

PubMed Central

Chapes, Stephen K.; Ben-Arieh, David; Wu, Chih-Hang

2016-01-01

We present an agent-based model (ABM) to simulate a hepatic inflammatory response (HIR) in a mouse infected by Salmonella that sometimes progressed to problematic proportions, known as “sepsis”. Based on over 200 published studies, this ABM describes interactions among 21 cells or cytokines and incorporates 226 experimental data sets and/or data estimates from those reports to simulate a mouse HIR in silico. Our simulated results reproduced dynamic patterns of HIR reported in the literature. As shown in vivo, our model also demonstrated that sepsis was highly related to the initial Salmonella dose and the presence of components of the adaptive immune system. We determined that high mobility group box-1, C-reactive protein, and the interleukin-10: tumor necrosis factor-α ratio, and CD4+ T cell: CD8+ T cell ratio, all recognized as biomarkers during HIR, significantly correlated with outcomes of HIR. During therapy-directed silico simulations, our results demonstrated that anti-agent intervention impacted the survival rates of septic individuals in a time-dependent manner. By specifying the infected species, source of infection, and site of infection, this ABM enabled us to reproduce the kinetics of several essential indicators during a HIR, observe distinct dynamic patterns that are manifested during HIR, and allowed us to test proposed therapy-directed treatments. Although limitation still exists, this ABM is a step forward because it links underlying biological processes to computational simulation and was validated through a series of comparisons between the simulated results and experimental studies. PMID:27556404

Appendices to the model description document for a computer program for the emulation/simulation of a space station environmental control and life support system

NASA Technical Reports Server (NTRS)

Yanosy, James L.

1988-01-01

A Model Description Document for the Emulation Simulation Computer Model was already published. The model consisted of a detailed model (emulation) of a SAWD CO2 removal subsystem which operated with much less detailed (simulation) models of a cabin, crew, and condensing and sensible heat exchangers. The purpose was to explore the utility of such an emulation simulation combination in the design, development, and test of a piece of ARS hardware, SAWD. Extensions to this original effort are presented. The first extension is an update of the model to reflect changes in the SAWD control logic which resulted from test. Also, slight changes were also made to the SAWD model to permit restarting and to improve the iteration technique. The second extension is the development of simulation models for more pieces of air and water processing equipment. Models are presented for: EDC, Molecular Sieve, Bosch, Sabatier, a new condensing heat exchanger, SPE, SFWES, Catalytic Oxidizer, and multifiltration. The third extension is to create two system simulations using these models. The first system presented consists of one air and one water processing system. The second consists of a potential air revitalization system.

Appendices to the user's manual for a computer program for the emulation/simulation of a space station environmental control and life support system

NASA Technical Reports Server (NTRS)

Yanosy, James L.

1988-01-01

A user's Manual for the Emulation Simulation Computer Model was published previously. The model consisted of a detailed model (emulation) of a SAWD CO2 removal subsystem which operated with much less detailed (simulation) models of a cabin, crew, and condensing and sensible heat exchangers. The purpose was to explore the utility of such an emulation/simulation combination in the design, development, and test of a piece of ARS hardware - SAWD. Extensions to this original effort are presented. The first extension is an update of the model to reflect changes in the SAWD control logic which resulted from the test. In addition, slight changes were also made to the SAWD model to permit restarting and to improve the iteration technique. The second extension is the development of simulation models for more pieces of air and water processing equipment. Models are presented for: EDC, Molecular Sieve, Bosch, Sabatier, a new condensing heat exchanger, SPE, SFWES, Catalytic Oxidizer, and multifiltration. The third extension is to create two system simulations using these models. The first system presented consists of one air and one water processing system, the second a potential Space Station air revitalization system.

Simulating cholinesterase inhibition in birds caused by dietary insecticide exposure

USGS Publications Warehouse

Corson, M.S.; Mora, M.A.; Grant, W.E.

1998-01-01

We describe a stochastic simulation model that simulates avian foraging in an agricultural landscape to evaluate factors affecting dietary insecticide exposure and to predict post-exposure cholinesterase (ChE) inhibition. To evaluate the model, we simulated published field studies and found that model predictions of insecticide decay and ChE inhibition reasonably approximated most observed results. Sensitivity analysis suggested that foraging location usually influenced ChE inhibition more than diet preferences or daily intake rate. Although organophosphorus insecticides usually caused greater inhibition than carbamate insecticides, insecticide toxicity appeared only moderately important. When we simulated impact of heavy insecticide applications during breeding seasons of 15 wild bird species, mean maximum ChE inhibition in most species exceeded 20% at some point. At this level of inhibition, birds may experience nausea and/or may exhibit minor behavioral changes. Simulated risk peaked in April–May and August–September and was lowest in July. ChE inhibition increased with proportion of vegetation in the diet. This model, and ones like it, may help predict insecticide exposure of and sublethal ChE inhibition in grassland animals, thereby reducing dependence of ecological risk assessments on field studies alone.

Response of Flight Nurses in a Simulated Helicopter Environment.

PubMed

Kaniecki, David M; Hickman, Ronald L; Alfes, Celeste M; Reimer, Andrew P

The purpose of this study was to determine if a helicopter flight simulator could provide a useful educational platform by creating experiences similar to those encountered by actual flight nurses. Flight nurse (FN) and non-FN participants completed a simulated emergency scenario in a flight simulator. Physiologic and psychological stress during the simulation was measured using heart rate and perceived stress scores. A questionnaire was then administered to assess the realism of the flight simulator. Subjects reported that the overall experience in the flight simulator was comparable with a real helicopter. Sounds, communications, vibrations, and movements in the simulator most approximated those of a real-life helicopter environment. Perceived stress levels of all participants increased significantly from 27 (on a 0-100 scale) before simulation to 51 at the peak of the simulation and declined thereafter to 28 (P < .001). Perceived stress levels of FNs increased significantly from 25 before simulation to 54 at the peak of the simulation and declined thereafter to 30 (P < .001). Perceived stress levels of non-FNs increased significantly from 31 before simulation to 49 at the peak of the simulation and declined thereafter to 25 (P < .001). There were no significant differences in perceived stress levels between FNs and non-FNs before (P = .58), during (P = .63), or after (P = .55) simulation. FNs' heart rates increased significantly from 77 before simulation to 100 at the peak of the simulation and declined thereafter to 72 (P < .001). The results of this study suggest that simulation of a critical care scenario in a high-fidelity helicopter flight simulator can provide a realistic helicopter transport experience and create physiologic and psychological stress for participants. Copyright © 2017 Air Medical Journal Associates. Published by Elsevier Inc. All rights reserved.

Dynamics and statics of nonaxisymmetric liquid bridges

NASA Technical Reports Server (NTRS)

Alexander, J. Iwan D.; Resnick, Andy; Zhang, Yiqiang; Fedoseyev, A.

1994-01-01

We finished the construction of the experimental apparatus and the design and testing of some of the visualization and data acquisition techniques. Experimental work focused on three areas: force measurements, loss of stability to nonaxisymmetric bridges, and vibration behavior. The experimental work is summarized in section 2. Selected results from our force measurement experiments are outlined in section 3. In addition we worked on the theory of the dynamic stability of axisymmetric bridges and undertook numerical simulation of the effects of inclined gravity vectors on the minimum volume stability limit for static bridges. The results and status of our theoretical work and numerical simulation are described in section 4. Papers published and in preparation, conference presentations, etc., are described in section 5. Work planned for the third year is discussed in section 6. References cited in the report are listed in section 7.

Monte Carlo simulations of nematic and chiral nematic shells

NASA Astrophysics Data System (ADS)

Wand, Charlie R.; Bates, Martin A.

2015-01-01

We present a systematic Monte Carlo simulation study of thin nematic and cholesteric shells with planar anchoring using an off-lattice model. The results obtained using the simple model correspond with previously published results for lattice-based systems, with the number, type, and position of defects observed dependent on the shell thickness with four half-strength defects in a tetrahedral arrangement found in very thin shells and a pair of defects in a bipolar (boojum) configuration observed in thicker shells. A third intermediate defect configuration is occasionally observed for intermediate thickness shells, which is stabilized in noncentrosymmetric shells of nonuniform thickness. Chiral nematic (cholesteric) shells are investigated by including a chiral term in the potential. Decreasing the pitch of the chiral nematic leads to a twisted bipolar (chiral boojum) configuration with the director twist increasing from the inner to the outer surface.

A beating heart cell model to predict cardiotoxicity: effects of the dietary supplement ingredients higenamine, phenylethylamine, ephedrine and caffeine.

PubMed

Calvert, Richard; Vohra, Sanah; Ferguson, Martine; Wiesenfeld, Paddy

2015-04-01

Some dietary supplements may contain cardiac stimulants and potential cardiotoxins. In vitro studies may identify ingredients of concern. A beating human cardiomyocyte cell line was used to evaluate cellular effects following phenylethylamine (PEA), higenamine, ephedrine or caffeine treatment. PEA and higenamine exposure levels simulated published blood levels in humans or animals after intravenous administration. Ephedrine and caffeine levels approximated published blood levels following human oral intake. At low or midrange levels, each chemical was examined plus or minus 50 µM caffeine, simulating human blood levels reported after consumption of caffeine-enriched dietary supplements. To measure beats per minute (BPM), peak width, etc., rhythmic rise and fall in intracellular calcium levels following 30 min of treatment was examined. Higenamine 31.3 ng/ml or 313 ng/ml significantly increased BPM in an escalating manner. PEA increased BPM at 0.8 and 8 µg/ml, while 80 µg/ml PEA reduced BPM and widened peaks. Ephedrine produced a significant BPM dose response from 0.5 to 5.0 µM. Caffeine increased BPM only at a toxic level of 250 µM. Adding caffeine to PEA or higenamine but not ephedrine further increased BPM. These in vitro results suggest that additional testing may be warranted in vivo to further evaluate these effects. Published by Elsevier Ltd.

Combined PEST and Trial-Error approach to improve APEX calibration

USDA-ARS?s Scientific Manuscript database

The Agricultural Policy Environmental eXtender (APEX), a physically-based hydrologic model that simulates management impacts on the environment for small watersheds, requires improved understanding of the input parameters for improved simulations. However, most previously published studies used the ...

Shielding Effect of Lead Glasses on Radiologists' Eye Lens Exposure in Interventional Procedures.

PubMed

Hu, Panpan; Kong, Yan; Chen, Bo; Liu, Qianqian; Zhuo, Weihai; Liu, Haikuan

2017-04-20

To study the shielding effect of radiologists' eye lens with lead glasses of different equivalent thicknesses and sizes in interventional radiology procedures. Using the human voxel phantom with a more accurate model of the eye and MCNPX software, eye lens doses of the radiologists who wearing different kinds of lead glasses were simulated, different beam projections were taken into consideration during the simulation. Measurements were also performed with the physical model to verify simulation results. Simulation results showed that the eye lens doses were reduced by a factor from 3 to 9 when wearing a 20 cm2-sized lead glasses with the equivalent thickness ranging from 0.1 to 1.0 mm Pb. The increase of dose reduction factor (DRF) was not significant whenever increase the lead equivalent of glasses of which larger than 0.35 mm. Furthermore, the DRF was proportional to the size of glass lens from 6 to 30 cm2 with the same lead equivalent. The simulation results were in well agreements with the measured ones. For more reasonable and effective protection of the eye lens of interventional radiologists, a pair of glasses with a lead equivalent of 0.5 mm Pb and large-sized (at least 27 cm2 per glass) lens are recommended. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Determination of elastomeric foam parameters for simulations of complex loading.

PubMed

Petre, M T; Erdemir, A; Cavanagh, P R

2006-08-01

Finite element (FE) analysis has shown promise for the evaluation of elastomeric foam personal protection devices. Although appropriate representation of foam materials is necessary in order to obtain realistic simulation results, material definitions used in the literature vary widely and often fail to account for the multi-mode loading experienced by these devices. This study aims to provide a library of elastomeric foam material parameters that can be used in FE simulations of complex loading scenarios. Twelve foam materials used in footwear were tested in uni-axial compression, simple shear and volumetric compression. For each material, parameters for a common compressible hyperelastic material model used in FE analysis were determined using: (a) compression; (b) compression and shear data; and (c) data from all three tests. Material parameters and Drucker stability limits for the best fits are provided with their associated errors. The material model was able to reproduce deformation modes for which data was provided during parameter determination but was unable to predict behavior in other deformation modes. Simulation results were found to be highly dependent on the extent of the test data used to determine the parameters in the material definition. This finding calls into question the many published results of simulations of complex loading that use foam material parameters obtained from a single mode of testing. The library of foam parameters developed here presents associated errors in three deformation modes that should provide for a more informed selection of material parameters.

Simulation of regimes of convection and plume dynamics by the thermal Lattice Boltzmann Method

NASA Astrophysics Data System (ADS)

Mora, Peter; Yuen, David A.

2018-02-01

We present 2D simulations using the Lattice Boltzmann Method (LBM) of a fluid in a rectangular box being heated from below, and cooled from above. We observe plumes, hot narrow upwellings from the base, and down-going cold chutes from the top. We have varied both the Rayleigh numbers and the Prandtl numbers respectively from Ra = 1000 to Ra =1010 , and Pr = 1 through Pr = 5 ×104 , leading to Rayleigh-Bénard convection cells at low Rayleigh numbers through to vigorous convection and unstable plumes with pronounced vortices and eddies at high Rayleigh numbers. We conduct simulations with high Prandtl numbers up to Pr = 50, 000 to simulate in the inertial regime. We find for cases when Pr ⩾ 100 that we obtain a series of narrow plumes of upwelling fluid with mushroom heads and chutes of downwelling fluid. We also present simulations at a Prandtl number of 0.7 for Rayleigh numbers varying from Ra =104 through Ra =107.5 . We demonstrate that the Nusselt number follows power law scaling of form Nu ∼Raγ where γ = 0.279 ± 0.002 , which is consistent with published results of γ = 0.281 in the literature. These results show that the LBM is capable of reproducing results obtained with classical macroscopic methods such as spectral methods, and demonstrate the great potential of the LBM for studying thermal convection and plume dynamics relevant to geodynamics.

Efforts to integrate CMIP metadata and standards into NOAA-GFDL's climate model workflow

NASA Astrophysics Data System (ADS)

Blanton, C.; Lee, M.; Mason, E. E.; Radhakrishnan, A.

2017-12-01

Modeling centers participating in CMIP6 run model simulations, publish requested model output (conforming to community data standards), and document models and simulations using ES-DOC. GFDL developed workflow software implementing some best practices to meet these metadata and documentation requirements. The CMIP6 Data Request defines the variables that should be archived for each experiment and specifies their spatial and temporal structure. We used the Data Request's dreqPy python library to write GFDL model configuration files as an alternative to hand-crafted tables. There was also a largely successful effort to standardize variable names within the model to reduce the additional overhead of translating "GFDL to CMOR" variables at a later stage in the pipeline. The ES-DOC ecosystem provides tools and standards to create, publish, and view various types of community-defined CIM documents, most notably model and simulation documents. Although ES-DOC will automatically create simulation documents during publishing by harvesting NetCDF global attributes, the information must be collected, stored, and placed in the NetCDF files by the workflow. We propose to develop a GUI to collect the simulation document precursors. In addition, a new MIP for CMIP6-CPMIP, a comparison of computational performance of climate models-is documented using machine and performance CIM documents. We used ES-DOC's pyesdoc python library to automatically create these machine and performance documents. We hope that these and similar efforts will become permanent features of the GFDL workflow to facilitate future participation in CMIP-like activities.

Urn models for response-adaptive randomized designs: a simulation study based on a non-adaptive randomized trial.

PubMed

Ghiglietti, Andrea; Scarale, Maria Giovanna; Miceli, Rosalba; Ieva, Francesca; Mariani, Luigi; Gavazzi, Cecilia; Paganoni, Anna Maria; Edefonti, Valeria

2018-03-22

Recently, response-adaptive designs have been proposed in randomized clinical trials to achieve ethical and/or cost advantages by using sequential accrual information collected during the trial to dynamically update the probabilities of treatment assignments. In this context, urn models-where the probability to assign patients to treatments is interpreted as the proportion of balls of different colors available in a virtual urn-have been used as response-adaptive randomization rules. We propose the use of Randomly Reinforced Urn (RRU) models in a simulation study based on a published randomized clinical trial on the efficacy of home enteral nutrition in cancer patients after major gastrointestinal surgery. We compare results with the RRU design with those previously published with the non-adaptive approach. We also provide a code written with the R software to implement the RRU design in practice. In detail, we simulate 10,000 trials based on the RRU model in three set-ups of different total sample sizes. We report information on the number of patients allocated to the inferior treatment and on the empirical power of the t-test for the treatment coefficient in the ANOVA model. We carry out a sensitivity analysis to assess the effect of different urn compositions. For each sample size, in approximately 75% of the simulation runs, the number of patients allocated to the inferior treatment by the RRU design is lower, as compared to the non-adaptive design. The empirical power of the t-test for the treatment effect is similar in the two designs.

Percolation connectivity, pore size, and gas apparent permeability: Network simulations and comparison to experimental data

NASA Astrophysics Data System (ADS)

Li, M.; Tang, Y. B.; Bernabé, Y.; Zhao, J. Z.; Li, X. F.; Li, T.

2017-07-01

We modeled single-phase gas flow through porous media using percolation networks. Gas permeability is different from liquid permeability. The latter is only related to the geometry and topology of the pore space, while the former depends on the specific gas considered and varies with gas pressure. As gas pressure decreases, four flow regimes can be distinguished as viscous flow, slip flow, transition flow, and free molecular diffusion. Here we use a published conductance model presumably capable of predicting the flow rate of an arbitrary gas through a cylindrical pipe in the four regimes. We incorporated this model into pipe network simulations. We considered 3-D simple cubic, body-centered cubic, and face-centered cubic lattices, in which we varied the pipe radius distribution and the bond coordination number. Gas flow was simulated at different gas pressures. The simulation results showed that the gas apparent permeability kapp obeys an identical scaling law in all three lattices, kapp (z-zc)β, where the exponent β depends on the width of the pipe radius distribution, z is the mean coordination number, and zc its critical value at the percolation threshold. Surprisingly, (z-zc) had a very weak effect on the ratio of the apparent gas permeability to the absolute liquid permeability, kapp/kabs, suggesting that the Klinkenberg gas slippage correction factor is nearly independent of connectivity. We constructed models of kapp and kapp/kabs based on the observed power law and tested them by comparison with published experimental data on glass beads and other materials.

Promoting A-Priori Interoperability of HLA-Based Simulations in the Space Domain: The SISO Space Reference FOM Initiative

NASA Technical Reports Server (NTRS)

Moller, Bjorn; Garro, Alfredo; Falcone, Alberto; Crues, Edwin Z.; Dexter, Daniel E.

2016-01-01

Distributed and Real-Time Simulation plays a key-role in the Space domain being exploited for missions and systems analysis and engineering as well as for crew training and operational support. One of the most popular standards is the 1516-2010 IEEE Standard for Modeling and Simulation (M&S) High Level Architecture (HLA). HLA supports the implementation of distributed simulations (called Federations) in which a set of simulation entities (called Federates) can interact using a Run-Time Infrastructure (RTI). In a given Federation, a Federate can publish and/or subscribes objects and interactions on the RTI only in accordance with their structures as defined in a FOM (Federation Object Model). Currently, the Space domain is characterized by a set of incompatible FOMs that, although meet the specific needs of different organizations and projects, increases the long-term cost for interoperability. In this context, the availability of a reference FOM for the Space domain will enable the development of interoperable HLA-based simulators for related joint projects and collaborations among worldwide organizations involved in the Space domain (e.g. NASA, ESA, Roscosmos, and JAXA). The paper presents a first set of results achieved by a SISO standardization effort that aims at providing a Space Reference FOM for international collaboration on Space systems simulations.

A DVE Time Management Simulation and Verification Platform Based on Causality Consistency Middleware

NASA Astrophysics Data System (ADS)

Zhou, Hangjun; Zhang, Wei; Peng, Yuxing; Li, Sikun

During the course of designing a time management algorithm for DVEs, the researchers always become inefficiency for the distraction from the realization of the trivial and fundamental details of simulation and verification. Therefore, a platform having realized theses details is desirable. However, this has not been achieved in any published work to our knowledge. In this paper, we are the first to design and realize a DVE time management simulation and verification platform providing exactly the same interfaces as those defined by the HLA Interface Specification. Moreover, our platform is based on a new designed causality consistency middleware and might offer the comparison of three kinds of time management services: CO, RO and TSO. The experimental results show that the implementation of the platform only costs small overhead, and that the efficient performance of it is highly effective for the researchers to merely focus on the improvement of designing algorithms.

SpineCreator: a Graphical User Interface for the Creation of Layered Neural Models.

PubMed

Cope, A J; Richmond, P; James, S S; Gurney, K; Allerton, D J

2017-01-01

There is a growing requirement in computational neuroscience for tools that permit collaborative model building, model sharing, combining existing models into a larger system (multi-scale model integration), and are able to simulate models using a variety of simulation engines and hardware platforms. Layered XML model specification formats solve many of these problems, however they are difficult to write and visualise without tools. Here we describe a new graphical software tool, SpineCreator, which facilitates the creation and visualisation of layered models of point spiking neurons or rate coded neurons without requiring the need for programming. We demonstrate the tool through the reproduction and visualisation of published models and show simulation results using code generation interfaced directly into SpineCreator. As a unique application for the graphical creation of neural networks, SpineCreator represents an important step forward for neuronal modelling.

Teaching Process Simulation in Eleven Easy Lessons Using Excel and Its Tools

NASA Astrophysics Data System (ADS)

Morris, Arthur E.

The primary market driver for improving process technology is innovation, which requires a skilled and educated workforce. However, many Materials Science and Engineering departments have eliminated extractive metallurgy and chemical thermodynamics from their curricula, yet these topics contain the necessary fundamentals for process innovation. As a result, most MS&E students are ill-prepared for careers in processing. The dearth of process-oriented MS&E curricula has prompted some Universities to develop a "shared" effort to offer distance education between multiple institutions [1]. A target audience for a shared process simulation course would not only benefit students, but also be a basis for an on-line course for practicing engineers faced with new or changing career choices. To fill the gap, the basics of a process simulation course was developed in an abbreviated form as series of eleven articles and Excel workbooks published in Industrial Heating magazine between July 2012 and July 2013.

Effect of Simulation on Undergraduate Nursing Students' Knowledge of Nursing Ethics Principles.

PubMed

Donnelly, Mary Broderick; Horsley, Trisha Leann; Adams, William H; Gallagher, Peggy; Zibricky, C Dawn

2017-12-01

Background Undergraduate nursing education standards include acquisition of knowledge of ethics principles and the prevalence of health-care ethical dilemmas mandates that nursing students study ethics. However, little research has been published to support best practices for teaching/learning ethics principles. Purpose This study sought to determine if participation in an ethics consultation simulation increased nursing students' knowledge of nursing ethics principles compared to students who were taught ethics principles in the traditional didactic format. Methods This quasi-experimental study utilized a pre-test/post-test design with randomized assignment of students at three universities into both control and experimental groups. Results Nursing students' knowledge of nursing ethics principles significantly improved from pre-test to post-test ( p = .002); however, there was no significant difference between the experimental and control groups knowledge scores ( p = .13). Conclusion Further research into use of simulation to teach ethics principles is indicated.

Prediction of drug-packaging interactions via molecular dynamics (MD) simulations.

PubMed

Feenstra, Peter; Brunsteiner, Michael; Khinast, Johannes

2012-07-15

The interaction between packaging materials and drug products is an important issue for the pharmaceutical industry, since during manufacturing, processing and storage a drug product is continuously exposed to various packaging materials. The experimental investigation of a great variety of different packaging material-drug product combinations in terms of efficacy and safety can be a costly and time-consuming task. In our work we used molecular dynamics (MD) simulations in order to evaluate the applicability of such methods to pre-screening of the packaging material-solute compatibility. The solvation free energy and the free energy of adsorption of diverse solute/solvent/solid systems were estimated. The results of our simulations agree with experimental values previously published in the literature, which indicates that the methods in question can be used to semi-quantitatively reproduce the solid-liquid interactions of the investigated systems. Copyright © 2012 Elsevier B.V. All rights reserved.

High-fidelity simulations of unsteady civil aircraft aerodynamics: stakes and perspectives. Application of zonal detached eddy simulation.

PubMed

Deck, Sébastien; Gand, Fabien; Brunet, Vincent; Ben Khelil, Saloua

2014-08-13

This paper provides an up-to-date survey of the use of zonal detached eddy simulations (ZDES) for unsteady civil aircraft applications as a reflection on the stakes and perspectives of the use of hybrid methods in the framework of industrial aerodynamics. The issue of zonal or non-zonal treatment of turbulent flows for engineering applications is discussed. The ZDES method used in this article and based on a fluid problem-dependent zonalization is briefly presented. Some recent landmark achievements for conditions all over the flight envelope are presented, including low-speed (aeroacoustics of high-lift devices and landing gear), cruising (engine-airframe interactions), propulsive jets and off-design (transonic buffet and dive manoeuvres) applications. The implications of such results and remaining challenges in a more global framework are further discussed. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Comprehensive pulsed electric field (PEF) system analysis for microalgae processing.

PubMed

Buchmann, Leandro; Bloch, Robin; Mathys, Alexander

2018-06-07

Pulsed electric field (PEF) is an emerging nonthermal technique with promising applications in microalgae biorefinery concepts. In this work, the flow field in continuous PEF processing and its influencing factors were analyzed and energy input distributions in PEF treatment chambers were investigated. The results were obtained using an interdisciplinary approach that combined multiphysics simulations with ultrasonic Doppler velocity profiling (UVP) and rheological measurements of Arthrospira platensis suspensions as a case study for applications in the biobased industry. UVP enabled non-invasive validation of multiphysics simulations. A. platensis suspensions follow a non-Newtonian, shear-thinning behavior, and measurement data could be fitted with rheological functions, which were used as an input for fluid dynamics simulations. Within the present work, a comprehensive system characterization was achieved that will facilitate research in the field of PEF processing. Copyright © 2018 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Multiphysics Simulation of Welding-Arc and Nozzle-Arc System: Mathematical-Model, Solution-Methodology and Validation

NASA Astrophysics Data System (ADS)

Pawar, Sumedh; Sharma, Atul

2018-01-01

This work presents mathematical model and solution methodology for a multiphysics engineering problem on arc formation during welding and inside a nozzle. A general-purpose commercial CFD solver ANSYS FLUENT 13.0.0 is used in this work. Arc formation involves strongly coupled gas dynamics and electro-dynamics, simulated by solution of coupled Navier-Stoke equations, Maxwell's equations and radiation heat-transfer equation. Validation of the present numerical methodology is demonstrated with an excellent agreement with the published results. The developed mathematical model and the user defined functions (UDFs) are independent of the geometry and are applicable to any system that involves arc-formation, in 2D axisymmetric coordinates system. The high-pressure flow of SF6 gas in the nozzle-arc system resembles arc chamber of SF6 gas circuit breaker; thus, this methodology can be extended to simulate arcing phenomenon during current interruption.

Genomic prediction in animals and plants: simulation of data, validation, reporting, and benchmarking.

PubMed

Daetwyler, Hans D; Calus, Mario P L; Pong-Wong, Ricardo; de Los Campos, Gustavo; Hickey, John M

2013-02-01

The genomic prediction of phenotypes and breeding values in animals and plants has developed rapidly into its own research field. Results of genomic prediction studies are often difficult to compare because data simulation varies, real or simulated data are not fully described, and not all relevant results are reported. In addition, some new methods have been compared only in limited genetic architectures, leading to potentially misleading conclusions. In this article we review simulation procedures, discuss validation and reporting of results, and apply benchmark procedures for a variety of genomic prediction methods in simulated and real example data. Plant and animal breeding programs are being transformed by the use of genomic data, which are becoming widely available and cost-effective to predict genetic merit. A large number of genomic prediction studies have been published using both simulated and real data. The relative novelty of this area of research has made the development of scientific conventions difficult with regard to description of the real data, simulation of genomes, validation and reporting of results, and forward in time methods. In this review article we discuss the generation of simulated genotype and phenotype data, using approaches such as the coalescent and forward in time simulation. We outline ways to validate simulated data and genomic prediction results, including cross-validation. The accuracy and bias of genomic prediction are highlighted as performance indicators that should be reported. We suggest that a measure of relatedness between the reference and validation individuals be reported, as its impact on the accuracy of genomic prediction is substantial. A large number of methods were compared in example simulated and real (pine and wheat) data sets, all of which are publicly available. In our limited simulations, most methods performed similarly in traits with a large number of quantitative trait loci (QTL), whereas in traits with fewer QTL variable selection did have some advantages. In the real data sets examined here all methods had very similar accuracies. We conclude that no single method can serve as a benchmark for genomic prediction. We recommend comparing accuracy and bias of new methods to results from genomic best linear prediction and a variable selection approach (e.g., BayesB), because, together, these methods are appropriate for a range of genetic architectures. An accompanying article in this issue provides a comprehensive review of genomic prediction methods and discusses a selection of topics related to application of genomic prediction in plants and animals.

Genomic Prediction in Animals and Plants: Simulation of Data, Validation, Reporting, and Benchmarking

PubMed Central

Daetwyler, Hans D.; Calus, Mario P. L.; Pong-Wong, Ricardo; de los Campos, Gustavo; Hickey, John M.

2013-01-01

The genomic prediction of phenotypes and breeding values in animals and plants has developed rapidly into its own research field. Results of genomic prediction studies are often difficult to compare because data simulation varies, real or simulated data are not fully described, and not all relevant results are reported. In addition, some new methods have been compared only in limited genetic architectures, leading to potentially misleading conclusions. In this article we review simulation procedures, discuss validation and reporting of results, and apply benchmark procedures for a variety of genomic prediction methods in simulated and real example data. Plant and animal breeding programs are being transformed by the use of genomic data, which are becoming widely available and cost-effective to predict genetic merit. A large number of genomic prediction studies have been published using both simulated and real data. The relative novelty of this area of research has made the development of scientific conventions difficult with regard to description of the real data, simulation of genomes, validation and reporting of results, and forward in time methods. In this review article we discuss the generation of simulated genotype and phenotype data, using approaches such as the coalescent and forward in time simulation. We outline ways to validate simulated data and genomic prediction results, including cross-validation. The accuracy and bias of genomic prediction are highlighted as performance indicators that should be reported. We suggest that a measure of relatedness between the reference and validation individuals be reported, as its impact on the accuracy of genomic prediction is substantial. A large number of methods were compared in example simulated and real (pine and wheat) data sets, all of which are publicly available. In our limited simulations, most methods performed similarly in traits with a large number of quantitative trait loci (QTL), whereas in traits with fewer QTL variable selection did have some advantages. In the real data sets examined here all methods had very similar accuracies. We conclude that no single method can serve as a benchmark for genomic prediction. We recommend comparing accuracy and bias of new methods to results from genomic best linear prediction and a variable selection approach (e.g., BayesB), because, together, these methods are appropriate for a range of genetic architectures. An accompanying article in this issue provides a comprehensive review of genomic prediction methods and discusses a selection of topics related to application of genomic prediction in plants and animals. PMID:23222650

Thermoluminescent chip detector for in vivo dosimetry in pelvis and head & neck cancer treatment.

PubMed

Leal, Marcela A; Viegas, Claudio; Viamonte, Alfredo; Campos, Anna; Braz, Delson; Clivland, Paul

2010-01-01

Our aim is to show the TL dosimetry as a confident QA method for radiotherapy treatments. Before in vivo entrance dose measurements using TLD-100 chips, ECLIPSE TPS-simulated treatments for a Rando anthropomorphic phantom, two for pelvis and one head & neck. In Vivo measurements results with (60)Co beam remained within +/-5% limits. Results for 6 and 15 MV are in conclusion. This is a National Cancer Institute/RJ/Brazil study under the 13.111-IAEA Coordinated Research Project. Copyright 2010. Published by Elsevier Ltd.

Spin Resonances for Stored Deuteron Beams in COSY. Vector Polarization. Tracking with Spink

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

Luccio,A.; Lehrach, A.

2008-04-01

Results of measurements of vector and tensor polarization of a deuteron beam in the storage ring COSY have been published by the SPIN{at}COSY collaboration. In this experiment a RF Dipole was used that produced spin flip. The strength of the RFD-induced depolarizing resonance was calculated from the amount of spin flipping and the results shown in the figures of the cited paper. In this note we present the simulation of the experimental data (vector polarization) with the spin tracking code Spink.

WE-H-BRA-04: Biological Geometries for the Monte Carlo Simulation Toolkit TOPASNBio

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

McNamara, A; Held, K; Paganetti, H

2016-06-15

Purpose: New advances in radiation therapy are most likely to come from the complex interface of physics, chemistry and biology. Computational simulations offer a powerful tool for quantitatively investigating radiation interactions with biological tissue and can thus help bridge the gap between physics and biology. The aim of TOPAS-nBio is to provide a comprehensive tool to generate advanced radiobiology simulations. Methods: TOPAS wraps and extends the Geant4 Monte Carlo (MC) simulation toolkit. TOPAS-nBio is an extension to TOPAS which utilizes the physics processes in Geant4-DNA to model biological damage from very low energy secondary electrons. Specialized cell, organelle and molecularmore » geometries were designed for the toolkit. Results: TOPAS-nBio gives the user the capability of simulating biological geometries, ranging from the micron-scale (e.g. cells and organelles) to complex nano-scale geometries (e.g. DNA and proteins). The user interacts with TOPAS-nBio through easy-to-use input parameter files. For example, in a simple cell simulation the user can specify the cell type and size as well as the type, number and size of included organelles. For more detailed nuclear simulations, the user can specify chromosome territories containing chromatin fiber loops, the later comprised of nucleosomes on a double helix. The chromatin fibers can be arranged in simple rigid geometries or within factual globules, mimicking realistic chromosome territories. TOPAS-nBio also provides users with the capability of reading protein data bank 3D structural files to simulate radiation damage to proteins or nucleic acids e.g. histones or RNA. TOPAS-nBio has been validated by comparing results to other track structure simulation software and published experimental measurements. Conclusion: TOPAS-nBio provides users with a comprehensive MC simulation tool for radiobiological simulations, giving users without advanced programming skills the ability to design and run complex simulations.« less

PUBLISHING SPILL IMPACT MAPS OVER THE WEB

EPA Science Inventory

This paper discusses the implementaiton of a web-based map publishing technology within a USEPA GIS laboratory. A sophisticated spill travel prediction model for the Ohio River has been installed within the GIS laboratory, and is used by personnel from the NRMRL. The spill simul...

A novel electron accelerator for MRI-Linac radiotherapy

PubMed Central

Whelan, Brendan; Gierman, Stephen; Holloway, Lois; Schmerge, John; Keall, Paul; Fahrig, Rebecca

2016-01-01

Purpose: MRI guided radiotherapy is a rapidly growing field; however, current electron accelerators are not designed to operate in the magnetic fringe fields of MRI scanners. As such, current MRI-Linac systems require magnetic shielding, which can degrade MR image quality and limit system flexibility. The purpose of this work was to develop and test a novel medical electron accelerator concept which is inherently robust to operation within magnetic fields for in-line MRI-Linac systems. Methods: Computational simulations were utilized to model the accelerator, including the thermionic emission process, the electromagnetic fields within the accelerating structure, and resulting particle trajectories through these fields. The spatial and energy characteristics of the electron beam were quantified at the accelerator target and compared to published data for conventional accelerators. The model was then coupled to the fields from a simulated 1 T superconducting magnet and solved for cathode to isocenter distances between 1.0 and 2.4 m; the impact on the electron beam was quantified. Results: For the zero field solution, the average current at the target was 146.3 mA, with a median energy of 5.8 MeV (interquartile spread of 0.1 MeV), and a spot size diameter of 1.5 mm full-width-tenth-maximum. Such an electron beam is suitable for therapy, comparing favorably to published data for conventional systems. The simulated accelerator showed increased robustness to operation in in-line magnetic fields, with a maximum current loss of 3% compared to 85% for a conventional system in the same magnetic fields. Conclusions: Computational simulations suggest that replacing conventional DC electron sources with a RF based source could be used to develop medical electron accelerators which are robust to operation in in-line magnetic fields. This would enable the development of MRI-Linac systems with no magnetic shielding around the Linac and reduce the requirements for optimization of magnetic fringe field, simplify design of the high-field magnet, and increase system flexibility. PMID:26936713

Estimating freshwater turtle mortality rates and population declines following hook ingestion.

PubMed

Steen, David A; Robinson, Orin J

2017-12-01

Freshwater turtle populations are susceptible to declines following small increases in the mortality of adults, making it essential to identify and understand potential threats. Freshwater turtles ingest fish hooks associated with recreational angling, and this is likely a problem because hook ingestion is a source of additive mortality for sea turtles. We used a Bayesian-modeling framework, observed rates of hook ingestion by freshwater turtles, and mortality of sea turtles from hook ingestion to examine the probability that a freshwater turtle in a given population ingests a hook and subsequently dies from it. We used the results of these analyses and previously published life-history data to simulate the effects of hook ingestion on population growth for 3 species of freshwater turtle. In our simulation, the probability that an individual turtle ingests a hook and dies as a result was 1.2-11%. Our simulation results suggest that this rate of mortality from hook ingestion is sufficient to cause population declines. We believe we have identified fish-hook ingestion as a serious yet generally overlooked threat to the viability of freshwater turtle populations. © 2017 Society for Conservation Biology.

Validation of columnar CsI x-ray detector responses obtained with hybridMANTIS, a CPU-GPU Monte Carlo code for coupled x-ray, electron, and optical transport

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

Sharma, Diksha; Badano, Aldo

2013-03-15

Purpose: hybridMANTIS is a Monte Carlo package for modeling indirect x-ray imagers using columnar geometry based on a hybrid concept that maximizes the utilization of available CPU and graphics processing unit processors in a workstation. Methods: The authors compare hybridMANTIS x-ray response simulations to previously published MANTIS and experimental data for four cesium iodide scintillator screens. These screens have a variety of reflective and absorptive surfaces with different thicknesses. The authors analyze hybridMANTIS results in terms of modulation transfer function and calculate the root mean square difference and Swank factors from simulated and experimental results. Results: The comparison suggests thatmore » hybridMANTIS better matches the experimental data as compared to MANTIS, especially at high spatial frequencies and for the thicker screens. hybridMANTIS simulations are much faster than MANTIS with speed-ups up to 5260. Conclusions: hybridMANTIS is a useful tool for improved description and optimization of image acquisition stages in medical imaging systems and for modeling the forward problem in iterative reconstruction algorithms.« less

Simulation of 2D Kinetic Effects in Plasmas using the Grid Based Continuum Code LOKI

NASA Astrophysics Data System (ADS)

Banks, Jeffrey; Berger, Richard; Chapman, Tom; Brunner, Stephan

2016-10-01

Kinetic simulation of multi-dimensional plasma waves through direct discretization of the Vlasov equation is a useful tool to study many physical interactions and is particularly attractive for situations where minimal fluctuation levels are desired, for instance, when measuring growth rates of plasma wave instabilities. However, direct discretization of phase space can be computationally expensive, and as a result there are few examples of published results using Vlasov codes in more than a single configuration space dimension. In an effort to fill this gap we have developed the Eulerian-based kinetic code LOKI that evolves the Vlasov-Poisson system in 2+2-dimensional phase space. The code is designed to reduce the cost of phase-space computation by using fully 4th order accurate conservative finite differencing, while retaining excellent parallel scalability that efficiently uses large scale computing resources. In this poster I will discuss the algorithms used in the code as well as some aspects of their parallel implementation using MPI. I will also overview simulation results of basic plasma wave instabilities relevant to laser plasma interaction, which have been obtained using the code.

Current state of virtual reality simulation in robotic surgery training: a review.

PubMed

Bric, Justin D; Lumbard, Derek C; Frelich, Matthew J; Gould, Jon C

2016-06-01

Worldwide, the annual number of robotic surgical procedures continues to increase. Robotic surgical skills are unique from those used in either open or laparoscopic surgery. The acquisition of a basic robotic surgical skill set may be best accomplished in the simulation laboratory. We sought to review the current literature pertaining to the use of virtual reality (VR) simulation in the acquisition of robotic surgical skills on the da Vinci Surgical System. A PubMed search was conducted between December 2014 and January 2015 utilizing the following keywords: virtual reality, robotic surgery, da Vinci, da Vinci skills simulator, SimSurgery Educational Platform, Mimic dV-Trainer, and Robotic Surgery Simulator. Articles were included if they were published between 2007 and 2015, utilized VR simulation for the da Vinci Surgical System, and utilized a commercially available VR platform. The initial search criteria returned 227 published articles. After all inclusion and exclusion criteria were applied, a total of 47 peer-reviewed manuscripts were included in the final review. There are many benefits to utilizing VR simulation for robotic skills acquisition. Four commercially available simulators have been demonstrated to be capable of assessing robotic skill. Three of the four simulators demonstrate the ability of a VR training curriculum to improve basic robotic skills, with proficiency-based training being the most effective training style. The skills obtained on a VR training curriculum are comparable with those obtained on dry laboratory simulation. The future of VR simulation includes utilization in assessment for re-credentialing purposes, advanced procedural-based training, and as a warm-up tool prior to surgery.

DNA strand breaks induced by electrons simulated with Nanodosimetry Monte Carlo Simulation Code: NASIC.

PubMed

Li, Junli; Li, Chunyan; Qiu, Rui; Yan, Congchong; Xie, Wenzhang; Wu, Zhen; Zeng, Zhi; Tung, Chuanjong

2015-09-01

The method of Monte Carlo simulation is a powerful tool to investigate the details of radiation biological damage at the molecular level. In this paper, a Monte Carlo code called NASIC (Nanodosimetry Monte Carlo Simulation Code) was developed. It includes physical module, pre-chemical module, chemical module, geometric module and DNA damage module. The physical module can simulate physical tracks of low-energy electrons in the liquid water event-by-event. More than one set of inelastic cross sections were calculated by applying the dielectric function method of Emfietzoglou's optical-data treatments, with different optical data sets and dispersion models. In the pre-chemical module, the ionised and excited water molecules undergo dissociation processes. In the chemical module, the produced radiolytic chemical species diffuse and react. In the geometric module, an atomic model of 46 chromatin fibres in a spherical nucleus of human lymphocyte was established. In the DNA damage module, the direct damages induced by the energy depositions of the electrons and the indirect damages induced by the radiolytic chemical species were calculated. The parameters should be adjusted to make the simulation results be agreed with the experimental results. In this paper, the influence study of the inelastic cross sections and vibrational excitation reaction on the parameters and the DNA strand break yields were studied. Further work of NASIC is underway. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Large eddy simulation for predicting turbulent heat transfer in gas turbines.

PubMed

Tafti, Danesh K; He, Long; Nagendra, K

2014-08-13

Blade cooling technology will play a critical role in the next generation of propulsion and power generation gas turbines. Accurate prediction of blade metal temperature can avoid the use of excessive compressed bypass air and allow higher turbine inlet temperature, increasing fuel efficiency and decreasing emissions. Large eddy simulation (LES) has been established to predict heat transfer coefficients with good accuracy under various non-canonical flows, but is still limited to relatively simple geometries and low Reynolds numbers. It is envisioned that the projected increase in computational power combined with a drop in price-to-performance ratio will make system-level simulations using LES in complex blade geometries at engine conditions accessible to the design process in the coming one to two decades. In making this possible, two key challenges are addressed in this paper: working with complex intricate blade geometries and simulating high-Reynolds-number (Re) flows. It is proposed to use the immersed boundary method (IBM) combined with LES wall functions. A ribbed duct at Re=20 000 is simulated using the IBM, and a two-pass ribbed duct is simulated at Re=100 000 with and without rotation (rotation number Ro=0.2) using LES with wall functions. The results validate that the IBM is a viable alternative to body-conforming grids and that LES with wall functions reproduces experimental results at a much lower computational cost. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Simulation based teaching in interventional radiology training: is it effective?

PubMed

Patel, R; Dennick, R

2017-03-01

To establish the educational effectiveness of simulation teaching in interventional radiology training. Electronic databases (MEDLINE, ERIC, Embase, OvidSP, and Cochrane Library) were searched (January 2000 to May 2015). Studies specifically with educational outcomes conducted on radiologists were eligible. All forms of simulation in interventional training were included. Data were extracted based on the population, intervention, comparison, and outcome (PICO) model. Kirkpatrick's hierarchy was used to establish educational intervention effectiveness. The quality of studies was assessed using the Cochrane risk of bias tool. Search resulted in 377 articles, of which 15 met the inclusion criteria. Thirteen of the 15 studies achieved level 2 of Kirkpatrick's hierarchy with only one reaching level 4. Statistically significant improvements in performance metrics as objective measures, demonstrating trainee competence were seen in 12/15 studies. Subjective improvements in confidence were noted in 13/15. Only one study demonstrated skills transferability and improvements in patient outcomes. Results demonstrate the relevance of simulated training to current education models in improving trainee competence; however, this is limited to the simulated environment as there is a lack of literature investigating its predictive validity and the effect on patient outcomes. The requirement for further research in this field is highlighted. Simulation is thus currently only deemed useful as an adjunct to current training models with the potential to play an influential role in the future of the interventional radiology training curriculum. Copyright © 2016. Published by Elsevier Ltd.

Dynamic optimization of walker-assisted FES-activated paraplegic walking: simulation and experimental studies.

PubMed

Nekoukar, Vahab; Erfanian, Abbas

2013-11-01

In this paper, we propose a musculoskeletal model of walker-assisted FES-activated paraplegic walking for the generation of muscle stimulation patterns and characterization of the causal relationships between muscle excitations, multi-joint movement, and handle reaction force (HRF). The model consists of the lower extremities, trunk, hands, and a walker. The simulation of walking is performed using particle swarm optimization to minimize the tracking errors from the desired trajectories for the lower extremity joints, to reduce the stimulations of the muscle groups acting around the hip, knee, and ankle joints, and to minimize the HRF. The results of the simulation studies using data recorded from healthy subjects performing walker-assisted walking indicate that the model-generated muscle stimulation patterns are in agreement with the EMG patterns that have been reported in the literature. The experimental results on two paraplegic subjects demonstrate that the proposed methodology can improve walking performance, reduce HRF, and increase walking speed when compared to the conventional FES-activated paraplegic walking. Copyright © 2013 IPEM. Published by Elsevier Ltd. All rights reserved.

Development and validation of rear impact computer simulation model of an adult manual transit wheelchair with a seated occupant.

PubMed

Salipur, Zdravko; Bertocci, Gina

2010-01-01

It has been shown that ANSI WC19 transit wheelchairs that are crashworthy in frontal impact exhibit catastrophic failures in rear impact and may not be able to provide stable seating support and thus occupant protection for the wheelchair occupant. Thus far only limited sled test and computer simulation data have been available to study rear impact wheelchair safety. Computer modeling can be used as an economic and comprehensive tool to gain critical knowledge regarding wheelchair integrity and occupant safety. This study describes the development and validation of a computer model simulating an adult wheelchair-seated occupant subjected to a rear impact event. The model was developed in MADYMO and validated rigorously using the results of three similar sled tests conducted to specifications provided in the draft ISO/TC 173 standard. Outcomes from the model can provide critical wheelchair loading information to wheelchair and tiedown manufacturers, resulting in safer wheelchair designs for rear impact conditions. (c) 2009 IPEM. Published by Elsevier Ltd. All rights reserved.

Validation of columnar CsI x-ray detector responses obtained with hybridMANTIS, a CPU-GPU Monte Carlo code for coupled x-ray, electron, and optical transport.

PubMed

Sharma, Diksha; Badano, Aldo

2013-03-01

hybridMANTIS is a Monte Carlo package for modeling indirect x-ray imagers using columnar geometry based on a hybrid concept that maximizes the utilization of available CPU and graphics processing unit processors in a workstation. The authors compare hybridMANTIS x-ray response simulations to previously published MANTIS and experimental data for four cesium iodide scintillator screens. These screens have a variety of reflective and absorptive surfaces with different thicknesses. The authors analyze hybridMANTIS results in terms of modulation transfer function and calculate the root mean square difference and Swank factors from simulated and experimental results. The comparison suggests that hybridMANTIS better matches the experimental data as compared to MANTIS, especially at high spatial frequencies and for the thicker screens. hybridMANTIS simulations are much faster than MANTIS with speed-ups up to 5260. hybridMANTIS is a useful tool for improved description and optimization of image acquisition stages in medical imaging systems and for modeling the forward problem in iterative reconstruction algorithms.

Application of multiphase modelling for vortex occurrence in vertical pump intake - a review

NASA Astrophysics Data System (ADS)

Samsudin, M. L.; Munisamy, K. M.; Thangaraju, S. K.

2015-09-01

Vortex formation within pump intake is one of common problems faced for power plant cooling water system. This phenomenon, categorised as surface and sub-surface vortices, can lead to several operational problems and increased maintenance costs. Physical model study was recommended from published guidelines but proved to be time and resource consuming. Hence, the use of Computational Fluid Dynamics (CFD) is an attractive alternative in managing the problem. At the early stage, flow analysis was conducted using single phase simulation and found to find good agreement with the observation from physical model study. With the development of computers, multiphase simulation found further enhancement in obtaining accurate results for representing air entrainment and sub-surface vortices which were earlier not well predicted from the single phase simulation. The purpose of this paper is to describe the application of multiphase modelling with CFD analysis for investigating vortex formation for a vertically inverted pump intake. In applying multiphase modelling, there ought to be a balance between the acceptable usage for computational time and resources and the degree of accuracy and realism in the results as expected from the analysis.

A Modeling Approach for Plastic-Metal Laser Direct Joining

NASA Astrophysics Data System (ADS)

Lutey, Adrian H. A.; Fortunato, Alessandro; Ascari, Alessandro; Romoli, Luca

2017-09-01

Laser processing has been identified as a feasible approach to direct joining of metal and plastic components without the need for adhesives or mechanical fasteners. The present work sees development of a modeling approach for conduction and transmission laser direct joining of these materials based on multi-layer optical propagation theory and numerical heat flow simulation. The scope of this methodology is to predict process outcomes based on the calculated joint interface and upper surface temperatures. Three representative cases are considered for model verification, including conduction joining of PBT and aluminum alloy, transmission joining of optically transparent PET and stainless steel, and transmission joining of semi-transparent PA 66 and stainless steel. Conduction direct laser joining experiments are performed on black PBT and 6082 anticorodal aluminum alloy, achieving shear loads of over 2000 N with specimens of 2 mm thickness and 25 mm width. Comparison with simulation results shows that consistently high strength is achieved where the peak interface temperature is above the plastic degradation temperature. Comparison of transmission joining simulations and published experimental results confirms these findings and highlights the influence of plastic layer optical absorption on process feasibility.

On the mechanisms of secondary flows in a gas vortex unit

PubMed Central

Niyogi, Kaustav; Torregrosa, Maria M.; Marin, Guy B.; Shtern, Vladimir N.

2018-01-01

The hydrodynamics of secondary flow phenomena in a disc‐shaped gas vortex unit (GVU) is investigated using experimentally validated numerical simulations. The simulation using ANSYS FLUENT® v.14a reveals the development of a backflow region along the core of the central gas exhaust, and of a counterflow multivortex region in the bulk of the disc part of the unit. Under the tested conditions, the GVU flow is found to be highly spiraling in nature. Secondary flow phenomena develop as swirl becomes stronger. The backflow region develops first via the swirl‐decay mechanism in the exhaust line. Near‐wall jet formation in the boundary layers near the GVU end‐walls eventually results in flow reversal in the bulk of the unit. When the jets grow stronger the counterflow becomes multivortex. The simulation results are validated with experimental data obtained from Stereoscopic Particle Image Velocimetry and surface oil visualization measurements. © 2018 The Authors AIChE Journal published by Wiley Periodicals, Inc. on behalf of American Institute of Chemical Engineers AIChE J, 64: 1859–1873, 2018 PMID:29937545

Exploration of DGVM Parameter Solution Space Using Simulated Annealing: Implications for Forecast Uncertainties

NASA Astrophysics Data System (ADS)

Wells, J. R.; Kim, J. B.

2011-12-01

Parameters in dynamic global vegetation models (DGVMs) are thought to be weakly constrained and can be a significant source of errors and uncertainties. DGVMs use between 5 and 26 plant functional types (PFTs) to represent the average plant life form in each simulated plot, and each PFT typically has a dozen or more parameters that define the way it uses resource and responds to the simulated growing environment. Sensitivity analysis explores how varying parameters affects the output, but does not do a full exploration of the parameter solution space. The solution space for DGVM parameter values are thought to be complex and non-linear; and multiple sets of acceptable parameters may exist. In published studies, PFT parameters are estimated from published literature, and often a parameter value is estimated from a single published value. Further, the parameters are "tuned" using somewhat arbitrary, "trial-and-error" methods. BIOMAP is a new DGVM created by fusing MAPSS biogeography model with Biome-BGC. It represents the vegetation of North America using 26 PFTs. We are using simulated annealing, a global search method, to systematically and objectively explore the solution space for the BIOMAP PFTs and system parameters important for plant water use. We defined the boundaries of the solution space by obtaining maximum and minimum values from published literature, and where those were not available, using +/-20% of current values. We used stratified random sampling to select a set of grid cells representing the vegetation of the conterminous USA. Simulated annealing algorithm is applied to the parameters for spin-up and a transient run during the historical period 1961-1990. A set of parameter values is considered acceptable if the associated simulation run produces a modern potential vegetation distribution map that is as accurate as one produced by trial-and-error calibration. We expect to confirm that the solution space is non-linear and complex, and that multiple acceptable parameter sets exist. Further we expect to demonstrate that the multiple parameter sets produce significantly divergent future forecasts in NEP, C storage, and ET and runoff; and thereby identify a highly important source of DGVM uncertainty

Developing a Canadian Curriculum for Simulation-Based Education in Obstetrics and Gynaecology: A Delphi Study.

PubMed

Craig, Catherine; Posner, Glenn D

2017-09-01

As obstetrics and gynaecology (Ob/Gyn) residency training programs move towards a competence-based approach to training and assessment, the development of a national standardized simulation curriculum is essential. The primary goal of this study was to define the fundamental content for the Canadian Obstetrics and Gynecology Simulation curriculum. A modified Delphi technique was used to achieve consensus in three rounds by surveying residency program directors or their local simulation educator delegates in 16 accredited Canadian Ob/Gyn residency programs. A consensus rate of 80% was agreed upon. Survey results were collected over 11 months in 2016. Response rates for the Delphi were 50% for the first round, 81% for the second round, and 94% for the third round. The first survey resulted in 84 suggested topics. These were organized into four categories: obstetrics high acuity low frequency events, obstetrics common events, gynaecology high acuity low frequency events, and gynaecology common events. Using the modified Delphi method, consensus was reached on 6 scenarios. This study identified the content for a national simulation-based curriculum for Ob/Gyn residency training programs and is the first step in the development of this curriculum. Copyright © 2017 The Society of Obstetricians and Gynaecologists of Canada/La Société des obstétriciens et gynécologues du Canada. Published by Elsevier Inc. All rights reserved.

Pseudo hard-sphere potential for use in continuous molecular-dynamics simulation of spherical and chain molecules.

PubMed

Jover, J; Haslam, A J; Galindo, A; Jackson, G; Müller, E A

2012-10-14

We present a continuous pseudo-hard-sphere potential based on a cut-and-shifted Mie (generalized Lennard-Jones) potential with exponents (50, 49). Using this potential one can mimic the volumetric, structural, and dynamic properties of the discontinuous hard-sphere potential over the whole fluid range. The continuous pseudo potential has the advantage that it may be incorporated directly into off-the-shelf molecular-dynamics code, allowing the user to capitalise on existing hardware and software advances. Simulation results for the compressibility factor of the fluid and solid phases of our pseudo hard spheres are presented and compared both to the Carnahan-Starling equation of state of the fluid and published data, the differences being indistinguishable within simulation uncertainty. The specific form of the potential is employed to simulate flexible chains formed from these pseudo hard spheres at contact (pearl-necklace model) for m(c) = 4, 5, 7, 8, 16, 20, 100, 201, and 500 monomer segments. The compressibility factor of the chains per unit of monomer, m(c), approaches a limiting value at reasonably small values, m(c) < 50, as predicted by Wertheim's first order thermodynamic perturbation theory. Simulation results are also presented for highly asymmetric mixtures of pseudo hard spheres, with diameter ratios of 3:1, 5:1, 20:1 over the whole composition range.

Why Isn't There More High-fidelity Simulation Training in Diagnostic Radiology? Results of a Survey of Academic Radiologists.

PubMed

Cook, Tessa S; Hernandez, Jessica; Scanlon, Mary; Langlotz, Curtis; Li, Chun-Der L

2016-07-01

Despite its increasing use in training other medical specialties, high-fidelity simulation to prepare diagnostic radiology residents for call remains an underused educational resource. To attempt to characterize the barriers toward adoption of this technology, we conducted a survey of academic radiologists and radiology trainees. An Institutional Review Board-approved survey was distributed to the Association of University Radiologists members via e-mail. Survey results were collected electronically, tabulated, and analyzed. A total of 68 survey responses representing 51 programs were received from program directors, department chairs, chief residents, and program administrators. The most common form of educational activity for resident call preparation was lectures. Faculty supervised "baby call" was also widely reported. Actual simulated call environments were quite rare with only three programs reporting this type of educational activity. Barriers to the use of simulation include lack of faculty time, lack of faculty expertise, and lack of perceived need. High-fidelity simulation can be used to mimic the high-stress, high-stakes independent call environment that the typical radiology resident encounters during the second year of training, and can provide objective data for program directors to assess the Accreditation Council of Graduate Medical Education milestones. We predict that this technology will begin to supplement traditional diagnostic radiology teaching methods and to improve patient care and safety in the next decade. Published by Elsevier Inc.

Effects of Aircraft Wake Dynamics on Measured and Simulated NO(x) and HO(x) Wake Chemistry. Appendix B

NASA Technical Reports Server (NTRS)

Lewellen, D. C.; Lewellen, W. S.

2001-01-01

High-resolution numerical large-eddy simulations of the near wake of a B757 including simplified NOx and HOx chemistry were performed to explore the effects of dynamics on chemistry in wakes of ages from a few seconds to several minutes. Dilution plays an important basic role in the NOx-O3 chemistry in the wake, while a more interesting interaction between the chemistry and dynamics occurs for the HOx species. These simulation results are compared with published measurements of OH and HO2 within a B757 wake under cruise conditions in the upper troposphere taken during the Subsonic Aircraft Contrail and Cloud Effects Special Study (SUCCESS) mission in May 1996. The simulation provides a much finer grained representation of the chemistry and dynamics of the early wake than is possible from the 1 s data samples taken in situ. The comparison suggests that the previously reported discrepancy of up to a factor of 20 - 50 between the SUCCESS measurements of the [HO2]/[OH] ratio and that predicted by simplified theoretical computations is due to the combined effects of large mixing rates around the wake plume edges and averaging over volumes containing large species fluctuations. The results demonstrate the feasibility of using three-dimensional unsteady large-eddy simulations with coupled chemistry to study such phenomena.

Numerical Simulations of Subscale Wind Turbine Rotor Inboard Airfoils at Low Reynolds Number

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

Blaylock, Myra L.; Maniaci, David Charles; Resor, Brian R.

2015-04-01

New blade designs are planned to support future research campaigns at the SWiFT facility in Lubbock, Texas. The sub-scale blades will reproduce specific aerodynamic characteristics of utility-scale rotors. Reynolds numbers for megawatt-, utility-scale rotors are generally above 2-8 million. The thickness of inboard airfoils for these large rotors are typically as high as 35-40%. The thickness and the proximity to three-dimensional flow of these airfoils present design and analysis challenges, even at the full scale. However, more than a decade of experience with the airfoils in numerical simulation, in the wind tunnel, and in the field has generated confidence inmore » their performance. Reynolds number regimes for the sub-scale rotor are significantly lower for the inboard blade, ranging from 0.7 to 1 million. Performance of the thick airfoils in this regime is uncertain because of the lack of wind tunnel data and the inherent challenge associated with numerical simulations. This report documents efforts to determine the most capable analysis tools to support these simulations in an effort to improve understanding of the aerodynamic properties of thick airfoils in this Reynolds number regime. Numerical results from various codes of four airfoils are verified against previously published wind tunnel results where data at those Reynolds numbers are available. Results are then computed for other Reynolds numbers of interest.« less

The LapSim virtual reality simulator: promising but not yet proven.

PubMed

Fairhurst, Katherine; Strickland, Andrew; Maddern, Guy

2011-02-01

The acquisition of technical skills using surgical simulators is an area of active research and rapidly evolving technology. The LapSim is a virtual reality simulator that currently allows practice of basic laparoscopic skills and some procedures. To date, no reviews have been published with reference to a single virtual reality simulator. A PubMed search was performed using the keyword "LapSim," with further papers identified from the citations of original search articles. Use of the LapSim to develop surgical skills has yielded overall results, although inconsistencies exist. Data regarding the transferability of learned skills to the operative environment are encouraging as is the validation work, particularly the use of a combination of measured parameters to produce an overall comparative performance score. Although the LapSim currently does not have any proven significant advantages over video trainers in terms of basic skills instruction and although the results of validation studies are variable, the potential for such technology to have a huge impact on surgical training is apparent. Work to determine standardized learning curves and proficiency criteria for different levels of trainees is incomplete. Moreover, defining which performance parameters measured by the LapSim accurately determine laparoscopic skill is complex. Further technological advances will undoubtedly improve the efficacy of the LapSim, and the results of large multicenter trials are anticipated.

Analysis of Measured and Simulated Supraglottal Acoustic Waves.

PubMed

Fraile, Rubén; Evdokimova, Vera V; Evgrafova, Karina V; Godino-Llorente, Juan I; Skrelin, Pavel A

2016-09-01

To date, although much attention has been paid to the estimation and modeling of the voice source (ie, the glottal airflow volume velocity), the measurement and characterization of the supraglottal pressure wave have been much less studied. Some previous results have unveiled that the supraglottal pressure wave has some spectral resonances similar to those of the voice pressure wave. This makes the supraglottal wave partially intelligible. Although the explanation for such effect seems to be clearly related to the reflected pressure wave traveling upstream along the vocal tract, the influence that nonlinear source-filter interaction has on it is not as clear. This article provides an insight into this issue by comparing the acoustic analyses of measured and simulated supraglottal and voice waves. Simulations have been performed using a high-dimensional discrete vocal fold model. Results of such comparative analysis indicate that spectral resonances in the supraglottal wave are mainly caused by the regressive pressure wave that travels upstream along the vocal tract and not by source-tract interaction. On the contrary and according to simulation results, source-tract interaction has a role in the loss of intelligibility that happens in the supraglottal wave with respect to the voice wave. This loss of intelligibility mainly corresponds to spectral differences for frequencies above 1500 Hz. Copyright © 2016 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

SU-F-T-50: Evaluation of Monte Carlo Simulations Performance for Pediatric Brachytherapy Dosimetry

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

Chatzipapas, C; Kagadis, G; Papadimitroulas, P

Purpose: Pediatric tumors are generally treated with multi-modal procedures. Brachytherapy can be used with pediatric tumors, especially given that in this patient population low toxicity on normal tissues is critical as is the suppression of the probability for late malignancies. Our goal is to validate the GATE toolkit on realistic brachytherapy applications, and evaluate brachytherapy plans on pediatrics for accurate dosimetry on sensitive and critical organs of interest. Methods: The GATE Monte Carlo (MC) toolkit was used. Two High Dose Rate (HDR) 192Ir brachytherapy sources were simulated (Nucletron mHDR-v1 and Varian VS2000), and fully validated using the AAPM and ESTROmore » protocols. A realistic brachytherapy plan was also simulated using the XCAT anthropomorphic computational model .The simulated data were compared to the clinical dose points. Finally, a 14 years old girl with vaginal rhabdomyosarcoma was modelled based on clinical procedures for the calculation of the absorbed dose per organ. Results: The MC simulations resulted in accurate dosimetry in terms of dose rate constant (Λ), radial dose gL(r) and anisotropy function F(r,θ) for both sources.The simulations were executed using ∼1010 number of primaries resulting in statistical uncertainties lower than 2%.The differences between the theoretical values and the simulated ones ranged from 0.01% up to 3.3%, with the largest discrepancy (6%) being observed in the dose rate constant calculation.The simulated DVH using an adult female XCAT model was also compared to a clinical one resulting in differences smaller than 5%. Finally, a realistic pediatric brachytherapy simulation was performed to evaluate the absorbed dose per organ and to calculate DVH with respect to heterogeneities of the human anatomy. Conclusion: GATE is a reliable tool for brachytherapy simulations both for source modeling and for dosimetry in anthropomorphic voxelized models. Our project aims to evaluate a variety of pediatric brachytherapy schemes using a population of pediatric phantoms for several pathological cases. This study is part of a project that has received funding from the European Union Horizon2020 research and innovation programme under the MarieSklodowska-Curiegrantagreement.No691203.The results published in this study reflect only the authors view and the Research Executive Agency (REA) and the European Commission is not responsible for any use that may be madeof the information it contains.« less

Cost-effectiveness of supervised exercise therapy in heart failure patients.

PubMed

Kühr, Eduardo M; Ribeiro, Rodrigo A; Rohde, Luis Eduardo P; Polanczyk, Carisi A

2011-01-01

Exercise therapy in heart failure (HF) patients is considered safe and has demonstrated modest reduction in hospitalization rates and death in recent trials. Previous cost-effectiveness analysis described favorable results considering long-term supervised exercise intervention and significant effectiveness of exercise therapy; however, these evidences are now no longer supported. To evaluate the cost-effectiveness of supervised exercise therapy in HF patients under the perspective of the Brazilian Public Healthcare System. We developed a Markov model to evaluate the incremental cost-effectiveness ratio of supervised exercise therapy compared to standard treatment in patients with New York Heart Association HF class II and III. Effectiveness was evaluated in quality-adjusted life years in a 10-year time horizon. We searched PUBMED for published clinical trials to estimate effectiveness, mortality, hospitalization, and utilities data. Treatment costs were obtained from published cohort updated to 2008 values. Exercise therapy intervention costs were obtained from a rehabilitation center. Model robustness was assessed through Monte Carlo simulation and sensitivity analysis. Cost were expressed as international dollars, applying the purchasing-power-parity conversion rate. Exercise therapy showed small reduction in hospitalization and mortality at a low cost, an incremental cost-effectiveness ratio of Int$26,462/quality-adjusted life year. Results were more sensitive to exercise therapy costs, standard treatment total costs, exercise therapy effectiveness, and medications costs. Considering a willingness-to-pay of Int$27,500, 55% of the trials fell below this value in the Monte Carlo simulation. In a Brazilian scenario, exercise therapy shows reasonable cost-effectiveness ratio, despite current evidence of limited benefit of this intervention. Copyright © 2011 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

Evaluation of Cloud-resolving and Limited Area Model Intercomparison Simulations using TWP-ICE Observations. Part 1: Deep Convective Updraft Properties

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

Varble, A. C.; Zipser, Edward J.; Fridlind, Ann

2014-12-27

Ten 3D cloud-resolving model (CRM) simulations and four 3D limited area model (LAM) simulations of an intense mesoscale convective system observed on January 23-24, 2006 during the Tropical Warm Pool – International Cloud Experiment (TWP-ICE) are compared with each other and with observed radar reflectivity fields and dual-Doppler retrievals of vertical wind speeds in an attempt to explain published results showing a high bias in simulated convective radar reflectivity aloft. This high bias results from ice water content being large, which is a product of large, strong convective updrafts, although hydrometeor size distribution assumptions modulate the size of this bias.more » Snow reflectivity can exceed 40 dBZ in a two-moment scheme when a constant bulk density of 100 kg m-3 is used. Making snow mass more realistically proportional to area rather than volume should somewhat alleviate this problem. Graupel, unlike snow, produces high biased reflectivity in all simulations. This is associated with large amounts of liquid water above the freezing level in updraft cores. Peak vertical velocities in deep convective updrafts are greater than dual-Doppler retrieved values, especially in the upper troposphere. Freezing of large rainwater contents lofted above the freezing level in simulated updraft cores greatly contributes to these excessive upper tropospheric vertical velocities. Strong simulated updraft cores are nearly undiluted, with some showing supercell characteristics. Decreasing horizontal grid spacing from 900 meters to 100 meters weakens strong updrafts, but not enough to match observational retrievals. Therefore, overly intense simulated updrafts may partly be a product of interactions between convective dynamics, parameterized microphysics, and large-scale environmental biases that promote different convective modes and strengths than observed.« less

The effect of modeled recharge distribution on simulated groundwater availability and capture.

PubMed

Tillman, F D; Pool, D R; Leake, S A

2015-01-01

Simulating groundwater flow in basin-fill aquifers of the semiarid southwestern United States commonly requires decisions about how to distribute aquifer recharge. Precipitation can recharge basin-fill aquifers by direct infiltration and transport through faults and fractures in the high-elevation areas, by flowing overland through high-elevation areas to infiltrate at basin-fill margins along mountain fronts, by flowing overland to infiltrate along ephemeral channels that often traverse basins in the area, or by some combination of these processes. The importance of accurately simulating recharge distributions is a current topic of discussion among hydrologists and water managers in the region, but no comparative study has been performed to analyze the effects of different recharge distributions on groundwater simulations. This study investigates the importance of the distribution of aquifer recharge in simulating regional groundwater flow in basin-fill aquifers by calibrating a groundwater-flow model to four different recharge distributions, all with the same total amount of recharge. Similarities are seen in results from steady-state models for optimized hydraulic conductivity values, fit of simulated to observed hydraulic heads, and composite scaled sensitivities of conductivity parameter zones. Transient simulations with hypothetical storage properties and pumping rates produce similar capture rates and storage change results, but differences are noted in the rate of drawdown at some well locations owing to the differences in optimized hydraulic conductivity. Depending on whether the purpose of the groundwater model is to simulate changes in groundwater levels or changes in storage and capture, the distribution of aquifer recharge may or may not be of primary importance. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

Simulating ungulate herbivory across forest landscapes: A browsing extension for LANDIS-II

USGS Publications Warehouse

DeJager, Nathan R.; Drohan, Patrick J.; Miranda, Brian M.; Sturtevant, Brian R.; Stout, Susan L.; Royo, Alejandro; Gustafson, Eric J.; Romanski, Mark C.

2017-01-01

Browsing ungulates alter forest productivity and vegetation succession through selective foraging on species that often dominate early succession. However, the long-term and large-scale effects of browsing on forest succession are not possible to project without the use of simulation models. To explore the effects of ungulates on succession in a spatially explicit manner, we developed a Browse Extension that simulates the effects of browsing ungulates on the growth and survival of plant species cohorts within the LANDIS-II spatially dynamic forest landscape simulation model framework. We demonstrate the capabilities of the new extension and explore the spatial effects of ungulates on forest composition and dynamics using two case studies. The first case study examined the long-term effects of persistently high white-tailed deer browsing rates in the northern hardwood forests of the Allegheny National Forest, USA. In the second case study, we incorporated a dynamic ungulate population model to simulate interactions between the moose population and boreal forest landscape of Isle Royale National Park, USA. In both model applications, browsing reduced total aboveground live biomass and caused shifts in forest composition. Simulations that included effects of browsing resulted in successional patterns that were more similar to those observed in the study regions compared to simulations that did not incorporate browsing effects. Further, model estimates of moose population density and available forage biomass were similar to previously published field estimates at Isle Royale and in other moose-boreal forest systems. Our simulations suggest that neglecting effects of browsing when modeling forest succession in ecosystems known to be influenced by ungulates may result in flawed predictions of aboveground biomass and tree species composition.

Conducting multicenter research in healthcare simulation: Lessons learned from the INSPIRE network.

PubMed

Cheng, Adam; Kessler, David; Mackinnon, Ralph; Chang, Todd P; Nadkarni, Vinay M; Hunt, Elizabeth A; Duval-Arnould, Jordan; Lin, Yiqun; Pusic, Martin; Auerbach, Marc

2017-01-01

Simulation-based research has grown substantially over the past two decades; however, relatively few published simulation studies are multicenter in nature. Multicenter research confers many distinct advantages over single-center studies, including larger sample sizes for more generalizable findings, sharing resources amongst collaborative sites, and promoting networking. Well-executed multicenter studies are more likely to improve provider performance and/or have a positive impact on patient outcomes. In this manuscript, we offer a step-by-step guide to conducting multicenter, simulation-based research based upon our collective experience with the International Network for Simulation-based Pediatric Innovation, Research and Education (INSPIRE). Like multicenter clinical research, simulation-based multicenter research can be divided into four distinct phases. Each phase has specific differences when applied to simulation research: (1) Planning phase , to define the research question, systematically review the literature, identify outcome measures, and conduct pilot studies to ensure feasibility and estimate power; (2) Project Development phase , when the primary investigator identifies collaborators, develops the protocol and research operations manual, prepares grant applications, obtains ethical approval and executes subsite contracts, registers the study in a clinical trial registry, forms a manuscript oversight committee, and conducts feasibility testing and data validation at each site; (3) Study Execution phase , involving recruitment and enrollment of subjects, clear communication and decision-making, quality assurance measures and data abstraction, validation, and analysis; and (4) Dissemination phase , where the research team shares results via conference presentations, publications, traditional media, social media, and implements strategies for translating results to practice. With this manuscript, we provide a guide to conducting quantitative multicenter research with a focus on simulation-specific issues.

Heterogeneous multiscale Monte Carlo simulations for gold nanoparticle radiosensitization.

PubMed

Martinov, Martin P; Thomson, Rowan M

2017-02-01

To introduce the heterogeneous multiscale (HetMS) model for Monte Carlo simulations of gold nanoparticle dose-enhanced radiation therapy (GNPT), a model characterized by its varying levels of detail on different length scales within a single phantom; to apply the HetMS model in two different scenarios relevant for GNPT and to compare computed results with others published. The HetMS model is implemented using an extended version of the EGSnrc user-code egs_chamber; the extended code is tested and verified via comparisons with recently published data from independent GNP simulations. Two distinct scenarios for the HetMS model are then considered: (a) monoenergetic photon beams (20 keV to 1 MeV) incident on a cylinder (1 cm radius, 3 cm length); (b) isotropic point source (brachytherapy source spectra) at the center of a 2.5 cm radius sphere with gold nanoparticles (GNPs) diffusing outwards from the center. Dose enhancement factors (DEFs) are compared for different source energies, depths in phantom, gold concentrations, GNP sizes, and modeling assumptions, as well as with independently published values. Simulation efficiencies are investigated. The HetMS MC simulations account for the competing effects of photon fluence perturbation (due to gold in the scatter media) coupled with enhanced local energy deposition (due to modeling discrete GNPs within subvolumes). DEFs are most sensitive to these effects for the lower source energies, varying with distance from the source; DEFs below unity (i.e., dose decreases, not enhancements) can occur at energies relevant for brachytherapy. For example, in the cylinder scenario, the 20 keV photon source has a DEF of 3.1 near the phantom's surface, decreasing to less than unity by 0.7 cm depth (for 20 mg/g). Compared to discrete modeling of GNPs throughout the gold-containing (treatment) volume, efficiencies are enhanced by up to a factor of 122 with the HetMS approach. For the spherical phantom, DEFs vary with time for diffusion, radionuclide, and radius; DEFs differ considerably from those computed using a widely applied analytic approach. By combining geometric models of varying complexity on different length scales within a single simulation, the HetMS model can effectively account for both macroscopic and microscopic effects which must both be considered for accurate computation of energy deposition and DEFs for GNPT. Efficiency gains with the HetMS approach enable diverse calculations which would otherwise be prohibitively long. The HetMS model may be extended to diverse scenarios relevant for GNPT, providing further avenues for research and development. © 2016 American Association of Physicists in Medicine.

Trends of 'urolithiasis: interventions, simulation, and laser technology' over the last 16 years (2000-2015) as published in the literature (PubMed): a systematic review from European section of Uro-technology (ESUT).

PubMed

Pietropaolo, Amelia; Proietti, Silvia; Geraghty, Rob; Skolarikos, Andreas; Papatsoris, Athanasios; Liatsikos, Evangelos; Somani, Bhaskar K

2017-11-01

To look at the bibliometric publication trends on 'Urolithiasis' and aspects of treatment and training associated with it over a period of 16 years from 2000 to 2015. To this end, we conducted this study to look at the publication trends associated with urolithiasis, including the use of simulation, laser technology, and all types of interventions for it. We performed a systematic review of the literature using PubMed over the last 16 years, from January 2000 to December 2015 for all published papers on 'Urolithiasis'. While there were no language restrictions, English language articles and all non-English language papers with published English abstracts were also included. Case reports, animal and laboratory studies, and those studies that did not have a published abstract were excluded from our analysis. We also analyzed the data in two time periods, period-1 (2000-2007) and period-2 (2008-2015). During the last 16 years, a total of 5343 papers were published on 'Urolithiasis', including 4787 in English language and 556 in non-English language. This included papers on URS (n = 1200), PCNL (n = 1715), SWL (n = 887), open stone surgery (n = 87), laparoscopic stone surgery (n = 209), pyelolithotomy (n = 35), simulation in Endourology (n = 82), and use of laser for stone surgery (n = 406). When comparing the two time periods, during period 2, the change was +171% (p = 0.007), +279% (p < 0.001), and -17% (p = 0.2) for URS, PCNL, and SWL, respectively. While there was a rise in laparoscopic surgery (+116%), it decreased for open stone surgery (-11%) and pyelolithotomy (-47%). A total of 82 papers have been published on simulation for stone surgery including 48 papers for URS (67% rise in period-2, p = 0.007), and 34 papers for PCNL (480% rise in period-2, p < 0.001). A rising trend for the use of laser was also seen in period 2 (increase of 126%, p < 0.02, from 124 papers to 281 papers). Published papers on intervention for Urolithiasis have risen over the last 16 years. While there has been a steep rise of URS and minimally invasive PCNL techniques, SWL and open surgery have shown a slight decline over this period. A similar increase has also been seen for the use of simulation and lasers in Endourology.

Impact of audio-visual storytelling in simulation learning experiences of undergraduate nursing students.

PubMed

Johnston, Sandra; Parker, Christina N; Fox, Amanda

2017-09-01

Use of high fidelity simulation has become increasingly popular in nursing education to the extent that it is now an integral component of most nursing programs. Anecdotal evidence suggests that students have difficulty engaging with simulation manikins due to their unrealistic appearance. Introduction of the manikin as a 'real patient' with the use of an audio-visual narrative may engage students in the simulated learning experience and impact on their learning. A paucity of literature currently exists on the use of audio-visual narratives to enhance simulated learning experiences. This study aimed to determine if viewing an audio-visual narrative during a simulation pre-brief altered undergraduate nursing student perceptions of the learning experience. A quasi-experimental post-test design was utilised. A convenience sample of final year baccalaureate nursing students at a large metropolitan university. Participants completed a modified version of the Student Satisfaction with Simulation Experiences survey. This 12-item questionnaire contained questions relating to the ability to transfer skills learned in simulation to the real clinical world, the realism of the simulation and the overall value of the learning experience. Descriptive statistics were used to summarise demographic information. Two tailed, independent group t-tests were used to determine statistical differences within the categories. Findings indicated that students reported high levels of value, realism and transferability in relation to the viewing of an audio-visual narrative. Statistically significant results (t=2.38, p<0.02) were evident in the subscale of transferability of learning from simulation to clinical practice. The subgroups of age and gender although not significant indicated some interesting results. High satisfaction with simulation was indicated by all students in relation to value and realism. There was a significant finding in relation to transferability on knowledge and this is vital to quality educational outcomes. Copyright © 2017. Published by Elsevier Ltd.

Numerical Simulation of Screech Tones from Supersonic Jets: Physics and Prediction

NASA Technical Reports Server (NTRS)

Tam, Christopher K. W.; Zaman, Khairul Q. (Technical Monitor)

2002-01-01

The objectives of this project are to: (1) perform a numerical simulation of the jet screech phenomenon; and (2) use the data of the simulations to obtain a better understanding of the physics of jet screech. The original grant period was for three years. This was extended at no cost for an extra year to allow the principal investigator time to publish the results. We would like to report that our research work and results (supported by this grant) have fulfilled both objectives of the grant. The following is a summary of the important accomplishments: (1) We have now demonstrated that it is possible to perform accurate numerical simulations of the jet screech phenomenon. Both the axisymmetric case and the fully three-dimensional case were carried out successfully. It is worthwhile to note that this is the first time the screech tone phenomenon has been successfully simulated numerically; (2) All four screech modes were reproduced in the simulation. The computed screech frequencies and intensities were in good agreement with the NASA Langley Research Center data; (3) The staging phenomenon was reproduced in the simulation; (4) The effects of nozzle lip thickness and jet temperature were studied. Simulated tone frequencies at various nozzle lip thickness and jet temperature were found to agree well with experiments; (5) The simulated data were used to explain, for the first time, why there are two axisymmetric screech modes and two helical/flapping screech modes; (6) The simulated data were used to show that when two tones are observed, they co-exist rather than switching from one mode to the other, back and forth, as some previous investigators have suggested; and (7) Some resources of the grant were used to support the development of new computational aeroacoustics (CAA) methodology. (Our screech tone simulations have benefited because of the availability of these improved methods.)

Application of the U.S. Geological Survey's precipitation-runoff modeling system to the Prairie Dog Creek basin, southeastern Montana

USGS Publications Warehouse

Cary, L.E.

1984-01-01

The U.S. Geological Survey 's precipitation-runoff modeling system was tested using 2 year 's data for the daily mode and 17 storms for the storm mode from a basin in southeastern Montana. Two hydrologic response unit delineations were studied. The more complex delineation did not provide superior results. In this application, the optimum numbers of hydrologic response units were 16 and 18 for the two alternatives. The first alternative with 16 units was modified to facilitate interfacing with the storm mode. A parameter subset was defined for the daily mode using sensitivity analysis. Following optimization, the simulated hydrographs approximated the observed hydrograph during the first year, a year of large snowfall. More runoff was simulated than observed during the second year. There was reasonable correspondence between the observed snowpack and the simulated snowpack the first season but poor the second. More soil moisture was withdrawn than was indicated by soil moisture observations. Optimization of parameters in the storm mode resulted in much larger values than originally estimated, commonly larger than published values of the Green and Ampt parameters. Following optimization, variable results were obtained. The results obtained are probably related to inadequate representation of basin infiltration characteristics and to precipitation variability. (USGS)

SU-D-19A-05: The Dosimetric Impact of Using Xoft Axxent® Electronic Brachytherapy Source TG-43 Dosimetry Parameters for Treatment with the Xoft 30 Mm Diameter Vaginal Applicator

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

Simiele, S; Micka, J; Culberson, W

2014-06-01

Purpose: A full TG-43 dosimetric characterization has not been performed for the Xoft Axxent ® electronic brachytherapy source (Xoft, a subsidiary of iCAD, San Jose, CA) within the Xoft 30 mm diameter vaginal applicator. Currently, dose calculations are performed using the bare-source TG-43 parameters and do not account for the presence of the applicator. This work focuses on determining the difference between the bare-source and sourcein- applicator TG-43 parameters. Both the radial dose function (RDF) and polar anisotropy function (PAF) were computationally determined for the source-in-applicator and bare-source models to determine the impact of using the bare-source dosimetry data. Methods:more » MCNP5 was used to model the source and the Xoft 30 mm diameter vaginal applicator. All simulations were performed using 0.84p and 0.03e cross section libraries. All models were developed based on specifications provided by Xoft. The applicator is made of a proprietary polymer material and simulations were performed using the most conservative chemical composition. An F6 collision-kerma tally was used to determine the RDF and PAF values in water at various dwell positions. The RDF values were normalized to 2.0 cm from the source to accommodate the applicator radius. Source-in-applicator results were compared with bare-source results from this work as well as published baresource results. Results: For a 0 mm source pullback distance, the updated bare-source model and source-in-applicator RDF values differ by 2% at 3 cm and 4% at 5 cm. The largest PAF disagreements were observed at the distal end of the source and applicator with up to 17% disagreement at 2 cm and 8% at 8 cm. The bare-source model had RDF values within 2.6% of the published TG-43 data and PAF results within 7.2% at 2 cm. Conclusion: Results indicate that notable differences exist between the bare-source and source-in-applicator TG-43 simulated parameters. Xoft Inc. provided partial funding for this work.« less

Modeling the Cost Effectiveness of Malaria Control Interventions in the Highlands of Western Kenya

PubMed Central

Stuckey, Erin M.; Stevenson, Jennifer; Galactionova, Katya; Baidjoe, Amrish Y.; Bousema, Teun; Odongo, Wycliffe; Kariuki, Simon; Drakeley, Chris; Smith, Thomas A.; Cox, Jonathan; Chitnis, Nakul

2014-01-01

Introduction Tools that allow for in silico optimization of available malaria control strategies can assist the decision-making process for prioritizing interventions. The OpenMalaria stochastic simulation modeling platform can be applied to simulate the impact of interventions singly and in combination as implemented in Rachuonyo South District, western Kenya, to support this goal. Methods Combinations of malaria interventions were simulated using a previously-published, validated model of malaria epidemiology and control in the study area. An economic model of the costs of case management and malaria control interventions in Kenya was applied to simulation results and cost-effectiveness of each intervention combination compared to the corresponding simulated outputs of a scenario without interventions. Uncertainty was evaluated by varying health system and intervention delivery parameters. Results The intervention strategy with the greatest simulated health impact employed long lasting insecticide treated net (LLIN) use by 80% of the population, 90% of households covered by indoor residual spraying (IRS) with deployment starting in April, and intermittent screen and treat (IST) of school children using Artemether lumefantrine (AL) with 80% coverage twice per term. However, the current malaria control strategy in the study area including LLIN use of 56% and IRS coverage of 70% was the most cost effective at reducing disability-adjusted life years (DALYs) over a five year period. Conclusions All the simulated intervention combinations can be considered cost effective in the context of available resources for health in Kenya. Increasing coverage of vector control interventions has a larger simulated impact compared to adding IST to the current implementation strategy, suggesting that transmission in the study area is not at a level to warrant replacing vector control to a school-based screen and treat program. These results have the potential to assist malaria control program managers in the study area in adding new or changing implementation of current interventions. PMID:25290939

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.

PubMed

Bergmann, Frank T; Adams, Richard; Moodie, Stuart; Cooper, Jonathan; Glont, Mihai; Golebiewski, Martin; Hucka, Michael; Laibe, Camille; Miller, Andrew K; Nickerson, David P; Olivier, Brett G; Rodriguez, Nicolas; Sauro, Herbert M; Scharm, Martin; Soiland-Reyes, Stian; Waltemath, Dagmar; Yvon, Florent; Le Novère, Nicolas

2014-12-14

With the ever increasing use of computational models in the biosciences, the need to share models and reproduce the results of published studies efficiently and easily is becoming more important. To this end, various standards have been proposed that can be used to describe models, simulations, data or other essential information in a consistent fashion. These constitute various separate components required to reproduce a given published scientific result. We describe the Open Modeling EXchange format (OMEX). Together with the use of other standard formats from the Computational Modeling in Biology Network (COMBINE), OMEX is the basis of the COMBINE Archive, a single file that supports the exchange of all the information necessary for a modeling and simulation experiment in biology. An OMEX file is a ZIP container that includes a manifest file, listing the content of the archive, an optional metadata file adding information about the archive and its content, and the files describing the model. The content of a COMBINE Archive consists of files encoded in COMBINE standards whenever possible, but may include additional files defined by an Internet Media Type. Several tools that support the COMBINE Archive are available, either as independent libraries or embedded in modeling software. The COMBINE Archive facilitates the reproduction of modeling and simulation experiments in biology by embedding all the relevant information in one file. Having all the information stored and exchanged at once also helps in building activity logs and audit trails. We anticipate that the COMBINE Archive will become a significant help for modellers, as the domain moves to larger, more complex experiments such as multi-scale models of organs, digital organisms, and bioengineering.

Visualization of light propagation in visible Chinese human head for functional near-infrared spectroscopy

NASA Astrophysics Data System (ADS)

Li, Ting; Gong, Hui; Luo, Qingming

2011-04-01

Using the visible Chinese human data set, which faithfully represents human anatomy, we visualize the light propagation in the head in detail based on Monte Carlo simulation. The simulation is verified to agree with published experimental results in terms of a differential path-length factor. The spatial sensitivity profile turns out to seem like a fat tropical fish with strong distortion along the folding cerebral surface. The sensitive brain region covers the gray matter and extends to the superficial white matter, leading to a large penetration depth (>3 cm). Finally, the optimal source-detector separation is suggested to be narrowed down to 3-3.5 cm, while the sensitivity of the detected signal to brain activation reaches the peak of 8%. These results indicate that the cerebral cortex folding geometry actually has substantial effects on light propagation, which should be necessarily considered for applications of functional near-infrared spectroscopy.

GPU-based simulations of fracture in idealized brick and mortar composites

NASA Astrophysics Data System (ADS)

William Pro, J.; Kwei Lim, Rone; Petzold, Linda R.; Utz, Marcel; Begley, Matthew R.

2015-07-01

Stiff ceramic platelets (or bricks) that are aligned and bonded to a second ductile phase with low volume fraction (mortar) are a promising pathway to produce stiff, high-toughness composites. For certain ranges of constituent properties, including those of some synthetic analogs to nacre, one can demonstrate that the deformation is dominated by relative brick motions. This paper describes simulations of fracture that explicitly track the motions of individual rigid bricks in an idealized microstructure; cohesive tractions acting between the bricks introduce elastic, plastic and rupture behaviors. Results are presented for the stresses and damage near macroscopic cracks with different brick orientations relative to the loading orientation. The anisotropic macroscopic initiation toughness is computed for small-scale yielding conditions and is shown to be independent of specimen geometry and loading configuration. The results are shown to be in agreement with previously published experiments on synthetic nacre.

Formation of the Giant Planets by Concurrent Accretion of Solids and Gas

NASA Technical Reports Server (NTRS)

Hubickyj, Olenka

1997-01-01

Models were developed to simulate planet formation. Three major phases are characterized in the simulations: (1) planetesimal accretion rate, which dominates that of gas, rapidly increases owing to runaway accretion, then decreases as the planet's feeding zone is depleted; (2) occurs when both solid and gas accretion rates are small and nearly independent of time; and (3) starts when the solid and gas masses are about equal and is marked by runaway gas accretion. The models applicability to planets in our Solar System are judged using two basic "yardsticks". The results suggest that the solar nebula dissipated while Uranus and Neptune were in the second phase, during which, for a relatively long time, the masses of their gaseous envelopes were small but not negligible compared to the total masses. Background information, results and a published article are included in the report.

Protection of Lactobacillus acidophilus NRRL-B 4495 under in vitro gastrointestinal conditions with whey protein/pullulan microcapsules.

PubMed

Çabuk, Burcu; Tellioğlu Harsa, Şebnem

2015-12-01

In this research, whey protein/pullulan (WP/pullulan) microcapsules were developed in order to assess its protective effect on the viability of Lactobacillus acidophilus NRRL-B 4495 under in vitro gastrointestinal conditions. Results demonstrated that WP/pullulan microencapsulated cells exhibited significantly (p ≤ 0.05) higher resistance to simulated gastric acid and bile salt. Pullulan incorporation into protein wall matrix resulted in improved survival as compared to free cells after 3 h incubation in simulated gastric solution. Moreover WP/pullulan microcapsules were found to release over 70% of encapsulated L. acidophilus NRRL-B 4495 cells within 1 h. The effect of encapsulation during refrigerated storage was also studied. Free bacteria exhibited 3.96 log reduction while, WP/pullulan encapsulated bacteria showed 1.64 log reduction after 4 weeks of storage. Copyright © 2015 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Space Shuttle flying qualities and flight control system assessment study, phase 2

NASA Technical Reports Server (NTRS)

Myers, T. T.; Johnston, D. E.; Mcruer, D. T.

1983-01-01

A program of flying qualities experiments as part of the Orbiter Experiments Program (OEX) is defined. Phase 1, published as CR-170391, reviewed flying qualities criteria and shuttle data. The review of applicable experimental and shuttle data to further define the OEX plan is continued. An unconventional feature of this approach is the use of pilot strategy model identification to relate flight and simulator results. Instrumentation, software, and data analysis techniques for pilot model measurements are examined. The relationship between shuttle characteristics and superaugmented aircraft is established. STS flights 1 through 4 are reviewed from the point of view of flying qualities. A preliminary plan for a coordinated program of inflight and simulator research is presented.

Flow injection analysis simulations and diffusion coefficient determination by stochastic and deterministic optimization methods.

PubMed

Kucza, Witold

2013-07-25

Stochastic and deterministic simulations of dispersion in cylindrical channels on the Poiseuille flow have been presented. The random walk (stochastic) and the uniform dispersion (deterministic) models have been used for computations of flow injection analysis responses. These methods coupled with the genetic algorithm and the Levenberg-Marquardt optimization methods, respectively, have been applied for determination of diffusion coefficients. The diffusion coefficients of fluorescein sodium, potassium hexacyanoferrate and potassium dichromate have been determined by means of the presented methods and FIA responses that are available in literature. The best-fit results agree with each other and with experimental data thus validating both presented approaches. Copyright © 2013 The Author. Published by Elsevier B.V. All rights reserved.

Development of axisymmetric lattice Boltzmann flux solver for complex multiphase flows

NASA Astrophysics Data System (ADS)

Wang, Yan; Shu, Chang; Yang, Li-Ming; Yuan, Hai-Zhuan

2018-05-01

This paper presents an axisymmetric lattice Boltzmann flux solver (LBFS) for simulating axisymmetric multiphase flows. In the solver, the two-dimensional (2D) multiphase LBFS is applied to reconstruct macroscopic fluxes excluding axisymmetric effects. Source terms accounting for axisymmetric effects are introduced directly into the governing equations. As compared to conventional axisymmetric multiphase lattice Boltzmann (LB) method, the present solver has the kinetic feature for flux evaluation and avoids complex derivations of external forcing terms. In addition, the present solver also saves considerable computational efforts in comparison with three-dimensional (3D) computations. The capability of the proposed solver in simulating complex multiphase flows is demonstrated by studying single bubble rising in a circular tube. The obtained results compare well with the published data.

System Design under Uncertainty: Evolutionary Optimization of the Gravity Probe-B Spacecraft

NASA Technical Reports Server (NTRS)

Pullen, Samuel P.; Parkinson, Bradford W.

1994-01-01

This paper discusses the application of evolutionary random-search algorithms (Simulated Annealing and Genetic Algorithms) to the problem of spacecraft design under performance uncertainty. Traditionally, spacecraft performance uncertainty has been measured by reliability. Published algorithms for reliability optimization are seldom used in practice because they oversimplify reality. The algorithm developed here uses random-search optimization to allow us to model the problem more realistically. Monte Carlo simulations are used to evaluate the objective function for each trial design solution. These methods have been applied to the Gravity Probe-B (GP-B) spacecraft being developed at Stanford University for launch in 1999, Results of the algorithm developed here for GP-13 are shown, and their implications for design optimization by evolutionary algorithms are discussed.

Measurement of drug facilitated sexual assault agents in simulated sweat by ion mobility spectrometry.

PubMed

Demoranville, Leonard T; Verkouteren, Jennifer R

2013-03-15

Ion mobility spectrometry has found widespread use for the detection of explosives and illicit drugs. The technique offers rapid results with high sensitivity and little sample preparation. As such, it is well suited for field deployed screening settings. Here the response of ion mobility spectrometers for three drug-facilitated sexual assault (DFSA) agents - flunitrazepam, ketamine, and MDMA - and related metabolites has been studied in the presence of a simulated sweat. While all three DFSA agents present certain challenges for qualitative identification, IMS can provide useful information to guide the early treatment and investigation of sexual assault cases. Used as a presumptive test, the identification of DFSA agents would later require confirmatory analysis by other techniques. Published by Elsevier B.V.

Optimization of the design of Gas Cherenkov Detectors for ICF diagnosis

NASA Astrophysics Data System (ADS)

Liu, Bin; Hu, Huasi; Han, Hetong; Lv, Huanwen; Li, Lan

2018-07-01

A design method, which combines a genetic algorithm (GA) with Monte-Carlo simulation, is established and applied to two different types of Cherenkov detectors, namely, Gas Cherenkov Detector (GCD) and Gamma Reaction History (GRH). For accelerating the optimization program, open Message Passing Interface (MPI) is used in the Geant4 simulation. Compared with the traditional optical ray-tracing method, the performances of these detectors have been improved with the optimization method. The efficiency for GCD system, with a threshold of 6.3 MeV, is enhanced by ∼20% and time response improved by ∼7.2%. For the GRH system, with threshold of 10 MeV, the efficiency is enhanced by ∼76% in comparison with previously published results.

FFT multislice method--the silver anniversary.

PubMed

Ishizuka, Kazuo

2004-02-01

The first paper on the FFT multislice method was published in 1977, a quarter of a century ago. The formula was extended in 1982 to include a large tilt of an incident beam relative to the specimen surface. Since then, with advances of computing power, the FFT multislice method has been successfully applied to coherent CBED and HAADF-STEM simulations. However, because the multislice formula is built on some physical approximations and approximations in numerical procedure, there seem to be controversial conclusions in the literature on the multislice method. In this report, the physical implication of the multislice method is reviewed based on the formula for the tilted illumination. Then, some results on the coherent CBED and the HAADF-STEM simulations are presented.

Simulation of bone-conducted sound transmission in a three-dimensional finite-element model of a human skull

NASA Astrophysics Data System (ADS)

Chang, You; Kim, Namkeun; Stenfelt, Stefan

2015-12-01

Bone conduction (BC) is the transmission of sound to the inner ear through the bones of the skull. This type of transmission is used in humans fitted with BC hearing aids as well as to classify between conductive and sensorineural hearing losses. The objective of the present study is to develop a finite-element (FE) model of the human skull based on cryosectional images of a female cadaver head in order to gain better understanding of the sound transmission. Further, the BC behavior was validated in terms of sound transmission against experimental data published in the literature. Results showed the responses of the simulated skull FE model were consistent with the experimentally reported data.

Anti-windup adaptive PID control design for a class of uncertain chaotic systems with input saturation.

PubMed

Tahoun, A H

2017-01-01

In this paper, the stabilization problem of actuators saturation in uncertain chaotic systems is investigated via an adaptive PID control method. The PID control parameters are auto-tuned adaptively via adaptive control laws. A multi-level augmented error is designed to account for the extra terms appearing due to the use of PID and saturation. The proposed control technique uses both the state-feedback and the output-feedback methodologies. Based on Lyapunov׳s stability theory, new anti-windup adaptive controllers are proposed. Demonstrative examples with MATLAB simulations are studied. The simulation results show the efficiency of the proposed adaptive PID controllers. Copyright © 2016 ISA. Published by Elsevier Ltd. All rights reserved.

An Experimentally Robust Model of Monomeric Apolipoprotein A-I Created from a Chimera of Two X-ray Structures and Molecular Dynamics Simulations

PubMed Central

2015-01-01

High-density lipoprotein (HDL) retards atherosclerosis by accepting cholesterol from the artery wall. However, the structure of the proposed acceptor, monomeric apolipoprotein A-I (apoA-I), the major protein of HDL, is poorly understood. Two published models for monomeric apoA-I used cross-linking distance constraints to derive best fit conformations. This approach has limitations. (i) Cross-linked peptides provide no information about secondary structure. (ii) A protein chain can be folded in multiple ways to create a best fit. (iii) Ad hoc folding of a secondary structure is unlikely to produce a stable orientation of hydrophobic and hydrophilic residues. To address these limitations, we used a different approach. We first noted that the dimeric apoA-I crystal structure, (Δ185–243)apoA-I, is topologically identical to a monomer in which helix 5 forms a helical hairpin, a monomer with a hydrophobic cleft running the length of the molecule. We then realized that a second crystal structure, (Δ1–43)apoA-I, contains a C-terminal structure that fits snuggly via aromatic and hydrophobic interactions into the hydrophobic cleft. Consequently, we combined these crystal structures into an initial model that was subjected to molecular dynamics simulations. We tested the initial and simulated models and the two previously published models in three ways: against two published data sets (domains predicted to be helical by H/D exchange and six spin-coupled residues) and against our own experimentally determined cross-linking distance constraints. We note that the best fit simulation model, superior by all tests to previously published models, has dynamic features of a molten globule with interesting implications for the functions of apoA-I. PMID:25423138

Corrigendum to "Monte Carlo simulations of the secondary neutron ambient and effective dose equivalent rates from surface to suborbital altitudes and low Earth orbit".

PubMed

El-Jaby, Samy

2016-06-01

A recent paper published in Life Sciences in Space Research (El-Jaby and Richardson, 2015) presented estimates of the secondary neutron ambient and effective dose equivalent rates, in air, from surface altitudes up to suborbital altitudes and low Earth orbit. These estimates were based on MCNPX (LANL, 2011) (Monte Carlo N-Particle eXtended) radiation transport simulations of galactic cosmic radiation passing through Earth's atmosphere. During a recent review of the input decks used for these simulations, a systematic error was discovered that is addressed here. After reassessment, the neutron ambient and effective dose equivalent rates estimated are found to be 10 to 15% different, though, the essence of the conclusions drawn remains unchanged. Crown Copyright © 2016. Published by Elsevier Ltd. All rights reserved.

Task-dependent changes of corticospinal excitability during observation and motor imagery of balance tasks.

PubMed

Mouthon, A; Ruffieux, J; Wälchli, M; Keller, M; Taube, W

2015-09-10

Non-physical balance training has demonstrated to be efficient to improve postural control in young people. However, little is known about the potential to increase corticospinal excitability by mental simulation in lower leg muscles. Mental simulation of isolated, voluntary contractions of limb muscles increase corticospinal excitability but more automated tasks like walking seem to have no or only minor effects on motor-evoked potentials (MEPs) evoked by transcranial magnetic stimulation (TMS). This may be related to the way of performing the mental simulation or the task itself. Therefore, the present study aimed to clarify how corticospinal excitability is modulated during AO+MI, MI and action observation (AO) of balance tasks. For this purpose, MEPs and H-reflexes were elicited during three different mental simulations (a) AO+MI, (b) MI and (c) passive AO. For each condition, two balance tasks were evaluated: (1) quiet upright stance (static) and (2) compensating a medio-lateral perturbation while standing on a free-swinging platform (dynamic). AO+MI resulted in the largest facilitation of MEPs followed by MI and passive AO. MEP facilitation was significantly larger in the dynamic perturbation than in the static standing task. Interestingly, passive observation resulted in hardly any facilitation independent of the task. H-reflex amplitudes were not modulated. The current results demonstrate that corticospinal excitability during mental simulation of balance tasks is influenced by both the type of mental simulation and the task difficulty. As H-reflexes and background EMG were not modulated, it may be argued that changes in excitability of the primary motor cortex were responsible for the MEP modulation. From a functional point of view, our findings suggest best training/rehabilitation effects when combining MI with AO during challenging postural tasks. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Dermatopathology effects of simulated solar particle event radiation exposure in the porcine model.

PubMed

Sanzari, Jenine K; Diffenderfer, Eric S; Hagan, Sarah; Billings, Paul C; Gridley, Daila S; Seykora, John T; Kennedy, Ann R; Cengel, Keith A

2015-07-01

The space environment exposes astronauts to risks of acute and chronic exposure to ionizing radiation. Of particular concern is possible exposure to ionizing radiation from a solar particle event (SPE). During an SPE, magnetic disturbances in specific regions of the Sun result in the release of intense bursts of ionizing radiation, primarily consisting of protons that have a highly variable energy spectrum. Thus, SPE events can lead to significant total body radiation exposures to astronauts in space vehicles and especially while performing extravehicular activities. Simulated energy profiles suggest that SPE radiation exposures are likely to be highest in the skin. In the current report, we have used our established miniature pig model system to evaluate the skin toxicity of simulated SPE radiation exposures that closely resemble the energy and fluence profile of the September, 1989 SPE using either conventional radiation (electrons) or proton simulated SPE radiation. Exposure of animals to electron or proton radiation led to dose-dependent increases in epidermal pigmentation, the presence of necrotic keratinocytes at the dermal-epidermal boundary and pigment incontinence, manifested by the presence of melanophages in the derm is upon histological examination. We also observed epidermal hyperplasia and a reduction in vascular density at 30 days following exposure to electron or proton simulated SPE radiation. These results suggest that the doses of electron or proton simulated SPE radiation results in significant skin toxicity that is quantitatively and qualitatively similar. Radiation-induced skin damage is often one of the first clinical signs of both acute and non-acute radiation injury where infection may occur, if not treated. In this report, histopathology analyses of acute radiation-induced skin injury are discussed. Copyright © 2015 The Committee on Space Research (COSPAR). Published by Elsevier Ltd. All rights reserved.

Impact of WRF model PBL schemes on air quality simulations over Catalonia, Spain.

PubMed

Banks, R F; Baldasano, J M

2016-12-01

Here we analyze the impact of four planetary boundary-layer (PBL) parametrization schemes from the Weather Research and Forecasting (WRF) numerical weather prediction model on simulations of meteorological variables and predicted pollutant concentrations from an air quality forecast system (AQFS). The current setup of the Spanish operational AQFS, CALIOPE, is composed of the WRF-ARW V3.5.1 meteorological model tied to the Yonsei University (YSU) PBL scheme, HERMES v2 emissions model, CMAQ V5.0.2 chemical transport model, and dust outputs from BSC-DREAM8bv2. We test the performance of the YSU scheme against the Assymetric Convective Model Version 2 (ACM2), Mellor-Yamada-Janjic (MYJ), and Bougeault-Lacarrère (BouLac) schemes. The one-day diagnostic case study is selected to represent the most frequent synoptic condition in the northeast Iberian Peninsula during spring 2015; regional recirculations. It is shown that the ACM2 PBL scheme performs well with daytime PBL height, as validated against estimates retrieved using a micro-pulse lidar system (mean bias=-0.11km). In turn, the BouLac scheme showed WRF-simulated air and dew point temperature closer to METAR surface meteorological observations. Results are more ambiguous when simulated pollutant concentrations from CMAQ are validated against network urban, suburban, and rural background stations. The ACM2 scheme showed the lowest mean bias (-0.96μgm -3 ) with respect to surface ozone at urban stations, while the YSU scheme performed best with simulated nitrogen dioxide (-6.48μgm -3 ). The poorest results were with simulated particulate matter, with similar results found with all schemes tested. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Cost-effectiveness of omega-3 fatty acid supplements in parenteral nutrition therapy in hospitals: a discrete event simulation model.

PubMed

Pradelli, Lorenzo; Eandi, Mario; Povero, Massimiliano; Mayer, Konstantin; Muscaritoli, Maurizio; Heller, Axel R; Fries-Schaffner, Eva

2014-10-01

A recent meta-analysis showed that supplementation of omega-3 fatty acids in parenteral nutrition (PN) regimens is associated with a statistically and clinically significant reduction in infection rate, and length of hospital stay (LOS) in medical and surgical patients admitted to the ICU and in surgical patients not admitted to the ICU. The objective of this present study was to evaluate the cost-effectiveness of the addition of omega-3 fatty acids to standard PN regimens in four European countries (Italy, France, Germany and the UK) from the healthcare provider perspective. Using a discrete event simulation scheme, a patient-level simulation model was developed, based on outcomes from the Italian ICU patient population and published literature. Comparative efficacy data for PN regimens containing omega-3 fatty acids versus standard PN regimens was taken from the meta-analysis of published randomised clinical trials (n = 23 studies with a total of 1502 patients), and hospital LOS reduction was further processed in order to split the reduction in ICU stay from that in-ward stays for patients admitted to the ICU. Country-specific cost data was obtained for Italian, French, German and UK healthcare systems. Clinical outcomes included in the model were death rates, nosocomial infection rates, and ICU/hospital LOS. Probabilistic and deterministic sensitivity analyses were undertaken to test the reliability of results. PN regimens containing omega-3 fatty acids were more effective on average than standard PN both in ICU and in non-ICU patients in the four countries considered, reducing infection rates and overall LOS, and resulting in a lower total cost per patient. Overall costs for patients receiving PN regimens containing omega-3 fatty acids were between €14 144 to €19 825 per ICU patient and €5484 to €14 232 per non-ICU patient, translating into savings of between €3972 and €4897 per ICU patient and savings of between €561 and €1762 per non-ICU patient. Treatment costs were completely offset by the reduction in hospital stay costs and antibiotic costs. Sensitivity analyses confirmed the robustness of these findings. These results suggest that the supplementation of PN regimens with omega-3 fatty acids would be cost effective in Italian, French, German and UK hospitals. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

A Variable-Instar Climate-Driven Individual Beetle-Based Phenology Model for the Invasive Asian Longhorned Beetle (Coleoptera: Cerambycidae).

PubMed

Trotter, R Talbot; Keena, Melody A

2016-12-01

Efforts to manage and eradicate invasive species can benefit from an improved understanding of the physiology, biology, and behavior of the target species, and ongoing efforts to eradicate the Asian longhorned beetle (Anoplophora glabripennis Motschulsky) highlight the roles this information may play. Here, we present a climate-driven phenology model for A. glabripennis that provides simulated life-tables for populations of individual beetles under variable climatic conditions that takes into account the variable number of instars beetles may undergo as larvae. Phenology parameters in the model are based on a synthesis of published data and studies of A. glabripennis, and the model output was evaluated using a laboratory-reared population maintained under varying temperatures mimicking those typical of Central Park in New York City. The model was stable under variations in population size, simulation length, and the Julian dates used to initiate individual beetles within the population. Comparison of model results with previously published field-based phenology studies in native and invasive populations indicates both this new phenology model, and the previously published heating-degree-day model show good agreement in the prediction of the beginning of the flight season for adults. However, the phenology model described here avoids underpredicting the cumulative emergence of adults through the season, in addition to providing tables of life stages and estimations of voltinism for local populations. This information can play a key role in evaluating risk by predicting the potential for population growth, and may facilitate the optimization of management and eradication efforts. Published by Oxford University Press on behalf of Entomological Society of America 2016. This work is written by US Government employees and is in the public domain in the US.

Open surgical simulation--a review.

PubMed

Davies, Jennifer; Khatib, Manaf; Bello, Fernando

2013-01-01

Surgical simulation has benefited from a surge in interest over the last decade as a result of the increasing need for a change in the traditional apprentice model of teaching surgery. However, despite the recent interest in surgical simulation as an adjunct to surgical training, most of the literature focuses on laparoscopic, endovascular, and endoscopic surgical simulation with very few studies scrutinizing open surgical simulation and its benefit to surgical trainees. The aim of this review is to summarize the current standard of available open surgical simulators and to review the literature on the benefits of open surgical simulation. Open surgical simulators currently used include live animals, cadavers, bench models, virtual reality, and software-based computer simulators. In the current literature, there are 18 different studies (including 6 randomized controlled trials and 12 cohort studies) investigating the efficacy of open surgical simulation using live animal, bench, and cadaveric models in many surgical specialties including general, cardiac, trauma, vascular, urologic, and gynecologic surgery. The current open surgical simulation studies show, in general, a significant benefit of open surgical simulation in developing the surgical skills of surgical trainees. However, these studies have their limitations including a low number of participants, variable assessment standards, and a focus on short-term results often with no follow-up assessment. The skills needed for open surgical procedures are the essential basis that a surgical trainee needs to grasp before attempting more technical procedures such as laparoscopic procedures. In this current climate of medical practice with reduced hours of surgical exposure for trainees and where the patient's safety and outcome is key, open surgical simulation is a promising adjunct to modern surgical training, filling the void between surgeons being trained in a technique and a surgeon achieving fluency in that open surgical procedure. Better quality research is needed into the benefits of open surgical simulation, and this would hopefully stimulate further development of simulators with more accurate and objective assessment tools. © 2013 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.

SIMULATION OF OZONE EFFECTS ON EIGHT TREE SPECIES AT SHENANDOAH NATIONAL PARK

EPA Science Inventory

As part of an assessment of potential effects of air pollutants on the vegetation of Shenandoah National Park (SHEN), we simulated the growth of eight important tree species using TREGRO, a mechanistic model of individual tree growth. Published TREGRO parameters for black cherry...

A permeation theory for single-file ion channels: one- and two-step models.

PubMed

Nelson, Peter Hugo

2011-04-28

How many steps are required to model permeation through ion channels? This question is investigated by comparing one- and two-step models of permeation with experiment and MD simulation for the first time. In recent MD simulations, the observed permeation mechanism was identified as resembling a Hodgkin and Keynes knock-on mechanism with one voltage-dependent rate-determining step [Jensen et al., PNAS 107, 5833 (2010)]. These previously published simulation data are fitted to a one-step knock-on model that successfully explains the highly non-Ohmic current-voltage curve observed in the simulation. However, these predictions (and the simulations upon which they are based) are not representative of real channel behavior, which is typically Ohmic at low voltages. A two-step association/dissociation (A/D) model is then compared with experiment for the first time. This two-parameter model is shown to be remarkably consistent with previously published permeation experiments through the MaxiK potassium channel over a wide range of concentrations and positive voltages. The A/D model also provides a first-order explanation of permeation through the Shaker potassium channel, but it does not explain the asymmetry observed experimentally. To address this, a new asymmetric variant of the A/D model is developed using the present theoretical framework. It includes a third parameter that represents the value of the "permeation coordinate" (fractional electric potential energy) corresponding to the triply occupied state n of the channel. This asymmetric A/D model is fitted to published permeation data through the Shaker potassium channel at physiological concentrations, and it successfully predicts qualitative changes in the negative current-voltage data (including a transition to super-Ohmic behavior) based solely on a fit to positive-voltage data (that appear linear). The A/D model appears to be qualitatively consistent with a large group of published MD simulations, but no quantitative comparison has yet been made. The A/D model makes a network of predictions for how the elementary steps and the channel occupancy vary with both concentration and voltage. In addition, the proposed theoretical framework suggests a new way of plotting the energetics of the simulated system using a one-dimensional permeation coordinate that uses electric potential energy as a metric for the net fractional progress through the permeation mechanism. This approach has the potential to provide a quantitative connection between atomistic simulations and permeation experiments for the first time.

The effects of clutter-rejection filtering on estimating weather spectrum parameters

NASA Technical Reports Server (NTRS)

Davis, W. T.

1989-01-01

The effects of clutter-rejection filtering on estimating the weather parameters from pulse Doppler radar measurement data are investigated. The pulse pair method of estimating the spectrum mean and spectrum width of the weather is emphasized. The loss of sensitivity, a measure of the signal power lost due to filtering, is also considered. A flexible software tool developed to investigate these effects is described. It allows for simulated weather radar data, in which the user specifies an underlying truncated Gaussian spectrum, as well as for externally generated data which may be real or simulated. The filter may be implemented in either the time or the frequency domain. The software tool is validated by comparing unfiltered spectrum mean and width estimates to their true values, and by reproducing previously published results. The effects on the weather parameter estimates using simulated weather-only data are evaluated for five filters: an ideal filter, two infinite impulse response filters, and two finite impulse response filters. Results considering external data, consisting of weather and clutter data, are evaluated on a range cell by range cell basis. Finally, it is shown theoretically and by computer simulation that a linear phase response is not required for a clutter rejection filter preceeding pulse-pair parameter estimation.

Incorporation of Fixed Installation Costs into Optimization of Groundwater Remediation with a New Efficient Surrogate Nonlinear Mixed Integer Optimization Algorithm

NASA Astrophysics Data System (ADS)

Shoemaker, Christine; Wan, Ying

2016-04-01

Optimization of nonlinear water resources management issues which have a mixture of fixed (e.g. construction cost for a well) and variable (e.g. cost per gallon of water pumped) costs has been not well addressed because prior algorithms for the resulting nonlinear mixed integer problems have required many groundwater simulations (with different configurations of decision variable), especially when the solution space is multimodal. In particular heuristic methods like genetic algorithms have often been used in the water resources area, but they require so many groundwater simulations that only small systems have been solved. Hence there is a need to have a method that reduces the number of expensive groundwater simulations. A recently published algorithm for nonlinear mixed integer programming using surrogates was shown in this study to greatly reduce the computational effort for obtaining accurate answers to problems involving fixed costs for well construction as well as variable costs for pumping because of a substantial reduction in the number of groundwater simulations required to obtain an accurate answer. Results are presented for a US EPA hazardous waste site. The nonlinear mixed integer surrogate algorithm is general and can be used on other problems arising in hydrology with open source codes in Matlab and python ("pySOT" in Bitbucket).

Complication Reducing Effect of the Information Technology-Based Diabetes Management System on Subjects with Type 2 Diabetes

PubMed Central

Cho, Jae-Hyoung; Lee, Jin-Hee; Oh, Jeong-Ah; Kang, Mi-Ja; Choi, Yoon-Hee; Kwon, Hyuk-Sang; Chang, Sang-Ah; Cha, Bong-Yun; Son, Ho-Young; Yoon, Kun-Ho

2008-01-01

Objective We introduced a new information technology-based diabetes management system, called the Internet-based glucose monitoring system (IBGMS), and demonstrated its short-term and long-term favorable effects. However, there has been no report on clinical effects of such a new diabetes management system on the development of diabetic complications so far. This study was used to simulate the complication reducing effect of the IBGMS, given in addition to existing treatments in patients with type 2 diabetes. Research Design and Methods The CORE Diabetes Model, a peer-reviewed, published, validated computer simulation model, was used to project long-term clinical outcomes in type 2 diabetes patients receiving the IBGMS in addition to their existing treatment. The model combined standard Markov submodels to simulate the incidence and progression of diabetes-related complications. Results The addition of IBGMS was associated with improvements in reducing diabetic complications, mainly microangiopathic complications, including diabetic retinopathy, diabetic neuropathy, diabetic nephropathy, and diabetic foot ulcer. The IBGMS also delayed the development of all diabetic complications for more than 1 year. Conclusions This study demonstrated that the simulated IBGMS, compared to existing treatment, was associated with a reduction of diabetic complications. As a result, it provides valuable evidence for practical application to the public in the world. PMID:19885180

Advances in dynamic modeling of colorectal cancer signaling-network regions, a path toward targeted therapies

PubMed Central

Kolch, Walter; Kholodenko, Boris N.; Ambrosi, Cristina De; Barla, Annalisa; Biganzoli, Elia M.; Nencioni, Alessio; Patrone, Franco; Ballestrero, Alberto; Zoppoli, Gabriele; Verri, Alessandro; Parodi, Silvio

2015-01-01

The interconnected network of pathways downstream of the TGFβ, WNT and EGF-families of receptor ligands play an important role in colorectal cancer pathogenesis. We studied and implemented dynamic simulations of multiple downstream pathways and described the section of the signaling network considered as a Molecular Interaction Map (MIM). Our simulations used Ordinary Differential Equations (ODEs), which involved 447 reactants and their interactions. Starting from an initial “physiologic condition”, the model can be adapted to simulate individual pathologic cancer conditions implementing alterations/mutations in relevant onco-proteins. We verified some salient model predictions using the mutated colorectal cancer lines HCT116 and HT29. We measured the amount of MYC and CCND1 mRNAs and AKT and ERK phosphorylated proteins, in response to individual or combination onco-protein inhibitor treatments. Experimental and simulation results were well correlated. Recent independently published results were also predicted by our model. Even in the presence of an approximate and incomplete signaling network information, a predictive dynamic modeling seems already possible. An important long term road seems to be open and can be pursued further, by incremental steps, toward even larger and better parameterized MIMs. Personalized treatment strategies with rational associations of signaling-proteins inhibitors, could become a realistic goal. PMID:25671297

Mesoscale Effective Property Simulations Incorporating Conductive Binder

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

Trembacki, Bradley L.; Noble, David R.; Brunini, Victor E.

Lithium-ion battery electrodes are composed of active material particles, binder, and conductive additives that form an electrolyte-filled porous particle composite. The mesoscale (particle-scale) interplay of electrochemistry, mechanical deformation, and transport through this tortuous multi-component network dictates the performance of a battery at the cell-level. Effective electrode properties connect mesoscale phenomena with computationally feasible battery-scale simulations. We utilize published tomography data to reconstruct a large subsection (1000+ particles) of an NMC333 cathode into a computational mesh and extract electrode-scale effective properties from finite element continuum-scale simulations. We present a novel method to preferentially place a composite binder phase throughout the mesostructure,more » a necessary approach due difficulty distinguishing between non-active phases in tomographic data. We compare stress generation and effective thermal, electrical, and ionic conductivities across several binder placement approaches. Isotropic lithiation-dependent mechanical swelling of the NMC particles and the consideration of strain-dependent composite binder conductivity significantly impact the resulting effective property trends and stresses generated. Lastly, our results suggest that composite binder location significantly affects mesoscale behavior, indicating that a binder coating on active particles is not sufficient and that more accurate approaches should be used when calculating effective properties that will inform battery-scale models in this inherently multi-scale battery simulation challenge.« less

On the performance of a high head Francis turbine at design and off-design conditions

NASA Astrophysics Data System (ADS)

Aakti, B.; Amstutz, O.; Casartelli, E.; Romanelli, G.; Mangani, L.

2015-01-01

In the present paper, fully 360 degrees transient and steady-state simulations of a Francis turbine were performed at three operating conditions, namely at part load (PL), best efficiency point (BEP), and high load (HL), using different numerical approaches for the pressure-velocity coupling. The simulation domain includes the spiral casing with stay and guide vanes, the runner and the draft tube. The main target of the investigations is the numerical prediction of the overall performance of the high head Francis turbine model as well as local and integral quantities of the complete machine in different operating conditions. All results were compared with experimental data published by the workshop organization. All CFD simulations were performed at model scale with a new in-house, 3D, unstructured, object-oriented finite volume code within the framework of the open source OpenFOAM library. The novel fully coupled pressure-based solver is designed to solve the incompressible RANS- Equations and is capable of handling multiple references of frame (MRF). The obtained results show that the overall performance is well captured by the simulations. Regarding the local flow distributions within the inlet section of the draft-tube, the axial velocity is better estimated than the circumferential component.

Parametric electrical impedance tomography for measuring bone mineral density in the pelvis using a computational model.

PubMed

Kimel-Naor, Shani; Abboud, Shimon; Arad, Marina

2016-08-01

Osteoporosis is defined as bone microstructure deterioration resulting a decrease of bone's strength. Measured bone mineral density (BMD) constitutes the main tool for Osteoporosis diagnosis, management, and defines patient's fracture risk. In the present study, parametric electrical impedance tomography (pEIT) method was examined for monitoring BMD, using a computerized simulation model and preliminary real measurements. A numerical solver was developed to simulate surface potentials measured over a 3D computerized pelvis model. Varying cortical and cancellous BMD were simulated by changing bone conductivity and permittivity. Up to 35% and 16% change was found in the real and imaginary modules of the calculated potential, respectively, while BMD changes from 100% (normal) to 60% (Osteoporosis). Negligible BMD relative error was obtained with SNR>60 [dB]. Position changes errors indicate that for long term monitoring, measurement should be taken at the same geometrical configuration with great accuracy. The numerical simulations were compared to actual measurements that were acquired from a healthy male subject using a five electrodes belt bioimpedance device. The results suggest that pEIT may provide an inexpensive easy to use tool for frequent monitoring BMD in small clinics during pharmacological treatment, as a complementary method to DEXA test. Copyright © 2016. Published by Elsevier Ltd.

Multiaxial mechanical properties and constitutive modeling of human adipose tissue: a basis for preoperative simulations in plastic and reconstructive surgery.

PubMed

Sommer, Gerhard; Eder, Maximilian; Kovacs, Laszlo; Pathak, Heramb; Bonitz, Lars; Mueller, Christoph; Regitnig, Peter; Holzapfel, Gerhard A

2013-11-01

A preoperative simulation of soft tissue deformations during plastic and reconstructive surgery is desirable to support the surgeon's planning and to improve surgical outcomes. The current development of constitutive adipose tissue models, for the implementation in multilayer computational frameworks for the simulation of human soft tissue deformations, has proved difficult because knowledge of the required mechanical parameters of fat tissue is limited. Therefore, for the first time, human abdominal adipose tissues were mechanically investigated by biaxial tensile and triaxial shear tests. The results of this study suggest that human abdominal adipose tissues under quasi-static and dynamic multiaxial loadings can be characterized as a nonlinear, anisotropic and viscoelastic soft biological material. The nonlinear and anisotropic features are consequences of the material's collagenous microstructure. The aligned collagenous septa observed in histological investigations causes the anisotropy of the tissue. A hyperelastic model used in this study was appropriate to represent the quasi-static multiaxial mechanical behavior of fat tissue. The constitutive parameters are intended to serve as a basis for soft tissue simulations using the finite element method, which is an apparent method for obtaining promising results in the field of plastic and reconstructive surgery. Copyright © 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Explaining the heterogeneity of functional connectivity findings in multiple sclerosis: An empirically informed modeling study.

PubMed

Tewarie, Prejaas; Steenwijk, Martijn D; Brookes, Matthew J; Uitdehaag, Bernard M J; Geurts, Jeroen J G; Stam, Cornelis J; Schoonheim, Menno M

2018-06-01

To understand the heterogeneity of functional connectivity results reported in the literature, we analyzed the separate effects of grey and white matter damage on functional connectivity and networks in multiple sclerosis. For this, we employed a biophysical thalamo-cortical model consisting of interconnected cortical and thalamic neuronal populations, informed and amended by empirical diffusion MRI tractography data, to simulate functional data that mimic neurophysiological signals. Grey matter degeneration was simulated by decreasing within population connections and white matter degeneration by lowering between population connections, based on lesion predilection sites in multiple sclerosis. For all simulations, functional connectivity and functional network organization are quantified by phase synchronization and network integration, respectively. Modeling results showed that both cortical and thalamic grey matter damage induced a global increase in functional connectivity, whereas white matter damage induced an initially increased connectivity followed by a global decrease. Both white and especially grey matter damage, however, induced a decrease in network integration. These empirically informed simulations show that specific topology and timing of structural damage are nontrivial aspects in explaining functional abnormalities in MS. Insufficient attention to these aspects likely explains contradictory findings in multiple sclerosis functional imaging studies so far. © 2018 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.

Mesoscale Effective Property Simulations Incorporating Conductive Binder

DOE PAGES

Trembacki, Bradley L.; Noble, David R.; Brunini, Victor E.; ...

2017-07-26

Lithium-ion battery electrodes are composed of active material particles, binder, and conductive additives that form an electrolyte-filled porous particle composite. The mesoscale (particle-scale) interplay of electrochemistry, mechanical deformation, and transport through this tortuous multi-component network dictates the performance of a battery at the cell-level. Effective electrode properties connect mesoscale phenomena with computationally feasible battery-scale simulations. We utilize published tomography data to reconstruct a large subsection (1000+ particles) of an NMC333 cathode into a computational mesh and extract electrode-scale effective properties from finite element continuum-scale simulations. We present a novel method to preferentially place a composite binder phase throughout the mesostructure,more » a necessary approach due difficulty distinguishing between non-active phases in tomographic data. We compare stress generation and effective thermal, electrical, and ionic conductivities across several binder placement approaches. Isotropic lithiation-dependent mechanical swelling of the NMC particles and the consideration of strain-dependent composite binder conductivity significantly impact the resulting effective property trends and stresses generated. Lastly, our results suggest that composite binder location significantly affects mesoscale behavior, indicating that a binder coating on active particles is not sufficient and that more accurate approaches should be used when calculating effective properties that will inform battery-scale models in this inherently multi-scale battery simulation challenge.« less

A spectral element method with adaptive segmentation for accurately simulating extracellular electrical stimulation of neurons.

PubMed

Eiber, Calvin D; Dokos, Socrates; Lovell, Nigel H; Suaning, Gregg J

2017-05-01

The capacity to quickly and accurately simulate extracellular stimulation of neurons is essential to the design of next-generation neural prostheses. Existing platforms for simulating neurons are largely based on finite-difference techniques; due to the complex geometries involved, the more powerful spectral or differential quadrature techniques cannot be applied directly. This paper presents a mathematical basis for the application of a spectral element method to the problem of simulating the extracellular stimulation of retinal neurons, which is readily extensible to neural fibers of any kind. The activating function formalism is extended to arbitrary neuron geometries, and a segmentation method to guarantee an appropriate choice of collocation points is presented. Differential quadrature may then be applied to efficiently solve the resulting cable equations. The capacity for this model to simulate action potentials propagating through branching structures and to predict minimum extracellular stimulation thresholds for individual neurons is demonstrated. The presented model is validated against published values for extracellular stimulation threshold and conduction velocity for realistic physiological parameter values. This model suggests that convoluted axon geometries are more readily activated by extracellular stimulation than linear axon geometries, which may have ramifications for the design of neural prostheses.

Reimplementation of the Biome-BGC model to simulate successional change.

PubMed

Bond-Lamberty, Ben; Gower, Stith T; Ahl, Douglas E; Thornton, Peter E

2005-04-01

Biogeochemical process models are increasingly employed to simulate current and future forest dynamics, but most simulate only a single canopy type. This limitation means that mixed stands, canopy succession and understory dynamics cannot be modeled, severe handicaps in many forests. The goals of this study were to develop a version of Biome-BGC that supported multiple, interacting vegetation types, and to assess its performance and limitations by comparing modeled results to published data from a 150-year boreal black spruce (Picea mariana (Mill.) BSP) chronosequence in northern Manitoba, Canada. Model data structures and logic were modified to support an arbitrary number of interacting vegetation types; an explicit height calculation was necessary to prioritize radiation and precipitation interception. Two vegetation types, evergreen needle-leaf and deciduous broadleaf, were modeled based on site-specific meteorological and physiological data. The new version of Biome-BGC reliably simulated observed changes in leaf area, net primary production and carbon stocks, and should be useful for modeling the dynamics of mixed-species stands and ecological succession. We discuss the strengths and limitations of Biome-BGC for this application, and note areas in which further work is necessary for reliable simulation of boreal biogeochemical cycling at a landscape scale.

Use of mechanistic simulations as a quantitative risk-ranking tool within the quality by design framework.

PubMed

Stocker, Elena; Toschkoff, Gregor; Sacher, Stephan; Khinast, Johannes G

2014-11-20

The purpose of this study is to evaluate the use of computer simulations for generating quantitative knowledge as a basis for risk ranking and mechanistic process understanding, as required by ICH Q9 on quality risk management systems. In this specific publication, the main focus is the demonstration of a risk assessment workflow, including a computer simulation for the generation of mechanistic understanding of active tablet coating in a pan coater. Process parameter screening studies are statistically planned under consideration of impacts on a potentially critical quality attribute, i.e., coating mass uniformity. Based on computer simulation data the process failure mode and effects analysis of the risk factors is performed. This results in a quantitative criticality assessment of process parameters and the risk priority evaluation of failure modes. The factor for a quantitative reassessment of the criticality and risk priority is the coefficient of variation, which represents the coating mass uniformity. The major conclusion drawn from this work is a successful demonstration of the integration of computer simulation in the risk management workflow leading to an objective and quantitative risk assessment. Copyright © 2014. Published by Elsevier B.V.

Comment to: "Martini straight: Boosting performance using a shorter cutoff and GPUs" by D.H. de Jong, S. Baoukina, H.I. Ingólfsson, and S.J. Marrink

NASA Astrophysics Data System (ADS)

Benedetti, Florian; Loison, Claire

2018-07-01

In a recent study published in this journal, de Jong et al. investigated the efficiency improvement reached thanks to new parameter sets for molecular dynamics simulations using the coarse-grained Martini force-field and its implementation in the Gromacs simulation package (de Jong et al., 2016). The advantages of the new sets are the computational efficiency and the conservation of the equilibrium properties of the Martini model. This article reports additional tests on the total energy conservation for zwitterionic lipid bilayer membranes. The results show that the conclusion by de Jong et al. on the total energy conservation of the new parameter sets, based on short simulations and homogeneous systems, is not generalizable to long lipid bilayer simulations. The energy conservation of the three parameter sets compared in their article (common, new and new-RF) differ if one analyzes sufficiently long trajectories or if one measures the total energy drifts. In practice, when total energy conservation is important for a Martini lipid bilayer simulation, we would consider either keeping the common set, or carefully testing the new-RF set for energy leaks or sources before production use.

A simulation of dementia epidemiology and resource use in Australia.

PubMed

Standfield, Lachlan B; Comans, Tracy; Scuffham, Paul

2018-06-01

The number of people in the developed world who have dementia is predicted to rise markedly. This study presents a validated predictive model to assist decision-makers to determine this population's future resource requirements and target scarce health and welfare resources appropriately. A novel individual patient discrete event simulation was developed to estimate the future prevalence of dementia and related health and welfare resource use in Australia. When compared to other published results, the simulation generated valid estimates of dementia prevalence and resource use. The analysis predicted 298,000, 387,000 and 928,000 persons in Australia will have dementia in 2011, 2020 and 2050, respectively. Health and welfare resource use increased markedly over the simulated time-horizon and was affected by capacity constraints. This simulation provides useful estimates of future demands on dementia-related services allowing the exploration of the effects of capacity constraints. Implications for public health: The model demonstrates that under-resourcing of residential aged care may lead to inappropriate and inefficient use of hospital resources. To avoid these capacity constraints it is predicted that the number of aged care beds for persons with dementia will need to increase more than threefold from 2011 to 2050. © 2017 The Authors.

Fe/starch nanoparticle - Pseudomonas aeruginosa: Bio-physiochemical and MD studies.

PubMed

Mofradnia, Soheil Rezazadeh; Tavakoli, Zahra; Yazdian, Fatemeh; Rashedi, Hamid; Rasekh, Behnam

2018-05-03

In this research, we attempt to study biosurfactant production by Pseudomonas aeruginosa using Fe/starch nanoparticles. Fe/starch showed no bacterial toxicity at 1 mg/ml and increased the growth rate and biosurfactant production up to 23.21 and 20.73%, respectively. Surface tension, dry weight cell, and emulsification indexes (E24) were measured. Biosurfactant production was considered via computational techniques and molecular dynamic (MD) simulation through flexible and periodic conditions (by material studio software) as well. The results of software predictions demonstrate by radial distribution function (RDF), density, energy and temperature graphs. According to the present experimental results, increased 30% growth of the bacterium has been observed and the subsequent production of biosurfactant. The difference between the experimental results and simulation data were achieved up to 0.17 g/cm 3 , which confirms the prediction of data by the software due to a difference of <14.5% (ideal error value is 20%). Copyright © 2017. Published by Elsevier B.V.

Rate-equation modelling and ensemble approach to extraction of parameters for viral infection-induced cell apoptosis and necrosis

NASA Astrophysics Data System (ADS)

Domanskyi, Sergii; Schilling, Joshua E.; Gorshkov, Vyacheslav; Libert, Sergiy; Privman, Vladimir

2016-09-01

We develop a theoretical approach that uses physiochemical kinetics modelling to describe cell population dynamics upon progression of viral infection in cell culture, which results in cell apoptosis (programmed cell death) and necrosis (direct cell death). Several model parameters necessary for computer simulation were determined by reviewing and analyzing available published experimental data. By comparing experimental data to computer modelling results, we identify the parameters that are the most sensitive to the measured system properties and allow for the best data fitting. Our model allows extraction of parameters from experimental data and also has predictive power. Using the model we describe interesting time-dependent quantities that were not directly measured in the experiment and identify correlations among the fitted parameter values. Numerical simulation of viral infection progression is done by a rate-equation approach resulting in a system of "stiff" equations, which are solved by using a novel variant of the stochastic ensemble modelling approach. The latter was originally developed for coupled chemical reactions.

Rate-equation modelling and ensemble approach to extraction of parameters for viral infection-induced cell apoptosis and necrosis

NASA Astrophysics Data System (ADS)

Domanskyi, Sergii; Schilling, Joshua; Gorshkov, Vyacheslav; Libert, Sergiy; Privman, Vladimir

We develop a theoretical approach that uses physiochemical kinetics modelling to describe cell population dynamics upon progression of viral infection in cell culture, which results in cell apoptosis (programmed cell death) and necrosis (direct cell death). Several model parameters necessary for computer simulation were determined by reviewing and analyzing available published experimental data. By comparing experimental data to computer modelling results, we identify the parameters that are the most sensitive to the measured system properties and allow for the best data fitting. Our model allows extraction of parameters from experimental data and also has predictive power. Using the model we describe interesting time-dependent quantities that were not directly measured in the experiment and identify correlations among the fitted parameter values. Numerical simulation of viral infection progression is done by a rate-equation approach resulting in a system of ``stiff'' equations, which are solved by using a novel variant of the stochastic ensemble modelling approach. The latter was originally developed for coupled chemical reactions.

Modelling of peak temperature during friction stir processing of magnesium alloy AZ91

NASA Astrophysics Data System (ADS)

Vaira Vignesh, R.; Padmanaban, R.

2018-02-01

Friction stir processing (FSP) is a solid state processing technique with potential to modify the properties of the material through microstructural modification. The study of heat transfer in FSP aids in the identification of defects like flash, inadequate heat input, poor material flow and mixing etc. In this paper, transient temperature distribution during FSP of magnesium alloy AZ91 was simulated using finite element modelling. The numerical model results were validated using the experimental results from the published literature. The model was used to predict the peak temperature obtained during FSP for various process parameter combinations. The simulated peak temperature results were used to develop a statistical model. The effect of process parameters namely tool rotation speed, tool traverse speed and shoulder diameter of the tool on the peak temperature was investigated using the developed statistical model. It was found that peak temperature was directly proportional to tool rotation speed and shoulder diameter and inversely proportional to tool traverse speed.

Integration of high-fidelity simulator in third-year paediatrics clerkship.

PubMed

Ortiz, Nerian; Pedrogo, Yasmin; Bonet, Nydia

2011-06-01

Simulation in medicine is a useful tool for assessing clinical competencies. The liaison committee on medical education expects students to have simulation experiences in the curriculum. The integration of simulators has been encouraged for clinical clerkships. The use of the human simulator in a safe environment should result in enhanced teamworking, communication and critical thinking skills. During the academic year 2007-08, a formative activity using the simulator was implemented in the paediatrics clerkship. The objectives included exposing students to an emergent general paediatric medical scenario using the human simulator. It was imperative that students would adequately go through the critical thinking process. The paediatrics clerkship has incorporated a formative activity using the high-fidelity simulator. A faculty member debriefed the students, and feedback was offered. A total of 124 students participated in the activity. Ninety-eight percent agreed that the use of the simulator in a scenario such as the one presented allowed for a better understanding of the clinical issues studied in the clerkship. More than 85 percent of the students recommended the integration of the simulator in other major clinical clerkships. Performance in the objective structured clinical exam (OSCE) at the end of the clerkship has improved after the implementation of this formative activity. The use of the high-fidelity simulator during the paediatrics clerkship has been identified as an excellent teaching tool. This formative activity has been deemed successful by the students, who feel that it serves as an extra tool to strengthen learned concepts and skills. © Blackwell Publishing Ltd 2011.

In Silico Analyses of Substrate Interactions with Human Serum Paraoxonase 1

DTIC Science & Technology

2008-01-01

substrate interactions of HuPON1 remains elusive. In this study, we apply homology modeling, docking, and molecular dynamic (MD) simulations to probe the...mod- eling; docking; molecular dynamics simulations ; binding free energy decomposition. 486 PROTEINS Published 2008 WILEY-LISS, INC. yThis article is a...apply homology modeling, docking, and molecular dynamic (MD) simulations to probe the binding interactions of HuPON1 with representative substrates. The

Investigating the Transonic Flutter Boundary of the Benchmark Supercritical Wing

NASA Technical Reports Server (NTRS)

Heeg, Jennifer; Chwalowski, Pawel

2017-01-01

This paper builds on the computational aeroelastic results published previously and generated in support of the second Aeroelastic Prediction Workshop for the NASA Benchmark Supercritical Wing configuration. The computational results are obtained using FUN3D, an unstructured grid Reynolds-Averaged Navier-Stokes solver developed at the NASA Langley Research Center. The analysis results focus on understanding the dip in the transonic flutter boundary at a single Mach number (0.74), exploring an angle of attack range of ??1 to 8 and dynamic pressures from wind off to beyond flutter onset. The rigid analysis results are examined for insights into the behavior of the aeroelastic system. Both static and dynamic aeroelastic simulation results are also examined.

The development of an industrial-scale fed-batch fermentation simulation.

PubMed

Goldrick, Stephen; Ştefan, Andrei; Lovett, David; Montague, Gary; Lennox, Barry

2015-01-10

This paper describes a simulation of an industrial-scale fed-batch fermentation that can be used as a benchmark in process systems analysis and control studies. The simulation was developed using a mechanistic model and validated using historical data collected from an industrial-scale penicillin fermentation process. Each batch was carried out in a 100,000 L bioreactor that used an industrial strain of Penicillium chrysogenum. The manipulated variables recorded during each batch were used as inputs to the simulator and the predicted outputs were then compared with the on-line and off-line measurements recorded in the real process. The simulator adapted a previously published structured model to describe the penicillin fermentation and extended it to include the main environmental effects of dissolved oxygen, viscosity, temperature, pH and dissolved carbon dioxide. In addition the effects of nitrogen and phenylacetic acid concentrations on the biomass and penicillin production rates were also included. The simulated model predictions of all the on-line and off-line process measurements, including the off-gas analysis, were in good agreement with the batch records. The simulator and industrial process data are available to download at www.industrialpenicillinsimulation.com and can be used to evaluate, study and improve on the current control strategy implemented on this facility. Crown Copyright © 2014. Published by Elsevier B.V. All rights reserved.

Figures of Merit for Lunar Simulants

NASA Technical Reports Server (NTRS)

Slane, Frederick A.; Rickman, Douglas L.

2012-01-01

At an earlier SRR the concept for an international standard on Lunar regolith simulants was presented. The international standard, ISO 10788, Lunar Simulants, has recently been published. This paper presents the final content of the standard. Therefore, we are presenting an update of the following: The collection and analysis of lunar samples from 1969 to present has yielded large amounts of data. Published analyses give some idea of the complex nature of the regolith at all scales, rocks, soils and the smaller particulates commonly referred to as dust. Data recently acquired in support of NASA s simulant effort has markedly increased our knowledge and quantitatively demonstrates that complexity. It is anticipated that future analyses will further add to the known complexity. In an effort to communicate among the diverse technical communities performing research on or research using regolith samples and simulants, a set of Figures of Merit (FoM) have been devised. The objective is to allow consistent and concise comparative communication between researchers from multiple organizations and nations engaged in lunar exploration. This paper describes Figures of Merit in a new international standard for Lunar Simulants. The FoM methodology uses scientific understanding of the lunar samples to formulate parameters which are reproducibly quantifiable. Contaminants and impurities in the samples are also addressed.

The simulators: truth and power in the psychiatry of José Ingenieros.

PubMed

Caponi, Sandra

2016-01-01

Using Michel Foucault's lectures on "Psychiatric power" as its starting point, this article analyzes the book Simulación de la locura (The simulation of madness), published in 1903 by the Argentine psychiatrist José Ingenieros. Foucault argues that the problem of simulation permeates the entire history of modern psychiatry. After initial analysis of José Ingenieros's references to the question of simulation in the struggle for existence, the issue of simulation in pathological states in general is examined, and lastly the simulation of madness and the problem of degeneration. Ingenieros participates in the epistemological and political struggle that took place between experts-psychiatrists and simulators over the question of truth.

Simulating energy cascade of shock wave formation process in a resonator by gas kinetic scheme

NASA Astrophysics Data System (ADS)

Qu, Chengwu; Zhang, Xiaoqing; Feng, Heying

2017-12-01

The temporal-spatial evolution of gas oscillation was simulated by gas kinetic scheme (GKS) in a cylindrical resonator, driven by a piston at one end and rigidly closed at the other end. Periodic shock waves propagating back and forth were observed in the resonator under finite amplitude of gas oscillation. The studied results demonstrated that the acoustic pressure is a saw-tooth waveform and the oscillatory velocity is a square waveform at the central position of the resonant tube. Moreover, it was found by harmonic analysis that there was no presence of obvious feature for pressure node in such a typical standing wave resonator, and the distribution of acoustic fields displayed a one-dimensional feature for the acoustic pressure while a quasi-one-dimensional form for oscillatory velocity, which demonstrated the nonlinear effects. The simulation results for axial distribution of acoustic intensity showed a good consistency with the published experimental data in the open literature domain, which provides a verification for the effectiveness of the GKS model proposed. The influence of displacement amplitude of the driving piston on the formation of shock wave was numerically investigated, and the simulated results revealed the cascade process of harmonic wave energy from the fundamental wave to higher harmonics. In addition, this study found that the acoustic intensity at the driving end of the resonant tube would increase linearly with the displacement amplitude of the piston due to nonlinear effects, rather than the exponential variation by linear theory. This research demonstrates that the GKS model is strongly capable of simulating nonlinear acoustic problems.

Mathematical Modeling of Early Cellular Innate and Adaptive Immune Responses to Ischemia/Reperfusion Injury and Solid Organ Allotransplantation

PubMed Central

Day, Judy D.; Metes, Diana M.; Vodovotz, Yoram

2015-01-01

A mathematical model of the early inflammatory response in transplantation is formulated with ordinary differential equations. We first consider the inflammatory events associated only with the initial surgical procedure and the subsequent ischemia/reperfusion (I/R) events that cause tissue damage to the host as well as the donor graft. These events release damage-associated molecular pattern molecules (DAMPs), thereby initiating an acute inflammatory response. In simulations of this model, resolution of inflammation depends on the severity of the tissue damage caused by these events and the patient’s (co)-morbidities. We augment a portion of a previously published mathematical model of acute inflammation with the inflammatory effects of T cells in the absence of antigenic allograft mismatch (but with DAMP release proportional to the degree of graft damage prior to transplant). Finally, we include the antigenic mismatch of the graft, which leads to the stimulation of potent memory T cell responses, leading to further DAMP release from the graft and concomitant increase in allograft damage. Regulatory mechanisms are also included at the final stage. Our simulations suggest that surgical injury and I/R-induced graft damage can be well-tolerated by the recipient when each is present alone, but that their combination (along with antigenic mismatch) may lead to acute rejection, as seen clinically in a subset of patients. An emergent phenomenon from our simulations is that low-level DAMP release can tolerize the recipient to a mismatched allograft, whereas different restimulation regimens resulted in an exaggerated rejection response, in agreement with published studies. We suggest that mechanistic mathematical models might serve as an adjunct for patient- or sub-group-specific predictions, simulated clinical studies, and rational design of immunosuppression. PMID:26441988

Simulation and Gaming: The Best of ERIC.

ERIC Educational Resources Information Center

Coombs, Don H., Comp.

Most of the 101 citations included in this annotated bibliography on simulation and gaming were derived from a search of the Educational Resources Information Center (ERIC) indexes. Entries were published between 1972 and 1975. The bibliography is divided into nine sections: theory and research; social studies materials; environment, land use, and…

Video Simulations to Develop Preservice Mathematics Teachers' Discourse Practices

ERIC Educational Resources Information Center

Amador, Julie M.

2018-01-01

The incorporation of video technology in teacher education programmes is increasingly prevalent, with teacher educators commonly using three traditional forms of videos: published video, preservice teachers' own videos and colleagues' videos. This study explored a fourth type of video, self-created scripted video simulations in which preservice…

Simulation of aerobic and anaerobic biodegradation processes at a crude oil spill site

USGS Publications Warehouse

Essaid, Hedeff I.; Bekins, Barbara A.; Godsy, E. Michael; Warren, Ean; Baedecker, Mary Jo; Cozzarelli, Isabelle M.

1995-01-01

A two-dimensional, multispecies reactive solute transport model with sequential aerobic and anaerobic degradation processes was developed and tested. The model was used to study the field-scale solute transport and degradation processes at the Bemidji, Minnesota, crude oil spill site. The simulations included the biodegradation of volatile and nonvolatile fractions of dissolved organic carbon by aerobic processes, manganese and iron reduction, and methanogenesis. Model parameter estimates were constrained by published Monod kinetic parameters, theoretical yield estimates, and field biomass measurements. Despite the considerable uncertainty in the model parameter estimates, results of simulations reproduced the general features of the observed groundwater plume and the measured bacterial concentrations. In the simulation, 46% of the total dissolved organic carbon (TDOC) introduced into the aquifer was degraded. Aerobic degradation accounted for 40% of the TDOC degraded. Anaerobic processes accounted for the remaining 60% of degradation of TDOC: 5% by Mn reduction, 19% by Fe reduction, and 36% by methanogenesis. Thus anaerobic processes account for more than half of the removal of DOC at this site.

Applying the Nernst equation to simulate redox potential variations for biological nitrification and denitrification processes.

PubMed

Chang, Cheng-Nan; Cheng, Hong-Bang; Chao, Allen C

2004-03-15

In this paper, various forms of Nernst equations have been developed based on the real stoichiometric relationship of biological nitrification and denitrification reactions. Instead of using the Nernst equation based on a one-to-one stoichiometric relation for the oxidizing and the reducing species, the basic Nernst equation is modified into slightly different forms. Each is suitable for simulating the redox potential (ORP) variation of a specific biological nitrification or denitrification process. Using the data published in the literature, the validity of these developed Nernst equations has been verified by close fits of the measured ORP data with the calculated ORP curve. The simulation results also indicate that if the biological process is simulated using an incorrect form of Nernst equation, the calculated ORP curve will not fit the measured data. Using these Nernst equations, the ORP value that corresponds to a predetermined degree of completion for the biochemical reaction can be calculated. Thus, these Nernst equations will enable a more efficient on-line control of the biological process.

A finite-element model for simulation of two-dimensional steady-state ground-water flow in confined aquifers

USGS Publications Warehouse

Kuniansky, E.L.

1990-01-01

A computer program based on the Galerkin finite-element method was developed to simulate two-dimensional steady-state ground-water flow in either isotropic or anisotropic confined aquifers. The program may also be used for unconfined aquifers of constant saturated thickness. Constant head, constant flux, and head-dependent flux boundary conditions can be specified in order to approximate a variety of natural conditions, such as a river or lake boundary, and pumping well. The computer program was developed for the preliminary simulation of ground-water flow in the Edwards-Trinity Regional aquifer system as part of the Regional Aquifer-Systems Analysis Program. Results of the program compare well to analytical solutions and simulations .from published finite-difference models. A concise discussion of the Galerkin method is presented along with a description of the program. Provided in the Supplemental Data section are a listing of the computer program, definitions of selected program variables, and several examples of data input and output used in verifying the accuracy of the program.

Laser Doppler pulp vitality measurements: simulation and measurement

NASA Astrophysics Data System (ADS)

Ertl, T.

2017-02-01

Frequently pulp vitality measurement is done in a dental practice by pressing a frozen cotton pellet on the tooth. This method is subjective, as the patient's response is required, sometimes painful and has moderate sensitivity and specificity. Other methods, based on optical or electrical measurement have been published, but didńt find wide spread application in the dental offices. Laser Doppler measurement of the blood flow in the pulp could be an objective method to measure pulp vitality, but the influence of the gingival blood flow on the measurements is a concern. Therefore experiments and simulations were done to learn more about the gingival blood flow in relation to the pulpal blood flow and how to minimize the influence. First patient measurements were done to show the feasibility clinically. Results: Monte Carlo simulations and bench experiments simulating the blood flow in and around a tooth show that both basic configurations, transmission and reflection measurements are possible. Most favorable is a multi-point measurement with different distances from the gingiva. Preliminary sensitivity / specificity are promising and might allow an objective and painless measurement of tooth vitality.

Intelligent Exit-Selection Behaviors during a Room Evacuation

NASA Astrophysics Data System (ADS)

Zarita, Zainuddin; Lim Eng, Aik

2012-01-01

A modified version of the existing cellular automata (CA) model is proposed to simulate an evacuation procedure in a classroom with and without obstacles. Based on the numerous literature on the implementation of CA in modeling evacuation motions, it is notable that most of the published studies do not take into account the pedestrian's ability to select the exit route in their models. To resolve these issues, we develop a CA model incorporating a probabilistic neural network for determining the decision-making ability of the pedestrians, and simulate an exit-selection phenomenon in the simulation. Intelligent exit-selection behavior is observed in our model. From the simulation results, it is observed that occupants tend to select the exit closest to them when the density is low, but if the density is high they will go to an alternative exit so as to avoid a long wait. This reflects the fact that occupants may not fully utilize multiple exits during evacuation. The improvement in our proposed model is valuable for further study and for upgrading the safety aspects of building designs.

Molecular dynamics studies of a hexameric purine nucleoside phosphorylase.

PubMed

Zanchi, Fernando Berton; Caceres, Rafael Andrade; Stabeli, Rodrigo Guerino; de Azevedo, Walter Filgueira

2010-03-01

Purine nucleoside phosphorylase (PNP) (EC.2.4.2.1) is an enzyme that catalyzes the cleavage of N-ribosidic bonds of the purine ribonucleosides and 2-deoxyribonucleosides in the presence of inorganic orthophosphate as a second substrate. This enzyme is involved in purine-salvage pathway and has been proposed as a promising target for design and development of antimalarial and antibacterial drugs. Recent elucidation of the three-dimensional structure of PNP by X-ray protein crystallography left open the possibility of structure-based virtual screening initiatives in combination with molecular dynamics simulations focused on identification of potential new antimalarial drugs. Most of the previously published molecular dynamics simulations of PNP were carried out on human PNP, a trimeric PNP. The present article describes for the first time molecular dynamics simulations of hexameric PNP from Plasmodium falciparum (PfPNP). Two systems were simulated in the present work, PfPNP in ligand free form, and in complex with immucillin and sulfate. Based on the dynamical behavior of both systems the main results related to structural stability and protein-drug interactions are discussed.

Helicopter simulator standards

NASA Technical Reports Server (NTRS)

Boothe, Edward M.

1992-01-01

The initial advisory circular was produced in 1984 (AC 120-XX). It was not finalized, however, because the FAR's for pilot certification did not recognize helicopter simulators and, therefore, permitted no credit for their use. That is being rectified, and, when the new rules are published, standards must be available for qualifying simulators. Because of the lack of a data base to support specification of these standards, the FAA must rely on the knowledge of experts in the simulator/training industry. A major aim of this workshop is to form a working group of these experts to produce a set of standards for helicopter training simulators.

Conformational flexibility of human casein kinase catalytic subunit explored by metadynamics.

PubMed

Gouron, Aurélie; Milet, Anne; Jamet, Helene

2014-03-04

Casein kinase CK2 is an essential enzyme in higher organisms, catalyzing the transfer of the γ phosphate from ATP to serine and threonine residues on protein substrates. In a number of animal tumors, CK2 activity has been shown to escape normal cellular control, making it a potential target for cancer therapy. Several crystal structures of human CK2 have been published with different conformations for the CK2α catalytic subunit. This variability reflects a high flexibility for two regions of CK2α: the interdomain hinge region, and the glycine-rich loop (p-loop). Here, we present a computational study simulating the equilibrium between three conformations involving these regions. Simulations were performed using well-tempered metadynamics combined with a path collective variables approach. This provides a reference pathway describing the conformational changes being studied, based on analysis of free energy surfaces. The free energies of the three conformations were found to be close and the paths proposed had low activation barriers. Our results indicate that these conformations can exist in water. This information should be useful when designing inhibitors specific to one conformation. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Percolation Network Study on the Gas Apparent Permeability of Rock

NASA Astrophysics Data System (ADS)

Wang, Y.; Tang, Y. B.; Li, M.

2017-12-01

We modeled the gas single phase transport behaviors of monomodal porous media using percolation networks. Different from the liquid absolute permeability, which is only related to topology and morphology of pore space, the gas permeability depends on pore pressure as well. A published gas flow conductance model, included usual viscous flow, slip flow and Knudsen diffusion in cylinder pipe, was used to simulated gas flow in 3D, simple cubic, body-center cubic and face-center cubic networks with different hydraulic radius, different coordination number, and different pipe radius distributions under different average pore pressure. The simulation results showed that the gas apparent permeability kapp obey the `universal' scaling law (independence of network lattices), kapp (z-zc)β, where exponent β is related to pore radius distribution, z is coordination number and zc=1.5. Following up on Bernabé et al.'s (2010) study of the effects of pore connectivity and pore size heterogeneity on liquid absolute permeability, gas apparent permeability kapp model and a new joint gas-liquid permeability (i.e., kapp/k∞) model, which could explain the Klinkenberg phenomenon, were proposed. We satisfactorily tested the models by comparison with published experimental data on glass beads and other datasets.

iBIOMES Lite: Summarizing Biomolecular Simulation Data in Limited Settings

PubMed Central

2015-01-01

As the amount of data generated by biomolecular simulations dramatically increases, new tools need to be developed to help manage this data at the individual investigator or small research group level. In this paper, we introduce iBIOMES Lite, a lightweight tool for biomolecular simulation data indexing and summarization. The main goal of iBIOMES Lite is to provide a simple interface to summarize computational experiments in a setting where the user might have limited privileges and limited access to IT resources. A command-line interface allows the user to summarize, publish, and search local simulation data sets. Published data sets are accessible via static hypertext markup language (HTML) pages that summarize the simulation protocols and also display data analysis graphically. The publication process is customized via extensible markup language (XML) descriptors while the HTML summary template is customized through extensible stylesheet language (XSL). iBIOMES Lite was tested on different platforms and at several national computing centers using various data sets generated through classical and quantum molecular dynamics, quantum chemistry, and QM/MM. The associated parsers currently support AMBER, GROMACS, Gaussian, and NWChem data set publication. The code is available at https://github.com/jcvthibault/ibiomes. PMID:24830957

Feasibility of producing a short, high energy s-band linear accelerator using a klystron power source.

PubMed

Baillie, Devin; St Aubin, J; Fallone, B G; Steciw, S

2013-04-01

To use a finite-element method (FEM) model to study the feasibility of producing a short s-band (2.9985 GHz) waveguide capable of producing x-rays energies up to 10 MV, for applications in a linac-MR, as well as conventional radiotherapy. An existing waveguide FEM model developed by the authors' group is used to simulate replacing the magnetron power source with a klystron. Peak fields within the waveguide are compared with a published experimental threshold for electric breakdown. The RF fields in the first accelerating cavity are scaled, approximating the effect of modifications to the first coupling cavity. Electron trajectories are calculated within the RF fields, and the energy spectrum, beam current, and focal spot of the electron beam are analyzed. One electron spectrum is selected for Monte Carlo simulations and the resulting PDD compared to measurement. When the first cavity fields are scaled by a factor of 0.475, the peak magnitude of the electric fields within the waveguide are calculated to be 223.1 MV∕m, 29% lower than the published threshold for breakdown at this operating frequency. Maximum electron energy increased from 6.2 to 10.4 MeV, and beam current increased from 134 to 170 mA. The focal spot FWHM is decreased slightly from 0.07 to 0.05 mm, and the width of the energy spectrum increased slightly from 0.44 to 0.70 MeV. Monte Carlo results show dmax is at 2.15 cm for a 10 × 10 cm(2) field, compared with 2.3 cm for a Varian 10 MV linac, while the penumbral widths are 4.8 and 5.6 mm, respectively. The authors' simulation results show that a short, high-energy, s-band accelerator is feasible and electric breakdown is not expected to interfere with operation at these field strengths. With minor modifications to the first coupling cavity, all electron beam parameters are improved.

Particle-in-cell simulations of collisionless shock formation via head-on merging of two laboratory supersonic plasma jets

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

Thoma, C.; Welch, D. R.; Hsu, S. C.

2013-08-15

We describe numerical simulations, using the particle-in-cell (PIC) and hybrid-PIC code lsp[T. P. Hughes et al., Phys. Rev. ST Accel. Beams 2, 110401 (1999)], of the head-on merging of two laboratory supersonic plasma jets. The goals of these experiments are to form and study astrophysically relevant collisionless shocks in the laboratory. Using the plasma jet initial conditions (density ∼10{sup 14}–10{sup 16} cm{sup −3}, temperature ∼ few eV, and propagation speed ∼20–150 km/s), large-scale simulations of jet propagation demonstrate that interactions between the two jets are essentially collisionless at the merge region. In highly resolved one- and two-dimensional simulations, we showmore » that collisionless shocks are generated by the merging jets when immersed in applied magnetic fields (B∼0.1–1 T). At expected plasma jet speeds of up to 150 km/s, our simulations do not give rise to unmagnetized collisionless shocks, which require much higher velocities. The orientation of the magnetic field and the axial and transverse density gradients of the jets have a strong effect on the nature of the interaction. We compare some of our simulation results with those of previously published PIC simulation studies of collisionless shock formation.« less

Systematic Review of Patient-Specific Surgical Simulation: Toward Advancing Medical Education.

PubMed

Ryu, Won Hyung A; Dharampal, Navjit; Mostafa, Ahmed E; Sharlin, Ehud; Kopp, Gail; Jacobs, William Bradley; Hurlbert, Robin John; Chan, Sonny; Sutherland, Garnette R

Simulation-based education has been shown to be an effective tool to teach foundational technical skills in various surgical specialties. However, most of the current simulations are limited to generic scenarios and do not allow continuation of the learning curve beyond basic technical skills to prepare for more advanced expertise, such as patient-specific surgical planning. The objective of this study was to evaluate the current medical literature with respect to the utilization and educational value of patient-specific simulations for surgical training. We performed a systematic review of the literature using Pubmed, Embase, and Scopus focusing on themes of simulation, patient-specific, surgical procedure, and education. The study included randomized controlled trials, cohort studies, and case-control studies published between 2005 and 2016. Two independent reviewers (W.H.R. and N.D) conducted the study appraisal, data abstraction, and quality assessment of the studies. The search identified 13 studies that met the inclusion criteria; 7 studies employed computer simulations and 6 studies used 3-dimensional (3D) synthetic models. A number of surgical specialties evaluated patient-specific simulation, including neurosurgery, vascular surgery, orthopedic surgery, and interventional radiology. However, most studies were small in size and primarily aimed at feasibility assessments and early validation. Early evidence has shown feasibility and utility of patient-specific simulation for surgical education. With further development of this technology, simulation-based education may be able to support training of higher-level competencies outside the clinical settingto aid learners in their development of surgical skills. Copyright © 2017 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.

Simulation of image detectors in radiology for determination of scatter-to-primary ratios using Monte Carlo radiation transport code MCNP/MCNPX.

PubMed

Smans, Kristien; Zoetelief, Johannes; Verbrugge, Beatrijs; Haeck, Wim; Struelens, Lara; Vanhavere, Filip; Bosmans, Hilde

2010-05-01

The purpose of this study was to compare and validate three methods to simulate radiographic image detectors with the Monte Carlo software MCNP/MCNPX in a time efficient way. The first detector model was the standard semideterministic radiography tally, which has been used in previous image simulation studies. Next to the radiography tally two alternative stochastic detector models were developed: A perfect energy integrating detector and a detector based on the energy absorbed in the detector material. Validation of three image detector models was performed by comparing calculated scatter-to-primary ratios (SPRs) with the published and experimentally acquired SPR values. For mammographic applications, SPRs computed with the radiography tally were up to 44% larger than the published results, while the SPRs computed with the perfect energy integrating detectors and the blur-free absorbed energy detector model were, on the average, 0.3% (ranging from -3% to 3%) and 0.4% (ranging from -5% to 5%) lower, respectively. For general radiography applications, the radiography tally overestimated the measured SPR by as much as 46%. The SPRs calculated with the perfect energy integrating detectors were, on the average, 4.7% (ranging from -5.3% to -4%) lower than the measured SPRs, whereas for the blur-free absorbed energy detector model, the calculated SPRs were, on the average, 1.3% (ranging from -0.1% to 2.4%) larger than the measured SPRs. For mammographic applications, both the perfect energy integrating detector model and the blur-free energy absorbing detector model can be used to simulate image detectors, whereas for conventional x-ray imaging using higher energies, the blur-free energy absorbing detector model is the most appropriate image detector model. The radiography tally overestimates the scattered part and should therefore not be used to simulate radiographic image detectors.

Sensitivity of charge transport measurements to local inhomogeneities

NASA Astrophysics Data System (ADS)

Koon, Daniel; Wang, Fei; Hjorth Petersen, Dirch; Hansen, Ole

2012-02-01

We derive analytic expressions for the sensitivity of resistive and Hall measurements to local variations in a specimen's material properties in the combined linear limit of both small magnetic fields and small perturbations, presenting exact, algebraic expressions both for four-point probe measurements on an infinite plane and for symmetric, circular van der Pauw discs. We then generalize the results to obtain corrections to the sensitivities both for finite magnetic fields and for finite perturbations. Calculated functions match published results and computer simulations, and provide an intuitive, visual explanation for experimental misassignment of carrier type in n-type ZnO and agree with published experimental results for holes in a uniform material. These results simplify calculation and plotting of the sensitivities on an NxN grid from a problem of order N^5 to one of order N^3 in the arbitrary case and of order N^2 in the handful of cases that can be solved exactly, putting a powerful tool for inhomogeneity analysis in the hands of the researcher: calculation of the sensitivities requires little more than the solution of Laplace's equation on the specimen geometry.

Effects of sample size on KERNEL home range estimates

USGS Publications Warehouse

Seaman, D.E.; Millspaugh, J.J.; Kernohan, Brian J.; Brundige, Gary C.; Raedeke, Kenneth J.; Gitzen, Robert A.

1999-01-01

Kernel methods for estimating home range are being used increasingly in wildlife research, but the effect of sample size on their accuracy is not known. We used computer simulations of 10-200 points/home range and compared accuracy of home range estimates produced by fixed and adaptive kernels with the reference (REF) and least-squares cross-validation (LSCV) methods for determining the amount of smoothing. Simulated home ranges varied from simple to complex shapes created by mixing bivariate normal distributions. We used the size of the 95% home range area and the relative mean squared error of the surface fit to assess the accuracy of the kernel home range estimates. For both measures, the bias and variance approached an asymptote at about 50 observations/home range. The fixed kernel with smoothing selected by LSCV provided the least-biased estimates of the 95% home range area. All kernel methods produced similar surface fit for most simulations, but the fixed kernel with LSCV had the lowest frequency and magnitude of very poor estimates. We reviewed 101 papers published in The Journal of Wildlife Management (JWM) between 1980 and 1997 that estimated animal home ranges. A minority of these papers used nonparametric utilization distribution (UD) estimators, and most did not adequately report sample sizes. We recommend that home range studies using kernel estimates use LSCV to determine the amount of smoothing, obtain a minimum of 30 observations per animal (but preferably a?Y50), and report sample sizes in published results.

Modeling the impact of biota on polychlorinated biphenyls (PCBs) fate and transport in Lake Ontario using a population-based multi-compartment fugacity approach.

PubMed

Sun, Xiangfei; Ng, Carla A; Small, Mitchell J

2018-06-12

Organisms have long been treated as receptors in exposure studies of polychlorinated biphenyls (PCBs) and other persistent organic pollutants (POPs). The influences of environmental pollution on organisms are well recognized. However, the impact of biota on PCB transport in an environmental system has not been considered in sufficient detail. In this study, a population-based multi-compartment fugacity model is developed by reconfiguring the organisms as populated compartments and reconstructing all the exchange processes between the organism compartments and environmental compartments, especially the previously ignored feedback routes from biota to the environment. We evaluate the model performance by simulating the PCB concentration distribution in Lake Ontario using published loading records. The lake system is divided into three environment compartments (air, water, and sediment) and several organism groups according to the dominant local biotic species. The comparison indicates that the simulated results are well-matched by a list of published field measurements from different years. We identify a new process, called Facilitated Biotic Intermedia Transport (FBIT), to describe the enhanced pollution transport that occurs between environmental media and organisms. As the hydrophobicity of PCB congener increases, the organism population exerts greater influence on PCB mass flows. In a high biomass scenario, the model simulation indicates significant FBIT effects and biotic storage effects with hydrophobic PCB congeners, which also lead to significant shifts in systemic contaminant exchange rates between organisms and the environment. Copyright © 2018 Elsevier Ltd. All rights reserved.

TH-E-18A-01: Developments in Monte Carlo Methods for Medical Imaging

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

Badal, A; Zbijewski, W; Bolch, W

Monte Carlo simulation methods are widely used in medical physics research and are starting to be implemented in clinical applications such as radiation therapy planning systems. Monte Carlo simulations offer the capability to accurately estimate quantities of interest that are challenging to measure experimentally while taking into account the realistic anatomy of an individual patient. Traditionally, practical application of Monte Carlo simulation codes in diagnostic imaging was limited by the need for large computational resources or long execution times. However, recent advancements in high-performance computing hardware, combined with a new generation of Monte Carlo simulation algorithms and novel postprocessing methods,more » are allowing for the computation of relevant imaging parameters of interest such as patient organ doses and scatter-to-primaryratios in radiographic projections in just a few seconds using affordable computational resources. Programmable Graphics Processing Units (GPUs), for example, provide a convenient, affordable platform for parallelized Monte Carlo executions that yield simulation times on the order of 10{sup 7} xray/ s. Even with GPU acceleration, however, Monte Carlo simulation times can be prohibitive for routine clinical practice. To reduce simulation times further, variance reduction techniques can be used to alter the probabilistic models underlying the x-ray tracking process, resulting in lower variance in the results without biasing the estimates. Other complementary strategies for further reductions in computation time are denoising of the Monte Carlo estimates and estimating (scoring) the quantity of interest at a sparse set of sampling locations (e.g. at a small number of detector pixels in a scatter simulation) followed by interpolation. Beyond reduction of the computational resources required for performing Monte Carlo simulations in medical imaging, the use of accurate representations of patient anatomy is crucial to the virtual generation of medical images and accurate estimation of radiation dose and other imaging parameters. For this, detailed computational phantoms of the patient anatomy must be utilized and implemented within the radiation transport code. Computational phantoms presently come in one of three format types, and in one of four morphometric categories. Format types include stylized (mathematical equation-based), voxel (segmented CT/MR images), and hybrid (NURBS and polygon mesh surfaces). Morphometric categories include reference (small library of phantoms by age at 50th height/weight percentile), patient-dependent (larger library of phantoms at various combinations of height/weight percentiles), patient-sculpted (phantoms altered to match the patient's unique outer body contour), and finally, patient-specific (an exact representation of the patient with respect to both body contour and internal anatomy). The existence and availability of these phantoms represents a very important advance for the simulation of realistic medical imaging applications using Monte Carlo methods. New Monte Carlo simulation codes need to be thoroughly validated before they can be used to perform novel research. Ideally, the validation process would involve comparison of results with those of an experimental measurement, but accurate replication of experimental conditions can be very challenging. It is very common to validate new Monte Carlo simulations by replicating previously published simulation results of similar experiments. This process, however, is commonly problematic due to the lack of sufficient information in the published reports of previous work so as to be able to replicate the simulation in detail. To aid in this process, the AAPM Task Group 195 prepared a report in which six different imaging research experiments commonly performed using Monte Carlo simulations are described and their results provided. The simulation conditions of all six cases are provided in full detail, with all necessary data on material composition, source, geometry, scoring and other parameters provided. The results of these simulations when performed with the four most common publicly available Monte Carlo packages are also provided in tabular form. The Task Group 195 Report will be useful for researchers needing to validate their Monte Carlo work, and for trainees needing to learn Monte Carlo simulation methods. In this symposium we will review the recent advancements in highperformance computing hardware enabling the reduction in computational resources needed for Monte Carlo simulations in medical imaging. We will review variance reduction techniques commonly applied in Monte Carlo simulations of medical imaging systems and present implementation strategies for efficient combination of these techniques with GPU acceleration. Trade-offs involved in Monte Carlo acceleration by means of denoising and “sparse sampling” will be discussed. A method for rapid scatter correction in cone-beam CT (<5 min/scan) will be presented as an illustration of the simulation speeds achievable with optimized Monte Carlo simulations. We will also discuss the development, availability, and capability of the various combinations of computational phantoms for Monte Carlo simulation of medical imaging systems. Finally, we will review some examples of experimental validation of Monte Carlo simulations and will present the AAPM Task Group 195 Report. Learning Objectives: Describe the advances in hardware available for performing Monte Carlo simulations in high performance computing environments. Explain variance reduction, denoising and sparse sampling techniques available for reduction of computational time needed for Monte Carlo simulations of medical imaging. List and compare the computational anthropomorphic phantoms currently available for more accurate assessment of medical imaging parameters in Monte Carlo simulations. Describe experimental methods used for validation of Monte Carlo simulations in medical imaging. Describe the AAPM Task Group 195 Report and its use for validation and teaching of Monte Carlo simulations in medical imaging.« less

A National Needs Assessment to Identify Technical Procedures in Vascular Surgery for Simulation Based Training.

PubMed

Nayahangan, L J; Konge, L; Schroeder, T V; Paltved, C; Lindorff-Larsen, K G; Nielsen, B U; Eiberg, J P

2017-04-01

Practical skills training in vascular surgery is facing challenges because of an increased number of endovascular procedures and fewer open procedures, as well as a move away from the traditional principle of "learning by doing." This change has established simulation as a cornerstone in providing trainees with the necessary skills and competences. However, the development of simulation based programs often evolves based on available resources and equipment, reflecting convenience rather than a systematic educational plan. The objective of the present study was to perform a national needs assessment to identify the technical procedures that should be integrated in a simulation based curriculum. A national needs assessment using a Delphi process was initiated by engaging 33 predefined key persons in vascular surgery. Round 1 was a brainstorming phase to identify technical procedures that vascular surgeons should learn. Round 2 was a survey that used a needs assessment formula to explore the frequency of procedures, the number of surgeons performing each procedure, risk and/or discomfort, and feasibility for simulation based training. Round 3 involved elimination and ranking of procedures. The response rate for round 1 was 70%, with 36 procedures identified. Round 2 had a 76% response rate and resulted in a preliminary prioritised list after exploring the need for simulation based training. Round 3 had an 85% response rate; 17 procedures were eliminated, resulting in a final prioritised list of 19 technical procedures. A national needs assessment using a standardised Delphi method identified a list of procedures that are highly suitable and may provide the basis for future simulation based training programs for vascular surgeons in training. Copyright © 2017 European Society for Vascular Surgery. Published by Elsevier Ltd. All rights reserved.

Dose Titration Algorithm Tuning (DTAT) should supersede 'the' Maximum Tolerated Dose (MTD) in oncology dose-finding trials.

PubMed

Norris, David C

2017-01-01

Background . Absent adaptive, individualized dose-finding in early-phase oncology trials, subsequent 'confirmatory' Phase III trials risk suboptimal dosing, with resulting loss of statistical power and reduced probability of technical success for the investigational therapy. While progress has been made toward explicitly adaptive dose-finding and quantitative modeling of dose-response relationships, most such work continues to be organized around a concept of 'the' maximum tolerated dose (MTD). The purpose of this paper is to demonstrate concretely how the aim of early-phase trials might be conceived, not as 'dose-finding', but as dose titration algorithm (DTA) -finding. Methods. A Phase I dosing study is simulated, for a notional cytotoxic chemotherapy drug, with neutropenia constituting the critical dose-limiting toxicity. The drug's population pharmacokinetics and myelosuppression dynamics are simulated using published parameter estimates for docetaxel. The amenability of this model to linearization is explored empirically. The properties of a simple DTA targeting neutrophil nadir of 500 cells/mm 3 using a Newton-Raphson heuristic are explored through simulation in 25 simulated study subjects. Results. Individual-level myelosuppression dynamics in the simulation model approximately linearize under simple transformations of neutrophil concentration and drug dose. The simulated dose titration exhibits largely satisfactory convergence, with great variance in individualized optimal dosing. Some titration courses exhibit overshooting. Conclusions. The large inter-individual variability in simulated optimal dosing underscores the need to replace 'the' MTD with an individualized concept of MTD i . To illustrate this principle, the simplest possible DTA capable of realizing such a concept is demonstrated. Qualitative phenomena observed in this demonstration support discussion of the notion of tuning such algorithms. Although here illustrated specifically in relation to cytotoxic chemotherapy, the DTAT principle appears similarly applicable to Phase I studies of cancer immunotherapy and molecularly targeted agents.

Competing Pathways and Multiple Folding Nuclei in a Large Multidomain Protein, Luciferase.

PubMed

Scholl, Zackary N; Yang, Weitao; Marszalek, Piotr E

2017-05-09

Proteins obtain their final functional configuration through incremental folding with many intermediate steps in the folding pathway. If known, these intermediate steps could be valuable new targets for designing therapeutics and the sequence of events could elucidate the mechanism of refolding. However, determining these intermediate steps is hardly an easy feat, and has been elusive for most proteins, especially large, multidomain proteins. Here, we effectively map part of the folding pathway for the model large multidomain protein, Luciferase, by combining single-molecule force-spectroscopy experiments and coarse-grained simulation. Single-molecule refolding experiments reveal the initial nucleation of folding while simulations corroborate these stable core structures of Luciferase, and indicate the relative propensities for each to propagate to the final folded native state. Both experimental refolding and Monte Carlo simulations of Markov state models generated from simulation reveal that Luciferase most often folds along a pathway originating from the nucleation of the N-terminal domain, and that this pathway is the least likely to form nonnative structures. We then engineer truncated variants of Luciferase whose sequences corresponded to the putative structure from simulation and we use atomic force spectroscopy to determine their unfolding and stability. These experimental results corroborate the structures predicted from the folding simulation and strongly suggest that they are intermediates along the folding pathway. Taken together, our results suggest that initial Luciferase refolding occurs along a vectorial pathway and also suggest a mechanism that chaperones may exploit to prevent misfolding. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Inappropriate Fiddling with Statistical Analyses to Obtain a Desirable P-value: Tests to Detect its Presence in Published Literature

PubMed Central

Gadbury, Gary L.; Allison, David B.

2012-01-01

Much has been written regarding p-values below certain thresholds (most notably 0.05) denoting statistical significance and the tendency of such p-values to be more readily publishable in peer-reviewed journals. Intuition suggests that there may be a tendency to manipulate statistical analyses to push a “near significant p-value” to a level that is considered significant. This article presents a method for detecting the presence of such manipulation (herein called “fiddling”) in a distribution of p-values from independent studies. Simulations are used to illustrate the properties of the method. The results suggest that the method has low type I error and that power approaches acceptable levels as the number of p-values being studied approaches 1000. PMID:23056287

Inappropriate fiddling with statistical analyses to obtain a desirable p-value: tests to detect its presence in published literature.

PubMed

Gadbury, Gary L; Allison, David B

2012-01-01

Much has been written regarding p-values below certain thresholds (most notably 0.05) denoting statistical significance and the tendency of such p-values to be more readily publishable in peer-reviewed journals. Intuition suggests that there may be a tendency to manipulate statistical analyses to push a "near significant p-value" to a level that is considered significant. This article presents a method for detecting the presence of such manipulation (herein called "fiddling") in a distribution of p-values from independent studies. Simulations are used to illustrate the properties of the method. The results suggest that the method has low type I error and that power approaches acceptable levels as the number of p-values being studied approaches 1000.

Boundedness, Mittag-Leffler stability and asymptotical ω-periodicity of fractional-order fuzzy neural networks.

PubMed

Wu, Ailong; Zeng, Zhigang

2016-02-01

We show that the ω-periodic fractional-order fuzzy neural networks cannot generate non-constant ω-periodic signals. In addition, several sufficient conditions are obtained to ascertain the boundedness and global Mittag-Leffler stability of fractional-order fuzzy neural networks. Furthermore, S-asymptotical ω-periodicity and global asymptotical ω-periodicity of fractional-order fuzzy neural networks is also characterized. The obtained criteria improve and extend the existing related results. To illustrate and compare the theoretical criteria, some numerical examples with simulation results are discussed in detail. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

Simulation-based bronchoscopy training: systematic review and meta-analysis.

PubMed

Kennedy, Cassie C; Maldonado, Fabien; Cook, David A

2013-07-01

Simulation-based bronchoscopy training is increasingly used, but effectiveness remains uncertain. We sought to perform a comprehensive synthesis of published work on simulation-based bronchoscopy training. We searched MEDLINE, EMBASE, CINAHL, PsycINFO, ERIC, Web of Science, and Scopus for eligible articles through May 11, 2011. We included all original studies involving health professionals that evaluated, in comparison with no intervention or an alternative instructional approach, simulation-based training for flexible or rigid bronchoscopy. Study selection and data abstraction were performed independently and in duplicate. We pooled results using random effects meta-analysis. From an initial pool of 10,903 articles, we identified 17 studies evaluating simulation-based bronchoscopy training. In comparison with no intervention, simulation training was associated with large benefits on skills and behaviors (pooled effect size, 1.21 [95% CI, 0.82-1.60]; n=8 studies) and moderate benefits on time (0.62 [95% CI, 0.12-1.13]; n=7). In comparison with clinical instruction, behaviors with real patients showed nonsignificant effects favoring simulation for time (0.61 [95% CI, -1.47 to 2.69]) and process (0.33 [95% CI, -1.46 to 2.11]) outcomes (n=2 studies each), although variation in training time might account for these differences. Four studies compared alternate simulation-based training approaches. Inductive analysis to inform instructional design suggested that longer or more structured training is more effective, authentic clinical context adds value, and animal models and plastic part-task models may be superior to more costly virtual-reality simulators. Simulation-based bronchoscopy training is effective in comparison with no intervention. Comparative effectiveness studies are few.

Understanding bulk behavior of particulate materials from particle scale simulations

NASA Astrophysics Data System (ADS)

Deng, Xiaoliang

Particulate materials play an increasingly significant role in various industries, such as pharmaceutical manufacturing, food, mining, and civil engineering. The objective of this research is to better understand bulk behaviors of particulate materials from particle scale simulations. Packing properties of assembly of particles are investigated first, focusing on the effects of particle size, surface energy, and aspect ratio on the coordination number, porosity, and packing structures. The simulation results show that particle sizes, surface energy, and aspect ratio all influence the porosity of packing to various degrees. The heterogeneous force networks within particle assembly under external compressive loading are investigated as well. The results show that coarse-coarse contacts dominate the strong network and coarse-fine contacts dominate the total network. Next, DEM models are developed to simulate the particle dynamics inside a conical screen mill (comil) and magnetically assisted impaction mixer (MAIM), both are important particle processing devices. For comil, the mean residence time (MRT), spatial distribution of particles, along with the collision dynamics between particles as well as particle and vessel geometries are examined as a function of the various operating parameters such as impeller speed, screen hole size, open area, and feed rate. The simulation results can help better understand dry coating experimental results using comil. For MAIM system, the magnetic force is incorporated into the contact model, allowing to describe the interactions between magnets. The simulation results reveal the connections between homogeneity of mixture and particle scale variables such as size of magnets and surface energy of non-magnets. In particular, at the fixed mass ratio of magnets to non-magnets and surface energy the smaller magnets lead to better homogeneity of mixing, which is in good agreement with previously published experimental results. Last but not least, numerical simulations, along with theoretical analysis, are performed to investigate the interparticle force of dry coated particles. A model is derived and can be used to predict the probabilities of hose-host (HH), host-guest (HG), and guest-guest (GG) contacts. The results indicate that there are three different regions dominated by HH, HG, and GG contacts, respectively. Moreover, the critical SAC for the transition of HG to GG contacts is lower than previously estimated value. In summary, particle packing, particle dynamics associated with various particle processing devices, and interparticle force of dry coated particles are investigated in this thesis. The results show that particle scale information such as coordination number, collision dynamics, and contact force between particles from simulation results can help better understand bulk properties of assembly of individual particles.

Quantum Computation and Simulation Using Neutral Fermionic Atoms

DTIC Science & Technology

2014-06-06

labeled n = 1) Efimov trimer crosses the three-atom scattering threshold. Working in the context of nuclear physics in the early 1970’s, Vitaly Efimov...permit the observation of anti-ferromagnetic ordering in the Hubbard model. (a) Papers published in peer-reviewed journals ( N /A for none) Enter List of...Physics, (06 2011): 0. doi: TOTAL: 7 Number of Papers published in peer-reviewed journals: (b) Papers published in non-peer-reviewed journals ( N /A for

Pore-scale and continuum simulations of solute transport micromodel benchmark experiments

DOE PAGES

Oostrom, M.; Mehmani, Y.; Romero-Gomez, P.; ...

2014-06-18

Four sets of nonreactive solute transport experiments were conducted with micromodels. Three experiments with one variable, i.e., flow velocity, grain diameter, pore-aspect ratio, and flow-focusing heterogeneity were in each set. The data sets were offered to pore-scale modeling groups to test their numerical simulators. Each set consisted of two learning experiments, for which our results were made available, and one challenge experiment, for which only the experimental description and base input parameters were provided. The experimental results showed a nonlinear dependence of the transverse dispersion coefficient on the Peclet number, a negligible effect of the pore-aspect ratio on transverse mixing,more » and considerably enhanced mixing due to flow focusing. Five pore-scale models and one continuum-scale model were used to simulate the experiments. Of the pore-scale models, two used a pore-network (PN) method, two others are based on a lattice Boltzmann (LB) approach, and one used a computational fluid dynamics (CFD) technique. Furthermore, we used the learning experiments, by the PN models, to modify the standard perfect mixing approach in pore bodies into approaches to simulate the observed incomplete mixing. The LB and CFD models used the learning experiments to appropriately discretize the spatial grid representations. For the continuum modeling, the required dispersivity input values were estimated based on published nonlinear relations between transverse dispersion coefficients and Peclet number. Comparisons between experimental and numerical results for the four challenge experiments show that all pore-scale models were all able to satisfactorily simulate the experiments. The continuum model underestimated the required dispersivity values, resulting in reduced dispersion. The PN models were able to complete the simulations in a few minutes, whereas the direct models, which account for the micromodel geometry and underlying flow and transport physics, needed up to several days on supercomputers to resolve the more complex problems.« less

Testing for Questionable Research Practices in a Meta-Analysis: An Example from Experimental Parapsychology.

PubMed

Bierman, Dick J; Spottiswoode, James P; Bijl, Aron

2016-01-01

We describe a method of quantifying the effect of Questionable Research Practices (QRPs) on the results of meta-analyses. As an example we simulated a meta-analysis of a controversial telepathy protocol to assess the extent to which these experimental results could be explained by QRPs. Our simulations used the same numbers of studies and trials as the original meta-analysis and the frequencies with which various QRPs were applied in the simulated experiments were based on surveys of experimental psychologists. Results of both the meta-analysis and simulations were characterized by 4 metrics, two describing the trial and mean experiment hit rates (HR) of around 31%, where 25% is expected by chance, one the correlation between sample-size and hit-rate, and one the complete P-value distribution of the database. A genetic algorithm optimized the parameters describing the QRPs, and the fitness of the simulated meta-analysis was defined as the sum of the squares of Z-scores for the 4 metrics. Assuming no anomalous effect a good fit to the empirical meta-analysis was found only by using QRPs with unrealistic parameter-values. Restricting the parameter space to ranges observed in studies of QRP occurrence, under the untested assumption that parapsychologists use comparable QRPs, the fit to the published Ganzfeld meta-analysis with no anomalous effect was poor. We allowed for a real anomalous effect, be it unidentified QRPs or a paranormal effect, where the HR ranged from 25% (chance) to 31%. With an anomalous HR of 27% the fitness became F = 1.8 (p = 0.47 where F = 0 is a perfect fit). We conclude that the very significant probability cited by the Ganzfeld meta-analysis is likely inflated by QRPs, though results are still significant (p = 0.003) with QRPs. Our study demonstrates that quantitative simulations of QRPs can assess their impact. Since meta-analyses in general might be polluted by QRPs, this method has wide applicability outside the domain of experimental parapsychology.

A Review and Comparison of Methods for Recreating Individual Patient Data from Published Kaplan-Meier Survival Curves for Economic Evaluations: A Simulation Study

PubMed Central

Wan, Xiaomin; Peng, Liubao; Li, Yuanjian

2015-01-01

Background In general, the individual patient-level data (IPD) collected in clinical trials are not available to independent researchers to conduct economic evaluations; researchers only have access to published survival curves and summary statistics. Thus, methods that use published survival curves and summary statistics to reproduce statistics for economic evaluations are essential. Four methods have been identified: two traditional methods 1) least squares method, 2) graphical method; and two recently proposed methods by 3) Hoyle and Henley, 4) Guyot et al. The four methods were first individually reviewed and subsequently assessed regarding their abilities to estimate mean survival through a simulation study. Methods A number of different scenarios were developed that comprised combinations of various sample sizes, censoring rates and parametric survival distributions. One thousand simulated survival datasets were generated for each scenario, and all methods were applied to actual IPD. The uncertainty in the estimate of mean survival time was also captured. Results All methods provided accurate estimates of the mean survival time when the sample size was 500 and a Weibull distribution was used. When the sample size was 100 and the Weibull distribution was used, the Guyot et al. method was almost as accurate as the Hoyle and Henley method; however, more biases were identified in the traditional methods. When a lognormal distribution was used, the Guyot et al. method generated noticeably less bias and a more accurate uncertainty compared with the Hoyle and Henley method. Conclusions The traditional methods should not be preferred because of their remarkable overestimation. When the Weibull distribution was used for a fitted model, the Guyot et al. method was almost as accurate as the Hoyle and Henley method. However, if the lognormal distribution was used, the Guyot et al. method was less biased compared with the Hoyle and Henley method. PMID:25803659

Compression simulations of plant tissue in 3D using a mass-spring system approach and discrete element method.

PubMed

Pieczywek, Piotr M; Zdunek, Artur

2017-10-18

A hybrid model based on a mass-spring system methodology coupled with the discrete element method (DEM) was implemented to simulate the deformation of cellular structures in 3D. Models of individual cells were constructed using the particles which cover the surfaces of cell walls and are interconnected in a triangle mesh network by viscoelastic springs. The spatial arrangement of the cells required to construct a virtual tissue was obtained using Poisson-disc sampling and Voronoi tessellation in 3D space. Three structural features were included in the model: viscoelastic material of cell walls, linearly elastic interior of the cells (simulating compressible liquid) and a gas phase in the intercellular spaces. The response of the models to an external load was demonstrated during quasi-static compression simulations. The sensitivity of the model was investigated at fixed compression parameters with variable tissue porosity, cell size and cell wall properties, such as thickness and Young's modulus, and a stiffness of the cell interior that simulated turgor pressure. The extent of the agreement between the simulation results and other models published is discussed. The model demonstrated the significant influence of tissue structure on micromechanical properties and allowed for the interpretation of the compression test results with respect to changes occurring in the structure of the virtual tissue. During compression virtual structures composed of smaller cells produced higher reaction forces and therefore they were stiffer than structures with large cells. The increase in the number of intercellular spaces (porosity) resulted in a decrease in reaction forces. The numerical model was capable of simulating the quasi-static compression experiment and reproducing the strain stiffening observed in experiment. Stress accumulation at the edges of the cell walls where three cells meet suggests that cell-to-cell debonding and crack propagation through the contact edge of neighboring cells is one of the most prevalent ways for tissue to rupture.

Development and evaluation of a simulation exercise to prepare midwifery students for neonatal resuscitation.

PubMed

Carolan-Olah, Mary; Kruger, Gina; Brown, Vera; Lawton, Felicity; Mazzarino, Melissa

2016-01-01

Simulation provides opportunities for midwifery students to enhance their performance in emergency situations. Neonatal resuscitation is one such emergency and its management is a major concern for midwifery students. This project aimed to develop and evaluate a simulation exercise, for neonatal resuscitation, for 3rd year midwifery students. A quantitative survey design was employed using questions from two previously validated questionnaires: (1.) Student Satisfaction and Self-Confidence in Learning and (2.) the Clinical Teamwork Scale (CTS). Australian university. 40 final year midwifery students were invited to participate and 36 agreed to take part in the project. In pre-simulation questionnaires, students reported low levels of confidence in initiating care of an infant requiring resuscitation. Most anticipated that the simulation exercise would be useful to better prepare them respond to a neonatal emergency. Post-simulation questionnaires reported an increase in student confidence, with 30 of 36 students agreeing/ strongly agreeing that their confidence levels had improved. Nonetheless, an unexpected number of students reported a lack of familiarity with the equipment. The single simulation exercise evaluated in this project resulted in improved student confidence and greater knowledge and skills in neonatal resuscitation. However, deficits in handling emergency equipment, and in understanding the role of the student midwife/midwife in neonatal resuscitation, were also noted. For the future, the development and evaluation of a programme of simulation exercises, over a longer period, is warranted. This approach may reduce stress and better address student learning needs. Copyright © 2015. Published by Elsevier Ltd.

Precipitation Dynamical Downscaling Over the Great Plains

NASA Astrophysics Data System (ADS)

Hu, Xiao-Ming; Xue, Ming; McPherson, Renee A.; Martin, Elinor; Rosendahl, Derek H.; Qiao, Lei

2018-02-01

Detailed, regional climate projections, particularly for precipitation, are critical for many applications. Accurate precipitation downscaling in the United States Great Plains remains a great challenge for most Regional Climate Models, particularly for warm months. Most previous dynamic downscaling simulations significantly underestimate warm-season precipitation in the region. This study aims to achieve a better precipitation downscaling in the Great Plains with the Weather Research and Forecast (WRF) model. To this end, WRF simulations with different physics schemes and nudging strategies are first conducted for a representative warm season. Results show that different cumulus schemes lead to more pronounced difference in simulated precipitation than other tested physics schemes. Simply choosing different physics schemes is not enough to alleviate the dry bias over the southern Great Plains, which is related to an anticyclonic circulation anomaly over the central and western parts of continental U.S. in the simulations. Spectral nudging emerges as an effective solution for alleviating the precipitation bias. Spectral nudging ensures that large and synoptic-scale circulations are faithfully reproduced while still allowing WRF to develop small-scale dynamics, thus effectively suppressing the large-scale circulation anomaly in the downscaling. As a result, a better precipitation downscaling is achieved. With the carefully validated configurations, WRF downscaling is conducted for 1980-2015. The downscaling captures well the spatial distribution of monthly climatology precipitation and the monthly/yearly variability, showing improvement over at least two previously published precipitation downscaling studies. With the improved precipitation downscaling, a better hydrological simulation over the trans-state Oologah watershed is also achieved.

ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins

PubMed Central

2015-01-01

We present the ff14ipq force field, implementing the previously published IPolQ charge set for simulations of complete proteins. Minor modifications to the charge derivation scheme and van der Waals interactions between polar atoms are introduced. Torsion parameters are developed through a generational learning approach, based on gas-phase MP2/cc-pVTZ single-point energies computed of structures optimized by the force field itself rather than the quantum benchmark. In this manner, we sacrifice information about the true quantum minima in order to ensure that the force field maintains optimal agreement with the MP2/cc-pVTZ benchmark for the ensembles it will actually produce in simulations. A means of making the gas-phase torsion parameters compatible with solution-phase IPolQ charges is presented. The ff14ipq model is an alternative to ff99SB and other Amber force fields for protein simulations in programs that accommodate pair-specific Lennard–Jones combining rules. The force field gives strong performance on α-helical and β-sheet oligopeptides as well as globular proteins over microsecond time scale simulations, although it has not yet been tested in conjunction with lipid and nucleic acid models. We show how our choices in parameter development influence the resulting force field and how other choices that may have appeared reasonable would actually have led to poorer results. The tools we developed may also aid in the development of future fixed-charge and even polarizable biomolecular force fields. PMID:25328495

Closely Coupled Multi-Mode Radiators: A New Concept for Improving the Perfomance of Electrically Small Antennas

DTIC Science & Technology

2015-11-23

realized gain values of−5.0 dBiC and 3.1 dBiC, respectively. Details of the design, optimization, simulation, and the measured results of the fabricated...prototype of this Fig. 4. The measured input VSWR of the antenna prototype shown in Fig. 3. 7    antenna were published in IEEE Transactions on...suppressed. Other prototypes of these types of MEFSSs were also designed and fabricated and characterized. Details of the design and measurement

Methods for Reachability-based Hybrid Controller Design

DTIC Science & Technology

2012-05-10

approaches for airport runways ( Teo and Tomlin, 2003). The results of the reachability calculations were validated in extensive simulations as well as...UAV flight experiments (Jang and Tomlin, 2005; Teo , 2005). While the focus of these previous applications lies largely in safety verification, the work...B([15, 0],a0)× [−π,π])\\ V,∀qi ∈ Q, where a0 = 30m is the protected radius (chosen based upon published data of the wingspan of a Boeing KC -135

Frontiers in the Teaching of Physiology. Computer Literacy and Simulation.

ERIC Educational Resources Information Center

Tidball, Charles S., Ed.; Shelesnyak, M. C., Ed.

Provided is a collection of papers on computer literacy and simulation originally published in The Physiology Teacher, supplemented by additional papers and a glossary of terms relevant to the field. The 12 papers are presented in five sections. An affirmation of conventional physiology laboratory exercises, coping with computer terminology, and…

Linking population viability, habitat suitability, and landscape simulation models for conservation planning

Treesearch

Michael A. Larson; Frank R., III Thompson; Joshua J. Millspaugh; William D. Dijak; Stephen R. Shifley

2004-01-01

Methods for habitat modeling based on landscape simulations and population viability modeling based on habitat quality are well developed, but no published study of which we are aware has effectively joined them in a single, comprehensive analysis. We demonstrate the application of a population viability model for ovenbirds (Seiurus aurocapillus)...

Power and the Power Simulation: Then and Now

ERIC Educational Resources Information Center

Bolman, Lee; Deal, Terrence E.

2017-01-01

Lee Bolman and Terrence Deal think of how much has changed since the era of innocence when they first published "A Simple But Powerful Power Simulation"--before the advent of cell phones, personal computers, the Internet, e-mail, Facebook, and Twitter. So much has changed, and yet the fundamentals of human behavior, social interaction,…

Comparing Macroscale and Microscale Simulations of Porous Battery Electrodes

DOE PAGES

Higa, Kenneth; Wu, Shao-Ling; Parkinson, Dilworth Y.; ...

2017-06-22

This article describes a vertically-integrated exploration of NMC electrode rate limitations, combining experiments with corresponding macroscale (macro-homogeneous) and microscale models. Parameters common to both models were obtained from experiments or based on published results. Positive electrode tortuosity was the sole fitting parameter used in the macroscale model, while the microscale model used no fitting parameters, instead relying on microstructural domains generated from X-ray microtomography of pristine electrode material held under compression while immersed in electrolyte solution (additionally providing novel observations of electrode wetting). Macroscale simulations showed that the capacity decrease observed at higher rates resulted primarily from solution-phase diffusion resistance.more » This ability to provide such qualitative insights at low computational costs is a strength of macroscale models, made possible by neglecting electrode spatial details. To explore the consequences of such simplification, the corresponding, computationally-expensive microscale model was constructed. This was found to have limitations preventing quantitatively accurate predictions, for reasons that are discussed in the hope of guiding future work. Nevertheless, the microscale simulation results complement those of the macroscale model by providing a reality-check based on microstructural information; in particular, this novel comparison of the two approaches suggests a reexamination of salt diffusivity measurements.« less

Chitosan nanoparticles-trypsin interactions: Bio-physicochemical and molecular dynamics simulation studies.

PubMed

Salar, Safoura; Mehrnejad, Faramarz; Sajedi, Reza H; Arough, Javad Mohammadnejad

2017-10-01

Herein, we investigated the effect of the chitosan nanoparticles (CsNP) on the structure, dynamics, and activity of trypsin. The enzyme activity in complex with the nanoparticles slightly increased, which represents the interactions between the nanoparticles and the enzyme. The kinetic parameters of the enzyme, K m and k cat , increased after adding the nanoparticles, resulting in a slight increase in the catalytic efficiency (k cat /K m ). However, the effect of the nanoparticles on the kinetic stability of trypsin has not exhibited significant variations. Fluorescence spectroscopy did not show remarkable changes in the trypsin conformation in the presence of the nanoparticles. The circular dichroism (CD) spectroscopy results also revealed the secondary structure of trypsin attached to the nanoparticles slightly changed. Furthermore, we used molecular dynamics (MD) simulation to find more information about the interaction mechanisms between the nanoparticles and trypsin. The root mean square deviation (RMSD) of Cα atoms results have shown that in the presence of the nanoparticles, trypsin was stable. The simulation and the calculation of the binding free energy demonstrate that the nonpolar interactions are the most important forces for the formation of stable nanoparticle-trypsin complex. This study has explicitly elucidated that the nanoparticles have not considerable effect on the trypsin. Copyright © 2017. Published by Elsevier B.V.

Maintenance dose conversion between oral risperidone and paliperidone palmitate 1 month: Practical guidance based on pharmacokinetic simulations.

PubMed

Russu, Alberto; Kern Sliwa, Jennifer; Ravenstijn, Paulien; Singh, Arun; Mathews, Maju; Kim, Edward; Gopal, Srihari

2018-06-01

We assessed the dosage strengths of paliperidone palmitate 1-month (PP1M) long-acting injectable resulting in similar steady-state (SS) exposures to the dosage strengths of oral risperidone using pharmacokinetic (PK) simulations. Population PK simulations of SS PK were performed using the PK models of oral risperidone and PP1M. The concentrations of active moiety (risperidone + paliperidone) from risperidone were compared to paliperidone concentrations resulting from PP1M administration. Similarity was assessed via graphical evaluation of median and 90% prediction intervals of SS PK profiles over 28 days. Oral risperidone doses of 1, 2, 3, 4, and 6 mg/d are expected to result in similar SS PK as PP1M doses of 25, 50, 75, 100, and 150 mg eq. (which correspond to 39, 78, 117, 156, and 234 mg of paliperidone palmitate) respectively (ie 25-fold dose conversion factor from oral risperidone to PP1M). This study provides clinicians with a practical guidance to establish suitable maintenance dose levels of PP1M and oral risperidone when transitioning patients from one formulation to another. © 2018 The Authors. International Journal of Clinical Practice Published by John Wiley & Sons Ltd.

Simulations of magnetic hysteresis loops at high temperatures

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

Plumer, M. L.; Whitehead, J. P.; Fal, T. J.

2014-09-28

The kinetic Monte-Carlo algorithm as well as standard micromagnetics are used to simulate MH loops of high anisotropy magnetic recording media at both short and long time scales over a wide range of temperatures relevant to heat-assisted magnetic recording. Microscopic parameters, common to both methods, were determined by fitting to experimental data on single-layer FePt-based media that uses the Magneto-Optic Kerr effect with a slow sweep rate of 700 Oe/s. Saturation moment, uniaxial anisotropy, and exchange constants are given an intrinsic temperature dependence based on published atomistic simulations of FePt grains with an effective Curie temperature of 680 K. Ourmore » results show good agreement between micromagnetics and kinetic Monte Carlo results over a wide range of sweep rates. Loops at the slow experimental sweep rates are found to become more square-shaped, with an increasing slope, as temperature increases from 300 K. These effects also occur at higher sweep rates, typical of recording speeds, but are much less pronounced. These results demonstrate the need for accurate determination of intrinsic thermal properties of future recording media as input to micromagnetic models as well as the sensitivity of the switching behavior of thin magnetic films to applied field sweep rates at higher temperatures.« less

3D-QSAR (CoMFA, CoMSIA), molecular docking and molecular dynamics simulations study of 6-aryl-5-cyano-pyrimidine derivatives to explore the structure requirements of LSD1 inhibitors.

PubMed

Ding, Lina; Wang, Zhi-Zheng; Sun, Xu-Dong; Yang, Jing; Ma, Chao-Ya; Li, Wen; Liu, Hong-Min

2017-08-01

Recently, Histone Lysine Specific Demethylase 1 (LSD1) was regarded as a promising anticancer target for the novel drug discovery. And several small molecules as LSD1 inhibitors in different structures have been reported. In this work, we carried out a molecular modeling study on the 6-aryl-5-cyano-pyrimidine fragment LSD1 inhibitors using three-dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking and molecular dynamics simulations. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were used to generate 3D-QSAR models. The results show that the best CoMFA model has q 2 =0.802, r 2 ncv =0.979, and the best CoMSIA model has q 2 =0.799, r 2 ncv =0.982. The electrostatic, hydrophobic and H-bond donor fields play important roles in the models. Molecular docking studies predict the binding mode and the interactions between the ligand and the receptor protein. Molecular dynamics simulations results reveal that the complex of the ligand and the receptor protein are stable at 300K. All the results can provide us more useful information for our further drug design. Copyright © 2017. Published by Elsevier Ltd.

Muscle-tendon mechanics explain unexpected effects of exoskeleton assistance on metabolic rate during walking.

PubMed

Jackson, Rachel W; Dembia, Christopher L; Delp, Scott L; Collins, Steven H

2017-06-01

The goal of this study was to gain insight into how ankle exoskeletons affect the behavior of the plantarflexor muscles during walking. Using data from previous experiments, we performed electromyography-driven simulations of musculoskeletal dynamics to explore how changes in exoskeleton assistance affected plantarflexor muscle-tendon mechanics, particularly for the soleus. We used a model of muscle energy consumption to estimate individual muscle metabolic rate. As average exoskeleton torque was increased, while no net exoskeleton work was provided, a reduction in tendon recoil led to an increase in positive mechanical work performed by the soleus muscle fibers. As net exoskeleton work was increased, both soleus muscle fiber force and positive mechanical work decreased. Trends in the sum of the metabolic rates of the simulated muscles correlated well with trends in experimentally observed whole-body metabolic rate ( R 2 =0.9), providing confidence in our model estimates. Our simulation results suggest that different exoskeleton behaviors can alter the functioning of the muscles and tendons acting at the assisted joint. Furthermore, our results support the idea that the series tendon helps reduce positive work done by the muscle fibers by storing and returning energy elastically. We expect the results from this study to promote the use of electromyography-driven simulations to gain insight into the operation of muscle-tendon units and to guide the design and control of assistive devices. © 2017. Published by The Company of Biologists Ltd.

Wave-optics simulation of the double-pass beam propagation in modulating retro-reflector FSO systems using a corner cube reflector.

PubMed

Yang, Guowei; You, Shengzui; Bi, Meihua; Fan, Bing; Lu, Yang; Zhou, Xuefang; Li, Jing; Geng, Hujun; Wang, Tianshu

2017-09-10

Free-space optical (FSO) communication utilizing a modulating retro-reflector (MRR) is an innovative way to convey information between the traditional optical transceiver and the semi-passive MRR unit that reflects optical signals. The reflected signals experience turbulence-induced fading in the double-pass channel, which is very different from that in the traditional single-pass FSO channel. In this paper, we consider the corner cube reflector (CCR) as the retro-reflective device in the MRR. A general geometrical model of the CCR is established based on the ray tracing method to describe the ray trajectory inside the CCR. This ray tracing model could treat the general case that the optical beam is obliquely incident on the hypotenuse surface of the CCR with the dihedral angle error and surface nonflatness. Then, we integrate this general CCR model into the wave-optics (WO) simulation to construct the double-pass beam propagation simulation. This double-pass simulation contains the forward propagation from the transceiver to the MRR through the atmosphere, the retro-reflection of the CCR, and the backward propagation from the MRR to the transceiver, which can be realized by a single-pass WO simulation, the ray tracing CCR model, and another single-pass WO simulation, respectively. To verify the proposed CCR model and double-pass WO simulation, the effective reflection area, the incremental phase, and the reflected beam spot on the transceiver plane of the CCR are analyzed, and the numerical results are in agreement with the previously published results. Finally, we use the double-pass WO simulation to investigate the double-pass channel in the MRR FSO systems. The histograms of the turbulence-induced fading in the forward and backward channels are obtained from the simulation data and are fitted by gamma-gamma (ΓΓ) distributions. As the two opposite channels are highly correlated, we model the double-pass channel fading by the product of two correlated ΓΓ random variables (RVs).

Simulation of Hypervelocity Impact Effects on Reinforced Carbon-Carbon. Chapter 6

NASA Technical Reports Server (NTRS)

Park, Young-Keun; Fahrenthold, Eric P.

2004-01-01

Spacecraft operating in low earth orbit face a significant orbital debris impact hazard. Of particular concern, in the case of the Space Shuttle, are impacts on critical components of the thermal protection system. Recent research has formulated a new material model of reinforced carbon-carbon, for use in the analysis of hypervelocity impact effects on the Space Shuttle wing leading edge. The material model has been validated in simulations of published impact experiments and applied to model orbital debris impacts at velocities beyond the range of current experimental methods. The results suggest that momentum scaling may be used to extrapolate the available experimental data base, in order to predict the size of wing leading edge perforations at impact velocities as high as 13 km/s.

Programmable logic controller performance enhancement by field programmable gate array based design.

PubMed

Patel, Dhruv; Bhatt, Jignesh; Trivedi, Sanjay

2015-01-01

PLC, the core element of modern automation systems, due to serial execution, exhibits limitations like slow speed and poor scan time. Improved PLC design using FPGA has been proposed based on parallel execution mechanism for enhancement of performance and flexibility. Modelsim as simulation platform and VHDL used to translate, integrate and implement the logic circuit in FPGA. Xilinx's Spartan kit for implementation-testing and VB has been used for GUI development. Salient merits of the design include cost-effectiveness, miniaturization, user-friendliness, simplicity, along with lower power consumption, smaller scan time and higher speed. Various functionalities and applications like typical PLC and industrial alarm annunciator have been developed and successfully tested. Results of simulation, design and implementation have been reported. Copyright © 2014 ISA. Published by Elsevier Ltd. All rights reserved.

Variations of flow in human airways as a consequence of lung diseases

NASA Astrophysics Data System (ADS)

Lizal, Frantisek; Stejskal, David; Belka, Miloslav; Jedelsky, Jan; Jicha, Miroslav; Brat, Kristian; Herout, Vladimir; Lizalova Sujanska, Elena

2018-06-01

The efficiency of drug delivery administered by inhalation depends, among other factors, such as size and shape of aerosol particles, significantly also on the flow in the airways. As many lung diseases change both the breathing pattern and the shape of airways, we focus in this study on the influence of several selected diseases on the distribution of flow between the lung lobes and on changes the diseases induce on the course of flowrate. First, we present results of a literature survey focused on the published records of pathological breathing patterns. In the second part, we describe the newly designed breathing simulator and the implementation of the patterns into it. The last part is focused on the experimental verification of fidelity of the simulated breathing patterns.

Simulations of the Fuel Economy and Emissions of Hybrid Transit Buses over Planned Local Routes

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

Gao, Zhiming; LaClair, Tim J; Daw, C Stuart

2014-01-01

We present simulated fuel economy and emissions city transit buses powered by conventional diesel engines and diesel-hybrid electric powertrains of varying size. Six representative city drive cycles were included in the study. In addition, we included previously published aftertreatment device models for control of CO, HC, NOx, and particulate matter (PM) emissions. Our results reveal that bus hybridization can significantly enhance fuel economy by reducing engine idling time, reducing demands for accessory loads, exploiting regenerative braking, and shifting engine operation to speeds and loads with higher fuel efficiency. Increased hybridization also tends to monotonically reduce engine-out emissions, but trends inmore » the tailpipe (post-aftertreatment) emissions involve more complex interactions that significantly depend on motor size and drive cycle details.« less

Design and implementation of a control structure for quality products in a crude oil atmospheric distillation column.

PubMed

Sotelo, David; Favela-Contreras, Antonio; Sotelo, Carlos; Jiménez, Guillermo; Gallegos-Canales, Luis

2017-11-01

In recent years, interest for petrochemical processes has been increasing, especially in refinement area. However, the high variability in the dynamic characteristics present in the atmospheric distillation column poses a challenge to obtain quality products. To improve distillates quality in spite of the changes in the input crude oil composition, this paper details a new design of a control strategy in a conventional crude oil distillation plant defined using formal interaction analysis tools. The process dynamic and its control are simulated on Aspen HYSYS ® dynamic environment under real operating conditions. The simulation results are compared against a typical control strategy commonly used in crude oil atmospheric distillation columns. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

Modeling of milk flow in mammary ducts in lactating human female breast.

PubMed

Mortazavi, S Negin; Geddes, Donna; Hassanipour, Fatemeh

2014-01-01

A transient laminar Newtonian three-dimensional CFD simulation has been studied for milk flow in a phantom model of the 6-generations human lactating breast branching system. Milk is extracted by the cyclic pattern of suction from the alveoli through the duct and to the nipple. The real negative (suction) pressure data are applied as an outlet boundary condition in nipple. In this study, the commercial CFD code (Fluent Inc., 2004) is employed for the numerical solution of the milk flow. The milk intake flow rate from simulation is compared to the real clinical data from published paper. The results are in good agreement. It is believed that the methodology of the lactating human breast branching modeling proposed here can provide potential guidelines for further clinical and research application.

A simulator evaluation of an automatic terminal approach system

NASA Technical Reports Server (NTRS)

Hinton, D. A.

1983-01-01

The automatic terminal approach system (ATAS) is a concept for improving the pilot/machine interface with cockpit automation. The ATAS can automatically fly a published instrument approach by using stored instrument approach data to automatically tune airplane avionics, control the airplane's autopilot, and display status information to the pilot. A piloted simulation study was conducted to determine the feasibility of an ATAS, determine pilot acceptance, and examine pilot/ATAS interaction. Seven instrument-rated pilots each flew four instrument approaches with a base-line heading select autopilot mode. The ATAS runs resulted in lower flight technical error, lower pilot workload, and fewer blunders than with the baseline autopilot. The ATAS status display enabled the pilots to maintain situational awareness during the automatic approaches. The system was well accepted by the pilots.

Shape optimization of road tunnel cross-section by simulated annealing

NASA Astrophysics Data System (ADS)

Sobótka, Maciej; Pachnicz, Michał

2016-06-01

The paper concerns shape optimization of a tunnel excavation cross-section. The study incorporates optimization procedure of the simulated annealing (SA). The form of a cost function derives from the energetic optimality condition, formulated in the authors' previous papers. The utilized algorithm takes advantage of the optimization procedure already published by the authors. Unlike other approaches presented in literature, the one introduced in this paper takes into consideration a practical requirement of preserving fixed clearance gauge. Itasca Flac software is utilized in numerical examples. The optimal excavation shapes are determined for five different in situ stress ratios. This factor significantly affects the optimal topology of excavation. The resulting shapes are elongated in the direction of a principal stress greater value. Moreover, the obtained optimal shapes have smooth contours circumscribing the gauge.

Simulating forest productivity along a neotropical elevational transect: temperature variation and carbon use efficiency

NASA Astrophysics Data System (ADS)

Marthews, T.; Malhi, Y.; Girardin, C.; Silva-Espejo, J.; Aragão, L.; Metcalfe, D.; Rapp, J.; Mercado, L.; Fisher, R.; Galbraith, D.; Fisher, J.; Salinas-Revilla, N.; Friend, A.; Restrepo-Coupe, N.; Williams, R.

2012-04-01

A better understanding of the mechanisms controlling the magnitude and sign of carbon components in tropical forest ecosystems is important for reliable estimation of this important regional component of the global carbon cycle. We used the JULES vegetation model to simulate all components of the carbon balance at six sites along an Andes-Amazon transect across Peru and Brazil and compared the results to published field measurements. In the upper montane zone the model predicted a vegetation dieback, indicating a need for better parameterisation of cloud forest vegetation. In the lower montane and lowland zones simulated ecosystem productivity and respiration were predicted with reasonable accuracy, although not always within the error bounds of the observations. Model-predicted carbon use efficiency in this transect surprisingly did not increase with elevation, but remained close to the 'temperate' value 0.5. This may be explained by elevational changes in the balance between growth and maintenance respiration within the forest canopy, as controlled by both temperature- and pressure-mediated processes.

A methodology to determine the elastic moduli of crystals by matching experimental and simulated lattice strain pole figures using discrete harmonics

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

Wielewski, Euan; Boyce, Donald E.; Park, Jun-Sang

Determining reliable single crystal material parameters for complex polycrystalline materials is a significant challenge for the materials community. In this work, a novel methodology for determining those parameters is outlined and successfully applied to the titanium alloy, Ti-6Al-4V. Utilizing the results from a lattice strain pole figure experiment conducted at the Cornell High Energy Synchrotron Source, an iterative approach is used to optimize the single crystal elastic moduli by comparing experimental and simulated lattice strain pole figures at discrete load steps during a uniaxial tensile test. Due to the large number of unique measurements taken during the experiments, comparisons weremore » made by using the discrete spherical harmonic modes of both the experimental and simulated lattice strain pole figures, allowing the complete pole figures to be used to determine the single crystal elastic moduli. (C) 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.« less

Simulation analyses of space use: Home range estimates, variability, and sample size

USGS Publications Warehouse

Bekoff, Marc; Mech, L. David

1984-01-01

Simulations of space use by animals were run to determine the relationship among home range area estimates, variability, and sample size (number of locations). As sample size increased, home range size increased asymptotically, whereas variability decreased among mean home range area estimates generated by multiple simulations for the same sample size. Our results suggest that field workers should ascertain between 100 and 200 locations in order to estimate reliably home range area. In some cases, this suggested guideline is higher than values found in the few published studies in which the relationship between home range area and number of locations is addressed. Sampling differences for small species occupying relatively small home ranges indicate that fewer locations may be sufficient to allow for a reliable estimate of home range. Intraspecific variability in social status (group member, loner, resident, transient), age, sex, reproductive condition, and food resources also have to be considered, as do season, habitat, and differences in sampling and analytical methods. Comparative data still are needed.

Simulation of Ametropic Human Eyes

NASA Astrophysics Data System (ADS)

Tan, Bo; Chen, Ying-Ling; Lewis, James W. L.

2004-11-01

The computational simulation of the performance of human eyes is complex because the optical parameters of the eye depend on many factors, including age, gender, race, refractive status (accommodation and near- or far-sightedness). This task is made more difficult by the inadequacy of the population statistical characteristics of these parameters. Previously we simulated ametropic (near- or far-sighted) eyes using three independent variables: the axial length of the eye, the corneal surface curvature, and the intraocular refractive index gradient. The prescription for the correction of an ametropic eye is determined by its second-order coefficients of the wavefront aberrations. These corrections are typically achieved using contact lens, spectacle lens, or laser surgery (LASIK). However, the higher order aberrations, which are not corrected and are likely complicated or enhanced by the lower-order correction, could be important for visual performance in a darkened environment. In this paper, we investigate the higher order wavefront aberrations of synthetic ametropic eyes and compare results with measured data published in the past decade. The behavior of three types of ametropes is discussed.

A coarse-grained model for DNA origami.

PubMed

Reshetnikov, Roman V; Stolyarova, Anastasia V; Zalevsky, Arthur O; Panteleev, Dmitry Y; Pavlova, Galina V; Klinov, Dmitry V; Golovin, Andrey V; Protopopova, Anna D

2018-02-16

Modeling tools provide a valuable support for DNA origami design. However, current solutions have limited application for conformational analysis of the designs. In this work we present a tool for a thorough study of DNA origami structure and dynamics. The tool is based on a novel coarse-grained model dedicated to geometry optimization and conformational analysis of DNA origami. We explored the ability of the model to predict dynamic behavior, global shapes, and fine details of two single-layer systems designed in hexagonal and square lattices using atomic force microscopy, Förster resonance energy transfer spectroscopy, and all-atom molecular dynamic simulations for validation of the results. We also examined the performance of the model for multilayer systems by simulation of DNA origami with published cryo-electron microscopy and atomic force microscopy structures. A good agreement between the simulated and experimental data makes the model suitable for conformational analysis of DNA origami objects. The tool is available at http://vsb.fbb.msu.ru/cosm as a web-service and as a standalone version.

A Modal Model to Simulate Typical Structural Dynamic Nonlinearity [PowerPoint

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

Mayes, Randall L.; Pacini, Benjamin Robert; Roettgen, Dan

2016-01-01

Some initial investigations have been published which simulate nonlinear response with almost traditional modal models: instead of connecting the modal mass to ground through the traditional spring and damper, a nonlinear Iwan element was added. This assumes that the mode shapes do not change with amplitude and there are no interactions between modal degrees of freedom. This work expands on these previous studies. An impact experiment is performed on a structure which exhibits typical structural dynamic nonlinear response, i.e. weak frequency dependence and strong damping dependence on the amplitude of vibration. Use of low level modal test results in combinationmore » with high level impacts are processed using various combinations of modal filtering, the Hilbert Transform and band-pass filtering to develop response data that are then fit with various nonlinear elements to create a nonlinear pseudo-modal model. Simulations of forced response are compared with high level experimental data for various nonlinear element assumptions.« less

A Modal Model to Simulate Typical Structural Dynamic Nonlinearity

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

Pacini, Benjamin Robert; Mayes, Randall L.; Roettgen, Daniel R

2015-10-01

Some initial investigations have been published which simulate nonlinear response with almost traditional modal models: instead of connecting the modal mass to ground through the traditional spring and damper, a nonlinear Iwan element was added. This assumes that the mode shapes do not change with amplitude and there are no interactions between modal degrees of freedom. This work expands on these previous studies. An impact experiment is performed on a structure which exhibits typical structural dynamic nonlinear response, i.e. weak frequency dependence and strong damping dependence on the amplitude of vibration. Use of low level modal test results in combinationmore » with high level impacts are processed using various combinations of modal filtering, the Hilbert Transform and band-pass filtering to develop response data that are then fit with various nonlinear elements to create a nonlinear pseudo-modal model. Simulations of forced response are compared with high level experimental data for various nonlinear element assumptions.« less

The role of orbital dynamics and cloud-cloud collisions in the formation of giant molecular clouds in global spiral structures

NASA Technical Reports Server (NTRS)

Roberts, William W., Jr.; Stewart, Glen R.

1987-01-01

The role of orbit crowding and cloud-cloud collisions in the formation of GMCs and their organization in global spiral structure is investigated. Both N-body simulations of the cloud system and a detailed analysis of individual particle orbits are used to develop a conceptual understanding of how individual clouds participate in the collective density response. Detailed comparisons are made between a representative cloud-particle simulation in which the cloud particles collide inelastically with one another and give birth to and subsequently interact with young star associations and stripped down simulations in which the cloud particles are allowed to follow ballistic orbits in the absence of cloud-cloud collisions or any star formation processes. Orbit crowding is then related to the behavior of individual particle trajectories in the galactic potential field. The conceptual picture of how GMCs are formed in the clumpy ISMs of spiral galaxies is formulated, and the results are compared in detail with those published by other authors.

Modeling of the plasma extraction efficiency of an inductively coupled plasma-mass spectrometer interface using the direct simulation Monte Carlo method

NASA Astrophysics Data System (ADS)

Kivel, Niko; Potthast, Heiko-Dirk; Günther-Leopold, Ines; Vanhaecke, Frank; Günther, Detlef

The interface between the atmospheric pressure plasma ion source and the high vacuum mass spectrometer is a crucial part of an inductively coupled plasma-mass spectrometer. It influences the efficiency of the mass transfer into the mass spectrometer, it also contributes to the formation of interfering ions and to mass discrimination. This region was simulated using the Direct Simulation Monte Carlo method with respect to the formation of shock waves, mass transport and mass discrimination. The modeling results for shock waves and mass transport are in overall agreement with the literature. Insights into the effects and geometrical features causing mass discrimination could be gained. The overall observed collision based mass discrimination is lower than expected from measurements on real instruments, supporting the assumptions that inter-particle collisions play a minor role in this context published earlier. A full representation of the study, for two selected geometries, is given in form of a movie as supplementary data.

Cybersim: geographic, temporal, and organizational dynamics of malware propagation

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

Santhi, Nandakishore; Yan, Guanhua; Eidenbenz, Stephan

2010-01-01

Cyber-infractions into a nation's strategic security envelope pose a constant and daunting challenge. We present the modular CyberSim tool which has been developed in response to the need to realistically simulate at a national level, software vulnerabilities and resulting mal ware propagation in online social networks. CyberSim suite (a) can generate realistic scale-free networks from a database of geocoordinated computers to closely model social networks arising from personal and business email contacts and online communities; (b) maintains for each,bost a list of installed software, along with the latest published vulnerabilities; (d) allows designated initial nodes where malware gets introduced; (e)more » simulates, using distributed discrete event-driven technology, the spread of malware exploiting a specific vulnerability, with packet delay and user online behavior models; (f) provides a graphical visualization of spread of infection, its severity, businesses affected etc to the analyst. We present sample simulations on a national level network with millions of computers.« less

Evaluation of a Drowning Prevention Program Based on Testimonial Videos: A Randomized Controlled Trial.

PubMed

Shen, Jiabin; Pang, Shulan; Schwebel, David C

2016-06-01

Unintentional drowning is the most common cause of childhood death in rural China. Global intervention efforts offer mixed results regarding the efficacy of educational programs. Using a randomized controlled design, we evaluated a testimonial-based intervention to reduce drowning risk among 280 3rd- and 4th-grade rural Chinese children. Children were randomly assigned to view either testimonials on drowning risk (intervention) or dog-bite risk (control). Safety knowledge and perceived vulnerability were measured by self-report questionnaires, and simulated behaviors in and near water were assessed with a culturally appropriate dollhouse task. Children in the intervention group had improved children's safety knowledge and simulated behaviors but not perceived vulnerability compared with controls. The testimonial-based intervention's efficacy appears promising, as it improved safety knowledge and simulated risk behaviors with water among rural Chinese children. © The Author 2015. Published by Oxford University Press on behalf of the Society of Pediatric Psychology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Tunneling ionization and Wigner transform diagnostics in OSIRIS

NASA Astrophysics Data System (ADS)

Martins, S.; Fonseca, R. A.; Silva, L. O.; Deng, S.; Katsouleas, T.; Tsung, F.; Mori, W. B.

2004-11-01

We describe the ionization module implemented in the PIC code OSIRIS [1]. Benchmarks with previously published tunnel ionization results were made. Our ionization module works in 1D, 2D and 3D simulations with barrier suppression ionization or the ADK ionization model, and allows for moving ions. Several illustrative 3D numerical simulations were performed, namely of the propagation of a SLAC beam in a Li gas cell, for the parameters of [2]. We compare the performance of OSIRIS with/without the ionization module, concluding that much less simulation time is usually required when using the ionization module. A novel diagnostic over the electric field is implemented, the Wigner transform, that provides information on the local spectral content of the field. This diagnostic is applied to the analysis of the chirp induced in an ionizing laser pulse. [1] R. A. Fonseca et al., LNCS 2331, 342-351, (Springer, Heidelberg, 2002). [2] S. Deng et al., Phys. Rev. E 68, 047401 (2003).

A coarse-grained model for DNA origami

PubMed Central

Stolyarova, Anastasia V; Zalevsky, Arthur O; Panteleev, Dmitry Y; Pavlova, Galina V; Klinov, Dmitry V; Golovin, Andrey V; Protopopova, Anna D

2018-01-01

Abstract Modeling tools provide a valuable support for DNA origami design. However, current solutions have limited application for conformational analysis of the designs. In this work we present a tool for a thorough study of DNA origami structure and dynamics. The tool is based on a novel coarse-grained model dedicated to geometry optimization and conformational analysis of DNA origami. We explored the ability of the model to predict dynamic behavior, global shapes, and fine details of two single-layer systems designed in hexagonal and square lattices using atomic force microscopy, Förster resonance energy transfer spectroscopy, and all-atom molecular dynamic simulations for validation of the results. We also examined the performance of the model for multilayer systems by simulation of DNA origami with published cryo-electron microscopy and atomic force microscopy structures. A good agreement between the simulated and experimental data makes the model suitable for conformational analysis of DNA origami objects. The tool is available at http://vsb.fbb.msu.ru/cosm as a web-service and as a standalone version. PMID:29267876

Procedural instruction in invasive bedside procedures: a systematic review and meta-analysis of effective teaching approaches.

PubMed

Huang, Grace C; McSparron, Jakob I; Balk, Ethan M; Richards, Jeremy B; Smith, C Christopher; Whelan, Julia S; Newman, Lori R; Smetana, Gerald W

2016-04-01

Optimal approaches to teaching bedside procedures are unknown. To identify effective instructional approaches in procedural training. We searched PubMed, EMBASE, Web of Science and Cochrane Library through December 2014. We included research articles that addressed procedural training among physicians or physician trainees for 12 bedside procedures. Two independent reviewers screened 9312 citations and identified 344 articles for full-text review. Two independent reviewers extracted data from full-text articles. We included measurements as classified by translational science outcomes T1 (testing settings), T2 (patient care practices) and T3 (patient/public health outcomes). Due to incomplete reporting, we post hoc classified study outcomes as 'negative' or 'positive' based on statistical significance. We performed meta-analyses of outcomes on the subset of studies sharing similar outcomes. We found 161 eligible studies (44 randomised controlled trials (RCTs), 34 non-RCTs and 83 uncontrolled trials). Simulation was the most frequently published educational mode (78%). Our post hoc classification showed that studies involving simulation, competency-based approaches and RCTs had higher frequencies of T2/T3 outcomes. Meta-analyses showed that simulation (risk ratio (RR) 1.54 vs 0.55 for studies with vs without simulation, p=0.013) and competency-based approaches (RR 3.17 vs 0.89, p<0.001) were effective forms of training. This systematic review of bedside procedural skills demonstrates that the current literature is heterogeneous and of varying quality and rigour. Evidence is strongest for the use of simulation and competency-based paradigms in teaching procedures, and these approaches should be the mainstay of programmes that train physicians to perform procedures. Further research should clarify differences among instructional methods (eg, forms of hands-on training) rather than among educational modes (eg, lecture vs simulation). Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Modelling and simulation of a pervaporation process using tubular module for production of anhydrous ethanol

NASA Astrophysics Data System (ADS)

Hieu, Nguyen Huu

2017-09-01

Pervaporation is a potential process for the final step of ethanol biofuel production. In this study, a mathematical model was developed based on the resistance-in-series model and a simulation was carried out using the specialized simulation software COMSOL Multiphysics to describe a tubular type pervaporation module with membranes for the dehydration of ethanol solution. The permeance of membranes, operating conditions, and feed conditions in the simulation were referred from experimental data reported previously in literature. Accordingly, the simulated temperature and density profiles of pure water and ethanol-water mixture were validated based on existing published data.

Kinship, parental manipulation and evolutionary origins of eusociality.

PubMed

Kapheim, Karen M; Nonacs, Peter; Smith, Adam R; Wayne, Robert K; Wcislo, William T

2015-03-22

One of the hallmarks of eusociality is that workers forego their own reproduction to assist their mother in raising siblings. This seemingly altruistic behaviour may benefit workers if gains in indirect fitness from rearing siblings outweigh the loss of direct fitness. If worker presence is advantageous to mothers, however, eusociality may evolve without net benefits to workers. Indirect fitness benefits are often cited as evidence for the importance of inclusive fitness in eusociality, but have rarely been measured in natural populations. We compared inclusive fitness of alternative social strategies in the tropical sweat bee, Megalopta genalis, for which eusociality is optional. Our results show that workers have significantly lower inclusive fitness than females that found their own nests. In mathematical simulations based on M. genalis field data, eusociality cannot evolve with reduced intra-nest relatedness. The simulated distribution of alternative social strategies matched observed distributions of M. genalis social strategies when helping behaviour was simulated as the result of maternal manipulation, but not as worker altruism. Thus, eusociality in M. genalis is best explained through kin selection, but the underlying mechanism is likely maternal manipulation. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

The structure and intermolecular forces of DNA condensates.

PubMed

Yoo, Jejoong; Aksimentiev, Aleksei

2016-03-18

Spontaneous assembly of DNA molecules into compact structures is ubiquitous in biological systems. Experiment has shown that polycations can turn electrostatic self-repulsion of DNA into attraction, yet the physical mechanism of DNA condensation has remained elusive. Here, we report the results of atomistic molecular dynamics simulations that elucidated the microscopic structure of dense DNA assemblies and the physics of interactions that makes such assemblies possible. Reproducing the setup of the DNA condensation experiments, we measured the internal pressure of DNA arrays as a function of the DNA-DNA distance, showing a quantitative agreement between the results of our simulations and the experimental data. Analysis of the MD trajectories determined the DNA-DNA force in a DNA condensate to be pairwise, the DNA condensation to be driven by electrostatics of polycations and not hydration, and the concentration of bridging cations, not adsorbed cations, to determine the magnitude and the sign of the DNA-DNA force. Finally, our simulations quantitatively characterized the orientational correlations of DNA in DNA arrays as well as diffusive motion of DNA and cations. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Simulation of an Impact Test of the All-Composite Lear Fan Aircraft

NASA Technical Reports Server (NTRS)

Stockwell, Alan E.; Jones, Lisa E. (Technical Monitor)

2002-01-01

An MSC.Dytran model of an all-composite Lear Fan aircraft fuselage was developed to simulate an impact test conducted at the NASA Langley Research Center Impact Dynamics Research Facility (IDRF). The test was the second of two Lear Fan impact tests. The purpose of the second test was to evaluate the performance of retrofitted composite energy-absorbing floor beams. A computerized photogrammetric survey was performed to provide airframe geometric coordinates, and over 5000 points were processed and imported into MSC.Patran via an IGES file. MSC.Patran was then used to develop the curves and surfaces and to mesh the finite element model. A model of the energy-absorbing floor beams was developed separately and then integrated into the Lear Fan model. Structural responses of components such as the wings were compared with experimental data or previously published analytical data wherever possible. Comparisons with experimental results were used to guide structural model modifications to improve the simulation performance. This process was based largely on qualitative (video and still camera images and post-test inspections) rather than quantitative results due to the relatively few accelerometers attached to the structure.

Computational Planning in Facial Surgery.

PubMed

Zachow, Stefan

2015-10-01

This article reflects the research of the last two decades in computational planning for cranio-maxillofacial surgery. Model-guided and computer-assisted surgery planning has tremendously developed due to ever increasing computational capabilities. Simulators for education, planning, and training of surgery are often compared with flight simulators, where maneuvers are also trained to reduce a possible risk of failure. Meanwhile, digital patient models can be derived from medical image data with astonishing accuracy and thus can serve for model surgery to derive a surgical template model that represents the envisaged result. Computerized surgical planning approaches, however, are often still explorative, meaning that a surgeon tries to find a therapeutic concept based on his or her expertise using computational tools that are mimicking real procedures. Future perspectives of an improved computerized planning may be that surgical objectives will be generated algorithmically by employing mathematical modeling, simulation, and optimization techniques. Planning systems thus act as intelligent decision support systems. However, surgeons can still use the existing tools to vary the proposed approach, but they mainly focus on how to transfer objectives into reality. Such a development may result in a paradigm shift for future surgery planning. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

Role of Desolvation in Thermodynamics and Kinetics of Ligand Binding to a Kinase

PubMed Central

2015-01-01

Computer simulations are used to determine the free energy landscape for the binding of the anticancer drug Dasatinib to its src kinase receptor and show that before settling into a free energy basin the ligand must surmount a free energy barrier. An analysis based on using both the ligand-pocket separation and the pocket-water occupancy as reaction coordinates shows that the free energy barrier is a result of the free energy cost for almost complete desolvation of the binding pocket. The simulations further show that the barrier is not a result of the reorganization free energy of the binding pocket. Although a continuum solvent model gives the location of free energy minima, it is not able to reproduce the intermediate free energy barrier. Finally, it is shown that a kinetic model for the on rate constant in which the ligand diffuses up to a doorway state and then surmounts the desolvation free energy barrier is consistent with published microsecond time-scale simulations of the ligand binding kinetics for this system [Shaw, D. E. et al. J. Am. Chem. Soc.2011, 133, 9181−918321545110]. PMID:25516727

A Quantitative Dynamic Simulation of Bremia lactucae Airborne Conidia Concentration above a Lettuce Canopy.

PubMed

Fall, Mamadou Lamine; Van der Heyden, Hervé; Carisse, Odile

2016-01-01

Lettuce downy mildew, caused by the oomycete Bremia lactucae Regel, is a major threat to lettuce production worldwide. Lettuce downy mildew is a polycyclic disease driven by airborne spores. A weather-based dynamic simulation model for B. lactucae airborne spores was developed to simulate the aerobiological characteristics of the pathogen. The model was built using the STELLA platform by following the system dynamics methodology. The model was developed using published equations describing disease subprocesses (e.g., sporulation) and assembled knowledge of the interactions among pathogen, host, and weather. The model was evaluated with four years of independent data by comparing model simulations with observations of hourly and daily airborne spore concentrations. The results show an accurate simulation of the trend and shape of B. lactucae temporal dynamics of airborne spore concentration. The model simulated hourly and daily peaks in airborne spore concentrations. More than 95% of the simulation runs, the daily-simulated airborne conidia concentration was 0 when airborne conidia were not observed. Also, the relationship between the simulated and the observed airborne spores was linear. In more than 94% of the simulation runs, the proportion of the linear variation in the hourly-observed values explained by the variation in the hourly-simulated values was greater than 0.7 in all years except one. Most of the errors came from the deviation from the 1:1 line, and the proportion of errors due to the model bias was low. This model is the only dynamic model developed to mimic the dynamics of airborne inoculum and represents an initial step towards improved lettuce downy mildew understanding, forecasting and management.

A Quantitative Dynamic Simulation of Bremia lactucae Airborne Conidia Concentration above a Lettuce Canopy

PubMed Central

Fall, Mamadou Lamine; Van der Heyden, Hervé; Carisse, Odile

2016-01-01

Lettuce downy mildew, caused by the oomycete Bremia lactucae Regel, is a major threat to lettuce production worldwide. Lettuce downy mildew is a polycyclic disease driven by airborne spores. A weather-based dynamic simulation model for B. lactucae airborne spores was developed to simulate the aerobiological characteristics of the pathogen. The model was built using the STELLA platform by following the system dynamics methodology. The model was developed using published equations describing disease subprocesses (e.g., sporulation) and assembled knowledge of the interactions among pathogen, host, and weather. The model was evaluated with four years of independent data by comparing model simulations with observations of hourly and daily airborne spore concentrations. The results show an accurate simulation of the trend and shape of B. lactucae temporal dynamics of airborne spore concentration. The model simulated hourly and daily peaks in airborne spore concentrations. More than 95% of the simulation runs, the daily-simulated airborne conidia concentration was 0 when airborne conidia were not observed. Also, the relationship between the simulated and the observed airborne spores was linear. In more than 94% of the simulation runs, the proportion of the linear variation in the hourly-observed values explained by the variation in the hourly-simulated values was greater than 0.7 in all years except one. Most of the errors came from the deviation from the 1:1 line, and the proportion of errors due to the model bias was low. This model is the only dynamic model developed to mimic the dynamics of airborne inoculum and represents an initial step towards improved lettuce downy mildew understanding, forecasting and management. PMID:26953691

FF12MC: A revised AMBER forcefield and new protein simulation protocol

PubMed Central

2016-01-01

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

The challenges in developing a finite element injury model of the neck to predict the penetration of explosively propelled projectiles.

PubMed

Breeze, Johno; Newbery, T; Pope, D; Midwinter, M J

2014-09-01

Neck injuries sustained by UK service personnel serving on current operations from explosively propelled fragments result in significant mortality and long-term morbidity. Many of these injuries could potentially have been prevented had the soldiers been wearing their issued neck collars at the time of injury. The aim of this research is to develop an accurate method of predicting the resultant damage to cervical neurovascular structures from explosively propelled fragments. A finite element numerical model has been developed based on an anatomically accurate, anthropometrically representative 3D mathematical mesh of cervical neurovascular structures. Currently, the model simulates the passage of a fragment simulating projectile through all anatomical components of the neck using material models based upon 20% ballistic gelatin on the simplification that all tissue types act like homogenous muscle. The material models used to define the properties of each element within the model will be sequentially replaced by ones specific to each individual tissue within an anatomical structure. However, the cumulative effect of so many additional variables will necessitate experimental validation against both animal models and post-mortem human subjects to improve the credibility of any predictions made by the model. We believe this approach will in the future have the potential to enable objective comparisons between the mitigative effects of different body armour systems to be made with resultant time and financial savings. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Aortic Root Biomechanics After Sleeve and David Sparing Techniques: A Finite Element Analysis.

PubMed

Tasca, Giordano; Selmi, Matteo; Votta, Emiliano; Redaelli, Paola; Sturla, Francesco; Redaelli, Alberto; Gamba, Amando

2017-05-01

Aortic root aneurysm can be treated with valve-sparing procedures. The David and Yacoub techniques have shown excellent long-term results but are technically demanding. Recently, a new and simpler procedure, the Sleeve technique, was proposed with encouraging results. We aimed to quantify the biomechanics of the initially aneurysmal aortic root (AR) after the Sleeve procedure to assess whether it induces abnormal stresses, potentially undermining its durability. Two finite element (FE) models of the physiologic and aneurysmal AR were built, accounting for the anatomical asymmetry and the nonlinear and anisotropic mechanical properties of human AR tissues. On the aneurysmal model, the Sleeve and David techniques were simulated based on the corresponding published technical features. Aortic root biomechanics throughout 2 consecutive cardiac cycles were computed in each simulated configuration. Both sparing techniques restored physiologic-like kinematics of aortic valve (AV) leaflets but induced different leaflets stresses. The time course averaged over the leaflets' bellies was 35% higher in the David model than in the Sleeve model. Commissural stresses, which were equal to 153 and 318 kPa in the physiologic and aneurysmal models, respectively, became 369 and 208 kPa in the David and Sleeve models, respectively. No intrinsic structural problems were detected in the Sleeve model that might jeopardize the durability of the procedure. If corroborated by long-term clinical outcomes, the results obtained suggest that using this new technique could successfully simplify the surgical repair of AR aneurysms and reduce intraoperative complications. Copyright © 2017 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

Improved simulation of poorly drained forests using Biome-BGC.

PubMed

Bond-Lamberty, Ben; Gower, Stith T; Ahl, Douglas E

2007-05-01

Forested wetlands and peatlands are important in boreal and terrestrial biogeochemical cycling, but most general-purpose forest process models are designed and parameterized for upland systems. We describe changes made to Biome-BGC, an ecophysiological process model, that improve its ability to simulate poorly drained forests. Model changes allowed for: (1) lateral water inflow from a surrounding watershed, and variable surface and subsurface drainage; (2) adverse effects of anoxic soil on decomposition and nutrient mineralization; (3) closure of leaf stomata in flooded soils; and (4) growth of nonvascular plants (i.e., bryophytes). Bryophytes were treated as ectohydric broadleaf evergreen plants with zero stomatal conductance, whose cuticular conductance to CO(2) was dependent on plant water content. Individual model changes were parameterized with published data, and ecosystem-level model performance was assessed by comparing simulated output to field data from the northern BOREAS site in Manitoba, Canada. The simulation of the poorly drained forest model exhibited reduced decomposition and vascular plant growth (-90%) compared with that of the well-drained forest model; the integrated bryophyte photosynthetic response accorded well with published data. Simulated net primary production, biomass and soil carbon accumulation broadly agreed with field measurements, although simulated net primary production was higher than observed data in well-drained stands. Simulated net primary production in the poorly drained forest was most sensitive to oxygen restriction on soil processes, and secondarily to stomatal closure in flooded conditions. The modified Biome-BGC remains unable to simulate true wetlands that are subject to prolonged flooding, because it does not track organic soil formation, water table changes, soil redox potential or anaerobic processes.

Maintenance of health care providers clinical proficiency: Transdisciplinary analysis, modeling and intervention

DTIC Science & Technology

2015-10-13

attack, status epilepticus , and other clinical scenarios. Interservice/Industry Training, Simulation, and Education Conference (I/ITSEC) 2015 2015...volume: year; page numbers; status of publication (published; accepted, awaiting publication; submitted, under review; other); acknowledgement of...collection, if applicable; bibliographic information; year; type of publication (e.g., book, thesis or dissertation); status of publication (published

NUCLEAR HEATING IN LIF DOSEMETERS IN A FUSION NEUTRON FIELD, TRIAL OF DIRECT COMPARISON OF EXPERIMENTAL AND SIMULATED RESULTS.

PubMed

Pohorecki, Wladyslaw; Obryk, Barbara

2017-09-29

The results of nuclear heating measured by means of thermoluminescent dosemeters (TLD-LiF) in a Cu block irradiated by 14 MeV neutrons are presented. The integral Cu experiment relevant for verification of copper nuclear data at neutron energies characteristic for fusion facilities was performed in the ENEA FNG Laboratory at Frascati. Five types of TLDs were used: highly photon sensitive LiF:Mg,Cu,P (MCP-N), 7LiF:Mg,Cu,P (MCP-7) and standard, lower sensitivity LiF:Mg,Ti (MTS-N), 7LiF:Mg,Ti (MTS-7) and 6LiF:Mg,Ti (MTS-6). Calibration of the detectors was performed with gamma rays in terms of air-kerma (10 mGy of 137Cs air-kerma). Nuclear heating in the Cu block was also calculated with the use of MCNP transport code Nuclear heating in Cu and air in TLD's positions was calculated as well. The nuclear heating contribution from all simulated by MCNP6 code particles including protons, deuterons, alphas tritons and heavier ions produced by the neutron interactions were calculated. A trial of the direct comparison between experimental results and results of simulation was performed. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Mobile in Situ Simulation as a Tool for Evaluation and Improvement of Trauma Treatment in the Emergency Department.

PubMed

Amiel, Imri; Simon, Daniel; Merin, Ofer; Ziv, Amitai

2016-01-01

Medical simulation is an increasingly recognized tool for teaching, coaching, training, and examining practitioners in the medical field. For many years, simulation has been used to improve trauma care and teamwork. Despite technological advances in trauma simulators, including better means of mobilization and control, most reported simulation-based trauma training has been conducted inside simulation centers, and the practice of mobile simulation in hospitals' trauma rooms has not been investigated fully. The emergency department personnel from a second-level trauma center in Israel were evaluated. Divided into randomly formed trauma teams, they were reviewed twice using in situ mobile simulation training at the hospital's trauma bay. In all, 4 simulations were held before and 4 simulations were held after a structured learning intervention. The intervention included a 1-day simulation-based training conducted at the Israel Center for Medical Simulation (MSR), which included video-based debriefing facilitated by the hospital's 4 trauma team leaders who completed a 2-day simulation-based instructors' course before the start of the study. The instructors were also trained on performance rating and thus were responsible for the assessment of their respective teams in real time as well as through reviewing of the recorded videos; thus enabling a comparison of the performances in the mobile simulation exercise before and after the educational intervention. The internal reliability of the experts' evaluation calculated in the Cronbach α model was found to be 0.786. Statistically significant improvement was observed in 4 of 10 parameters, among which were teamwork (29.64%) and communication (24.48%) (p = 0.00005). The mobile in situ simulation-based training demonstrated efficacy both as an assessment tool for trauma teams' function and an educational intervention when coupled with in vitro simulation-based training, resulting in a significant improvement of the teams' function in various aspects of treatment. Copyright © 2015 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.

Old Dog New Tricks: Use of Point-based Crop Models in Grid-based Regional Assessment of Crop Management Technologies Impact on Future Food Security

NASA Astrophysics Data System (ADS)

Koo, J.; Wood, S.; Cenacchi, N.; Fisher, M.; Cox, C.

2012-12-01

HarvestChoice (harvestchoice.org) generates knowledge products to guide strategic investments to improve the productivity and profitability of smallholder farming systems in sub-Saharan Africa (SSA). A keynote component of the HarvestChoice analytical framework is a grid-based overlay of SSA - a cropping simulation platform powered by process-based, crop models. Calibrated around the best available representation of cropping production systems in SSA, the simulation platform engages the DSSAT Crop Systems Model with the CENTURY Soil Organic Matter model (DSSAT-CENTURY) and provides a virtual experimentation module with which to explore the impact of a range of technological, managerial and environmental metrics on future crop productivity and profitability, as well as input use. For each of 5 (or 30) arc-minute grid cells in SSA, a stack of model input underlies it: datasets that cover soil properties and fertility, historic and future climate scenarios and farmers' management practices; all compiled from analyses of existing global and regional databases and consultations with other CGIAR centers. Running a simulation model is not always straightforward, especially when certain cropping systems or management practices are not even practiced by resource-poor farmers yet (e.g., precision agriculture) or they were never included in the existing simulation framework (e.g., water harvesting). In such cases, we used DSSAT-CENTURY as a function to iteratively estimate relative responses of cropping systems to technology-driven changes in water and nutrient balances compared to zero-adoption by farmers, while adjusting model input parameters to best mimic farmers' implementation of technologies in the field. We then fed the results of the simulation into to the economic and food trade model framework, IMPACT, to assess the potential implications on future food security. The outputs of the overall simulation analyses are packaged as a web-accessible database and published on the web with an interface that allows users to explore the simulation results in each country with user-defined baseline and what-if scenarios. The results are dynamically presented on maps, charts, and tables. This paper discusses the development of the simulation platform and its underlying data layers, a case study that assessed the role of potential crop management technology development, and the development of a web-based application that visualizes the simulation results.

Variance estimation when using inverse probability of treatment weighting (IPTW) with survival analysis.

PubMed

Austin, Peter C

2016-12-30

Propensity score methods are used to reduce the effects of observed confounding when using observational data to estimate the effects of treatments or exposures. A popular method of using the propensity score is inverse probability of treatment weighting (IPTW). When using this method, a weight is calculated for each subject that is equal to the inverse of the probability of receiving the treatment that was actually received. These weights are then incorporated into the analyses to minimize the effects of observed confounding. Previous research has found that these methods result in unbiased estimation when estimating the effect of treatment on survival outcomes. However, conventional methods of variance estimation were shown to result in biased estimates of standard error. In this study, we conducted an extensive set of Monte Carlo simulations to examine different methods of variance estimation when using a weighted Cox proportional hazards model to estimate the effect of treatment. We considered three variance estimation methods: (i) a naïve model-based variance estimator; (ii) a robust sandwich-type variance estimator; and (iii) a bootstrap variance estimator. We considered estimation of both the average treatment effect and the average treatment effect in the treated. We found that the use of a bootstrap estimator resulted in approximately correct estimates of standard errors and confidence intervals with the correct coverage rates. The other estimators resulted in biased estimates of standard errors and confidence intervals with incorrect coverage rates. Our simulations were informed by a case study examining the effect of statin prescribing on mortality. © 2016 The Authors. Statistics in Medicine published by John Wiley & Sons Ltd. © 2016 The Authors. Statistics in Medicine published by John Wiley & Sons Ltd.

Future Climate Change in the Baltic Sea Area

NASA Astrophysics Data System (ADS)

Bøssing Christensen, Ole; Kjellström, Erik; Zorita, Eduardo; Sonnenborg, Torben; Meier, Markus; Grinsted, Aslak

2015-04-01

Regional climate models have been used extensively since the first assessment of climate change in the Baltic Sea region published in 2008, not the least for studies of Europe (and including the Baltic Sea catchment area). Therefore, conclusions regarding climate model results have a better foundation than was the case for the first BACC report of 2008. This presentation will report model results regarding future climate. What is the state of understanding about future human-driven climate change? We will cover regional models, statistical downscaling, hydrological modelling, ocean modelling and sea-level change as it is projected for the Baltic Sea region. Collections of regional model simulations from the ENSEMBLES project for example, financed through the European 5th Framework Programme and the World Climate Research Programme Coordinated Regional Climate Downscaling Experiment, have made it possible to obtain an increasingly robust estimation of model uncertainty. While the first Baltic Sea assessment mainly used four simulations from the European 5th Framework Programme PRUDENCE project, an ensemble of 13 transient regional simulations with twice the horizontal resolution reaching the end of the 21st century has been available from the ENSEMBLES project; therefore it has been possible to obtain more quantitative assessments of model uncertainty. The literature about future climate change in the Baltic Sea region is largely built upon the ENSEMBLES project. Also within statistical downscaling, a considerable number of papers have been published, encompassing now the application of non-linear statistical models, projected changes in extremes and correction of climate model biases. The uncertainty of hydrological change has received increasing attention since the previous Baltic Sea assessment. Several studies on the propagation of uncertainties originating in GCMs, RCMs, and emission scenarios are presented. The number of studies on uncertainties related to downscaling and impact models is relatively small, but more are emerging. A large number of coupled climate-environmental scenario simulations for the Baltic Sea have been performed within the BONUS+ projects (ECOSUPPORT, INFLOW, AMBER and Baltic-C (2009-2011)), using various combinations of output from GCMs, RCMs, hydrological models and scenarios for load and emission of nutrients as forcing for Baltic Sea models. Such a large ensemble of scenario simulations for the Baltic Sea has never before been produced and enables for the first time an estimation of uncertainties.

Seismoelectric numerical modeling on a grid

USGS Publications Warehouse

Haines, S.S.; Pride, S.R.

2006-01-01

Our finite-difference algorithm provides a new method for simulating how seismic waves in arbitrarily heterogeneous porous media generate electric fields through an electrokinetic mechanism called seismoelectric coupling. As the first step in our simulations, we calculate relative pore-fluid/grain-matrix displacement by using existing poroelastic theory. We then calculate the electric current resulting from the grain/fluid displacement by using seismoelectric coupling theory. This electrofiltration current acts as a source term in Poisson's equation, which then allows us to calculate the electric potential distribution. We can safely neglect induction effects in our simulations because the model area is within the electrostatic near field for the depth of investigation (tens to hundreds of meters) and the frequency ranges (10 Hz to 1 kHz) of interest for shallow seismoelectric surveys.We can independently calculate the electric-potential distribution for each time step in the poroelastic simulation without loss of accuracy because electro-osmotic feedback (fluid flow that is perturbed by generated electric fields) is at least 105 times smaller than flow that is driven by fluid-pressure gradients and matrix acceleration, and is therefore negligible. Our simulations demonstrate that, distinct from seismic reflections, the seismoelectric interface response from a thin layer (at least as thin as one-twentieth of the seismic wavelength) is considerably stronger than the response from a single interface. We find that the interface response amplitude decreases as the lateral extent of a layer decreases below the width of the first Fresnel zone. We conclude, on the basis of our modeling results and of field results published elsewhere, that downhole and/or crosswell survey geometries and time-lapse applications are particularly well suited to the seismoelectric method. ?? 2006 Society of Exploration Geophysicists.

Global land-atmosphere coupling associated with cold climate processes

NASA Astrophysics Data System (ADS)

Dutra, Emanuel

This dissertation constitutes an assessment of the role of cold processes, associated with snow cover, in controlling the land-atmosphere coupling. The work was based on model simulations, including offline simulations with the land surface model HTESSEL, and coupled atmosphere simulations with the EC-EARTH climate model. A revised snow scheme was developed and tested in HTESSEL and EC-EARTH. The snow scheme is currently operational at the European Centre for Medium-Range Weather Forecasts integrated forecast system, and in the default configuration of EC-EARTH. The improved representation of the snowpack dynamics in HTESSEL resulted in improvements in the near surface temperature simulations of EC-EARTH. The new snow scheme development was complemented with the option of multi-layer version that showed its potential in modeling thick snowpacks. A key process was the snow thermal insulation that led to significant improvements of the surface water and energy balance components. Similar findings were observed when coupling the snow scheme to lake ice, where lake ice duration was significantly improved. An assessment on the snow cover sensitivity to horizontal resolution, parameterizations and atmospheric forcing within HTESSEL highlighted the role of the atmospheric forcing accuracy and snowpack parameterizations in detriment of horizontal resolution over flat regions. A set of experiments with and without free snow evolution was carried out with EC-EARTH to assess the impact of the interannual variability of snow cover on near surface and soil temperatures. It was found that snow cover interannual variability explained up to 60% of the total interannual variability of near surface temperature over snow covered regions. Although these findings are model dependent, the results showed consistency with previously published work. Furthermore, the detailed validation of the snow dynamics simulations in HTESSEL and EC-EARTH guarantees consistency of the results.