Techno-economic process modelling and Monte Carlo simulation data of uncertainty quantification in field-grown plant-based manufacturing.
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ABSTRACT:
SUBMITTER: McNulty MJ
PROVIDER: S-EPMC8405912 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BACKGROUND: Exposure to air pollution is associated with a short-term increase in mortality, and this field has begun to focus on health impact assessment. OBJECTIVES: Our aim was to estimate the impact of PM10 on mortality within 2 days from the exposure in the Italian region of Lombardy for the year 2007, at the municipality level, examining exposure entailed by daily intermunicipality commuting and accounting for uncertainty propagation. METHODS: We combined data from different sources to derive probabilistic distributions for all input quantities used to calculate attributable deaths (mortality rates, PM10 concentrations, estimated PM10 effects, and commuting flows) and applied a Monte Carlo procedure to propagate uncertainty and sample the distribution of attributable deaths for each municipality. RESULTS: We estimated that annual average PM10 concentrations above the World Health Organization-recommended threshold of 20 ?g/m3 were responsible for 865 short-term deaths (80% credibility interval: 475, 1,401), 26% of which were attributable to PM10 above the European Union limit of 40 ?g/m3. Reducing annual average PM10 concentrations > 20 ?g/m3 by 20% would have reduced the number of attributable deaths by 36%. The largest estimated impacts were along the basin of the Po River and in the largest cities. Commuting contributed to the spatial distribution of the estimated impact. CONCLUSIONS: Our estimates, which incorporated uncertainty quantification, indicate that the short-term impact of PM10 on mortality in Lombardy in 2007 was notable, and that reduction in air pollution would have had a substantial beneficial effect on population health. Using commuting data helped to identify critical areas for prioritizing intervention.
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Project description:The typical experimental procedure for testing stress corrosion cracking initiation involves an interval-censored reliability test. Based on these test results, the parameters of a Weibull distribution, which is a widely accepted crack initiation model, can be estimated using maximum likelihood estimation or median rank regression. However, it is difficult to determine the appropriate number of test specimens and censoring intervals required to obtain sufficiently accurate Weibull estimators. In this study, we compare maximum likelihood estimation and median rank regression using a Monte Carlo simulation to examine the effects of the total number of specimens, test duration, censoring interval, and shape parameters of the true Weibull distribution on the estimator uncertainty. Finally, we provide the quantitative uncertainties of both Weibull estimators, compare them with the true Weibull parameters, and suggest proper experimental conditions for developing a probabilistic crack initiation model through crack initiation tests.
| S-EPMC5456946 | biostudies-literature
Project description:The coronavirus disease 2019 (COVID-19) has now spread throughout most countries in the world causing heavy life losses and damaging social-economic impacts. Following a stochastic point process modelling approach, a Monte Carlo simulation model was developed to represent the COVID-19 spread dynamics. First, we examined various expected performances (theoretical properties) of the simulation model assuming a number of arbitrarily defined scenarios. Simulation studies were then performed on the real COVID-19 data reported (over the period of 1 March to 1 May) for Australia and United Kingdom (UK). Given the initial number of COVID-19 infection active cases were around 10 for both countries, the model estimated that the number of active cases would peak around 29 March in Australia (≈ 1,700 cases) and around 22 April in UK (≈ 22,860 cases); ultimately the total confirmed cases could sum to 6,790 for Australia in about 75 days and 206,480 for UK in about 105 days. The results of the estimated COVID-19 reproduction numbers were consistent with what was reported in the literature. This simulation model was considered an effective and adaptable decision making/what-if analysis tool in battling COVID-19 in the immediate need, and for modelling any other infectious diseases in the future.
| S-EPMC7403316 | biostudies-literature
Project description:BackgroundMonte Carlo simulation is considered as the most accurate method for dose calculation in radiotherapy. PRIMO is a Monte-Carlo program with a user-friendly graphical interface.Material and methodA VitalBeam with 6MV and 6MV flattening filter free (FFF), equipped with the 120 Millennium multileaf collimator was simulated by PRIMO. We adjusted initial energy, energy full width at half maximum (FWHM), focal spot FWHM, and beam divergence to match the measurements. The water tank and ion-chamber were used in the measurement. Percentage depth dose (PDD) and off axis ratio (OAR) were evaluated with gamma passing rates (GPRs) implemented in PRIMO. PDDs were matched at different widths of standard square fields. OARs were matched at five depths. Transmission factor and dose leaf gap (DLG) were simulated. DLG was measured by electronic portal imaging device using a sweeping gap method.ResultFor the criterion of 2%/2 mm, 1%/2 mm and 1%/1 mm, the GPRs of 6MV PDD were 99.33-100%, 99-100%, and 99-100%, respectively; the GPRs of 6MV FFF PDD were 99.33-100%, 98.99-99.66%, and 97.64-98.99%, respectively; the GPRs of 6MV OAR were 96.4-100%, 90.99-100%, and 85.12-98.62%, respectively; the GPRs of 6MV FFF OAR were 95.15-100%, 89.32-100%, and 87.02-99.74%, respectively. The calculated DLG matched well with the measurement (6MV: 1.36 mm vs. 1.41 mm; 6MV FFF: 1.07 mm vs. 1.03 mm, simulation vs measurement). The transmission factors were similar (6MV: 1.25% vs. 1.32%; 6MV FFF: 0.8% vs. 1.12%, simulation vs measurement).ConclusionThe calculated PDD, OAR, DLG and transmission factor were all in good agreement with measurements. PRIMO is an independent (with respect to analytical dose calculation algorithm) and accurate Monte Carlo tool.
| S-EPMC9667592 | biostudies-literature
Project description:The invention and advancement of biological microscopy depends critically on an ability to accurately simulate imaging of complex biological structures embedded within complex scattering media. Unfortunately no technique exists for rigorous simulation of the complete imaging process, including the source, instrument, sample and detector. Monte-Carlo modelling is the gold standard for the modelling of light propagation in tissue, but is somewhat laborious to implement and does not incorporate the rejection of scattered light by the microscope. On the other hand microscopes may be rigorously and rapidly modelled using commercial ray-tracing software, but excluding the interaction with the biological sample. We report a hybrid Monte-Carlo optical ray-tracing technique for modelling of complete imaging systems of arbitrary complexity. We make the software available to enable user-friendly and rigorous virtual prototyping of biological microscopy of arbitrary complexity involving light scattering, fluorescence, polarised light propagation, diffraction and coherence. Examples are presented for the modelling and optimisation of representative imaging of neural cells using light-sheet and micro-endoscopic fluorescence microscopy and imaging of retinal vasculature using confocal and non-confocal scanning-laser ophthalmoscopes.
| S-EPMC6825179 | biostudies-literature
Project description:In this study, we apply four Monte Carlo simulation methods, namely, Monte Carlo, quasi-Monte Carlo, multilevel Monte Carlo and multilevel quasi-Monte Carlo to the problem of uncertainty quantification in the estimation of the average travel time during the transport of particles through random heterogeneous porous media. We apply the four methodologies to a model problem where the only input parameter, the hydraulic conductivity, is modelled as a log-Gaussian random field by using direct Karhunen-Loéve decompositions. The random terms in such expansions represent the coefficients in the equations. Numerical calculations demonstrating the effectiveness of each of the methods are presented. A comparison of the computational cost incurred by each of the methods for three different tolerances is provided. The accuracy of the approaches is quantified via the mean square error.
| S-EPMC5579089 | biostudies-literature
Project description:Conventional mammography can suffer from poor contrast between healthy and cancerous tissues due to the small difference in attenuation properties. Coherent scatter slot scan imaging is an imaging technique which provides additional information and is compatible with conventional mammography. A Monte Carlo simulation of coherent scatter slot scan imaging was performed to assess its performance and provide system optimization. Coherent scatter could be exploited using a system similar to conventional slot scan mammography system with antiscatter grids tilted at the characteristic angle of cancerous tissues. System optimization was performed across several parameters, including source voltage, tilt angle, grid distances, grid ratio, and shielding geometry. The simulated carcinomas were detectable for tumors as small as 5 mm in diameter, so coherent scatter analysis using a wide-slot setup could be promising as an enhancement for screening mammography. Employing coherent scatter information simultaneously with conventional mammography could yield a conventional high spatial resolution image with additional coherent scatter information.
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Project description:UnlabelledBackgroundCost-effective production of lignocellulosic biofuels remains a major financial and technical challenge at the industrial scale. A critical tool in biofuels process development is the techno-economic (TE) model, which calculates biofuel production costs using a process model and an economic model. The process model solves mass and energy balances for each unit, and the economic model estimates capital and operating costs from the process model based on economic assumptions. The process model inputs include experimental data on the feedstock composition and intermediate product yields for each unit. These experimental yield data are calculated from primary measurements. Uncertainty in these primary measurements is propagated to the calculated yields, to the process model, and ultimately to the economic model. Thus, outputs of the TE model have a minimum uncertainty associated with the uncertainty in the primary measurements.ResultsWe calculate the uncertainty in the Minimum Ethanol Selling Price (MESP) estimate for lignocellulosic ethanol production via a biochemical conversion process: dilute sulfuric acid pretreatment of corn stover followed by enzymatic hydrolysis and co-fermentation of the resulting sugars to ethanol. We perform a sensitivity analysis on the TE model and identify the feedstock composition and conversion yields from three unit operations (xylose from pretreatment, glucose from enzymatic hydrolysis, and ethanol from fermentation) as the most important variables. The uncertainty in the pretreatment xylose yield arises from multiple measurements, whereas the glucose and ethanol yields from enzymatic hydrolysis and fermentation, respectively, are dominated by a single measurement: the fraction of insoluble solids (fIS) in the biomass slurries.ConclusionsWe calculate a $0.15/gal uncertainty in MESP from the TE model due to uncertainties in primary measurements. This result sets a lower bound on the error bars of the TE model predictions. This analysis highlights the primary measurements that merit further development to reduce the uncertainty associated with their use in TE models. While we develop and apply this mathematical framework to a specific biorefinery scenario here, this analysis can be readily adapted to other types of biorefining processes and provides a general framework for propagating uncertainty due to analytical measurements through a TE model.
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Project description:MotivationInvestigating the 3D structure of chromatin provides new insights into transcriptional regulation. With the evolution of 3C next-generation sequencing methods like ChiA-PET and Hi-C, the surge in data volume has highlighted the need for more efficient chromatin spatial modelling algorithms. This study introduces the cudaMMC method, based on the Simulated Annealing Monte Carlo approach and enhanced by GPU-accelerated computing, to efficiently generate ensembles of chromatin 3D structures.ResultsThe cudaMMC calculations demonstrate significantly faster performance with better stability compared to our previous method on the same workstation. cudaMMC also substantially reduces the computation time required for generating ensembles of large chromatin models, making it an invaluable tool for studying chromatin spatial conformation.Availability and implementationOpen-source software and manual and sample data are freely available on https://github.com/SFGLab/cudaMMC.
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Project description:Traditional multiple-group confirmatory factor analysis (multiple-group CFA) is usually criticized for having too restrictive model assumption, namely the scalar measurement invariance. The new multiple-group analysis methodology, alignment, has become an effective alternative. The alignment evaluates measurement invariance and more importantly, permits factor mean comparisons without requiring scalar invariance which is usually required in traditional multiple-group CFA. Some simulation studies and empirical studies have investigated the applicability of alignment under different conditions, but some areas remain unexplored. Based on the simulation studies of Asparouhov and Muthén and of Flake and McCoach, this current simulation study is broken into two sections. The first study investigates the minimal group sizes required for alignment in three-factor models. The second study compares the performance of multiple-group CFA, multiple-group exploratory structural equation model (multiple-group ESEM), and alignment by including different proportions and magnitudes of cross-loadings in the models. Study 1 shows that when the model has no noninvariant parameters, the alignment requires relatively lower group sizes. Explicitly, the minimal group size required for alignment was 250 when the amount of groups was three, the minimal group size was 150 when the amount of groups was nine, and 200 when the amount of groups was 15. When there are noninvariant parameters in the model and the amount of groups is low, a group size of 350 is a safe rule of thumb. When there are noninvariant parameters in the model and the amount of groups is high, a group size of 250 is required for trustworthy results. The magnitude of noninvariance and the noninvariance rate do not affect the minimal group size required for alignment. Study 2 shows that multiple-group CFA provides accurate factor mean estimates when each factor had 20% factor loading (1 factor loading) with small-sized cross-loading. Multiple-group ESEM provides accurate factor mean estimates when the magnitude of cross-loading is small or when each factor had 20% factor loading (1 factor loading) with medium-sized cross-loading. Alignment provides accurate factor mean estimates when there are only small-sized cross-loadings in the model. The parameter estimates, coverage rates and ratios of average standard error to standard deviation for each methodology are not influenced by the amount of groups. Recommendations are concluded for using multiple-group CFA, multiple-group ESEM, traditional alignment and aligned ESEM (AESEM) based on the results. Multiple-group CFA is more suitable for use when scalar invariance is established. Multiple-group ESEM works best when there are small-sized or only a few medium-sized cross-loadings in the model. Traditional alignment allows for small-sized cross-loadings and a few noninvariant parameters in the model. AESEM integrates the advantages of alignment and ESEM, can provide accurate estimates when noninvariant parameters and cross-loadings both exist in the model. Compared to multiple-group CFA, multiple-group ESEM, the alignment methodology performs well in more situations.
| S-EPMC9263979 | biostudies-literature