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At least 793 records · Page 44

A data-driven approach to modeling cancer cell mechanics during microcirculatory transport

In order to understand the effect of cellular level features on the transport of circulating cancer cells in the microcirculation, there has been an increasing reliance on high-resolution in silico models. Accurate simulation of cancer cells flowing with blood cells requires resolving cellular-scale interactions in 3D, which is a significant computational undertaking warranting a cancer cell model that is both computationally efficient yet sufficiently complex to capture relevant behavior. Given that the characteristics of metastatic spread are known to depend on cancer type, it is crucial to account for mechanistic behavior representative of a specific cancer’s cells. To address this gap, in the present work we develop and validate a means by which an efficient and popular membrane model-based approach can be used to simulate deformable cancer cells and reproduce experimental data from specific cell lines. Here, cells are modeled using the immersed boundary method (IBM) within a lattice Boltzmann method (LBM) fluid solver, and the finite element method (FEM) is used to model cell membrane resistance to deformation. Through detailed comparisons with experiments, we (i) validate this model to represent cancer cells undergoing large deformation, (ii) outline a systematic approach to parameterize different cell lines to optimally fit experimental data over a range of deformations, and (iii) provide new insight into nucleated vs. non-nucleated cell models and their ability to match experiments. While many works have used the membrane-model based method employed here to model generic cancer cells, no quantitative comparisons with experiments exist in the literature for specific cell lines undergoing large deformation. Here, we describe a phenomenological, data-driven approach that can not only yield good agreement for large deformations, but explicitly detail how it can be used to represent different cancer cell lines. This model is readily incorporated into cell-resolved hemodynamic transport simulations, and thus offers significant potential to complement experiments towards providing new insights into various aspects of cancer progression.

59 BASIC BIOLOGICAL SCIENCES↗

Molecular beam mass spectrometry measurements of vibrationally excited N 2 in the effluent of an atmospheric plasma jet: a comparison with a state-to-state kinetic model

Vibrationally excited N 2 molecules are suggested to be one of the possible key species responsible for the observed synergistic effects in plasma catalysis for NH 3 synthesis. To assess the impact of vibrationally excited species in plasma-catalysis, quantitative measurements near interfaces are required, which remains challenging. In this letter, we report spatially resolved measurements of vibrationally excited N 2 in the effluent of an atmospheric pressure plasma jet by molecular beam mass spectrometry (MBMS). The mass spectrometry signals as a function of electron energy of the ionizer were fitted with the effective electron-impact ionization cross section of N 2 (v) considering the vibrational distribution function as determined by a detailed vibrational level resolved plasma kinetic calculation. Here, the reported method presented in this letter shows the capability of MBMS to measure vibrationally excited species of N 2 near interfaces when the vibrational distribution function is known or assumed and shows excellent agreement with state-to-state kinetic models of N 2 (v).

42 ENGINEERING↗

Comparison of point cloud and image-based models for calorimeter fast simulation

Score based generative models are a new class of generative models that have been shown to accurately generate high dimensional calorimeter datasets. Recent advances in generative models have used images with 3D voxels to represent and model complex calorimeter showers. Point clouds, however, are likely a more natural representation of calorimeter showers, particularly in calorimeters with high granularity. Furthermore, point clouds preserve all of the information of the original simulation, more naturally deal with sparse datasets, and can be implemented with more compact models and data files. In this work, two state-of-the-art score based models are trained on the same set of calorimeter simulation and directly compared.

47 OTHER INSTRUMENTATION↗

Galaxy assembly bias and large-scale distribution: a comparison between IllustrisTNG and a semi-analytic model

In this work, we compare large scale structure observables for stellar mass selected samples at z = 0, as predicted by two galaxy models, the hydrodynamical simulation IllustrisTNG and the Santa-Cruz semi-analytic model (SC-SAM). Although both models have been independently calibrated to match observations, rather than each other, we find good agreement between the two models for two-point clustering and galaxy assembly bias signatures. The models also show a qualitatively similar response of occupancy and clustering to secondary halo parameters other than mass, such as formation history and concentration, although with some quantitative differences. Thus, our results demonstrate that the galaxy–halo relationships in SC-SAM and TNG are quite similar to first order. However, we also find areas in which the models differ. For example, we note a strong correlation between halo gas content and environment in TNG, which is lacking in the SC-SAM, as well as differences in the occupancy predictions for low-mass haloes. Moreover, we show that higher order statistics, such as cumulants of the density field, help us to accurately describe the galaxy distribution and discriminate between models that show degenerate behaviour for two-point statistics. Our results suggest that SAMs are a promising cost-effective and intuitive method for generating mock catalogues for next generation cosmological surveys.

79 ASTRONOMY AND ASTROPHYSICS↗

Multi-Frequency Analysis of Simulated versus Observed Variability in Tropospheric Temperature

Studies seeking to identify a human-caused global warming signal generally rely on climate model estimates of the “noise” of intrinsic natural variability. Assessing the reliability of these noise estimates is of critical importance. We evaluate here the statistical significance of differences between climate model and observational natural variability spectra for global-mean mid- to upper-tropospheric temperature (TMT). We use TMT information from satellites and large multimodel ensembles of forced and unforced simulations. Our main goal is to explore the sensitivity of model-versus-data spectral comparisons to a wide range of subjective decisions. These include the choice of satellite and climate model TMT datasets, the method for separating signal and noise, the frequency range considered, and the statistical model used to represent observed natural variability. Of particular interest is the amplitude of the interdecadal noise against which an anthropogenic tropospheric warming signal must be detected. We find that on time scales of 5–20 years, observed TMT variability is (on average) overestimated by the last two generations of climate models participating in the Coupled Model Intercomparison Project. This result is relatively insensitive to different plausible analyst choices, enhancing confidence in previous claims of detectable anthropogenic warming of the troposphere and indicating that these claims may be conservative. A further key finding is that two commonly used statistical models of short-term and long-term memory have deficiencies in their ability to capture the complex shape of observed TMT spectra.

54 ENVIRONMENTAL SCIENCES↗

Comparison of AGR-3/4 Fission Product Transport Model to Measurements and Extraction of Diffusivities via Analytical Fits

A one-dimensional finite-element model based on the MOOSE framework has been constructed, and overall transport estimates are predicted based on available diffusivities and sorption isotherms in the extant literature. The predicted transport profiles are compared to experimental results, where such results are available, including total inventory analysis of gamma emitters, liquid scintillation results for Sr-90 concentrations, radial deconsolidation leach-burn-leach within compacts, tomographic reconstructions based on detailed gamma scanning and destructive physical sampling of several rings. The magnitude of expected transport to the sink ring is generally predicted by the model for silver and cesium, however, modeled detailed concentration profiles are not consistent with experimental results. Strontium and europium transport is not well characterized by model results.

07 ISOTOPE AND RADIATION SOURCES↗

Advanced Turbulence Models for Large-Scale Atmospheric Boundary Layer Flows

We present high-fidelity large-eddy-simulation (LES) modeling approaches for the turbulent atmospheric boundary layer (ABL) flows. Wind energy is a prime example of an application driven by ABL. Generation of electrical energy from farms of wind turbines at night in the stable ABL is a particularly interesting situation. In this report, we consider the well-known GEWEX (Global Energy and Water Cycle Experiment) Atmospheric Boundary Layer Study (GABLS) stably stratified benchmark LES case. We use a high-order spectral element code Nek5000/RS, which is supported under the DOE's Exascale Computing Project (ECP) Center for Efficient Exascale Discretizations (CEED) project, targeting application simulations on various acceleration-device based exascale computing platforms. In our earlier ANL report, we demonstrated our newly developed subgrid-scale (SGS) models based on high-pass filter (HPF), mean-field eddy viscosity (MFEV), and Smagorinsky (SMG) with no-slip and traction boundary conditions, provided with low-order statistics, convergence and turbulent structure analysis. In this report, we extend the range of our SGS modeling approaches in the context of the mean-field eddy viscosity (MFEV), to include the solution of an SGS turbulent kinetic energy equation (TKE). We demonstrate the model fidelity of Nek5000/RS in comparison to that of AMR-Wind, a block-structured second-order finite-volume code with adaptive-mesh-refinement capabilities, with which we studied scaling performance for both codes in comparison on DOE's leadership computing platforms.

17 WIND ENERGY↗

Non-locality of mean scalar transport in two-dimensional Rayleigh–Taylor instability using the macroscopic forcing method

The importance of non-locality of mean scalar transport in two-dimensional Rayleigh–Taylor Instability (RTI) is investigated. The macroscopic forcing method is utilized to measure spatio-temporal moments of the eddy diffusivity kernel representing passive scalar transport in the ensemble averaged fields. Presented in this work are several studies assessing the importance of the higher-order moments of the eddy diffusivity, which contain information about non-locality, in models for RTI. First, it is demonstrated through a comparison of leading-order models that a purely local eddy diffusivity is insufficient to capture the mean field evolution of the mass fraction in RTI. Therefore, higher-order moments of the eddy diffusivity operator are not negligible. Models are then constructed by utilizing the measured higher-order moments. It is demonstrated that an explicit operator based on the Kramers–Moyal expansion of the eddy diffusivity kernel is insufficient. An implicit operator construction that matches the measured moments is shown to offer improvements relative to the local model in a converging fashion.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Discrete fracture network model benchmarks developed and applied in a DECOVALEX-2023 repository performance assessment study

This study presents newly developed benchmarks for modeling flow and transport within discrete fracture networks (DFNs) and useful methods for analyzing the results. The new benchmarks are designed to test modeling approaches for use in probabilistic performance assessment models of deep geologic repositories in fractured rock. The benchmarks simulate flow and transport through a 1 km 3 block of fractured rock. The first simulates migration of a short pulse of tracer through a simple network of four intersecting fractures. The second adds 1089 stochastically generated fractures. The third changes the pulse to a continuous point source. Evaluation of model performance relies on moment analysis and comparison of the results of different models. The expected nondimensional first moment of the conservative tracer for each benchmark is 1. The benchmarks were simulated by teams from Canada, Czechia, Germany, Korea, Sweden, Taiwan, and the United States as part of a DECOVALEX-2023 study (decovalex.org). The teams used various approaches, including explicit DFN modeling, DFN upscaling to an equivalent continuous porous medium (ECPM), and a combination of both methods. Transport mechanisms are modeled using either the advection-dispersion equation or particle tracking. Results demonstrate strong agreement among the models in breakthrough behavior up to the 75th percentile. Significant deviations in first moments and well-clustered outputs led to the identification of inaccuracies in several models. Such findings exemplify the benefit of exercising these benchmarks and using the presented methods to test DFN flow and transport models.

Benchmark↗

A visco-plastic constitutive model for accurate densification and shape predictions in powder metallurgy hot isostatic pressing

Powder metallurgy hot isostatic pressing (PM-HIP) is an advanced manufacturing process that produces near net shape parts with high material utilization and uniform microstructures. Despite being used frequently to produce small-scale components, the application of PM-HIP to large-scale components is limited due to inadequate understanding of its complex mechanisms that cause unpredictable post-HIP shape distortions. A computational model can provide necessary information about the intermediate and final stages of the HIP process that can help understand it better and make accurate predictions. Generally, two types of computational models are employed for PM-HIP of metal powders, namely, plastic and visco-plastic models. Between these, the plastic model is preferred due to its cheaper calibration approach requiring less experimental data. However, the plastic model sometimes produces incorrect predictions when slight variations of the HIP conditions are encountered in practical situations. Therefore, this work presents a visco-plastic model that addresses these limitations of the plastic model. A novel modified calibration approach is employed for the visco-plastic model that utilizes less experimental data than existing approaches. With the new approach, the data requirement is same for both plastic and visco-plastic models. This also enables a quantitative comparison of plastic and visco-plastic models, which have been only qualitatively compared in the past. When calibrated with the same experimental data, both the models are found to produce similar results. In conclusion, the calibrated visco-plastic model is applied to several complex geometries, and the predictions are found to be in good agreement with experimental observations.

Hot isostatic pressing↗

On the impact of the galaxy window function on cosmological parameter estimation

One important source of systematics in galaxy redshift surveys comes from the estimation of the galaxy window function. Up until now, the impact of the uncertainty in estimating the galaxy window function on parameter inference has not been properly studied. In this paper, we show that the uncertainty and the bias in estimating the galaxy window function will be salient for ongoing and next-generation galaxy surveys using a simulation-based approach. With a specific case study of cross-correlating emission-line galaxies from the DESI Legacy Imaging Surveys and the Planck cosmic microwave background lensing map, we show that neural network-based regression approaches to modelling the window function are superior in comparison to linear regression-based models. Here, we additionally show that the definition of the galaxy overdensity estimator can impact the overall signal-to-noise of observed power spectra. Finally, we show that the additive biases coming from the window functions can significantly bias the modes of the inferred parameters and also degrade their precision. Thus, a careful understanding of the window functions will be essential to conduct cosmological experiments.

79 ASTRONOMY AND ASTROPHYSICS↗

Statistical model of the stimulated forward Brillouin scattering driven by a randomized laser beam in plasma

The modeling of a spatially incoherent laser beam remains a central problem of the parametric instabilities in the context of inertial confinement fusion. This letter gives a simplified and comprehensive overview of the recent analytical developments regarding the modeling of these laser beams and a comparison with a dedicated experiment. Our model accounts for the first time for the statistical standard deviation of the gain and accurately captures the entanglement between wave mixing processes and the speckle correlations thus resolving the longstanding contradictions between the random phase approximation and the model of independent speckles. It is successfully compared to a recent laser beam spray experiment and the associated paraxial simulations, demonstrating that backscattering predictions require accounting for the beam spray. Furthermore, our framework thus provides a way to evaluate and guide the analysis of parametric instabilities in high laser energy experiments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Rotational excitations in rare-earth nuclei: A comparative study within three cranking models with different mean fields and treatments of pairing correlations

High-spin rotational bands in rare-earth Er (Z = 68), Tm (Z = 69), and Yb (Z = 70) isotopes are investigated by three different nuclear models. These are (i) the cranked relativistic Hartree-Bogoliubov (CRHB) approach with approximate particle number projection by means of the Lipkin-Nogami (LN) method, (ii) the cranking covariant density functional theory (CDFT) with pairing correlations treated by a shell-model-like approach (SLAP) or the so-called particle-number conserving (PNC) method, and (iii) cranked shell model (CSM) based on the Nilsson potential with pairing correlations treated by the PNC method. A detailed comparison between these three models in the description of the ground-state rotational bands of even-even Er and Yb isotopes is performed. The similarities and differences between these models in the description of the moments of inertia, the features of band crossings, and equilibrium deformations and pairing energies of the even-even nuclei under study are discussed. These quantities are considered as a function of rotational frequency and proton and neutron numbers. The changes in the properties of the first band crossings with increasing neutron number in this mass region are investigated. On average, a comparable accuracy of the description of available experimental data is achieved in these models. However, the differences between model predictions become larger above the first band crossings. Because of the time-consuming nature of numerical calculations in the CDFT-based models, a systematic study of the rotational properties of both ground-state and excited-state bands in odd-mass Tm nuclei is carried out only by the PNC-SCM. With few exceptions, the rotational properties of experimental 1-quasiparticle and 3-quasiparticle bands in 165,167,169,171 Tm are reproduced reasonably well. As a result, the appearance of backbendings or upbendings in these nuclei is well understood from the analysis of the variations of the occupation probabilities of the single-particle states and their contributions to total angular momentum alignment with rotational frequency.

150 ≤ A ≤ 189↗

Decarbonization Scenarios in the United States: Comparing Biofuels Growth in Two Models - GCAM and BSM

Scenarios for deep decarbonization rely on biomass for biofuels, biopower, and bioproducts, often including negative emissions via carbon capture and storage or utilization. Despite the prominence of biomass in many deep decarbonization pathways, critical questions remain about biomass allocation, effects of transportation electrification, the pace of growth, and implications for agriculture and land use. We address these questions through a unique comparison of carbon pricing effects on the growth of biomass utilization and its effects on land use in the United States by comparing results from a multisectoral integrated assessment model, the Global Change Analysis Model [GCAM], with results from a biomass-to-biofuels system dynamics model, the Biomass Scenario Model [BSM]. We contribute to model comparison efforts by analyzing the biomass deployment needed for a scenario consistent with a "Middle of the Road" Shared Socioeconomic Pathway [SSP2] and a representative concentration pathway of 2.6 W/m2. The GCAM scenarios solve for global equilibrium conditions that are consistent with this pathway, including demands for biomass across all economic sectors and representing bioenergy with carbon capture and storage as a technology option. The BSM scenarios assess those biomass and biofuel results for the United States and identify challenges associated with that pace and amount of expansion. In the scenario analysis, we harmonize key factors such as carbon price trajectory, domestic ethanol fuel demand, ethanol blending, and arable land availability, and vary them in both models. In GCAM, we vary the carbon price, transportation electrification, ethanol blending constraints, and arable land availability inputs and the value of the carbon in land; in BSM, in addition to directly inputting certain GCAM results, we vary the maximum rate of biorefinery construction, flexibility of feedstock types across conversion processes, and policy incentives such as tax credits and renewable identification number payments. The selected carbon price trajectory results in a rapid increase in biofuel production in the United States, reaching about 9.4 EJ/year in 2060 in the highest scenario analyzed in GCAM. Results differ between the two models in timing and ultimate quantity of biomass and biofuel production. GCAM biofuel quantities generally exceed BSM amounts because CCS is applied to biofuel pathways in GCAM, and because of differences in capacity expansion and related dynamics of land allocation, biomass production, and price dynamics. These dynamics include rapid biorefinery capacity expansion in high demand cases. To satisfy this biomass demand, GCAM rapidly equilibrates land allocation, but the BSM limits the rate at which this re-allocation can occur. A further contrast with the equilibrium approach in GCAM is that the BSM represents a delay between planting and harvesting woody biomass resources. As a result of these model contrasts, feedstock costs in BSM increase more than in GCAM, and the absence of CCS in the BSM also reduces the relative economic attractiveness of biofuels production. The bottlenecks, lags, and price increases also lead to potential for volatility in feedstock price and land allocation to biomass in the BSM. GCAM has more biomass production than BSM in all scenarios, partly because of the broader, economy-wide coverage of GCAM, in contrast to BSM's exclusive focus on biofuels. In both models, trends like those of biofuels production were observed for biomass production: minimal growth without a carbon price and policy incentives, and increases with a carbon price, particularly with carbon capture and storage, because the inputs assume that biopower and biofuels decrease greenhouse gas emissions. In high policy scenarios, biomass demand is high, and the consequent high biomass prices due to the land re-allocation bottleneck in the BSM limit biofuel production even if the biorefinery capacity is expanded. However, because biomass prices do not increase as much in the low policy scenario, growth is slower and the land-reallocation bottleneck no longer dominates, such that the effect of increased capacity can be seen. Across both the models, a change in assumptions from less to more land availability increases biofuel production in both GCAM and BSM, as the upward pressure on feedstock price and volatility are both reduced.

biofuels↗

Comparison of URANS and LES predictions for the open phase of the OECD NEA CSNI fluid structure interaction CFD benchmark

The OECD NEA CSNI WGAMA CFD Task Group ran a benchmark in 2020 and 2021 to assess the predictive capabilities of coupled fluid structure interaction (FSI) CFD analysis methods. This paper presents the predictions made for the open phase of the benchmark using URANS and LES turbulence modelling approaches, and a comparison of the results to the experimental data. The benchmark comprised a channel containing two inline cylinders in cross-flow. The cylinders were fixed at one end, free at the other, and had measured resonant frequencies and damping properties. The URANS modelling used ANSYS Fluent 2-way coupled to ANSYS Mechanical. The LES modelling used Nek5000, 1-way coupled to Diablo. Comparisons with cross-channel velocity profiles are presented, both for the mean flow and its RMS. Comparisons are also made to the frequency spectra for point measurements of fluid velocity and pressure, and for the accelerations of the free end of each cylinder. URANS predicts the average velocity profiles relatively well, and is able to predict the velocity and acceleration spectra at the shedding frequency. However, the frequency content at the 4th harmonic of the shedding frequency is low in the URANS flow fields, and so does not excite accelerations at the resonant frequency of the cylinders. LES makes better predictions of the average profiles, and the velocity spectra agree well at both the shedding frequency and at higher frequencies. In conclusion, the 1-way coupled LES results show good agreement for acceleration spectra.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗