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At least 469 records · Page 26

An approximate inertial manifold (AIM) based closure for turbulent flows

A closure model for turbulent flows is developed based on a dynamical system theory. An appropriately discretized formulation of the governing equations is considered for this process. The key ingredient is an approximation of the system’s attractor, where all the trajectories in phase space are confined. This approximate inertial manifold based approach provides a path to track trajectories of the system in a lower-dimensional subspace. Unlike conventional coarse-graining approaches, the turbulent field is decomposed into resolved and unresolved dynamics using the properties of the governing equations. The novelty of the approach relies on the reconstruction of the unresolved field constrained by the governing equations. A posteriori tests for homogeneous isotropic turbulence and the Kuramoto–Sivashinsky equation show promising results for considerable dimension reduction with strong convergence properties. The proposed model outperforms the dynamic Smagorinsky model, and the computational overhead is competitive with similar approaches.

97 MATHEMATICS AND COMPUTING↗

Avoiding pitfalls in molecular simulation of vapor sorption: Example of propane and isobutane in metal–organic frameworks for adsorption cooling applications

This study introduces recommendations for conducting molecular simulations of vapor adsorption, with an emphasis on enhancing the accuracy, reproducibility, and comparability of results. The first aspect we address is consistency in the implementation of some details of typical molecular models, including tail corrections and cutoff distances, due to their significant influence on generated data. We highlight the importance of explicitly calculating the saturation pressures at relevant temperatures using methods such as Gibbs ensemble Monte Carlo simulations and illustrate some pitfalls in extrapolating saturation pressures using this method. For grand canonical Monte Carlo (GCMC) simulations, the input fugacity is usually calculated using an equation of state, which often requires the critical parameters of the fluid. We show the importance of using critical parameters derived from the simulation with the same model to ensure internal consistency between the simulated explicit adsorbate phase and the implicit bulk phase in GCMC. We show the advantages of presenting isotherms on a relative pressure scale to facilitate easier comparison among models and with experiment. Extending these guidelines to a practical case study, we evaluate the performance of various isoreticular metal–organic frameworks (MOFs) in adsorption cooling applications. This includes examining the advantages of using propane and isobutane as working fluids and identifying MOFs with a superior performance.

36 MATERIALS SCIENCE↗

Continental Scale Hydrostratigraphy: Comparing Geologically Informed Data Products to Analytical Solutions

Abstract This study synthesizes two different methods for estimating hydraulic conductivity (K) at large scales. We derive analytical approaches that estimate K and apply them to the contiguous United States. We then compare these analytical approaches to three‐dimensional, national gridded K data products and three transmissivity (T) data products developed from publicly available sources. We evaluate these data products using multiple approaches: comparing their statistics qualitatively and quantitatively and with hydrologic model simulations. Some of these datasets were used as inputs for an integrated hydrologic model of the Upper Colorado River Basin and the comparison of the results with observations was used to further evaluate the K data products. Simulated average daily streamflow was compared to daily flow data from 10 USGS stream gages in the domain, and annually averaged simulated groundwater depths are compared to observations from nearly 2000 monitoring wells. We find streamflow predictions from analytically informed simulations to be similar in relative bias and Spearman's rho to the geologically informed simulations. R ‐squared values for groundwater depth predictions are close between the best performing analytically and geologically informed simulations at 0.68 and 0.70 respectively, with RMSE values under 10 m. We also show that the analytical approach derived by this study produces estimates of K that are similar in spatial distribution, standard deviation, mean value, and modeling performance to geologically‐informed estimates. The results of this work are used to inform a follow‐on study that tests additional data‐driven approaches in multiple basins within the contiguous United States.

54 ENVIRONMENTAL SCIENCES↗

Quantitative cross-species translators of cardiac myocyte electrophysiology: Model training, experimental validation, and applications

Animal experimentation is key in the evaluation of cardiac efficacy and safety of novel therapeutic compounds. However, interspecies differences in the mechanisms regulating excitation-contraction coupling can limit the translation of experimental findings from animal models to human physiology and undermine the assessment of drugs’ efficacy and safety. Here, we built a suite of translators for quantitatively mapping electrophysiological responses in ventricular myocytes across species. We trained these statistical operators using a broad dataset obtained by simulating populations of our biophysically detailed computational models of action potential and Ca 2+ transient in mouse, rabbit, and human. We then tested our translators against experimental data describing the response to stimuli, such as ion channel block, change in beating rate, and β-adrenergic challenge. We demonstrate that this approach is well suited to predicting the effects of perturbations across different species or experimental conditions and suggest its integration into mechanistic studies and drug development pipelines.

60 APPLIED LIFE SCIENCES↗

PCMDI Metrics Package

The Program for Climate Model Diagnosis & Intercomparison (PCMDI) Metrics Package (PMP) is used to provide "quick-look" objective comparisons of Earth System Models (ESMs) with one another and available observations. The PMP provides a diverse suite of analysis utilities each of which produce summary statistics that gauge the consistency between climate model simulations and available observations. The primary application of the PMP is to evaluate simulations from the Coupled Model Intercomparison Project (CMIP). It can also be used to provide objective performance summaries during the model development process as well as selected research purposes.

Ullrich, PaulA [Lawrence Livermore National Labora↗

Improving Protein–Ligand Interaction Modeling with cryo-EM Data, Templates, and Deep Learning in 2021 Ligand Model Challenge

Elucidating protein–ligand interaction is crucial for studying the function of proteins and compounds in an organism and critical for drug discovery and design. The problem of protein–ligand interaction is traditionally tackled by molecular docking and simulation, which is based on physical forces and statistical potentials and cannot effectively leverage cryo-EM data and existing protein structural information in the protein–ligand modeling process. In this work, we developed a deep learning bioinformatics pipeline (DeepProLigand) to predict protein–ligand interactions from cryo-EM density maps of proteins and ligands. DeepProLigand first uses a deep learning method to predict the structure of proteins from cryo-EM maps, which is averaged with a reference (template) structure of the proteins to produce a combined structure to add ligands. The ligands are then identified and added into the structure to generate a protein–ligand complex structure, which is further refined. The method based on the deep learning prediction and template-based modeling was blindly tested in the 2021 EMDataResource Ligand Challenge and was ranked first in fitting ligands to cryo-EM density maps. These results demonstrate that the deep learning bioinformatics approach is a promising direction for modeling protein–ligand interactions on cryo-EM data using prior structural information.

59 BASIC BIOLOGICAL SCIENCES↗

Loosely Conditioned Emulation of Global Climate Models With Generative Adversarial Networks

Climate models encapsulate our best understanding of the Earth system, allowing research to be conducted on its future under alternative assumptions of how human-driven climate forces are going to evolve. An important application of climate models is to provide metrics of mean and extreme climate changes, particularly under these alternative future scenarios, as these quantities drive the impacts of climate on society and natural systems. Because of the need to explore a wide range of alternative scenarios and other sources of uncertainties in a computationally efficient manner, climate models can only take us so far, as they require significant computational resources, especially when attempting to characterize extreme events, which are rare and thus demand long and numerous simulations in order to accurately represent their changing statistics. Here we use deep learning in a proof of concept that lays the foundation for emulating global climate model output for different scenarios. We train two "loosely conditioned" Generative Adversarial Networks (GANs) that emulate daily precipitation output from a fully coupled Earth system model: one GAN modeling Fall-Winter behavior and the other Spring-Summer. Our GANs are trained to produce spatiotemporal samples: 32 days of precipitation over a 64x128 regular grid discretizing the globe. We evaluate the generator with a set of related performance metrics based upon KL divergence, and find the generated samples to be nearly as well matched to the test data as the validation data is to test. We also find the generated samples to accurately estimate the mean number of dry days and mean longest dry spell in the 32 day samples. Our trained GANs can rapidly generate numerous realizations at a vastly reduced computational expense, compared to large ensembles of climate models, which greatly aids in estimating the statistics of extreme events.

climate emulation, extreme climate, impacts, machi↗

COMPUTATIONAL MODELING OF IGNITION AND PREMIXED FLAME PROPAGATION INITIATED BY A PRE-CHAMBER TURBULENT JET

Addressing the pressing need for reduced carbon emissions, Turbulent Jet Ignition (TJI) emerges as a promising technology for ultra-lean combustion, offering enhanced thermal efficiencies and minimized cyclic variability in spark-ignited engines. To facilitate rapid testing and integration of this technology, a robust computational modeling framework is crucial. This study delves into the predictive capabilities of computational models for main-chamber ignition and premixed flame propagation using a single-cycle TJI rig measured by Biswas et al. (Applied Thermal Engineering, vol 106, 2016). Employing an open-source compressible flow simulation solver with Large Eddy Simulation (LES) for turbulence modeling, the investigation integrates the conventional Laminar Finite Rate Chemistry (LFRC) model alongside the transported Probability Density Method (PDF) for turbulence-chemistry interaction. A fully-consistent Eulerian Monte-Carlo Fields (EMCF) method is utilized to approximate the transported PDF, while Interaction by Exchange with Mean is employed to close micro-mixing terms in stochastic differential equations. A reduced chemical reaction mechanism with 21 species and 84 reactions (DRM-19) is used for solving chemical kinetics, and a double Gaussian energy deposition model is used to approximate the spark ignition in the pre-chamber. An unstructured O-grid mesh with 0.3 million cells in the prechamber and 1 million cells in the main chamber is employed. Results are divided into two phases: pre-chamber initialization and full TJI simulations. Validation of the predicted pre-chamber flame propagation and the lean ignition in the main-chamber is carried out by using available experimental data. Under quiescent conditions, both the LFRC and transported PDF methods largely underestimate the flame speed and subsequent pressure growth in the pre-chamber. A linear momentum forcing technique is applied to investigate the impact of initial turbulence in the pre-chamber, demonstrating a notable influence on flame propagation. Fine-tuning of the forcing coefficient reproduces the sudden pressure growth observed in the experiment. The experimentally validated pre-chamber simulation serves as the initial condition for the full TJI simulations. It is found that the LFRC model fails to predict lean-ignition in the main-chamber, resulting in a misfiring event. Incorporation of turbulence-chemistry interaction using the transported PDF method substantially improves the prediction of the ignition event in the main-chamber, achieving fair qualitative agreement and quantitative validation of combustion parameters within ±10% of the reported experimental data. The rich simulation results consisting of a full set of statistical description of the thermo-chemical states enable us to gain deep insights into the ignition mechanisms in the main chamber, which is limited when done experimentally. A novel dual ignition phenomenon is revealed in the TJI rig for the first time. Initially, a primary ignition kernel is formed at a downstream location which eventually detaches from the main jet. As the jet momentum decreases, a secondary ignition event follows, this time at a more upstream location which eventually combines with the primary ignition kernel to form a single connected flame front. Investigation of these ignition sequences in chemical composition space reveal distinct differences between the two. The primary ignition event in the main-chamber is followed by a large concentration of active radicals from the pre-chamber jet, accelerating the chain-branching steps, characterizing what has been referred to as flame ignition. In contrast, the secondary ignition occurs in the absence of active radicals in the pre-chamber jet, hence characterized as jet ignition. Further analysis of the effect of pre-chamber jet characteristics on lean ignition in the main-chamber is conducted by setting up cases with different initial pressure ratios (por) between the two chambers, a non-dimensional parameter, ranging from 1.2 to 3.2. As the initial pressure ratio increases, jet momentum increases, with dual ignition observed in cases above por= 2.2. Case with por= 3.2 lead to misfiring. The effect of ignition sequence on global combustion characteristics of TJI is analyzed. Dual ignition events lead to non-monotonicity in combustion characteristics such as global reaction progress variable, flame penetration, and global heat release rate. In dual ignition events, although the rate of fuel consumption and global heat release rate is initially lower, the secondary ignition leads to a sudden increase in flame surface area, resulting in a sudden jump and promoting the overall performance of the TJI system.

42 ENGINEERING↗

Phase-field model of precipitation processes with coherency loss

A phase-field model is proposed to simulate coherency loss coupled with microstructure evolution. A special field variable is employed to describe the degree of coherency loss of each particle and its evolution is governed by a Ginzburg-Landau type kinetic equation. For the sake of computational efficiency, a flood-fill algorithm is introduced that can drastically reduce the required number of field variables, which allows the model to efficiently simulate a large number of particles sufficient for characterizing their statistical features during Ostwald ripening. The model can incorporate size dependence of coherency loss, metastability of coherent particles, and effectively incorporate the underlying mechanisms of coherency loss by introducing a so-called differential energy criterion. The model is applied to simulate coarsening of Al 3 Sc precipitates in aluminum alloy and comprehensively compared with experiments. Our results clearly show how the particle size distribution is changed during coherency loss and affects the coarsening rate.

36 MATERIALS SCIENCE↗

Baycal

Bayesian Model Calibration (BayCal) toolkit is a software plugin for Risk Analysis Virtual Environment (RAVEN) framework, arming at inversely quantifying the uncertainties associated with simulation model parameters based on available experiment data. BayCal seeks statistical inference of the uncertain input parameters that are consistent with the available measurement data or observed data. The unique feature of BayCal is the capability to be linked with RAVEN to build corresponding calibration workflows for complex multi-physics simulations. In addition to be able to use the machine learning capability of RAVEN to significantly reduce the computational cost of expensive simulation models, another distinctive feature of BayCal is the capability to deal with high-dimensional correlated model outputs, such as time series observations at multiple locations, via principal component analysis (PCA) technique.

Wang, Congjian↗

Optimization of a Cyclone Using Multiphase Flow Computational Fluid Dynamics

The U.S. Department of Energy National Energy Technology Laboratory's (NETL) 50 kW th chemical looping reactor (CLR) has an underperforming cyclone, which was designed using empirical correlations. To improve the performance of this cyclone using computational fluid dynamics (CFD)-based modeling simulations, four critical design parameters including the vortex tube radius and length, barrel radius, and the inlet width and height were optimized. Here, NETL's open source multiphase flow with interphase exchange (MFiX) CFD code has been used to model a series of cyclones by systematically varying the geometric design parameters. To perform the optimization process, the surrogate modeling and sensitivity analysis followed by the optimization capability in nodeworks was used. The basic methodology for the process is to employ a statistical design of experiments (DOE) method to generate sampling simulations that fill the design space. Corresponding CFD models are then created, executed, and postprocessed. A response surface is created to characterize the relationship between input parameters and the quantities of interest (QoI). Finally, the CFD-surrogate is used by an optimization method to find the optimal design condition based on the objective and constraints prescribed. The resulting optimal cyclone has a larger diameter and longer vortex tube, a larger diameter barrel, and a taller and narrower solids inlet. The improved design has a predicted pressure drop 11 times lower than the original design while reducing the mass loss by a factor of 2.3.

42 ENGINEERING↗

On the Statistical Uncertainty of Monte Carlo-Calculated Scattering Sensitivities

Sensitivity coefficients calculated with Monte Carlo codes are widely used for nuclear data uncertainty quantification in the modeling and simulation of complex 3D reactor systems. This study systematically compares sensitivity coefficients and associated statistical uncertainties for the multiplication factor and fuel temperature reactivity across multiple Monte Carlo codes (SCALE/KENO, SCALE/Shift, MCNP, and Serpent) using simple models representing light-water reactors and advanced reactor concepts. For multiplication factor sensitivities, statistical uncertainties are generally acceptable, although scattering sensitivities show significantly larger statistical uncertainties than, for example, fission and capture reactions. Fuel temperature reactivity sensitivities show significantly larger statistical uncertainties across all reactions. Elastic scattering sensitivities are the most problematic: all Monte Carlo codes fail to resolve energy-dependent coefficients, and they produce dramatically different energy-collapsed values. Critically, the use of these sensitivity coefficients in nuclear data uncertainty propagation leads to reduced statistical uncertainties in individual uncertainty contributions. This can lead to the masking of unusable sensitivity coefficients and producing misleading uncertainty results. The findings of this study show that new or enhanced methods are needed to improve Monte Carlo elastic scattering sensitivity calculations. Additionally, this study shows the relevance of verifying sensitivity coefficients through direct perturbation calculations for individual nuclide reactions, instead of only for total cross sections as commonly done.

Bostelmann, Rike [ORNL] (ORCID:0000000165968088)↗

Backlighting extended gas halos around luminous red galaxies: Kinematic Sunyaev-Zel’dovich effect from DESI Y1 and ACT data

The gas density profile around galaxies, shaped by feedback and affecting the galaxy lensing signal, is imprinted on the cosmic microwave background (CMB) by the kinematic Sunyaev-Zel’dovich effect (kSZ). We precisely measure this effect (𝑆/𝑁 ≈ 10) via velocity stacking with 825,283 spectroscopically confirmed luminous red galaxies (LRG) from the Dark Energy Spectroscopic Instrument Year 1 (DESI Y1) survey, which overlap with the Atacama Cosmology Telescope (ACT) Data Release 6 temperature maps over ≥ 4,000 deg 2 . We explore the kSZ dependence with various galaxy parameters and find no significant trend with redshift but clear trends with stellar mass and absolute magnitude in 𝑔, 𝑟, and 𝑧 bands. Our analysis suggests that the gas extends beyond the dark matter halo (99.5% confidence level, i.e., probability to exceed (PTE)⁢ = 0.005). We find a tentative preference for hydrodynamical simulation models with stronger feedback that drives gas further out (Illustris 𝑧 = 0.5, PTE⁢ = 0.37) over weaker-feedback cases (IllustrisTNG 𝑧 = 0.8, PTE⁢ = 0.045), though with limited statistical significance. In all cases, a free multiplicative amplitude was fit to the simulated profiles, and further modeling work is required to firm up these conclusions. We find consistency between kSZ profiles around spectroscopic and photometric LRG, with comparable statistical power, thus increasing our confidence in the photometric analysis. Additionally, we present the first kSZ measurement around the DESI Y1 bright galaxy sample (BGS) and the emission-line galaxies (ELG) whose features match qualitative expectations. Finally, we forecast 𝑆/𝑁 ∼ 50 for future stacked kSZ measurements using data from the ACT, the DESI Y3, and the Rubin Observatory. Furthermore, these measurements will serve as an input for galaxy formation models and baryonic uncertainties in galaxy lensing.

79 ASTRONOMY AND ASTROPHYSICS↗

Microscopic Origin of Twist-Dependent Electron Transfer Rate in Bilayer Graphene

Using molecular simulation and continuum dielectric theory, we consider how electrochemical kinetics are modulated by the twist angle in bilayer graphene electrodes. By establishing a connection between the twist angle and the screening length of charge carriers within the electrode, we investigate how tunable metallicity modifies the statistics of the electron transfer energy gap. Constant potential molecular simulations show that the activation free energy for electron transfer increases with screening length, leading to a non-monotonic dependence on the twist angle. Here, the twist angle alters the density of states, tuning the number of thermally accessible channels for electron transfer and the reorganization energy by affecting the stability of the vertically excited state through attenuated image charge interactions. Understanding these effects allows us to express the Marcus rate of interfacial electron transfer as a function of the twist angle in a manner consistent with experimental observations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Simulating low-energy neutrino interactions with MARLEY

Monte Carlo event generators are a critical tool for the interpretation of data obtained by neutrino experiments. Several modern event generators are available which are well-suited to the GeV energy scale used in studies of accelerator neutrinos. However, theoretical modeling differences make their immediate application to lower energies difficult. In this paper, I present a new event generator, MARLEY, which is designed to better address the simulation needs of the low-energy (tens of MeV and below) neutrino community. The code is written in C++14 with an optional interface to the popular ROOT data analysis framework. The current release of MARLEY (version 1.2.0) emphasizes simulations of the reaction 40 Ar ( ν e , e − ) 40 K ⁎ but is extensible to other channels with suitable user input. This paper provides detailed documentation of MARLEY's implementation and usage, including guidance on how generated events may be analyzed and how MARLEY may be interfaced with external codes such as Geant4. Further information about MARLEY is available on the official website at http://www.marleygen.org. Program title:MARLEY 1.2.0 CPC Library link to program files:https://doi.org/10.17632/4v7zxnc8j3.1 Developer's respository link:http://github.com/MARLEY-MC/marley Code Ocean capsule:https://codeocean.com/capsule/9868179 Licensing provisions: GNU General Public License 3.0 Programming language: C++14 External routines/libraries used: GNU Scientific Library [1,2] (required), ROOT [3,4] (optional) Nature of problem: Simulation of neutrino-nucleus scattering events at energies of tens-of-MeV and below Solution method: Initial two-to-two scattering kinematics are sampled using the allowed approximation differential cross section and tables of precomputed nuclear matrix elements. Subsequent de-excitations of the remnant nucleus are simulated using a Monte Carlo implementation of the Hauser-Feshbach statistical model and tabulated γ-ray decay schemes for discrete nuclear levels. Additional comments including restrictions and unusual features: Input data are provided with the code that are suitable for producing simulations of the charged-current reaction 40 Ar ( ν e , e − ) 40 K ⁎ , coherent elastic neutrino-nucleus scattering on spin-zero target nuclei, and neutrino-electron elastic scattering on any atomic target. Preparation of new reaction input files (whose format is documented in Appendix B) would enable other reaction channels and nuclear targets to be handled by the existing code framework. Although there is no maximum neutrino energy enforced by the code itself, realistic neutrino-nucleus scattering events may be generated up to roughly 50 MeV. Above this energy, the effects of forbidden nuclear transitions, which are neglected in the current treatment of the cross sections (see section 2.1), become increasingly important.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Meltwater runoff and glacier mass balance in the high Arctic: 1991–2022 simulations for Svalbard

The Arctic is undergoing increased warming compared to the global mean, which has major implications for freshwater runoff into the oceans from seasonal snow and glaciers. Here, we present high-resolution (2.5 km) simulations of glacier mass balance, runoff, and snow conditions on Svalbard from 1991–2022, one of the fastest warming regions in the world. The simulations are created using the CryoGrid community model forced by Copernicus Arctic Regional ReAnalysis (CARRA) (1991–2021) and AROME-ARCTIC forecasts (2016–2022). Updates to the water percolation and runoff schemes are implemented in the CryoGrid model for the simulations. In situ observations available for Svalbard, including automatic weather station data, stake measurements, and discharge observations, are used to carefully evaluate the quality of the simulations and model forcing. We find a slightly negative climatic mass balance (CMB) over the simulation period of -0.08 mw.e.yr -1 but with no statistically significant trend. The most negative annual CMB is found for Nordenskiöldland (-0.73 mw.e.yr -1 ), with a significant negative trend of -0.27 mw.e. per decade for the region. Although there is no trend in the annual CMB, we do find a significant increasing trend in the runoff from glaciers of 0.14 mw.e. per decade. The average runoff was found to be 0.8 mw.e.yr -1 . We also find a significant negative trend in the refreezing of -0.13 mw.e. per decade. Using AROME-ARCTIC forcing, we find that 2021/22 has the most negative CMB and highest runoff over the 1991–2022 simulation period investigated in this study. We find the simulated climatic mass balance and runoff using CARRA and AROME-ARCTIC forcing are similar and differ by only 0.1 mw.e.yr -1 in climatic mass balance and by 0.2 mw.e.yr -1 in glacier runoff when averaged over all of Svalbard. There is, however, a clear difference over Nordenskiöldland, where AROME-ARCTIC simulates significantly higher mass balance and significantly lower runoff. This indicates that AROME-ARCTIC may provide similar high-quality predictions of the total mass balance of Svalbard as CARRA, but regional uncertainties should be taken into consideration. The simulations produced for this study are made publicly available at a daily and monthly resolution, and these high-resolution simulations may be re-used in a wide range of applications including studies on glacial runoff, ocean currents, and ecosystems.

54 ENVIRONMENTAL SCIENCES↗

LAW Simulant Recipes for Evaluation of Real-Time, In-Line Monitoring Instruments

Statistically designed recipes were generated for evaluation of in-line instrumentation for the Real-Time In-Line Monitoring (RTIM) program in support of the Hanford Direct-Feed Low Activity Waste (DFLAW) program. The composition matrices were prepared based on Low Activity Waste (LAW) feed vector, melter feed, and Effluent Management Facility (EMF) feed information provided by the flowsheet integration modelling for the DFLAW portion of the Waste Treatment Plant (WTP) mission. These composition matrices were converted to recipes for the LAW feed using the approaches for LAW simulant recipes developed by Savannah River National Laboratory (SRNL). Recipes for the glass forming chemicals (GFCs) were developed based on expected mineral forms to be used to for each element to be added to the recipe. The recipe matrices are shown in the Appendix.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗