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At least 235 records · Page 13

ORT: a workflow linking genome-scale metabolic models with reactive transport codes

Abstract Motivation Nutrient and contaminant behavior in the subsurface are governed by multiple coupled hydrobiogeochemical processes which occur across different temporal and spatial scales. Accurate description of macroscopic system behavior requires accounting for the effects of microscopic and especially microbial processes. Microbial processes mediate precipitation and dissolution and change aqueous geochemistry, all of which impacts macroscopic system behavior. As ‘omics data describing microbial processes is increasingly affordable and available, novel methods for using this data quickly and effectively for improved ecosystem models are needed. Results We propose a workflow (‘Omics to Reactive Transport—ORT) for utilizing metagenomic and environmental data to describe the effect of microbiological processes in macroscopic reactive transport models. This workflow utilizes and couples two open-source software packages: KBase (a software platform for systems biology) and PFLOTRAN (a reactive transport modeling code). We describe the architecture of ORT and demonstrate an implementation using metagenomic and geochemical data from a river system. Our demonstration uses microbiological drivers of nitrification and denitrification to predict nitrogen cycling patterns which agree with those provided with generalized stoichiometries. While our example uses data from a single measurement, our workflow can be applied to spatiotemporal metagenomic datasets to allow for iterative coupling between KBase and PFLOTRAN. Availability and implementation Interactive models available at https://pflotranmodeling.paf.subsurfaceinsights.com/pflotran-simple-model/. Microbiological data available at NCBI via BioProject ID PRJNA576070. ORT Python code available at https://github.com/subsurfaceinsights/ort-kbase-to-pflotran. KBase narrative available at https://narrative.kbase.us/narrative/71260 or static narrative (no login required) at https://kbase.us/n/71260/258. Supplementary information Supplementary data are available at Bioinformatics online.

54 ENVIRONMENTAL SCIENCES↗

The Need for Urban‐Resolving Climate Modeling Across Scales

Abstract Increasing urbanization, evolving urban landscapes, and growing populations require an accurate representation of urban areas and urban processes at microscale, regional, and global scales and their feedback across the scales. Important urban processes should be represented in climate models, and current approaches used are discussed. We discuss strategies for urban‐resolving climate research to capture the effect of climate on urban regions and the non‐linear urban processes on climate. Advancing urban‐resolving climate modeling will take us closer to capabilities that can truly capture relevant natural and human components.

Sharma, Ashish↗

Determination of permeability for hydrocarbon release due to excavation-induced stress redistribution in rock salt

Due to a stress redistribution after the excavation of an underground tunnel for radioactive waste disposal, an Ed/DZ (excavation disturbed/damaged zone) will be generated in the near field of the opening, resulting in significant changes in the hydraulic and mechanical properties of the rock mass in the zone. Initially more or less randomly distributed hydrocarbons at grain boundaries in rock salt, which sometimes can only be observed with ultraviolet light, can then be mobilised and migrate at a potentially significant rate towards the excavation. Within the international cooperative project DECOVALEX 2019, the migration mechanism of such fluid inclusions in rock salt is being studied intensively. Specifically, a multi-scale modelling strategy has been developed. A macroscale coupled hydro-mechanical modelling of an underground excavation was performed to determine hydraulic and time-dependent deviatoric stress conditions, by taking into account the rock salt creep behaviour. Under the obtained macro-scale constraints, micro-scale modelling of a pathway dilation along halite grain boundaries was performed using different model strategies: a) coupled hydromechanical modelling with a consideration of hydraulic pressure-induced dilatant deformation, b) nonlinear dynamic model taking account of fluid migration, stress-dependent grain boundary wetting and shear-induced dilatancy of salt, and c) phase-field modelling of flow pathway propagation. The permeability increase resulting from the pathway dilation is estimated to be as high as two orders of magnitude. Based on the permeability determined, a series of pressure buildups measured from a borehole with a high hydrocarbon release rate, a total of 430 build-ups within a monitoring time of 938 days, can be simulated with a macro-scale compressible flow model accounting for different zones around the opening.

58 GEOSCIENCES↗

Bridging particle and reactor scales in the simulation of biomass fast pyrolysis by coupling particle resolved simulation and coarse grained CFD-DEM

Efficient utilization of biomass is challenging due to the complexity of the feedstock at molecular, particle, and reactor scales. Direct coupling of particle scale model and reactor scale simulation is computationally infeasible. In this work, the results from a particle resolved simulation were used to calibrate the heat transfer and reaction kinetics of particles. A hybrid drag model was used to consider the different fluidization properties of sands and biomass particles. The computation cost was reduced using a coarse-grained Discrete Element Method (DEM). The simulated conversion rate, char yield, tar yield, and pyrolysis gas yield compare well with experiment. The residence time and axial distributions of biomass were also analyzed. This novel multi-scale method provides an efficient and accurate tool for the modeling of biomass pyrolysis reactors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Efficient Computation Of Surface Sunlit Fractions In Urban-Scale Building Modeling Using Ray-Tracing Techniques

For building energy simulation at an urban-scale, solar shading calculations can be significantly slow when a large number of shading surfaces are considered in the solar shading calculations, due to the computational complexity of the geometry calculations. We developed a new algorithm using the ray-tracing technique to pre-calculate the sunlit fractions of all exterior surfaces in an urban district altogether. The ray tracing-based calculator is accelerated using General Purpose Graphics Processing Units (GPGPUs) and the Optix ray tracing library, and provides an efficient, flexible, and robust means for computing the sunlit fraction of large numbers of urban surfaces of complex geometries.

Luo, Xuan↗

Definition of the Stiesdal Offshore TetraSpar Floating Wind System for OC6 Phase IV

The Offshore Code Comparison Collaboration, Continued, with Correlation, and unCertainty (OC6) is an international project focused on verifying and validating modeling tools used in the analysis of floating offshore wind systems. The fourth phase of the project aims to assess the ability of the tools to model a novel floating wind design. The TetraSpar was designed by Stiesdal Offshore Technologies and was selected as the subject platform for the project. The platform is a unique design that features spar-like stability with a very low center of gravity, but does not require rare deep-water ports. This combination is achieved with a system made of two separate steel structures, a hull at the water's surface that supports the wind turbine tower, and a keel that is suspended below the main body. This lower keel has a very high density and drives the total platform's low center of gravity. The TetraSpar, with hull and keel, spar-type stability, and relatively slender components, is unique compared to platforms studied in earlier phases of OC3-OC6 projects, and it offers an opportunity to evaluate the applicability of modeling tools to a novel design, especially unique hydrodynamics and compliant cables. Scaled model tests of the TetraSpar design were performed in 2018-2019 by the University of Maine. The data collected in the model tests provides a detailed description of the response of the platform in various controlled and relatively well understood conditions. Comparison with this data provides a good opportunity for validation of numerical models. The OC6 Phase IV work focuses on the specific parameters used in these scaled model tests. Descriptions of the platform and the test campaign in this document are based on the report written by Allen and Fowler of the University of Maine in 2019.

17 WIND ENERGY↗

SPiRaL: a multiresolution global tomography model of seismic wave speeds and radial anisotropy variations in the crust and mantle

SUMMARY SPiRaL is a joint global-scale model of wave speeds (P and S) and anisotropy (vertical transverse isotropy, VTI) variations in the crust and mantle. The model is comprised of >2.1 million nodes with five parameters at each node that capture velocity variations for P- and S-waves travelling at arbitrary directions in transversely isotropic media with a vertical symmetry axis (VTI). The crust (including ice, water, sediments and crystalline layers) is directly incorporated into the model. The default node spacing is approximately 2° in the lower mantle and 1° in the crust and upper mantle. The grid is refined with ∼0.25° minimum node spacing in highly sampled regions of the crust and upper mantle throughout North America and Eurasia. The data considered in the construction of SPiRaL includes millions of body wave traveltimes (crustal, regional and teleseismic phases with multiples) and surface wave (Rayleigh and Love) dispersion. A multiresolution inversion approach is employed to capture long-wavelength heterogeneities commonly depicted in global-scale tomography images as well as more localized details that are typically resolved in more focused regional-scale studies. Our previous work has demonstrated that such global-scale models with regional-scale detail can accurately predict both teleseismic and regional body wave traveltimes, which is necessary for more accurate location of small seismic events that may have limited signal at teleseismic distances. SPiRaL was constructed to predict traveltimes for event location and long-period waveform dispersion for seismic source inversion applications in regions without sufficiently tuned models. SPiRaL may also serve as a starting model for full-waveform inversion (FWI) with the goal of fitting waves with periods 10–50 s over multiple broad regions (thousands of kilometres) and potentially the globe. To gain insight to this possibility, we simulated waveforms for a small set of events using SPiRaL and independent waveform-based models for comparison. For the events tested, the performance of the traveltime-based SPiRaL model is shown to be generally on par with regional 3-D waveform-based models in three regions (western United States, Middle East, Korean Peninsula) suggesting SPiRaL may serve as a starting model for FWI over broad regions.

58 GEOSCIENCES↗

High-resolution hourly surrogate modeling framework for physics-based large-scale building stock modeling

Surrogate modeling can play a key role in reducing high computational burdens for large-scale physics-based modeling and uncertainty quantification. With the rapid development of large-scale building stock energy modeling, surrogate modeling has also begun to be widely applied in this field; however, most existing surrogate models lack hourly time resolution for regional-scale modeling, which is essential for understanding building demand profiles and grid impacts. Further, there is generally a lack of necessary data and feature engineering frameworks specific to building modeling for efficiently managing large datasets and complex computations. Furthermore, this paper proposes a modeling framework for large-scale (city-/region-scale), high-resolution, high-fidelity surrogate building stock energy models. Our developed framework consists of six modules: (1) building stock energy modeling (ComStock TM and ResStock TM ), (2) data engineering for large simulation data, (3) high performance computing workflow, (4) feature engineering, (5) machine learning model development, and (6) model performance evaluation. Two case studies apply the developed framework in both residential and commercial building stock analysis to demonstrate its computational efficiency and surrogate modeling accuracies. Results show that surrogate models, when efficiently trained using the HPC workflow module, reach a high level of modeling accuracy for two case studies.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Advancing quantitative models of soil microbiology, ecology, and biochemistry

Rapid advances in soil biology are increasingly reflected in mathematical models. From molecular to global scales, models contribute to fundamental understanding and prediction of critical soil processes, such as carbon sequestration. Recent models explicitly incorporate microbial control over soil carbon and nutrient cycling, an approach that offers greater biological realism but raises new challenges in model parameterization and stability. Although they have proliferated at community and ecosystem scales, microbial-explicit models have yet to be incorporated into most Earth system models. Applying soil models across scales requires integration with data to support parameterization and validation using approaches such as Bayesian data assimilation. In conclusion, to catalyze future progress, we recommend breaking down barriers between modeling and empirical disciplines while broadening access to the computational infrastructure that supports soil biological modeling.

Xie, Wally↗

Atomic-scale mechanisms of void strengthening in tungsten

Neutron and heavy-ion irradiation of tungsten produces nanometer-size vacancy voids, gas-filled bubbles and dislocation loops. These defect features can affect mechanical properties and the impact can be quite significant because of their high density. Understanding the basic mechanisms of mechanical properties degradation is necessary for predicting radiation effects. Predictions can be made using discrete dislocation dynamics or/and finite element approaches which, however, need local interaction mechanisms as inputs. Such knowledge can be provided only by atomic-scale modeling. This paper reports the results of an extensive atomic-scale modeling study of the interactions between moving edge dislocations and voids in tungsten. Furthermore, the main focus is on the effects of the void size and ambient temperature. Critical resolved shear stress was calculated for voids up to 9 nm in diameter. Atomistic results are compared with the theoretical approach and with those obtained earlier for voids in body centered cubic (bcc) iron. An important role of the void surface has been revealed.

36 MATERIALS SCIENCE↗

Equivalent Point Sources for Simulating Nuclear/Radiological Search Operations

Modeling and simulation can be used to estimate the detection of different types and strengths of radioactive sources. Simulations of shielded gamma-ray sources in complex environments, such as searches in urban areas using vehicle-mounted detectors, can demonstrate what source strengths and shielding combinations should be able to be detected. For faster calculations, gamma-emitting sources that could have different shielding layers can be simulated ahead of time, resulting in equivalent point source emission distributions that can be used in larger simulation models. Larger-scale models will then run faster using equivalent point sources because the shielding layers around the sources have already been accounted for. Accompanying this paper are 260 equivalent point source emission files for 72 sources with different shielding layers, formatted for three different Monte Carlo codes. Users wanting to request versions of the SCALE and/or MCNP software can find details here: https://rsicc.ornl.gov/

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Development and scaling of MeV x-ray radiography at NIF-ARC

We investigate the generation of MeV x-rays using the Advanced Radiography Capability laser system at the National Ignition Facility using 1, 10, and 38 ps pulse durations, with laser energies reaching up to 4 kJ and using compound parabolic concentrators. Hydrodynamic simulations using up-to-date measurements of the contrast of the ARC laser are conducted, allowing us to employ an electron scaling model that incorporates scale length and pulse duration, which aligns closely with the observed temperature distributions. Comparable x-ray sources, in terms of dose, are generated when using a 10 ps pulse duration with 2.4 kJ at ∼1.9 ± 0.4 × 10 18 W/cm 2 and when using a 38 ps pulse duration with 4 kJ at 9.9 ± 0.4 × 10 17 W/cm 2 , both achieving ∼16 rad in air at 1 m for x-ray energies > 0.5 MeV. Radiographs performed on the laser “line-of-sight” show significant improvements in image quality than radiographs performed at 65 degrees to the laser axis. We verify the radiography performance using Monte Carlo Simulations.

Physics - Plasma physics↗

Characterizing the seismic response of a molten salt nuclear reactor

Abstract One Generation IV nuclear reactor, which uses a fluoride salt as a coolant, graphite reflector blocks as a moderator, and circulating buoyant TRISO pebbles as fuel is at an advanced stage of development. To characterize the seismic behavior of components of this reactor, validate numerical models for analysis, and develop recommendations for design, a set of earthquake‐simulator experiments on a scaled model of the reactor vessel and its internals was executed on a six‐degree‐of‐freedom earthquake simulator. The model was seismically isolated at its base using two types of spherical sliding bearings. The scaled model involved representations of the prototype reactor vessel, core barrel, reflector blocks, coolant, and spherical fuel pebbles. The material and geometric properties of different test components were selected based on a dynamic similitude scaling analysis and an approximate length scale of 0.4. Four sets of three‐component earthquake motions were used as inputs for testing. Instrumentation on the test specimen recorded the dynamic responses of the outer vessel, core barrel, and reflector‐block assembly, the hydrodynamic responses (sloshing and hydrodynamic pressure) of the liquid coolant, pebble consolidation under earthquake shaking, and the behavior of the isolation systems. This paper describes the design of the experiments and presents key results from the tests. The dynamic responses of the outer vessel, core barrel, and the reflector blocks revealed that the components responded as a unit for the intense shaking used in the experiments. The sloshing response of the fluid in a thin annulus near the perimeter of the vessel was heavily damped. The change in the packing fraction of the pebble bed under repeated, intense 3D earthquake shaking was less than 3%. Seismically isolating the vessel substantially reduced demands on its internal components.

Engineering↗

OReole-FM: successes and challenges toward billion-parameter foundation models for high-resolution satellite imagery

While the pretraining of Foundation Models (FMs) for remote sensing (RS) imagery is on the rise, models remain restricted to a few hundred million parameters. Scaling models to billions of parameters has been shown to yield unprecedented benefits including emergent abilities, but requires data scaling and computing resources typically not available outside industry R&D labs. In this work, we pair high-performance computing resources including Frontier supercomputer, America's first exascale system, and high-resolution optical RS data to pretrain billion-scale FMs. Our study assesses performance of different pretrained variants of vision Transformers across image classification, semantic segmentation and object detection benchmarks, which highlight the importance of data scaling for effective model scaling. Moreover, we discuss construction of a novel TIU pretraining dataset, model initialization, with data and pretrained models intended for public release. By discussing technical challenges and details often lacking in the related literature, this work is intended to offer best practices to the geospatial community toward efficient training and benchmarking of larger FMs.

Ambrozio Dias, Philipe↗

MATBOX, an Open-Source Microstructure Analysis Toolbox for Meshing, Generation, Segmentation, and Characterization of 3D Heterogenous Volumes

Battery performance is strongly correlated with electrode microstructural properties. To account for its impact, lithium-ion battery (LIB) models either abstract the microstructural heterogeneity of composite electrodes using effective macroscopic properties (macro- or meso- scale models) or directly solve the system of equations on the microstructure geometry or mesh (microstructure-scale models). Therefore, to be adequate, both families of models require information from the microstructure geometry, which can be provided by the numerical tool presented in this work. MATBOX is a MATLAB open-source application [1] developed by NREL for performing various microstructure-related tasks including microstructure numerical generation, image filtering and microstructure segmentation, microstructure characterization and correlation, visualization, and microstructure meshing. MATBOX was originally developed for the analysis of LIB electrode microstructures; however, the algorithms provided by the toolbox are widely applicable to other heterogeneous materials. The toolbox provides a user-friendly experience thanks to a Graphical-User Interface, requires no coding by the user, and is well documented. This presentation will illustrate various MATBOX features for the characterization of a LIB electrode, including a fully automated Representative Volume Element (RVE) analysis, the numerical generation of complex 'virtual' microstructure, including dual-layer electrodes and carbon-binder additive phase, and the meshing of a complex NMC/graphite full cell microstructure suitable for 3D finite-element modeling. Other modules (segmentation, visualization, and correlation) will be briefly presented. Thanks to its modular, open-source approach, MATBOX can easily incorporate third-party algorithms to eventually build a standard in the field that will benefit the whole scientific community. Effective diffusion coefficient [2], additive phase numerical generation [3], and meshing [4] third-party algorithms have been already integrated in the toolbox with more to come.

DIRECT ENERGY CONVERSION,MATHEMATICS AND COMPUTING↗

A linked-scale coupled model of mass erosion and redistribution in plasma-exposed micro-foam surfaces

Surface evolution due to exposure to harsh environments is of importance in many scientific and technological applications. In plasma-exposed materials, the surface receives charged particles from the plasma, leading to a series of processes that drive the system far from equilibrium and may lead to the severe deterioration of the surface properties. Although surface morphological changes are driven by atomic collisions taking place over picoseconds and nanometers, these processes result in mass loss and redistribution of matter over much larger length and time scales. This necessitates a multi-scale approach capable of capturing the range of processes linking primary atomic collision events with engineering-level surface geometry changes. In this paper, we develop a computational model to simulate the morphological evolution and effective erosion rate of micro-architected tungsten foams during low-energy plasma ion bombardment. Furthermore, the model acts on several length scales, with the energy and angular dependence of the sputtering yield of flat tungsten surfaces determined using the SRIM code based on the binary collision approximation. This information is introduced into a low-fluence, short-term Monte Carlo raytracing model, and further into a high-fluence, long-term particle transport model. In the latter, material particles representing billions of atoms are described in a digitized 3-D representation of the foam structure from X-ray tomography data, and are sputtered off and redeposited using the atomistic information. We show that the redeposition of sputtered atoms leads to partial self-healing in the bottom layers with a sharp reduction in the sputtering coefficient of low density foams, roughly 25% of the solid W value. This is in qualitative agreement with recent experiments on low porosity W structures. At high fluence, the foam structure degrades considerably as there are fewer ligaments available to recapture sputtered atoms and, consequently, the sputtering rate increases again.

36 MATERIALS SCIENCE↗