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DOE OSTI2020

A Review of Computational Models for the Flow of Milled Biomass Part I: Discrete-Particle Models

Biomass is a renewable and sustainable energy resource. Current design of biomass handling and feeding equipment leverage both experiments and numerical modeling. This paper reviews the state-of-the-art discrete element methods (DEM) for the flow of milled biomass (Part I), accompanied by a comprehensive review on continuum-based computational models (Part II). The present review on DEM is primarily focused on the features and suitability of various particle shape models for different types of milled biomass because particle shape is the predominant attribute controlling the flow behavior of complex-shaped granular material. The general strengths and weaknesses in the applicability of those models for the milled biomass modeling are summarized. In particular, comments are provided to balance the numerical model capabilities and the computational cost for the development of DEM models. To our best knowledge, this is the first-of-its-kind review on DEM specifically for biomass. Our study indicates that the current DEM models require further development, calibration, and validation based on a deep understanding of biomass particle contact mechanics and experimental data support before they can be reliably used for predictive simulations in handling and feeding systems.

42 ENGINEERING↗

DOE OSTI2020

A Review of Computational Models for the Flow of Milled Biomass Part II: Continuum-Mechanics Models

The design of efficient material-handling systems for milled lignocellulosic biomass is challenging due to their complex particle morphologies and frictional interactions. Computational modeling, including the discrete element method (DEM) and continuum-based finite-element/volume methods, may offer scientific insight and predictive capabilities for the flow of milled biomass in hoppers and feeders. Herein, this article (Part II) presents a review of current state-of-the-art continuum models for the flow of milled biomass, whereas DEM models are reviewed in a companion article (Part I). Advances of numerical methods to solve the global governing equations are discussed first, followed by a comprehensive review of constitutive models for granular materials, including Drucker–Prager, hypoplastic, Cambridge-type, inertial-rheology, and nonlocal granular fluidity models. Specifically, we provide in-depth discussion on the suitability of those models for milled lignocellulosic biomass materials in terms of nonlinear elasticity, dependence of flow strength on pressure, density and shear rate, and compaction (dilation) associated with hardening (softening). Furthermore, our study shows that, despite the recent advances in continuum granular flow modeling, the most suitable constitutive models still need further development to account for material parametrization, multiflow regimes, and multiscale behavior before they can be reliably used to optimize the design and operation of biomass handling systems.

09 BIOMASS FUELS↗

DOE OSTI2020

Parameterizing Perennial Bioenergy Crops in Version 5 of the Community Land Model Based on Site‐Level Observations in the Central Midwestern United States

Abstract With projected expansion of biofuel production at a global scale, there is a pressing need to develop adequate representation of bioenergy crops in land surface models to help effectively quantify the biogeophysical and biogeochemical effects of its associated land use changes. This study implements two new perennial bioenergy crops, Miscanthus and switchgrass, into the Community Land Model Version 5 based on site‐level observations from the midwestern United States by modifying parameters associated with photosynthesis, phenology, allocation, decomposition, and carbon cost of nitrogen uptake and integrating concomitantly land management practices. Sensitivity analyses indicate that carbon and energy fluxes of the perennial crops are most sensitive to photosynthesis and phenology parameters. Validation of simulated fluxes against site‐level measurements demonstrates that the model is capable of capturing the overall patterns of energy and carbon fluxes, as well as physiological transitions from leaf emergence to senescence. Compared to annual crops, perennial crops feature longer growing season, greater leaf areas, and higher productivity, leading to increased transpiration, lower annual runoff, and larger carbon uptake. The model simulations suggest that with higher CO 2 assimilation rates and lower demands for nutrients and water, high‐yielding perennial crops are promising alternatives of bioenergy feedstocks compared to traditional annual crops not only for mitigating climate change but also for environmental conservation purposes by reducing fertilizer application and therefore alleviating surface‐ and ground‐water contaminations. Although the local‐scale simulations shed light on potential benefits of using perennial grasses as bioenergy feedstocks, quantifying consequences of their plantations at larger scales warrants additional investigation.

Cheng, Yanyan↗

DOE OSTI2020

Improving a Multilevel Turbulence Closure Model for a Shallow Lake in Comparison With Other 1-D Models

Lakes differ from lands in water availability, heat capacity, albedo, and roughness, which affect local surface-atmospheric interactions. This study modified a multilevel upper ocean model (UOM) for lake applications and evaluated its performance in Lake Taihu (China) with comprehensive measurements against three popular one-dimensional (1-D) lake models. These models were based on different concepts, including the self-similarity (FLake), the wind-driven eddy diffusion (LISSS), the k-ε turbulence closure (SIMSTRAT), and a simplified turbulence closure (UOM). The surface flux scheme in these models was unified to exclude the discrepancies in representing air-lake exchanges. All models in their default formulations presented obvious cold water temperature biases and largely underestimated the lake surface temperature (LST) diurnal range. For each model, these deficiencies were significantly reduced by incorporating new physics schemes or calibrated tunable parameters based on systematic sensitivity tests. The primary modifications for UOM included (1) a new scheme of decreased surface roughness lengths to better characterize the shallow lake, (2) a solar radiation penetration scheme with increased light extinction coefficient and surface absorption fraction to account for the high water turbidity, and (3) turbulent Prandtl number increased by a factor of 20 to reduce the turbulent vertical mixing. All other models were improved in these three aspects (roughness, extinction, and mixing) within their original formulations. Given these improvements, UOM showed superior performance to other models in capturing LST diurnal cycle and daily to seasonal variations, as well as summer-autumn vertical stratification changes. The new UOM is well suited for application in shallow lakes.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Twisting the Hubbard model into the momentum-mixing Hatsugai–Kohmoto model

The Hubbard model is a standard theoretical tool for studying materials with strong electron–electron interactions, such as cuprate superconductors. Unfortunately, interaction-driven phenomena, such as a transition into the strongly correlated Mott insulator phase, are difficult to treat with established theoretical techniques. However, the exactly solvable Hatsugai–Kohmoto model displays similar Mott physics. In this work we show how the Hatsugai–Kohmoto model can be deformed continuously into the Hubbard model. The trick is to systematically reintroduce all the momentum mixing that the original Hatsugai–Kohmoto model omits. This can be accomplished by grouping n momenta into a cell and hybridizing them, resulting in the momentum-mixing Hatsugai–Kohmoto model. We recover the Bethe ansatz ground-state energy of the one-dimensional Hubbard model to within 1% from only ten mixed momenta. Overall, the convergence scales as 1/n2 as opposed to the inverse linear behaviour of standard finite-cluster techniques. Our results for a square lattice reproduce all the known features from state-of-the-art simulations also with only a few mixed momenta. Consequently, we believe that the momentum-mixing Hatsugai–Kohmoto model offers an alternative tool for strongly correlated quantum matter.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2024

Probabilistic and maximum entropy modeling of chemical reaction systems: Characteristics and comparisons to mass action kinetic models

We demonstrate and characterize a first-principles approach to modeling the mass action dynamics of metabolism. Starting from a basic definition of entropy expressed as a multinomial probability density using Boltzmann probabilities with standard chemical potentials, we derive and compare the free energy dissipation and the entropy production rates. We express the relation between entropy production and the chemical master equation for modeling metabolism, which unifies chemical kinetics and chemical thermodynamics. Because prediction uncertainty with respect to parameter variability is frequently a concern with mass action models utilizing rate constants, we compare and contrast the maximum entropy model, which has its own set of rate parameters, to a population of standard mass action models in which the rate constants are randomly chosen. We show that a maximum entropy model is characterized by a high probability of free energy dissipation rate and likewise entropy production rate, relative to other models. We then characterize the variability of the maximum entropy model predictions with respect to uncertainties in parameters (standard free energies of formation) and with respect to ionic strengths typically found in a cell.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2019

Nonlinear Modeling of Ground Motions at Lotung LSST Site with Nested Surface Soil Constitutive Model

Seismic analyses of nuclear facilities require the use of validated numerical models that can realistically reproduce the response of soils during earthquakes. The nested surface nonlinear, hysteretic soil constitutive model is one of the soil constitutive models that is vastly used due to (i) lower number of free parameters compared to other nonlinear soil constitutive models, and (ii) because of the ease of calibrating these parameters using the commonly available soil data, i.e., G/G max and damping curves as a function of shear strain. This material model is available in commercial finite element software packages (LS-DYNA and Abaqus) as well in the open source finite element tool (Mastodon). The purpose of this study is to estimate the parameters required for this material model from the soil data available for the Lotung site and to demonstrate that this nonlinear soil constitutive model used in a time domain, finite element analysis can reasonably reproduce the actual measured soil motions recorded at Lotung during the LSST07 event on May 20, 1986. Results are introduced from all the three softwares mentioned above using the same material model.

42 ENGINEERING↗

DOE OSTI2020

Impact of ocean model resolution on understanding the delayed warming of the Southern Ocean

Abstract Currently available historical climate change simulations indicate a relatively delayed Southern Ocean warming, particularly poleward of the Antarctic Circumpolar Current (ACC) compared much of the rest of the globe. However, even this simulated delayed warming is inconsistent with observational estimates which show a cooling trend poleward of the ACC for the period 1979–2014. A fully coupled model run at two resolutions, i.e. ocean eddy parameterized and ocean eddy resolving, driven by historical and fixed CO2 concentration is used to investigate forced trends south of the ACC. We analyze the 1961–2005 Southern Ocean surface and upper ocean temperatures trends simulated by the model and observational estimates to understand the observed trends in the SO. At both resolutions, the models successfully reproduce the observed warming response for the northern flank of the ACC. The eddy resolving simulations, however, are able to reproduce the observed near Antarctic cooling in contrast to the eddy parameterized simulation which shows a warming trend. The cause of this inconsistency between the observations and the ocean eddy parameterized climate models is still a matter of debate, and we show here results that suggest resolved ocean meso-scale processes may be an integral part of capturing the observed trends in the Southern Ocean.

Environmental Sciences & Ecology↗

DOE OSTI2023

Complementing model species with model clades

Abstract Model species continue to underpin groundbreaking plant science research. At the same time, the phylogenetic resolution of the land plant tree of life continues to improve. The intersection of these 2 research paths creates a unique opportunity to further extend the usefulness of model species across larger taxonomic groups. Here we promote the utility of the Arabidopsis thaliana model species, especially the ability to connect its genetic and functional resources, to species across the entire Brassicales order. We focus on the utility of using genomics and phylogenomics to bridge the evolution and diversification of several traits across the Brassicales to the resources in Arabidopsis, thereby extending scope from a model species by establishing a “model clade.” These Brassicales-wide traits are discussed in the context of both the model species Arabidopsis and the family Brassicaceae. We promote the utility of such a “model clade” and make suggestions for building global networks to support future studies in the model order Brassicales.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Deep Learning-Based Dynamic Modeling of Three-Phase Voltage Source Inverters

Inverter-based resource (IBR) models are necessary to analyze modern power system stability and create effective control strategies. Modeling IBRs in converter-rich power systems is crucial, yet challenging due to the lack of commercial information on converter topologies and control parameters. This paper proposes novel convolutional neural network (CNN)–based data-driven techniques for modeling IBRs, addressing adaptability and proprietary concerns without requiring internal system physics knowledge. The proposed method is tested using real grid-tied commercial IBR transient data and demonstrates effectiveness and accuracy. Furthermore, the developed modeling approach is integrated and implemented in the open-source power distribution simulation and analysis tool, GridLAB-D, to illustrate the potentiality of dynamic analysis of large-scale power systems with high IBRs.

deep learning, artificial intelligence↗

DOE OSTI2021

Networked HIL Simulation System for Modeling Large-scale Power Systems

This paper presents a networked hardware-in-the-loop (HIL) simulation system for modeling large-scale power systems. Researchers have developed many HIL test systems for power systems in recent years. Those test systems can model both microsecond-level dynamic responses of power electronic systems and millisecond-level transients of transmission and distribution grids. By integrating individual HIL test systems into a network of HIL test systems, we can create large-scale power grid digital twins with flexible structures at required modeling resolution that fits for a wide range of system operating conditions. This will not only significantly reduce the need for field tests when developing new technologies but also greatly shorten the model development cycle. In this paper, we present a networked OPAL-RT based HIL test system for developing transmission-distribution coordinative Volt-VAr regulation technologies as an example to illustrate system setups, communication requirements among different HIL simulation systems, and system connection mechanisms. Impacts of communication delays, information exchange cycles, and computing delays are illustrated. Simulation results show that the performance of a networked HIL test system is satisfactory.

Xie, Fuhong↗

DOE OSTI2023

Impact of Detailed Parameter Modeling of Open-Cycle Gas Turbines on Production Cost Simulation: Preprint

Flexible resources are increasingly important as variable renewable energy deployment in the power system increases. Although many systems are transitioning away from fossil fuels, open-cycle gas turbines are likely to play an important balancing role for some time, thus requiring accurate modeling of their operational parameters. This paper explores the impact of detailed representation of three operational parameters - start- up costs, run-up rates, and forced outage rates - in the production cost model of a system as it adopts higher levels of wind and solar. Using PLEXOS simulations of the NREL-118 bus test system, the study examines how more detailed parameter modeling affects outcomes such as the number of start-ups and shutdowns, ramping and total generation costs for open-cycle gas turbines, as renewable energy levels increase. The results suggest the value of detailed parameter modeling and continued research on combustion turbines' ability to provide flexibility.

economic dispatch↗

DOE OSTI2020

Improving collaborations between empiricists and modelers to advance grassland community dynamics in ecosystem models

Climate change, increasing atmospheric CO 2 , and land use change have altered biogeochemical and hydrologic cycles world-wide, with grassland systems being particularly vulnerable to resulting vegetation shifts (Komatsu et al., 2019). Therefore, incorporating plant community dynamics into ecosystem models is critical for accurate forecasting of ecosystem responses to global change (Levine, 2016). Process-based ecosystem models, which simulate the biogeochemical transfers of mass and energy among biota, the subsurface, and atmosphere, require representation of dynamic composition of organisms within ecosystems. For example, these models simulate leaf and plant-level characteristics, such as electron transport rate and allometry of carbon (C) allocation, to predict how net primary productivity and other ecosystem processes respond to abiotic drivers. These models are particularly useful in scaling from organismal to ecosystem levels but are still underdeveloped in their ability to capture community change, especially in grassland ecosystems. To represent compositional changes, these models must simulate competition, mortality, establishment, and reproduction of plant populations within communities. Yet, current ecosystem modeling approaches to forecast plant community change have derived from studies of forested systems and are either too coarse to capture fine-scale community dynamics (e.g. dynamic global vegetation models (DGVMs)) or too complex to be used at large spatial scales (e.g. forest gap models).

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Estimating uncertainty: A Bayesian approach to modelling photosynthesis in C3 leaves

The Farquhar-von Caemmerer-Berry (FvCB) model is extensively used to model pho-tosynthesis from gas exchange measurements. Since its publication, many methods have been developed to measure, or more accurately estimate, parameters of this model. Here, we have created a tool that uses Bayesian statistics to fit photosyn-thetic parameters using concurrent gas exchange and chlorophyll fluorescence mea-surements whilst evaluating the reliability of the parameter estimation. We have tested this tool on synthetic data and experimental data from rice leaves. Our results indicate that reliable parameter estimation can be achieved whilst only keeping one parameter, Km, that is, Michaelis constant for CO2 by Rubisco, prefixed. Additionally, we show that including detailed low CO2 measurements at low light levels increases reliability and suggests this as a new standard measurement protocol. By providing an estimated distribution of parameter values, the tool can be used to evaluate the quality of data from gas exchange and chlorophyll fluorescence measurement proto-cols. Compared to earlier model fitting methods, the use of a Bayesian statistics-based tool minimizes human interaction during fitting, reducing the subjectivity which is essential to most existing tools. A user friendly, interactive Bayesian tool script is provided.

Bayesian statistics, leaf photosynthesis, mesophyl↗

DOE OSTI2023

Evaluation of Spray and Combustion Models for Simulating Dilute Combustion in a Direct-Injection Spark-Ignition Engine

Dilute combustion in spark-ignition engines has the potential to improve thermal efficiency by mitigating knock and by reducing throttling and wall heat losses. However, ignition and combustion processes can become unstable for dilute operation due to a lowered laminar flame speed, resulting in excessive cycle-to-cycle variability (CCV) of the combustion process. To compensate for the slower combustion in less reactive mixtures, a modified intake port geometry can be employed to generate a strong tumble flow in the cylinder and elevate turbulence levels around the spark plug, thereby promoting a faster transition to turbulent deflagration. Consequently, optimizing combustion chamber geometry and operating strategy is crucial to maximizing the benefits of using dilute combustion with enhanced in-cylinder turbulence across a wide range of operating conditions. Computational fluid dynamics (CFD) simulations can be utilized for virtual engine optimization tasks, but this would require the models to be truly predictive regarding the impact of changes to the engine design and operational parameters.In this study, multicycle large-eddy simulations (LES) are performed for a direct-injection spark-ignition engine to investigate the model performance in predicting engine combustion characteristics with respect to changes in the intake configuration. A tumble plate that blocks the lower part of the intake port inlet is used to vary the tumble. A set of CFD models that have been recently developed are employed, which takes into account the drag of nonspherical droplets, flash-boiling behavior of liquid sprays, spray-wall interaction, surrogate formulation of a research-grade E10 gasoline, and fast chemical kinetic solvers. Simulation results are compared to experimental engine data in terms of cylinder pressure, apparent heat release rate, mass fraction burned timing, and flame images. It is found that LES employing the state-of-the-art CFD models are capable of properly predicting the spray processes and reproducing the measured mean cylinder pressure for the case with the tumble plate. On the other hand, the LES over-predicts the combustion rate during the early combustion stage and under-estimates the CCV, and these discrepancies become larger when the tumble plate is removed.

computational fluid dynamics simulation↗

DOE OSTI2025

Micromechanical Surrogate Machine Learning Model for Creep Deformation Modeling

Process variability during the manufacture of gas turbine engine hot section components can significantly affect the material’s resulting microstructure. In casting, for instance, geometric variation within a component (thin sections versus thick sections, radial location) influences cooling rates and the resulting grain size. The high temperature creep response is known to be sensitive to grain size owing to a diffusional creep mechanism which occurs more readily along grain boundaries. Microstructural variation correspondingly drives mechanical behavior which propagates into component scale performance uncertainty. These factors are essential when planning inspection, maintenance, and repair strategies within a reliability framework. These benefits provide opportunities to increase overall energy efficiency through refined margins. Critically, there is an opportunity to bolster existing data-driven reliability models using physics-driven process-structure-property relations. Here we present recent work establishing a framework for evaluating the probabilistic creep performance of high-temperature materials. A novel microstructure-sensitive crystal plasticity finite element model is established that captures both grain boundary and crystallographic deformation effects. The computationally expensive physics model is calibrated using a statistical approach and this high-fidelity model is subsequently used to train a computationally efficient machine learning surrogate model. The surrogate model is essential for sampling a large ensemble of simulated structure-property pair results. The ensemble data are then mined to extract salient trends to be incorporated into a microstructure-sensitive reliability model. The proposed approach represents a novel way to capture microstructure-sensitive trends from physics-based models within a modern reliability framework.

Fernandez-Zelaia, Patxi [ORNL]↗

DOE OSTI2026

Dataset for Top Model Decision Tree: Selecting Segmentation Models for Reliable Quantitative Analysis in Low- and Ultralow-Dose CryoEM

Motivation Multiple deep learning model architectures can be used to segment bacterial membranes in cryoEM images. However, an AI-based tool advancement is often presented with only a single segmentation model for broad use, and this single model may show inconsistent results across datasets from different users. Here, we present the Top Model Decision Tree, a model screening framework to screen for the best model to generate bacterial inner and outer membrane masks based on user priorities. We use pre-trained segmentation models from YOLOv11, YOLO26, U-Net, Detectron2 and SAM3 fine-tuned on bacterial inner and outer membranes imaged with cryoEM. Run the Framework This notebook must be opened in Google Colab. Mount Google Drive and run with a GPU-based runtime. Open the notebook and follow steps to git clone in folders and files within this repository. There will be a repeating top_model_decision_tree.ipynb (notebook clone) that will not be used. Save your .png binary mask files and .csv table outputs within your Google Drive or download before closing the notebook. The models and all analysis/training scripts are available at [GitHub: https://github.com/Lynnicia/CryoEM_membranes_top_model_decision_tree and https://github.com/Sireesiru/Semantic-Segmentation-of-bacterial-cell-envelope-using-U-Nets.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

From Escherichia coli mutant 13 C labeling data to a core kinetic model: A kinetic model parameterization pipeline

Kinetic models of metabolic networks offer the promise of quantitative phenotype prediction. The mechanistic characterization of enzyme catalyzed reactions allows for tracing the effect of perturbations in metabolite concentrations and reaction fluxes in response to genetic and environmental perturbation that are beyond the scope of stoichiometric models. In this study, we develop a two-step computational pipeline for the rapid parameterization of kinetic models of metabolic networks using a curated metabolic model and available 13 C-labeling distributions under multiple genetic and environmental perturbations. The first step involves the elucidation of all intracellular fluxes in a core model of E. coli containing 74 reactions and 61 metabolites using 13 C-Metabolic Flux Analysis ( 13 C-MFA). Here, fluxes corresponding to the mid-exponential growth phase are elucidated for seven single gene deletion mutants from upper glycolysis, pentose phosphate pathway and the Entner-Doudoroff pathway. The computed flux ranges are then used to parameterize the same (i.e., k-ecoli74) core kinetic model for E. coli with 55 substrate-level regulations using the newly developed K-FIT parameterization algorithm. The K-FIT algorithm employs a combination of equation decomposition and iterative solution techniques to evaluate steady-state fluxes in response to genetic perturbations. k-ecoli74 predicted 86% of flux values for strains used during fitting within a single standard deviation of 13 C-MFA estimated values. By performing both tasks using the same network, errors associated with lack of congruity between the two networks are avoided, allowing for seamless integration of data with model building. Product yield predictions and comparison with previously developed kinetic models indicate shifts in flux ranges and the presence or absence of mutant strains delivering flux towards pathways of interest from training data significantly impact predictive capabilities. Using this workflow, the impact of completeness of fluxomic datasets and the importance of specific genetic perturbations on uncertainties in kinetic parameter estimation are evaluated.

59 BASIC BIOLOGICAL SCIENCES↗