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A Study on the Role of Electric Field in Low-Temperature Plasma Catalytic Ammonia Synthesis via Integrated Density Functional Theory and Microkinetic Modeling
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ParFlow-CLM model simulation files for Maina et al., Journal of Hydrology, 2022
This dataset contains the files to run a ParFlow-CLM integrated hydrologic model simulation for Maina et al., HESS, 2022. It also contains the associated daily pressure output of those simulations. Simulations are for a hillslope-similarity approach based on seasonal groundwater changes in the East River, Colorado. Comparisons are made to different clustering, or functional zonation approaches. We assess the ability of these clustering approaches to identify and categorize hillslopes with similar static characteristics, hydroclimate, land surface processes, and subsurface dynamics in a mountainous watershed. ParFlow binary files (.pfb) are model specific, and can be modified/viewed with conversion to .sa, .silo, or .vtk file formats. ParFlow input scripts are in the .tcl file format. Associated post-processing scripts are included as .f90 files.
A Review and Comparison of Different Sensitivity Analysis Techniques in Practice
There exist many methods for sensitivity analysis readily available to the practitioner. While each seeks to help the modeler answer the same general question – How do sources of uncertainty or changes in the model inputs relate to uncertainty in the output? – different methods are associated with different assumptions, constraints, and required resources, leading to conclusions that may vary in interpretability and level of detail. Thus, it is crucial that the practitioner selects the desired sensitivity analysis method judiciously, making sure to match the selected approach to the specifics of their problem and to their desired objectives. In this chapter, we provide a practical overview of a collection of widely used, widely available sensitivity analysis methods. We focus on global sensitivity approaches, which seek to characterize how uncertainty in the model output may be allocated to sources of uncertainty in model inputs across the entire input space. Generally, this will require the practitioner to specify a probability distribution over the input space. On the other hand, methods for local sensitivity analysis do not require this specification but they have more limited utility, providing insight into sources of uncertainty associated only with a particular, specified location in the input space. Our hope is that this chapter may serve as a decision-making tool for practitioners, helping to guide the selection of a sensitivity analysis approach that will best fit their needs. To support this goal, we have selected a suite of approaches to cover, which, while not exhaustive, we believe provides a flexible and robust sensitivity analysis toolkit. All methods included are widely used and available in standard software packages.
Validation and Sensitivity Analysis of a 1-D Lake Model Across Global Lakes
Lakes have important influence on weather and climate from local to global scales. However, their prediction using numerical models is notoriously difficult because lakes are highly heterogeneous across the globe, but observations are sparse. In this study, we assessed the performance of a 1-D lake model in simulating the thermal structures of 58 lakes with diverse morphometric and geographic characteristics by following the phase 2a local lake protocol of the Inter-sectoral Impact Model Intercomparison Project (ISIMIP2a). After calibration, the root-mean-square errors (RMSE) were below 2 °C for 70% and 75% of the lakes for epilimnion and full-profile temperature simulations, with an average of 1.71 °C and 1.43 °C, respectively. The model performance mainly depended on lake shape rather than location, supporting the possibility of grouping model parameters by lake shape for global applications. Furthermore, through machine-learning based parameter sensitivity tests, we identified turbulent heat fluxes, wind-driven mixing and water transparency as the major processes controlling lake thermal and mixing regimes. Snow density was also important for modeling the ice phenology of high-latitude lakes. The relative influence of the key processes and the corresponding parameters mainly depended on lake latitude and depth. Turbulent heat fluxes showed a decreasing importance in affecting epilimnion temperature with increasing latitude. Wind-driven mixing was less influential to lake stratification for deeper lakes while the impact of light extinction, on the contrary, showed a positive correlation with depth. Our findings may guide improvements in 1-D lake model parameterizations to achieve higher fidelity in simulating global lake thermal dynamics.
Sensitivity Analysis of MFiX-PIC Parameters Using Nodeworks, PSUADE, and DAKOTA
The study presented in this report was aimed to demonstrate UQ analysis performed not only with Nodeworks, but also two other well-established UQ software tools from the U.S. DOE’s National Laboratories (PSUADE from Lawrence Livermore National Laboratory and DAKOTA from Sandia National Laboratory). It is important to emphasize that the motivation of this study was not to determine the best UQ software, but to verify if the global sensitivity analyses from the end-to-end workflow in Nodeworks are consistent with the results of other two UQ software. The components of Nodeworks from Python’s ecosystem have been tested as standalone libraries. However, an assessment study for the complete workflow targeting a specific UQ analysis has not been performed for Nodeworks. Hence, this study is expected to serve as an equivalent of solution verification for Nodeworks using other established UQ tools as reference solution. For this purpose, three distinct flow configurations (i.e., settling bed, bubbling fluidized, and circulating fluidized bed) have been used as representative multiphase flow problems of interest. The results of the systematic simulation campaigns performed in an earlier study using the particle-in-cell (PIC) approach in the Multiphase Flow with Interphase eXchanges (MFIX) suite of solvers (i.e., MFiX-PIC) was utilized. The same set of tabulated results was provided as input to the different UQ software for global sensitivity analysis. Results for the three cases indicate that based on the Sobol’ Sensitivity Indices method the order of importance ranking determined by Nodeworks for the Sobol’ Total Sensitivity Indices is consistent with PSUADE and DAKOTA in each case for the five model parameters considered. The input files for Nodeworks for the three cases are also shared through NETL’s Gitlab repository for the reader interested in reproducibility and further analysis (See Section 1.2).
Visual HPC Workflows for the Analysis of System Dynamics Models
Visual analytics supported by high performance computing (HPC) accelerates and enhances the discovery, exploration, and analysis of causal patterns in complex system dynamics (SD) models. We present a suite of visualization-assisted ensemble-based techniques for hypothesis generation and testing, and for sensitivity analysis. By employing HPC to provide parallel, on-demand simulation of SD models, one can “steer” an ensemble of simulated scenarios in real time as one first formulates and then informally tests those hypotheses: this provides rapid feedback for analysts to refine their understanding of the causal relationships emergent from a model. Such understandings can be followed and augmented by rigorous application of statistical methods, namely global variance-based sensitivity analysis, Monte-Carlo filtering, adaptive regional sensitivity analysis, and self-organized maps: here timely computation relies on HPC, while effective presentation emphasizes high-dimensional multivariate data visualization. Immersive visualization in virtual 3D environments provides an excellent adjunct to the traditional 2D graphics typically used for SD models, as it generates an embodied understanding of model behavior and facilitates an active, collaborative critique of model structure and output. Finally, we summarize prospects for HPC-enabled visual analytics applied to SD modeling.
Impact of Rock Wettability and Mineralization on CO 2 Storage Efficiency in Basalt Reservoirs
Basalt formations have emerged as highly promising targets for geological CO 2 storage due to their abundance of reactive silicate minerals that can rapidly convert dissolved CO 2 into stable carbonate minerals. The efficiency of CO 2 trapping in basalts, however, depends not only on their geochemical reactivity but also on reservoir wettability, which governs how CO 2 partitions among structural, residual, solubility, and mineral trapping mechanisms. However, wettability and mineral kinetics have largely been examined separately, wettability for plume migration and kinetics in terms of mineralization, leaving their coupled impact unquantified. Here, we systematically integrate th ese processes in a reservoir-scale reactive transport model to quantify the impact of three distinct wettability conditions (water-wet, mixed-wet, and CO 2 -wet) on plume migration, mineral precipitation, pore-scale blockage, and long-term immobilization. Results show that under ideal conditions (no mineralization), water-wet systems exhibited plume aspect ratios up to 28% higher than CO 2 -wet systems and promoted at least 60% greater residual trapping. When mineralization was incorporated, mineral trapping accounted for 57%, 53%, and 46% of the total immobilized CO 2 in water-wet, mixed-wet, and CO 2 -wet systems, respectively. Dissolved CO 2 contributed 43-46%, while residual trapping remained below 5%, and mobile CO 2 was substantially reduced due to mineralization, demonstrating that as the system becomes more water-wet, CO 2 is more effectively converted into stable carbonate minerals, although extensive mineral precipitation may lead to pore clogging. A global Sobol-Morris sensitivity analysis further reveals that the kinetic parameters of reactive minerals are the most influential factor, followed by wettability, while salinity has only a minor influence. Furthermore, these findings highlight that wettability is not merely a flow property but a fundamental control on CO 2 mineralization in basalts, with direct implications for site selection for storage projects.
Patient-Specific Mathematical Model of the Clear Cell Renal Cell Carcinoma Microenvironment
The interactions between cells and molecules in the tumor microenvironment can give insight into the initiation and progression of tumors and their optimal treatment options. In this paper, we developed an ordinary differential equation (ODE) mathematical model of the interaction network of key players in the clear cell renal cell carcinoma (ccRCC) microenvironment. We then performed a global gradient-based sensitivity analysis to investigate the effects of the most sensitive parameters of the model on the number of cancer cells. The results indicate that parameters related to IL-6 have high a impact on cancer cell growth, such that decreasing the level of IL-6 can remarkably slow the tumor’s growth.
Quantitative assessment of eddy viscosity rans models for turbulent mixed convection in a differentially heated plane channel
Turbulent mixed convection between two vertical, infinite parallel plates at different temperatures is studied using various two-equation turbulence models. The numerical simulations are performed at a turbulent Reynolds number of Re τ = 150 and a Grashof number of Gr = 9.6 × 10 5 . Comparisons are made against the highly trusted DNS results. Consistent with the DNS approach, the current simulations are performed using constant properties and the Boussinesq approximation to predict the influence of buoyancy. Previous studies have provided assessments of two-equation turbulence models for various scenarios, but often rely on a qualitative “eye” test in order to determine the most appropriate model to predict a given flow. This study aims to provide a new form of quantitative assessment that accounts for both the physics captured by the turbulence model as well as the magnitude of the system response quantities (SRQ) using a modified symmetric mean absolute percent error (SMAPE) method. This method is designed to be approachable to researchers at any level and can be applied to system response quantities from multiple research fields. Uncertainty quantification is also performed to determine the discretization error for each turbulence model. Recommendations are made as to which turbulence models best capture the physics – hydrodynamically and thermally – using both local and global validation metrics. Lastly, a sensitivity analysis is performed on the damping functions used in the most accurate models. This underpins the potential of model developments and adjustments most worth pursuing for buoyant flows. Finally, this framework provides a more physics-based comparative analysis of the selected turbulence models.
Techno-Economic Analysis and Global Warming Potential of a Novel Offshore Macroalgae Biorefinery
The success of a large scale macroalgae-based biorefinery is dependent on the demonstration of favorable system economics and environmental sustainability. This study uses detailed process modeling to quantify the mass and energy flows through the various unit operations required for a novel free-floating macroalgae biorefinery concept. The modular process model served as the foundation for the techno-economic and global warming potential analyses used to quantify the sustainability of the proposed concept. This work includes detailed techno-economic results for a complete macroalgae cultivation and conversion system with multiple hatchery configurations and several emerging technologies. System optimization was achieved through the evaluation of various technology options for each unit operation. Technologies considered include traditional twine and textile substrate hatchery configurations, drone assisted seeding and biomass transport, mechanized line seeding and harvesting, adhesive spore mixtures that simplify seeding operations and improve hatchery energetics, and hydrothermal liquefaction to produce upgradable biocrude. Outputs from the system include renewable diesel (R100), naphtha, biochar, nitrogen and phosphorus fertilizers, and aqueous/solid waste streams. Three different system pathways were explored, yielding a biomass production cost ranging from $210 to $565 per dry metric ton and a minimum fuel selling price from $1.35 to $2.91 per liter of gasoline equivalent. Stochastic manipulation of the process model and sensitivity analyses support these results. The global warming potential analysis shows net greenhouse gas emissions ranging from 14 to 29 gCO2-eq MJ-1, supported by stochastic and sensitivity analyses. The recommendations from this work highlight critical areas for research and development investment such that a sustainable macroalgae cultivation and conversion system can be realized.
Machine Learning Driven Sensitivity Analysis of E3SM Land Model Parameters for Wetland Methane Emissions
Methane (CH 4 ) is globally the second most critical greenhouse gas after carbon dioxide, contributing to 16%–25% of the observed atmospheric warming. Wetlands are the primary natural source of methane emissions globally. However, wetland methane emission estimates from biogeochemistry models contain considerable uncertainty. One of the main sources of this uncertainty arises from the numerous uncertain model parameters within various physical, biological, and chemical processes that influence methane production, oxidation, and transport. Sensitivity Analysis (SA) can help identify critical parameters for methane emission and achieve reduced biases and uncertainties in future projections. This study performs SA for 19 selected parameters responsible for critical biogeochemical processes in the methane module of the Energy Exascale Earth System Model (E3SM) land model (ELM). The impact of these parameters on various CH 4 fluxes is examined at 14 FLUXNET- CH 4 sites with diverse vegetation types. Given the extensive number of model simulations needed for global variance-based SA, we employ a machine learning (ML) algorithm to emulate the complex behavior of ELM methane biogeochemistry. We found that parameters linked to CH 4 production and diffusion generally present the highest sensitivities despite apparent seasonal variation. Comparing simulated emissions from perturbed parameter sets against FLUXNET-CH 4 observations revealed that better performances can be achieved at each site compared to the default parameter values. This presents a scope for further improving simulated emissions using parameter calibration with advanced optimization techniques.
Quantification of hydraulic trait control on plant hydrodynamics and risk of hydraulic failure within a demographic structured vegetation model in a tropical forest (FATES–HYDRO V1.0)
Abstract. Vegetation plays a key role in the global carbon cycle and thus is an important component within Earth system models (ESMs) that project future climate. Many ESMs are adopting methods to resolve plant size and ecosystem disturbance history, using vegetation demographic models. These models make it feasible to conduct more realistic simulation of processes that control vegetation dynamics. Meanwhile, increasing understanding of the processes governing plant water use, and ecosystem responses to drought in particular, has led to the adoption of dynamic plant water transport (i.e., hydrodynamic) schemes within ESMs. However, the extent to which variations in plant hydraulic traits affect both plant water stress and the risk of mortality in trait-diverse tropical forests is understudied. In this study, we report on a sensitivity analysis of an existing hydrodynamic scheme (HYDRO) model that is updated and incorporated into the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) (FATES–HYDRO V1.0). The size- and canopy-structured representation within FATES is able to simulate how plant size and hydraulic traits affect vegetation dynamics and carbon–water fluxes. To better understand this new model system, and its functionality in tropical forest systems in particular, we conducted a global parameter sensitivity analysis at Barro Colorado Island, Panama. We assembled 942 observations of plant hydraulic traits on 306 tropical plant species for stomata, leaves, stems, and roots and determined the best-fit statistical distribution for each trait, which was used in model parameter sampling to assess the parametric sensitivity. We showed that, for simulated leaf water potential and loss of hydraulic conductivity across different plant organs, the four most important traits were associated with xylem conduit taper (buffers increasing hydraulic resistance with tree height), stomatal sensitivity to leaf water potential, maximum stem hydraulic conductivity, and the partitioning of total hydraulic resistance above vs. belowground. Our analysis of individual ensemble members revealed that trees at a high risk of hydraulic failure and potential tree mortality generally have a lower conduit taper, lower maximum xylem conductivity, lower stomatal sensitivity to leaf water potential, and lower resistance to xylem embolism for stem and transporting roots. We expect that our results will provide guidance on future modeling studies using plant hydrodynamic models to predict the forest responses to droughts and future field campaigns that aim to better parameterize plant hydrodynamic models.
Sensitivity analysis of numerical modeling input parameters on floating offshore wind turbine loads
Abstract. Floating wind turbines must withstand a unique and challenging set of loads from the wind and ocean environment. To de-risk development, accurate predictions of these loads are necessary. Uncertainty in modeling predictions leads to larger required safety factors, increasing project costs and the levelized cost of energy. Complex aero-hydro-elastic modeling tools use many input parameters to represent the wind, waves, current, aerodynamic loads, hydrodynamic loads, and structural properties. It is helpful to understand which of these parameters ultimately drives a design. In this work, an ultimate and fatigue-proxy load sensitivity analysis was performed with 35 different input parameters, using an elementary effects approach to identify the most influential parameters for a case study involving the National Renewable Energy Laboratory (NREL) 5 MW baseline wind turbine atop the OC4-DeepCwind semisubmersible during normal operation. The importance of each parameter was evaluated using 14 response quantities of interest across three operational wind speed conditions. The study concludes that turbulent wind velocity standard deviation is the parameter with the strongest sensitivity; this value is important not just for turbine loads, but also for the global system response. The system center of mass in the wind direction is found to have the highest impact on the system rotation and tower loads. The current velocity is found to be the most dominating parameter for the system global motion and consequently the mooring loads. All tested wind turbulence parameters in addition to the standard deviation are also found to be influential. Wave characteristics are influential for some fatigue-proxy loading but do not significantly impact the extreme ultimate loads in these operational load cases. The required number of random seeds for stochastic environmental conditions is considered to ensure that the sensitivities are due to the input parameters and not due to the seed. The required number of analysis points in the parameter space is identified so that the conclusions represent a global sensitivity. The results are specific to the platform, turbine, and choice of parameter ranges, but the demonstrated approach can be applied widely to guide focus in parameter uncertainty.
Shrub Expansion Simulations at Trail Valley Creek Tundra site using E3SM Land Model (ELM) Arctic-focused Version
The warming of the Arctic is causing substantial compositional, structural, and functional changes in tundra vegetation including shrub and densification in parts of the Arctic. Assessing the impact of these changes in vegetation composition on the Arctic’s carbon and energy budgets is important to constrain projected local and global surface-atmosphere exchanges. We conduct a sensitivity analysis of the projected surface energy fluxes, soil carbon pools, and carbon dioxide fluxes (net ecosystem exchange, gross primary production, and ecosystem respiration) between present day and 2100 to different shrub expansion rates and air temperature increases under future emission scenarios (intermediate – RCP4.5, and high – RCP8.5) using the Arctic-focused version of the Energy Exascale Earth System Model (E3SM) Land Model (ELM). We focus on Trail Valley Creek (TVC), a mineral upland tundra site located in the western Canadian Arctic, which is experiencing tall shrub densification and expansion. In this study, we run TVC under two different warming scenarios RCP4.5 and RCP 8.5 and simulate different shrubification rates projected until year 2100. In this repository, we include all the forcing, input, parameters, and output data corresponding to all the simulations performed. flmd.csv includes a detailed description of the datasets files.
Region and cloud regime dependence of parametric sensitivity in E3SM atmosphere model
Abstract The Department of Energy (DOE)’s Energy Exascale Earth System Model (E3SM), including its atmosphere model (EAM), has many relatively new features. In a previous study we conducted a systematic parametric sensitivity analysis for EAM based on short, perturbed parameter ensemble (PPE) simulations, mainly focusing on global mean climate features and metrics. While parameter values in global climate models are generally invariant in space and time, model response to parameters perturbation may vary by regions and climate regimes, which motivates the need to better understand the EAM model behaviors and physics at regional scale and process level. In this study, using the same set of PPE simulations and a similar sensitivity analysis framework, we identify parameters that cause largest sensitivities over different regions and compare model responses in fast atmospheric processes to the parameters across different cloud regimes for several important cloud-related fidelity metrics. We find that cloud forcing has opposite response to some parameters over mid-latitude vs. tropical land. We also analyze how the parametric sensitivity varies as stratocumulus transitions to shallow convection and to deep convection over ocean. Low cloud forcing and shortwave cloud forcing in the subtropical eastern Pacific are most sensitive to the parameters controlling the width of the probability density function (PDF) of the subgrid vertical velocity ( w’ ) ( gamma ) and the damping of the w’ skewness ( c8 ) near the coast but become more sensitive to the parameter affecting the damping of the w’ variance ( c1 ) further offshore. Detailed interpretation of the spatial dependence of parametric sensitivity is provided. We also investigate how the parametric sensitivity evolves with prediction duration. This study improves our process-level understanding of cloud physics and parameterization and provides insights for developing more advanced regime-aware parameterization schemes in global climate model.
Influence of Tibetan Plateau sensible heat on pre-monsoon dust burdens over South Asia: Observational and modeling evidence
Tibetan Plateau sensible heating (TPSH) effect is recognized as a key driver of the South Asian climate; however its role in regulating the regional dust burdens over South Asia during the pre-monsoon season remains unclear. Using long-term reanalysis and/or observational dust and TPSH data, we show that the dust optical depth at 550 nm (DOD 550 ) over South Asia is significantly positively correlated with TPSH at the interannual scale. DOD 550 over South Asia increases (decreases) by 20 % (12 %) in the strongest (weakest) TPSH years. The phenomenon of TPSH-dust relationships is reinforced by sensitivity experiments by altering TPSH from global climate models. Further mechanism analysis reveals that TPSH perturbation induces regional circulation anomalies over South Asia, which features a low-tropospheric cyclonic response around the Tibetan Plateau. This cyclonic anomaly strengthens the prevailing northwesterly winds, increasing regional dust emissions and transportation over South Asia. This novel mechanism helps understand the South Asian dust change.
Reaction Mechanism Generator v3.0: Advances in Automatic Mechanism Generation
In chemical kinetics research, kinetic models containing hundreds of species and tens of thousands of elementary reactions are commonly used to understand and predict the behavior of reactive chemical systems. Reaction Mechanism Generator (RMG) is a software suite developed to automatically generate such models by incorporating and extrapolating from a database of known thermochemical and kinetic parameters. Here, we present the recent version 3 release of RMG and highlight improvements since the previously published description of RMG v1.0. Most notably, RMG can now generate heterogeneous catalysis models in addition to the previously available gas- and liquid-phase capabilities. For model analysis, new methods for local and global uncertainty analysis have been implemented to supplement first-order sensitivity analysis. The RMG database of thermochemical and kinetic parameters has been significantly expanded to cover more types of chemistry. The present release includes parallelization for faster model generation and a new molecule isomorphism approach to improve computational performance. RMG has also been updated to use Python 3, ensuring compatibility with the latest cheminformatics and machine learning packages. Overall, RMG v3.0 includes many changes which improve the accuracy of the generated chemical mechanisms and allow for exploration of a wider range of chemical systems.