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DOE OSTI2021

Three-Dimensional Free Gas Flow Focuses Basin-Wide Microbial Methane to Concentrated Methane Hydrate Reservoirs in Geological System

Here, we present a systematic model that links the generation, migration, phase partitioning, and accumulation of methane into a closed loop as the sediment is deposited from the seafloor and buried through the base of hydrate stability zone (BHSZ). In our model, methane is generated by biodegradation of organic carbon in muds. Hydrate does not form and methane is not trapped until a coarse-grained layer is deposited, because the small pores prevent hydrate formation in muds. Instead, methane diffuses into sands/silts where methane solidifies into hydrate. As hydrate-bearing sands/silts pass through the BHSZ during sediment burial, methane hydrate dissociates, and releases free gas. The released and the newly generated free gas below the BHSZ concentrates into a vertical/dipping zone with low capillary entry pressure and high permeability and flows upward driven its buoyancy. When free gas reaches the hydrate stability zone (HSZ), capillary forces drive free gas to flow laterally, preferentially enter sands/silts, feed hydrate growth, and elevate hydrate saturation. With three-dimensional focused free gas flow, microbial methane that is generated from a much larger fetch area of the entire basin, both above and below the BHSZ, is concentrated into coarse-grained layers at structural closures for hydrate formation. Our model illustrates how geological evolution, microbial methane generation, and gas flow by buoyancy couple to generate concentrated hydrate deposits in geological system. These insights can be used to explore for high-concentration methane hydrate and are important for understanding the methane budget and carbon cycle under the seafloor.

58 GEOSCIENCES↗

DOE OSTI2025

The role of thermal stratification on the co‐spectral properties of momentum transport above an Amazonian forest

The influence of thermal stratification on the turbulent kinetic energy balance has been widely studied; however, its influence on the turbulent stress remains less explored in the presence of tall vegetated canopies and less ideal micrometeorological conditions. Here, the impact of thermal stratification on turbulent momentum flux is considered in the roughness sublayer (RSL) and the atmospheric surface layer (ASL) using the Amazon Tall Tower Observatory (ATTO) in Brazil. A scalewise co‐spectral budget (CSB) model is developed using standard closure schemes for the pressure–velocity decorrelation. The CSB revealed that the co‐spectrum ${F}_{wu}\left({k}_x\right)$ between longitudinal (u') and vertical (w') velocity fluctuations is impacted by the energy spectrum of the vertical velocity ${E}_{ww}\left({k}_x\right)$ and the much less studied longitudinal heat‐flux co‐spectrum ${F}_{u{\theta}_{\mathrm{v}}}\left({k}_x\right)$, where ${\theta}_{\mathrm{v}}^{\prime }$ are temperature fluctuations and ${k}_x$ is the longitudinal wavenumber. Under stable, very stable, and dynamic–convective conditions, the scaling exponent ${F}_{wu}\left({k}_x\right)$ in for the inertial subrange (ISR) scales is dominated by ${F}_{u{\theta}_{\mathrm{v}}}\left({k}_x\right)$ instead of ${E}_{ww}\left({k}_x\right)$. A near ${k}_x^{-7/3}$scaling in ${F}_{u{\theta}_{\mathrm{v}}}\left({k}_x\right)$ robust to large variations in thermal stratification is found, whereas the Kolmogorov ISR scaling for ${E}_{ww}\left({k}_x\right)\sim {k}_x^{-5/3}$ is not found. The scale‐dependent decorrelation time between u' and w' is dominated by ${\epsilon}^{-1/3}{k}_x^{-2/3}$ in the ISR, but is nearly constant for eddies larger than the vertical velocity integral scale, regardless of stability. Implications of these findings for generalized stability correction functions that are based on the turbulent stress budget instead of the turbulent kinetic energy budget are discussed.

canopy turbulence↗

DOE OSTI2022

Data-driven, multi-moment fluid modeling of Landau damping

Deriving governing equations of complex physical systems based on first principles can be quite challenging when there are certain unknown terms and hidden physical mechanisms in the systems. In this work, we apply a deep learning architecture to learn fluid partial differential equations (PDEs) of a plasma system based on the data acquired from a fully kinetic model. Here, the learned multi-moment fluid PDEs are demonstrated to incorporate kinetic effect such as Landau damping. Based on the learned fluid closure, the data-driven, multi-moment fluid modeling can well reproduce all the physical quantities derived from the fully kinetic model. The calculated damping rate of Landau damping is consistent with both the fully kinetic simulation and the linear theory. The data-driven fluid modeling of PDEs for complex physical systems may be applied to improve the fluid closure and reduce the computational cost of multi-scale modeling of global systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2026

Second Order Closures for the Radiative Transfer Equation: Some Are Unstable

The largest existing simulations of cosmic reionization model radiative transfer with moment methods that require a closure relation. The two most commonly used closure relations are M1 and OTVET; both close the moment hierarchy at the first moment. We explore the properties of a higher, second-order closure. We show that direct generalizations of M1 and OTVET to one higher order are physically unstable - i.e., the closure equations themselves result in unstable solutions, not just their numerical implementation. In fact, a generalization of OTVET to any order higher than the first one is unstable. We are also able to show that any local (i.e., depending only on the local moments of the radiation field, like M1) second-order closure that depends only on the radiation intensity and radiation flux, but does not explicitly depend on the radiation pressure, is physically unstable. This result restricts the choice of possible second-order closure relations.

Gnedin, Nickolay Y. [Fermilab; Chicago U., Astron.↗

DOE OSTI2021

Direct observations and characterization of crack closure during microstructurally small fatigue crack growth via in-situ high-energy X-ray characterization

This study provides direct observation of the crack closure mechanism of a naturally occurring, tortuous, 3D microstructurally small fatigue crack (SFC) in additively manufactured Inconel 718. In-situ non-destructive characterization is performed using high-energy X-ray diffraction techniques to capture the evolution of the 3D microstructure and micromechanical response in the vicinity of the crack front. Based on the stress state of twelve grains analyzed at the crack tip, the crack closure events of the SFC front was found to be spatially heterogeneous with respect to loading progression governed by the local stress state of the grains (specifically the stress reversal from compression to tension). From this analysis, three grains that displayed different degrees of crack closure were further investigated, based on the orientation of the crack relative to the grains and the associated modality of crack growth. The stress normal to the crack plane and the associated degree of Mode I crack behavior were correlated with events of the crack opening earlier during the loading cycle. This was further corroborated by diffraction spot spreading analysis that quantified the crystallographic lattice distortion caused by the opening crack. Additionally, the detailed characterization of the opening behavior of the grains located at the crack tip and their associated states of stress elucidates the mechanism governing crack closure and will inform future modeling efforts of this phenomenon.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Challenges in quantifying unparameterized spatial uncertainties in deep geologic repositories for nuclear waste

Spatially heterogeneous uncertainties are prevalent in geophysical modeling applications, such as probabilistic post-closure performance assessment (PA) of deep geologic repositories for nuclear waste. Such uncertainties are often highly influential to model outputs, so it is desirable to identify the most important mechanisms by which they influence model predictions. However, these uncertainties are often unparameterized in the sense that there is no set of parameters that can be specified to yield a particular realization of the uncertainty. Additionally, the uncertainty is not intrinsically endowed with a parameterization that captures a realization’s mechanistic influence on model outputs. Therefore, in this work we present a novel methodology to develop and assess a set of proxy variables that aim to represent this influence. We show how they can be computed, downselected, and incorporated into the construction of statistical surrogate models mapping model inputs to outputs. We present our methodology in the context of a motivating application problem in deep geologic repository PA and discuss the challenges in capturing the effects of these spatial heterogeneities in uncertainty analyses.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2020

A long short-term memory embedding for hybrid uplifted reduced order models

In this paper, we introduce an uplifted reduced order modeling (UROM) approach through the integration of standard projection based methods with long short-term memory (LSTM) embedding. Our approach has three modeling layers or components. In the first layer, we utilize an intrusive projection approach to model dynamics represented by the largest modes. The second layer consists of an LSTM model to account for residuals beyond this truncation. This closure layer refers to the process of including the residual effect of the discarded modes into the dynamics of the largest scales. However, the feasibility of generating a low rank approximation tails off for higher Kolmogorov n -width systems due to the underlying nonlinear processes. The third uplifting layer, called super-resolution, addresses this limited representation issue by expanding the span into a larger number of modes utilizing the versatility of LSTM. Therefore, our model integrates a physics-based projection model with a memory embedded LSTM closure and an LSTM based super-resolution model. In several applications, we exploit the use of Grassmann manifold to construct UROM for unseen conditions. We performed numerical experiments by using the Burgers and Navier-Stokes equations with quadratic nonlinearity. Finally, our results show robustness of the proposed approach in building reduced order models for parameterized systems and confirm the improved trade-off between accuracy and efficiency.

42 ENGINEERING↗

DOE OSTI2023

A multifidelity deep operator network approach to closure for multiscale systems

Projection-based reduced order models (PROMs) have shown promise in representing the behavior of multiscale systems using a small set of generalized (or latent) variables. Despite their success, PROMs can be susceptible to inaccuracies, even instabilities, due to the improper accounting of the interaction between the resolved and unresolved scales of the multiscale system (known as the closure problem). In the current work, we interpret closure as a multifidelity problem and use a multifidelity deep operator network (DeepONet) framework to address it. In addition, to enhance the stability and/or accuracy of the multifidelity-based closure, we employ the recently developed ``in-the-loop" training approach from the literature on coupling physics and machine learning models. The resulting approach is tested on shock advection for the one-dimensional viscous Burgers equation and vortex merging for the two-dimensional Navier-Stokes equations. Furthermore, the numerical experiments show significant improvement of the predictive ability of the closure-corrected PROM over the un-corrected one both in the interpolative and the extrapolative regimes.

42 ENGINEERING↗

DOE OSTI2026

Improbability of Post-Closure Criticality in Compacted Criticality Control Overpacks after Room Closure at Waste Isolation Pilot Plant

As part of its periodic re-certification of the Waste Isolation Pilot Plant (WIPP), an operating repository in bedded salt for the disposal of transuranic (TRU) waste from atomic energy defense activities, the United States Environmental Protection Agency expects a re-evaluation of features, events, and processes, such as post-closure nuclear criticality. Although salt creep beneficially encapsulates the TRU waste in the closed WIPP repository, the spacing between an array of waste packages is disrupted as the salt creep closes disposal rooms and containers lose structural integrity. For most TRU waste, the possibility of post-closure criticality is exceedingly small either because the salt neutronically isolates TRU waste canisters or because closure of a disposal room from salt creep does not sufficiently compact the low mass of fissile material. The criticality evaluation was updated, however, because of the introduction of criticality control overpack (CCO) containers, which may dispose up to 380 fissile gram equivalent plutonium-239 in each container. The criticality potential is evaluated through high-fidelity geomechanical modeling of a disposal room filled with CCO containers during two representative conditions: (1) large salt block fall, and (2) gradual disposal room closure from salt creep. Geomechanical models of roof fall demonstrate three tiers of CCO containers are not greatly disrupted. Geomechanical models of gradual room closure from salt creep (without brine seepage and subsequent gas generation to permit maximum room closure) were used to predict irregular arrays of closely packed CCOs after 1000 years, when room closure has asymptotically approached maximum compaction. Models of spheres or cylinders with 380 fissile gram equivalent of plutonium (as oxide) at the predicted irregular compacted spacing demonstrate that an array of CCO containers is not critical when surrounded by salt and magnesium oxide, provided the mass of hydrogenous material shipped in CCO containers (usually plastics) is controlled or boron carbide (a neutron poison) is mixed with the fissile contents.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2026

Low-stress creep behavior of multiple salt caverns under cyclic operations

Here, the use of multiple salt caverns for large-scale underground hydrogen storage offers a strategic solution to the growing demand for efficient and flexible energy storage, due to the inherent low permeability, high mechanical strength, and self-healing properties of the salt formation. Despite these advantages, the long-term geomechanical response of salt caverns under cyclic injection and withdrawal remains a significant challenge for ensuring operational stability. This mechanistic study highlights the critical role of low-stress creep, also known as pressure solution creep, in governing deformation of salt caverns during cyclic operations. Unlike conventional creep mechanisms that dominate under high-stress conditions, low-stress creep becomes particularly relevant under the moderate stress changes induced by repeated injection and withdrawal, which provides a previously underexplored control on cavern closure. Our three-dimensional computational model integrates the low-stress creep mechanism into the Munson–Dawson creep equation across a spectrum of operational scenarios including variations in cavern pressure cycles, injection-withdrawal frequencies, and caprock mechanical property. The low-stress creep components accelerate the cavern creep closure, which is amplified with shorter cycle frequency and larger pressure difference. Sensitivity analyses capture the complex interactions between multiple caverns and surround formations at the field scale that allows for a quantitative assessment of deformation patterns and closure rates over time and thereby informs the design and operation of sustainable underground hydrogen storage system.

Cyclic operation↗

DOE OSTI2026

elm-diagnostics

elm-diagnostics is a Python package for computing diagnostic analyses and visualizations for the E3SM Land Model (ELM) component and is meant to support new feature development in ELM. The tool reads model history files and performs quantitative analyses including budget-closure checking, variable transformations, temporal aggregations, and statistical summaries to support model evaluation, validation, and scientific interpretation. The framework is designed for extensibility, with modular architecture enabling straightforward addition of new diagnostic methods, derived variables, analysis types, visualization approaches, and model-specific adaptations

Hoffman, Matt [Los Alamos National Laboratory]↗

DOE OSTI2021

Benchmarking NIMROD continuum kinetic formulations through the steady-state poloidal flow

In this work, continuum kinetic formulations are employed as a mechanism to include closure physics in an extended magnetohydrodynamics model. Two continuum kinetic approaches have been implemented in the plasma fluid code NIMROD [Sovinec et al., “Nonlinear magnetohydrodynamics with high-order finite elements,” J. Comput. Phys. 195, 355 (2004)] including a Chapman–Enskog-like (CEL) formulation and a more conventional df approach. Ion kinetic closure schemes are employed to describe the neoclassical flow properties in axisymmetric toroidal geometry. In particular, predictions for steady-state values of poloidal flow profiles in tokamak geometry are provided using both the df formulation and two different solution techniques for the CEL approach. These results are benchmarked against analytic theory predictions as well as results from the drift kinetic code DK4D. The continuum kinetic formulations employed here show agreement with both the analytic theory and DK4D results, and offer a novel velocity space representation involving higher-order finite elements in pitch angle.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

Simulating Mixed‐Phase Open Cellular Clouds Observed During COMBLE: Evaluation of Parameterized Turbulence Closure

Marine cold-air outbreaks, or CAOs, are airmass transformations whereby relatively cold boundary layer (BL) air is transported over relatively warm water. To more deeply understand BL and mixed-phase cloud properties during CAO conditions, the Cold-Air Outbreaks in the Marine Boundary Layer Experiment (COMBLE) took place from late 2019 into early 2020. During COMBLE, the U.S. Department of Energy's first Atmospheric Radiation Measurement Mobile Facility (AMF1) was deployed to Andenes, Norway, far downstream (~1,000 km) from the Arctic pack ice. This study examines the two most intense CAOs sampled at the AMF1 site. The observed BL structures are open cellular with high (~3–5 km) and cold (–30 to –50 °C) cloud tops, and they often have pockets of high liquid water paths (LWPs; up to ~1,000 g m –2 ) associated with strong updrafts and enhanced turbulence. We use a high-resolution mesoscale model to explore how well four turbulence closure methods represent open cellular clouds. After applying a radar simulator to model outputs for direct evaluation, cloud top properties agree well with AMF1 observations (within ~10%), but radar reflectivity and LWP agreement is more variable. Results suggest that the turbulent Prandtl number may play an important role for the simulated BL and cloud properties. All simulations produce enhanced precipitation rates that are well-correlated with a cloud transition. Finally, the eddy-diffusivity/mass-flux approach produces the deepest cloud layer and therefore the largest and most coherent cellular structures. Furthermore, we recommend the use of a non-local turbulence closure approach to better capture turbulent processes in intense CAOs.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Deep learning interfacial momentum closures in coarse-mesh CFD two-phase flow simulation using validation data

Multiphase flow phenomena have been widely observed in the industrial applications while it remains a challenging yet unsolved problems. Three-dimensional computational fluid dynamics (CFD) approaches resolve the flow fields on a finer special and temporal scales which can complement the dedicated experimental study. However, closures have to be introduced to reflect the underlying physics in multiphase flow. Among them, the interfacial forces, including drag, lift, turbulent dispersion and wall lubrication forces, play in important role on the bubble’s distribution and migration in liquid-vapor two-phase flow. Development of those closures traditionally rely on the experimental data and analytical derivation with simplified assumptions which usually cannot deliver a universal solution across wide range of flow conditions. In this paper, a data-driven approach, named as Feature Similarity Measurement (FSM), is developed and applied to improve the simulation capability of two-phase flow with coarse-mesh CFD approach. Interfacial momentum transfer in adiabatic bubbly flow serves as the focus of the present study. Both a mature and a simplified set of interfacial closures are taken as the low fidelity data. Experimental data and fine mesh CFD simulations results are adopted as high-fidelity data. Qualitative and quantitative analysis are performed in this paper which reveals that FSM can substantially improve the prediction of coarse mesh CFD model regardless of the choice of interfacial closures and it provides scalability and consistency across discontinuous flow regimes. Furthermore, it demonstrates that data-driven method can aid the multiphase flow modeling by exploring the connections between local physical features and simulation errors.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

SootLib: A soot model library for combustion simulation

Soot formation in combustion is an important process that affects radiative heat transfer, flame temperatures, and emissions with health and environmental impacts. Soot formation involves complex chemistry for nucleation, growth, oxidation, and coagulation processes. The soot particles vary widely in size and accurate modeling requires representation of the particle size distribution (PSD). Modeling soot is not trivial, and is only one of several physical processes active in combustion systems. This paper presents a software package called SootLib, which is an open-source library for modeling soot formation and other aerosol systems. SootLib is written in C++, is documented with Doxygen, and is available on GitHub. The library includes several models for soot chemistry and coagulation, and it represents the PSD using either a sectional model or the method of moments (MOM). Four closure approaches for the MOM are implemented allowing up to eight moments: monodispersed, an assumed-shape lognormal distribution, the quadrature method of moments, and the method of moments with interpolative closure. SootLib provides an interface for inclusion in other combustion packages including CFD or reacting flow solvers. The range of models allows comparisons and sensitivity studies, and the modularity facilitates extension to other soot models.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

The vertical-velocity skewness in the inertial sublayer of turbulent wall flows

Empirical evidence is provided that within the inertial sublayer (i.e. logarithmic region) of adiabatic turbulent flows over smooth walls, the skewness of the vertical-velocity component 𝑆 𝑤 displays universal behaviour, being a positive constant and constrained within the range 𝑆 𝑤 ≈ 0.1–0.16, regardless of flow configuration and Reynolds number. A theoretical model is then proposed to explain this behaviour, including the observed range of variations of 𝑆 𝑤 . The proposed model clarifies why 𝑆 𝑤 cannot be predicted from down-gradient closure approximations routinely employed in large-scale meteorological and climate models. The proposed model also offers an alternative and implementable approach for such large-scale models.

turbulent boundary layers↗

DOE OSTI2023

Automated Symbolic Upscaling: 2. Model Generation for Extended Applicability Regimes

Abstract In this second part of the two paper series, we detail an algorithmic procedure for systematically implementing the generalized closure form strategy presented in Part 1. This strategy extends the applicability of homogenized models with respect to classical homogenization theory, as demonstrated in Part 1 where upscaled models are rigorously derived in moderately reactive physical regimes. After encoding the algorithm into Symbolica, an automated upscaling framework, we upscale two reactive mass transport problems and numerically validate the resulting nonlinear homogenized models by showing the absolute error estimates predicted by homogenization theory are satisfied. In both problems, nontrivial closure forms and closure problems are automatically formulated using the encoded strategy with no human interaction, nor prior knowledge regarding the closure required for the systems. We hope these demonstrations spark further interest in automated analytical frameworks for multiscale modeling, as such capabilities are invaluable for generating rigorous multiscale models of complex phenomena in porous media.

Pietrzyk, Kyle↗

DOE OSTI2025

Molecular model of TFIIH recruitment to the transcription-coupled repair machinery

Transcription-coupled repair (TCR) is a vital nucleotide excision repair sub-pathway that removes DNA lesions from actively transcribed DNA strands. Binding of CSB to lesion-stalled RNA Polymerase II (Pol II) initiates TCR by triggering the recruitment of downstream repair factors. Yet it remains unknown how transcription factor IIH (TFIIH) is recruited to the intact TCR complex. Combining existing structural data with AlphaFold predictions, we build an integrative model of the initial TFIIH-bound TCR complex. We show how TFIIH can be first recruited in an open repair-inhibited conformation, which requires subsequent CAK module removal and conformational closure to process damaged DNA. In our model, CSB, CSA, UVSSA, elongation factor 1 (ELOF1), and specific Pol II and UVSSA-bound ubiquitin moieties come together to provide interaction interfaces needed for TFIIH recruitment. STK19 acts as a linchpin of the assembly, orienting the incoming TFIIH and bridging Pol II to core TCR factors and DNA. Molecular simulations of the TCR-associated CRL4CSA ubiquitin ligase complex unveil the interplay of segmental DDB1 flexibility, continuous Cullin4A flexibility, and the key role of ELOF1 for Pol II ubiquitination that enables TCR. Collectively, these findings elucidate the coordinated assembly of repair proteins in early TCR.

Paul, Tanmoy↗