Hacking Limnology Workshops and DSOS23 : Growing a Workforce for the Nexus of Data Science, Open Science, and the Aquatic Sciences
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16 TIDAL AND WAVE POWER↗
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Establishing fluvial silicon regimes and their stability across the Northern Hemisphere
Abstract Fluvial silicon (Si) plays a critical role in controlling primary production, water quality, and carbon sequestration through supporting freshwater and marine diatom communities. Geological, biogeochemical, and hydrological processes, as well as climate and land use, dictate the amount of Si exported by streams. Understanding Si regimes—the seasonal patterns of Si concentrations—can help identify processes driving Si export. We analyzed Si concentrations from over 200 stream sites across the Northern Hemisphere to establish distinct Si regimes and evaluated how often sites moved among regimes over their period of record. We observed five distinct regimes across diverse stream sites, with nearly 60% of sites exhibiting multiple regime types over time. Our results indicate greater spatial and interannual variability in Si seasonality than previously recognized and highlight the need to characterize the watershed and climate variables that affect Si cycling across diverse ecosystems.
54 ENVIRONMENTAL SCIENCES↗
Evaluation of preservation protocols for oxygen-sensitive minerals within laminated aquatic sediments
Laminated sediments can record seasonal changes in sedimentation of material from anoxic waters, including minerals of the redox-sensitive elements Fe, Mn, and S that form under varying oxygen levels, mineral saturation conditions, and from microbial metabolism. However, preserving the oxygen-sensitive minerals for identification is challenging when preservation of the spatial arrangement of laminae is also required. In this study, we compare methods for embedding sedimentary materials from anoxic waters and sediments from Brownie Lake, Minnesota, USA for analysis of the speciation for Fe, Mn, and S using synchrotron-based X-ray absorption near edge spectroscopy (XANES). We found that acetone dehydration and resin replacement in a 100% N 2 glovebox successfully preserved the speciation of Fe and Mn minerals within laminated sediments. However, acetone removed some sulfur species from sediments, and epoxies contained sulfur species, which challenged identification of native sulfur species. Results from this study will aid researchers who are interested in spatial analysis of oxygen sensitive sediments, soils, or microbial mats in choosing a preservation method.
58 GEOSCIENCES↗
An anisotropic viscoplasticity model for shale based on layered microstructure homogenization
Viscoplastic deformation of shale is frequently observed in many subsurface applications. Many studies have suggested that this viscoplastic behavior is anisotropic—specifically, transversely isotropic—and closely linked to the layered composite structure at the microscale. In this work, we develop a two-scale constitutive model for shale in which anisotropic viscoplastic behavior naturally emerges from semianalytical homogenization of a bilayer microstructure. The microstructure is modeled as a composite of soft layers, representing a ductile matrix formed by clay and organics, and hard layers, corresponding to a brittle matrix composed of stiff minerals. This layered microstructure renders the macroscopic behavior anisotropic, even when the individual layers are modeled with isotropic constitutive laws. Using a common correlation between clay and organic content and magnitude of creep, we apply a viscoplastic modified Cam-Clay plasticity model to the soft layers, while treating the hard layers as a linear elastic material to minimize the number of calibration parameters. We then describe the implementation of the proposed model in a standard material update subroutine. The model is validated with laboratory creep data on samples from three gas shale formations. We also demonstrate the computational behavior of the proposed model through simulation of time-dependent borehole closure in a shale formation with different bedding plane directions.
58 GEOSCIENCES↗
Simulation of coupled multiphase flow and geomechanics in porous media with embedded discrete fractures
In fractured natural formations, the equations governing fluid flow and geomechanics are strongly coupled. Hydrodynamical properties depend on the mechanical configuration, and they are therefore difficult to accurately resolve using uncoupled methods. In recent years, significant research has focused on discretization strategies for these coupled systems, particularly in the presence of complicated fracture network geometries. In this work, we explore a finite-volume discretization for the multiphase flow equations coupled with a finite-element scheme for the mechanical equations. Fractures are treated as lower dimensional surfaces embedded in a background grid. Interactions are captured using the embedded discrete fracture model (EDFM) and the embedded finite element method (EFEM) for the flow and the mechanics, respectively. This nonconforming approach significantly alleviates meshing challenges. EDFM considers fractures as lower dimension finite volumes that exchange fluxes with the rock matrix cells. The EFEM method provides, instead, a local enrichment of the finite-element space inside each matrix cell cut by a fracture element. Both the use of piecewise constant and piecewise linear enrichments are investigated. They are also compared to an extended finite element approach. One key advantage of EFEM is the element-based nature of the enrichment, which reduces the geometric complexity of the implementation and leads to linear systems with advantageous properties. Synthetic numerical tests are presented to study the convergence and accuracy of the proposed method. It is also applied to a realistic scenario, involving a heterogeneous reservoir with a complex fracture distribution, to demonstrate its relevance for field applications.
58 GEOSCIENCES↗
An extended numerical manifold method for unsaturated soil-water interaction analysis at micro-scale
To investigate unsaturated soil-water interaction at micro-scale, this work extends the numerical manifold method (NMM) by incorporating a soil-water coupling model considering specific capillary water distribution and capillary force calculation. The soil skeleton is constructed by a soil skeleton generation algorithm with random polygons. To more realistically capture the interaction between soil grains and capillary water, a capillary mechanics-based geometric algorithm is proposed to iteratively calculate the capillary water distribution. The capillary forces corresponding to the capillary water distribution are calculated based on the Young-Laplace equation. The proposed capillary water solving framework is first verified by reproducing the soil-water characteristic curve and the capillary water distribution of an ideal contact-disk model against analytical solutions. To further validate the ability of the capillary water solving framework to predict hydraulic behavior of the real soil, a laboratory test on the Toyoura sand is reproduced numerically. Then an ideal direct shear test is performed to further validate the two-way soil-water coupling procedure, in which a comparison between the numerical and analytical results regarding the shear strength and matric suction is presented. Finally, microscopic hydraulic and compression tests are conducted on two soil specimens with the same porosity and mean grain diameter but different uniformity coefficients. The results elucidate that the extended method is a potential tool to explore unsaturated soil behaviors at micro-scale.
58 GEOSCIENCES↗
Spectral deferred correction methods for high-order accuracy in poroelastic problems
In this work, we investigate high-order accuracy in time integration by examining two operator splitting methods for poroelastic problems: the two-pass and the spectral deferred correction (SDC) methods. To enhance the order of accuracy, the two-pass method partitions a coupled operator symmetrically, whereas the SDC method corrects truncation errors by establishing an error equation. These high-order methods are applied to underlying solution strategies, i.e., monolithic, fixed-stress sequential, and undrained sequential methods. We observe that semi-discretized systems from spatial discretization have forms similar to those of index-1 differential algebraic equations (DAEs), causing order reduction against the two-pass method when it is used in conjunction with either the monolithic or sequential method. On the other hand, the SDC in conjunction with the monolithic method exhibits the desired second-order accuracy in poroelastic problems while increasing the order of accuracy for index-1 DAEs. However, the SDC in conjunction with either of the two sequential methods does not achieve the desired order of accuracy, and maintains first order because the flow equation for poroelasticity has an additional approximation associated with the volumetric strain rate term, which does not yield exactly the same forms as those of conventional DAEs. Thus, the monolithic SDC method can achieve higher-order accuracy, but may require higher computational costs because it involves solving matrix systems larger than those for the sequential methods.
02 PETROLEUM↗
A phase-field model for quasi-dynamic nucleation, growth, and propagation of rate-and-state faults
Despite its critical role in the study of earthquake processes, numerical simulation of the entire stages of fault rupture remains a formidable task. The main challenges in simulating a fault rupture process include the complex evolution of fault geometry, frictional contact, and off-fault damage over a wide range of spatial and temporal scales. Here, in this paper, we develop a phase-field model for quasi-dynamic fault nucleation, growth, and propagation, which features two standout advantages: (i) it does not require any sophisticated algorithms to represent fault geometry and its evolution; and (ii) it allows for modeling fault nucleation, propagation, and off-fault damage processes with a single formulation. Built on a recently developed phase-field framework for shear fractures with frictional contact, the proposed formulation incorporates rate- and state-dependent friction, radiation damping, and their impacts on fault mechanics and off-fault damage. We show that the numerical results of the phase-field model are consistent with those obtained from well-verified approaches that model the fault as a surface of discontinuity, without suffering from the mesh convergence issue in the existing continuous approaches to fault rupture (e.g., the stress glut method). Further, through numerical examples of fault propagation in various settings, we demonstrate that the phase-field approach may open new opportunities for investigating complex earthquake processes that have remained overly challenging for the existing numerical methods.
58 GEOSCIENCES↗
Extended Barton–Bandis model for rock joints under cyclic loading: Formulation and implicit algorithm
In this paper, the Barton–Bandis model for rock joints is extended to cyclic loading conditions, without any new material parameter. Also developed herein is an implicit solution algorithm for the extended Barton–Bandis model, which can also be used for the original Barton–Bandis model for which an implicit algorithm has been unavailable. To this end, we first cast the Barton–Bandis model into an incremental elasto-plastic framework, deriving an expression for the elastic shear stiffness being consistent with the original model formulation. We then extend the model formulation to cyclic loading conditions, incorporating the dependence of shear stress and dilation on the joint position and the shearing direction. The extension is achieved by introducing a few state-dependent variables which can be calculated with the existing material parameters. For robust and accurate utilization of the model, we also develop an implicit algorithm based on return mapping, which is unconditionally stable and guarantees the satisfaction of the strength criterion. We verify that the proposed model formulation and algorithm produce virtually the same results as the original Barton–Bandis model under monotonic shearing conditions. Here, we then validate the extended Barton–Bandis model against experimental data on natural rock joints under cycling loading conditions. The present work thus enables the Barton–Bandis model, which has been exceptionally popular in research and practice, to be applicable to a wider range of problems in rock mechanics and rock engineering.
58 GEOSCIENCES↗
Implementation and verification of a user-defined element (UEL) for coupled thermal-hydraulic-mechanical-chemical (THMC) processes in saturated geological media
Efficient and accurate modeling of the coupled thermal-hydraulic-mechanical-chemical (THMC) processes in various rock formations is indispensable for designing energy geo-structures such as underground repositories for high-level nuclear wastes. Here, this work focuses on developing and verifying an implicit finite element solver for generic coupled THMC problems in geological settings. Starting from the mass, momentum, and energy balance laws, a specialized set of governing equations and a thermoporoelastic constitutive model is derived. This system is then solved by an implicit finite element (FE) scheme. Specifically, the residuals and the Jacobians are scripted in a user-defined element (UEL) subroutine which is then combined with the general-purpose FE software Abaqus Standard to solve initial-boundary value problems. Considering the complexity of the system, the UEL development follows a stepwise manner by first solving the coupled hydraulic-mechanical (HM) and thermal-hydraulic-mechanical (THM) equations before moving on to the full THMC problem. Each implementation step consists of at least one verification test by comparing computed results with closed-form analytical solutions to ensure that the various coupling effects are correctly realized. To demonstrate the robustness of the algorithm and to validate the UEL, a three-dimensional case study is performed with reference to the in-situ heating test of ATLAS at Belgium in 1980s. A hypothetical radionuclide leakage event is then simulated by activating the chemical-concentration degree of freedom and prescribing a constant high concentration at the heater's surface. The model predicts a limited contaminated regime after six years considering both diffusion and advection effects on species transport.
12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
Sequential formulation of all‐way coupled finite strain thermoporomechanics for largely deformable gas hydrate deposits
We develop a numerically stable sequential formulation of thermoporomechanics for largely deformable gas hydrate deposits, extended from the fixed stress split of infinitesimal transformation. Constitutive equations are based on the total Lagrangian approach for both flow and geomechanics, including dynamic full tensor permeability and thermal conductivity updated from the deformation gradient. For space discretization, we take the cell-centered finite volume and node-based finite element method for flow and geomechanics, respectively. Then, we propose a sequential implicit method for all-way coupled thermoporomechanics, where the nonisothermal multiphase flow problem of gas hydrates is solved implicitly first and then the geomechanics problem is solved implicitly at the next step. During solution of the flow problem, we fix the rate of first Pioal total stress for numerical stability as well as apply porosity correction and entropy correction to account for geomechanical effects. We test numerical examples where flow and geomechanics parameters are based on deep oceanic gas hydrate deposits. When applying depressurization, even though the results between the infinitesimal transformation and finite strain geomechanics are similar in the early stages due to small deformation, we find differences between them in the late times as deformation becomes large. Accordingly, permeability and thermal conductivity tensors become nonisotropic full tensors although they are initially isotropic. Furthermore, we identify numerical stability of the developed sequential method from the test cases that exhibit the highly complex coupled gas hydrate systems with large deformation. Thus, the proposed sequential formulation can be applied in largely deformable gas hydrate systems.
42 ENGINEERING↗
Data-driven nonlocal model for fragmentation in the crushing of solids
A technique is proposed for reproducing particle size distributions in three-dimensional simulations of the crushing and comminution of solid materials. The method is designed to produce realistic distributions over a wide range of loading conditions, especially for small fragments. In contrast to most existing methods, the new model does not explicitly treat the small-scale process of fracture. Instead, it uses measured fragment distributions from laboratory tests as the basic material property that is incorporated into the algorithm, providing a data-driven approach. The algorithm is implemented within a nonlocal peridynamic solver, which simulates the underlying continuum mechanics and contact interactions between fragments after they are formed. Finally, the technique is illustrated in reproducing fragmentation data from drop weight testing on sandstone samples.
58 GEOSCIENCES↗
A Phase-field Model for Quasi-dynamic Rupture Nucleation and Propagation of In-plane Faults
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Geosciences↗
Anthromes and forest carbon responses to global change
Human effects on ecosystems date back thousands of years, and anthropogenic biomes—anthromes—broadly incorporate the effects of human population density and land use on ecosystems. Forests are integral to the global carbon cycle, containing large biomass carbon stocks, yet their responses to land use and climate change are uncertain but critical to informing climate change mitigation strategies, ecosystem management, and Earth system modeling. Using an anthromes perspective and the site locations from the Global Forest Carbon (ForC) Database, we compare intensively used, cultured, and wildland forest lands in tropical and extratropical regions. We summarize recent past (1900-present) patterns of land use intensification, and we use a feedback analysis of Earth system models from the Coupled Model Intercomparison Project Phase 6 to estimate the sensitivity of forest carbon stocks to CO 2 and temperature change for different anthromes among regions. Modeled global forest carbon stock responses are positive for CO 2 increase but neutral to negative for temperature increase. Across anthromes (intensively used, cultured, and wildland forest areas), modeled forest carbon stock responses of temperate and boreal forests are less variable than those of tropical forests. Tropical wildland forest areas appear especially sensitive to CO 2 and temperature change, with the negative temperature response highlighting the potential vulnerability of the globally significant carbon stock in tropical forests. The net effect of anthropogenic activities—including land-use intensification and environmental change and their interactions with natural forest dynamics—will shape future forest carbon stock changes. These interactive effects will likely be strongest in tropical wildlands.
54 ENVIRONMENTAL SCIENCES↗
Diurnal cycle of precipitation over the tropics and central United States: intercomparison of general circulation models
Diurnal precipitation is a fundamental mode of variability that climate models have difficulty in accurately simulating. Here, in this work, the diurnal cycle of precipitation (DCP) in participating climate models from the Global Energy and Water Exchanges' DCP project is evaluated over the tropics and central United States. Common model biases such as excessive precipitation over the tropics, too frequent light-to-moderate rain, and the failure to capture propagating convection in the central United States still exist. Over the central United States, the issues of too weak rainfall intensity in climate runs is well improved in their hindcast runs with initial conditions from numerical weather prediction analyses. But the improvement is minimal over the central Amazon. Incorporating the role of the large-scale environment in convective triggering processes helps resolve the phase-locking issue in many models where precipitation often incorrectly peaks near noon due to maximum insolation over land. Allowing air parcels to be lifted above the boundary layer improves the simulation of nocturnal precipitation which is often associated with the propagation of mesoscale systems. Including convective memory in cumulus parameterizations acts to suppress light-to-moderate rain and promote intense rainfall; however, it also weakens the diurnal variability. Simply increasing model resolution (with cumulus parameterizations still used) cannot fully resolve the biases of low-resolution climate models in DCP. The hierarchy modeling framework from this study is useful for identifying the missing physics in models and testing new development of model convective processes over different convective regimes.
58 GEOSCIENCES↗
Carbonate clumped isotope analysis (Δ 47 ) of 21 carbonate standards determined via gas‐source isotope‐ratio mass spectrometry on four instrumental configurations using carbonate‐based standardization and multiyear data sets
Rationale Clumped isotope geochemistry examines the pairing or clumping of heavy isotopes in molecules and provides information about the thermodynamic and kinetic controls on their formation. The first clumped isotope measurements of carbonate minerals were first published 15 years ago, and since then, interlaboratory offsets have been observed, and laboratory and community practices for measurement, data analysis, and instrumentation have evolved. Here we briefly review historical and recent developments for measurements, share Tripati Lab practices for four different instrument configurations, test a recently published proposal for carbonate‐based standardization on multiple instruments using multi‐year data sets, and report values for 21 different carbonate standards that allow for recalculations of previously published data sets. Methods We examine data from 4628 standard measurements on Thermo MAT 253 and Nu Perspective IS mass spectrometers, using a common acid bath (90°C) and small‐sample (70°C) individual reaction vessels. Each configuration was investigated by treating some standards as anchors (working standards) and the remainder as unknowns (consistency standards). Results We show that different acid digestion systems and mass spectrometer models yield indistinguishable results when instrument drift is well characterized. For linearity correction, mixed gas‐and‐carbonate standardization or carbonate‐only standardization yields similar results. No difference is observed in the use of three or eight working standards for the construction of transfer functions. Conclusions We show that all configurations yield similar results if instrument drift is robustly characterized and validate a recent proposal for carbonate‐based standardization using large multiyear data sets. Δ 47 values are reported for 21 carbonate standards on both the absolute reference frame (ARF; also refered to as the Carbon Dioxide Equilibrated Scale or CDES) and the new InterCarb‐Carbon Dioxide Equilibrium Scale (I‐CDES) reference frame, facilitating intercomparison of data from a diversity of labs and instrument configurations and restandardization of a broad range of sample sets between 2006, when the first carbonate measurements were published, and the present.
58 GEOSCIENCES↗
Comparison of δ 13 C analyses of individual foraminifer ( Orbulina universa ) shells by secondary ion mass spectrometry and gas source mass spectrometry
Rationale: The use of secondary ion mass spectrometry (SIMS) to perform micrometer-scale in situ carbon isotope (δ 13 C) analyses of shells of marine microfossils called planktic foraminifers holds promise to explore calcification and ecological processes. The potential of this technique, however, cannot be realized without comparison to traditional whole-shell δ 13 C values measured by gas source mass spectrometry (GSMS). Methods: Paired SIMS and GSMS δ 13 C values measured from final chamber fragments of the same shell of the planktic foraminifer Orbulina universa are compared. The SIMS–GSMS δ 13 C differences (Δ 13 C SIMS-GSMS ) were determined via paired analysis of hydrogen peroxide-cleaned fragments of modern cultured specimens and of fossil specimens from deep-sea sediments that were either untreated, sonicated, and cleaned with hydrogen peroxide or vacuum roasted. After treatment, fragments were analyzed by a CAMECA IMS 1280 SIMS instrument and either a ThermoScientific MAT-253 or a Fisons Optima isotope ratio mass spectrometer (GSMS). Results: Paired analyses of cleaned fragments of cultured specimens (n = 7) yield no SIMS–GSMS δ 13 C difference. However, paired analyses of untreated (n = 18) and cleaned (n = 12) fragments of fossil shells yield average Δ 13 C SIMS-GSMS values of 0.8‰ and 0.6‰ (±0.2‰, 2 SE), respectively, while vacuum roasting of fossil shell fragments (n = 11) removes the SIMS–GSMS δ 13 C difference. Conclusions: The noted Δ 13 C SIMS-GSMS values are most likely due to matrix effects causing sample–standard mismatch for SIMS analyses but may also be a combination of other factors such as SIMS measurement of chemically bound water. The volume of material analyzed via SIMS is ~10 5 times smaller than that analyzed by GSMS; hence, the extent to which these Δ 13 C SIMS-GSMS values represent differences in analyte or instrument factors remains unclear.
58 GEOSCIENCES↗
Mapping the Residual Stress Distribution in Polycrystalline Quartz Tiger's Eye Using Raman Spectroscopy
Stress distribution maps in polycrystalline materials are needed to reveal stress pathways caused by short‐and long‐range interactions of crystallites. Stress induced changes to wavenumbers in Raman spectroscopy is a well‐known phenomenon that occurs when a crystalline material undergoes elastic strain. Using spatially resolved Raman spectroscopy, we have developed a technique to experimentally measure grain‐scale residual stresses across a sample of polycrystal quartz Tiger's Eye. The results of this technique are validated using multiple criteria, including evaluation of the residual stress map itself and the accuracy of the measurements taken. The residual map of Tiger's Eye shows striking similarity to observed characteristics of other polycrystalline residual stress distributions, revealing heterogenous areas of high and low magnitude stresses. The stress magnitudes are consistent with residual stress magnitudes previously measured from polycrystalline quartz. Characterization of Tiger's Eye quartz also revealed the geometric nature of the iron oxide inclusions, not previously observed in Tiger's Eye quartz. With this technique, we present a residual stress map of Tiger's Eye quartz that shows with accuracy a heterogeneous stress state with inter‐ and intra‐granular detail.
36 MATERIALS SCIENCE↗