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At least 1,243 records · Page 69

Investigation of methane mass transfer and sorption in Marcellus shale under variable net-stress

Natural gas in shale exists as free and adsorbed gas, subject to prevailing pore pressures and stress conditions. Accordingly, to accurately estimate/predict the shale gas recovery potential, a central requirement is to represent gas transport and sorption behavior under varying stress conditions. The objective of this work is to facilitate the interpretation of laboratory-scale experiments, at relevant conditions, in an attempt to bridge the gap in scales between laboratory- and field-scale observations. We have conducted a series of high-pressure experiments on a full-diameter core sample from the Marcellus shale. These include gas loading (pressure-decay) and depletion (production) experiments with pure methane (CH 4 ) at variable stress conditions to characterize transport and sorption behavior under reservoir-relevant conditions. Here we have formulated and applied a novel integral model for mass transfer and storage in multi-porosity shale systems that allows us to effectively investigate transport and sorption phenomena: We delineate gas transport by interpreting helium (He) pressure-decay experiments and demonstrate how to use the information gained to calculate the relevant transport coefficients of CH 4 and other gases. A separate measurement of the CH 4 sorption isotherm on a smaller sample (a shale cube) was interpreted and combined with the transport description to predict the production behavior of CH 4 from the experiments with the full-diameter core. Our experiments demonstrate that the representation of sorption hysteresis is crucial for predicting and guiding shale gas production: At the end of both gas production experiments, approximately 20% of the initial gas in place remained in the core. Without accounting for sorption hysteresis, our modeling demonstrates that the CH 4 production could be overestimated by 10%. We demonstrate that our integral, triple-porosity model provides an effective approach for the interpretation and prediction of gas transport and sorption behavior during loading and production experiments on shale cores under variable net-stress conditions. In summary, our work combines measurements and modeling of mass transfer and sorption in shales at different scales to validate a characterization approach that facilitates an improved understanding of shale gas production. Furthermore, the triple-porosity model utilized in our work defines a potential pathway for the translation of laboratory-scale experimentation to larger-scale applications.

58 GEOSCIENCES↗

Tau-jet signatures of vectorlike quark decays to heavy charged and neutral Higgs bosons

We study 4 b + 2 τ and 4 b + 1 τ signatures of heavy neutral and charged Higgs bosons originating from cascade decays of pair-produced new quarks. Decays of vectorlike quarks through heavy Higgses can easily dominate in the two Higgs doublet model of type-II, and the studied signatures are common to many possible decay chains. We design search strategies for these final states and discuss the mass ranges of heavy Higgs bosons and new quarks that can be explored at the Large Hadron Collider as functions of branching ratios in a model independent way. We further combine the results with a similar study focusing on decays which lead to a 6 b final state and interpret the sensitivity to charged and neutral Higgs bosons and vectorlike quarks in the type-II two Higgs doublet model. We find that the LHC reach for their masses extends to well above 2 TeV in the case of an SU(2) doublet quark and to at least 1.8 TeV for a bottom-like SU(2) singlet quark in the whole range of tan β between 1 and 50.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Dynamics of vacancy-induced modes in the non-Abelian Kitaev spin liquid

Here, we study the dynamical response of vacancy-induced quasiparticle excitations in the site-diluted Kitaev spin liquid with a magnetic field. Due to the flux-binding effect and the emergence of dangling Majorana fermions around each spin vacancy, the low-energy physics is governed by a set of vacancy-induced quasi-zero-energy modes. These localized modes result in unique characteristics of the dynamical spin correlation functions, which intriguingly mimic the single-quasiparticle density of states and further exhibit a quasi-zero-frequency peak. By recognizing the potential observability of these local correlation functions via scanning tunneling microscopy (STM), we show how the STM response is sensitive to the local flux configuration, the magnetic field strength, and the vacancy concentration. Constructing a simple model of the localized modes, we also elucidate how the local correlation functions can be interpreted in terms of the hybridization between these modes.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Quantum biological insights into CRISPR-Cas9 sgRNA efficiency from explainable-AI driven feature engineering

Abstract CRISPR-Cas9 tools have transformed genetic manipulation capabilities in the laboratory. Empirical rules-of-thumb have been developed for only a narrow range of model organisms, and mechanistic underpinnings for sgRNA efficiency remain poorly understood. This work establishes a novel feature set and new public resource, produced with quantum chemical tensors, for interpreting and predicting sgRNA efficiency. Feature engineering for sgRNA efficiency is performed using an explainable-artificial intelligence model: iterative Random Forest (iRF). By encoding quantitative attributes of position-specific sequences for Escherichia coli sgRNAs, we identify important traits for sgRNA design in bacterial species. Additionally, we show that expanding positional encoding to quantum descriptors of base-pair, dimer, trimer, and tetramer sequences captures intricate interactions in local and neighboring nucleotides of the target DNA. These features highlight variation in CRISPR-Cas9 sgRNA dynamics between E. coli and H. sapiens genomes. These novel encodings of sgRNAs enhance our understanding of the elaborate quantum biological processes involved in CRISPR-Cas9 machinery.

59 BASIC BIOLOGICAL SCIENCES↗

Call for Participation: Collaborative Benchmarking of Functional-Structural Root Architecture Models. The Case of Root Water Uptake

Three-dimensional models of root growth, architecture and function are becoming important tools that aid the design of agricultural management schemes and the selection of beneficial root traits. However, while benchmarking is common in many disciplines that use numerical models, such as natural and engineering sciences, functional-structural root architecture models have never been systematically compared. The following reasons might induce disagreement between the simulation results of different models: different representation of root growth, sink term of root water and solute uptake and representation of the rhizosphere. Presently, the extent of discrepancies is unknown, and a framework for quantitatively comparing functional-structural root architecture models is required. We propose, in a first step, to define benchmarking scenarios that test individual components of complex models: root architecture, water flow in soil and water flow in roots. While the latter two will focus mainly on comparing numerical aspects, the root architectural models have to be compared at a conceptual level as they generally differ in process representation. Therefore, defining common inputs that allow recreating reference root systems in all models will be a key challenge. In a second step, benchmarking scenarios for the coupled problems are defined. We expect that the results of step 1 will enable us to better interpret differences found in step 2. This benchmarking will result in a better understanding of the different models and contribute toward improving them. Improved models will allow us to simulate various scenarios with greater confidence and avoid bugs, numerical errors or conceptual misunderstandings. This work will set a standard for future model development.

Plant Sciences↗

Investigation of hydrometeorological influences on reservoir releases using explainable machine learning methods

Long short-term memory (LSTM) networks have demonstrated successful applications in accurately and efficiently predicting reservoir releases from hydrometeorological drivers including reservoir storage, inflow, precipitation, and temperature. However, due to its black-box nature and lack of process-based implementation, we are unsure whether LSTM makes good predictions for the right reasons. In this work, we use an explainable machine learning (ML) method, called SHapley Additive exPlanations (SHAP), to evaluate the variable importance and variable-wise temporal importance in the LSTM model prediction. In application to 30 reservoirs over the Upper Colorado River Basin, United States, we show that LSTM can accurately predict the reservoir releases with NSE ≥ 0.69 for all the considered reservoirs despite of their diverse storage sizes, functionality, elevations, etc. Additionally, SHAP indicates that storage and inflow are more influential than precipitation and temperature. Moreover, the storage and inflow show a relatively long-term influence on the release up to 7 days and this influence decreases as the lag time increases for most reservoirs. These findings from SHAP are consistent with our physical understanding. However, in a few reservoirs, SHAP gives some temporal importances that are difficult to interpret from a hydrological point of view, probably because of its ignorance of the variable interactions. SHAP is a useful tool for black-box ML model explanations, but the hydrological processes inferred from its results should be interpreted cautiously. More investigations of SHAP and its applications in hydrological modeling is needed and will be pursued in our future study.

54 ENVIRONMENTAL SCIENCES↗

Deep energy-pressure regression for a thermodynamically consistent EOS model

Abstract In this paper, we aim to explore novel machine learning (ML) techniques to facilitate and accelerate the construction of universal equation-Of-State (EOS) models with a high accuracy while ensuring important thermodynamic consistency. When applying ML to fit a universal EOS model, there are two key requirements: (1) a high prediction accuracy to ensure precise estimation of relevant physics properties and (2) physical interpretability to support important physics-related downstream applications. We first identify a set of fundamental challenges from the accuracy perspective, including an extremely wide range of input/output space and highly sparse training data. We demonstrate that while a neural network (NN) model may fit the EOS data well, the black-box nature makes it difficult to provide physically interpretable results, leading to weak accountability of prediction results outside the training range and lack of guarantee to meet important thermodynamic consistency constraints. To this end, we propose a principled deep regression model that can be trained following a meta-learning style to predict the desired quantities with a high accuracy using scarce training data. We further introduce a uniquely designed kernel-based regularizer for accurate uncertainty quantification. An ensemble technique is leveraged to battle model overfitting with improved prediction stability. Auto-differentiation is conducted to verify that necessary thermodynamic consistency conditions are maintained. Our evaluation results show an excellent fit of the EOS table and the predicted values are ready to use for important physics-related tasks.

97 MATHEMATICS AND COMPUTING↗

Review: Pre-Darcy flows in low-permeability porous media

The widely used Darcy’s law specifies a linear relation between the Darcy velocity of fluid flow and the pressure gradient that drives the flow. However, studies have shown that Darcy velocity can exhibit a nonlinear dependence on the pressure gradient in low-permeability porous media such as clay and shale when the pressure gradient is adequately low. This phenomenon is referred to as low-velocity non-Darcian flow or pre-Darcy flow. This paper provides a comprehensive review of the theories, experimental data, and modeling methods for pre-Darcy flow in low-permeability porous media. The review begins by outlining the fundamental mechanisms underlying pre-Darcy flow that regulate the unique characteristics such as nonlinear dependence of the Darcy velocity on the pressure gradient and its relevance to fluid–rock interactions. The review then proceeds to present a thorough compilation of experimental investigations performed in various low-permeability geomaterials including tight sandstones, shales, and clays. Next, empirical and theoretical models and simulation methods that have been developed to fit and interpret experimental data are reviewed. Finally, the review underscores the challenges encountered in conducting and interpreting pre-Darcy flow experiments and suggests future research directions. By analyzing previous experimental investigations, this review aims to offer a valuable resource for researchers and practitioners seeking to enhance their understanding of fluid dynamics in low-permeability geomaterials. This provides insights into the application of pre-Darcy flow in numerous natural and engineered processes such as shale oil and gas recovery, contaminant transport in low-permeability aquifers, and geological disposal of nuclear waste.

58 GEOSCIENCES↗

Frontiers in divalent $f$-block chemistry

Divalent f-block chemistry has undergone rapid expansion in recent years, driven by advances in the stabilization of low-valent lanthanide and actinide complexes. Although f-elements were historically accessed in the +3 or higher oxidation states, the isolation of +2 species has revealed unusual spectroscopic signatures, distinct bonding motifs, and multiple accessible electronic configurations that influence their chemical and physical properties. These developments have generated opportunities in areas including quantum information science, molecular magnetism, catalysis, and luminescence. Computational chemistry has played a pivotal role in interpreting the electronic structure and reactivity of these systems. However, accurately modeling divalent f-block complexes remains challenging because of strong electronic correlation, multiconfigurational character, and the presence of close-in-energy competing electronic states. As experimental capabilities and theoretical methodologies continue to advance, a comprehensive assessment of divalent chemistry is both timely and needed. In this Review, we integrate experimental and theoretical perspectives to provide a systematic analysis of divalent lanthanide and actinide complexes across the f-block series. We critically assess the role of ligands in determining competing ground-state configurations (f n d 1 vs. f n+1 ) resulting in their distinct spectroscopic, magnetic, and bonding properties. Finally, we discuss emerging strategies for predictive modeling and rational design of low-valent f-block molecular systems, with potential applications ranging from dinitrogen reduction to quantum technologies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Experimental study of the partitioning of some platinum group elements (Pd and Ir) between orthopyroxene and silicate melt

Past experiments and observations on natural samples have largely focused on the roles of olivine and chromite in controlling the behaviour of the platinum-group elements (PGE) during melting and solidification, whereas other phases, such as pyroxene, have gone largely uncharacterized. Here, to address this, experiments have been done to measure the partitioning of Pd (with a subset of results for Ir), between orthopyroxene and silicate melt at 1340 °C, 0.1 MPa and log fO 2 of FMQ - 1 to FMQ + 6 (FMQ = Fayalite-Magnetite-Quartz). The X-ray Absorption Near-Edge Structure (XANES) was measured in a subset of experiment glasses. Glass concentrations of Pd (corrected to unit Pd activity) increase from ~6 to ~650 ug/g over the fO 2 range of experiments. The slope of the solubility-fO 2 relation is consistent with Pd 1+ as the dominant oxidation state, with evidence for Pd 0 and Pd 2+ at the lowest and highest experiment fO 2 , respectively. Consistent with this result, the XANES reveal spectral features similar to Pd 0 and Pd 2+ spectral reference materials (specRM) at the most reduced and oxidized synthesis conditions, respectively. Other lines of evidence require the presence of a third melt species, here interpreted to be Pd 1+ . Values of orthopyroxene/melt partition coefficients for Pd (D Pd Opx/melt ) are 0.0051 (+/-0.006) at log fO 2 < ΔFMQ + 3, increasing with fO 2 to a maximum of 0.013 at ~FMQ + 6. Sodium partition coefficients, expected to be similar to Pd, range from 0.0061 (+/-0.00061) at FMQ + 3, increase to 0.007–0.009 at higher fO 2 , but with no clear systematic trend. A value for D Ir Opx-melt of ~0.6 was measured at ~FMQ + 4, indicating significantly more compatible behaviour for Ir relative to Pd. Partitioning results are interpreted in the context of the Blundy-Wood elastic strain model in which the variation in partitioning is related to ionic radius mismatch to an optimal crystallographic site size. Based on the trend in ionic radius with oxidation state, the estimated ionic radius of Pd 1+ in octahedral coordination is similar to Na 1+ , and comparison to previous orthopyroxene-melt partitioning experiments suggests D Pd1+ opx/melt and DNaopx/melt should be nearly identical, consistent with the results of this study. The ionic radius of VI-fold Pd 2+ is close to the optimal M2 site size, so an increased proportion of this species with fO 2 accounts for the larger values of D Pd opx/melt at the highest fO 2 investigated. The much larger partition coefficient for Ir is consistent with the presence of Ir 2+ , whose estimated ionic radius is close to Fe 2+ and Mg 2+ , as well as predictions for the optimal M1 site size. With the assumption that D Pd opx/melt = D Na opx/melt , combined with a revised value for the Pd content of the primitive mantle, a melting model is presented that better reproduces the Pd concentration of high degree melts from sulfide-free mantle sources.

58 GEOSCIENCES↗

Joint impedance and facies inversion of time-lapse seismic data for improving monitoring of CO 2 incidentally stored from CO 2 EOR

Time-lapse seismic monitoring is an effective and proven technology for mapping the distribution of CO 2 in a subsurface reservoir. When injected CO 2 displaces other reservoir fluids, porous-medium properties are changed and thus the seismic impedance changes, causing time-lapse seismic amplitude differences in the injection zones. The analysis and interpretation of images created from these amplitude differences can provide information about reservoir architecture and the CO 2 migration within the reservoir. Incorporating seismic inversion and rock physics into the interpretation of time-lapse seismic data can considerably improve the modeling and monitoring to detect and assess the location of CO 2 over time. The joint inversion method presented in this paper has an integral representation of the geology in the inversion algorithm using elastic facies, which provides information about the spatial distribution of the geologic heterogeneities controlling the movement of fluids in the reservoir. The method was successfully applied to time-lapse seismic data from a mature oil field undergoing CO 2 enhanced oil recovery. The estimated seismic acoustic impedances and facies reflect the characteristics of individual geologic facies and fluid conditions of the reservoir subject to CO 2 injection. Finally, the probabilities estimated by the joint impedance and facies inversion for the reservoir's litho-fluid facies can be used for forecasting CO 2 saturation and pressure changes within the target reservoir.

4D seismic↗

Nematic fluctuations in iron-oxychalcogenide Mott insulators

Nematic fluctuations occur in a wide range physical systems from biological molecules to cuprates and iron pnictide high- T c superconductors. It is unclear whether nematicity in pnictides arises from electronic spin or orbital degrees of freedom. We studied the iron-based Mott insulators La 2 O 2 Fe 2 OM 2 M = (S, Se), which are structurally similar to pnictides. Nuclear magnetic resonance revealed a critical slowing down of nematic fluctuations and complementary Mössbauerr spectroscopy data showed a change of electrical field gradient. The neutron pair distribution function technique detected local C 2 fluctuations while neutron diffraction indicates that global C 4 symmetry is preserved. A geometrically frustrated Heisenberg model with biquadratic and single-ion anisotropic terms provides the interpretation of the low temperature magnetic fluctuations. The nematicity is not due to spontaneous orbital order, instead it is linked to geometrically frustrated magnetism based on orbital selectivity. This study highlights the interplay between orbital order and spin fluctuations in nematicity.

36 MATERIALS SCIENCE↗

Improved AlphaFold modeling with implicit experimental information

Machine-learning prediction algorithms such as AlphaFold and RoseTTAFold can create remarkably accurate protein models, but these models usually have some regions that are predicted with low confidence or poor accuracy. We hypothesized that by implicitly including new experimental information such as a density map, a greater portion of a model could be predicted accurately, and that this might synergistically improve parts of the model that were not fully addressed by either machine learning or experiment alone. An iterative procedure was developed in which AlphaFold models are automatically rebuilt on the basis of experimental density maps and the rebuilt models are used as templates in new AlphaFold predictions. We show that including experimental information improves prediction beyond the improvement obtained with simple rebuilding guided by the experimental data. This procedure for AlphaFold modeling with density has been incorporated into an automated procedure for interpretation of crystallographic and electron cryo-microscopy maps.

59 BASIC BIOLOGICAL SCIENCES↗

Chemical bonding in americium oxides probed by X-ray spectroscopy

The electronic structure and the chemical state in Am binary oxides and Am-doped UO 2 were studied by means of X-ray absorption spectroscopy at shallow Am core (4d and 5d) edges. In particular, the Am 5f states were probed and the nature of their bonding to the oxygen states was analyzed. The interpretation of the experimental data was supported by the Anderson impurity model (AIM) calculations which took into account the full multiplet structure due to the interaction between 5f electrons as well as the interaction with the core hole. The sensitivity of the branching ratio of the Am 4d 3/2 and 4d 5/2 X-ray absorption lines to the chemical state of Am was shown using Am binary oxides as reference systems. The observed ratio for Am-doped UO 2 suggests that at least at low Am concentrations, americium is in the Am(III) state in the UO 2 lattice. To confirm the validity of the applied AIM approach, the analysis of the Am 4f X-ray photoelectron spectra of AmO 2 and Am 2 O 3 was also performed which revealed a good agreement between experiment and calculations. As a whole, AmO 2 can be classified as the charge-transfer compound with the 5f occupancy (n ƒ ) equal to 5.73 electrons, while Am 2 O 3 is rather a Mott–Hubbard system with n ƒ = 6.05.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Spectroscopic analysis reveals that soil phosphorus availability and plant allocation strategies impact feedstock quality of nutrient-limited switchgrass

Abstract The perennial native switchgrass adapts better than other plant species do to marginal soils with low plant-available nutrients, including those with low phosphorus (P) content. Switchgrass roots and their associated microorganisms can alter the pools of available P throughout the whole soil profile making predictions of P availability in situ challenging. Plant P homeostasis makes monitoring of P limitation via measurements of plant P content alone difficult to interpret. To address these challenges, we developed a machine-learning model trained with high accuracy using the leaf tissue chemical profile, rather than P content. By applying this learned model in field trials across two sites with contrasting extractable soil P, we observed that actual plant available P in soil was more similar than expected, suggesting that adaptations occurred to alleviate the apparent P constraint. These adaptations come at a metabolic cost to the plant that have consequences for feedstock chemical components and quality. We observed that other biochemical signatures of P limitation, such as decreased cellulose-to-lignin ratios, were apparent, indicating re-allocation of carbon resources may have contributed to increased P acquisition. Plant P allocation strategies also differed across sites, and these differences were correlated with the subsequent year’s biomass yields.

59 BASIC BIOLOGICAL SCIENCES↗

Electron density measurement using a partially covered hairpin resonator in an inductively coupled plasma

Hairpin probes are used to determine electron densities via measuring the shift of the resonant frequency of the probe structure when immersed in a plasma. This manuscript presents new developments in hairpin probe hardware and theory that have enabled measurements in a high electron density plasma, up to approximately 10 12 cm -3 , corresponding to a plasma frequency of about 9 GHz. Hardware developments include the use of both quarter-wavelength and three-quarter-wavelength partially covered hairpin probes in a transmission mode together with an easily reproducible implementation of the associated microwave electronics using commercial off-the-shelf components. The three-quarter-wavelength structure is operated at its second harmonic with the purpose of measuring higher electron densities. New theory developments for interpreting the probe measurements include the use of a transmission line model to find an accurate relationship between the resonant frequency of the probe and the electron density, including effects of partially covering the probes with epoxy. Measurements are taken in an inductively coupled plasma sustained in argon at pressures below 50 mTorr. Results are compared with Langmuir probe and interferometry measurements.

47 OTHER INSTRUMENTATION↗

Sodium tracer measurements of an expanded dense aluminum plasma from e-beam isochoric heating

Spatially and temporally resolved visible absorption spectroscopy is performed on sodium D-lines present as surface contaminants on an expanded dense aluminum plasma plume. An 80-ns FWHM, intense, relativistic electron beam deposits 5.4 J into a 100- μ m-thick Al foil, which isochorically heats and subsequently hydrodynamically expands the material through the warm dense matter state and into a classical-like plasma state, with a coupling parameter of approximately 0.2 and a degeneracy parameter of approximately 270. The Na contamination, carried along with the expanding plume, shows saturated absorption features in the dense Al continuum for λ > 450 nm. X-ray photoelectron spectroscopy and laser-induced breakdown spectroscopy confirm Na is a surface contaminant with an atomic concentration of ~ 0.1 % when interrogating identical foil samples. Additioanlly, a spectroscopic-quality radiation transport model is used to post-process 2D hydrodynamic simulations to interpret the plasma conditions based on the measured Na 3p-3s doublet line profiles. A sodium number density of 3 × 10 15 cm -3 best matches the experimental spectra, which originate from a dense surface plasma with n e = 3.0 ± 0.8 × 10 18 cm -3 .

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

EVAP: A two-photon imaging tool to study conformational changes in endogenous Kv2 channels in live tissues

A primary goal of molecular physiology is to understand how conformational changes of proteins affect the function of cells, tissues, and organisms. Here, we describe an imaging method for measuring the conformational changes of the voltage sensors of endogenous ion channel proteins within live tissue, without genetic modification. We synthesized GxTX-594, a variant of the peptidyl tarantula toxin guangxitoxin-1E, conjugated to a fluorophore optimal for two-photon excitation imaging through light-scattering tissue. We term this tool EVAP (Endogenous Voltage-sensor Activity Probe). GxTX-594 targets the voltage sensors of Kv2 proteins, which form potassium channels and plasma membrane–endoplasmic reticulum junctions. GxTX-594 dynamically labels Kv2 proteins on cell surfaces in response to voltage stimulation. To interpret dynamic changes in fluorescence intensity, we developed a statistical thermodynamic model that relates the conformational changes of Kv2 voltage sensors to degree of labeling. We used two-photon excitation imaging of rat brain slices to image Kv2 proteins in neurons. We found puncta of GxTX-594 on hippocampal CA1 neurons that responded to voltage stimulation and retain a voltage response roughly similar to heterologously expressed Kv2.1 protein. Our findings show that EVAP imaging methods enable the identification of conformational changes of endogenous Kv2 voltage sensors in tissue.

59 BASIC BIOLOGICAL SCIENCES↗