pyMS-Vis, an Open-Source Python Application for Visualizing and Investigating Deconvoluted Top-Down Mass Spectrometric Experiments: A Histone Proteoform Case Study
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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Designing Particle Morphologies for Materials with Solid Transport Limitations: A Case Study of Lithium and Manganese Rich Cathode Oxides
A lithium and manganese rich nickel-manganese-cobalt oxide (LMR-NMC) cathode is a promising candidate for next-generation batteries due to its high specific capacity, low cost, and low cobalt content. However, the material suffers from poor rate capability due to the diffusion limitations of lithium in the cathode particles. Understanding the material performance requires careful control of the morphology of the cathode particles, taking into account the primary and agglomerated diffusion pathways and the presence of pores, some of which could be closed from electrolyte infiltration. Here, in this study, we use a microstructure-based mathematical model combined with experimental data to understand the role of the complex cathode particle morphology in the rate performance of the material. Scanning electron microscopy images of cathodes made under different synthesis conditions, which results in different agglomerate morphologies, serve as the input into the mathematical model. The model is then compared to rate data to understand the controlling parameters. The presence of intra-agglomerate closed pores results in a large agglomerate diffusion length in comparison to the ideal condition, where the primary particles are agglomerated in an open and dispersed manner such that the entire interfacial area is available for electrochemical reaction. Smaller primary and agglomerate diffusion lengths result in better electrochemical performance. This points us toward designing the morphology of the cathode particles to compensate for the diffusion limitation of LMR-NMC while maximizing the density.
Tewari, Deepti↗
A Deep Learning Based Framework to Identify Undocumented Orphaned Oil and Gas Wells from Historical Maps: A Case Study for California and Oklahoma
Undocumented Orphaned Wells (UOWs) are wells without an operator that have limited or no documentation with regulatory authorities. An estimated 310,000 to 800,000 UOWs exist in the United States (US), whose locations are largely unknown. These wells can potentially leak methane and other volatile organic compounds to the atmosphere, and contaminate groundwater. In this study, we developed a novel framework utilizing a state-of-the-art computer vision neural network model to identify the precise locations of potential UOWs. The U-Net model is trained to detect oil and gas well symbols in georeferenced historical topographic maps, and potential UOWs are identified as symbols that are further than 100 m from any documented well. A custom tool was developed to rapidly validate the potential UOW locations. We applied this framework to four counties in California and Oklahoma, leading to the discovery of 1301 potential UOWs across >40,000 km 2 . We confirmed the presence of 29 UOWs from satellite images and 15 UOWs from magnetic surveys in the field with a spatial accuracy on the order of 10 m. This framework can be scaled to identify potential UOWs across the US since the historical maps are available for the entire nation.
54 ENVIRONMENTAL SCIENCES↗
Locating Undocumented Wells Using Historical Oil and Gas Exploration Maps: A Case Study in Osage County, Oklahoma
Undocumented oil and gas wells lack reliable information about their locations and characteristics, making them difficult to identify. These wells can result in unanticipated delays and costs in the development of nearby surface and subsurface resources, and, if improperly plugged, can cause contamination. This study leverages historical petroleum exploration maps to locate such wells, focusing on Osage County, Oklahoma. Two sets of early 20th century oil and gas exploration maps by the United States Geological Survey were georeferenced and analyzed using a computer vision model to detect well symbols. The locations of detected wells were compared to the location of known wells in the database from the Bureau of Indian Affairs Osage Agency to identify potential undocumented wells. The analysis yielded over 500 potential undocumented wells, with dry holes constituting the largest fraction. Field verification confirmed the presence of some undocumented wells. Comparison with prior work revealed limited overlap, underscoring the complementary value of historical oil and gas maps for locating undocumented wells. This approach demonstrates the utility of integrating historical cartographic resources with modern geospatial and machine learning techniques to improve the identification and management of undocumented wells.
Energy - Petroleum↗
CAML: Commutative Algebra Machine Learning─A Case Study on Protein–Ligand Binding Affinity Prediction
Recently, Suwayyid and Wei introduced commutative algebra as an emerging paradigm for machine learning and data science. In this work, we propose commutative algebra machine learning (CAML) for the prediction of protein−ligand binding affinities. Specifically, we apply persistent Stanley−Reisner theory, a key concept in combinatorial commutative algebra, to the affinity predictions of protein−ligand binding and metalloprotein−ligand binding. We present three new algorithms, i.e., element-specific commutative algebra, category-specific commutative algebra, and commutative algebra on bipartite complexes, to tackle the complexity of data involved in (metallo) protein−ligand complexes. We show that the proposed CAML outperforms other state-of-theart methods in (metallo) protein−ligand binding affinity predictions, indicating the great potential of commutative algebra learning.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Commutative Algebra Modeling in Materials Science – A Case Study on Metal–Organic Frameworks (MOFs)
Metal-organic frameworks (MOFs) are a class of important crystalline and highly porous materials whose hierarchical geometry and chemistry hinder interpretable predictions in materials properties. Commutative algebra is a branch of abstract algebra that has been rarely applied in data and material sciences. We introduce the first ever commutative algebra modeling and prediction in materials science. Specifically, category-specific commutative algebra (CSCA) is proposed as a new framework for MOF representation and learning. It integrates element-based categorization with multiscale algebraic invariants to encode both local coordination motifs and global network organization of MOFs. These algebraically consistent, chemically aware representations enable compact, interpretable, and data efficient modeling of MOF properties such as Henry’s constants and uptake capacities for common gases. Compared to traditional geometric and graph-based approaches, CSCA achieves comparable or superior predictive accuracy while substantially improving interpretability and stability across data sets. By aligning commutative algebra with the chemical hierarchy, the CSCA establishes a rigorous and generalizable paradigm for understanding structure and property relationships in porous materials and provides a nonlinear algebra-based framework for data-driven material discovery.
Khaemba, Caleb S.↗
Assessing the Sensitivity of Pourbaix Diagrams to Computational Protocols: Electrochemical Stability of Ni Oxides as a Case Study
Pourbaix diagrams stand as a useful tool in assessing and visualizing materials’ electrochemical stability and are widely used for electrocatalyst design. However, their reliability hinges on the accuracy of the chemical potentials of involved phases, which may bear uncertainties and can be significantly impacted by decision-making steps in the computational protocol. Here, this study introduces a robust sensitivity analysis framework, exemplified through a detailed examination of the computational Pourbaix diagram of Ni, the oxides of which are used as high-activity and cost-friendly catalysts for many electrochemical reactions. Quantities of interest derived from the Pourbaix diagram include the appearance and stability domain of the catalytically active Ni oxide phases along with the onset electrochemical potentials of phase transitions. These metrics can guide the design of operational conditions for Ni oxide electrocatalysts. We find that the employed DFT exchange-correlation functional has the most significant influence on the computed Pourbaix diagram. Uncertainties on crystal structures, along with their related ab initio energetics, are also found to affect the size of the phase stability domain. Higher-order coupling among input parameters is found to play a crucial role in influencing the appearance and distribution of Ni phases in the diagram. Our findings suggest a need to consider variations and uncertainties associated with the computational procedures on predicted Pourbaix diagrams for materials design.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Pathway to High Rate Capability in Interconnected Composite Electrolytes: A Case Study with a Single-Ion-Conducting Polymer
In a three-dimensional interconnected polymer/ceramic composite electrolyte (3D composite), both the polymer and ceramic electrolyte phases are individually connected with a polymer-rich surface layer to provide conformal contact with the electrodes. This work investigates how the transference number of the polymer phase affects the electrochemical properties of the 3D composite. Here, we fabricate a 3D composite using a “single-ion” conducting polymer electrolyte (PE), Li 1+x+y Al x Ti 2–x Si y P 3–y O 12 (LICGC) ceramic, and compare its electrochemical properties with the neat polymer, and with a 3D composite made with a dual-ion-conducting PE (we reported previously). Our results reveal that changing the polymer phase from a dual-ion-conducting PE to a single-ion-conducting PE results in a 9-fold increase in the limiting current density, although the interfacial impedance between the polymer and LICGC ceramic remains high (and contributes significantly to the total impedance of the 3D composite). Further, the limiting current density of the 3D composite is dictated by the PE and minimally affected by the ceramic scaffold. The ceramic scaffold, however, helps to ease the concentration gradient buildup within the PE and moderately improves the overall transference number. The LICGC scaffold does not provide any additional Li dendrite resistance due to its high reactivity with Li.
25 ENERGY STORAGE↗
Catalysis in Extreme Field Environments: A Case Study of Strongly Ionized SiO 2 Nanoparticle Surfaces
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77 NANOSCIENCE AND NANOTECHNOLOGY↗
Toward Unified Autonomous Scattering Experiments: A Cross-Facility Case Study at ALS and PETRA III
Autonomous experiments rely on the integration of control, data acquisition, analysis, and decision-making frameworks. While such systems have been demonstrated at individual facilities, adapting them to additional instruments remains challenging due to differences in local infrastructure. We present a modular workflow that connects existing open-source tools for data access (Tiled), workflow orchestration (Prefect), analysis and visualization (pyFAI, Plotly Dash), and Gaussian-process-based adaptive sampling (gpCAM) into a unified framework for autonomous scattering experiments. The same configuration operates across two synchrotron beamlines (ALS 7.3.3 and PETRA III P03) with only minimal facility-specific adjustments, as shown in proof-of-concept demonstrations. This validates that a consistent design emphasizing modularity and shared interfaces can ease deployment across diverse experimental environments. The resulting framework provides a flexible foundation for extending autonomous control and analysis capabilities beyond a single beamline or instrument.
47 OTHER INSTRUMENTATION↗
The Effect of Hydrothermal Alteration and Microcracks on Hydraulic Properties and Poroelastic Deformation: A Case Study of the Blue Mountain Geothermal Field
Abstract Geothermal energy plays a vital role in decarbonizing electricity and heat supply. Effective utilization of geothermal resources hinges on identifying or generating permeable reservoir zones and understanding how effective pressure variations affect fluid circulation and reservoir properties by poroelastic deformation. Hydrothermal alteration can modify the petrophysical properties of geothermal reservoir rocks, which may increase or decrease its productivity. Understanding these alteration effects is essential to predict and optimize long‐term sustainable geothermal operations. Here, we investigate the impact of hydrothermal alteration on poroelastic and hydraulic properties of diverse lithologies in a series of deformation tests performed at several confining (0–80 MPa) and pore pressure (10–30 MPa) levels. Experimental results of hydrothermally altered dikes and phyllites obtained from the Blue Mountain geothermal field (Nevada, USA) are compared to thermally cracked La Peyratte granite (France) and correlated with petrophysical properties, mineral composition, and microstructures. Argillic alteration of dikes increases porosity and storage capacity but lowers thermal conductivity and increases pore compressibility. Conversely, silicate precipitation in phyllites increases stiffness and thermal conductivity but also reduces porosity and permeability. Experimentally determined effective pressure coefficients range from 0.1 to 0.9, differ for permeability and volumetric strain and decrease with increasing effective pressure. The presence of compliant microcracks and crack‐like pores significantly increases the stress sensitivity of La Peyratte granite and silicified phyllites. This study demonstrates how thermal and chemical alteration impacts poromechanical and petrophysical characteristics of geothermal targets, which ultimately govern reservoir stability and subsidence, induced seismicity as well as fluid and heat extraction efficiency during geothermal operations.
Schuster, Valerian [Helmholtz Centre Potsdam GFZ G↗
Quantifying the Resolution Sensitivity of the Kain–Fritsch Scheme Across the Gray Zone by Isolating Interactions: A TWP‐ICE Case Study
The resolution sensitivity of the Kain–Fritsch (KF) convection scheme and the role of interactions between the physics and dynamics within the gray zone (<10 km) were investigated using the Separate Physics and Dynamics Experiment (SPADE) framework. Two groups of experiments were conducted using the Weather Research and Forecasting (WRF) model via traditional (Tradition) runs and SPADE runs with resolutions of 1, 2, 4, and 8 km during the wet period of the Tropical Warm Pool–International Cloud Experiment (TWP‐ICE). Results show that the KF scheme simulates the weakened convective processes well as the resolution increases in both groups, and the changes in the convective variables with resolution in SPADE are smaller than in the Tradition group. This indicates the important effects of interactions between model components on convection parameterizations as the resolution changes. Additionally, the microphysics variables remain nearly unchanged with resolution in SPADE and weaken slightly in Tradition as the resolution decreases, suggesting the relatively weaker influences of model interactions for the resolved‐cloud parameterization. Therefore, the scale‐aware behavior of KF scheme is further strengthened in Tradition runs, primarily through inhibiting the strength of stratiform processes through physics–dynamics interactions and physical components.
54 ENVIRONMENTAL SCIENCES↗
Sensitivity of Regional WRF‐Chem Air Quality and Weather Simulations to Biomass‐Burning Emission Data Sets: A Case Study of the Impact of Canadian Wildfire on the US°
This study focuses on the period from June 26 to 29, 2023, when record‐breaking Canadian wildfires severely impacted air quality in the Midwest United States. Using the Weather Research and Forecasting Model with Chemistry (WRF‐Chem) and four biomass‐burning data sets (Fire Inventory from NCAR version 1, Fire Inventory from NCAR version 2.5, Quick Fire Emissions Data set [QFED], and Regional ABI‐VIIRS Emission), we analyzed aerosol transport from Canada to the US and assessed the model's accuracy in predicting PM 2.5 , O 3 , CO and aerosol weather feedback. Model simulations were compared with ground‐based and remote sensing observations as well as field measurements from the Community Research on Climate and Urban Science (CROCUS) project. Our findings show that the movement of a low‐pressure system from the Great Lakes to the Atlantic, combined with the high‐pressure system over the Atlantic, caused the transport of aerosols from Canadian wildfires to the US. Results show WRF‐Chem significantly underestimated key atmospheric components: aerosol optical depth (AOD) by over 50%, PM 2.5 by 65%–90% and peak O 3 concentrations by 50%–55% across four biomass burning data sets. Additionally, CO and NO 2 concentrations were underpredicted. The substantial underestimation of PM 2.5 led to an overestimation of temperature by up to 3.6 °C primarily due to excessive downward shortwave radiation, which resulted from the underestimation of direct aerosol effects and an increase in sensible heat flux. Among the biomass‐burning data sets, QFED produced the most accurate AOD and PM 2.5 predictions due to improved wildfire emission estimates, leading to a 1.0 to 1.5 °C reduction in temperature overestimation during the daytime. These findings underscore the need for improving wildfire emission estimates for trace gases and aerosols to enhance air quality and weather feedback predictions.
WRF-chem model↗
Neural network potentials with effective charge separation for non-equilibrium dynamics of ionic solids: a ZnO case study
Developing neural network potentials (NNPs) accurate under non-equilibrium dynamics is challenging, as such systems require extensive sampling beyond equilibrium phases. Here we construct high-fidelity NNPs for zinc oxide (ZnO), a polymorphic ionic solid, using density functional theory (DFT) reference data. To efficiently capture transitional configurations, we combine enhanced-sampling molecular dynamics with empirical potentials, data distillation, and pretraining on short-range atomic energies (A-Train), followed by transfer learning with DFT-relabeled datasets. This hierarchical approach improves transferability across polymorphs and stress states. We further introduce effective charge separation, treating long-range Coulombic terms analytically while short-range residual interactions are learned by the NNP. The optimal effective charges fall in the range 0.5–1.0 q e , consistent with dielectric-screened values derived from formal charges but distinct from Bader estimates. Motivated by this observation, we propose a simple data-driven protocol in which effective charges are optimized by comparing DFT reference energies with explicit Coulomb calculations, without additional NNP training. This strategy improves accuracy and transferability in DFT-level predictions of energies, forces, and stress. Together, these results provide a practical charge-selection framework for robust NNP development in ionic solids, enabling reliable simulation of polymorphic phase transformations and non-equilibrium dynamics.
Chemistry↗
Case study on climate change effects and food security in Southeast Asia
Agriculture, a cornerstone of human civilization, faces rising challenges from climate change, resource limitations, and stagnating yields. Precise crop production forecasts are crucial for shaping trade policies, development strategies, and humanitarian initiatives. This study introduces a comprehensive machine learning framework designed to predict crop production. We leverage CMIP5 climate projections under a moderate carbon emission scenario to evaluate the future suitability of agricultural lands and incorporate climatic data, historical agricultural trends, and fertilizer usage to project yield changes. Our integrated approach forecasts significant regional variations in crop production across Southeast Asia by 2028, identifying potential cropland utilization. Specifically, the cropland area in Indonesia, Malaysia, Philippines, and Viet Nam is projected to decline by more than 10% if no action is taken, and there is potential to mitigate that loss. Moreover, rice production is projected to decline by 19% in Viet Nam and 7% in Thailand, while the Philippines may see a 5% increase compared to 2021 levels. Our findings underscore the critical impacts of climate change and human activities on agricultural productivity, offering essential insights for policy-making and fostering international cooperation.
54 ENVIRONMENTAL SCIENCES↗
Best practices for methylome characterization in novel species: a case study in the microalgae Microchloropsis
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59 BASIC BIOLOGICAL SCIENCES↗