Deciphering Dynamic Structural and Mechanistic Complexity in Cu/CeO2/ZSM-5 Catalysts for the Reverse Water-Gas Shift Reaction
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99 GENERAL AND MISCELLANEOUS↗
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Discovery of SARS-CoV-2 Papain-like Protease Inhibitors through a Combination of High-Throughput Screening and a FlipGFP-Based Reporter Assay
The papain-like protease (PL pro ) of SARS-CoV-2 is a validated antiviral drug target. Through a fluorescence resonance energy transfer-based high-throughput screening and subsequent lead optimization, we identified several PL pro inhibitors including Jun9-72-2 and Jun9-75-4 with improved enzymatic inhibition and antiviral activity compared to GRL0617, which was reported as a SARS-CoV PL pro inhibitor. Significantly, we developed a cell-based FlipGFP assay that can be applied to predict the cellular antiviral activity of PL pro inhibitors in the BSL-2 setting. X-ray crystal structure of PL pro in complex with GRL0617 showed that binding of GRL0617 to SARS-CoV-2 induced a conformational change in the BL2 loop to a more closed conformation. Molecular dynamics simulations showed that Jun9-72-2 and Jun9-75-4 engaged in more extensive interactions than GRL0617. Overall, the PL pro inhibitors identified in this study represent promising candidates for further development as SARS-CoV-2 antivirals, and the FlipGFP-PL pro assay is a suitable surrogate for screening PL pro inhibitors in the BSL-2 setting.
60 APPLIED LIFE SCIENCES↗
Generalized representative structures for atomistic systems
A new method is presented to generate atomic structures that reproduce the essential characteristics of arbitrary material systems, phases, or ensembles. Previous methods allow one to reproduce the essential characteristics (e.g. the chemical disorder) of a large random alloy within a small crystal structure. The ability to generate small representations of random alloys, along with the restriction to crystal systems, results from using the fixed-lattice cluster correlations to describe structural characteristics. A more general description of the structural characteristics of atomic systems is obtained using complete sets of atomic environment descriptors. These are used within for generating representative atomic structures without restriction to fixed lattices. A general data-driven approach is provided here utilizing the atomic cluster expansion (ACE) basis. The N-body ACE descriptors are a complete set of atomic environment descriptors that span both chemical and spatial degrees of freedom and are used within for describing atomic structures. The generalized representative structure (GRS) method presented within generates small atomic structures that reproduce ACE descriptor distributions corresponding to arbitrary structural and chemical complexity. It is shown that systematically improvable representations of crystalline systems on fixed parent lattices, amorphous materials, liquids, and ensembles of atomic structures may be produced efficiently through optimization algorithms. With the GRS method, we highlight reduced representations of atomistic machine-learning training datasets that contain similar amounts of information and small 40–72 atom representations of liquid phases. The ability to use GRS methodology as a driver for informed novel structure generation is also demonstrated. The advantages over other data-driven methods and state-of-the-art methods restricted to high-symmetry systems are highlighted.
atomic cluster expansion↗
Pose Classification Using Three-Dimensional Atomic Structure-Based Neural Networks Applied to Ion Channel–Ligand Docking
The identification of promising lead compounds showing pharmacological activities toward a biological target is essential in early stage drug discovery. With the recent increase in available small-molecule databases, virtual high-throughput screening using physics-based molecular docking has emerged as an essential tool in assisting fast and cost-efficient lead discovery and optimization. However, the best scored docking poses are often suboptimal, resulting in incorrect screening and chemical property calculation. We address the pose classification problem by leveraging data-driven machine learning approaches to identify correct docking poses from AutoDock Vina and Glide screens. To enable effective classification of docking poses, we present two convolutional neural network approaches: a three-dimensional convolutional neural network (3D-CNN) and an attention-based point cloud network (PCN) trained on the PDBbind refined set. We demonstrate the effectiveness of our proposed classifiers on multiple evaluation data sets including the standard PDBbind CASF-2016 benchmark data set and various compound libraries with structurally different protein targets including an ion channel data set extracted from Protein Data Bank (PDB) and an in-house KCa3.1 inhibitor data set. Our experiments show that excluding false positive docking poses using the proposed classifiers improves virtual high-throughput screening to identify novel molecules against each target protein compared to the initial screen based on the docking scores.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Bloom filter de-identifier
A bloom filter is a binary data structure that is designed to be memory efficient and able to determine whether an element is present in a set. The bloom filter is a probabilistic data structure. It can tell you whether an element, or set of elements, is likely to exist within a set. It can also tell you whether an element, or set of elements, does not exist within a set. So false positives are probable, but false negatives are not. Our novel approach utilizes the bloom filter to determine how many bigrams (two letter sequence) each value has in common. The resulting metric approximates the relative similarity of two text values.
Bleeker, Amelia↗
Structural Analysis Report for Sandia High Altitude Aerosol Research (SHAAR) Payloads
Sandia National Laboratories has interest in mounting enclosures to gather scientific data aboard NASA scientific balloons. This report documents the structural integrity of three separate payloads considered ‘piggybacks.’ To date, there are no design criteria for piggybacks, therefore each piggyback shall follow the same design requirements set by NASA per the Gondola Structural Design Requirements. This analysis report shall describe how each payload meets the design requirements laid out in the Gondola Design Requirements.
47 OTHER INSTRUMENTATION↗
Toward Drilling the Perfect Geothermal Well: An International Research Coordination Network for Geothermal Drilling Optimization Supported by Deep Machine Learning and Cloud Based Data Aggregation
The EDGE project, supported by the U.S. Department of Energy Geothermal Technologies Office under award DE-EE0008793, established a data-driven framework for improving the efficiency, cost-effectiveness, and reliability of geothermal well drilling. The project focused on developing scalable data infrastructure, advanced machine learning and probabilistic models, and integrated analytics tools to support continuous drilling optimization. A central objective was to reduce geothermal drilling costs by up to seventy percent while minimizing the risk of well failure through predictive diagnostics and adaptive planning. Over the project period, a comprehensive data repository was designed and deployed, incorporating records from over one hundred geothermal wells across varied geological settings. This repository supported both structured and unstructured data and adhered to FAIR data principles, enabling provenance tracking, quality control, and standardized metadata. The project introduced automated ingestion pipelines and a cloud-hosted platform that facilitated access to raw, processed, and derived datasets. This infrastructure served as the foundation for model development and analysis. Machine learning workflows were developed to predict key drilling metrics including rate of penetration, non-productive time, and total drilling costs. Self-organizing maps and dimensionality reduction methods were used to uncover operational patterns and outliers, while supervised learning algorithms such as random forests and deep neural networks were applied to forecast performance outcomes. The models were validated on heterogeneous datasets from both U.S. and Icelandic fields, demonstrating variable but significant predictive accuracy. The results indicated that finer temporal resolution, inclusion of lithological data, and consistency in operational annotations could substantially improve model performance. The project also implemented process mining techniques to reconstruct state-transition models from drilling event logs. These models enabled the identification of deviations from optimal workflows and provided insights into recurring failure modes. Analysis of non-productive time highlighted the impact of equipment failures, geological challenges, and human factors, offering opportunities for targeted mitigation strategies. The EDGE Dashboard was developed as a web-based expert system integrating data visualization, model outputs, and user-driven queries. It provided an accessible interface for operators to explore historical data, evaluate predicted outcomes, and compare drilling scenarios. Initial feedback from project partners suggested that the dashboard could serve as a foundation for more advanced advisory and optimization tools. Overall, the EDGE project demonstrated the feasibility and value of applying modern data science techniques to geothermal drilling. It delivered a set of interoperable tools and models that can support more efficient, lower-risk well development. The findings point toward a viable path for transitioning from advisory analytics to semi-autonomous drilling systems, contingent on continued collaboration, expanded datasets, and field validation. The project results have immediate relevance for drilling operations, data management practices, and future geothermal R&D efforts aimed at achieving reliable, cost-competitive geothermal energy at scale.
15 GEOTHERMAL ENERGY↗
Molecular-dynamics simulation methods for macromolecular crystallography
It is investigated whether molecular-dynamics (MD) simulations can be used to enhance macromolecular crystallography (MX) studies. Historically, protein crystal structures have been described using a single set of atomic coordinates. Because conformational variation is important for protein function, researchers now often build models that contain multiple structures. Methods for building such models can fail, however, in regions where the crystallographic density is difficult to interpret, for example at the protein–solvent interface. To address this limitation, a set of MD–MX methods that combine MD simulations of protein crystals with conventional modeling and refinement tools have been developed. In an application to a cyclic adenosine monophosphate-dependent protein kinase at room temperature, the procedure improved the interpretation of ambiguous density, yielding an alternative water model and a revised protein model including multiple conformations. The revised model provides mechanistic insights into the catalytic and regulatory interactions of the enzyme. The same methods may be used in other MX studies to seek mechanistic insights.
59 BASIC BIOLOGICAL SCIENCES↗
PersGNN: Applying Topological Data Analysis and Geometric Deep Learning to Structure-Based Protein Function Prediction
Understanding protein structure-function relationships is a key challenge in computational biology, with applications across the biotechnology and pharmaceutical industries. While it is known that protein structure directly impacts protein function, many functional prediction tasks use only protein sequence. In this work, we isolate protein structure to make functional annotations for proteins in the Protein Data Bank in order to study the expressiveness of different structure-based prediction schemes. We present PersGNN - an end-to-end trainable deep learning model that combines graph representation learning with topological data analysis to capture a complex set of both local and global structural features. While variations of these techniques have been successfully applied to proteins before, we demonstrate that our hybridized approach, PersGNN, outperforms either method on its own as well as a baseline neural network that learns from the same information. PersGNN achieves a 9.3% boost in area under the precision recall curve (AUPR) compared to the best individual model, as well as high F1 scores across different gene ontology categories, indicating the transferability of this approach.
Swenson, Nicolas↗
A D-term Modeling Code (DMC) for Simultaneous Calibration and Full-Stokes Imaging of Very Long Baseline Interferometric Data
In this paper we present DMC, a model and associated tool for polarimetric imaging of very long baseline interferometry data sets that simultaneously reconstructs the full-Stokes emission structure along with the station-based gain and leakage calibration terms. DMC formulates the imaging problem in terms of posterior exploration, which is achieved using Hamiltonian Monte Carlo sampling. The resulting posterior distribution provides a natural quantification of uncertainty in both the image structure and the data calibration. We run DMC on both synthetic and real data sets, the results of which demonstrate its ability to accurately recover both the image structure and calibration quantities, as well as to assess their corresponding uncertainties. The framework underpinning DMC is flexible, and its specific implementation is under continued development.
47 OTHER INSTRUMENTATION↗
Shape restricted additive hazards models: Monotone, unimodal, and U‐shape hazard functions
We consider estimation of the semiparametric additive hazards model with an unspecified baseline hazard function where the effect of a continuous covariate has a specific shape but otherwise unspecified. Such estimation is particularly useful for a unimodal hazard function, where the hazard is monotone increasing and monotone decreasing with an unknown mode. A popular approach of the proportional hazards model is limited in such setting due to the complicated structure of the partial likelihood. Our model defines a quadratic loss function, and its simple structure allows a global Hessian matrix that does not involve parameters. Thus, once the global Hessian matrix is computed, a standard quadratic programming method can be applicable by profiling all possible locations of the mode. However, the quadratic programming method may be inefficient to handle a large global Hessian matrix in the profiling algorithm due to a large dimensionality, where the dimension of the global Hessian matrix and number of hypothetical modes are the same order as the sample size. We propose the quadratic pool adjacent violators algorithm to reduce computational costs. The proposed algorithm is extended to the model with a time‐dependent covariate with monotone or U‐shape hazard function. In simulation studies, our proposed method improves computational speed compared to the quadratic programming method, with bias and mean square error reductions. We analyze data from a recent cardiovascular study.
Mathematical & Computational Biology↗
Smectite phase separation is driven by hydration-mediated interfacial charge
Smectite clay minerals have an outsize impact on the response of clay-rich media to common stimuli, such as hydration and ion exchange, motivating extensive effort to understand behaviors resulting from these processes such as swelling and exfoliation. Smectites are common and historic systems for investigating colloidal and interfacial phenomena, with two swelling regimes commonly identified across myriad clays: osmotic swelling at high water activity and crystalline swelling at low water activity. However, no current swelling model seamlessly spans the full ranges of water, salt and clay content encountered in natural or engineered settings. Here, we show that structures previously rationalized as either osmotic or crystalline coexist as a rich array of distinct colloidal phases that differ by water content, layer stacking thickness, and curvature. We present an analytical model for intermolecular potentials among water, salt and clay in both mono- and divalent electrolytes that predicts swelling pressures across high and low water activities. Our results indicate that all clay swelling is osmotic swelling, but that the osmotic pressure of charged mineral interfaces becomes attractive and dominates that of the electrolyte at high clay activities. Global energy minima are often not reached on experimental timescales due to many local energy minima that promote long-lived intermediate states with vast differences in clay, ion, and water mobilities, leading to hyperdiffusive layer dynamics driven by variable hydration-mediated interfacial charge.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
New precious metal containing normal spinels: LiRhRu 1-x Ir x O 4 , LiFeIr 1-x Ru x O 4 , and LiCoIr 1-x Ru x O 4
Large spin-orbit-coupled cations in geometrically frustrated crystal structures have the most suitable setting for exploring novel exotic states of matter. Spinel oxides (AM 2 O 4 ) are well-known examples of geometrically frustrated systems. In this study, we report for the first time the synthesis of compositions LiRhRu 1-x Ir x O 4 (x = 0–0.5), LiFeIr 1-x Ru x O 4 (x = 0–0.5), and LiCoIr 1-x Ru x O 4 (x = 0–0.3) containing precious metal cations on edge-sharing octahedral M-sites, and systematically investigate their magnetic and electrical properties. 57 Fe Mössbauer spectroscopy revealed that iron is trivalent in all LiFeIr 1-x Ru x O 4 solid solutions. Magnetic measurements indicate deviations from theoretical spin-only magnetic moment values, indicating the influence of spin-orbit coupling owing to the presence of 4d and 5d block elements. The LiFeIr 1-x Ru x O 4 series shows spin-glass-like freezing behavior with T g ≈ 20 K, and a small frustration index (f ≈ 1-2), indicating that the frustration originates from site disorder. LiRhRu 1-x Ir x O 4 and LiCoIr 1-x Ru x O 4 exhibit strongly geometrically frustrated magnetism. Electrical resistivity measurements as a function of temperature indicate that all phases are semiconducting. Seebeck coefficient measurements show that LiRhRu 1-x Ir x O 4 and LiFeIr 1-x Ru x O 4 are p-type semiconductors with holes as the major charge carriers. A sign reversal of the Seebeck coefficient indicates both holes and electrons as carriers for LiCoIr 1-x RuxO 4 (x = 0–0.2), but only holes as major carriers for x = 0.3. Here, the Seebeck coefficient and power factor increase drastically in the LiRhRu 1-x Ir x O 4 solid solution with Ir substitution, reaching a maximum of ≈ +125 μV/K and ≈2.3×10 -6 W/mK 2 at ∼650 K for x = 0.5.
Charge carriers↗
Biosensor Guided Polyketide Synthases Engineering for Optimization of Domain Exchange Boundaries
Type I modular polyketide synthases (PKSs) are multi-domain enzymes functioning like assembly lines. Many engineering attempts have been made for the last three decades to replace, delete and insert new functional domains into PKSs to produce novel molecules. However, inserting heterologous domains often destabilize PKSs, causing loss of activity and protein misfolding. To address this challenge, here we develop a fluorescence-based solubility biosensor that can quickly identify engineered PKSs variants with minimal structural disruptions. Using this biosensor, we screen a library of acyltransferase (AT)-exchanged PKS hybrids with randomly assigned domain boundaries, and we identify variants that maintain wild type production levels. We then probe each position in the AT linker region to determine how domain boundaries influence structural integrity and identify a set of optimized domain boundaries. Overall, we have successfully developed an experimentally validated, high-throughput method for making hybrid PKSs that produce novel molecules.
59 BASIC BIOLOGICAL SCIENCES↗
A nanoporous capacitive electrochemical ratchet for continuous ion separations
Directed ion transport in liquid electrolyte solutions underlies many phenomena in natural and industrial settings. While nature has evolved structures that drive continuous ion flow without Faradaic redox reactions, establishing this process in synthetic systems has been challenging. Here, in this study, we report an ion pump that drives aqueous ions against a force using a capacitive ratchet mechanism independent of redox reactions. Modulation of an electric potential between thin metallic layers on either face of a nanoporous alumina wafer immersed in solution results in persistent voltages and ionic currents. This occurs due to the nonlinear capacitive nature of electric double layers, whose repeated charging and discharging sustains a continuous ion flux. Using this approach, we demonstrate ratchet-driven electrodialysis that reaches a 50% decrease in the conductivity of the solution in a dilution cell. These ratchet-based ion pumps can enable continuous desalination and selective ion separation using an electrically powered device with no moving parts.
Kautz, Rylan [University of California, Irvine, CA↗
Observation of a promethium complex in solution
Lanthanide rare-earth metals are ubiquitous in modern technologies, but we know little about chemistry of the 61st element, promethium (Pm), a lanthanide that is highly radioactive and inaccessible. Despite its importance, Pm has been conspicuously absent from the experimental studies of lanthanides, impeding our full comprehension of the so-called lanthanide contraction phenomenon: a fundamental aspect of the periodic table that is quoted in general chemistry textbooks. Here we demonstrate a stable chelation of the 147 Pm radionuclide (half-life of 2.62 years) in aqueous solution by the newly synthesized organic diglycolamide ligand. The resulting homoleptic Pm III complex is studied using synchrotron X-ray absorption spectroscopy and quantum chemical calculations to establish the coordination structure and a bond distance of promethium. These fundamental insights allow a complete structural investigation of a full set of isostructural lanthanide complexes, ultimately capturing the lanthanide contraction in solution solely on the basis of experimental observations. Our results show accelerated shortening of bonds at the beginning of the lanthanide series, which can be correlated to the separation trends shown by diglycolamides. The characterization of the radioactive Pm III complex in an aqueous environment deepens our understanding of intra-lanthanide behaviour and the chemistry and separation of the f-block elements.
38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
AI-accelerated protein-ligand docking for SARS-CoV-2 is 100-fold faster with no significant change in detection
Protein-ligand docking is a computational method for identifying drug leads. The method is capable of narrowing a vast library of compounds down to a tractable size for downstream simulation or experimental testing and is widely used in drug discovery. While there has been progress in accelerating scoring of compounds with artificial intelligence, few works have bridged these successes back to the virtual screening community in terms of utility and forward-looking development. We demonstrate the power of high-speed ML models by scoring 1 billion molecules in under a day (50 k predictions per GPU seconds). We showcase a workflow for docking utilizing surrogate AI-based models as a pre-filter to a standard docking workflow. Our workflow is ten times faster at screening a library of compounds than the standard technique, with an error rate less than 0.01% of detecting the underlying best scoring 0.1% of compounds. Our analysis of the speedup explains that another order of magnitude speedup must come from model accuracy rather than computing speed. In order to drive another order of magnitude of acceleration, we share a benchmark dataset consisting of 200 million 3D complex structures and 2D structure scores across a consistent set of 13 million “in-stock” molecules over 15 receptors, or binding sites, across the SARS-CoV-2 proteome. We believe this is strong evidence for the community to begin focusing on improving the accuracy of surrogate models to improve the ability to screen massive compound libraries 100 × or even 1000 × faster than current techniques and reduce missing top hits. The technique outlined aims to be a fast drop-in replacement for docking for screening billion-scale molecular libraries.
59 BASIC BIOLOGICAL SCIENCES↗
Explainable machine learning for incipient anomaly detection in compact molten salt heat exchanger with overlapping feature distributions
High-temperature molten salt-cooled reactors (MSCRs) are a promising next-generation nuclear technology option, offering efficient power conversion and inherent safety features. However, the reliability of these systems depends on the robust operation of heat exchangers (HXs), which are susceptible to failure due to temperature gradients and channel plugging caused by fluid freezing. Conventional monitoring methods, relying on inlet and outlet measurements, lack the spatial resolution needed to detect early-stage faults. We propose a novel design of a compact salt-to-salt matrix-type HX design consisting of interleaved arrays of parallel tubes, with integrated synthetic fiber optic distributed temperature sensing (DTS) to enable localized detection of incipient faults. To evaluate performance of this design, we generate high-fidelity synthetic data using heat transfer computational modeling to simulate channel plugging, and introduce sensor noise for realistic modeling of measurements. The dataset comprises of 97% normal operation and 3% anomaly cases, with each anomaly class representing 1% of the data. These early anomalies result in overlapping temperature profiles between normal and faulty channels, producing a non-separable dataset that challenges traditional classification techniques. We benchmark eight supervised machine learning (ML) models and demonstrate that XGBoost achieves the highest performance. To improve transparency, we develop an explainability framework combining Shapley values and partially ordered sets (POSETs) to quantify and structurally analyze feature importance. This approach identifies both dominant predictors and ambiguous feature relationships, enhancing trust and interpretability. Our results highlight the potential of combining DTS and explainable ML with intelligent feature selection to improve predictive maintenance and ensure operational resilience in advanced nuclear systems.
Prantikos, Konstantinos [Argonne National Laborato↗