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At least 1,045 records · Page 58

Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV-2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations

Starting from our previous finding of 14 known drugs as inhibitors of the main protease (M pro ) of SARS-CoV-2, the virus responsible for COVID-19, we have redesigned the weak hit perampanel to yield multiple noncovalent, nonpeptidic inhibitors with ca. 20 nM IC 50 values in a kinetic assay. Free-energy perturbation (FEP) calculations for M pro -ligand complexes provided valuable guidance on beneficial modifications that rapidly delivered the potent analogues. The design efforts were confirmed and augmented by determination of high-resolution X-ray crystal structures for five analogues bound to M pro . Results of cell-based antiviral assays further demonstrated the potential of the compounds for treatment of COVID-19. In addition to the possible therapeutic significance, the work clearly demonstrates the power of computational chemistry for drug discovery, especially FEP-guided lead optimization.

99 GENERAL AND MISCELLANEOUS↗

Dynamical Large Deviations of Two-Dimensional Kinetically Constrained Models Using a Neural-Network State Ansatz

We use a neural-network ansatz originally designed for the variational optimization of quantum systems to study dynamical large deviations in classical ones. We use recurrent neural networks to describe the large deviations of the dynamical activity of model glasses, kinetically constrained models in two dimensions. We present the first finite size-scaling analysis of the large-deviation functions of the two-dimensional Fredrickson-Andersen model, and explore the spatial structure of the high-activity sector of the South-or-East model. These results provide a new route to the study of dynamical large-deviation functions, and highlight the broad applicability of the neural-network state ansatz across domains in physics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Monolithically Integrated $\varepsilon$-Ge/In x Ga 1-x As Quantum Well Laser Design: Experimental and Theoretical Investigation

Here, we have analyzed the electrical and optical phenomenon occurring in a $\varepsilon$-Ge/In x Ga 1-x -Ge/In x Ga 1-x As quantum well (QW) laser through self-consistent physical solvers calibrated using in-house experimental results. A separate confinement heterostructure QW design is proposed to enable lasing from tensile strained germanium ($\varepsilon$-Ge/In x Ga 1-x -Ge) in the range of 1.55 um to 4 um wavelengths as a function of QW thickness and indium (In) composition. Different recombination mechanisms were analyzed as a function of tensile strain in $\varepsilon$-Ge/In x Ga 1-x -Ge QW. Minority carrier lifetime and band alignment are key attributes of a QW laser, which were measured using microwave photoconductive decay and x-ray photoelectron spectroscopy (as a function of In composition), respectively. The transition point of Ge to a direct bandgap material is re-affirmed to be at $\varepsilon$-Ge/In x Ga 1-x = 1.6% (In ~24%) and the transition from type I to type II for $\varepsilon$-Ge/In x Ga 1-x -Ge/In x Ga 1-x As QW is found to be at In ~55%. Also, the transition to a TM mode dominant laser is identified at In ~15%. Using a tunable waveguide design to optimize confinement as a function of In composition, strain, wavelength, QW thickness, refractive index, and geometry, the $\varepsilon$-Ge/In x Ga 1-x -Ge QW laser design provided a net material gain of ~2000 cm -1 and a threshold current density of ~5 kA/cm 2 , which is an improvement over existing Ge based lasers. In conclusion, the impact of In composition and QW thickness on the band structure, polarized gain spectra, and various lasing metrics were analyzed to show $\varepsilon$-Ge/In x Ga 1-x -Ge/InGaAs QW lasers as promising for integrated photonics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

PVDeg: Enhancing Usability and AI-Driven Multi-Mechanism Degradation Modeling

PVDeg version 0.7.0, released in December 2025, introduced major enhancements to improve usability and performance. This update reorganized tutorials and tool notebooks to create a more intuitive experience, enabling users to easily follow and adapt workflows for their specific analyses. In addition to structural improvements, both the notebooks and core logic underwent significant optimization for efficiency, robustness, and style. These refinements were supported by new testing frameworks built on nbval and pytest, adherence to PEP8 standards, and extensive code refactoring, which collectively simplify onboarding for new developers. Looking ahead, version 0.8.0 will deliver advanced AI-driven capabilities. The primary focus is to further develop and automate the degradation workflow, designed to analyze PV module degradation across diverse locations and system configurations. By integrating large language models (LLMs) to scan literature and compile a comprehensive database of materials and degradation rates, this feature will enable modeling of multiple materials and mechanisms within a single, streamlined workflow. Users will be able to evaluate degradation impacts on different system architectures under varying environmental conditions, facilitating informed decisions on bill-of-materials optimization for specific deployment scenarios. These advancements position PVDeg as a powerful, user-friendly tool for accelerating PV reliability research and system design.

14 SOLAR ENERGY↗

Assessment and Performance of Flexible Quench Antenna Array Diagnostics for Superconducting Magnets

FNAL has been developing multiple versions of flexible quench antennas (flex-QA), including some specially optimized for high sensitivity and/or high resolution, to characterize quench events and transients during current ramping in superconducting magnets. A fundamental feature in our use of these is the creation of grid-like structures of sensitive elements to cover coil surfaces, with the aim of getting precise localization of magnetic flux-change events. The flex-QA are coupled with fast data-acquisition, allowing comprehensive analysis of signals at the relevant fine time scales. In addition to arrays of various flex-QA types being used during cryogenic testing of superconducting magnets, we also are utilizing a newly developed room temperature test stand to better understand QA response characteristics. The data from actual superconducting magnet tests, warm test stand measurements, and simulation data on the same QA designs allows us to draw conclusions on operational feasibility and plan better for improvements of our sensors. In this paper we present data from the multiple tests performed and analysis results. Flex-QA designs are compared, and their features, options, and optimization discussed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

X-ray Diffraction Studies of Single-Crystal Materials for Broad Battery Applications

Single-crystal materials have attracted growing interest in battery research due to their well-defined crystallographic orientation, absence of grain boundaries, and enhanced mechanical and electrochemical stability. This Review provides a comprehensive overview of recent advances in the synthesis, structural evolution, and performance optimization of single-crystal electrodes and solid electrolytes. Particular focus is placed on the application of advanced X-ray diffraction (XRD) techniques, including operando synchrotron diffraction, reciprocal space mapping, and Bragg coherent diffraction imaging, which have enabled in-depth investigations of lattice strain, cation disorder, phase transitions, and defect formation. Representative case studies across Ni-rich layered oxides, spinel-type cathodes, and garnet-based electrolytes are examined to highlight the structural features unique to single crystals. Additionally, the synergistic integration of XRD with machine learning, tomography, and spectroscopy is discussed as a powerful direction for real-time analysis and predictive modeling. Furthermore, these insights provide critical guidance for the rational design of high-performance single-crystal materials in lithium, sodium, and solid-state battery systems.

25 ENERGY STORAGE↗

Deep Learning Coordinate-Free Quantum Chemistry

Computing quantum chemical properties of small molecules and polymers can provide insights valuable to physicists, chemists and biologists when designing new materials, catalysts, biological probes and drugs. Deep learning can compute quantum chemical properties accurately in a fraction of the time required by commonly used methods such as density functional theory (DFT). However, many of these deep learning architectures require energy minimized molecular geometries as input, which is also computationally expensive, and decreasing the reproducibility and throughput of these methods. In this study, we demonstrate that accurate quantum chemical computations can be performed without optimized geometries by operating in the coordinate-free domain using deep learning on graph encodings. Furthermore, we also find that the choice of graph-encoding architecture substantially affects the performance of these methods. The Wave architecture outperforms graph convolution architectures, particularly on complex molecules. Furthermore, the structures of these graph encoding architectures provide an opportunity to probe an important, outstanding question in quantum mechanics: What types of quantum chemical properties can be represented by local-variable models? We find that Wave, a local-variable model, is more accurately calculates quantum chemical properties. Graph convolutional architectures require global variables, and are not as effective as as Wave. We anticipate that coordinate-free, deep-learning models of quantum chemistry will become valuable tools in chemistry and biology, enabling researchers to rapidly screen chemical databases or identify new molecules using automated, de-novo design algorithms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Robust Molecular Predictive Methods for Novel Polymer Discovery and Applications

Polymeric materials are ubiquitous in modern society and they play an instrumental role in almost all industries, undoubtedly including the energy and environment sectors. Increased demand of energy and awareness to sustainability both necessitates the development of novel polymers with enhanced properties. Unfortunately, their structural and behavioral complexity render such discovery challenging and impeded. To address this problem, scientists are developing various computational modeling techniques and leveraging their power to depict the relationship between structural characteristics of polymers and their properties (such as rheological behaviors), and use such prediction to guide the design and syntheses of novel polymeric materials with enhanced performances. Unfortunately, predicting the relationships between polymer structure and composition with rheological properties via atomistic modeling is still a major challenge because of the extended time and length scales involved. Studying dynamic shear viscosity and linear viscoelasticity using molecular models requires capabilities that have been elusive, including representation of large molecular weight chains with an effective internal scale capable of describing entanglement, shear-rates that are in the s-1 scale with accurate quantitative stresses, and chemically-realistic combinations of both homogeneous and heterogeneous systems. Motivated by these unmet challenges, the overall technical objective of this DOE-STTR Phase II project is to develop robust molecular predictive methods for advanced polymer discovery and applications and especially for designing and demonstrating the “smart” polymer-based waterflooding enhanced oil recovery (EOR) process. In particular, we apply state-of-the-art molecular modeling methods developed by our academic partner, Materials Stimulation Center (MSC) at California Institute of Technology (Caltech), to facilitate and accelerate the experimental discovery processes. During the Phase I of this project, we had focused on development and demonstration of the molecular modeling methods to describe rheological properties of non-Newtonian polymer fluids, and to improve our fundamental understandings of shear-thickening mechanism and kinetics. In Phase II, we further apply the theoretical models to guide our experimental programs to improve our design of smart rheology modifier (SRM) polymers and their optimization for EOR. Specifically, we have three objectives in the Phase II study: (1) to further improve out computational modeling methods, coupling with the advanced machine learning algorithms; (2) to develop cost-effective and efficient SRM-flooding process suitable for EOR applications under typical reservoir conditions; and (3) to further explore the application of our molecular predictive models for innovative material discovery in other industrial applications. The recent development of our multiscale predictive framework allows the successful prediction of rheological properties from the chemical structure for polymers of experimentally relevant molecular weights, and provides an in-silico machine learning engine for screening novel compositions and structures with optimized non-Newtonian response, required for both shear-thinning and shear-thickening applications. Our framework provides: (1) procedures and tools for systematic coarsening from atomistic models and reverse mapping of coarse-grain models to atomistic, (2) unique ab initio methods to characterize the atomistic origin of colloidal and interfacial interactions and phenomena, (3) systematic structure and composition builders based on practical descriptors that drive rheological changes in polymer melts and diluted polymer mixtures, (4) a rheological properties engine capable of predicting viscosity in the zero-shear limit and under realistic dynamic conditions (for shear-rates commensurate with experiments) for large heterogeneous systems, (5) coarse-grain force fields with improved non-bond descriptions based on accurate quantum mechanics, (6) an in-silico screening machine learning engine that feeds from the systematic model builders to cover the descriptors search space, computes the rheological properties from converged trajectories spanning sub-milliseconds and ranks them for each structure/composition using an automated viscosity-vs-shear rate fitness function that can be tuned for shear-thickening, shear-thinning and other rheological responses.

02 PETROLEUM↗

Portability for GPU-accelerated molecular docking applications for cloud and HPC: can portable compiler directives provide performance across all platforms?

High-throughput structure-based screening of drug-like molecules has become a common tool in biomedical research. Recently, acceleration with graphics processing units (GPUs) has provided a large performance boost for molecular docking programs. Both cloud and high-performance computing (HPC) resources have been used for large screens with molecular docking programs; while NVIDIA GPUs have dominated cloud and HPC resources, new vendors such as AMD and Intel are now entering the field, creating the problem of software portability across different GPUs. Ideally, software productivity could be maximized with portable programming models that are able to maintain high performance across architectures. While in many cases compiler directives have been used as an easy way to offload parallel regions of a CPU-based program to a GPU accelerator, they may also be an attractive programming model for providing portability across different GPU vendors, in which case the porting process may proceed in the reverse direction: from low-level, architecture-specific code to higher-level directive-based abstractions. MiniMDock is a new mini-application (miniapp) designed to capture the essential computational kernels found in molecular docking calculations, such as are used in phar-maceutical drug discovery efforts, in order to test different solutions for porting across GPU architectures. Here we extend MiniMDock to GPU offloading with OpenMP directives, and compare to performance of kernels using CUDA and HIP on NVIDIA and AMD GPUs, respectively, as well as across different compilers, exploring performance bottlenecks. We document this reverse-porting process, from highly optimized device code to a higher-level version using directives, compare code structure, and describe barriers that were overcome in this effort.

Thavappiragasam, Mathialakan↗

From atomistic models to machine learning: Predictive design of nanocarbons under extreme conditions

The formation of technologically valuable nanocarbon structures under extreme conditions, such as those produced during high-explosive detonations, remains poorly understood but holds significant potential for the development of controlled synthesis pathways. While detonation shockwaves provide the high-pressure, high-temperature environment required for nanodiamond formation, subsequent cooling and decompression dictate whether the diamond phase is preserved or transformed into other nanocarbon structures. Here, in this study, we employ GPU-accelerated reactive molecular dynamics (ReaxFF) simulations to investigate the graphitization and structural remodeling of detonation nanodiamond under nonlinear quench and pressure-release trajectories. We further investigate how the initial nanodiamond morphology; cuboctahedral, octahedral, or hexagonal prism influences the resulting transformation products. Evolution of nanostructure, allotrope (via simulated x-ray diffraction), carbon hybridization, and ring statistics are tracked during a two-stage quench from 5000 K to 60 GPa. Rapid cooling combined with slow decompression optimizes cubic diamond retention, whereas slow cooling with rapid pressure release promotes surface-to-core graphitization, producing concentric sp 2 -hybridized layers and hollowed inner shells. Octahedral nanodiamonds evolve into carbon nano-onions, initially forming bucky diamonds that progressively transform into fully sp 2 -hybridized structures, while hexagonal prisms preferentially form parallel-stacked graphite layers resembling carbon dots. Transient hexagonal diamond (lonsdaleite) emerges as an interfacial phase, suggesting potential reversibility in the shock-induced graphite-to-diamond transformation pathway transformation route. To extend predictive capabilities, we trained machine learning (ML) regressors on over 10 5 node-hours of molecular dynamics (MD) trajectories. A multilayer perceptron (MLP) model reliably predicts the number of graphitized layers from temperature–pressure trajectories with a coefficient of determination (R 2 ) exceeding 0.90. This high predictive fidelity enables efficient, high-throughput mapping of the synthesis parameter space for optimized graphitization outcomes. Collectively, morphological control combined with optimized quench–decompression conditions promote the selective synthesis of nanocarbon allotropes. This work establishes a data-driven framework for the rational, a priori design of carbon nanomaterials for applications in energy storage, sensing, and biomedicine.

Detonation nanodiamond remodeling↗

Topology Optimization of Manufacturable Photonic Crystals With Complete Bandgaps [Dissertation]

Periodic structures consisting of dielectric material, i.e. photonic crystals, are capable of prohibiting electromagnetic waves within frequency ranges referred to as bandgaps. This principle was first demonstrated with alternating slabs of material and later demonstrated with three-dimensional (3D) structures capable of reflecting waves from any incident angle. A number of potential applications for photonic bandgap structures exist, including loss-less sharp corner waveguides, fiber optics, and radome design. Further, many optical devices could benefit from the perfect-mirror behavior of photonic crystals.

36 MATERIALS SCIENCE↗

Quantitative and mechanistic insights into proton dynamics for fast energy storage

Proton conduction in hydrogen-bond-rich protic electrolytes enables fast mass and charge transport, crucial for electrochemical energy storage and power conversion. Such transport can give proton-based batteries exceptional rate capability and low-temperature operation beyond other working ions. Here we show that in phosphoric acid (H 3 PO 4 ) electrolytes, vehicular and structural proton transport coexist, and their contributions to conductivity can be quantitatively distinguished. We link structural diffusion directly to hydrogen-bond strength, enabling the precise tuning of proton migration. Guided by this, we reveal a double conductivity peak from regulated structural diffusion. The optimal electrolyte (5.8-M H 3 PO 4 ) achieves high overall (232.9 mS cm −1 ) and structural (164.9 mS cm−1) conductivity. A MoO 3 ‖CuFe-TBA battery with this electrolyte outperforms a deep-eutectic benchmark (8.3-M H 3 PO 4 ), delivering >17,474 W kg −1 at room temperature and retaining 15.1 Wh kg −1 at −75 °C. These findings provide a framework for designing advanced protic electrolytes across electrochemical systems.

Li, Ziyue [Fudan University, Shanghai (China, Peop↗

Spotlight: efficient automated global optimization in rietveld analysis of diffraction data

Performing reliable Rietveld analysis on tens or hundreds of powder diffraction datasets from parametric or time-resolved experiments often poses a bottleneck in extracting meaningful results from the data. While automated analysis of data has recently been demonstrated, high temperature annealing studies, during which phase transformations occur and lattice parameters may change due to repartitioning of elements, are prime examples where automation by a simple phase identification from a database of room temperature structures or automation by sequential refinements is likely to fail. To enable reliable, efficient, automated Rietveld analysis, we present a Python package named Spotlight , building on established Rietveld packages such as MAUD, GSAS , or GSAS-II , which extends the refinement of best fit parameters to a global optimization using an ensemble of optimizers leveraging hierarchical parallel execution on high-performance computing clusters. Spotlight further enables the efficient design of refinement plans through the iterative automated machine-learning of a surrogate for the refinement on which the global optimizations are performed until results from the surrogate converge to the response surface data. We demonstrate Spotlight with the analysis of uranium molybdenum and Ti–6Al–4V datasets, as well as in two open-source tutorials analyzing aluminium oxide and lead sulphate.

36 MATERIALS SCIENCE↗

AI-optimized detector design for the future Electron-Ion Collider: the dual-radiator RICH case

Advanced detector R&D requires performing computationally intensive and detailed simulations as part of the detector-design optimization process. Here, we propose a general approach to this process based on Bayesian optimization and machine learning that encodes detector requirements. As a case study, we focus on the design of the dual-radiator Ring Imaging Cherenkov (dRICH) detector under development as a potential component of the particle-identification system at the future Electron-Ion Collider (EIC). The EIC is a US-led frontier accelerator project for nuclear physics, which has been proposed to further explore the structure and interactions of nuclear matter at the scale of sea quarks and gluons. We show that the detector design obtained with our automated and highly parallelized framework outperforms the baseline dRICH design within the assumptions of the current model. Our technique can be applied to any detector R&D, provided that realistic simulations are available.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DiffLense: a conditional diffusion model for super-resolution of gravitational lensing data

Abstract Gravitational lensing data is frequently collected at low resolution due to instrumental limitations and observing conditions. Machine learning-based super-resolution techniques offer a method to enhance the resolution of these images, enabling more precise measurements of lensing effects and a better understanding of the matter distribution in the lensing system. This enhancement can significantly improve our knowledge of the distribution of mass within the lensing galaxy and its environment, as well as the properties of the background source being lensed. Traditional super-resolution techniques typically learn a mapping function from lower-resolution to higher-resolution samples. However, these methods are often constrained by their dependence on optimizing a fixed distance function, which can result in the loss of intricate details crucial for astrophysical analysis. In this work, we introduce DiffLense , a novel super-resolution pipeline based on a conditional diffusion model specifically designed to enhance the resolution of gravitational lensing images obtained from the Hyper Suprime-Cam Subaru Strategic Program (HSC-SSP). Our approach adopts a generative model, leveraging the detailed structural information present in Hubble space telescope (HST) counterparts. The diffusion model, trained to generate HST data, is conditioned on HSC data pre-processed with denoising techniques and thresholding to significantly reduce noise and background interference. This process leads to a more distinct and less overlapping conditional distribution during the model’s training phase. We demonstrate that DiffLense outperforms existing state-of-the-art single-image super-resolution techniques, particularly in retaining the fine details necessary for astrophysical analyses.

Computer Science↗

Determining the Adsorption Energetics of 2,3-Butanediol on RuO 2 (110): Coupling First-Principles Calculations With Global Optimizers

As climate change continues to pose a threat to the Earth due to the disrupted carbon cycles and fossil fuel resources remain finite, new sources of sustainable hydrocarbons must be explored. 2,3-butanediol is a potential source to produce butene because of its sustainability as a biomass-derived sugar. Butene is an attractive product because it can be used as a precursor to jet fuel, categorizing this work in the alcohol-to-jet pathway. While studies have explored the conversion of 2,3-butanediol to butene, little is understood about the fundamental reaction itself. We quantify the energetics for three pathways that were reported in the literature in the absence of a catalyst. One of these pathways forms a 1,3-butadiene intermediate, which is a highly exothermic process and thus is unlikely to occur since 2,3-butanediol likely gets thermodynamically trapped at this intermediate. We further determined the corresponding energetics of 2,3-butanediol adsorption on an ensemble of predetermined binding sites when it interacts with a defect-free stoichiometric RuO 2 (110) surface. Within this ensemble of adsorption sites, the most favorable site has 2,3-butanediol covering a Ru 5–coordinated cation. This approach is compared to that obtained using the global optimization algorithm as implemented in the Northwest Potential Energy Surface Search Engine. When using such a global optimization algorithm, we determined a more favorable ground-state structure that was missed during the manual adsorption site testing, with an adsorption energy of -2.61 eV as compared to -2.34 eV when using the ensemble-based approach. We hypothesize that the dehydration reaction requires a stronger chemical bond, which could necessitate the formation of oxygen vacancies. As such, this study has taken the first step toward the utilization of a global optimization algorithm for the rational design of Ru-based catalysts toward the formation of butene from sustainable resources.

09 BIOMASS FUELS↗

Modeling commercial-scale CO 2 storage in the gas hydrate stability zone with PFLOTRAN v6.0

Abstract. Safe and secure carbon dioxide (CO2) storage is likely to be critical for mitigating some of the most dangerous effects of climate change. In the last decade, there has been a significant increase in activity associated with reservoir characterization and site selection for large-scale CO2 storage projects across the globe. These prospective storage sites tend to be selected for their optimal structural, petrophysical, and geochemical trapping potential. However, it has also been suggested that storing CO2 in reservoirs within the CO2 hydrate stability zone (GHSZ), characterized by high pressures and low temperatures (e.g., Arctic or marine environments), could provide a natural thermodynamic barrier to gas leakage. Evaluating the prospect of commercial-scale, long-term storage of CO2 in the GHSZ requires reservoir-scale modeling capabilities designed to account for the unique physics and thermodynamics associated with these systems. We have developed the HYDRATE flow mode and the accompanying fully implicit parallel well model in the massively parallel subsurface flow and reactive transport simulator PFLOTRAN to model CO2 injection into the marine GHSZ. We have applied these capabilities to a set of CO2 injection scenarios designed to reveal the challenges and opportunities for commercial-scale CO2 storage in the GHSZ.

carbon storage↗

Co-free gradient lithium-rich cathode for high-energy batteries with optimized cyclability

Lithium-rich layered oxides (LLOs) hold the promise for high-energy battery cathodes. However, its application has been hindered by voltage decay associated with irreversible reactions at high voltages despite decades of intensive efforts. Here, we first theoretically studied the molecular orbitals of Mn-based Li-rich configurations. We found that the π-bond ring formed within the LiMn 6 structure could participate in stable redox reactions as one unit, but Co could disrupt its symmetry. We thus designed and synthesized Co-free concentration-gradient LLOs (CF-CG-LLOs) materials. The combination of concentration gradient and Co removal leads to exceptional capacity retention without any fading over 100 cycles of the pouch cell. More importantly, it exhibits an extraordinarily low voltage decay of 0.15 mV/cycle, accompanied by a high Coulombic efficiency of 99.86%. This concept and demonstration of CF-CG-LLO cathodes reveal a viable avenue toward low-cost, high-energy-density battery cathodes.

25 ENERGY STORAGE↗